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ISSN: 1545-5963

A Copula-based Granger Causality Measure for the Analysis of Neural Spike Train Data (Abstract)

Meng Hu , Meng Hu is with the School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, PA 19104, USA. (e-mail: vhumeng@ gmail.com).

NovoExD: De novo peptide sequencing for ETD/ECD spectra (Abstract)

Yan Yan , Yan Yan is with the Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9 Canada. (email: yan.yan@usask.ca)

Modeling the geometry and dynamics of theEndoplasmic Reticulum network (Abstract)

Congping Lin , Congping Lin is with the Mathematics at the University of Exeter, UK (e-mail: c.lin@exeter.ac.uk).

Predicting protein functions by using unbalanced random walk algorithm on three biological networks (Abstract)

Wei Peng , Wei Peng is with the School of Information Science and Engineering, Central South University, Changsha, P. R. China, 410083 and the Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650093, PR China. (email: weipeng1980@gmail.com)

United complex centrality for identification of essential proteins from PPI networks (Abstract)

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

Optimal Fault Detection and Diagnosis in Transcriptional Circuits using Next-Generation Sequencing (Abstract)

Ulisses Braga-Neto , Arghavan Bahadorinejad is with the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843 USA. (email: arghavan@tamu.edu)

Identifying Spurious Interactions in the Protein-Protein Interaction Networks Using Local Similarity Preserving Embedding (Abstract)

Lin Zhu , Lin Zhu is with the College of Electronics and Information Engineering, Tongji, University, China. (e-mail: lizhonyx@163.com).

An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra (Abstract)

Yi Liu , Yi Liu is with the Department of Computer Science, The University of Western Ontario, London, ON, CA, N6H 4T7. (e-mail: yliu766@uwo.ca).

MeTDiff: a Novel Differential RNA Methylation Analysis for MeRIP-Seq Data (Abstract)

Xiaodong Cui , Xiaodong Cui is with the Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, 78249. (e-mail: xdchoi@gmail.com).

A Two-phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM (Abstract)

Fa Zhang , Fa Zhang is with the Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. 100190. (email: zhangfa@ict.ac.cn)

Learning Parameter-Advising Sets for Multiple Sequence Alignment (Abstract)

Daniel DeBlasio , D. DeBlasio is with the Department of Computer Science at the University of Arizona, Tucson, AZ 85721, USA. (email:deblasio@cs.arizona.edu)

Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides (Abstract)

Mansuck Kim , Mansuck Kim is with the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843.(email:mk22893@neo.tamu.edu)

An Effective Application of Bacteria Quorum Sensing and Circular Elimination in MOPSO (Abstract)

Shan Cheng , S. Cheng is with Hubei Key Laboratory of Cascaded Hydropower Stations Operation & Control, and Hubei Provincial Collaborative Center for New Energy Microgrid, China Three Gorges University.(email:hpucquyzu@ctgu.edu.cn)

A Novel Cluster Head Selection Algorithm Based on Fuzzy Clustering and Particle Swarm Optimization (Abstract)

Qingjian Ni , Qingjian Ni is with School of Computer Science and Engineering, Southeast University, Nanjing, 211189, China.(email:nqj@seu.edu.cn)

Microbiome Data Representation by Joint Nonnegative Matrix Factorization with Laplacian Regularization (Abstract)

Xingpeng Jiang , Xingpeng Jiang is with the School of Computer Science, Central China Normal University, Wuhan, Hubei, China. (e-mail: xingpengjiang@gmail.com).

Three-Dimensional Path Planning for Uninhabited Combat Aerial Vehicle Based on Predator-Prey Pigeon-Inspired Optimization in Dynamic Environment (Abstract)

Bo Zhang , Bo Zhang is with the State Key Laboratory of Virtual Reality Technology and Systems, School of Automation Science and Electrical Engineering, Beihang University, Beijing, 100191, P. R. China. (e-mail: hbduan@buaa.edu.cn).

Fireworks Algorithm with Enhanced Fireworks Interaction (Abstract)

Bei Zhang , Bei Zhang is with the College of Computer Science & Technology, Zhejiang University of Technology, Hangzhou, 310023 China. (email: zhangbei-zjut@outlook.com)

Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data (Abstract)

Yize Zhao , Yize Zhao is with the Statistical and Applied Mathematical Sciences Institute, Research Triangle Park, NC 27709.

Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline (Abstract)

Noushin Ghaffari , Noushin Ghaffari is with the AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77845.(Email: nghaffari@tamu.edu)

Gender Identification of Human Brain Image with A Novel 3D Descriptor (Abstract)

Lin Yuan , Lin Yuan is with the College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, 410073, China.

Analysis of Organization of the Interactome Using Dominating Sets: a Case Study on Cell Cycle Interaction Networks (Abstract)

Huiru Zheng , Huiru Zheng is with the Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, BT37 0QB, Northern Ireland, U.K.(Email: h.zheng@ulster.ac.uk)

Pathway Analysis with Signaling Hypergraphs (Abstract)

Anna Ritz , Anna Ritz is with the Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061.(Email: annaritz@vt.edu)

Muscle Tissue Labeling of Human Lower Limb in Multi-Channel mDixon MR Imaging: Concepts and Applications (Abstract)

Matthias Becker , Matthias Becker is with the MIRALab, University of Geneva, Battelle, Building A, 7 route de Drize, 1227 Carouge, Switzerland.(Email: becker@miralab.ch)

Symbiosis-based Alternative Learning Multi-Swarm Particle Swarm Optimization (Abstract)

Ben Niu , Ben Niu is with the College of Management, Shenzhen University,Shenzhen, China, and the Department of Industrial and System Engineering, The Hong Kong Polytechnic University, HK.(Email: drniuben@gmail.com)

Solving NP-Hard Problems with Physarum-Based Ant Colony System (Abstract)

Yuxin Liu , Yuxin Liu is with the College of Computer and Information Science & College of Software, Southwest University, Chongqing, China, 400715.(Email: xinjia@swu.edu.cn)

A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants (Abstract)

Zhiyong Wang , Zhiyong Wang is with the Toyota Technological Institute at Chicago, Chicago, IL, 60637 USA.(Email: indicator@gmail.com)

Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming (Abstract)

Daniel Veltri , Daniel Veltri is with the School of Systems Biology, George Mason University Fairfax, VA 22030. (email: dveltri@gmu.edu)

CORTICAL THINNING AND COGNITIVE IMPAIRMENT IN PARKINSON’S DISEASE WITHOUT DEMENTIA (Abstract)

Lijun Zhang , L. Zhang is with the Institute for Personalized Medicine, Pennsylvania State University, Hershey PA 17033.(email:lxhang6@hmc.psu.edu)

A New Magnetotactic Bacteria Optimization Algorithm Based on Moment Migration (Abstract)

Hongwei Mo , Hongwei Mo is with the Department of Automation, Harbin Engineering University, Harbin, China, 150001. (email: honwei2004@126.com)

A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-class Sensitivity Information (Abstract)

Fei Han , Fei Han is with the School of Computer Science and Communication Engineering, Jiangsu University, Zhenjiang, Jiangsu, China.(Email: hanfei@mail.ujs.edu.cn)

A GRASP-based Heuristic for the Sorting by Length-Weighted Inversions Problem (Abstract)

Thiago da Silva Arruda , Thiago da Silva Arruda is with the Institute of Computing, University of Campinas, Campinas, Sao Paulo, Brazil, 13083-852.(Email: thiago.arruda@students.ic.unicamp.br)

Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering (Abstract)

En-Shiun Annie Lee , En-Shiun Annie Lee is with the Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.(email:annie.lee@uwaterloo.ca)

Multi-objective Particle Swarm Optimization Approach for Cost-based Feature Selection in Classification (Abstract)

Yong Zhang , Yong Zhang is with the School of Information and Electronic Engineering, China University of Mining and Technology, Xuzhou 221008, China. (email: yongzh401@126.com.)

Complex network measures in Autism Spectrum Disorders (Abstract)

Joao Ricardo Sato , Joao Ricardo Sato is with the Center of Mathematics, Computation, and Cognition, the Universidade Federal do ABC, Rua Santa Adelia, 166, Santo André, SP, 09210-170, Brazil. (e-mail: jrsato@gmail.com.)

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)

A framework for identifying genotypic information from clinical records: exploiting integrated ontology structures to transfer annotations between ICD codes and Gene Ontologies (Abstract)

Seyedsasan Hashemikhabir , Seyedsasan Hashemikhabir is with the Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202. (email: hashemis@iu.edu)

IAS: Interaction specific GO term associations for predicting protein-protein interaction networks (Abstract)

Satwica Yerneni , Satwica Yerneni is with the Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN-55905, USA. (e-mail: Yerneni.Satwica@mayo.edu)

Nucleosome Positioning of Intronless Genes in the Human Genome (Abstract)

Xiangfei Cheng , Xiangfei Cheng is with the State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China. (email: chengxiangfeiangel@163.com)

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification (Abstract)

Jason Knight , Jason M. Knight is with the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843.(Email: jknight@tamu.edu)

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU (Abstract)

Jing Zhang , Jing Zhang is with the Dept. of Computer Science at Virginia Tech (e-mail: zjing14@vt.edu).

Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in human and mouse (Abstract)

Rodrigo Ramalho , Rodrigo F. Ramalho is with the Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405.(Email: rfrusp@gmail.com)

Multi-view Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering (Abstract)

Yong Zhang , Yong Zhang is with the College of Computer Science, Central China Normal University, Wuhan, Hubei 430079, China (e-mail: yzhang@mail.ccnu.edu.cn).

Improving identification of key players in aging via network de-noising and core inference (Abstract)

Boyoung Yoo , Boyoung Yoo is with the Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. (email: byoo@nd.edu.)

SparseNCA: Sparse Network Component Analysis for Recovering Transcription Factor Activities with Incomplete Prior Information (Abstract)

Amina Noor , Amina Noor is with the Department of Psychiatry, University of California, San Diego, CA, 92121.(Email: amina.noor@gmail.com)

Discovering Gene Regulatory Elements Using Coverage-based Heuristics (Abstract)

Rami Al-Ouran , Rami Al-Ouran is with the Department of Electrical Engineering and Computer Science, Ohio University, Athens, OH 45701. (email: ra102506@ohio.edu)

A Cooperative Framework for Fireworks Algorithm (Abstract)

Shaoqiu Zheng , Shaoqiu Zheng is with the Department of Machine Intelligence, School of Electronics Engineering and Computer Science, Peking University, Key Laboratory of Machine Perception (Ministry of Education), Peking University, Beijing,100871, P.R. China. (email: qiu11340203@163.com)

Calcium Ion Fluctuations Alter Channel Gating in a Stochastic Luminal Calcium Release Site Model (Abstract)

Hao Ji , Hao Ji is with the Department of Computer Science, Old Dominion University, Norfolk, VA, 23529.(Email: hji@cs.odu.edu)

PyMut: a web tool for overlapping gene loss-of-function mutation design (Abstract)

Ke Liu , Kei Liu is with the MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China. (e-mail: keliu_wh@163.com).

Towards extracting supporting information about predicted protein-protein interactions (Abstract)

Adam Roth , Adam Roth is with the Adam Roth is with Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 501, Pittsburgh, PA, 15206.
Sandeep Subramanian , Adam Roth is with the Adam Roth is with Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 501, Pittsburgh, PA, 15206.
Madhavi K. Ganapathiraju , Adam Roth is with the Adam Roth is with Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 501, Pittsburgh, PA, 15206.

