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ISSN: 1545-5963

Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data (Abstract)

Bo Tian , School of Software,Dalian University of Technology, Dalian, China.(email:zyhe@dlut.edu.cn)
Papers

Matching Split Distance for Unrooted Binary Phylogenetic Trees (Abstract)

Damian Bogdanowicz , Gdansk University of Technology, Gdansk
Krzysztof Giaro , Gdansk University of Technology, Gdansk

Drug target prediction by multi-view low rank embedding (Abstract)

Menglan Cai , School of Mathematics and Statistics, Xi’an Jiaotong University Xi’an, 710049, China (e-mail: caimenglan@stu.xjtu.edu.cn).
Special Section on the Eighth International Symposium on Bioinformatics Research and Application

An Integer Programming Formulation of the Parsimonious Loss of Heterozygosity Problem (Abstract)

Daniele Catanzaro , Université Libre de Bruxelles (ULB), Brussels
Martine Labbe , Université Libre de Bruxelles (ULB), Brussels
Bjarni V. Halldorsson , Reykjavik University, Reykjavik

Inapproximability of (1,2)-Exemplar Distance (Abstract)

Laurent Bulteau , Université de Nantes, Nantes
Minghui Jiang , Utah State University, Logan

A Transcript Perspective on Evolution (Abstract)

Yann Christinat , Ecole Polytechnique Federale de Lausanne, Lausanne
Bernard M.E. Moret , Ecole Polytechnique Federale de Lausanne, Lausanne

Reconstruction of Transcriptional Regulatory Networks by Stability-based Network Component Analysis (Abstract)

Xi Chen , Virginia Polytechnic Institute and State University, Arlington
Jianhua Xuan , Virginia Polytechnic Institute and State University, Arlington
Chen Wang , Virginia Polytechnic Institute and State University, Arlington
Ayesha N. Shajahan , Georgetown University Medical Center, Washington
Rebecca B. Riggins , Georgetown University Medical Center, Washington
Robert Clarke , Georgetown University Medical Center, Washington

Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems (Abstract)

Andre Wehe , University of Florida, Gainesville and Iowa State University, Ames
J. Gordon Burleigh , University of Florida, Gainesville
Oliver Eulenstein , Iowa State University, Ames
Special Section on the International Workshop on Data Mining in Bioinformatics

Biological Sequence Analysis with Multivariate String Kernels (Abstract)

Pavel P. Kuksa , NEC Laboratories America Inc, Princeton

Text Categorization of Biomedical Data Sets Using Graph Kernels and a Controlled Vocabulary (Abstract)

Said Bleik , New Jersey Institute of Technology, Newark
Meenakshi Mishra , University of Kansas, Lawrence
Jun Huan , University of Kansas, Lawrence
Min Song , Yonsei University, Seol
Special Section on the Eighth International Symposium on Bioinformatics Research and Application

Protein Chain Pair Simplification Under the Discrete Fréchet Distance (Abstract)

Tim Wylie , Montana State University, Bozeman
Binhai Zhu , Montana State University, Bozeman
Regular Papers

Multivariate Hypergeometric Similarity Measure (Abstract)

Chanchala D. Kaddi , Georgia Institute of Technology, Atlanta
R. Mitchell Parry , Appalachian State University, Boone
May D. Wang , Georgia Institute of Technology, Atlanta
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab-Initio Protein Structure Prediction (Abstract)

Kevin Molloy , George Mason University, Fairfax
Sameh Saleh , George Mason University, Fairfax
Amarda Shehu , George Mason University, Fairfax
Special Section on the Eighth International Symposium on Bioinformatics Research and Application

Novel Multi-Sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles (Abstract)

Ayshwarya Subramanian , Carnegie Mellon University, Pittsburgh
Stanley Shackney , Oncotherapeutics, Pittsburgh
Russell Schwartz , Carnegie Mellon University, Pittsburgh
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Improved Multiple Sequence Alignments Using Coupled Pattern Mining (Abstract)

K. S. M. Tozammel Hossain , Virginia Tech, Blacksburg
Debprakash Patnaik , Amazon Inc., Seattle
Srivatsan Laxman , Microsoft Research, Bangalore
Prateek Jain , Microsoft Research, Bangalore
Chris Bailey-Kellogg , Dartmouth College, Hanover
Naren Ramakrishnan , Virginia Tech, Blacksburg
Papers

Utilizing Both Topological and Attribute Information for Protein Complex Identification in PPI Networks (Abstract)

Allen L. Hu , The Hong Kong Polytechnic University, Hong Kong
Keith C. C. Chan , The Hong Kong Polytechnic University, Hong Kong
Special Section on the Eighth International Symposium on Bioinformatics Research and Application

Network-based Drug Ranking and Repositioning with respect to DrugBank Therapeutic Categories (Abstract)

Matteo Re , Universita degli Studi di Milano, Milano
Giorgio Valentini , Universita degli Studi di Milano, Milano
Papers

Hybrid Fuzzy Cluster Ensemble Framework for Tumor Clustering from Bio-molecular Data (Abstract)

Zhiwen Yu , South China University of Technology, Guangzhou and Hong Kong Polytechnic University, Hong Kong
Hantao Chen , South China University of Technology, Guangzhou
Jane You , Hong Kong Polytechnic University, Hong Kong
Guoqiang Han , South China University of Technology, Guangzhou
Le Li , South China University of Technology, Guangzhou
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal alignment. (Abstract)

Oben M. Tataw , University of California, Riverside, Riverside
Gonehal Venugopala Reddy , University of California, Riverside, Riverside
Eamonn J. Keogh , University of California, Riverside, Riverside
Amit K. Roy-Chowdhury , University of California, Riverside, Riverside
Regular Papers

Operon Prediction using Chaos Embedded Particle Swarm Optimization (Abstract)

Li-Yeh Chuang , I-Shou University, Kaohsiung
Cheng-Huei Yang , National Kaohsiung Institute of Marine Technology, Kaohsiung
Jui-Hung Tsai , National Kaohsiung University of Applied Sciences, Kaohsiung
Cheng-Hong Yang , National Kaohsiung University of Applied Sciences, Kaohsiung
Papers

A Combination of Feature Extraction Methods with an Ensemble of Different Classifiers for Protein Structural Class Prediction Problem (Abstract)

Abdollah Dehzangi , Griffith University, and National ICT Australia (NICTA), Brisbane
Kuldip Paliwal , Griffith University, Brisbane
Alok Sharma , Griffith University, Brisbane and University of the South Pacific, Fiji
Omid Dehzangi , University of Texas at Dallas, Dallas
Abdul Sattar , Griffith University, and National ICT Australia (NICTA), Brisbane
Special Section on the Eighth International Symposium on Bioinformatics Research and Application

Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of its Proteins (Abstract)

Si Li , National University of Singapore, Singapore
Kwok Pui Choi , National University of Singapore, Singapore
Taoyang Wu , National University of Singapore, Singapore and University of East Anglia, Norwich
Louxin Zhang , National University of Singapore, Singapore
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Reverse Engineering Molecular Hypergraphs (Abstract)

Ahsanur Rahman , Virginia Tech, Blacksburg
Christopher L. Poirel , Virginia Tech, Blacksburg
David J. Badger , Virginia Tech, Blacksburg
Craig Estep , Virginia Tech, Blacksburg
T. M. Murali , Virginia Tech, Blacksburg
Papers

Comparison of Feature Selection Methods for Cross-Laboratory Microarray Analysis (Abstract)

Hsi-Che Liu , Mackay Medical College and Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital, New Taipei
Pei-Chen Peng , National Taiwan University, Taipei
Tzung-Chien Hsieh , National Taiwan University, Taipei
Ting-Chi Yeh , Mackay Medical College and Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital, New Taipei
Chih-Jen Lin , National Taiwan University, Taipei
Chien-Yu Chen , National Taiwan University, Taipei
Jen-Yin Hou , Mackay Medical College and Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital, New Taipei
Lee-Yung Shih , Chang Gung Memorial Hospital, Taipei, and Chang Gung University, Taoyuan
Der-Cherng Liang , Mackay Medical College and Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital, New Taipei
Regular Papers

An Adaptive Window Length Strategy For Eukaryotic CDS Prediction (Abstract)

Devendra K. Shakya , Samrat Ashok Technological Institute, Vidisha
Rajiv Saxena , Jaypee University of Engineering and Technology, Raghogarh, Guna
Sanjeev N. Sharma , Samrat Ashok Technological Institute, Vidisha
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Non-overlapping Clone Pooling for High-Throughput Sequencing (Abstract)

Reginaldo M. Kuroshu , Universidade Federal de São Paulo, São José dos Campos
Special Section on the International Workshop on Data Mining in Bioinformatics
Regular Papers

Probabilistic Model Checking Analysis of Palytoxin Effects on Cell Energy Reactions of the Na^+/K^+-ATPase (Abstract)

Fernando A. F. Braz , Universidade Federal de Minas Gerais, Belo Horizonte
Jader S. Cruz , Universidade Federal de Minas Gerais, Belo Horizonte
Alessandra C. Faria-Campos , Universidade Federal de Minas Gerais, Belo Horizonte
Sergio V. A. Campos , Universidade Federal de Minas Gerais, Belo Horizonte
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Coalescent-based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data (PDF)

Ming-Chi Tsai , CMU-Pitt PhD Program in Computational Biology, Pittsburgh
Guy E. Blelloch , Carnegie Mellon University, Pittsburgh
R. Ravi , Carnegie-Mellon University, Pittsburgh
Russell Schwartz , Carnegie Mellon University, Pittsburgh
Short Papers

Strategy for Naturelike Designer Transcription Factors with Reduced Toxicity (Abstract)

Christian Bach , University of Bridgeport, Bridgeport
Prabir Patra , University of Bridgeport, Bridgeport
Jani M. Pallis , University of Bridgeport, Bridgeport
William Sherman , Brookhaven National Labs, Long Island, Upton
Hassan Bajwa , University of Bridgeport, Bridgeport

A Combinatorial Perspective of the Protein Inference Problem (Abstract)

Chao Yang , The Hong Kong University of Science and Technology, Hong Kong
Zengyou He , Dalian University of Technology, Dalian
Weichuan Yu , The Hong Kong University of Science and Technology, Hong Kong
Regular Papers

Computing the Joint Distribution of Tree Shape and Tree Distance for Gene Tree Inference and Recombination Detection (Abstract)

Yujin Chung , University of Wisconsin, Madison
Nicole T. Perna , University of Wisconsin, Madison
Cécile Ané , University of Wisconsin, Madison
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Expanded Explorations into the Optimization of an Energy Function for Protein Design (Abstract)

Yao-ming Huang , University of California, San Francisco, San Francisco
Chris Bystroff , Rensselaer Polytechnic Institute, Troy
Short Papers

Naïve Bayesian Classifiers with Multinomial Models for rRNA Taxonomic Assignment (Abstract)

Kuan-Liang Liu , National Cheng Kung University, Tainan
Tzu-Tsung Wong , National Cheng Kung University, Tainan
Regular Papers

Statistical Detection of Boolean Regulatory Relationships (Abstract)

Ting Chen , Texas A&M University, College Station
Ulisses M. Braga-Neto , Texas A&M University, College Station

EEG/ERP Adaptive Noise Canceller Design with Controlled Search Space (CSS) approach in Cuckoo and other Optimization Algorithms (Abstract)

M. K. Ahirwal , PanditDwarka Prasad Mishra Indian Institute of Information Technology, Design & Manufacturing Jabalpur, Jabalpur
A. Kumar , PanditDwarka Prasad Mishra Indian Institute of Information Technology, Design & Manufacturing Jabalpur, Jabalpur
G. K. Singh , Indian Institute of Technology Roorkee, India, Jabalpur and University of Malaya, Malaysia
Short Papers

Explicit Expression for the Steady State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model (Abstract)

Yoram Zarai , Tel-Aviv University, Tel-Aviv
Michael Margaliot , Tel-Aviv University, Tel-Aviv
Tamir Tuller , Tel-Aviv University, Tel-Aviv
Regular Papers

Intensity-Based Skeletonization of CryoEM Grayscale Images Using a True Segmentation-Free Algorithm (Abstract)

Kamal Al Nasr , Howard University, Washington D.C.
Chunmei Liu , Howard University, Washington D.C.
Mugizi Rwebangira , Howard University, Washington D.C.
Legand Burge , Howard University, Washington D.C.
Jing He , Old Dominion University, Norfolk
Special Section on the ACM Conference on Bioinformatics Computational Biology and Biomedicine

Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure (Abstract)

Seth Blumenthal , Lehigh University, Bethlehem
Yisheng Tang , Lehigh University, Bethlehem
Wenjie Yang , Lehigh University, Bethlehem
Brian Chen , Lehigh University, Bethlehem
Regular Papers

FRESCO: Referential Compression of Highly-Similar Sequences (PDF)

Sebastian Wandelt , Humboldt-University of Berlin, Berlin
Ulf Leser , Humboldt-University of Berlin, Berlin
Papers

Measure the Semantic Similarity of GO terms Using Aggregate Information Content (Abstract)

Xuebo Song , Clemson University, Clemson
Lin Li , Murray State Univerisity, Murray
Pradip K. Srimani , Clemson Univeristy, Clemson
Philip S. Yu , University of Illinois, Chicago
James Z. Wang , Clemson Univeristy, Clemson

Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage (Abstract)

Falk Hüffner , TU Berlin, Berlin
Christian Komusiewicz , TU Berlin, Berlin
Adrian Liebtrau , Friedrich-Schiller-Universität Jena, Berlin
Rolf Niedermeier , TU Berlin, Berlin

Quantifying Significance of MHC II Residues (Abstract)

Ying Fan , City University of Hong Kong, Hong Kong
Ruoshui Lu , City University of Hong Kong, Hong Kong
Lusheng Wang , City University of Hong Kong, Hong Kong
Massimo Andreatta , City University of Hong Kong, Hong Kong
Shuai Cheng Li , City University of Hong Kong, Hong Kong
Perspectives Papers

Genome-guided Transcriptome Assembly in the Age of Next Generation Sequencing (PDF)

Liliana D. Florea , Johns Hopkins University School of Medicine, Baltimore
Steven L. Salzberg , Johns Hopkins School of Medicine and Bloomberg School of Public Health, Baltimore
Short Papers

Protein Structure Optimisation With a "Lamarckian" Ant Colony Algorithm. (Abstract)

Mark T. Oakley , University of Birmingham, Birmingham
Elizabeth Grace Richardson , University of Birmingham, Birmingham
Harriet Carr , University of Birmingham, Birmingham
Roy L. Johnston , University of Birmingham, Birmingham
Regular Papers

An Exact Algorithm For The Zero Exemplar Breakpoint Distance Problem (Abstract)

Daming Zhu , Shandong University, Jinan
Lusheng Wang , City University of Hong Kong, Hong Kong

Predicting Protein-Ligand Binding Sites using Support Vector Machine with Protein Properties (Abstract)

Ginny Y. Wong , The Hong Kong Polytechnic University, Hong Kong
Frank H.F. Leung , The Hong Kong Polytechnic University, Hong Kong
Sai-Ho Ling , University of Technology Sydney, Sydney
Papers

Evolution and Controllability of Cancer Networks: A Boolean Perspective (Abstract)

Sriganesh Srihari , The University of Queensland, Brisbane
Venkatesh Raman , The Institute of Mathematical Sciences, Chennai
Hon Wai Leong , National University of Singapore, Singapore
Mark A. Ragan , The University of Queensland, Brisbane

Identifying cis-Regulatory Elements and Modules using Conditional Random Fields (Abstract)

Yanglan Gan , Donghua University, Shanghai
Jihong Guan , Tongji University, Shanghai
Shuigeng Zhou , Fudan University, Shanghai
Weixiong Zhang , Jianghan University, Wuhan and Washington University in St. Louis, St. Louis
Regular Papers

Designing Pooling Systems for Noisy High-Throughput Protein-Protein Interaction Experiments using Boolean Compressed Sensing (Abstract)

Ramy Mourad , American University of Beirut, Beirut
Zaher Dawy , American University of Beirut, Beirut
Faruck Morcos , Rice University, Houston
Papers

Intelligent Consensus Modeling for Proline Cis-Trans Isomerization Prediction (Abstract)

Paul D. Yoo , Khalifa University, Abu Dhabi
Sami Muhaidat , Khalifa University, Abu Dhabi
Kamal Taha , Khalifa University, Abu Dhabi
Jamal Bentahar , Concordia University, Montreal
Abdallah Shami , The University of Western Ontario, London

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation (Abstract)

Laleh Soltan Ghoraie , University of Waterloo, Waterloo
Forbes Burkowski , University of Waterloo, Waterloo
Shuai Cheng Li , City University of Hong Kong, Hong Kong
Mu Zhu , University of Waterloo, Canada, Waterloo

Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo (PDF)

Jing Guo , Nanyang Technological University, Singapore
Ritika Jain , Nanyang Technological University, Singapore
Rui Fan , Nanyang Technological University, Singapore
Chee Keong Kwoh , Nanyang Technological University, Singapore

Incorporation of Biological Pathway Knowledge in the Construction of Priors for Optimal Bayesian Classification (Abstract)

Mohammad Shahrokh Esfahani , Texas A&M University, College Station
Edward R. Dougherty , Texas A&M University, College Station and Translational Genomics Research Institute, Pheonix

DNA Copy Number Selection Using Robust Structured Sparsity-Inducing Norms (Abstract)

Vangelis Metsis , The University of Texas at Arlington, Arlington
Fillia Makedon , The University of Texas at Arlington, Arlington
Dinggang Shen , University of North Carolina at Chapel Hill, Chapel Hill
Heng Huang , The University of Texas at Arlington, Arlington
Survey Papers

Wavelet Analysis in Current Cancer Genome Research: A Survey (Abstract)

Tao Meng , University of Miami, Coral Gables
Ahmed T. Soliman , University of Miami, Coral Gables
Mei-Ling Shyu , University of Miami, Coral Gables
Yimin Yang , Florida International University, Miami
Shu-Ching Chen , Florida International University , Miami
S.S. Iyengar , Florida International University, Miami
John Yordy , University of Texas Southwestern Medical Center, Dallas
Puneeth Iyengar , University of Texas Southwestern Medical Center, Dallas
Papers

A New Unsupervised Binning Approach for Metagenomic Sequences Based on N-grams and Automatic Feature Weighting (Abstract)

Ruiqi Liao , Fudan University, Shanghai
Ruichang Zhang , Fudan University, Shanghai
Jihong Guan , Tongji University, Shanghai
Shuigeng Zhou , Fudan University, Shanghai

Coupling Graphs, Efficient Algorithms and B-cell Epitope Prediction (PDF)

Liang Zhao , Nanyang Technological University, Singapore
Steven C.H. Hoi , Nanyang Technological University, Singapore
Zhenhua Li , Nanyang Technological University, Singapore
Limsoon Wong , National University of Singapore, Singapore
Hung Nguyen , University of Technology Sydney, Sydney
Jinyan Li , University of Technology Sydney, Sydney
Regular Papers

A Probabilistic Latent Semantic Analysis Model for Co-Clustering the Mouse Brain Atlas (Abstract)

Shuiwang Ji , Old Dominion University, Norfolk
Wenlu Zhang , Old Dominion University, Norfolk
Rongjian Li , Old Dominion University, Norfolk
Papers

Gene Name Disambiguation using Multi- Scope Species Detection (Abstract)

Jui-Chen Hsiao , National Cheng Kung University, Tainan
Chih-Hsuan Wei , National Cheng Kung University, Tainan
Hung-Yu Kao , National Cheng Kung University, Tainan

Protein Function Prediction with Incomplete Annotations (Abstract)

Guoxian Yu , Southwest University, Chongqing and South China University of Technology, Guangzhou
Huzefa Rangwala , George Mason University, Fairfax
Carlotta Domeniconi , George Mason University, Fairfax
Guoji Zhang , South China University of Technology, Guangzhou
Zhiwen Yu , South China University of Technology, Guangzhou

Maximizing Deep Coalescence Cost (Abstract)

Pawel Gorecki , University of Warsaw, Warsaw
Oliver Eulenstein , Iowa State University, Ames

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model (Abstract)

Sandhya Prabhakaran , University of Basel, Basel
Melanie Rey , University of Basel, Basel
Osvaldo Zagordi , University of Zurich, Zürich
Niko Beerenwinkel , ETH Zürich, Zürich
Volker Roth , University of Basel, Basel

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set (Abstract)

Leyi Wei , Xiamen University, Xiamen
Minghong Liao , Xiamen University, Xiamen
Yue Gao , National University of Singapore, Singapore
Rongrong Ji , Xiamen University, Xiamen
Zengyou He , Dalian University of Technology, Dalian
Quan Zou , Xiamen University, Xiamen

A New Path Based Hybrid Measure for Gene Ontology Similarity (Abstract)

Sanghamitra Bandyopadhyay , Indian Statistical Institute, Kolkata
Koushik Mallick , Indian Statistical Institute, Kolkata

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data (Abstract)

Sanghamitra Bandyopadhyay , Indian Statistical Institute, Kolkata
Saurav Mallik , Indian Statistical Institute, Kolkata
Anirban Mukhopadhyay , University of Kalyani, Nadia

Multiple Sequence Alignment with Hidden Markov Models Learned by Random Drift Particle Swarm Optimization (Abstract)

Jun Sun , Jiangnan University, Wuxi
Vasile Palade , University of Oxford, Oxford
Xiaojun Wu , Jiangnan University, Wuxi
Wei Fang , Jiangnan University, Wuxi

Herarchical Probabilistic Interaction Modeling for Multiple Gene Expression Replicates (Abstract)

Kristopher Patton , K. Patton is a PhD candidate in the Department of Statistics, Michigan State University (e-mail: pattonkr@stt.msu.edu).

Ligand-K* Sequence Elimination: a novel algorithm for ensemble-based redesign of receptor-ligand binding (Abstract)

Qingliang Shen , Qingliang Shen is with College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China.

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph (Abstract)

Pieter Meysman , Pieter Meysman is with the Advanced Database Research and Modeling (ADReM) of the University of Antwerp. (email: pieter.meysman@uantwerpen.be)

A fast PC algorithm for high dimensional causal discovery with multi-core PCs (Abstract)

Thuc Le , Thuc Duy Le is with the School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095.(Email: thuc.le@unisa.edu.au)

Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning (Abstract)

Shokoufeh Mirzaei , Shokoufeh Mirzaei is with the California State Polytechnic University, Pomona; Industrial and Manufacturing Engineering Department, 3801 W Temple Ave, Pomona , CA 91768.(Email: smirzaei@cpp.edu)

Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction (Abstract)

Ritambhara Singh , Department of Computer Science, University of Virginia, Charlottesville VA, 22903. (E-mail: rs3zz@virginia.edu)

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies (PDF)

Nina Luhmann , International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld University, Germany (e-mail: nina.luhmann@uni-bielefeld.de)

HMMCAS: a web tool for the identification and domain annotations of Cas proteins (Abstract)

Jian Huang , Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054.(email:chai@immunet.cn)

Construction of refined protein interaction network for predicting essential proteins (Abstract)

Min Li , School of Information Science and Engineering, Central South University, Changsha 410083, China. (email: limin@mail.csu.edu.cn)

Identifying sigma70 promoters with novel pseudo nucleotide composition (Abstract)

Hao Lin , Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China. (e-mail: hlin@uestc.edu.cn).

Identifying bacterial essential genes based on a feature-integrated method (Abstract)

Yan Lin , National Natural Science Foundation of China. (email: ylin@tju.edu.cn)

Predicting antimicrobial peptides by using increment of diversity with quadratic discriminant analysis method (Abstract)

Pengmian Feng , Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, 063000, China (e-mail: fengpengmian@gmail.com).

Coupling Effect of Double Lungs on a VCV Ventilator with Automatic Secretion Clearance Function (Abstract)

Yan Shi , School of Automation Science and Electrical Engineering, Beihang University, Beijing 100191, China, and The State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou 310058, China

Characteristics of Myosin V Processivity (Abstract)

Jun-Ping Zhang , School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China (e-mail: zjpbm@imu.edu.cn).

Fast prediction of protein methylation sites using a sequence-based feature selection technique (Abstract)

Leyi Wei , School of Computer Science and Technology, Tianjin University, Tianjin, China (e-mail: weileyi@tju.edu.cn).

