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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)

Incorporation of Solvent Effect into Multi-objective Evolutionary Algorithm for Improved Protein Structure Prediction (Abstract)

Mengchu Zhou , Department of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, NJ 07102 USA. (e-mail: zhou@njit.edu).

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).

Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation (PDF)

Yue Zhang , Mathematics and Statistics, University of Ottawa, Ottawa, Ontario Canada (e-mail: yzhan481@uottawa.ca)
Chunfang Zheng , Mathematics and Statistics, University of Ottawa, Ottawa, Ontario Canada (e-mail: chunfang313@gmail.com)
David Sankoff , Mathematics and Statistics, University of Ottawa, Ottawa, Ontario Canada (e-mail: sankoff@uottawa.ca)

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).

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).

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)

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).

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)

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.

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 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)

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)

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)

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)

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.

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)

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)

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.

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)

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)

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).

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)

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).

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)

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)

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)

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)

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)

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)

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).

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)

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)

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)

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)

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)

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)

The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms (Abstract)

Shihua Zhang , National Center for Mathematics and Interdisciplinary Sciences, Academy ofMathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China, and School of Mathematics Sciences, University of Chinese Academy of Sciences. (email: zsh@amss.ac.cn)

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.

A New Efficient Algorithm for the Frequent Gene Team Problem (Abstract)

Biing-Feng Wang , Department of Computer Science, National Tsing Hua University Hsinchu, Taiwan 30013, Republic of China. (email: bfwang@cs.nthu.edu.tw)

Querying of Disparate Association and Interaction Data in Biomedical Applications (Abstract)

Shi Qiao , Microsoft Corporation, One Microsoft Way Building 17, Redmond, WA 98052, USA.(email: shqiao@microsoft.com)

Network Community Detection based on the Physarum-inspired Computational Framework (Abstract)

Chao Gao , College of Computer and Information Science & College of Software, Southwest University, Chongqing, China, 400715 (e-mail: cgao@swu.edu.cn).

Prediction of HIV Drug Resistance by combining Sequence and Structural Properties (Abstract)

Zoya Khalid , Department of Biological Sciences and Bioengineering , Sabanci University, Istanbul, Turkey.(Email: zoyakhalid@sabanciuniv.edu)

A review of machine learning and statistical approaches for detecting SNP interactions in high-dimensional genomic data (Abstract)

Suneetha Uppu , Department of Computing, Curtin University, Bentley, Perth, WA-6102, USA. (email: suneetha.uppu@postgrad.curtin.edu.au)

Network-regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery (Abstract)

Shihua Zhang , National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.(Email: zsh@amss.ac.cn)

Classification of Alzheimer’s Disease Using Whole Brain Hierarchical Network (Abstract)

Jianxin Wang , School of Information Science and Engineering, Central South University, Changsha 410083, China.(Email: jxwang@mail.csu.edu.cn)

A Memetic Algorithm for 3-D Protein Structure Prediction Problem (Abstract)

Marcio Dorn , Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil (e-mail: mdorn@inf.ufrgs.br)

Conformational sampling of a biomolecular rugged energy landscape (Abstract)

Jakub Rydzewski , Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland (e-mail: jr@fizyka.umk.pl).

Evolutionary Graph Clustering for Protein Complex Identification (Abstract)

Tiantian He , Department of Computing, The Hong Kong Poly-technic University, Hung Hom, Hong Kong SAR.(Email: csthe@comp.polyu.edu.hk)

Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization (Abstract)

Sumanta Ray , Department of Computer Science and Engineering, Aliah University, Kolkata-700156, West Bengal,India

A Just-in-Time Learning based Monitoring and Classification Method for Hyper/Hypocalcemia Diagnosis (Abstract)

Feng Qian , Key Laboratory of Advanced Control and Optimization for Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, P. R. China, 200237 (E-mail: fqian@ecust.edu.cn)

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)

Regularized Non-negative Matrix Factorization for Identifying Differential Genes and Clustering Samples: a Survey (Abstract)

Jin-Xing Liu , School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong, 276826 China, and with the Bio-Computing Research Center, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.(email: sdcavell@126.com)

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).

An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-images (Abstract)

Wei Shao , School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China (e-mail: shaowei20022005@nuaa.edu.cn).

Constructing DNA Barcode Sets based on Particle Swarm Optimization (Abstract)

Qiang Zhang , Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China

PerPAS: Topology-Based Single Sample Pathway Analysis Method (Abstract)

Chengyu Liu , Research Programs Unit, Genome-Scale Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland (e-mail: czliu@cs.helsinki.fi).

Swarm Robots Search for Multiple Targets Based on an Improved Grouping Strategy (Abstract)

Qirong Tang , Laboratory of Robotics and Multibody System, Tongji University, Shanghai 201804, P. R. China (e-mail: qirong.tang@outlook.com)

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).

A Comparative Study for Identifying the Chromosome-Wide Spatial Clusters from High-Throughput Chromatin Conformation Capture data (Abstract)

Xiangtao Li , Department of Computer Science and Information Technology, Northeast Normal University, Changchun, Jilin, 130117 China. (e-mail: lixt314@nenu.edu.cn)

Robust Dynamic Multi-objective Vehicle Routing Optimization Method (Abstract)

Yi-nan Guo , China University of Mining and Technology, Xuzhou, 221116 P.R.China (e-mail: guoyinan@cumt.edu.cn).

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)

BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement (Abstract)

Aurelie Pirayre , IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France (e-mail: pirayre.aurelie@bbox.fr)

Immunological Approach for Full NURBS Reconstruction of Outline Curves from Noisy Data Points in Medical Imaging (Abstract)

Andres Iglesias , Department of Information Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, 274-8510, Funabashi, Japan, and the Department of Applied Mathematics and Computational Sciences, E.T.S.I. Caminos, Canales y Puertos, University of Cantabria, Avda. de los Castros, s/n, 39005, Santander, Spain (e-mail: iglesias@unican.es)

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).