Characteristic Gene Selection based on Robust Graph Regularized Non-negative Matrix Factorization (Abstract)

Dong Wang , Dong Wang is with the School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong 276826, China. (email: dongwshark@126.com)

Gene regulatory network inference from perturbed time-series expression data via ordered dynamical expansion of non-steady state actors (Abstract)

Mahdi Zamanighomi , Mahdi Zamanighomi is with the Department of Statistics, Stanford University, Stanford, CA, 94305 USA.(Email: mzamani@stanford.edu)

Encoding Data Using Biological Principles: the Multisample Variant Format for Phylogenomics and Population Genomics (Abstract)

James Pease , James B. Pease is with the Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, USA, 48109.(Email: jbpease@umich.edu)

A graph-theoretical approach for motif discovery in protein sequences (Abstract)

Elena Czeizler , E. Czeizler is with Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University.(email:elena.czeizler@aalto.fi)

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net (Abstract)

Lin Zhang , Lin Zhang is with the School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, 221116, China.(email:lin.zhang@cumt.edu.cn)

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees (Abstract)

Misagh Kordi , Misgah Kordi is with the Department of Computer Science and Engineering at the University of Connecticut, Storrs, USA.(email:misagh.kordi@uconn.edu)

Graphical Representation and Similarity Analysis of Protein Sequences Based on Fractal Interpolation (Abstract)

Hailong Hu , Hailong Hu is with the College of Science, Zhejiang Sci-Tech University, Zhejiang A&F University, Hangzhou, 311300, China. (email: huhailonga@163.com)

An application of invertibility of Boolean control networks to the control of the mammalian cell cycle (Abstract)

Kuize Zhang , K. Zhang is with College of Automation, Harbin Engineering University, Harbin, 150001, PR China.(email:zkz0017@163.com)

Sorting Circular Permutations by Super Short Reversals (Abstract)

Gustavo Rodrigues Galvao , G. R. Galvao is with the Institute of Computing, University of Campinas, Brazil.(email:ggalvao@ic.unicamp.br)

On the variable ordering in subgraph isomorphism algorithms (Abstract)

Vincenzo Bonnici , Vincenzo Bonnici is with the Department of Computer Science, University of Verona, Italy,(email:vincenzo.bonnici@univr.it)

A Visual Interface for Querying Heterogeneous Phylogenetic Databases (Abstract)

Hasan Jamil , Hasan M Jamil is with the Department of Computer Science, University of Idaho, Janssen Engineering, Room 236, Moscow, ID, 83844, USA. (email: jamil@uidaho.edu.)

Extracting Coevolutionary Features in Protein Sequences for Predicting Protein-protein Interactions (Abstract)

Lun Hu , Lun Hu is with the School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430070 China. He is also with the Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China (email: hulun@whut.edu.cn)

Predicting nsSNPs the disrupt protein-protein interactions using docking (Abstract)

Norman Goodacre , Norman Goodacre is with Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington DC 20007.(email:nfg4@georgetown.edu)

An annotation agnostic algorithm for detecting nascent RNA transcripts in GRO-seq (Abstract)

Joseph Azofeifa , J. Azofiefa is with the Department of Computer Science, University of Colorado, Boulder, CO 80309.(email:joseph.azofeifa@colorado.edu)

Transductive Learning for Multi-Label Protein Subchloroplast Localization Prediction (Abstract)

Shibiao Wan , Shibiao Wan is with the Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hong Kong SAR, China. (e-mail: shibiao.wan@connect.polyu.hk).

A new scheme to characterize and identify protein ubiquitination sites (Abstract)

Van-Nui Nguyen , Van-Nui Nguyen is with the Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan (email: nuinvtnu@gmail.com)

Genome-wide Semi-automated Annotation of Transporter Systems (Abstract)

Oscar Dias , Oscar Dias is with the Centre of Biological Enginnering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.(Email: odias@deb.uminho.pt)

Optimal Landmark Selection for Registration of 4D Confocal Image Stacks in Arabidopsis (Abstract)

Katya Mkrtchyan , K. Mkrtchyan is with the Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, 92521.

Searching Genome-wide Multi-locus Associations for Multiple Diseases Based on Bayesian Inference (Abstract)

Xuan Guo , Xuan Guo is with the Department of Computer Science, Georgia State University, Atlanta, GA, 30303.(email: xguo9@student.gsu.edu)

Algorithms and complexity results for genome mapping problems (Abstract)

Ashok Rajaraman , Ashok Rajaraman is with the Simon Fraser University.(Email: arajaram@illinois.edu)

A Resolution of the Static Formulation Question for the Problem of Computing the History Bound (Abstract)

Julia Matsieva , J. Matsieva is with the Department of Computer Science, University of California, Davis, Davis, 95616.(email:jmatsieva@ucdavis.edu)

Unconstrained Diameters for Deep Coalescence (Abstract)

Pawel Gorecki , Paweł Gorecki is with the Dept. of Mathematics, Informatics and Mechanics, University of Warsaw, Poland (email: gorecki@mimuw.edu.pl)

A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits (Abstract)

Behrang Mahjani , Behrang Mahjani is with the Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden.(Email: behrang.mahjani@it.uu.se)

Prediction and validation of disease genes using HeteSim Scores (Abstract)

XIANGXIANG ZENG , X. Zeng is with Department of Computer Science, Xiamen Unviersity, Xiamen 361005, Fujian, China.(email:xzeng@xmu.edu.cn)

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization (Abstract)

Ali Ezzat , Ali Ezzat is with the School of Computer Engineering, Nanyang Technological University, Singapore 639798.(email:aly002@ntu.edu.sg)

A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency (Abstract)

Weihua Zheng , Weihua Zheng is with the College of Information Science and Engineering, Hunan University, Changsha 410082, China. (email: zhengdavid@hnu.edu.cn)

Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks (Abstract)

Vo Hong Thanh , Vo Hong Thanh is with the Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy.(email: vo@cosbi.eu)

RNA Visualization: Relevance and the Current State-of-the-art Focusing on Pseudoknots (Abstract)

Boris Shabash , Boris Shabash is with the Department of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6. (e-mail: bshabash@sfu.ca).

Predicting the Absorption Potential of Chemical Compounds through a Deep Learning Approach (Abstract)

Moonshik Shin , Moonshik Shin is with the Department of Bio and Brain Engineering, Korea Advanced Institue of Science and Technology (KAIST), Dajeon, Korea. E‐mail:{msshin.kr, djjang, khlee, dhlee}@kaist.ac.kr

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Unit based on Homopolymer Compaction (Abstract)

Seunghyun Park , Seunghyun Park is with the Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea and is also with the School of Electrical Engineering, Korea University, Seoul 02841, Republic of Korea. (email: ilvu13@snu.ac.kr)

Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems (Abstract)

Tianle Ma , Tianle Ma is with the Department of Computer Science and Engineering, University at Buffalo (SUNY), Buffalo, NY, 14260. (e-mail: tianlema@buffalo.edu).