Multitask Protein Function Prediction Through Task Dissimilarity (Abstract)

Marco Frasca , Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Comelico 39 Milano, 20137, Italy (e-mail: marco.frasca@unimi.it).

Identification and Functional Inference for Tumor-associated Long Non-coding RNA (Abstract)

Ying Li , College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, China (e-mail: liying@jlu.edu.cn)

Recovering hidden diagonal structures via non-negative matrix factorization with multiple constraints (Abstract)

Hongmin Cai , School of Computer Science & Engineering, South China University of Technology, Guangzhou 510006, China. (e-mail: hmcai@scut.edu.cn).

Integrating Multiple Heterogeneous Networks for Novel LncRNA-disease Association Inference (Abstract)

Lei Deng , School of Software, Central South University, Changsha, 410075, China (e-mail: leideng@csu.edu.cn).

An Improved Approach for N-linked Glycan Structure Identification from HCD MS/MS Spectra (Abstract)

Weiping Sun , Department of Computer Science, University of Western Ontario, London, ON, N6A5B7 Canada (e-mail: wsun63@csd.uwo.ca).

Learning a structural and functional representation for gene expressions: To systematically dissect complex cancer phenotypes (Abstract)

Yanbo Wang , Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P.R.China.

Essential Protein Detection by Random Walk on Weighted Protein-Protein Interaction Networks (Abstract)

Jihong Guan , Department of Computer Science and Technology, Tongji University, Shanghai, China.(email:jhguang@tongji.edu.cn)

KATZLGO: Large-scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks (Abstract)

LEI DENG , School of Software, Central South University, Changsha, 410075, China, and also the Shanghai Key Laboratory of Intelligent Information Processing, Shanghai, 200433, China (e-mail: leideng@csu.edu.cn)

Subspace Weighting Co-Clustering of Gene Expression Data (Abstract)

Qingyao Wu , College of Computer Science and Software, Shenzhen University, Shenzhen 518060, P.R. China.(email:xjchen@szu.edu.cn)

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks (Abstract)

Min Li , School of Information Science and Engineering, Central South University, Changsha 410083, China.(email: limin@mail.csu.edu.cn)

Protein-protein interaction interface residue pair prediction based on deep learning architecture (Abstract)

Xinqi Gong , Institute for Mathematical Sciences, Renmin University of China No. 59 Zhongguancun Street, Haidian District Beijing, 100872, P.R. China.(email:xinqigong@ruc.edu.cn)

Highly Accurate and Efficient Data-Driven Methods For Genotype Imputation (Abstract)

Olivia Choudhury , Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556. (e-mail: ochoudhu@nd.edu).

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees (Abstract)

Mukul S. Bansal , Department of Computer Science & En- gineering and the Institute for Systems Genomics at the University of Connecticut, Storrs, USA (e-mail: mukul.bansal@uconn.edu).

A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer (Abstract)

Shaoliang Peng , School of Computer Science, National University of Defense Technology Changsha, China (e-mail: pengshaoliang@nudt.edu.cn)

Computing Manhattan Path-Difference MedianTrees: a Practical Local Search Approach (Abstract)

Alexey Markin , Computer Science, Iowa State University, 1177 Ames, Iowa United States 50011-2140 (e-mail: amarkin@iastate.edu)
Oliver Eulenstein , Computer Science, Iowa State University, Ames, Iowa United States (e-mail: oeulenst@iastate.edu)

Genome-wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-learning Approach (Abstract)

Roman Sergeevich Sergeev , Mathematical Cybernetics, Obyedinennyj institut problem informatiki Natsional'noj akademii nauk Belarusi, 231799 Minsk, Minsk region Belarus 220012 (e-mail: roma.sergeev@gmail.com)
Ivan Kavaliou , Epam Systems Inc Belarus, 393418 Minsk, Minsk region Belarus (e-mail: ivanich3d@gmail.com)
Uladzislau Sataneuski , Obyedinennyj institut problem informatiki Natsional'noj akademii nauk Belarusi, 231799 Minsk, Minsk Belarus (e-mail: satanevsky.vlad@yandex.by)
Andrei Gabrielian , Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, 35037 Bethesda, Maryland United States (e-mail: andrei.gabrielian@nih.gov)
Alex Rosenthal , Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, 35037 Bethesda, Maryland United States (e-mail: alexr@niaid.nih.gov)
Michael Tartakovsky , Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, 35037 Bethesda, Maryland United States (e-mail: mike.tartakovsky@nih.gov)
Alexander Tuzikov , Obyedinennyj institut problem informatiki Natsional'noj akademii nauk Belarusi, 231799 Minsk, Minsk region Belarus (e-mail: tuzikov@newman.bas-net.by)

A 2-Approximation Scheme for Sorting Signed Permutations by Reversals, Transpositions, Transreversals, and Block-Interchanges (Abstract)

FanChang HAO , Department of Information Science and Technology, Shangdong University of Political Science and Law, Jinan, Shandong China (e-mail: haofine@gmail.com)
Melvin ZHANG , Cosmiqo International Pte Ltd, Singapore, Singapore Singapore (e-mail: melvinzhang@gmail.com)
Hon Wai Leong , Department of Computer Science, National University of Singapore, Singapore, Singapore Singapore (e-mail: leonghw@comp.nus.edu.sg)

EmDL: Extracting miRNA-Drug Interactions from Literature (Abstract)

Wenbin Xie , computer science and technology, Tongji University, 12476 Shanghai, shanghai China 201804 (e-mail: sun_xie123@163.com)
Hong Yan , Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong Hong Kong KLN (e-mail: h.yan@cityu.edu.hk)
Xing-Ming Zhao , Tongji University, Shanghai, ShangHai China (e-mail: xm_zhao@tongji.edu.cn)

Calculating the Unrooted Subtree Prune-and-Regraft Distance (PDF)

Chris Whidden , Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington United States 98109 (e-mail: cwhidden@fhcrc.org)
Frederick Matsen , Fred Hutchinson Cancer Research Center, Seattle, Washington United States (e-mail: matsen@fhcrc.org)

Network clustering analysis using mixture exponential-family random graph models and its application in genetic interaction data (Abstract)

Yishu Wang , School of Mathematical Sciences, Qingdao University, Qingdao, Shandong China (e-mail: yishu6661@126.com)
Hongyu Zhao , Yale University, New Haven, Connecticut United States (e-mail: hongyu.zhao@yale.edu)
Minghua Deng , Beijing, Beijing China (e-mail: dengmh@math.pku.edu.cn)
Huaying Fang , Beijing, Beijing China (e-mail: hyfang@stanford.edu)
Dejie Yang , Beijing, Beijing China (e-mail: yangdejiejay@163.com)

Identification of protein complexes by using a spatial and temporal active protein interaction network (Abstract)

Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Xiangmao Meng , Computer Science, Central South University, Changsha, Hunan China (e-mail: mxmanhui@csu.edu.cn)
Ruiqing Zheng , Computer Science, Central South University, Changsha, Hunan China (e-mail: rqzheng@csu.edu.cn)
Fang-Xiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yaohang Li , Computer Science, Old Dominion University, 6042 Norfolk, Virginia United States (e-mail: yaohang@cs.odu.edu)
Yi Pan , Computer Science, Georgia State University, Atlanta, Georgia United States 30303 (e-mail: pan@cs.gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

FastEtch: A Fast Sketch-based Assembler for Genomes (PDF)

Priyanka Ghosh , Washington State University, 6760 Pullman, Washington United States 99164-1009 (e-mail: pghosh@eecs.wsu.edu)
Ananth Kalyanaraman , School of EECS, Washington State University, Pullman, Washington United States 99164-2752 (e-mail: ananth@eecs.wsu.edu)

Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins using Frequent Subgraph Mining (Abstract)

Tanay Kumar Saha , Indiana University Purdue University at Indianapolis, 10668 Indianapolis, Indiana United States 46254 (e-mail: tksaha@iupui.edu)
Ataur Katebi , Department of Veterinary Microbiology and Preventive Medicine, Ames, Iowa United States (e-mail: arkatebi@gmail.com)
Wajdi Dhifli , Institute of Systems and Synthetic Biology, Evry, Evry France (e-mail: wajdi.dhifli@univ-lille2.fr)
Mohammad Al Hasan , Computer Science, Indiana University Purdue University Indianapolis, Indianapolis, Indiana United States (e-mail: alhasan@cs.iupui.edu)

Parallel Stochastic discrete event simulation of calcium dynamics in neuron. (Abstract)

Mohammad Nazrul Ishlam Patoary , Computer Science, McGill University, montreal, Quebec Canada (e-mail: mohammad.patoary@mail.mcgill.ca)
Carl Tropper , Computer Science, McGill University, montreal, Quebec Canada H3A2K6 (e-mail: carl@cs.mcgill.ca)
Robert A. McDougal , Neurobiology, Yale University, New Haven, Connecticut United States (e-mail: robert.mcdougal@yale.edu)
Lin Zhongwei , Computer Science, National University of Defense Technology, Chendu, Hunan China (e-mail: zwlin@nudt.edu.cn)
William W. Lytton , Physiology and Pharmacology, Downstate Medical School, New York City, New York United States (e-mail: bill@neurosim.downstate.edu)

Clustering and Integrating of Heterogeneous Microbiome Data by Joint Symmetric Nonnegative Matrix Factorization with Laplacian Regularization (Abstract)

Yuanyuan Ma , Huazhong Normal University, 12446 Wuhan, Hubei China (e-mail: chonghua_1983@126.com)
Xiaohua Hu , Huazhong Normal University, 12446 Wuhan, Hubei China (e-mail: xh29@drexel.edu)
Tingting He , School of Computer, Central China Normal University, Wuhan, Hubei China (e-mail: tthe@mail.ccnu.edu.cn)
Xingpeng Jiang , Huazhong Normal University, 12446 Wuhan, Hubei China (e-mail: xpjiang@mail.ccnu.edu.cn)

ERDS-exome: a Hybrid Approach for Copy Number Variant Detection from Whole-exome Sequencing Data (Abstract)

Renjie Tan , Harbin Institute of Technology, 47822 Harbin, Heilongjiang China 150001 (e-mail: renjie.tan@outlook.com)
Jixuan Wang , Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: jixuan@cs.toronto.edu)
Xiaoliang Wu , Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 215376650@qq.com)
Liran Juan , School of Life Science and Technology, Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 527293317@qq.com)
Likun Zheng , School of Computer Science and technology, Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: ztj.hit@gmail.com)
Rui Ma , Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 909328425@qq.com)
Qing Zhan , School of Computer Science and Technology, Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 1055984355@qq.com)
Tao Wang , School of Life Science and Technology, Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 1260165153@qq.com)
Shuilin Jin , Department of Mathematics, Harbin Institute of Technology, 47822 Harbin, Heilongjiang China (e-mail: 2395778@qq.com)
Qinghua Jiang , Harbin Institute of Technology, Harbin, Heilongjiang China (e-mail: qhjiang@hit.edu.cn)
Yadong Wang , the Department of Computer Science and Engineering, Harbin Institute of Technology, Harbin, Heilongjiang China 150001 (e-mail: ydwang@hit.edu.cn)

Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL) (Abstract)

Mohammad Arifur Rahman , Computer Science, George Mason University Volgenau School of Information Technology and Engineering, 143375 Fairfax, Virginia United States 22030 (e-mail: mrahma23@gmu.edu)
Nathan LaPierre , Computer Science, George Mason University, Fairfax, Virginia United States (e-mail: nlapier2@gmu.edu)
Huzefa Rangwala , Computer Science, George Mason University, Fairfax, Virginia United States 22030 (e-mail: rangwala@cs.gmu.edu)

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems (Abstract)

Tony Pan , School of Computational Science and Engineering, Georgia Institute of Technology, 1372 Decatur, Georgia United States 30033 (e-mail: tpan7@gatech.edu)
Patrick Flick , Computational Science and Engineering, Georgia Institute of Technology, 1372 Atlanta, Georgia United States (e-mail: patrick.flick@gatech.edu)
Chirag Jain , Georgia Institute of Technology, 1372 Atlanta, Georgia United States 30332-0002 (e-mail: cjain7@gatech.edu)
Yongchao Liu , School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, Georgia United States 30332 (e-mail: yliu860@gatech.edu)
Srinivas Aluru , School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia United States 30332 (e-mail: aluru@cc.gatech.edu)

Linear time algorithms to construct populations fitting multiple constraint distributions at genomic scales (Abstract)

Enrico Siragusa , Computational Genomics, IBM Thomas J Watson Research Center, 71353 Yorktown Heights, New York United States 10598-0218 (e-mail: esiragu@us.ibm.com)
Niina Haiminen , Computational Genomics, IBM Thomas J Watson Research Center, 71353 Yorktown Heights, New York United States (e-mail: nshaimin@us.ibm.com)
Filippo Utro , Computational Genomics, IBM Thomas J Watson Research Center, 71353 Yorktown Heights, New York United States (e-mail: futro@us.ibm.com)
Laxmi Parida , Computational Genomics, IBM Thomas J Watson Research Center, 71353 Yorktown Heights, New York United States (e-mail: parida@us.ibm.com)

Efficient Local Search for Euclidean Path-Difference Median Trees (Abstract)

Alexey Markin , Computer Science, Iowa State University, 1177 Ames, Iowa United States (e-mail: amarkin@iastate.edu)
Oliver Eulenstein , Computer Science, Iowa State University, Ames, Iowa United States (e-mail: oeulenst@iastate.edu)

Human pathway-based disease network (Abstract)

Liang Yu , School of Computer Science and Technology, Xidian University, Xian, Shaanxi China 710071 (e-mail: lyu@xidian.edu.cn)
Lin Gao , School of Computer Science and Technology, Xidian University, Xian, Shaanxi China (e-mail: lgao@mail.xidian.edu.cn)

Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling (Abstract)

Muhibur Rasheed , Computer Science, University of Texas at Austin, Austin, Texas United States (e-mail: muhibur@utexas.edu)
Nathan Clement , Computer Science, University of Texas at Austin, Austin, Texas United States 78705 (e-mail: nclement@cs.utexas.edu)
Abhishek Bhowmick , Computer Science, University of Texas at Austin, Austin, Texas United States (e-mail: ab.abhishek.bhowmick@gmail.com)
Chandrajit L. Bajaj , Computer Science, University of Texas at Austin, Austin, Texas United States (e-mail: bajaj@cs.utexas.edu)

Protein-protein interaction identification using a similarity-constrained graph model (Abstract)

Yun Niu , College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu Province China 211106 (e-mail: yniu@nuaa.edu.cn)
Hongmei Wu , College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu Province China (e-mail: whm_1991@nuaa.edu.cn)
Yuwei Wang , College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu Province China (e-mail: ywwang@nuaa.edu.cn)

Constructing Pathway-based Priors Within a Gaussian Mixture Model for Bayesian Regression and Classification (Abstract)

Shahin Boluki , Electrical Engineering, Texas A & M University, College Station, Texas United States 77843 (e-mail: s.boluki@tamu.edu)
Mohammad Shahrokh Esfahani , Oncology, School of Medicince, Stanford University, Stanford, California United States 94305-5458 (e-mail: shahrokh@stanford.edu)
Xiaoning Qian , Texas A&M, College Station, Texas United States (e-mail: xqian@ece.tamu.edu)
Edward Russell Dougherty , Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas United States (e-mail: edward@ece.tamu.edu)

The Robust Classification Model Based on Combinatorial Features (Abstract)

Xiaohui Lin , Dalian University of Technology, Dalian, Liaoning China (e-mail: datas@dlut.edu.cn)
Xin Huang , Dalian University of Technology, 12399 Dalian, Liaoning China (e-mail: 845838820@mail.dlut.edu.cn)
Lina Zhou , Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning China (e-mail: lnzhou@126.com)
Weijie Ren , Dalian University of Technology, 12399 Dalian, Liaoning China (e-mail: 253058773@qq.com)
Jun Zeng , Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning China (e-mail: zjxm69602@yeah.net)
Weihong Yao , Dalian University of Technology, 12399 Dalian, Liaoning China (e-mail: weihongy@dlut.edu.cn)
Xingyuan Wang , Dalian University of Technology, Dalian, Liaoning China (e-mail: wangxy@dlut.edu.cn)

An RJMCMC-Based Method for Tracking and Resolving Collisions of Drosophila Larvae (Abstract)

Tim Michels , Computer Science, Christian-Albrechts-Universitat zu Kiel Institut fur Informatik, 64344 Kiel, Schleswig-Holstein Germany (e-mail: tmi@informatik.uni-kiel.de)
Dimitri Berh , Mathmatics and Computer Science, Westfalische Wilhelms Universitat Munster Fachbereich 10 Mathematik und Informatik, 234671 Munster, Nordrhein-Westfalen Germany (e-mail: d.berh@uni-muenster.de)
Xiaoyi Jiang , Department of Mathematics and Computer Science, University of Minster, Minster, NRW Germany (e-mail: xjiang@uni-muenster.de)

Estrogenic active stilbene derivatives as anti-cancer agents: A DFT and QSAR study (Abstract)

Bilal Nizami , Department of Biochemistry and Microbiology, Rhodes university, Research Unit in Bioinformatics (RUBi), Grahamstown, Eastern Cape South Africa (e-mail: nizamibilal1064@gmail.com)
Elham Mousavinezhad Sarasia , Durban, Kwazulu-Natal South Africa (e-mail: elham.mousavi@yahoo.com)
Mehbub I. K. Momin , Durban, KwazuluNatal South Africa (e-mail: mehbub2315@gmail.com)
Bahareh Honarparvar , UKZN, Durban, Kuazulu-Natal South Africa (e-mail: honarparvar@ukzn.ac.za)

Theory and A Heuristic for the Minimum Path Flow Decomposition Problem (PDF)

Mingfu Shao , Computational Biology Department, Carnegie Mellon University, 6612 Pittsburgh, Pennsylvania United States 15213-3815 (e-mail: shaomingfu@gmail.com)
Carl Kingsford , Carnegie Mellon University, Pittsburgh, Pennsylvania United States (e-mail: carlk@cs.cmu.edu)

A Feature Sampling Strategy for Analysis of High Dimensional Genomic Data (Abstract)

Jie Zhang , Adobe Systems Inc, 58584 San Jose, California United States 95110-2704 (e-mail: jiezhang535161432@gmail.com)
Zhigen Zhao , Department of Statistical Science, Temple University, Philadelphia, Pennsylvania United States (e-mail: zhaozhg@temple.edu)
Kai Zhang , Temple University Computer and Information Sciences Department, 329677 Philadelphia, Pennsylvania United States (e-mail: zhang.kai@temple.edu)
Zhi Wei , Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey United States (e-mail: zhiwei@njit.edu)

Bayesian Network Construction and Genotype-Phenotype Inference Using GWAS Statistics (Abstract)

Lu Zhang , Computer Science and Computer Engineering, University of Arkansas Fayetteville, 3341 Fayetteville, Arkansas United States 72701-4002 (e-mail: lz006@uark.edu)
Qiuping Pan , CSCE, University of Arkansas Fayetteville, 3341 Fayetteville, Arkansas United States 72701-4002 (e-mail: qpan@uark.edu)
Yue Wang , AcuSys, Inc, Alexandria, Virginia United States (e-mail: vwangyue@gmail.com)
Xintao Wu , Computer Science and Computer Engineering, University of Arkansas, Fayetteville, Arkansas United States 72701 (e-mail: xintaowu@uark.edu)
Xinghua Shi , Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina United States 28223 (e-mail: X.Shi@uncc.edu)

Detecting Population-differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection (Abstract)

Huanan Zhang , University of Minnesota Twin Cities, 5635 Minneapolis, Minnesota United States (e-mail: huanan@cs.umn.edu)
David Roe , University of Minnesota Twin Cities, 5635 Minneapolis, Minnesota United States 55455 (e-mail: roex0050@umn.edu)
Rui Kuang , Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota United States (e-mail: kuang@cs.umn.edu)

Bi-level error correction for PacBio long reads (Abstract)

Yuansheng Liu , Advanced Analytics Institute, University of Technology Sydney Faculty of Engineering and Information Technology, 120558 Sydney, New South Wales Australia (e-mail: yyuanshengliu@gmail.com)
Chaowang Lan , Advanced Analytics Institute, University of Technology Sydney Faculty of Engineering and Information Technology, 120558 Sydney, New South Wales Australia (e-mail: Chaowang.Lan@student.uts.edu.au)
Michael Blumenstein , School of Software, University of Technology, Sydney, Sydney, New South Wales Australia (e-mail: michael.blumenstein@uts.edu.au)
Jinyan Li , Advanced Analytics Institute, University of Technology, Sydney, -Broadway, New South Wales Australia 2007 (e-mail: jinyan.li@uts.edu.au)

Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows (Abstract)

Jakob L. Andersen , Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo, Tokyo Japan (e-mail: jakob@caput.dk)
Christoph Flamm , Institute for Theoretical Chemistry, University of Vienna, Vienna, None Austria (e-mail: xtof@tbi.univie.ac.at)
Daniel Merkle , Department of Mathematics and Computer Science, Syddansk Universitet, 6174 Odense, Fyn Denmark 5230 (e-mail: daniel@imada.sdu.dk)
Peter F. Stadler , Computer Science, Univ. Leipzig, Leipzig, Saxony Germany D-04107 (e-mail: studla@bioinf.uni-leipzig.de)

Detection and Recognition for Life State of Cell Cancer Using Two-Stage Cascade CNNs (Abstract)

Haigen Hu , Computer Science and Technology, Zhejiang University of Technology - Pingfeng Campus, 154477 Hangzhou, Zhejiang China 310023 (e-mail: hghu@zjut.edu.cn)
Qiu Guan , College of Computer Science and Technology, Zhejiang University of Technology, 12624 Hangzhou, Zhejiang China (e-mail: gq@zjut.edu.cn)
Shengyong Chen , College of Computer Science and Technology, Zhejiang University of Technology - Pingfeng Campus, 154477 Hangzhou, Zhejiang Province China (e-mail: sy@ieee.org)
Zhiwei Ji , School of Information & Electronic Engineering, Zhejiang Gongshang University, 12625 Hangzhou, Zhejiang China (e-mail: jzw18@hotmail.com)
Lin Yao , College of Life Sciences, Fujian Normal University, 12425 Fuzhou, Fujian China (e-mail: yaolin@fjnu.edu.cn)

New Deep Learning Methods for Protein Loop Modeling (Abstract)

Son Phong Nguyen , Department of Computer Science, University of Missouri, Columbia, Missouri United States 65211 (e-mail: spnf2f@mail.missouri.edu)
Zhaoyu Li , Department of Computer Science, University of Missouri, Columbia, Missouri United States (e-mail: zlht3@mail.missouri.edu)
Dong Xu , Computer Science, University of Missouri-Columnbia, Coulumbia, Missouri United States 65211 (e-mail: xudong@missouri.edu)
Yi Shang , University of Missouri, Columbia, Columbia, Missouri United States 65211 (e-mail: shangy@missouri.edu)

Statistical Association Mapping of Population-Structured Genetic Data (Abstract)

Amir Najafi , Computer Engineering, Sharif University of Technology, 68260 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: najafy@ce.sharif.edu)
Sepehr Janghorbani , Computer Engineering, Sharif University of Technology, 68260 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: janghorbani@ce.sharif.edu)
Seyed Abolfazl Motahari , Computer Engineering, Sharif University of Technology, 68260 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: motahari@sharif.edu)
Emad Fatemizadeh , Electrical Engineering, Sharif University of Technology, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: fatemizadeh@sharif.edu)

Unsupervised Discovery of Geometrically Common Structural Motifs and Long-Range Contacts in Protein 3D Structures (Abstract)

Florian Kaiser , Applied Computer and Biosciences, Hochschule Mittweida, 64355 Mittweida, Saxony Germany (e-mail: florian.kaiser@hs-mittweida.de)
Dirk Labudde , Hochschule Mittweida, 64355 Mittweida, Saxiny Germany 09648 (e-mail: dirk.labudde@hs-mittweida.de)

An Integrated Framework for Identifying Mutated Driver Pathway and Cancer Progression (Abstract)