D-Map: Random walking on gene network inference maps towards differential avenue discovery (Abstract)

Emmanouil Athanasiadis , Emmanouil Athanasiadis is with the Systems Biology Center, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27 Athens, Greece. (email: mathan@bioacademy.gr)

Leveraging FPGAs for Accelerating Short Read Alignment (Abstract)

James Arram , James Arram is with the Department of Computing, Imperial College London.(Email: jma11@ic.ac.uk)

3D genome reconstruction with ShRes3D+ and Hi-C data (Abstract)

Jiangeng Li , Jiangeng Li is with the College of Electronic and Control Engineering, and the Beijing Key Laboratory of Computational Intelligence and Intelligent System, Beijing University of Technology, Beijing, China. (email: lijg@bjut.edu.cn)

Autumn Algorithm – Computation of Hybridization Networks for Realistic Phylogenetic Trees (Abstract)

Daniel Huson , Daniel H. Huson is with the Center for Bioinformatics (ZBIT), University of Tubingen, Germany. (email: huson@informatik.uni-tuebingen.de)

DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations (Abstract)

Weiyun Ma , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Dmitriy Smirnov , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Juliet Forman , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Annalise Schweickart , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Carter Slocum , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Srinidhi Srinivasan , W. Ma is with the Harvey Mudd College, Claremont, California, USA.
Ran Libeskind-Hadas , W. Ma is with the Harvey Mudd College, Claremont, California, USA.

Super-thresholding: Supervised Thresholding of Protein Crystal Images (Abstract)

Imren Dinc , Imren Dinc is with the DataMedia Research Lab, Computer Science Department, University of Alabama in Huntsville, Huntsville, Alabama 35899, United States (e-mail: id0002@uah.edu).

Building ancestral recombination graphs for whole genomes (Abstract)

Thao Thi Phuong Nguyen , Thao Thi Phuong Nguyen is with the Institute of Information Technol-ogy, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam. (email: thaontp@ioit.ac.vn)

An IR-based Approach Utilising Query Expansion for Plagiarism Detection in MEDLINE (Abstract)

Rao Muhammad Adeel Nawab , Rao Muhammad Adeel Nawab is with the Department of Computer Science, COMSATS Institute of Information Technology, Defence Road, Off Raiwind Road, Lahore, Pakistan. (email: adeelnawab@ciitlahore.edu.pk)

A linear bound on the number of states in optimal convex characters for maximum parsimony distance (Abstract)

Olivier Boes , Olivier Boes is with the Deparment of Knowledge Engineering (DKE), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands. (email: o.boes@maastrichtuniversity.nl)

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images (Abstract)

Abhishek Biswas , Abhishek Biswas is with the Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529. USA. (email: abiswas@cs.odu.edu.)

Metabolic flux analysis in isotope labeling experiments using the adjoint approach (Abstract)

Stephane Mottelet , Stephane Mottelet is with the Department EA4297 TIMR, Sorbonne University, Universit´e de technologie de Compi`egne, rue du docteur Schweitzer, F-60203 Compi`egne, France.
Gil Gaullier , Stephane Mottelet is with the Department EA4297 TIMR, Sorbonne University, Universit´e de technologie de Compi`egne, rue du docteur Schweitzer, F-60203 Compi`egne, France.
Georges Sadaka , Stephane Mottelet is with the Department EA4297 TIMR, Sorbonne University, Universit´e de technologie de Compi`egne, rue du docteur Schweitzer, F-60203 Compi`egne, France.

Codon Context Optimization in Synthetic Gene Design (Abstract)

Dimitris Papamichail , D. Papamichail is with the Department of Computer Science, The College of New Jersey, 2000 Pennington Road, Ewing , NJ, 08628–0718.USA.(email:papmicd@tcnj.edu)

REPA: Applying Pathway Analysis to Genome-wide Transcription Factor Binding Data (Abstract)

Pranjal Patra , Pranjal Patra is with the Department of Computer Science, Memorial University of Newfoundland. (email: pp7002@mun.ca)

Pubcast and Genecast: Browsing and explor-ing publications and associated curated con-tent in biology through mobile devices. (Abstract)

Scott Goldweber , S. Goldweber is with The Department of Biochemistry & Molecular Medi-cine, George Washington University Medical Center, Washington, DC 20037, United States of America.(email:goldweber@gwu.edu)

Identifying Cell Populations in Flow Cytometry Data Using Phenotypic Signatures (Abstract)

Maziyar Baran Pouyan , M. Baran Pouyan is with Quality of Life and Technology Lab, The University of Texas at Dallas, Richardson, TX, 75080.

ISEA: iterative seed-extension algorithm for de novo assembly using paired-end information and insert size distribution (Abstract)

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

Algorithms for Pedigree Comparison (Abstract)

Zhi-Zhong Chen , Zhi-Zhong Chen is with the Division of Information System Design, Tokyo Denki University, Hatoyama, Saitama, Japan, 350-0394. (email: zzchen@mail.dendai.ac.jp)

Prediction of novel drugs for hepatocellular carcinoma based on multi-source random walk (Abstract)

Liang Yu , Liang Yu is with the School of Computer Science and Technology, Xidian University, Xian 710071, China. (email: lyu@xidian.edu.cn)

Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources (Abstract)

Yuansheng Liu , Yuansheng Liu is with the School of Software, Dalian University of Technology, Dalian, 116024, China. (email: yyuanshengliu@gmail.com)

PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-scale Data (Abstract)

Feng He , Feng He is with the School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China. (email: hefeng19890620@126.com)

A Characterization of Minimum Spanning Tree-like Metric Spaces (Abstract)

Momoko Hayamizu , Momoko Hayamizu is with the Department of Statistical Science, The Graduate University for Advanced Studies, Tokyo, Japan. (email: hayamizu@ism.ac.jp)

Accelerating Computation of Large Biological Datasets using MapReduce Framework (Abstract)

Chao Wang , C. Wang is with the University of Science and Technology of China, Hefei, 230027, Anhui, China.(email:cswang@ustc.edu.cn)

Classical mechanics approach applied to analysis of genetic oscillators (Abstract)

Anastasiia Vasylchenkova , Anastasiia Vasylchenkova is with the School of Physics and Technologies, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine. (email: vasylchenkova.anastasiia@yandex.ru)

Algorithmic Mapping and Characterization of the Drug-Induced Phenotypic-Response Space of Parasites Causing Schistosomiasis (Abstract)

Rahul Singh , Rahul Singh is with the Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA (e-mail: rahul@sfsu.edu).