Wei Zhang , Hunan University, 12569 Changsha, Hunan China 410082 (e-mail: zhangwei6409520@hnu.edu.cn)
Shulin Wang , Hunan University, 12569 Changsha, Hunan China (e-mail: jt_slwang@hotmail.com)

Credibility of Evolutionary Events in Gene Trees (Abstract)

Agnieszka Mykowiecka , Uniwersytet Warszawski Wydzial Matematyki Informatyki i Mechaniki, 121883 Warszawa, Mazowieckie Poland 02-097 (e-mail: agnieszka.mykowiecka@mimuw.edu.pl)
Pawel Gorecki , Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, mazowieckie Poland 02-097 (e-mail: gorecki@mimuw.edu.pl)

GapReduce: a gap filling algorithm based on partitioned read sets (Abstract)

Junwei Luo , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: luojunwei@csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Juan Shang , Computer Science, Central South University, ChangSha, Hunan China (e-mail: shangjuan@csu.edu.cn)
Huimin Luo , School of Information Science and Engineering, Central South University, 12570 Changsha, Hunan China (e-mail: luohuimin@csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)

ProtDet-CCH: Protein remote homology detection by combining Long Short-Term Memory and ranking methods (Abstract)

Bin Liu , Harbin Institute of Technology, Harbin, Heilongjiang China (e-mail: bliu@insun.hit.edu.cn)
Shumin Li , Shenzhen, Guandong China (e-mail: Shuminli20001@qq.com)

A Unified Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq data (Abstract)

Kefei Liu , Indiana University School of Medicine, 12250 Indianapolis, Indiana United States 46202 (e-mail: kefliu@iu.edu)
Jieping Ye , University of Michigan, Ann Arbor, Ann Arbor, Michigan United States 48109-2218 (e-mail: jpye@umich.edu)
Yang Yang , School of Computer Science and Engineering, Beihang University, Beijing, Beijing China (e-mail: yangyangfuture@buaa.edu.cn)
Li Shen , Indiana University, Indianapolis, Indiana United States 46260 (e-mail: shenli@iu.edu)
Hui Jiang , Biostatistics, University of Michigan, Ann Arbor, Michigan United States 48109 (e-mail: jianghui@umich.edu)

Fast Algorithms for Computing Path-Difference Distances (Abstract)

Biing-Feng Wang , Computer Science, National Tsing Hua University, Hsinchu, Taiwan Taiwan (e-mail: bfwang@cs.nthu.edu.tw)
Chih-Yu Li , Computer Science, National Tsing Hua University, Hsinchu, Taiwan Taiwan (e-mail: cyuli@cs.nthu.edu.tw)

Estimation of the Spatial Chromatin Structure Based on a Multiresolution Bead-Chain Model (Abstract)

Claudia Caudai , Istituto di Scienza e Tecnologie dell'Informazione, Consiglio Nazionale delle Ricerche, 9327 Pisa, PI Italy (e-mail: claudia.caudai@isti.cnr.it)
Emanuele Salerno , Istituto di Scienza e Tecnologie dell'Informazione, Consiglio Nazionale delle Ricerche, 9327 Pisa, PI Italy 56124 (e-mail: emanuele.salerno@isti.cnr.it)
Monica Zoppe , Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, 9327 Pisa, PI Italy (e-mail: mzoppe@ifc.cnr.it)
Anna Tonazzini , Istituto di Scienza e Tecnologie dall'Informazione, Consiglio Nazionale delle Ricerche, Pisa, Italy Italy 56124 (e-mail: anna.tonazzini@isti.cnr.it)

Modelling and Control of Gene Regulatory Networks for Perturbation Mitigation (PDF)

Mathias Foo , School of Engineering, University of Warwick, 2707 Coventry, West Midlands United Kingdom of Great Britain and Northern Ireland CV4 7AL (e-mail: M.Foo@warwick.ac.uk)
Jongrae Kim , School of Mechanical Engineering, University of Leeds, 4468 Leeds, West Yorkshire United Kingdom of Great Britain and Northern Ireland (e-mail: menjkim@leeds.ac.uk)
Declan Bates , School of Engineering, University of Warwick, 2707 Coventry, West Midlands United Kingdom of Great Britain and Northern Ireland (e-mail: D.Bates@warwick.ac.uk)

Safely Filling Gaps with Partial Solutions Common to All Solutions (PDF)

Leena Salmela , Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, NA Finland (e-mail: leena.salmela@cs.Helsinki.FI)
Alexandru Ioan Tomescu , Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Helsinki Finland (e-mail: tomescu@cs.helsinki.fi)

Stable IL-1$\beta$-Activation in an Inflammasome Signalling Model Depends on Positive and Negative Feedbacks and Tight Regulation of Protein Production (Abstract)

Fernando Lopez-Caamal , Department of Chemical Engineering, Universidad de Guanajuato, 14654 Guanajuato, Guanajuato Mexico 36000 (e-mail: fernando.lopez@ugto.mx)
Huber Heinrich , Institute for Automation Engineering, Systems Theory and Automatic Control Laboratory, Otto-von-Guericke Universitat Magdeburg, Magdeburg, Sachsen-Anhalt Germany (e-mail: heinrich.huber@ovgu.de)

An Adaptive Robust Control Strategy in a Cancer Tumor-Immune System under Uncertainties (Abstract)

Arta Jamshidi , Control Department, Univeristy of Tehran, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: arta.jamshidi@gmail.com)

Learning to Refine Expansion Terms for Biomedical Information Retrieval using Semantic Resources (Abstract)

Bo Xu , School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning China (e-mail: xubo2011@mail.dlut.edu.cn)
Hongfei Lin , Dept. of Computer Science and Engineering, Dalian University of Technology, Dalian, Liaoning China (e-mail: hflin@dlut.edu.cn)
Yuan Lin , Dalian University of Technology, Dalian, Liaoning China (e-mail: zhlin@dlut.edu.cn)

High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer (Abstract)

Shaoliang Peng , School of Computer Science, National University of Defense Technology, 58294 Changsha, Hunan China (e-mail: pengshaoliang@nudt.edu.cn)
Xiaoyu Zhang , School of Computer Science, National University of Defense Technology, 58294 Changsha, Hunan China (e-mail: zhangxiaoyu11@nudt.edu.cn)
Yutong Lu , Computer Science and Technology, National University of Defense Technology, Changsha, Hunan China 410073 (e-mail: yutong.lu@nscc-gz.cn)
Xiangke Liao , CSE, NUDT, Changsha, Hunan China (e-mail: xkliao@nudt.edu.cn)
Kai Lu , School of Computer Science, National University of Defense Technology, 58294 changsha, Hunan China (e-mail: 13407316868@139.com)
Canqun Yang , School of Computer Science, National University of Defense Technology, Changsha, Hunan China (e-mail: canqun@nudt.edu.cn)
Jie Liu , School of Computer Science, National University of Defense Technology, Changsha, Hunan China (e-mail: jieliu@nudt.edu.cn)
Weiliang Zhu , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, Shanghai China (e-mail: wlzhu@simm.ac.cn)
Dongqing Wei , College of Life Sciences and Biotechnology and State Key Laboratory of Microbial Metabolism, Shanghai, Shanghai China (e-mail: dqwei@sjtu.edu.cn)

A multimodal deep neural network for human breast cancer prognosis prediction by integrating multi-dimensional data (Abstract)

Dongdong Sun , School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: sddchina@mail.ustc.edu.cn)
Minghui Wang , School of Information Science and Technology, and Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, Anhui China (e-mail: mhwang@ustc.edu.cn)
Ao Li , School of Information Science and Technology, and Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, Anhui China (e-mail: aoli@ustc.edu.cn)

IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads (Abstract)

Jin Zhao , School of Computer Science and Technology, Shandong University, 12589 Jinan, Shandong Province China (e-mail: zhaojin_cc@163.com)
Haodi Feng , School of Computer Science and Technology, Shandong University, Jinan, Shandong Province China (e-mail: fenghaodi@sdu.edu.cn)
Daming Zhu , School of Computer Science and Technology, Shandong University, Jinan, Shandong Province China (e-mail: dmzhu@sdu.edu.cn)
Chi Zhang , Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana United States (e-mail: czhang87@iu.edu)
Ying Xu , Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia United States 30602-7229 (e-mail: xyn@bmb.uga.edu)

A fast exact functional test for directional association and cancer biology applications (Abstract)

Hua Zhong , Department of Computer Science, New Mexico State University, Las Cruces, New Mexico United States (e-mail: huazhong@nmsu.edu)
Mingzhou Song , Department of Computer Science, New Mexico State University, Las Cruces, New Mexico United States (e-mail: joemsong@cs.nmsu.edu)

Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data (Abstract)

Zaobo He , computer science, Georgia State University, atlanta, Georgia United States (e-mail: zhe4@student.gsu.edu)
Jiguo Yu , School of Computer Science, Qufu Normal Univeristy, Rizhao, Shandong China 276826 (e-mail: jiguoyu@sina.com)
Ji Li , Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: jli30@student.gsu.edu)
Qilong Han , Harbin, HeiLongJiang China (e-mail: hanqilong@hrbeu.edu.cn)
Guangchun Luo , Computer Science, University of Electronic Science and Technology of China, Chengdu, Sichuan China (e-mail: gcluo@uestc.edu.cn)
Yingshu Li , Department of Computer Science, Georgia State University, Atlanta, Georgia United States 30302 (e-mail: yili@gsu.edu)

Microarray Missing Value Imputation: A Regularized Local Learning Method (Abstract)

Aiguo Wang , Gerontechnology Lab, Hefei univercity of Technology, Hefei, Anhui China (e-mail: eric.ag.wang@qq.com)
Ye Chen , Gerontechnology Lab, Hefei univercity of Technology, Hefei, Anhui China (e-mail: 315866108@qq.com)
Ning An , Gerontechnology Lab, Hefei univercity of Technology, Hefei, Anhui China (e-mail: ning.g.an@acm.org)
Jing Yang , Gerontechnology Lab, Hefei university of Technology, Hefei, Anhui China (e-mail: jsjyj0801@163.com)
Lian Li , Gerontechnology Lab, Hefei univercity of Technology, Hefei, Anhui China (e-mail: lilian@hfut.edu.cn)
Lili Jiang , Department of Computing Science, Umea Universitet, 8075 Umea, Umea Sweden (e-mail: lili.jiang@cs.umu.se)

A robust simulator for physiologically structured population models (Abstract)

Michiel Van Dyck , Department of Mathematics and Computer Science, Universiteit Antwerpen Faculteit Wetenschappen, 98722 Antwerpen, Antwerpen Belgium (e-mail: michiel.vandyck@uantwerpen.be)
Xavier Woot de Trixhe , Janssen Pharmaceutica NV, 50148 Beerse, Antwerpen Belgium (e-mail: xwootdet@its.jnj.com)
An Vermeulen , Janssen Pharmaceutica NV, 50148 Beerse, Antwerpen Belgium (e-mail: avermeul@its.jnj.com)
Wim Vanroose , Universiteit Antwerpen Faculteit Wetenschappen, 98722 Antwerpen, Antwerpen Belgium (e-mail: wim.vanroose@uantwerpen.be)

Comorbidity Scoring with Causal Disease Networks (Abstract)

Jong Ho Jhee , Industrial engineering, Ajou University, 34919 Suwon, Gyeonggi Korea (the Republic of) 16499 (e-mail: baical77@ajou.ac.kr)
Sunjoo Bang , Industrial engineering, Ajou University, 34919 Suwon, Gyeonggi Korea (the Republic of) (e-mail: smalsunjoo@ajou.ac.kr)
Dong-gi Lee , Industrial engineering, Ajou University, 34919 Suwon, Gyeonggi Korea (the Republic of) (e-mail: ldg1226@ajou.ac.kr)
Hyunjung Shin , Department of Industrial and Information Systems Engineering, Ajou University, Suwon, Korea Korea, Republic of 443-749 (e-mail: shin@ajou.ac.kr)

Secure Wavelet Matrix: Alphabet-Friendly Privacy-Preserving String Search for Bioinformatics (PDF)

Hiroki Sudo , Waseda Daigaku, 13148 Shinjuku-ku, Tokyo Japan (e-mail: hsudo108@ruri.waseda.jp)
Masanobu Jimbo , Waseda Daigaku, 13148 Shinjuku-ku, Tokyo Japan (e-mail: jimwase@asagi.waseda.jp)
Koji Nuida , Sangyo Gijutsu Sogo Kenkyujo, 13508 Chiyoda-ku, Tokyo Japan (e-mail: k.nuida@aist.go.jp)
Kana Shimizu , Waseda Daigaku, 13148 Shinjuku-ku, Tokyo Japan 169-8050 (e-mail: shimizu.kana@waseda.jp)

Stage-Dependent Gene Expression Profiling in Colorectal Cancer (Abstract)

Man-Sun Kim , Department of Horticulture, Chungnam National University College of Agriculture and Life Sciences, 271684 Daejeon, N/A Korea (the Republic of) (e-mail: kms77@cnu.ac.kr)
Dongsan Kim , Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 34968 Daejeon, N/A Korea (the Republic of) (e-mail: dongsan@kaist.ac.kr)
Jeong-Rae Kim , Department of Mathematics, University of Seoul, 35010 Dongdaemun-gu, Seoul Korea (the Republic of) (e-mail: jrkim@uos.ac.kr)

Systematic Inspection of the Clinical Relevance of TP53 Missense Mutations in Gastric Cancer (PDF)

SeongRyeol Moon , Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, 65440 Incheon, Seoul Korea (the Republic of) (e-mail: moonsr1982@gmail.com)
Curt Balch , Complex Biological Systems Alliance, North Andover, Massachusetts United States (e-mail: curt.balch@gmail.com)
Sungjin Park , College of Medicine, Gachon University, 65440 Incheon, Seoul Korea (the Republic of) (e-mail: oscar.park@gmail.com)
Jinhyuk Lee , KOBIC, Korea Research Institute of Bioscience and Biotechnology, 54679 Daejeon, Daejeon Korea (the Republic of) (e-mail: jinhyuk@kribb.re.kr)
Jiyong Sung , Gachon University, 65440 Incheon, Seoul Korea (the Republic of) (e-mail: jysung329@gmail.com)
Seungyoon Nam , College of Medicine, Gachon University, 65440 Incheon, Seoul Korea (the Republic of) 13120 (e-mail: seungyoon.nam@gmail.com)

Designing optimal experiments to discriminate interaction graph models (PDF)

Sven Thiele , Max-Planck-Institut fur Dynamik komplexer technischer Systeme, 28307 Magdeburg, Sachsen-Anhalt Germany 39016 (e-mail: sthiele78@gmail.com)
Steffen Klamt , Max-Planck-Institut fur Dynamik komplexer technischer Systeme, 28307 Magdeburg, Sachsen-Anhalt Germany (e-mail: klamt@mpi-magdeburg.mpg.de)

Computational prediction of sigma-54 promoters in bacterial genomes by integrating motif finding and machine learning strategies (Abstract)

Bingqiang Liu , Mathematics, Shandong University, 12589 Jinan, Other China 250100 (e-mail: bingqiang@sdu.edu.cn)
Ling Han , Mathematics, Shandong University, 12589 Jinan, Other China (e-mail: 1427992316@qq.com)
Xiangrong Liu , Computer Science, Xiamen University, 12466 Xiamen, Fujian China (e-mail: xrliu@xmu.edu.cn)
Jichang Wu , Mathematics, Shandong University, 12589 Jinan, Other China (e-mail: jichangwu@126.com)
Qin Ma , South Dakota State University, 2019 Brookings, South Dakota United States 57007-2201 (e-mail: Qin.Ma@sdstate.edu)

Identification of local clusters of mutation hotspots in cancer-related genes and their biological relevance (Abstract)

Je-Keun Rhee , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) 06591 (e-mail: jkrhee@catholic.ac.kr)
Jinseon Yoo , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) (e-mail: dbwlstjs0@gmail.com)
Kyu Ryung Kim , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) (e-mail: kyuryung.kim@catholic.ac.kr)
Jeeyoon Kim , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) (e-mail: jeeyk017@catholic.ac.kr)
Yong-Jae Lee , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) (e-mail: leayong123@catholic.ac.kr)
Byoung Chul Cho , Yonsei University College of Medicine, 37991 Seodaemun-gu, Seoul Korea (the Republic of) (e-mail: CBC1971@yuhs.ac)
Tae-Min Kim , Catholic University of Korea School of Medicine, 37128 Seoul, Seoul Korea (the Republic of) (e-mail: tmkim@catholic.ac.kr)

EBWS: Essential Bioinformatics Web Services for Sequence Analyses (Abstract)

Dimitrios Kaloudas , Sofia, non Bulgaria (e-mail: dimitris.kaloudas@gmail.com)
Nikolet Pavlova , Sofia, non Bulgaria (e-mail: nikolet.pavlova@gmail.com)
Robert Penchovsky , Department of Genetics, Faculty of Biology, Sofia University Saint Kliment Ohridski, Sofia, Sofia Bulgaria 1165 (e-mail: robert.penchovsky@hotmail.com)

A MODEL for DISTRIBUTED PROCESSING and ANALYSES of NGS DATA under MAP-REDUCE PARADIGM (Abstract)

Sandip Samaddar , Computer Science and Engineering, Heritage Institute of Technology, 231983 Kolkata, West Bengal India (e-mail: sandip.samaddar@heritageit.edu)
Rituparna Sinha , Information Technology, Heritage Institute of Technology, 231983 Kolkata, West Bengal India (e-mail: rituparna.sinha@heritageit.edu)
Rajat K. De , Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal India 700108 (e-mail: rajat@isical.ac.in)

Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm (PDF)

Viacheslav Kapilevich , Graduate School of Information Science and Technology, Osaka University, Suita, Osaka Japan (e-mail: skkap@ist.osaka-u.ac.jp)
Shigeto Seno , Graduate School of Information Science and Technology, Osaka University, Suita, Osaka Japan (e-mail: senoo@ist.osaka-u.ac.jp)
Hideo Matsuda , Graduate School of Information Science and Technology, Osaka University, Suita, Osaka Japan (e-mail: matsuda@ist.osaka-u.ac.jp)
Yoichi Takenaka , Faculty of Informatics, Kansai University, Takatsuki, Osaka Japan (e-mail: takenaka@kansai-u.ac.jp)

Automated ICD-9 Coding via A Deep Learning Approach (Abstract)

Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Zhihui Fei , Changsha, Hunan China (e-mail: zhihuifei@foxmail.com)
Min Zeng , Changsha, Hunan China (e-mail: zengmin1990@163.com)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yaohang Li , Norfolk, Virginia United States (e-mail: yaohang@cs.odu.edu)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Constructing Disease Similarity Networks Based on Disease Module Theory (Abstract)

Peng Ni , School of Information Science and Engineering, Central South University, Changsha, Hunan China (e-mail: nipeng@csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Ping Zhong , School of Information Science and Engineering, Central South University, Changsha, Hunan China (e-mail: ping.zhong@csu.edu.cn)
Yaohang Li , Department of Computer Science, Old Dominion University, 6042 Norfolk, Virginia United States (e-mail: yaohang@cs.odu.edu)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)

High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites (Abstract)

Qinhu Zhang , Tongji University, 12476 Shanghai, Shanghai China 200092 (e-mail: 472765713@qq.com)
Lin Zhu , Tongji University, Shanghai, Shanghai China (e-mail: lizhonyx@163.com)
De-Shuang Huang , Computer Science Department, Tongji University, Shanghai, ShangHai China (e-mail: dshuang@tongji.edu.cn)

ParaCells: A GPU Architecture for Cell-Centered Models in Computational Biology (Abstract)

You Song , Software School, Beihang University, Beijing, Beijing China (e-mail: songyou@buaa.edu.cn)
Siyu Yang , Software School, Beihang University, Beijing, Beijing China (e-mail: yangsiyu1992@gmail.com)
JinZhi Lei , Zhou PeiYuan Center for Applied Mathematics, Tsinghua University, Beijing, Beijing China 100084 (e-mail: jzlei@tsinghua.edu.cn)

Biomarker Identification for Cancer Disease Using Biclustering Approach: An Empirical Study (Abstract)

Koyel Mandal , CSE, Tezpur University, Tezpur, Assam India (e-mail: koyel@tezu.ernet.in)
Rosy Sarmah , CSE, Tezpur University, Tezpur, Assam India 784028 (e-mail: rosy8@tezu.ernet.in)
Dhruba Kumar Bhattacharyya , Computer Science and Engineering, Tezpur University, Tezpur, Assam India 784028 (e-mail: dkb@tezu.ernet.in)

Controllability Analysis of A Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families (Abstract)

Pei Wang , Henan University, School of Mathematics and Information Sciences, Kaifeng, Henan China (e-mail: wp0307@126.com)
Daojie Wang , Henan University, State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; College of Life Sciences, Kaifeng, Henan China (e-mail: wangdj@henu.edu.cn)
Jinhu Lu , Chinese Academy of Sciences, Beijing, Beijing China (e-mail: jhlu@iss.ac.cn)

Bioimage Classification with Handcrafted and Learned Features (Abstract)

Loris Nanni , DEIS, University of Bologna, Bologna, Bologna Italy 40136 (e-mail: loris.nanni@unibo.it)
Sheryl Brahnam , CIS, Missouristate University, Springfield, Missouri United States 65804 (e-mail: sbrahnam@missouristate.edu)
Stefano Ghidoni , Department of Information Engineering, University of Padua, Padua, Padua Italy (e-mail: Stefano.ghidoni@unipd.it)
Alessandra Lumini , DEIS, University di Bologna, Cesena, FC Italy 47521 (e-mail: alessandra.lumini@unibo.it)

Submodular generalized matching for peptide identification in tandem mass spectrometry (Abstract)

Wenruo Bai , Department of Electrical Engineering, University of Washington, 7284 Seattle, Washington United States (e-mail: wrbai@uw.edu)
Jeffrey Bilmes , Department of Electrical Engineering, University of Washington, 7284 Seattle, Washington United States (e-mail: bilmes@uw.edu)
William Stafford Noble , Department of Genome Sciences, University of Washington, 7284 Seattle, Washington United States (e-mail: william-noble@uw.edu)

Measuring Boundedness for Protein Complex Identification in PPI Networks (Abstract)

Tiantian He , COMP, The Hong Kong Polytechnic University, Hung Hom, Kowloon Hong Kong (e-mail: csthe@comp.polyu.edu.hk)
Keith C.C. Chan , Computing, Hong Kong Polytechnic University, Hong Kong, Hong Kong Hong Kong Nil (e-mail: cskcchan@comp.polyu.edu.hk)

Differentiating prostate cancer from benign prostatic hyperplasia using PSAD based on machine learning: Single-center retrospective study in China (Abstract)

Yiyan Zhang , School of Life science, Beijing Institute of Technology, 47833 Beijing, Beijing China 100081 (e-mail: zhangyiyan0307@163.com)
Qin Li , School of Life science, Beijing Institute of Technology, 47833 Beijing, Beijing China (e-mail: linqin@bit.edu.cn)
Yi Xin , School of Life science, Beijing Institute of Technology, 47833 Beijing, Beijing China (e-mail: emeko@bit.edu.cn)
Weiqi Lv , School of Life science, Beijing Institute of Technology, 47833 Beijing, Beijing China (e-mail: lwq_voice@126.com)

BitMapper2: a GPU-accelerated all-mapper based on the sparse q-gram index (Abstract)

Haoyu Cheng , University of Science and Technology of China, 12652 Hefei, Anhui China 230026 (e-mail: chhy@mail.ustc.edu.cn)
Yong Zhang , University of Science and Technology of China, 12652 Hefei, Anhui China (e-mail: zy1990@mail.ustc.edu.cn)
Yun Xu , Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: xuyun@ustc.edu.cn)

Transfer Learning for Molecular Cancer classification using Deep Neural Networks (Abstract)

Rahul Kumar Sevakula , Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh India 208016 (e-mail: rahul.sevakula@gmail.com)
Vikas Singh , Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh India (e-mail: vikkyk@iitk.ac.in)
Nishchal K. Verma , Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh India 208016 (e-mail: nishchal.iitk@gmail.com)
Chandan Kumar , Indian Institute of Technology Guwahati, 28678 Guwahati, Assam India (e-mail: chandankr251297@gmail.com)
Yan Cui , University of Tennessee Health Science Center, 12326 Memphis, Tennessee United States (e-mail: ycui2@uthsc.edu)

Flexible Non-negative Matrix Factorization to Unravel Disease-related Genes (Abstract)

Xue Jiang , college of computer and control engineering, Nankai University, 12538 Tianjin, Tianjin China 300071 (e-mail: jiangxue@mail.nankai.edu.cn)
Hang Zhang , Tianjin, Tianjin China (e-mail: zhanghan@nankai.edu.cn)
Zhao Zhang , Tianjin, Tianjin China (e-mail: zhangzhao0807@sina.com)
Xiongwen Quan , Tianjin, Tianjin China (e-mail: quanxw@nankai.edu.cn)

Machine Vision System for 3D Plant Phenotyping (Abstract)

Ayan Chaudhury , Computer Science, Western University, 6221 London, Ontario Canada N6A 3K7 (e-mail: achaud29@uwo.ca)
John L. Barron , 1151 Richmond Street, Univ. of Western Ontario, London, Ontario Canada N6A 5B7 (e-mail: barron@csd.uwo.ca)

A probabilistic framework for molecular network structure inference by means of mechanistic modeling (PDF)

Juho Timonen , Department of Computer Science, Aalto University School of Science, Espoo, Uusimaa Finland (e-mail: juho.timonen@aalto.fi)
Henrik Mannerstrom , Department of Computer Science, Aalto University School of Science, Espoo, Uusimaa Finland (e-mail: henrik.mannerstrom@aalto.fi)
Harri Lahdesmaki , Department of Computer Science, Aalto University School of Science, Espoo, Uusimaa Finland (e-mail: harri.lahdesmaki@aalto.fi)
Jukka Intosalmi , Department of Computer Science, Aalto University School of Science, Espoo, Uusimaa Finland (e-mail: jukka.intosalmi@aalto.fi)

A novel cluster-based computational method to identify miRNA regulatory modules (Abstract)

Jiawei Luo , Hunan University, the College of Information Science and Engineering, Changsha, Hunan China (e-mail: luojiawei@hnu.edu.cn)
Chu Pan , Information Science and Electronic Engineering, Hunan University, Changsha, Hunan China (e-mail: panchu@hnu.edu.cn)

Inferring large-scale gene regulatory networks using a randomized algorithm based on singular value decomposition (Abstract)

Anjing Fan , School of Mathematics and Statistics, Wuhan University, wuhan, Hubei China (e-mail: anjingfan@whu.edu.cn)
Haitao Wang , Wuhan University, wuhan, Hubei China (e-mail: 773950750@qq.com)
Hua Xiang , School of Mathematics and Statistics, Wuhan University, wuhan, Hubei China (e-mail: hxiang@whu.edu.cn)
Xiufen Zou , Wuhan University, Wuhan, HuBei China 430072 (e-mail: xfzou@whu.edu.cn)

Dynamical Detection of Boundaries and Cavities in Biophysical Cell-based Simulations of Growing Tumor Tissues (Abstract)

Sabrina Stella , Physics, University of Trieste, Trieste, TS Italy (e-mail: Sabrina.Stella@ts.infn.it)
Roberto Chignola , Department of Biotechnology, University of Verona, Verona, Verona Italy (e-mail: roberto.chignola@univr.it)
Edoardo Milotti , Physics, University of Trieste, Trieste, TS Italy (e-mail: milotti@units.it)

A Novel Method for LncRNA-Disease Association Prediction Based on an lncRNA-disease Association Network (Abstract)

pengyao ping , College of Information Engineering, Xiangtan University, 12665 Xiangtan, HuNan China (e-mail: 956272448@qq.com)
Lei Wang , college of computer engineering applied mathematics, Changsha University, 121868 Changsha, Hunan China (e-mail: wanglei@xtu.edu.cn)
Linai Kuang , college of computer engineering applied mathematics, Changsha University, 121868 Changsha, Hunan China (e-mail: zhc680518@163.com)
Songtao Ye , Xiangtan University, 12665 Xiangtan, HuNan China 411105 (e-mail: 985326696@qq.com)
Muhammad Faisal Buland Iqbal , Xiangtan University, 12665 Xiangtan, HuNan China 411105 (e-mail: 1146105816@qq.com)
Tingrui Pei , Xiangtan University, 12665 Xiangtan, HuNan China 411105 (e-mail: 308407367@qq.com)

Efficient Mining Multi-mers in a Variety of Biological Sequences (Abstract)

Jingsong Zhang , Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, Shanghai China (e-mail: jasun@dmbio.info)
Jianmei Guo , Alibaba Group, Hangzhou, Zhejiang China (e-mail: gjm@ecust.edu.cn)
Ming Zhang , The Second Military Medical University, Shanghai, Shanghai China (e-mail: mingzhang@dmbio.info)
Xiangtian Yu , Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, Shanghai China (e-mail: graceyu1985@163.com)
Xiaoqing Yu , Department of Applied Mathematics, Shanghai Institute of Technology, Shanghai, Shanghai China (e-mail: xqyu@sit.edu.cn)
Weifeng Guo , School of Automation, Northwestern Polytechnical University, 26487 Xi'an, shaanxi China (e-mail: shaonianweifeng@126.com)
Tao Zeng , Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, Shanghai China (e-mail: zengtao@sibs.ac.cn)
Luonan Chen , Chinese Academy of Sciences, Shanghai Institute of Biological Sciences, Shanghai, ShangHai China (e-mail: lnchen@sibs.ac.cn)

A Composite Mode Differential Gene Regulatory Architecture based on Temporal Expression Profiles (Abstract)

Aurpan Majumder , Electronics and Communication Engineering, National Institute of Technology, 210919 Durgapur, West Bengal India 713209 (e-mail: aurpan.nitd@gmail.com)
Mrityunjay Sarkar , Electronics and Communication Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal India (e-mail: mrityu1488@gmail.com)
Prolay Sharma , Instrumentation and Electronics Engineering, Jadavpur University, 30167 Kolkata, West Bengal India (e-mail: prolaysharma08@gmail.com)

A Multi-Laplacian Prior and Augmented Lagrangian Approach to the Exploratory Analysis of Time-Varying Gene and Transcriptional Regulatory Networks for Gene Microarray Data (Abstract)

Li Zhang , School of Biomedical Engineering, Health Science Center, Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, 47890 Shenzhen, Guangdong China (e-mail: lzhang@szu.edu.cn)
H. C. Wu , Department of Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: andrewhcwu@eee.hku.hk)
C. H. Ho , Department of Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: chho@eee.hku.hk)
S. C. Chan , Department of Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: scchan@eee.hku.hk)

Protein Domain Level Cancer Drug Targets in the Network of MAPK pathways (Abstract)

MD Aksam V.K , VIT University, 30026 Vellore, Tamil nadu India 632014 (e-mail: mdaksamvk@gmail.com)
Chandrasekaran V.M. , VIT University, 30026 Vellore, Tamil Nadu India (e-mail: vmcsn@vit.ac.in)
Sundaramurthy Pandurangan , PointCross Life Sciences, Inc., Bangalore, karnataka India (e-mail: pksmurthy2020@gmail.com)

Phylogenetic Reconstruction for Copy-Number Evolution Problems (Abstract)

Ruofan Xia , Computer Science and Engineering, University of south carolina, Columbia, South Carolina United States 29208 (e-mail: sxia@email.sc.edu)
Yu Lin , Research School of Computer Science, Research School of Computer Science, Australian National University, Canberra, Australian Capital Territory Australia (e-mail: biolinyu@gmail.com)
Jun Zhou , Computer Science and Engineering, Univ. South Carolina, Columbia, South Carolina United States 29063 (e-mail: zhou23@email.sc.edu)
Tieming Geng , Computer Science and Engineering, University of South Carolina, Columbia, South Carolina United States (e-mail: TGENG@email.sc.edu)
Feng Bing , Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina United States (e-mail: bingf@email.sc.edu)
Jijun Tang , Computer Science and Engineering, Univ. South Carolina, Columbia, South Carolina United States 29063 (e-mail: jtang@cse.sc.edu)

Control of Gene Regulatory Networks using Bayesian Inverse Reinforcement Learning (Abstract)

Mahdi Imani , Electrical and Computer Engineering, Texas A and M University System, 2655 College Statoion, Texas United States 77843 (e-mail: m.imani88@tamu.edu)
Ulisses Braga-Neto , Texas A&M University, College Station, Texas United States 77843-3128 (e-mail: ulisses@ece.tamu.edu)

MIMOSA: Algorithms for Microbial Profiling (Abstract)

Ozkan Ufuk Nalbantoglu , Erciyes Universitesi, 52958 Kayseri, Kayseri Turkey 38039 (e-mail: nalbantoglu@erciyes.edu.tr)
Khalid Sayood , University of Nebraska-Lincoln College of Engineering, 315578 Lincoln, Nebraska United States (e-mail: ksayood@unl.edu)

GLAlign: A Novel Algorithm for Local Network Alignment (Abstract)

Marianna Milano , university of catanzaro, catanzaro, Catanzaro Italy (e-mail: m.milano@unicz.it)
Pietro Hiram Guzzi , Surgical Medical Sciences, University Magna Graecia, catanzaro, calabria Italy (e-mail: hguzzi@gmail.com)
Mario Cannataro , Medical and Surgical Sciences, University of Catanzaro, Catanzaro, CZ Italy 88100 (e-mail: cannataro@unicz.it)

Modelling Microbial Fuel Cells using lattice Boltzmann methods (Abstract)

Michail-Antisthenis Tsompanas , Unconventional Computing Centre, University of the West of England, 1981 Bristol, Avon United Kingdom of Great Britain and Northern Ireland (e-mail: antisthenis.tsompanas@uwe.ac.uk)
Andy Adamatzky , Uncoventional Computing Centre, University of the West of England, Bristol, Avon United Kingdom of Great Britain and Northern Ireland (e-mail: andrew.adamatzky@uwe.ac.uk)
Ioannis Ieropoulos , Bristol Bioenergy Centre, BRL, University of the West of England, 1981 Bristol, Avon United Kingdom of Great Britain and Northern Ireland (e-mail: ioannis.ieropoulos@brl.ac.uk)
Neil Phillips , Unconventional Computing Centre, University of the West of England, 1981 Bristol, Avon United Kingdom of Great Britain and Northern Ireland (e-mail: Neil.Phillips@uwe.ac.uk)
Georgios Ch. Sirakoulis , Department of Electrical and Computer Engineering, Democritus University of Thrace, Xanthi, Thrace Greece GR 67100 (e-mail: gsirak@ee.duth.gr)
John Greenman , Bristol Bioenergy Centre, BRL, University of the West of England, 1981 Bristol, Avon United Kingdom of Great Britain and Northern Ireland (e-mail: John.Greenman@uwe.ac.uk)

An integrative framework for protein interaction network and methylation data to discover epigenetic modules (Abstract)

Xiaoke Ma , School of Computer Science and Technology, Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: xkma@xidian.edu.cn)
Peng Gang Sun , Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: psun@mail.xidian.edu.cn)
Zhong-Yuan Zhang , Central University of Finance and Economics, Beijing, Beijing China (e-mail: zhyuanzh@gmail.com)

Computational drug repositioning with random walk on a heterogeneous network (Abstract)

Huimin Luo , School of Information Science and Engineering, Central South University, 12570 Changsha, Hunan China (e-mail: luohuimin@csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Junwei Luo , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: luojunwei@csu.edu.cn)
Peng Ni , School of Information Science and Engineering, Central South University, Changsha, Hunan China (e-mail: nipeng@csu.edu.cn)
Kaijie Zhao , School of Information Science and Engineering, Central South University, 12570 Changsha, Hunan China (e-mail: kay.zkj@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)

Identifying Candidate Genetic Associations with MRI-derived AD-related ROI via Tree-guided Sparse Learning (Abstract)

Xiaoke Hao , School of Artificial Intelligence and Data Science, Hebei University of Technology, 12606 Tianjin, Tianjin China (e-mail: robinhc@163.com)
Xiaohui Yao , Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania United States (e-mail: yao2@umail.iu.edu)
Shannon Risacher , Indianapolis, Indiana United States (e-mail: srisache@iupui.edu)
Andrew Saykin , Indianapolis, Indiana United States (e-mail: asaykin@iupui.edu)
Jintai Yu , Nanjing Medical University, Nanjing, Jiangsu China (e-mail: yu-jintai@163.com)
Huifu Wang , Nanjing Medical University, Nanjing, Jiangsu China (e-mail: wanghuifu2010@126.com)
Lan Tan , Qingdao Municipal Hospital, Qingdao, Shandong China (e-mail: dr.tanlan@163.com)
Li Shen , Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania United States (e-mail: Li.Shen@pennmedicine.upenn.edu)
Daoqiang Zhang , School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu China (e-mail: dqzhang@nuaa.edu.cn)

Identifying gene network rewiring by combining gene expression and gene mutation data (Abstract)

Jia-Juan Tu , Wuhan, Hubei China (e-mail: adaline_juan@mails.ccnu.edu.cn)
Le Ou-Yang , Shenzhen University, 47890 Shenzhen, Guangdong China 518060 (e-mail: leouyang@szu.edu.cn)
Xiaohua Hu , College of Information Science and Technology, Drexel University, Philadelphia, Pennsylvania United States 19104 (e-mail: xh29@drexel.edu)
Xiao-Fei Zhang , School of Mathematics and Statistics, Central China Normal University, Wuhan, Hubei China 430079 (e-mail: zhangxf@mail.ccnu.edu.cn)

A distributed feature selection algorithm based on distance correlation with an application to microarrays (Abstract)

Aida Brankovic , Politecnico di Milano Dipartimento di Elettronica Informazione e Bioingegneria, 124243 Milano, Milan Italy 20133 (e-mail: aida.brankovic@polimi.it)
Marjan Hosseini , Milano, Milan Italy (e-mail: marjan.hosseini@mail.polimi.it)
Luigi Piroddi , Politecnico di Milano Dipartimento di Elettronica Informazione e Bioingegneria, 124243 Milano, Milan Italy (e-mail: luigi.piroddi@polimi.it)

A Deep Learning Approach for Targeted Contrast-Enhanced Ultrasound Based Prostate Cancer Detection (Abstract)

Yujie Feng , Chongqing University Cancer Hospital, Chongqing, Chongqing China (e-mail: yujiegeng@qq.com)
Fan Yang , Chongqing University, 47913 Chongqing, Sichuan China (e-mail: 825603843@qq.com)
Xichuan Zhou , College of Communication Engineering, Chongqing University, 47913 Chongqing, Chongqing China 400044 (e-mail: zxc@cqu.edu.cn)
Yanli Guo , Southwest Hospital, Chongqing, Chongqing China (e-mail: yanliguo@qq.com)
Fang Tang , Chongqing University, 47913 Chongqing, Sichuan China (e-mail: eefrank@cqu.edu.cn)
Fengbo Ren , School of Computing Informatics and Decision Systems Engineering Arizona State University, Tempe, Arizona United States (e-mail: renfengbo@asu.edu)
Jishun Guo , Guangzhou, Guangdong China (e-mail: JishunGuo@gaei.cn)
Shuiwang Ji , School of Electrical Engineering & Computer Science, Washington State University, Pullman, Washington United States 99164 (e-mail: sji@eecs.wsu.edu)

Identification of differentially expressed genes to establish new Biomarker for cancer prediction (Abstract)

Amit Paul , Computer Science and Engineering, ST.Thomas' College of Engineering and Technology, Calcutta, West Bengal India (e-mail: amitpaul83@gmail.com)
Jaya Sil , Computer Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, West Bengal India (e-mail: jayasil@hotmail.com)

A Parametric Targetability Evaluation Approach for Vitiligo Proteome extracted through Integration of Gene Ontologies and Protein Interaction Topologies (Abstract)

Anvita Gupta Malhotra , Biological Science and Engineering, Maulana Azad National Institute of Technology, 29678 Bhopal, M.P India (e-mail: anvitagupta16@gmail.com)
Sudha Singh , Bhopal, M.P India (e-mail: sudhasingh99@gmail.com)
Mohit Jha , Bhopal, M.P India (e-mail: mohitjha23@gmail.com)
Khushhali Menaria Pandey , Bhopal, M.P India (e-mail: kmpbiomanit@gmail.com)

Enhancement of Protein β-sheet Topology Prediction using Maximum Weight Disjoint Path Cover (Abstract)

Toktam Dehghani , Computer Engineering, Ferdowsi University of Mashhad, 48440 Mashhad, Razavi Khorasan Iran (the Islamic Republic of) (e-mail: dehghani.toktam@mail.um.ac.ir)
Mahmoud Naghibzadeh , Computer Engineering, Ferdowsi University of Mashhad, 48440 Mashhad, Razavi Khorasan Iran (the Islamic Republic of) (e-mail: naghibzadeh@um.ac.ir)
Javad Sadri , Computer Science & Software Engineering, Concordia University, 5618 Montreal, Quebec Canada (e-mail: j_sadri@encs.concordia.ca)

Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images (Abstract)

Gregor Urban , Department of Information and Computer Science, University of California, Irvine, Irvine, California United States (e-mail: gurban@uci.edu)
Kevin M. Bache , Department of Information and Computer Science, University of California, Irvine, Irvine, California United States (e-mail: kbache@uci.edu)
Duc Phan , Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California United States (e-mail: ducp@uci.edu)
Agua Sobrino , Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California United States (e-mail: asobrino@uci.edu)
Alexander Konstantinovich Shmakov , Department of Information and Computer Science, University of California, Irvine, Irvine, California United States (e-mail: ashmakov@uci.edu)
Stephanie J. Hachey , Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California United States (e-mail: shachey13@gmail.com)
Chris Hughes , Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California United States (e-mail: cchughes@uci.edu)
Pierre Baldi , University of California, Irvine, Irvine, California United States 92697-3425 (e-mail: pfbaldi@ics.uci.edu)

3gClust: Human Protein Cluster Analysis (Abstract)

Anup Kumar Halder , CSE, Jadavpur University, Kolkata, West Bengal India (e-mail: anup21.halder@gmail.com)
Piyali Chatterjee , Computer Science and Engineering, Netaji Subhash Engineering College, 418379 Kolkata, West Bengal India (e-mail: piyali.gini@gmail.com)
Mita Nasipuri , Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal India (e-mail: mnasipuri@cse.jdvu.ac.in)
Dariusz Plewczynski , Warszawski Uniwersytet Medyczny, 37803 Warszawa, Warsaw Poland (e-mail: d.plewczynski@cent.uw.edu.pl)
Subhadip Basu , CSE, Jadavpur University, Kolkata, West Bengal India 700090 (e-mail: subhadip@cse.jdvu.ac.in)

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny (Abstract)

Laura Urbini , Universite Claude Bernard, Inria Rhone-Alpes, Villeurbanne cedex, Rhone-Alpes France (e-mail: laura.urbini@inria.fr)
Blerina Sinaimeri , Universite Claude Bernard, Inria Rhone-Alpes, Villeurbanne cedex, Rhone-Alpes France (e-mail: blerina.sinaimeri@inria.fr)
Catherine Matias , Université Pierre et Marie Curie / CNRS, Paris, Ile-de-France France (e-mail: catherine.matias@math.cnrs.fr)
Marie-France Sagot , Universite Claude Bernard, Inria Rhone-Alpes, Villeurbanne cedex, Rhone-Alpes France (e-mail: marie-france.sagot@inria.fr)

ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data (Abstract)

Claudia Caudai , Istituto di Scienza e Tecnologie dell'Informazione, Consiglio Nazionale delle Ricerche, 9327 Pisa, PI Italy (e-mail: claudia.caudai@isti.cnr.it)
Emanuele Salerno , Istituto di Scienza e Tecnologie dell'Informazione, Consiglio Nazionale delle Ricerche, 9327 Pisa, PI Italy 56124 (e-mail: emanuele.salerno@isti.cnr.it)
Monica Zoppe , Isntitute of Clinical Physiology, Pisa, Pisa Italy 56124 (e-mail: mzoppe@ifc.cnr.it)
Ivan Merelli , Institute for Biomedical Technologies, Italian National Research Council, Milan, Segrate Italy 20090 (e-mail: ivan.merelli@itb.cnr.it)
Anna Tonazzini , Istituto di Scienza e Tecnologie dall'Informazione, Consiglio Nazionale delle Ricerche, Pisa, Italy Italy 56124 (e-mail: anna.tonazzini@isti.cnr.it)

Nature-Inspired Multiobjective Epistasis Elucidation from Genome-Wide Association Studies (Abstract)

Xiangtao Li , College of Computer Science, Northeast Normal University, Changchun, 130117, P.R. China, Changchun, Jilin China (e-mail: lixt314@nenu.edu.cn)
Shixiong Zhang , Kowloon, Kowloon Tong Hong Kong (e-mail: sxzhang7-c@my.cityu.edu.hk)
Ka-Chun Wong , City University of hong Kong, Kowloon Tong, Kowloon Hong Kong (e-mail: kc.w@cityu.edu.hk)

Identifying “Many-to-Many” Relationships Between Gene-Expression Data and Drug-Response Data Via Sparse Binary Matching (Abstract)

Jiulun Cai , School of Computer Science and Engineering, South China University of Technology, 26467 Guangzhou, Guangdong China (e-mail: 371127784@qq.com)
Hongmin Cai , South China University of Technology, Guangzhou, Guangdong China 510006 (e-mail: hmcai@scut.edu.cn)
JIazhou Chen , School of Computer Science and Engineering, South China University of Technology, 26467 Guangzhou, Guangdong China (e-mail: 349221336@qq.com)
Xi Yang , School of Information Science and Technology, Guangdong University of Foreign Studies, 12385 Guangzhou, Guangdong China (e-mail: 519428418@qq.com)

Efficient Algorithms for Finding the Closest l-mers in Biological Data (Abstract)

Xingyu Cai , Computer Science and Engineering, University of Connecticut, Storrs, Connecticut United States 06269 (e-mail: xingyu.cai@uconn.edu)
Abdullah-Al Mamun , CSE, University of Connecticut System, 242752 Storrs, Connecticut United States (e-mail: abdullah.am.cs@gmail.com)
Sanguthevar Rajasekaran , CSE, Univ. of Connecticut, Storrs, Connecticut United States 06269-4155 (e-mail: rajasek@engr.uconn.edu)

Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers (Abstract)

Lun Hu , Computer Science and Technology, Wuhan University of Technology, 12565 Wuhan, Hubei China (e-mail: hulun@whut.edu.cn)
Xiaohui Yuan , Computer Science and Technology, Wuhan University of Technology, 12565 Wuhan, Hubei China (e-mail: yuanxiaohui@whut.edu.cn)
Xing Liu , School of Computer Science and Technology, Wuhan University of Technology, 12565 Wuhan, Hubei China (e-mail: liu.xing@whut.edu.cn)
Shengwu Xiong , Computer Science and Technology, Wuhan University of Technology, 12565 Wuhan, Hubei China (e-mail: xiongsw@whut.edu.cn)
Xin Luo , Chongqing Institute of Green and Intelligent Technology, 376348 Chongqing, Sichuan China (e-mail: luoxin21@cigit.ac.cn)

Using Emulation to Engineer and Understand Simulations of Biological Systems (PDF)

Kieran Alden , Department of Electronic Engineering, University of York, York, North Yorkshire United Kingdom of Great Britain and Northern Ireland (e-mail: kieran.alden@york.ac.uk)
Jason Cosgrove , Department of Electronic Engineering, University of York, York, North Yorkshire United Kingdom of Great Britain and Northern Ireland (e-mail: jason.cosgrove@york.ac.uk)
Mark Coles , Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire United Kingdom of Great Britain and Northern Ireland (e-mail: mark.coles@kennedy.ox.ac.uk)
Jon Timmis , Department of Electronic Engineering, University of York, York, North Yorkshire United Kingdom of Great Britain and Northern Ireland (e-mail: jon.timmis@york.ac.uk)

Robust Inductive Matrix Completion Strategy to Explore Associations between LincRNAs and Human Disease Phenotypes (Abstract)