Protein Complex Detection via Effective Integration of Base Clustering Solutions and Co-complex Affinity Scores (Abstract)

Min Wu , Min Wu is with the Institute for Infocomm Research (I2R), A*Star, Singapore 138632 (e-mail: wumin@i2r.a-star.edu.sg).

Finite-Time Stability Analysis of Reaction-Diffusion Genetic Regulatory Networks with Time-Varying Delays (Abstract)

Xiaofei Fan , Xiaofei Fan is with the School of Mathematical Science, Heilongjiang University, Harbin 150080, China (e- mail: 2141037@s.hlju.edu.cn).

A new feature vector based on Gene Ontology terms for protein-protein interaction prediction (Abstract)

Sanghamitra Bandyopadhyay , S. Bandyopadhyay is with Machine Intelligence Unit, Indian Statistical Institute, Kolkata-700108, India.(email:sanghami@isical.ac.in)

Robust Reachability of Boolean Control Networks (Abstract)

Fangfei Li , F. Li is with the Department of Mathematics, East China University of Science and Technology, Shanghai 200237, China.(email:li fangfei@163.com)

A heterogeneous network based method for identifying GBM-related genes by integrating multi-dimensional data (Abstract)

Chen Peng , Chen Peng is with the School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China. (email: pxc@ mail.ustc.edu.cn)

Genomic distance with high indel costs (Abstract)

Poly H. Hannah , Poly H. da Silva is with the UFF, Universidade Federal Fluminense (e-mail: poly.hannah@gmail.com).

A novel adaptive penalized logistic regression for uncovering biomarker associated with anti-cancer drug sensitivity (Abstract)

Heewon Park , Heewon Park is with the Faculty of Global and Science Studies, Yamaguchi University, Yamaguchi Prefecture, Japan.(Email: hwpark@yamaguchi-u.ac.jp)

Detecting Copy Number Variants from NGS with Sparse and Smooth Constraints (Abstract)

Yue Zhang , Yue Zhang is with the Electrical and Information College of Jinan University, Zhuhai, China.(Email: yuezhang@comp.hkbu.edu.hk)

Pattern Classification of Instantaneous Cognitive Task-load Through GMM Clustering, Laplacian Eigenmap and Ensemble SVMs (Abstract)

Jianhua Zhang , Jianhua Zhang is with the Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China. (email: zhangjh@ecust.edu.cn)

DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets (Abstract)

Hongbo Zhang , Hongbo Zhang is with Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering Tongji University, Shanghai 201804, China.(email:hongbozhang0808@163.com)

Derivative-free optimization of rate parameters of capsid assembly models from bulk in vitro data (PDF)

Lu Xie , Lu Xie is with the Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA USA and Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA USA 15213.(Email: lxie1@andrew.cmu.edu)

A Generalized Lattice based Probabilistic Approach for Metagenomic Clustering (Abstract)

Manjari Jha , Manjari Jha is with the School of Electrical Engineering and Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA. (e-mail: manjari@psu.edu).

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity (Abstract)

Sugeerth Murugesan , Sugeerth Murugesan is with the Department of Computer Science, University of California, Davis, One Shields Avenue, Davis CA 95616, USA (e-mail: smuru@ucdavis.edu).

IsAProteinDB: An Indexed Database of Trypsinized Proteins for Fast Peptide Mass Fingerprinting (Abstract)

Antonio d'Acierno , Antonio d’Acierno is with the Institute of Food Science, National Council of Research of Italy, via Roma 63, 83100, Avellino, Italy (e-mail: dacierno.a@isa.cnr.it).

Circular Order Aggregation and its Application to Cell-cycle Genes Expressions (Abstract)

Sandra Barragan , Sandra Barragan is with the Departamento de Estadıstica e I.O., Universidad de Valladolid, 47011 Valladolid, Spain. (email: sandraba@eio.uva.es)

Normalizing kernels in the Billera-Holmes-Vogtmann treespace (Abstract)

Grady Weyenberg , Grady Weyenberg is with the Integrative Epidemiology Unit of University of Bristol.(Email: grady.weyenberg@uky.edu)

Enhancing Protein Conformational Space Sampling Using Distance Profile-Guided Differential Evolution (Abstract)

Guijun Zhang , Gui-Jun Zhang is with the College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China. (e-mail: zgj@zjut.edu.cn).

An eigen-binding site based method for the analysis of anti-EGFR drug resistance in lung cancer treatment (Abstract)

Lichun Ma , Lichun Ma is with the Department of Electronic Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China. (email: lichunma2-c@my.cityu.edu.hk)

txCoords: A Novel Web Application for Transcriptomic Peak Re-mapping (Abstract)

Zhangming Yan , Zhangming Yan is with the MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China. (email:yzm09@mails.tsinghua.edu.cn)

Benchmark dataset for Whole Genome sequence compression (Abstract)

Biji C.L. , Biji C.L is with the Department of Computational Biology and Bioinfor-matics, Thiruvananthapuram- 695581, Kerala, India.(email:biji-jomy@gmail.com)

Effectively identifying compound-protein interactions by learning from positive and unlabeled examples (Abstract)

Zhanzhan Cheng , Zhanzhan Cheng is with the Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai, China. (e-mail: chengzhanzhan@fudan.edu.cn).

Improving Biochemical Named Entity Recognition Performance Using PSO Classifier Selection and Bayesian Combination Method (Abstract)

Abbas Akkasi , Abbas Akkasi is with the A.A, Computer Engineering Department, Eastern Mediterranean University, Famagusta, North Cyprus , Via Mersin 10, Turkey (e-mail: abbas.akkasi@gmail.com).