Ashis Biswas , Computer Science and Engineering, The University of Texas, Arlington, Texas United States (e-mail: ashis.biswas@mavs.uta.edu)
Mingon Kang , Computer Science, Kennesaw State University, 15617 Kennesaw, Georgia United States (e-mail: mkang9@kennesaw.edu)
Dongchul Kim , University of Texas Rio Grande Valley, 12331 Brownsville, Texas United States (e-mail: dongchul.kim@utrgv.edu)
Jean Gao , Computer Science and Engineering, The University of Texas, Arlington, Texas United States 76019 (e-mail: gao@uta.edu)

HetRCNA: a novel method to identify recurrent copy number alternations from heterogeneous tumor samples based on matrix decomposition framework (Abstract)

Jianing Xi , School of Information Science and Technology, Unversity of Science and Technology of China, Hefei, Anhui China (e-mail: xjn@mail.ustc.edu.cn)
Ao Li , School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: aoli@ustc.edu.cn)
Minghui Wang , School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: mhwang@ustc.edu.cn)

Detection of Driver Modules with Rarely Mutated Genes in Cancers (Abstract)

Li Feng , Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: lifeng_10_28@163.com)
Lin Gao , School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi China (e-mail: lgao@mail.xidian.edu.cn)
Bingbo Wang , Xidian University, Xian, Shaanxi China 710071 (e-mail: w_bingbo@163.com)

Quantifying direct dependencies in biological networks by multiscale association analysis (Abstract)

Jifan Shi , School of Mathematical Sciences, Peking University, Beijing, Beijing China (e-mail: shijifan123@126.com)
Juan Zhao , Institute of Biochemistry and Cell Biology, 85426 Shanghai, Shanghai China 200031 (e-mail: zjhywdsy@163.com)
Xiaoping Liu , Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Shanghai city, Shanghai China (e-mail: liuxiaoping@sibs.ac.cn)
Luonan Chen , Chinese Academy of Sciences, Shanghai Institute of Biological Sciences, Shanghai, ShangHai China 200031 (e-mail: lnchen@sibs.ac.cn)
Tiejun Li , Mathematics, Peking University, Beijing, Beijing China 100871 (e-mail: tieli@math.pku.edu.cn)

ELF: Extract Landmark Features by optimizing topology maintenance, redundancy, and specificity (Abstract)

Zhanying Feng , Insitute of Applied Mathematics, Academy of Mathematics and Systems Science, 85320 Beijing, Beijing China (e-mail: zhanyingfeng@gmail.com)
Yong Wang , Insitute of Applied Mathematics, Academy of mathematics and systems science, Beijing, Beijing China 100190 (e-mail: ywang@amss.ac.cn)

A branch point on differentiation trajectory is the bifurcating event revealed by dynamical network biomarker analysis of single-cell data (Abstract)

Ziwei Chen , Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, Beijing China (e-mail: 13370145897@163.com)
Xiangqi Bai , Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, Beijing China (e-mail: xqbai@amss.ac.cn)
Liang Ma , Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Beijing China (e-mail: mal@big.ac.cn)
Xiawei Wang , Biostatistics, University of California - Davis, Davis, California United States (e-mail: xwang932@wisc.edu)
Xiuqin Liu , the College of mathematics and physics, University of Science and Technology Beijing, Beijing, Beijing China (e-mail: mathlxq@amss.ac.cn)
Yuting Liu , Beijing Jiaotong University, 47829 Beijing, Beijing China (e-mail: ytliu@bjtu.edu.cn)
Luonan Chen , Chinese Academy of Sciences, Shanghai Institute of Biological Sciences, Shanghai, ShangHai China (e-mail: lnchen@sibs.ac.cn)
Lin Wan , Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, Beijing China 100190 (e-mail: lwan@amss.ac.cn)

Comparison of computational methods for imputing single-cell RNA-sequencing data (Abstract)

Lihua Zhang , Applied mathematics, Academy of Mathematics and Systems Science, 85320 Beijing, Beijing China 100190 (e-mail: zhanglihua@amss.ac.cn)
Shihua Zhang , Academy of Mathematics and Systems Science, CAS, Beijing, Beijing China (e-mail: zsh@amss.ac.cn)

Deep Learning for Plant Species Classification using Leaf Vein Morphometric (Abstract)

Jing Wei Tan , Institute of Biological Sciences, Bioinformatics Programme, University of Malaya Faculty of Science, 69873 Kuala Lumpur, Kuala Lumpur Malaysia (e-mail: jingwei_92@siswa.um.edu.my)
Siow-Wee Chang , Institute of Biological Sciences, Bioinformatics Programme, University of Malaya Faculty of Science, 69873 Kuala Lumpur, Kuala Lumpur Malaysia (e-mail: siowwee@um.edu.my)
Sameem Binti Abdul Kareem , Artificial Intelligent, University Malaya, Kuala Lumpur, Kuala Lumpur Malaysia (e-mail: sameem@um.edu.my)
Hwa Jen Yap , Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Selangor Malaysia (e-mail: hjyap737@um.edu.my)
Kien-Thai Yong , Institute of Biological Sciences, University of Malaya Faculty of Science, 69873 Kuala Lumpur, Kuala Lumpur Malaysia (e-mail: yongkt@um.edu.my)

Multi-factored gene-gene proximity measures exploiting biological knowledge extracted from Gene Ontology : application in gene clustering (Abstract)

Sudipta Acharya , Indian Institute of Technology Patna, 250259 Patna, Bihar India 801103 (e-mail: sudipta.pcs13@iitp.ac.in)
Sriparna Saha , Department of CSE, IIT Patna, Patna, bihar India (e-mail: sriparna.saha@gmail.com)
Prasanna Pradhan , Sikkim Manipal Institute of Technology, 210966 Gangtok, Sikkim India (e-mail: ppprashant64@gmail.com)

Stepwise Tikhonov Regularisation: Application to the Prediction of HIV-1 Drug Resistance (Abstract)

Ramon Delgado , School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, New South Wales Australia (e-mail: Ramon.delgado@uon.edu.au)
Zhiyong Chen , School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, New South Wales Australia (e-mail: zhiyong.chen@newcastle.edu.au)
Richard H. Middleton , Centre for Complex Dynamic Systems and Control, The University of Newcastle, Callaghan, New South Wales Australia 2308 (e-mail: Richard.Middleton@newcastle.edu.au)

Drug Side-effect Profiles Prediction: From Empirical Risk Minimization to Structural Risk Minimization (Abstract)

Hao Jiang , Renmin University of China, Beijing, Beijing China (e-mail: jiangh@ruc.edu.cn)
Yushan Qiu , Shenzhen, GuangDong China (e-mail: yushan.qiu@szu.edu.cn)
Wenpin Hou , Hong Kong, Hong Kong Hong Kong (e-mail: whou@hotmail.com)
Xiaoqing Cheng , Mathematics, The University of Hong Kong, Hong Kong, Hong Kong Hong Kong (e-mail: mechxqxiaofen@gmail.com)
Manyi Yim , Austin, Texas United States (e-mail: manyi.yim@utexas.edu)
Wai-Ki Ching , Department of Mathematics, The University of Hong Kong, Hong Kong, Hong Kong Hong Kong (e-mail: wching@hku.hk)

Rich Chromatin Structure Prediction from Hi-C Data (Abstract)

Laraib Malik , Computer Science, Stony Brook University, Stony Brook, New York United States (e-mail: lmalik@cs.stonybrook.edu)
Rob Patro , Computer Science, Stony Brook University, Stony Brook, New York United States (e-mail: rob.patro@cs.stonybrook.edu)

imPhy: Imputing Phylogenetic Trees with Missing Information using Mathematical Programming (Abstract)

Niko Yasui , Computing Science, University of Alberta, Edmonton, Alberta Canada (e-mail: yasuiniko@gmail.com)
Chrysafis Vogiatzis , Industrial and Manufacturing Engineering, North Dakota State University, 3323 Fargo, North Dakota United States 58108-6050 (e-mail: chrysafis.vogiatzis@ndsu.edu)
Ruriko Yoshida , Naval Postgraduate School, 48848 Monterey, California United States 93943-5155 (e-mail: ryoshida@nps.edu)
Kenji Fukumizu , Institute of Statistical Mathematics, Tachikawa, Tokyo Japan 190-8562 (e-mail: fukumizu@ism.ac.jp)

Assessing the Effectiveness of Causality Inference Methods for Gene Regulatory Networks (Abstract)

Syed Sazzad Ahmed , CSE, Assam Don Bosco University, 317240 Guwahati, Assam India (e-mail: syed.ahmed@dbuniversity.ac.in)
Swarup Roy , Information Technology, North Eastern Hill University, Shillong, Meghalaya India 793022 (e-mail: contact.swarup@gmail.com)
Jugal K. Kalita , Computer Science, University of Colorado, Colorado Springs, Colorado United States 80918 (e-mail: jkalita@uccs.edu)

On Sharing Intentions, and Personal and Interdependent Privacy Considerations for Genetic Data: A Vignette Study (Abstract)

Jake Weidman , Informatics, The Pennsylvania State University, State College, Pennsylvania United States (e-mail: jyw5163@ist.psu.edu)
William Aurite , Informatics, The Pennsylvania State University, State College, Pennsylvania United States (e-mail: wza5064@ist.psu.edu)
Jens Grossklags , Chair for Cyber Trust, Technical University of Munich, Munich, Bavaria Germany (e-mail: jens.grossklags@in.tum.de)

Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data (Abstract)

Donghe Li , Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Seoul Korea (the Republic of) (e-mail: lidonghe111@gmail.com)
Wonji Kim , Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Seoul Korea (the Republic of) (e-mail: dnjswlzz11@gmail.com)
Longfei Wang , Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Seoul Korea (the Republic of) (e-mail: longfeistat@gmail.com)
Kyong-Ah Yoon , Seoul, Seoul Korea (the Republic of) (e-mail: kayoon@konkuk.ac.kr)
Boyoung Park , Department of Cancer Control and Population Health, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyunggi Korea (the Republic of) (e-mail: hayejine@ncc.re.kr)
Charny Park , Clinical Genomic Analysis Branch, Research Institute, National Can-cer Center, Goyang, South Korea., Seoul, Seoul Korea (the Republic of) (e-mail: charn78@ncc.re.kr)
Sun-Young Kong , College of Veterinary Medicine, Konkuk University, Seoul, Korea, Seoul, Seoul Korea (the Republic of) (e-mail: ksy@ncc.re.kr)
Yongdeuk Hwang , Seoul, Seoul Korea (the Republic of) (e-mail: ydhwang@suwon.ac.kr)
Daehyun Baek , Center for RNA Research, Institute for Basic Science,Seoul, Korea, Seoul, Seoul Korea (the Republic of) (e-mail: baek@snu.ac.kr)
Eun Sook Lee , Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea, Seoul, Seoul Korea (the Republic of) (e-mail: eslee@ncc.re.kr)
Sungho Won , Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Seoul Korea (the Republic of) (e-mail: won1@snu.ac.kr)

A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models (Abstract)

Atsuko Miyawaki-Kuwakado , Fukuoka, Fukuoka Japan (e-mail: a-miyawaki@brs.kyushu-u.ac.jp)
Soichiro Komori , Graduate School of Bioresource and Bioenvironmental Sciences School of Agriculture, Kyushu Daigaku, 12923 Fukuoka, Fukuoka Japan 812-8581 (e-mail: s-komori@brs.kyushu-u.ac.jp)
Fumihide Shiraishi , Kyushu University, Fukuoka, Fukuoka Japan (e-mail: fumishira@brs.kyushu-u.ac.jp)

MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data (Abstract)

Jean Louis Raisaro , IC, Ecole polytechnique federale de Lausanne Faculte Informatique et Communications, 30685 Lausanne, Vaud Switzerland 1015 (e-mail: jeanlouis.raisaro@gmail.com)
Juan Troncoso-Pastoriza , Laboratory of Computer Applications 1, Ecole Polytechnique Federale de Lausanne, 27218 Lausanne, VD Switzerland 1015 (e-mail: juan.troncoso-pastoriza@epfl.ch)
Mickael Misbach , IC, Ecole polytechnique federale de Lausanne Faculte Informatique et Communications, 30685 Lausanne, Vaud Switzerland (e-mail: mickael.misbach@epfl.ch)
Joao Sa Sousa , IC, Ecole polytechnique federale de Lausanne Faculte Informatique et Communications, 30685 Lausanne, Vaud Switzerland (e-mail: joao.gomesdesaesousa@epfl.ch)
Sylvain Pradervand , Centre Hospitalier Universitaire Vaudois, 30635 Lausanne, VD Switzerland (e-mail: Sylvain.Pradervand@chuv.ch)
Edoardo Missiaglia , Centre Hospitalier Universitaire Vaudois, 30635 Lausanne, VD Switzerland (e-mail: edoardo.missiaglia@chuv.ch)
Olivier Michielin , Centre Hospitalier Universitaire Vaudois, 30635 Lausanne, VD Switzerland (e-mail: olivier.michielin@chuv.ch)
Bryan Ford , IC, Ecole polytechnique federale de Lausanne Faculte Informatique et Communications, 30685 Lausanne, Vaud Switzerland (e-mail: bryan.ford@epfl.ch)
Jean-Pierre Hubaux , Batiment BC, Swiss Federal Institute of Technology - I&C LCA(EPFL), Lausanne, VD Switzerland CH-1015 (e-mail: jean-pierre.hubaux@epfl.ch)

A supervised ensemble approach for sensitive microRNA target prediction (Abstract)

Ranjan Kumar Maji , Bose Institute - Centenary Campus, 224867 Kolkata, West Bengal India (e-mail: maji@jcbose.ac.in)
Sunirmal Khatua , Computer Science and Engineering, University of Calcutta, Kolkata, West Bengal India 700075 (e-mail: enggnimu_ju@yahoo.com)
Zhumur Ghosh , Bioinformatics Centre, Bose Institute - Centenary Campus, 224867 Kolkata, West Bengal India 700054 (e-mail: zhumur@jcbose.ac.in)

A novel scaffolding algorithm based on contig error correction and path extension (Abstract)

Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Li Tang , Computer Science, Central South University, Changsha, Hunan China (e-mail: tangli_csu@csu.edu.cn)
Zhongxiang Liao , Central South University, 12570 Changsha, Hunan China (e-mail: 1090771360@qq.com)
Junwei Luo , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: luojunwei@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Computer Science, Georgia State University, Atlanta, Georgia United States 30303 (e-mail: pan@cs.gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Pareto optimization of combinatorial mutagenesis libraries (Abstract)

Deeptak Verma , Computer Science, Dartmouth College, Hanover, New Hampshire United States 03755 (e-mail: deeptak.verma@dartmouth.edu)
Gevorg Grigoryan , Computer Science, Dartmouth College, Hanover, New Hampshire United States 03755 (e-mail: gevorg.grigoryan@gmail.com)
Chris Bailey-Kellogg , Computer Science, Dartmouth, Hanover, New Hampshire United States 03755 (e-mail: cbk@cs.dartmouth.edu)

AN APPLICATION OF THE BAYESIAN PERIODICITY TEST TO IDENTIFY DIURNAL RHYTHM GENES IN THE BRAIN (Abstract)

Mehmet Kocak , Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee United States 38103 (e-mail: mkocak1@uthsc.edu)
Khyobeni Mozhui , Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee United States (e-mail: kmozhui@uthsc.edu)

Disruption of the Protein Complexes from Weighted Complex Networks (Abstract)

Mahnaz Habibi , Department of Biomedical Engineering, Electrical, IT and Computer Sciences, Islamic Azad University Qazvin Branch, Qazvin, Qazvin Iran (the Islamic Republic of) (e-mail: mhabibi@ipm.ir)
Pegah Khosravi , the School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Tehran Iran (the Islamic Republic of) (e-mail: pegah.khosravi@ipm.ir)

Drug Selection via Joint Push and Learning to Rank (Abstract)

Yicheng He , Computer and Information Science, Indiana University Purdue University Indianapolis, Indianapolis, Indiana United States (e-mail: heyich@iupui.edu)
Junfeng Liu , Computer and Information Science, Indiana University Purdue University Indianapolis, Indianapolis, Indiana United States (e-mail: liujunf@iupui.edu)
Xia Ning , Computer and Information Science, Indiana University Purdue University Indianapolis, Indianapolis, Indiana United States (e-mail: xning@iupui.edu)

Fast de Bruijn Graph Compaction in Distributed Memory Environments (Abstract)

Tony Pan , School of Computational Science and Engineering, Georgia Institute of Technology, 1372 Decatur, Georgia United States 30033 (e-mail: tpan7@gatech.edu)
Rahul Nihalani , School of Computational Science and Engineering, Georgia Institute of Technology, 1372 Decatur, Georgia United States (e-mail: rnihalani3@gatech.edu)
Srinivas Aluru , School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia United States 30332 (e-mail: aluru@cc.gatech.edu)

Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics (PDF)

David Sankoff , Mathematics and Statistics, University of Ottawa, Ottawa, Ontario Canada (e-mail: sankoff@uottawa.ca)
Chunfang Zheng , Mathematics and Statistics, University of Ottawa, 6363 Ottawa, Ontario Canada (e-mail: chunfang313@gmail.com)
Yue Zhang , Mathematics and Statistics, University of Ottawa, 6363 Ottawa, Ontario Canada (e-mail: yzhan481@uottawa.ca)
Joao Meidanis , Department of Mathematics and Statistics, University of Ottawa, 6363 Ottawa, Ontario Canada (e-mail: meidanis@ic.unicamp.br)
Eric Lyons , The School of Plant Sciences, University of Arizona, Tucson, Arizona United States (e-mail: ericlyons@email.arizona.edu)
Haibao Tang , The School of Plant Sciences, University of Arizona, 8041 Tucson, Arizona United States (e-mail: tanghaibao@gmail.com)

Privacy-Preserving Linkage of Genomic and Clinical Data Sets (PDF)

Dixie Baker , Martin, Blanck & Associates, Alexandria, Virginia United States (e-mail: Dixie.Baker@martin-blanck.com)
Bartha M. Knoppers , McGill University Faculty of Medicine, 12367 Montreal, Quebec Canada (e-mail: bartha.knoppers@mcgill.ca)
Mark Phillips , McGill University, Montreal, Quebec Canada (e-mail: mark.phillips2@mcgill.ca)
David van Enckevort , University Medical Center Groningen, Groningen, Groningen Netherlands (e-mail: david.van.enckevort@umcg.nl)
Petra Kaufmann , Bethesda, Maryland United States (e-mail: petra.kaufmann@nih.gov)
Hanns Lochmuller , Newcastle, Newcastle upon Tyne United Kingdom of Great Britain and Northern Ireland (e-mail: hanns.lochmuller@newcastle.ac.uk)
Domenica Taruscio , Rome, Rome Italy (e-mail: domenica.taruscio@iss.it)

Rapid Reconstruction of Time-varying Gene Regulatory Networks (Abstract)

Saptarshi Pyne , Department of Computer Science and Engineering, Indian Institute of Technology Guwahati, 28678 Guwahati, Assam India 781039 (e-mail: saptarshipyne01@gmail.com)
Alok Ranjan Kumar , Siemens Industry Software (India) Pvt. Ltd., Pune, Maharashtra India (e-mail: alok4039@gmail.com)
Ashish Anand , Department of Computer Science and Engineering, Indian Institute of Technology Guwahati, 28678 Guwahati, Assam India (e-mail: anand.ashish@iitg.ernet.in)

Optimal Bayesian Filtering for Biomarker Discovery: Performance and Robustness (Abstract)

Ali Foroughi pour , Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio United States 43210 (e-mail: foroughipour.1@osu.edu)
Lori Dalton , Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio United States (e-mail: dalton.lori@outlook.com)

Weakly-Supervised Convolutional Neural Network Architecture for Predicting Protein-DNA Binding (Abstract)

Qinhu Zhang , Tongji University, 12476 Shanghai, Shanghai China 200092 (e-mail: 472765713@qq.com)
Lin Zhu , Tongji University, Shanghai, Shanghai China (e-mail: lizhonyx@163.com)
Wenzheng Bao , tongji university, shanghai, shanghai China (e-mail: baowz55555@126.com)
De-shuang Huang , Computer Science Department, Tongji University, Shanghai, ShangHai China (e-mail: dshuang@tongji.edu.cn)

Deep Neural Networks for Exploration of Transcriptome of Adult Mouse Brain (Abstract)

Yujie Li , Computer Science, the University of Georgia, Athens, GA Georgia (e-mail: lyj@uga.edu)
Heng Huang , School of Automation, Northwestern Polytechnical University, 26487 Xi'an, Shaanxi China (e-mail: hh07999@uga.edu)
Hanbo Chen , Computer Science, the University of Georgia, Athens, Georgia United States 30605 (e-mail: cojoc.chen@gmail.com)
Tianming Liu , Computer Science, University of Georgia, Athens, Georgia United States (e-mail: tliu@cs.uga.edu)

End-to-end Representation Learning for Chemical-Chemical Interaction Prediction (Abstract)

Sunyoung Kwon , Electrical and Computer Engineering, Seoul National University, Seoul, seoul Korea (the Republic of) 08826 (e-mail: threads@snu.ac.kr)
Sungroh Yoon , Electrical and Computer Engineering, Seoul National University, Seoul, Seoul Korea, Republic of 151744 (e-mail: sryoon@snu.ac.kr)

Identifying lncRNA and mRNA Co-expression Modules from Matched Expression Data in Ovarian Cancer (Abstract)

Qiu Xiao , College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan China (e-mail: hnuyldf@hnu.edu.cn)
Jiawei Luo , Hunan University, the College of Information Science and Engineering, Changsha, Hunan China (e-mail: luojiawei@hnu.edu.cn)
Cheng Liang , College of Information Science and Engineering, Shandong Normal University, Jinan, Shandong China (e-mail: alcs417@hnu.edu.cn)
Guanghui Li , School of Information Engineering, East China Jiaotong University, Nanchang, Jiangxi China (e-mail: ghli16@hnu.edu.cn)
Jie Cai , the College of Information Science and Engineering, Hunan University, Changsha, Hunan China (e-mail: 5259350@qq.com)
Pingjian Ding , College of Computer Science and Electronic Engineering, Hunan University, Changsha, Changsha China (e-mail: dpj@hnu.edu.cn)
Ying Liu , College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan China (e-mail: liu_ying@hnu.edu.cn)

Exploring Frequented Regions in Pan-Genomic Graphs (Abstract)

Alan Cleary , Montana State University System, 1705 Bozeman, Montana United States (e-mail: alan.cleay@msu.montana.edu)
Thiruvarangan Ramaraj , National Center for Genome Resources, 33685 Santa Fe, New Mexico United States (e-mail: tr@ncgr.org)
Indika Kahanda , Montana State University System, 1705 Bozeman, Montana United States (e-mail: indika.kahanda@montana.edu)
Joann Mudge , National Center for Genome Resources, 33685 Santa Fe, New Mexico United States (e-mail: jm@ncgr.org)
Brendan Mumey , Montana State University System, 1705 Bozeman, Montana United States 59717 (e-mail: brendan.mumey@montana.edu)

Dual-layer Strengthened Collaborative Topic Regression Modeling for Predicting Drug Sensitivity (Abstract)

Hang Wang , Automation, University of Science and Technology of China, USTC, Hefei, Anhui China 230027 (e-mail: wanghang@mail.ustc.edu.cn)
Jianing Xi , Department of Electronic Science and Technology, Unversity of Science and Technology of China, Hefei, Anhui China (e-mail: xjn@mail.ustc.edu.cn)
Minghui Wang , Department of Electronic Science And Technology, University of Science and Technology of China, Hefei, Anhui China 230027 (e-mail: mhwang@ustc.edu.cn)
Ao Li , Department of Electronic Science And Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: aoli@ustc.edu.cn)

Extension of Partial Gene Transcripts by Iterative Mapping of RNA-Seq Raw Reads (Abstract)