Copy Number Variations Detection: unravelling the problem in tangible aspects (Abstract)

Francisco Nascimento , Francisco do Nascimento is with the UFPE, Recife, Brazil. (email: fnj@cin.ufpe.br)

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)

Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations (Abstract)

Xin Wang , Xin Wang is with the Department of Computer Science and Engineering, University of Connecticut, Connecticut, CT, 06279.. (e-mail: xin.wang@uconn.edu).

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method (Abstract)

Yun Liu , Yun Liu is with the College of Communication Engineering, Jilin University, China.(Email: laoniu313@qq.com)

An algorithm for motif-based network design (Abstract)

Tuomo Maki-Marttunen , Tuomo Maki-Marttunen is with the Department of Signal Processing,Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland. (email: tuomo.maki-marttunen@tut.fi)

Data Management for Heterogeneous Genomic Datasets (Abstract)

Stefano Ceri , Stefano Ceri is with the Dipartimento di Elettronica Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy (e-mail: ceri@elet.polimi.it).

High class-imbalance in pre-miRNA prediction: a novel approach based on deepSOM (Abstract)

Georgina Stegmayer , Georgina Stegmayer is with the Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Argentina (e-mail: gstegmayer@sinc.unl.edu.ar).

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data (Abstract)

Deqing Gu , Deqing Gu is with the State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.(Email: hellodannygood@sina.com)

Improve Biomedical Information Retrieval using Modified Learning to Rank Methods (Abstract)

Bo Xu , Bo Xu is with the School of Computer Science and Technology, Dalian University of Technology, Room A923, Chuangxinyuan Building,No.2, Linggong Road, Dalian 116023, Liaoning, China. (e-mail: xubo2011@mail.dlut.edu.cn).

Extending the Applicability of Graphlets to Directed Networks (Abstract)

David Aparicio , D. Aparício is with CRACS & INESC-TEC and the Department of Computer Science, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal.(email:daparicio@dcc.fc.up.pt

Detecting pairwise interactive effects of continuous random variables for bimarker identification with small sample size (Abstract)

Amin Ahmadi Adl , Amin Ahmadi Adl is with Department of Computer Science and Engineering, University of South Florida, Tampa, Florida, 33620.

Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree (PDF)

Daniel Savel , Daniel Savel is with the Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. (email: dan.savel@case.edu)

Modeling and Identification of Amnioserosa Cell Mechanical Behavior by Using Mass-Spring Lattices (Abstract)

Maxime Dureau , Maxime Dureau is with the Department of Mechanical Engineering, Universita degli Studi di Genova, P.le Kennedy, Pad. D, 16129 Genova Italy. (email: maxime.dureau@ens-lyon.fr)

A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing (Abstract)

Ahmad Al Kawam , Ahmad Al Kawam is with the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77840, USA. (email: ahmad.alkawam@tamu.edu)

Predicting microRNA-disease associations based on improved microRNA and disease similarities (Abstract)

Wei Lan , Wei Lan is with the School of Infor-mation Science and Engineering,Central South University,Changsha, P.R. China. (Email: weilan@csu.edu.cn)

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm (Abstract)

Tatiana Maximova , Tatiana Maximova is with the Department of Computer Science, George Mason University, Fairfax, VA, 22030, USA. (email: tmaximov@gmu.edu)

Strategies for Comparing Metabolic Profiles: Implications for the Inference of Biochemical Mechanisms from Metabolomics Data (PDF)

Zhen Qi , Zhen Qi is with the Department of Biomedical Engineering, Georgia Institute of Technology and Emory University Medical School, Atlanta, GA 30332, USA .(Email: zhen.qi@gatech.edu)

Multi-Block Bipartite Graph for Integrative Genomic Analysis (Abstract)

Mingon Kang , Mingon Kang is with the Department of Computer Science, Kennesaw State University, Marietta, GA, USA 30060.(Email: mingon.kang@tamuc.edu)

Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection (Abstract)

Robert Moskovitch , Department of Biomedical Inforamtics at Columbia University (e-mail: robert.moskovitch@columbia.edu)

Efficient approach to correct read alignment for pseudogene abundance estimates (Abstract)

Chelsea Ju , Chelsea J.-T. Ju is with the Department of Computer Science, University of California, Los Angeles, CA, 90095.(Email: chelseaju@cs.ucla.edu)

From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis (Abstract)

Hua Wang , Department of Electrical and Computer Engineering, Colorado School of Mines, Golden, CO 80401.

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)

Modeling Healthcare Quality via Compact Representations of Electronic Health Records (Abstract)

Jelena Stojanovic , Jelena Stojanovic is with the Center for Data Analytics and Biomedical Informatics, Temple University, Philadelphia, PA, 19122.(Email: jelena.stojanovic@temple.edu)

Applications of Transductive Spectral Graph Methods in a Military Medical Concussion Database (Abstract)

Peter B. Walker , Peter B. Walker is with the Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA. (email: peter.b.walker.mil@mail.mil)

Batch Mode TD(λ) for Controlling Partially Observable Gene Regulatory Networks (Abstract)

Utku Sirin , Utku Sirin is with the School of Computer and Communication Sciences, ´ Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland (e-mail: utku.sirin@epfl.ch).

Triangular Alignment (TAME): A Tensor-based Approach for Higher-order Network Alignment (Abstract)

Shahin Mohammadi , Shahin Mohammadi is with the Department of Computer Science, Purdue University, West Lafayette, IN 47907 (e-mail: mohammadi@purdue.edu).

Soft Ngram representation and modeling for protein remote homology detection (Abstract)

Pietro Lovato , Pietro Lovato is with the Department of Computer Science, University of Verona, Verona (Italy) (e-mail: pietro.lovato@univr.it).

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-level Rule-based Models in Cell Biology (Abstract)

Arne Bittig , A. Bittig is with the Modeling and Simulation Group, Institute of Computer Science, University of Rostock, Rostock, Germany.(email:arne.bittig@informatik.uni-rostock.de)

Significance and Functional Similarity for Identification of Disease Genes (Abstract)

Pradipta Maji , P. Maji is with the Biomedical Imaging and Bioinformatics Lab, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.(email:pmaji@isical.ac.in)

Effect of Aggregation Operators on Network-based Disease Gene Prioritization: A Case Study on Blood Disorders (Abstract)

Nivit Grewal , Nivit Grewal is with the Punjabi University Regional Centre for IT and Management, Mohali. (email: nivitgrewal@gmail.com)

Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding (Abstract)

Eddie Ma , Eddie Y. T. Ma is with the School of Computer Science, University of Guelph, Guelph, Ontario, Canada.(email:ema@uoguelph.ca)

Collective prediction of disease-associated miRNAs based on transduction learning (Abstract)

Jiawei Luo , Jiawei Luo is with the College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410083 China. (email: luojiawei@hnu.edu.cn)

A graphical model of smoking-induced global instability in lung cancer (Abstract)

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

Feature Selection for Optimized High-dimensional Biomedical Data using the Improved Shuffled Frog Leaping Algorithm (PDF)

Bin Hu , Bin Hu is with the The School of Information Science and EngineeringLanzhou University,Lanzhou, 730000, China.(Email: bh@lzu.edu.cn)

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)

Protein Inference from the Integration of Tandem MS Data and Interactome Networks (Abstract)

Jiancheng Zhong , Jiancheng Zhong is with the School of Information Science and Engineering, Central South University Changsha, 410083, China. (email: jczhong@csu.edu.cn)

Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error (Abstract)

Daniel Mohsenizadeh , Daniel N. Mohsenizadeh is with the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843 USA.(Email: danielmz@tamu.edu)

A Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling (Abstract)

Hongjie Wu , School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China, 215009. (e-mail: hongjie.wu@qq.com)

Towards Unsupervised Gene Selection: A Matrix Factorization Framework (Abstract)

Jianqiang Li , Jianqiang Li is with the School of Software Engineering Beijing University of Technology and Beijing Engineering Research Center for IoT Software and Systems.(Email: jianqiangli.bjut@gmail.com)

Structural Class Classification of 3D Protein Structure Based on Multi-view 2D Images (Abstract)

Chendra Hadi Suryanto , Chendra Hadi Suryanto is with the Department of Computer Science, Graduate School of Systems and Information Engineering, University of Tsukuba, Ibaraki, Japan 305-8573. (e-mail: chendra@cvlab.cs.tsukuba.ac).

Species tree inference from gene splits by Unrooted STAR methods (Abstract)

Elizabeth Allman , Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775. (E-mail: e.allman@alaska.edu)

hMuLab: a Biomedical Hybrid MUlti-LABel Classifier Based on Multiple Linear Regression (Abstract)

Pu Wang , Pu Wang is with the Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences; and Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China. (email: wangpu@siat.ac.cn)

Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks with Leakage Delays (Abstract)

M. Syed Ali , Department of Mathematics, Thiruvalluvar University, Vellore-632115, Tamil Nadu, India

Filter Design with Adaptation to Time-Delay Parameters for Genetic Regulatory Networks (Abstract)

Hongmei Jiao , Hongmei Jiao is with the Medical Academy, Yangzhou University, Yangzhou 25001, China, and also with Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China (e-mail: hmjiao@yzu.edu.cn).

Identifying Stages of Kidney Renal Cell Carcinoma by Combining Gene Expression and DNA Methylation Data (Abstract)

Su-Ping Deng , Su-Ping Deng is with the Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Caoan Road 4800, Shanghai 201804, China.(Email: dsptk2003@126.com)

ACID: association correction for imbalanced data in GWAS (Abstract)

Feng Bao , Feng Bao is with the Department of Automation, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing 100084, China. (email: bf14@mails.tsinghua.edu.cn)

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)

Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree (Abstract)

Jesper Jansson , Jesper Jansson is with the Laboratory of Mathematical Bioinformatics (Akutsu Laboratory), Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. (e-mail: jj@kuicr.kyoto-u.ac.jp).

Random sets of stadiums in square and collective behavior of bacteria (Abstract)

Roman Czapla , Roman Czapla is with the Institute of Computer Science, Pedagogical University, ul. Podchorazych 2, Krakow 30-084, Poland.(Email: czapla@up.krakow.pl)

Classification of Protein Structure Classes on Flexible Neutral Tree (Abstract)

Wenzheng Bao , School of Electronic and Information Engineering Tongji University, Shanghai,PR China, CO 201804.(Email: baowz55555@126.com)

A novel approach to identify the miRNA-mRNA causal regulatory modules in Cancer (Abstract)

Jiawei Luo , Jiawei Luo is with the college of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, Hunan, China. (email: luojiawei@hnu.edu.cn)

Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes (Abstract)

Tom Hartmann , Parallel Computing and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.(Email: thartmann@informatik.uni-leipzig.de)

Nonconvex Penalty Based Low-rank Representation and Sparse Regression for eQTL Mapping (Abstract)

Lin Yuan , Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Caoan Road 4800, Shanghai 201804, China.

Tanglegrams: a Reduction Tool for Mathematical Phylogenetics (PDF)

Frederick Matsen , Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. http://matsen.fredhutch.org/ (email: ematsen@gmail.com)

Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer (Abstract)

Behnam Behinaein , Department of Electrical and Computer En-gineering, Queen’s University, Kingston, ON, Canada, K7L 3N6.(Email: 9hbb@queensu.ca)

HEMEsPred: Structure-based Ligand-specific Heme Binding Residues Prediction by Using Fast-adaptive Ensemble Learning Scheme (Abstract)

Guifu Yang , School of Computer Science and Information Technology, Northeast Normal University, Changchun, China, 130117.

Inferring the Functions of Proteins from the Interrelationships between Functional Categories (Abstract)

Kamal Taha , Electrical & Computer Engineering Department, Khalifa University, Abu Dhabi, UAE (e-mail: kamal.taha@kustar.ac.ae).

Region Growing for Segmenting Green Microalgae Images (Abstract)

Vinicius Borges , Instituto de Ciencias Matematicas e de Computacao, University of Sao Paulo (USP), Sao Carlos, SP, Brazil.