Kumar Saurabh Singh , College of life and environmental sciences, University of Exeter Cornwall Campus, 151778 Penryn, Cornwall United Kingdom of Great Britain and Northern Ireland (e-mail: k.saurabh-singh@exeter.ac.uk)
Katherine Beadle , College of life and environmental sciences, University of Exeter Cornwall Campus, 151778 Penryn, Cornwall United Kingdom of Great Britain and Northern Ireland (e-mail: k.beadle@exeter.ac.uk)
Bartek J. Troczka , Biological Chemistry and Crop Protection, Rothamsted Research, 15552 Harpenden, Hertfordshire United Kingdom of Great Britain and Northern Ireland (e-mail: bartek.troczka@rothamsted.ac.uk)
Linda Field , Biological Chemistry and Crop Protection, Rothamsted Research, 15552 Harpenden, Hertfordshire United Kingdom of Great Britain and Northern Ireland (e-mail: lin.field@rothamsted.ac.uk)
Emyr Davies , Biological Chemistry and Crop Protection, Rothamsted Research, 15552 Harpenden, Hertfordshire United Kingdom of Great Britain and Northern Ireland (e-mail: emyr.davies@rothamsted.ac.uk)
Martin Williamson , Biological Chemistry and Crop Protection, Rothamsted Research, 15552 Harpenden, Hertfordshire United Kingdom of Great Britain and Northern Ireland (e-mail: martin.williamson@rothamsted.ac.uk)
Ralf Nauen , Crop Science Division, Bayer AG, 1569 Monheim, Monheim am Rhein Germany (e-mail: ralf.nauen@bayer.com)
Chris Bass , College of life and environmental sciences, University of Exeter Cornwall Campus, 151778 Penryn, Cornwall United Kingdom of Great Britain and Northern Ireland (e-mail: c.bass@exeter.ac.uk)

Incorporating prior knowledge about genetic variants into the analysis of genetic association data: An empirical Bayes approach (Abstract)

Ali Karimnezhad , Tehran, N/A Iran (the Islamic Republic of) (e-mail: a.karimnezhad@kntu.ac.ir)
David R. Bickel , Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario Canada K1H 8M5 (e-mail: davidbickel.com@dawningrealm.org)

Artificial Fish Swarm Optimization Based Method to Identify Essential Proteins (Abstract)

Xiujuan Lei , College of Computer Science, Shaanxi Normal University, 12401 Xi'an, Shaanxi China 710062 (e-mail: xjlei@snnu.edu.cn)
Xiaoqin Yang , Xi'an, Shaanxi China (e-mail: 15929771027@snnu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)

Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model (Abstract)

Rongrong Zhang , Department of Statistics, Purdue University, West Lafayette, Indiana United States (e-mail: zhan1602@purdue.edu)
Ming Hu , Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio United States 44195 (e-mail: hum@ccf.org)
Yu Michael Zhu , Department of Statistics, Purdue University, West Lafayette, Indiana United States 47907-2067 (e-mail: yuzhu@stat.purdue.edu)
Zhaohui Steve Qin , Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia United States (e-mail: zhaohui.qin@emory.edu)
Ke Deng , Mathematical Sciences Center, Tsinghua University, Beijing, Beijing China (e-mail: kdeng@tsinghua.edu.cn)
Jun Liu , Statistics, Harvard University, Cambridge, Massachusetts United States 02138 (e-mail: jliu@stat.harvard.edu)

EL_LSTM: Prediction of DNA-binding residue from Protein sequence by Combining Long Short-Term Memory and Ensemble Learning (PDF)

Jiyun Zhou , Computing, Hong Kong Polytechnic University, 26680 Kowloon, Hong Kong Hong Kong (e-mail: zhoujiyun2010@gmail.com)
Qin Lu , Department of Computing, The Hong Kong Polytechnic University, Hong Kong, Hong Kong China (e-mail: csluqin@comp.polyu.edu.hk)
Ruifeng Xu , Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: xuruifeng@hit.edu.cn)
Lin Gui , Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: guilin.nlp@gmail.com)
Hongpeng Wang , Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: wanghp@hit.edu.cn)

Interactive Semi-Supervised Learning for Microarray Analysis (Abstract)

Yijuan Lu , M. Sanchez and Y. Wang are with Department of Biology, University of Texas at San Antonio, TX, 78249. E-mail: {msanchez, yufeng.wang}@lonestar.utsa.edu.
Qi Tian , M. Sanchez and Y. Wang are with Department of Biology, University of Texas at San Antonio, TX, 78249. E-mail: {msanchez, yufeng.wang}@lonestar.utsa.edu.
Feng Liu , M. Sanchez and Y. Wang are with Department of Biology, University of Texas at San Antonio, TX, 78249. E-mail: {msanchez, yufeng.wang}@lonestar.utsa.edu.
Maribel Sanchez , M. Sanchez and Y. Wang are with Department of Biology, University of Texas at San Antonio, TX, 78249. E-mail: {msanchez, yufeng.wang}@lonestar.utsa.edu.
Yufeng Wang , M. Sanchez and Y. Wang are with Department of Biology, University of Texas at San Antonio, TX, 78249. E-mail: {msanchez, yufeng.wang}@lonestar.utsa.edu.

Approximate Graph Edit Distance in Quadratic Time (Abstract)

Kaspar Riesen , Kaspar Riesen is with the Institute for Information Systems, University of Applied Sciences and Arts Northwestern Switzerland, Riggenbachstrasse 16, CH-4600 Olten, Switzerland.(Email: riesen@iam.unibe.ch)

PolyCluster: Minimum Fragment Disagreement Clustering for Polyploid Phasing (Abstract)

Sepideh Mazrouee , Computer Science, University of California, Los Angeles, California United States (e-mail: sepideh@cs.ucla.edu)
Wei Wang , Computer Science, UCLA, Los Angeles, California United States 90095 (e-mail: weiwang@cs.ucla.edu)

Predicting FAD Interacting Residues with Feature Selection and Comprehensive Sequence Descriptors (Abstract)

Runtao Yang , School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, Shandong China (e-mail: runtao-sd@163.com)
Chengjin Zhang , Shandong University, School of Mechanical, Electrical and Information Engineering, Weihai, Shandong China (e-mail: cjzhang@sdu.edu.cn)
Rui Gao , Shandong University, School of Control Science and Engineering, Jinan, Shandong China (e-mail: gaorui@sdu.edu.cn)
Lina Zhang , School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, Shandong China (e-mail: zlnabc2010@163.com)
Qing Song , School of Electrical Engineering, University of Jinan., Jinan, Shandong China (e-mail: songqing1983@126.com)

Class Balanced Multifactor Dimensionality Reduction to Detect Gene—Gene Interactions (Abstract)

Cheng-Hong Yang , Electronic Eng., National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan Taiwan 807 (e-mail: chyang@cc.kuas.edu.tw)
Yu-Da Lin , Electronic Eng., National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan Taiwan (e-mail: e0955767257@yahoo.com.tw)
Li-Yeh Chuang , Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan Taiwan (e-mail: chuang@isu.edu.tw)

Improving de novo assembly based on read classification (Abstract)

xingyu Liao , School of Information Science and Engineering, Central South University, 12570 Changsha, HuNan China 410083 (e-mail: liaoxingyu@csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
You Zou , Computer Science, Central South University, ChangSha, Hunan China (e-mail: zouyou@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Computer Science, Georgia State University, Atlanta, Georgia United States 30303 (e-mail: pan@cs.gsu.edu)
Feng Luo , Department of Computer Science, Clemson University, Clemson, South Carolina United States 29634 (e-mail: luofeng@clemson.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Developing a Multi-Dose Computational Model for Drug-induced Hepatotoxicity Prediction based on Toxicogenomics Data (Abstract)

Ran Su , Tianjin University, Tianjin, Tianjin China (e-mail: ran.su@tju.edu.cn)
Huichen Wu , School of Software, Tianjin University, Tianjin, Tianjin China (e-mail: savegegardenlove@163.com)
Bo Xu , Tianjin Tumor Hospital, 74675 Tianjin, Tianjin China (e-mail: ran_s57@yahoo.com)
Xiaofeng Liu , Tianjin Tumor Hospital, 74675 Tianjin, Tianjin China (e-mail: qiamond@aliyun.com)
Leyi Wei , School of Computer Science and Technology, Tianjin University, 12605 Tianjin, Tianjin China 300354 (e-mail: weileyi@tju.edu.cn)

Deep Manifold Preserving Autoencoder for Classifying Breast Cancer Histopathological Images (Abstract)

Yangqin Feng , college of computer science, Sichuan University, 12530 Chengdu, SiChuan China 610065 (e-mail: fengyangqin@outlook.com)
Lei Zhang , college of computer science, Sichuan University, 12530 Chengdu, SiChuan China 610065 (e-mail: leizhang@scu.edu.cn)
Juan Mo , college of computer science, Sichuan University, 12530 Chengdu, Sichuan China (e-mail: mojuan2016@gmail.com)

Combining Context and Knowledge Representations for Chemical-disease Relation Extraction (Abstract)

Huiwei Zhou , Dalian University of Technology, Dalian, Liaoning China (e-mail: zhouhuiwei@dlut.edu.cn)
Yunlong Yang , Dalian University of Technology, 12399 Dalian, Liaoning China 116024 (e-mail: SDyyl_1949@mail.dlut.edu.cn)
Shixian Ning , Dalian University of Technology, Dalian, Liaoning China (e-mail: ningshixian@mail.dlut.edu.cn)
Zhuang Liu , Dalian, Liaoning China (e-mail: zhuangliu1992@mail.dlut.edu.cn)
Chengkun Lang , Dalian University of Technology, Dalian, Liaoning China (e-mail: kunkun@mail.dlut.edu.cn)
Yingyu Lin , Dalian University of Technology, Dalian, Liaoning China (e-mail: lyydut@sina.com)
Degen Huang , Dalian University of Technology, Dalian, Liaoning China (e-mail: huangdg@dlut.edu.cn)

A new algorithm for counting independent motifs in probabilistic networks (Abstract)

Aisharjya Sarkar , Computer and Information Science and Engineering, University of Florida, 3463 Gainesville, Florida United States (e-mail: sarkar@cise.ufl.edu)
Yuanfang Ren , Computer and Information Science and Engineering, University of Florida, 3463 Gainesville, Florida United States (e-mail: yuanfang@cise.ufl.edu)
Rasha Elhesha , Computer and Information Science and Engineering, University of Florida, 3463 Gainesville, Florida United States (e-mail: relhesha@cise.ufl.edu)
Tamer Kahveci , Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida United States 32611-6125 (e-mail: tamer@cise.ufl.edu)

Microarray-Based quality assessment as a supporting criterion for de novo transcriptome assembly selection (Abstract)

Patricia Carvajal-Lopez , Grupo de Investigación en Bioinformática, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur Mexico (e-mail: pcarvajal@pg.cibnor.mx)
Fernando D. Von Borstel , Grupo de Investigación en Bioinformática, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur Mexico (e-mail: fborstel@cibnor.mx)
Amada Torres , Grupo de Investigación en Bioinformática, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur Mexico (e-mail: amada.torres@gmail.com)
Gabriella Rustici , Genetics Department, University of Cambridge, Cambridge, CB2 3EH United Kingdom of Great Britain and Northern Ireland (e-mail: gr231@cam.ac.uk)
Joaquin Gutierrez , Grupo de Investigación en Bioinformática, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur Mexico (e-mail: joaquing04@cibnor.mx)
Eduardo Romero-Vivas , Centro de Investigaciones Biologicas del Noroeste, 42579 La Paz, Baja California Sur Mexico 23090 (e-mail: evivas@cibnor.mx)

Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach (Abstract)

Paola Bonizzoni , DISCo, University of Milano Bicocca, Milan, Milan Italy (e-mail: bonizzoni@disco.unimib.it)
Simone Ciccolella , DISCo, Univ. Milano-Bicocca, Milano, MI Italy (e-mail: s.ciccolella@campus.unimib.it)
Gianluca Della Vedova , DISCo, Univ. Milano-Bicocca, Milano, MI Italy (e-mail: gianluca.dellavedova@unimib.it)
Mauricio Soto Gomez , DISCo, Univ. Milano-Bicocca, Milano, MI Italy (e-mail: mauricio.sotogomez@unimib.it)

Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data (Abstract)

Shimpei Nishida , Waseda University, Tokyo, NA Japan (e-mail: s-p.104.q-n@ruri.waseda.jp)
Shun Sakuraba , The University of Tokyo, Tokyo, NA Japan (e-mail: sakuraba@cbms.k.u-tokyo.ac.jp)
Kiyoshi Asai , Graduate School of Frontier Science, The University of Tokyo, Chiba, NA Japan (e-mail: asai@k.u-tokyo.ac.jp)
Michiaki Hamada , Waseda University, Tokyo, NA Japan 1698555 (e-mail: mhamada@waseda.jp)

NMFGO: Gene function prediction via nonnegative matrix factorization with Gene Ontology (Abstract)

Guoxian Yu , College of Computer and Information Science, Southwest University, Beibei, Chongqing China 400715 (e-mail: guoxian85@gmail.com)
Keyao Wang , College of Computer and Information Science, Southwest University, 26463 Beibei, Chongqing China (e-mail: keyaowang@email.swu.edu.cn)
Guangyuan Fu , College of Computer and Information Sciences, Southwest University, 26463 Beibei, Chongqing China (e-mail: fugy@email.swu.edu.cn)
Maozu Guo , School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, 117781 Daxin, Beijing China (e-mail: guomaozu@bucea.edu.cn)
Jun Wang , College of Computer and Information Sciences, Southwest University, Beibei, Chongqing China (e-mail: kingjun@swu.edu.cn)

MultiMotifMaker: a multi-thread tool for identifying DNA methylation motifs from Pacbio reads (Abstract)

Tao Li , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: litao_csu@csu.edu.cn)
Xiankai Zhang , Central South University, 12570 Changsha, Hunan China (e-mail: xkzhang@csu.edu.cn)
Feng Luo , Department of Computer Science, Clemson University, Clemson, South Carolina United States 29634 (e-mail: luofeng@clemson.edu)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Multi-domain Networks Association for Biological Data Using Block Signed Graph Clustering (Abstract)

Ye Liu , Hong Kong, Hong Kong China (e-mail: 16482549@life.hkbu.edu.hk)
Michael K. Ng , Mathematics, Hong Kong Baptist University, Hong Kong, Hong Kong Hong Kong 852 (e-mail: mng@math.hkbu.edu.hk)
Stephen Wu , Tokyo, Tokyo Japan (e-mail: stewu@ism.ac.jp)

LPGNMF: Predicting Long Non-coding RNA and Protein Interaction Using Graph Regularized Nonnegative Matrix Factorization (Abstract)

Tianyi Zhang , Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: wgb17@mail.ustc.edu.cn)
Minghui Wang , Department of Electronic Science And Technology, University of Science and Technology of China, Hefei, Anhui China 230027 (e-mail: mhwang@ustc.edu.cn)
Jianing Xi , Department of Electronic Science and Technology, Unversity of Science and Technology of China, Hefei, Anhui China (e-mail: xjn@mail.ustc.edu.cn)
Ao Li , Department of Electronic Science And Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: aoli@ustc.edu.cn)

GaMRed – adaptive filtering of high-throughput biological data (Abstract)

Michal Marczyk , Department of Internal Medicine, Yale University School of Medicine, 12228 New Haven, Connecticut United States (e-mail: michal.marczyk@polsl.pl)
Roman Jaksik , Politechnika Slaska, 49569 Gliwice, Slaskie Poland (e-mail: roman.jaksik@polsl.pl)
Andrzej Polanski , Politechnika Slaska, 49569 Gliwice, Slaskie Poland (e-mail: andrzej.polanski@polsl.pl)
Joanna Polanska , Politechnika Slaska, 49569 Gliwice, Slaskie Poland (e-mail: joanna.polanska@polsl.pl)

Robust Microbial Markers for Non-Invasive Inflammatory Bowel Disease Identification (Abstract)

Benjamin Wingfield , Intelligent Systems Research Centre, University of Ulster - Magee Campus, 354957 Derry, County Derry United Kingdom of Great Britain and Northern Ireland BT48 7JL (e-mail: wingfield-b@ulster.ac.uk)
Sonya Coleman , School of Computing and Intelligent Systems, University of Ulster, Derry, Ulster United Kingdom of Great Britain and Northern Ireland (e-mail: sa.coleman@ulster.ac.uk)
Thomas M. McGinnity , College of Science and Technology, Nottingham Trent University, 6122 Nottingham, Nottinghamshire United Kingdom of Great Britain and Northern Ireland (e-mail: martin.mcginnity@ntu.ac.uk)
Anthony Bjourson , Northern Ireland Centre for Stratified Medicine, Ulster University, Derry, County Derry United Kingdom of Great Britain and Northern Ireland (e-mail: aj.bjourson@ulster.ac.uk)

Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks (Abstract)

Chao Fang , University of Missouri Columbia, 14716 Columbia, Missouri United States 65211 (e-mail: cf797@mail.missouri.edu)
Yi Shang , University of Missouri, Columbia, Columbia, Missouri United States 65211 (e-mail: shangy@missouri.edu)
Dong Xu , Computer Science, University of Missouri-Columnbia, Coulumbia, Missouri United States 65211 (e-mail: xudong@missouri.edu)

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods (Abstract)

Jyotsna Talreja Wassan , School of Computing and Mathematics, University of Ulster at Jordanstown, 42259 Newtownabbey, Northern Ireland United Kingdom of Great Britain and Northern Ireland BT37 0QB (e-mail: wassan-jt@ulster.ac.uk)
Haiying Wang , School of Computing and mathematics, University of Ulster, Belfast, Northern Ireland United Kingdom of Great Britain and Northern Ireland BT37 0QB (e-mail: hy.wang@ulster.ac.uk)
Fiona Browne , School of Computing and Mathematics, University of Ulster at Jordanstown, 42259 Newtownabbey, Co Antrim United Kingdom of Great Britain and Northern Ireland BT37 0QB (e-mail: f.browne@ulster.ac.uk)
Huiru Zheng , School of Computing and mathematics, University of Ulster, Belfast, N. Ireland United Kingdom of Great Britain and Northern Ireland BT37 0QB (e-mail: H.Zheng@ulster.ac.uk)

Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer (Abstract)

Lin Yuan , Tongji University, Shanghai, Shanghai China (e-mail: yuanlindc@126.com)
Le-Hang Guo , Shanghai, Shanghai China (e-mail: gopp1314@hotmail.com)
Chang-An Yuan , Nanning, Guangxi China (e-mail: cay@gxtc.edu.cn)
You-Hua Zhang , Hefei, Anhui China (e-mail: zhangyh@ahau.edu.cn)
Kyungsook Han , Inha, Inha Korea (the Democratic People's Republic of) (e-mail: wfxueyuan@126.com)
Asoke Nandi , London, London United Kingdom of Great Britain and Northern Ireland (e-mail: xgrgr@126.com)
Barry Honig , Alabama, Alabama United States (e-mail: xgrgr126@126.com)
De-Shuang Huang , Computer Science Department, Tongji University, Shanghai, ShangHai China (e-mail: dshuang@tongji.edu.cn)

DFseq: Distribution-free method to detect differential gene expression for RNA-sequencing data (Abstract)

Shengping Yang , Lubbock, Texas United States (e-mail: Shengping.Yang@ttuhsc.edu)
Jianrong Wu , Biostatistics, University of Kentucky College of Public Health, 50880 Lexington, Kentucky United States 40536-0003 (e-mail: jianrong.wu78@yahoo.com)

Softepigen: Primers design web-based tool for MS-HRM technique (Abstract)

Efrain Pinzon , Universidad de Santander, Bucaramanga, Santander Colombia (e-mail: ehpinzon@udes.edu.co)
Paola Rondon-Villarreal , Molecular Biology and Biotechnology Lab, Universidad de Santander, Bucaramanga, Santander Colombia (e-mail: diseno.molecular@udes.edu.co)
William A. Alvarez , SARET research Group, Universidad Manuela Beltran, Bucaramanga, Santander Colombia (e-mail: william.alvarez@umb.edu.co)
Hernan Guillermo Hernandez , PhD Program in dentistry, Universidad de Santo Tomas - Bucaramanga, 157899 Bucaramanga, Santander Colombia (e-mail: hernan.hernandez.md@gmail.com)

Extracting Biomedical Events with Parallel Multi-Pooling Convolutional Neural Networks (Abstract)

Lishuang Li , Dalian University of Technology, Dalian, Liaoning China 116023 (e-mail: lilishuang314@163.com)
Yang Liu , Dalian, LiaoNing China (e-mail: rick@mail.dlut.edu.cn)
Meiyue Qin , Dalian University of Technology, Dalian, Liaoning China (e-mail: qinmessiy@163.com)

Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences using Deep Neural Networks (Abstract)

Zhen Cao , Institute of Systems Science Academy of Mathematics and Systems Science Chinese Academy of Sciences, 74693 Beijing, Beijing China (e-mail: cz@amss.ac.cn)
Shihua Zhang , Academy of Mathematics and Systems Science, CAS, Beijing, Beijing China (e-mail: zsh@amss.ac.cn)

Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learning (Abstract)

Jianguo Chen , the College of Computer Science and Electronic Engineering, Hunan university, Changsha, Hunan China (e-mail: cccjianguo@163.com)
Kenli Li , College of Information Science and Engineering, Hunan unversity, Changsha, Hunan China 410082 (e-mail: lkl@hnu.edu.cn)
Kashif Bilal , COMSATS Institute of IT, Abbottabad, KPK Pakistan 90120 (e-mail: eishaalkashif@gmail.com)
Ahmed A. Metwally , Departments of Bioengineering and Computer Science, University of Illinois at Chicago, Chicago, Illinois United States (e-mail: ametwa2@uic.edu)
Keqin Li , Dept. of Computer Science, State University of New York, New Paltz, New York United States 12561 (e-mail: lik@newpaltz.edu)
Philip Yu , Computer Science, UIC, Chicago, Illinois United States 60607 (e-mail: psyu@uic.edu)

Utilising Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women (Abstract)

Paul Fergus , School of Computing and Mathematical Sciences, Liverpool John Moores University, Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: P.Fergus@ljmu.ac.uk)
Aday Montanez , Computer Science, Liverpool John Moores University, 4589 Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: C.A.CurbeloMontanez@2015.ljmu.ac.uk)
Basma Abdulaimma , Liverpool John Moores University, 4589 Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: B.T.Abdulaimma@2015.ljmu.ac.uk)
Paulo Lisboa , School of Computing and Mathematical Sciences, Liverpool John Moores University, Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: P.J.Lisboa@ljmu.ac.uk)
Carl Chalmers , Department of Computer Science, Liverpool John Moores University, Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: C.Chalmers@ljmu.ac.uk)
Beth Pineles , University of Maryland Medical Center, 21668 Baltimore, Maryland United States (e-mail: bpineles@gmail.com)

Preprocessing Sequence Coverage Data for Precise Detection of Copy Number Variations (Abstract)

Fatima Zare , computer science and engineering, university of connecticut, storrs, Connecticut United States (e-mail: fatemeh.zare@uconn.edu)
Sardar Ansari , Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan United States (e-mail: sardara@umich.edu)
Kayvan Najarian , Engineering, University of Michigan, Ann Arbor, Michigan United States 49109 (e-mail: kayvan@umich.edu)
Sheida Nabavi , computer science and engineering, university of connecticut, Storrs, Connecticut United States (e-mail: sheida.nabavi@uconn.edu)

A Gaussian Mixture-Model Exploiting Pathway Knowledge for Dissecting Cancer Heterogeneity (Abstract)

Rajan Kapoor , electrical Engineering, Texas A&M Engineering, 122656 College Station, Texas United States 77843-3128 (e-mail: r.kapoor@tamu.edu)
Aniruddha Datta , Electrical and Computer Engineering, Texas A&M University, College Station, Texas United States (e-mail: datta@ece.tamu.edu)
Chao Sima , Texas A&M University, Center for Bioinformatics and Genomic Systems Engineering, College Station, Texas United States (e-mail: simachao@tamu.edu)
Jianping Hua , Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 14736 College Station, Texas United States (e-mail: jianpinghua@tamu.edu)
Rosana Lopes , Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, 67283 College Station, Texas United States (e-mail: rlopes@cvm.tamu.edu)
Michael L. Bittner , Translational Genomics Research Institute, 10897 Phoenix, Arizona United States (e-mail: mbittner@tgen.org)

Bounded Fuzzy Possibilistic Method reveals information about lung cancer through analysis of metabolomics (Abstract)