Inferring unknown biological functions by integration of GO annotations and gene expression data (Abstract)

Guillermo Leale , Center for R&D of Information Systems (CIDISI), CONICET and Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET. (email: guileale@santafe-conicet.gov.ar)

Detecting Essential Proteins Based on Network Topology, Gene Expression Data and Gene Ontology Information (Abstract)

Wei Zhang , School of Science at East China Jiaotong University in Nanchang, China. (e-mail: wzhang math@whu.edu.cn)

Nonbinary tree-based phylogenetic networks (Abstract)

Leo van Iersel , Delft University of Technology, PO-box 5, 2600 AA, Delft, The Netherlands. (email: ljetten@outlook.com)

Classification of State Trajectories in Gene Regulatory Networks (Abstract)

Alireza Karbalayghareh , Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843. (e-mail: karbalayghareh@gmail.com).

Attention Recognition in EEG-Based Affective Learning Research Using CFS+KNN Algorithm (Abstract)

Xiaowei Li , School of Information Science and Engineering, Lanzhou University, Lanzhou, China. (email: lixwei@lzu.edu.cn)

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-based Features and Boosting Multiple SVMs (Abstract)

Jun Hu , School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Road, Nanjing, 210094, China. (e‐mail: junh_cs@126.com).

RAFP-Pred: Robust Prediction of Antifreeze Proteins using Localized Analysis of n-Peptide Compositions (Abstract)

Imran Naseem , School of Electrical, Electronic and Computer Engineering, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.(e-mail: imran.naseem@uwa.edu.au).

Complexity and algorithms for finding a perfect phylogeny from mixed tumor samples (Abstract)

Ademir Hujdurovic , University of Primorska, UP IAM and UP FAMNIT, Koper, Slovenia (e-mail: ademir.hujdurovic@upr.si).

A Global Network Alignment Method Using Discrete Particle Swarm Optimization (Abstract)

Maoguo Gong , Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, International Research Center for Intelligent Perception and Computation, Xidian University, Xian, Shaanxi Province 710071, China.(Email: gong@ieee.org)

GSEH: A novel approach to select prostate cancer-associated genes using gene expression heterogeneity (Abstract)

Sanghyun Park , Department of Computer Science, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul 120-749, South Korea (e-mail: sanghyun@yonsei.ac.kr).

Calculating the expected time to eradicate HIV-1 using a Markov Chain (Abstract)

Narayanan Viswanath , Govt. Engineering College, Thrissur, India, 680009, (e-mail: narayanan viswanath@yahoo.com).

Efficient Algorithms for Sequence Analysis with Entropic Profiles (Abstract)

Cinzia Pizzi , Department of Information Engineering, University of Padova, Italy (e-mail: cinzia.pizzi@dei.unipd.it)

Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data (Abstract)

Chun-Hou Zheng , College of Electrical Engineering and Automation, Anhui University, Hefei, Anhui 230601, China and also with Co-Innovation Center for Information Support and Assurance Technology, Anhui University, Hefei, Anhui 230601, China. (email: zhengch99@126.com)

Bi-level and Bi-objective p-Median Type Problems for Integrative Clustering: Application to Analysis of Cancer Gene-Expression and Drug-Response Data (Abstract)

Anton V. Ushakov , Matrosov Institute for System Dynamics and Control Theory, Siberian Branch of the Russian Academy of Sciences, Irkutsk, 664033 Russia. (email: aushakov@icc.ru)

Extracting stage-specific and dynamic modules through analyzing multiple networks associated with cancer progression (Abstract)

Xiaoke Ma , School of Computer Science and Technology, Xidian University, Xian, Shaanxi, 710071.(Email: xkma@xidian.edu.cn)

GPU-based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites (Abstract)

Matthias Leinweber , Department of Mathematics and Computer Science, Philipps- Universitat Marburg, 35032 Marburg, Germany (e-mail: leinweberm@mathematik.uni-marburg.de).

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs (Abstract)

Tatsuya Akutsu , Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan (e-mail: takutsu@kuicr.kyoto-u.ac.jp)

From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes (Abstract)

Amarda Shehu , Department of Computer Science, George Mason University, Fairfax, VA, 22030.(Email: amarda@gmu.edu)

Introducing a Stable Bootstrap Validation Framework for Reliable Genomic Signature Extraction (Abstract)

Nikolaos-Kosmas Chlis , Institute of Computational Biology, Helmholtz, Zentrum, Munchen, 85764 Neuherberg, Germany (e-mail: nchlis@isc.tuc.gr)

Application of Fractal Theory on Motifs Counting in Biological Networks (Abstract)

Javad Sadri , Department of Computer, Science and Research Branch, Azad University, Birjand, Iran.(Email: m.joveini@outlook.com)

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis (Abstract)

Sanghamitra Bandyopadhyay , Machine Intelligence Unit, Indian Statistical Institute, Kolkata-700108, India.(Email: sanghami@isical.ac.in)

Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme (Abstract)

Yu-Chiao Chiu , Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 16017, Taiwan.
Yidong Chen , Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 16017, Taiwan.
Eric Y. Chuang , Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 16017, Taiwan.
Papers

Matching Split Distance for Unrooted Binary Phylogenetic Trees (Abstract)

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

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

Guoqiang Han , South China University of Technology, Guangzhou
Hantao Chen , South China University of Technology, Guangzhou
Le Li , South China University of Technology, Guangzhou
Zhiwen Yu , South China University of Technology, Guangzhou and Hong Kong Polytechnic University, Hong Kong
Jane You , Hong Kong Polytechnic University, Hong Kong
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)

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

Operon Prediction using Chaos Embedded Particle Swarm Optimization (Abstract)

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

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

Omid Dehzangi , University of Texas at Dallas, Dallas
Alok Sharma , Griffith University, Brisbane and University of the South Pacific, Fiji
Kuldip Paliwal , Griffith University, Brisbane
Abdollah Dehzangi , Griffith University, and National ICT Australia (NICTA), Brisbane
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)

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

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

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

Sanjeev N. Sharma , Samrat Ashok Technological Institute, Vidisha
Rajiv Saxena , Jaypee University of Engineering and Technology, Raghogarh, Guna
Devendra K. Shakya , 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)

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

Cécile Ané , University of Wisconsin, Madison
Nicole T. Perna , University of Wisconsin, Madison
Yujin Chung , 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)

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

Statistical Detection of Boolean Regulatory Relationships (Abstract)

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

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

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

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

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

Rui Fan , Nanyang Technological University, Singapore
Ritika Jain , Nanyang Technological University, Singapore
Jing Guo , 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)

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

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

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

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