Hossein Yazdani , Computer Science, Politechnika Wroclawska, 49567 Wroclaw, Wroclaw Poland 50-370 (e-mail: yazdanihossein@yahoo.com)
Aazam Yazdani , Houston, Texas United States (e-mail: azam.yazdani@uth.tmc.edu)
Len Cheng , Harvard Medical School, 1811 Boston, Massachusetts United States (e-mail: lcheng@mgh.harvard.edu)
David Christiani , Harvard Medical School, 1811 Boston, Massachusetts United States (e-mail: dchris@hsph.harvard.edu)

Cophenetic Median Trees (Abstract)

Alexey Markin , Computer Science, Iowa State University, 1177 Ames, Iowa United States 50011-2140 (e-mail: amarkin@iastate.edu)
Oliver Eulenstein , Computer Science, Iowa State University, Ames, Iowa United States (e-mail: oeulenst@iastate.edu)

Detection of Colorectal Carcinoma Based on Microbiota Analysis using Generalized Regression Neural Networks and Nonlinear Feature Selection (Abstract)

Abazar Arabameri , Biomedical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: Arabameri@ee.kntu.ac.ir)
Davud Asemani , Radiology, Medical University of South Carolina, charleston, South Carolina United States (e-mail: asemani@eetd.kntu.ac.ir)
Pegah Teymourpour , Biomedical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: teymourpour@ee.kntu.ac.ir)

Gene Expressions, Hippocampal Volume Loss and MMSE Scores in Computation of Progression and Pharmacologic Therapy Effects for Alzheimer's Disease (Abstract)

Aydin Saribudak , Electrical Engineering, City College of New York, 14770 New York, New York United States 10031-9101 (e-mail: asaribu000@citymail.cuny.edu)
Adarsha A. Subick , Electrical Engineering, City College of New York, 14770 New York, New York United States (e-mail: asubick00@citymail.cuny.edu)
Na Hyun Kim , Electrical Engineering, City College of New York, 14770 New York, New York United States (e-mail: ericakimnhk@gmail.com)
Joshua A. Rutta , Electrical Engineering, City College of New York, 14770 New York, New York United States (e-mail: joshrutta7@gmail.com)
M. Umit Uyar , Electrical Engineering, City College of New York, 14770 New York, New York United States (e-mail: uyar@ccny.cuny.edu)

In Silico Design and Experimental Validation of Combination Therapy for Pancreatic Cancer (Abstract)

Haswanth Vundavilli , Electrical Engineering, Texas A&M University, College Station, Texas United States 77840 (e-mail: hashwanthvv@gmail.com)
Aniruddha Datta , Electrical and Computer Engineering, Texas A&M University, College Station, Texas United States (e-mail: datta@ece.tamu.edu)
Chao Sima , Texas A&M Engineering, 122656 College Station, Texas United States (e-mail: simachao@tamu.edu)
Jianping Hua , Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 14736 College Station, Texas United States (e-mail: jianpinghua@tamu.edu)
Rosana Lopes , Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas United States (e-mail: rlopes@exchange.tamu.edu)
Michael L. Bittner , Translational Genomics Research Institute, 10897 Phoenix, Arizona United States (e-mail: mbittner@tgen.org)

Inferring disease-associated microRNAs in heterogeneous networks with node attributes (Abstract)

Ping Xuan , Department of Computer Science and Technology, Heilongjiang University, 12432 Harbin, Heilongjiang China (e-mail: xuanpinghdu@gmail.com)
Tonghui Shen , Department of Computer Science and Technology, Heilongjiang University, 12432 Harbin, Heilongjiang China (e-mail: shentonghui@vip.qq.com)
Xiao Wang , Department of Computer Science and Technology, Tsinghua University, 12442 Beijing, Beijing China (e-mail: xiao_wang_tsinghua@163.com)
Tiangang Zhang , Department of Mathematical Science, Heilongjiang University, 12432 Harbin, Heilongjiang China (e-mail: tiangang_zhang01@126.com)
Weixiong Zhang , Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri United States (e-mail: weixiongzh_wustl@126.com)

ASAPP: Architectural Similarity-based Automated Pathway Prediction System and its Application in Host-Pathogen Interactions (Abstract)

Rishika Sen , Machine Intelligence Unit, Indian Statistical Institute, 30160 Kolkata, West Bengal India (e-mail: rishikasen_r@isical.ac.in)
Somnath Tagore , Columbia University Medical Center, Herbert Irving Cancer Research Center, Califano Laboratory of Systems Biology, New York, New York United States (e-mail: somnath.tagore@biu.ac.il)
Rajat K. De , Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal India 700108 (e-mail: rajat@isical.ac.in)

miRTRS: A Recommendation Algorithm for Predicting miRNA Targets (Abstract)

Hui Jiang , Computer Science, Central South University, ChangSha, Hunan China (e-mail: jianghui@csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Wei Lan , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: weilan@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)

Plant Species Identification from Occluded Leaf Images (Abstract)

Ayan Chaudhury , Computer Science, Western University, 6221 London, Ontario Canada N6A 3K7 (e-mail: achaud29@uwo.ca)
John L. Barron , 1151 Richmond Street, Univ. of Western Ontario, London, Ontario Canada N6A 5B7 (e-mail: barron@csd.uwo.ca)

Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction (Abstract)

Guijun Zhang , college of information engineering, Zhejiag university of technology, Hangzhou, Zhejiang China 310023 (e-mail: zgj@zjut.edu.cn)
Laifa Ma , Zhejiang University of Technology - Pingfeng Campus, 154477 Hangzhou, Zhejiang China 310023 (e-mail: mlf@zjut.edu.cn)
Xiaoqi Wang , Hangzhou, Zhejiang China (e-mail: wxqi@zjut.edu.cn)
Xiaogen Zhou , college of information engineering, Zhejiag university of technology, Hangzhou, Zhejiang China 310023 (e-mail: zxg@zjut.edu.cn)

Identifying Key Genes of Liver Cancer by Networking of Multiple Data Sets (Abstract)

Su-Ping Deng , Tongji University, Shanghai, Shanghai China (e-mail: dsptk2003@126.com)
Wei-Li Guo , Tongji University, Shanghai, Shanghai China (e-mail: guoweili_henu@126.com)

Term-based Personalization for Feature Selection in Clinical Handover Form Auto-filling (Abstract)

Hongyu Liu , East China Normal University, 12655 Shanghai, Shanghai China 200062 (e-mail: 51151201085@stu.ecnu.edu.cn)
Qinmin Hu , Department of Computer Science and Technology, East China Normal University, 12655 Shanghai, US & Canada only China (e-mail: qmhu@cs.ecnu.edu.cn)
Liang He , Department of Computer Science and Technology, East China Normal University, Shanghai, ShangHai China (e-mail: lhe@cs.ecnu.edu.cn)

Combining High Speed ELM Learning with a Deep Convolutional Neural Network Feature Encoding for Predicting Protein-RNA Interactions (Abstract)

Lei Wang , Zaozhuang, Shandong China (e-mail: leiwang@cumt.edu.cn)
Zhu-Hong You , Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, China University of Mining and Technology, Ürümqi, Xingjiang China (e-mail: zhuhongyou@ms.xjb.ac.cn)
De-shuang Huang , Computer Science Department, Tongji University, Shanghai, ShangHai China (e-mail: dshuang@tongji.edu.cn)
Fengfeng Zhou , Changchun, Jilin China (e-mail: FengfengZhou@gmail.com)

Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy and Tools (Abstract)

Hussain Ahmed Chowdhury , Computer Science and Engineering, Tezpur University, 784028 Napaam, Assam India (e-mail: hachowdhury09@yahoo.in)
Dhruba Kumar Bhattacharyya , Computer Science and Engineering, Tezpur University, Tezpur, Assam India 784028 (e-mail: dkb@tezu.ernet.in)
Jugal K. Kalita , Computer Science, University of Colorado, Colorado Springs, Colorado United States 80918 (e-mail: jkalita@uccs.edu)

Fast Short Read De-novo Assembly Using Overlap-Layout-Consensus Approach (Abstract)

Arash Bayat , School of Computer Science and Engineering, University of New South Wales, UNSW Sydney, New South Wales Australia (e-mail: a.bayat@unsw.edu.au)
Nandan P. Deshpande , Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, New South Wales Australia (e-mail: n.deshpande@unsw.edu.au)
Marc R. Wilkins , Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, New South Wales Australia (e-mail: m.wilkins@unsw.edu.au)
Sri Parameswaran , School of Computer Science and Engineering, University of New South Wales, UNSW Sydney, New South Wales Australia (e-mail: sridevan@cse.unsw.edu.au)

Identification of Novel Scaffolds with Dual Role as Antiepileptic and Anti-Breast Cancer (Abstract)

Shailima Rampogu , Gyeongsang National University, 26720 Jinju, Gyeongsangnam-do Korea (the Republic of) (e-mail: shailima.rampogu@gmail.com)
Ayoung Baek , Jinju, Jinju Korea (the Republic of) (e-mail: ayoung@gnu.ac.kr)
Rohit S. Bavi , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: rohitsbavi@gmail.com)
Minky Son , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: minky@gnu.ac.kr)
Guang Ping Cao , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: tsao@bio.gnu.ac.kr)
Raj Kumar , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: rajkumar250287@gmail.com)
Chanin Park , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: chaninpark0806@gmail.com)
Amir Zeb , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) (e-mail: zebamir85@gmail.com)
Rabia Mukthar Rana , Gyeongsang National University, 26720 Jinju, Gyeongsangnam-do Korea (the Republic of) (e-mail: rabia.mukhtar.rana@gmail.com)
Seok Ju Park , Inje University, 26719 Gimhae, Gyeongsangnam-do Korea (the Republic of) (e-mail: psjgenesis@hanmail.net)
Keun Woo Lee , Gyeongsang National University, 26720 Jinju, Jinju Korea (the Republic of) 52828 (e-mail: kwlee@gnu.ac.kr)

Identification of minimum set of master regulatory genes in gene regulatory networks (Abstract)

Somayeh Bakhteh , Applied Math, Azarbaijan Shahid Madani University, 125619 Tabriz, East Azerbaijan Iran (the Islamic Republic of) (e-mail: s.bakhteh@azaruniv.ac.ir)
Alireza Ghaffari-Hadigheh , Applied Math, Azarbaijan Shahid Madani University, 125619 Tabriz, East Azarbaijan Iran (the Islamic Republic of) (e-mail: hadigheha@azaruniv.ac.ir)
Nader Chaparzadeh , Biology, Azarbaijan Shahid Madani University, 125619 Tabriz, East Azerbaijan Iran (the Islamic Republic of) (e-mail: Nchapar@azaruniv.ac.ir)

Automated Cell Tracking using Motion Prediction-based Matching and Event Handling (Abstract)

Fatima Boukari , Delaware State University, Dover, Delaware United States (e-mail: fboukari@desu.edu)
Sokratis Makrogiannis , Delaware State University, Dover, Delaware United States (e-mail: smakrogiannis@desu.edu)

SVSR: a Program to Simulate Structural Variations and Generate Sequencing Reads for Multiple Platforms (Abstract)

Xiguo Yuan , the School of Computer Science and Technology, Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: xiguoyuan@mail.xidian.edu.cn)
Meihong Gao , School of Computer Science and Technology, Xidian University, 47905 Xian, Shaanxi China (e-mail: 13484907397@163.com)
Jun Bai , Department of Medical Oncology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi China (e-mail: edgemen@163.com)
Junbo Duan , Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xian, Shaanxi China (e-mail: junbo.duan@mail.xjtu.edu.cn)

MEC: Misassembly Error Correction in contigs based on distribution of paired-end reads and statistics of GC-contents (Abstract)

Binbin Wu , Computer Science, Central South University, ChangSha, Hunan China (e-mail: binbinwu@csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Xingyu Liao , School of Information Science and Engineering, Central South University, 12570 Changsha, HuNan China 410083 (e-mail: liaoxingyu@csu.edu.cn)
Junwei Luo , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: luojunwei@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Computer Science, Georgia State University, Atlanta, Georgia United States 30303 (e-mail: pan@cs.gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Heterogeneous Domain Adaptation for IHC Classification of Breast Cancer Subtypes (Abstract)

Firat Ismailoglu , Computer Engineering, Cumhuriyet Universitesi, 52954 Sivas, Sivas Turkey (e-mail: firism@gmail.com)
Rachel Cavill , Data Science and Knowledge Engineering, Maastricht University, Maastricht, Maastricht Netherlands (e-mail: rachel.cavill@maastrichtuniversity.nl)
Evgueni Smirnov , Data Science and Knowledge Engieering, Maastricht University, 5211 Maastricht, Limburg Netherlands (e-mail: smirnov@maastrichtuniversity.nl)
Shuang Zhou , Data Science and Knowledge Engieering, Maastricht University, 5211 Maastricht, Limburg Netherlands (e-mail: shuang.zhou@maastrichtuniversity.nl)
Pieter Collins , Data Science and Knowledge Engieering, Maastricht University, 5211 Maastricht, Limburg Netherlands (e-mail: pieter.collins@maastrichtuniversity.nl)
Ralf Peeters , Data Science and Knowledge Engieering, Maastricht University, 5211 Maastricht, Limburg Netherlands (e-mail: ralf.peeters@maastrichtuniversity.nl)

Faster Exact Computation of rSPR Distance via Better Approximation (Abstract)

Zhi-Zhong Chen , Mathematical Sciences, Tokyo Denki University, Hatomama, Saitama Japan 350-0394 (e-mail: zzchen@mail.dendai.ac.jp)
Youta Harada , Mathematical Sciences, Tokyo Denki University, Hatomama, Saitama Japan (e-mail: 17rmd27@ms.dendai.ac.jp)
Yuna Nakamura , Mathematical Sciences, Tokyo Denki University, Hatomama, Saitama Japan (e-mail: 14rd129@ms.dendai.ac.jp)
Lusheng Wang , Department of Computer Science, City University of Hong Kong, Hongkong, Hongkong China (e-mail: cswangl@cityu.edu.hk)

CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths (Abstract)

Qiwen Kang , University of Kentucky, Lexington, Kentucky United States (e-mail: qiwen.kang@uky.edu)
Christopher W. Schardl , University of Kentucky, Lexington, Kentucky United States (e-mail: chris.schardl@uky.edu)
Neil Moore , University of Kentucky, Lexington, Kentucky United States (e-mail: neil@cs.uky.edu)
Ruriko Yoshida , Naval Postgraduate School, 48848 Monterey, California United States 93943-5155 (e-mail: ryoshida@nps.edu)

Robust Recurrent CNV Detection in the Presence of Inter-Subject Variability (Abstract)

Mustafa Alshawaqfeh , Electrical and Communication Engineering, German Jordanian University, 125725 Amman, Amman Jordan (e-mail: mustafa.shawaqfeh@gju.edu.jo)
Ahmad Al Kawam , Electrical and Computer Engineering, Texas A&M University, College Station, Texas United States 77845 (e-mail: ahmad.alkawam@tamu.edu)
Erchin Serpedin , Electrical and COmputer Engineering, Texas A&M University Baylor College of Dentistry, 26516 College Station, Texas United States (e-mail: eserpedin@tamu.edu)
Aniruddha Datta , Electrical and Computer Engineering, Texas A&M University, College Station, Texas United States (e-mail: a-datta@tamu.edu)

COPCOP: A Novel Algorithm and Parallel Optimization Framework for Co-Evolutionary Domain Detection (Abstract)

Xiaoyu Zhang , College of Computer, National University of Defense Technology, 58294 Changsha, Hunan China (e-mail: x.zhang18@imperial.ac.uk)
Xiangke Liao , College of Computer, National University of Defense Technology, 58294 Changsha, Hunan China (e-mail: xkliao@nudt.edu.cn)
Hao Zhu , Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, 70570 Guangzhou, Guangdong China (e-mail: haozhu@smu.edu.cn)
Kenli Li , College of Computer Science and Electronic Engineering & National Supercomputer Centre in Changsha, Hunan unversity, Changsha, Hunan China (e-mail: lkl@hnu.edu.cn)
Benyun Shi , College of Information Engineering, Nanjing University of Finance & Economics, Nanjing, Jiangsu China (e-mail: benyunshi@outlook.com)
Shaoliang Peng , College of Computer, National University of Defense Technology, 58294 Changsha, Hunan China (e-mail: pengshaoliang@nudt.edu.cn)

Backpropagation Approach Supported by Image Compression Algorithm for the Classification of Chronic Condition Diseases (Abstract)

Abir Hussain , Computer Science, Liverpool John Moores University, 4589 Liverpool, Merseyside United Kingdom of Great Britain and Northern Ireland (e-mail: A.Hussain@ljmu.ac.uk)
Dhiya Al-Jumeily , School of COmputer Science, Liverpool John Moores University, Liverpool, Mersyside United Kingdom of Great Britain and Northern Ireland L17 8XW (e-mail: D.Aljumeily@ljmu.ac.uk)
Ahmed Aljaaf , Anbar, Ramadi Iraq (e-mail: A.J.Aljaaf@uoanbar.edu.iq)
Naeem Radi , Al Khawarizmi International College, 105957 Abu Dhabi, Abu Dhabi United Arab Emirates (e-mail: n.radi@khawarizmi.com)

A Note on GRegNetSim: A Tool for the Discrete Simulation and Analysis of Genetic Regulatory Networks (Abstract)

Meirav Zehavi , Ben-Gurion University of the Negev, 26732 Beer-Sheva, Beer-Sheva Israel 84105 (e-mail: zehavimeirav@gmail.com)
Dor Ganor , Technion, Haifa, Haifa Israel (e-mail: dor.ganor@gmail.com)
Ron Pinter , Technion Israel Institute of Technology Faculty of Computer Science, 196688 Haifa, Haifa Israel (e-mail: pinter@cs.technion.ac.il)

Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome (Abstract)

Huiru Zheng , School of Computing, University of Ulster, Belfast, N. Ireland United Kingdom of Great Britain and Northern Ireland (e-mail: H.Zheng@ulster.ac.uk)
Haiying Wang , School of Computing, University of Ulster, Belfast, Northern Ireland United Kingdom of Great Britain and Northern Ireland (e-mail: hy.wang@ulster.ac.uk)
Richard Dewhurst , Scotland's Rural College, 3123 Edinburgh, Edinburgh United Kingdom of Great Britain and Northern Ireland (e-mail: Richard.Dewhurst@sruc.ac.uk)
Rainer Roehe , Scotland's Rural College, 3123 Edinburgh, Edinburgh United Kingdom of Great Britain and Northern Ireland (e-mail: Rainer.Roehe@sruc.ac.uk)

Introducing Heuristic Information into Ant Colony Optimization Algorithm for Identifying Epistasis (Abstract)

Yingxia Sun , Qufu Normal University, Rizhao, Shandong China (e-mail: sunyingxia026@163.com)
Xuan Wang , Rizhao, Shandong China (e-mail: wangxuanfine@163.com)
Junliang Shang , Qufu Normal University, Rizhao, Shandong China 276826 (e-mail: shangjunliang110@163.com)
Jin-Xing Liu , Bio-Computing Research Center, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong China 518055 (e-mail: sdcavell@126.com)
Chun-Hou Zheng , Qufu Normal University - Rizhao Campus, 381718 Rizhao, Shandong China (e-mail: zhengch99@126.com)
Xiujuan Lei , Xian, Shanxi China (e-mail: xjlei@snnu.edu.com)

Adaptive Particle Filtering for Fault Detection in Partially-Observed Boolean Dynamical Systems (Abstract)

Arghavan Bahadorinejad , Apple Inc, 93243 Cupertino, California United States (e-mail: arghavan@tamu.edu)
Mahdi Imani , Electrical and Computer Engineering, Texas A and M University System, 2655 College Statoion, Texas United States 77843 (e-mail: m.imani88@tamu.edu)
Ulisses Braga-Neto , Texas A&M University, College Station, Texas United States 77843-3128 (e-mail: ulisses@ece.tamu.edu)

Two New Heuristic Methods for Protein Model Quality Assessment (Abstract)

Wenbo Wang , Electrical Engineering and Computer Science, University of Missouri Columbia, 14716 Columbia, Missouri United States (e-mail: wwr34@mail.missouri.edu)
Junlin Wang , Electrical Engineering and Computer Science, University of Missouri Columbia, 14716 Columbia, Missouri United States (e-mail: jwynf@mail.missouri.edu)
Dong Xu , Computer Science, University of Missouri-Columnbia, Coulumbia, Missouri United States 65211 (e-mail: xudong@missouri.edu)
Yi Shang , University of Missouri, Columbia, Columbia, Missouri United States 65211 (e-mail: shangy@missouri.edu)

Inference of model parameters using particle filter algorithm and Copula distributions (Abstract)

Zhimin Deng , School of Applied Mathematics, Guangdong University of Technology, 47870 Guangzhou, Guangdong China (e-mail: deng1689@aliyun.com)
Xinan Zhang , School of Mathematics and Statistics, Huazhong Normal University, 12446 Wuhan, Hubei China (e-mail: xinanzhang@mail.ccnu.edu.cn)
Tianhai Tian , Mathematics, Monash University, Melbourne, Victoria Australia (e-mail: Tianhai.Tian@monash.edu)

An Efficient Ensemble Learning Approach for Predicting Protein-Protein Interactions by Integrating Protein Primary Sequence and Evolutionary Information (Abstract)

Zhu-Hong You , Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, China University of Mining and Technology, Ürümqi, Xingjiang China (e-mail: zhuhongyou@ms.xjb.ac.cn)
Wenzhun Huang , Xi'an, Shanxi China (e-mail: huangwenzhun@xijing.edu.cn)
Shanwen Zhang , Xi'an, Shanxi China (e-mail: zhangshanwen@xijing.edu.cn)
Yu-An Huang , Xi'an, Shanxi China (e-mail: yahuang1991@gmail.com)
Chang-Qing Yu , Xi'an, Shanxi China (e-mail: yuchangqing@xijing.edu.cn)
Li-Ping Li , Xi'an, Shanxi China (e-mail: sqerllp@gmail.com)

Identifying TF Binding Motifs from Partial Set of Target Genes and its Application to Regulatory Network Inference (Abstract)

Guoyi Zhao , Electrical and Computer Engineering, University of Massachusetts Amherst, 14707 Amherst, Massachusetts United States (e-mail: guoyi@umass.edu)
Li Guo , Xi'an Jiaotong University, 12480 Xi'an, Shaanxi China (e-mail: guo_li@xjtu.edu.cn)
Yong Zhang , Biochemistry and Molecular Biology, University of Massachusetts Amherst, 14707 Amherst, Massachusetts United States (e-mail: zya226@gmail.com)
Lixin Gao , Electrical and Computer Engineering, University of Massachusetts Amherst, 14707 Amherst, Massachusetts United States (e-mail: lgao@ecs.umass.edu)
Li-Jun Ma , Biochemistry and Molecular Biology, University of Massachusetts Amherst, 14707 Amherst, Massachusetts United States (e-mail: llijun@biochem.umass.edu)

Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors (Abstract)

Ka-Chun Wong , City University of hong Kong, Kowloon Tong, Kowloon Hong Kong (e-mail: kc.w@cityu.edu.hk)
Shankai Yan , Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon Hong Kong (e-mail: sk.yan@cityu.edu.hk)
Qiuzhen Lin , College of Computer Sciences and Software Engineering, Shenzhen University, 47890 Shenzhen, Guangdong China 518060 (e-mail: qiuzhlin@szu.edu.cn)
Xiangtao Li , College of Computer Science, Northeast Normal University, Changchun, 130117, P.R. China, Changchun, Jilin China (e-mail: lixt314@nenu.edu.cn)
Chengbin Peng , Chinese Academy of Sciences, Ningbo Institute of Industrial Technology, Ningbo, Zhejiang China (e-mail: pengchengbin@nimte.ac.cn)

NTSHMDA: Prediction of Human Microbe-Disease Association based on Random Walk by Integrating Network Topological Similarity (Abstract)

Jiawei Luo , Hunan University, the College of Information Science and Engineering, Changsha, Hunan China 410000 (e-mail: luojiawei@hnu.edu.cn)
Yahui Long , College of Computer Science and Electronic Engineering, Hunan University Changsha, Hunan, 410082, China, Changsha, Hunan Province China (e-mail: yahuilong@hnu.edu.cn)

Stability Analysis of Biological Networks' Diffusion State (Abstract)

Volkan Altuntas , Information Technologies, Bursa Teknik Universitesi, 226838 Bursa, Marmara Turkey (e-mail: valtuntas@gmail.com)
Murat Gok , Computer Engineering, Yalova Universitesi, 187479 Yalova, Marmara Turkey (e-mail: murat.gok@yalova.edu.tr)
Tamer Kahveci , Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida United States 32611-6125 (e-mail: tamer@cise.ufl.edu)

Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor (Abstract)

Jose Manuel Herruzo , Computer Architecture, University of Malaga, Malaga, Malaga Spain (e-mail: jmherruzo@uma.es)
Sonia Gonzalez Navarro , Computer Architecture, University of Malaga, Malaga, Malaga Spain 29071 (e-mail: sonia@ac.uma.es)
Pablo Ibanez , Informatica e Ingenieria de Sistemnas, University of Zaragoza, Zaragoza, Zaragoza Spain 50018 (e-mail: imarin@unizar.es)
Victor Vinals Yufera , Informática e Ingenieréa de Sistemas, Universidad de Zaragoza, Zaragoza, Zaragoza Spain 50018 (e-mail: victor@unizar.es)
Jesus Alastruey , Informtica e Ingenieréa de Sistemas, Universidad de Zaragoza, Zaragoza, Zaragoza Spain 50018 (e-mail: jalastru@unizar.es)
Oscar Plata , Computer Architecture, University of Malaga, Malaga, Malaga Spain E29071 (e-mail: oplata@uma.es)

Intra-cluster distance minimization in DNA methylation analysis using an advanced Tabu-based iterative k-medoids clustering algorithm (T-CLUST) (Abstract)

Haluk Damgacioglu , Industrial Engineering, University of Miami, Coral Gables, Florida United States (e-mail: haluk.damgacioglu@miami.edu)
Emrah Celik , Aerospace and Mechanical Engineering, University of Miami, Coral Gables, Florida United States (e-mail: e.celik@miami.edu)
Nurcin Celik , Industrial Engineering, University of Miami, Coral Gables, Florida United States 33146 (e-mail: celik@miami.edu)

Quantitative Regular Expressions for Arrhythmia Detection (Abstract)

Houssam Abbas , Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, Pennsylvania United States (e-mail: habbas@seas.upenn.edu)
Alena Rodionova , Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, Pennsylvania United States 19104 (e-mail: rodionova.alv@gmail.com)
Konstantinos Mamouras , University of Pennsylvania, Philadelphia, Pennsylvania United States (e-mail: kmamouras@gmail.com)
Ezio Bartocci , Technische Universitat Wien, 27259 Wien, Wien Austria (e-mail: ezio.bartocci@tuwien.ac.at)
Scott Smolka , Computer Science, Stony Brook University, 12301 Stony Brook, New York United States (e-mail: sas@cs.stonybrook.edu)
Radu Grosu , Technische Universitat Wien, 27259 Wien, Wien Austria (e-mail: radu.grosu@tuwien.ac.at)

Hardware-Software Codesign based Accelerated and Reconfigurable Methodology for String Matching in Computational Bioinformatics Applications (Abstract)

Venkateshwarlu Yellaswamy Gudur , Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana India (e-mail: ee15resch02009@iith.ac.in)
Amit Acharyya , Electrical, Indian Institute of Technology Hyderabad, 233600 Hyderabad, Telengana India 502205 (e-mail: amit_acharyya@iith.ac.in)

Visual Life Sciences Workflow Design using Distributed and Heterogeneous Resources (Abstract)

Xin Mou , Computer Science, University of Idaho, Moscow, Idaho United States (e-mail: mou1609@vandals.uidaho.edu)
Hasan M. Jamil , Computer Science, University of Idaho, Moscow, Idaho United States 83844-1010 (e-mail: jamil@uidaho.edu)

Understanding Protein Networks using Vester’s Sensitivity Model (Abstract)

Liana Amaya Moreno , Maschinenbau, Helmut-Schmidt-Universitat Universitat der Bundeswehr Hamburg, 26554 Hamburg, Hamburg Germany 22043 (e-mail: lamayamo@hsu-hh.de)
Maryam Omidi , Universitatsklinikum Hamburg-Eppendorf, 37734 Hamburg, Hamburg Germany (e-mail: m.omidi@uke.de)
Marcus Wurlitzer , Universitatsklinikum Hamburg-Eppendorf, 37734 Hamburg, Hamburg Germany (e-mail: m.wurlitzer@uke.de)
Berengere Luthringer , Helmholtz-Zentrum Geesthacht Zentrum fur Materialforschung und Kustenforschung, 28338 Geesthacht, Schleswig-Holstein Germany (e-mail: Berengere.Luthringer@hzg.de)
Heike Helmholz , Helmholtz-Zentrum Geesthacht Zentrum fur Materialforschung und Kustenforschung, 28338 Geesthacht, Schleswig-Holstein Germany (e-mail: heike.helmholz@hzg.de)
Hartmut Schluter , Universitatsklinikum Hamburg-Eppendorf, 37734 Hamburg, Hamburg Germany (e-mail: hschluet@uke.de)
Regine Willumeit-Romer , Helmholtz-Zentrum Geesthacht Zentrum fur Materialforschung und Kustenforschung, 28338 Geesthacht, Schleswig-Holstein Germany (e-mail: regine.willumeit@hzg.de)
Armin Fugenschuh , Brandenburgische Technische Universitat Cottbus-Senftenberg, 38871 Cottbus, Brandenburg Germany (e-mail: fuegenschuh@b-tu.de)

Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition (Abstract)

Xiaohui Yang , Data Analysis Technology Lab, Henan University, 12411 Kaifeng, Henan China (e-mail: xhyanghenu@163.com)
Li Tian , School of Mathematics and Statistics, Henan University, 12411 Kaifeng, Henan China (e-mail: zihaibeitl@163.com)
Yunmei Chen , Department of Mathematics, University of Florida, Gainesville, Florida United States (e-mail: yun@ufl.edu)
Lijun Yang , School of Mathematics and Statistics, Henan University, Kaifeng, Henan China (e-mail: yanglijun@henu.edu.cn)
Shuang Xu , Xi'an Jiaotong University, 12480 Xi'an, Shaanxi China (e-mail: henuxs@foxmail.com)
Weming Wu , School of Mathematics and Statistics, Henan University, Kaifeng, Henan China (e-mail: wenmingWu55@163.com)

Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks (PDF)

Hannes Klarner , Mathematics, Freie Universität Berlin, Berlin, Berlin Germany (e-mail: Hannes.Klarner@FU-Berlin.de)
Heike Siebert , Mathematics, Freie Universität Berlin, Berlin, Berlin Germany (e-mail: Heike.Siebert@FU-Berlin.de)
Sarah Nee , Freie Universitat Berlin Fachbereich Mathematik und Informatik, 197351 Berlin, Berlin Germany 14195 (e-mail: sarah.nee@me.com)
Frederike Heinitz , Freie Universitat Berlin Fachbereich Mathematik und Informatik, 197351 Berlin, Berlin Germany 12059 (e-mail: afheinitz@zedat.fu-berlin.de)

Feed-forward and Feedback Control in Astrocytes for Ca2+-based Molecular Communications Nanonetworks (Abstract)

Michael Barros , TSSG, Waterford Institute of Technology, 8807 Waterford, Waterford Ireland (e-mail: mbarros@tssg.org)
Subhrakanti Dey , Signals and Systems, Uppsala University, Uppsala, Uppland Sweden (e-mail: Subhra.Dey@signal.uu.se)

Causal reasoning on Boolean control networks based on abduction: theory and application to Cancer drug discovery (Abstract)

Celia Biane , Computer Science, IBISC, Evry Univ, Paris-Saclay University, 91025 Evry, Ile-de-France France (e-mail: celia.biane@univ-evry.fr)
Franck Delaplace , Computer Science, IBISC, Evry Univ., Paris-Saclay University, 91025 Evry, Ile-de-France France (e-mail: franck.delaplace@ibisc.univ-evry.fr)

United neighborhood closeness centrality and orthology for predicting essential proteins (Abstract)

Gaoshi Li , Changsha, Hunan China (e-mail: ligaoshi@gxnu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Yaohang Li , Computer Science, Old Dominion University, Norfolk, Virginia United States 23508 (e-mail: yaohang@cs.odu.edu)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)

Prediction of DNA-binding residues in local segments of protein sequences with Fuzzy Cognitive Maps (Abstract)

Abdollah Amirkhani , Electrical Engineering, Iran University of Science and Technology, 56944 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: amirkhani@ieee.org)
Mojtaba Kolahdoozi , Electrical Engineering, Iran University of Science and Technology, 56944 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: mojtaba_kolahdooz@elec.iust.ac.ir)
Chen Wang , Computer Science, Virginia Commonwealth University, Richmond, Virginia United States (e-mail: wangc27@mymail.vcu.edu)
Lukasz Kurgan , Computer Science, Virginia Commonwealth University, Richmond, Virginia United States 23284-3019 (e-mail: lkurgan@vcu.edu)

Prediction of TF-binding site by inclusion of higher order position dependencies (PDF)

Jiyun Zhou , Computing, Hong Kong Polytechnic University, 26680 Hong Kong, Hong Kong Hong Kong (e-mail: zhoujiyun2010@gmail.com)
Qin Lu , Computing, The Hong Kong Polytechnic University, Hong Kong, Hong Kong Hong Kong (e-mail: csluqin@comp.polyu.edu.hk)
Ruifeng Xu , Computer science and technology, Harbin Institute Of Technology Shenzhen Graduate School, Shenzhen, Guangdong China (e-mail: xuruifeng@hit.edu.cn)
Lin Gui , Engineering and Applied Science, Aston University, 1722 Birmingham, Birmingham United Kingdom of Great Britain and Northern Ireland (e-mail: guilin.nlp@gmail.com)
Hongpeng Wang , Computer science and technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong China (e-mail: wanghp@hit.edu.cn)

nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale (Abstract)

Alexandre Victor Fassio , Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 28114 Belo Horizonte, Minas Gerais Brazil (e-mail: alexandrefassio@dcc.ufmg.br)
Lucianna H. Santos , Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 28114 Belo Horizonte, MG Brazil (e-mail: luciannahss@gmail.com)
Sabrina A. Silveira , Department of Computer Science, Universidade Federal de Vicosa, 28120 Vicosa, MG Brazil (e-mail: sabrina@ufv.br)
Rafaela S. Ferreira , Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 28114 Belo Horizonte, Minas Gerais Brazil (e-mail: rafaelasf@gmail.com)
Raquel Cardoso de Melo-Minardi , Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil (e-mail: raquelcm@dcc.ufmg.br)

Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-optimal Solutions (Abstract)

Syed Ali Ahmed , Computer Science, The Graduate Center City University of New York, New York, New York United States (e-mail: sahmed3@gradcenter.cuny.edu)
Saad Mneimneh , computer science, Hunter College of CUNY, new york, New York United States 10021 (e-mail: saad@hunter.cuny.edu)

Querying Representative and Informative Super-pixels for Filament Segmentation in Bioimages (Abstract)

Wei Shao , School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu China 210016 (e-mail: 527606857@qq.com)
Sheng-Jun Huang , Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu China 211106 (e-mail: huangsj@nuaa.edu.cn)
MingXia Liu , Department of Computer Science and Engineering, Nanjing University of Aeronautics and Astronautics, 47854 Nanjing, Jiangsu China (e-mail: mingxialiu@nuaa.edu.cn)
Daoqiang Zhang , Computer Science and Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu China 210016 (e-mail: dqzhang@nuaa.edu.cn)

Local Similarity Matrix for Cysteine Disulfide Connectivity Prediction from Protein Sequences (Abstract)

Norman John Mapes Jr , College of Engineering and Science, Louisiana Tech, Ruston, Louisiana United States 71270 (e-mail: johnmapesjr@gmail.com)
Christopher Rodriguez , College of Engineering and Science, Louisiana Tech, Ruston, Louisiana United States (e-mail: chrizrodz@gmail.com)
Pradeep Chowriappa , College of Engineering and Science, Louisiana Tech, Ruston, Louisiana United States (e-mail: mariopradeep@gmail.com)
Sumeet Dua , College of Engineering and Science, Louisiana Tech, Ruston, Louisiana United States (e-mail: sdua@latech.edu)

Modified Half-System based Method for Reverse Engineering of Gene Regulatory Networks (Abstract)

Abhinandan Khan , Computer Science and Engineering, University of Calcutta, 30163 Kolkata, West Bengal India (e-mail: khan.abhinandan@gmail.com)
Goutam Saha , Information Technology, North-Eastern Hill University, 29666 Shillong, Meghalaya India (e-mail: dr.goutamsaha@gmail.com)
Rajat Kumar Pal , Computer Science and Engineering, University of Calcutta, 30163 Kolkata, West Bengal India (e-mail: pal.rajatk@gmail.com)

(Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices (Abstract)

Hussain Ahmed Chowdhury , Computer Science and Engineering, Tezpur University, 28688 Napaam, Assam India (e-mail: hachowdhury09@yahoo.in)
Dhruba Kumar Bhattacharyya , Computer Science and Engineering, Tezpur University, Tezpur, Assam India 784028 (e-mail: dkb@tezu.ernet.in)
Jugal K. Kalita , Computer Science, University of Colorado, Colorado Springs, Colorado United States 80918 (e-mail: jkalita@uccs.edu)

TargetDBP: Accurate DNA-Binding Protein Prediction via Sequence-based Multi-View Feature Learning (Abstract)

Jun Hu , college of information engineering, Zhejiang University of Technology, Hangzhou, Zhejiang China (e-mail: junh_cs@126.com)
Xiaogen Zhou , college of information engineering, Zhejiag university of technology, Hangzhou, Zhejiang China 310023 (e-mail: zxg@zjut.edu.cn)
Yi-Heng Zhu , School of Computer Science and Engineering, Nanjing University of Science and Technology, 12436 Nanjing, Jiangsu China (e-mail: zhy930505@163.com)
Dong-Jun Yu , School of Computer Science and Engineering, Nanjing University of Science and Technology, 12436 Nanjing, Jiangsu China 210094 (e-mail: njyudj@126.com)
Guijun Zhang , college of information engineering, Zhejiag university of technology, Hangzhou, Zhejiang China 310023 (e-mail: zgj@zjut.edu.cn)

A reaction-based model of the state space of chemical reaction systems enables efficient simulations (Abstract)

Paola Lecca , Department of Mathematics, Universita degli Studi di Trento Dipartimento di Matematica, 201805 Trento, Italy Italy (e-mail: paola.lecca@unitn.it)
Angela Re , Center for Sustainable Future Technologies CSFT@Polito, Istituto Italiano di Tecnologia, Torino, Italy Italy (e-mail: Angela.Re@iit.it)

Low-Rank Joint Subspace Construction for Cancer Subtype Discovery (Abstract)

Aparajita Khan , Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal India (e-mail: aparajitak_r@isical.ac.in)
Pradipta Maji , Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal India (e-mail: pmaji@isical.ac.in)

Potential Effect of Tobacco Consumption Through Smoking and Chewing Tobacco on IL1beta Protein Expression in Chronic Periodontitis Patients: In Silico Molecular Docking Study (Abstract)

Poulami Majumder , Maulana Abul Kalam Azad University of Technology, 74998 Kolkata, west bengal India 700064 (e-mail: plm89.majumder@gmail.com)
Partha Pratim Ray , Computer Applications, Sikkim University, Gangtok, Sikkim India 737135 (e-mail: ppray@cus.ac.in)
Sujay Ghosh , University of Calcutta, 30163 Kolkata, West Bengal India (e-mail: g_sujoy@yahoo.com)
Subrata Kumar Dey , Maulana Abul Kalam Azad University of Technology, 74998 Kolkata, West Bengal India (e-mail: skd.humgenet@gmail.com)

A Data-driven Approach to Predict and Classify Epileptic Seizures from Brain-wide Calcium Imaging Video Data (Abstract)

Jingyi Zheng , Statistics, UC Davis, Davis, California United States (e-mail: jgzheng@ucdavis.edu)
Hsieh Fushing , Statistics, UC Davis, Davis, California United States (e-mail: fhsieh@ucdavis.edu)
Linqiang Ge , Computer Science, Georgia Southwestern State University, 1165 Americus, Georgia United States 31709-4376 (e-mail: linqiang.ge@gsw.edu)

Generation of level-k LGT Networks (Abstract)

Joan Carles Pons , Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Balearic Islands Spain (e-mail: joancarles.pons@uib.es)
Celine Scornavacca , Institut des Sciences de l'Evolution, Universite Montpellier Faculte des Sciences de Montpellier, 173567 Montpellier, Languedoc-Roussillon France (e-mail: celine.scornavacca@umontpellier.fr)
Gabriel Cardona , Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Balearic Islands Spain (e-mail: gabriel.cardona@uib.es)

BiModule: biclique modularity strategy for identifying transcription factor and microRNA co-regulatory modules (Abstract)

CHU PAN , Information Science and Electronic Engineering, Hunan University, Changsha, Hunan China (e-mail: panchu@hnu.edu.cn)
Jiawei Luo , Hunan University, the College of Information Science and Engineering, Changsha, Hunan China 410000 (e-mail: luojiawei@hnu.edu.cn)
Jiao ZHANG , Department of Computer Science, City University of Hong Kong, 53025 Hong Kong, --- Select One --- Hong Kong 999077 (e-mail: jiaozhang9-c@my.cityu.edu.hk)
Xin Li , Information Science and Electronic Engineering, Hunan University, Changsha, Hunan China (e-mail: lx1006@hnu.edu.cn)

Tissue-specific Subcellular Localization Prediction using Multi-label Markov Random Fields (Abstract)

Lu Zhu , Bioinformatics Department, Universitat Bielefeld Technische Fakultat, 197691 Bielefeld, North Rhine-Westphalia Germany (e-mail: lzhu@techfak.uni-bielefeld.de)
Ralf Hofestaedt , Bioinfomatics Department, Universitat Bielefeld Technische Fakultat, 197691 Bielefeld, Nordrhein-Westfalen Germany (e-mail: ralf.hofestaedt@uni-bielefeld.de)
Martin Ester , School of Computing Science, Simon Fraser University, Burnaby, British Columbia Canada (e-mail: ester@cs.sfu.ca)

An efficient trimming algorithm based on multi-feature fusion scoring model for NGS data (Abstract)

Xingyu Liao , School of Information Science and Engineering, Central South University, 12570 Changsha, HuNan China 410083 (e-mail: liaoxingyu@csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
You Zou , Computer Science, Central South University, ChangSha, Hunan China (e-mail: zouyou@csu.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yi Pan , Computer Science, Georgia State University, Atlanta, Georgia United States 30303 (e-mail: pan@cs.gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

A deep learning framework for identifying essential proteins by integrating multiple types of biological information (Abstract)

Min Zeng , Central South University, 12570 Changsha, Hunan China 410083 (e-mail: zengmin@csu.edu.cn)
Min Li , Computer Science, Central South University, Changsha, Hunan China (e-mail: limin@mail.csu.edu.cn)
Zhihui Fei , Changsha, Hunan China (e-mail: zhihuifei@foxmail.com)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)
Yaohang Li , Computer Science, Old Dominion University, Norfolk, Virginia United States 23508 (e-mail: yaohang@cs.odu.edu)
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, Georgia United States (e-mail: yipan@gsu.edu)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)

Accurately Detecting Protein Complexes by Graph Embedding and Combining Functions with Interactions (Abstract)

Heng Yao , Department of Computer Science and Technology, Tongji University, Shanghai, Shanghai China (e-mail: yaoheng@tongji.edu.cn)
Yunjia Shi , Department of Computer Science and Technology, Tongji University, 12476 Shanghai, Shanghai China (e-mail: 18817878627@tongji.edu.cn)
Jihong Guan , Department of Computer Science and Technology, Tongji University, Shanghai, Shanghai China (e-mail: jhguan@tongji.edu.cn)
Shuigeng Zhou , School of Computer Science, Fudan University, Shanghai, ShangHai China 200433 (e-mail: sgzhou@fudan.edu.cn)

Variable neighborhood search for partitioning sparse biological networks into the maximum edge-weighted $k$-plexes (Abstract)

Milana Grbic , Dept. of Mathematics and Informatics, Faculty of Natural Science and Mathematics, University of Banja Luka, Banja Luka, Republika Srpska Bosnia and Herzegovina 78000 (e-mail: milana.grbic@pmf.unibl.org)
Aleksandar Kartelj , Faculty of Mathematics, University of Belgrade, Belgrade, Belgrade Serbia (e-mail: aleksandar.kartelj@gmail.com)
Savka Jankovic , Faculty of Natural Science and Mathematics, University of Banja Luka, Banja Luka, Republika Srpska Bosnia and Herzegovina (e-mail: savka.jankovic@pmf.unibl.org)
Dragan Matic , Faculty of Natural Science and Mathematics, University of Banja Luka, Banja Luka, Republika Srpska Bosnia and Herzegovina (e-mail: dragan.matic@pmf.unibl.org)
Vladimir Filipovic , Faculty of Mathematics, University of Belgrade, Belgrade, Belgrade Serbia (e-mail: vladofilipovic@hotmail.com)

Shortest-Latency Opportunistic Routing in Asynchronous Wireless Sensor Networks with Independent Duty-Cycling (Abstract)

Xinming Zhang , School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui China 230027 (e-mail: xinming@ustc.edu.cn)
Lei Tao , School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: taolei@mail.ustc.edu.cn)
Fan Yan , School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui China (e-mail: yanfan@mail.ustc.edu.cn)
Dan Keun Sung , EECS, KAIST, Daejeon, Daejeon Korea, Republic of 305-701 (e-mail: dksung@ee.kaist.ac.kr)

PredictFP2: a new computational model to predict fusion peptide domain in all retroviruses (Abstract)

Sijia Wu , Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: wusijia@xidian.edu.cn)
Xiaoming Wu , Xi'an, Shaanxi China (e-mail: wxm@mail.xjtu.edu.cn)
Jie Tian , Institute of Automation, Chinese Academy of Sciences, Beijing, Beijing China (e-mail: jie.tian@ia.ac.cn)
Xiaobo Zhou , Medical Center Boulevard, Wake Forest School of Medicine, Winston-Salem, North Carolina United States (e-mail: zhouxb2015@163.com)
Liyu Huang , Xi'an, Shaanxi China (e-mail: huangly@mail.xidian.edu.cn)

Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation (Abstract)

Yuan Zhang , Department of Mathematics, Yuxi Normal University, 66360 Yuxi, Yunnan China (e-mail: zhyuan90@sina.com)
Haihong Liu , Department of mathematics, Yunnan Normal University, 66343 Kunming, Yunnan China (e-mail: lhhmath@aliyun.com)
Zhouhong Li , Department of mathematics, Yuxi Normal University, 66360 Yuxi, Yunnan China (e-mail: zhouhli@yeah.net)
Zhonghua Miao , School of Mechatronic Engineering and Automation, Shanghai University, 34747 Shanghai, Shanghai China (e-mail: zhhmiao@shu.edu.cn)
Jin Zhou , Shanghai Institute of Applied Math and Mech, Shanghai University, Shanghai, Shanghai China (e-mail: jinzhoushu@163.com)

Integration of imaging (epi)genomics data for the study of schizophrenia using group sparse joint nonnegative matrix factorization (Abstract)

Min Wang , School of Mathematical Sciences/Research Center for Image and Vision Computing, University of Electronic Science and Technology of China, 12599 Chengdu, Sichuan China (e-mail: minwang1989@126.com)
Ting-Zhu Huang , University of Electronic Science and Technology of China, 12599 Chengdu, Sichuan China (e-mail: tingzhuhuang@126.com)
Jian Fang , Biomedical Engineering, Tulane University, 5783 New Orleans, Louisiana United States 70118-5665 (e-mail: jfang3@tulane.edu)
Vince D. Calhoun , The Mind Research Network, University of New Mexico, Albuquerque, New Mexico United States (e-mail: vcalhoun@mrn.org)
Yu-Ping Wang , Tulane University, New Orleans, Louisiana United States (e-mail: wyp@tulane.edu)
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