Assessment of semantic similarity between proteins using information content and topological properties of the Gene Ontology graph (Abstract)

Subhadip Basu , Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, India.(email:subhadip@cse.jdvu.ac.in)

Optimization of Gene Set Annotations using Robust Trace-Norm Multitask Learning (Abstract)

Xianpeng Liang , Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, No. 4800 Caoan Road, Shanghai 201804, China. (e-mail: 1xp_liang@tongji.edu.cn).

Comparison of Machine Learning Approaches for Prediction of Advanced Liver Fibrosis in Chronic Hepatitis C Patients (Abstract)

Mahmoud Elhefnawi , Informatics and Systems Department and biomedical informatics and chemo informatics group, Engineering Research Division and centre of excellence for advanced sciences, National Research Centre, Giza, Egypt. (e-mail: mahef@aucegypt.edu).

A Spatial-Temporal Method to Detect Global Influenza Epidemics Using Heterogeneous Data Collected from the Internet (Abstract)

Xichuan Zhou , Key Laboratory of Dependable Service Computing in Cyber Physical Society Ministry of Education, College of Communication Engineering, Chongqing University, Chongqing, China, 400044 (e-mail: zxc@cqu.edu.cn).

LMMO: A Large Margin Approach for Refining Regulatory Motifs (Abstract)

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

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology (Abstract)

Mark Gerstein , Department of Molecular Biophysics and Biochemistry, Program of Computational Biology and Bioinformatics, Department of Computer Science, Yale University, New Haven, CT 06520. (e-mail: mark@gersteinlab.org).

A Bipartite Network and Resource Transfer-based Approach to Infer LncRNA-environmental Factor Associations (Abstract)

Jie Zhou , Guangdong Key Laboratory of Computer Network, School of Computer Science and Engineering, South China University of Technology, Guangzhou 510006, China (e-mail: jiezhou@scut.edu.cn)

Aggregation for Computing Multi-Modal Stationary Distributions in 1-D Gene Regulatory Networks (Abstract)

NESLIHAN AVCU , Department of Electrical and Electronics Engineering, Dokuz Eylul University, Izmir, 35160 Turkey (e-mail: neslihan.avcu@deu.edu.tr)

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)

Reviving the Two-state Markov Chain Approach (Abstract)

Qixia Yuan , Computer Science and Communications Research Unit, University of Luxembourg, Luxembourg City, Luxembourg (e-mail: qixia.yuan@uni.lu)

NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithm for Flexible Protein Structure Alignment (Abstract)

Samira Fotoohifiroozabadi , Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai 81310 Johor, Malaysia (e-mails: samira.fotoohi@gmail.com)
Safaai Deris , Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai 81310 Johor, Malaysia (e-mails: samira.fotoohi@gmail.com)

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)

Controlling mRNA Translation (Abstract)

Tamir Tuller , Dept. of Biomedical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel.(email:tamirtul@post.tau.ac.il)

Efficient Algorithms for Genomic Duplication Models (Abstract)

Jaroslaw Paszek , Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland (e-mail: jpaszek@mimuw.edu.pl).

Inferring gene-species assignments in the presence of horizontal gene transfer (Abstract)

Agnieszka Mykowiecka , Department of Mathematics, Informatics and Mechanics, University of Warsaw, Poland (e-mail: agnieszka.mykowiecka@mimuw.edu.pl).

Genome Rearrangement with ILP (Abstract)

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

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).

Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus (PDF)

Qian Xie , Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical (e-mail: 416900030@qq.com).

An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information (Abstract)

Erman Ayday , Computer Engineering Department, Bilkent University, Ankara, Turkey (e-mail: erman@cs.bilkent.edu.tr).

Biological Event Trigger Identification with Noise Contrastive Estimation (Abstract)

Nan Jiang , School of Computer Science and Engineering, Beihang University, Beijing 100191, China (e-mail: nanjiang@buaa.edu.cn).

Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks (Abstract)

Md Abdul Alim , Computer and Information Science and Engineering, University of Florida (E-mail: alim@cise.ufl.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 Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data (Abstract)

Dong-Jun Yu , School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei, Nanjing 210094, China. (e-mail: njyudj@mail.njust.edu.cn).

Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection (Abstract)

Shuai An , The Institute of Big Data, College of Computer and Control Engineering, Nankai University, Tianjin 300071, China (email: shuaian@mail.nankai.edu.cn)

A Two-stage Biomedical Event Trigger Detection Method Integrating Feature Selection and Word Embeddings (Abstract)

Xinyu He , Dalian, Liaoning China (e-mail: hexinyu@mail.dlut.edu.cn)
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)
XiaoMing Yu , Dalian, LiaoNing China (e-mail: Xiaoming-Yu@outlook.com)
Jun Meng , School of Computer Science and Technolog, School of Dalian University of Technology, Dalian, Liaoning China (e-mail: mengjun@dlut.edu.cn)

NewGOA: predicting new GO annotations of proteins by bi-random walks on a hybrid graph (Abstract)

Guoxian Yu , College of Computer and Information Science, Southwest University, Beibei, Chongqing China (e-mail: guoxian85@gmail.com)
Guangyuan Fu , College of Computer and Information Sciences, Southwest University, 26463 Beibei, Chongqing China (e-mail: fugy@email.swu.edu.cn)
Jun Wang , College of Computer and Information Sciences, Southwest University, Beibei, Chongqing China (e-mail: kingjun@swu.edu.cn)
Yingwen Zhao , College of Computer and Information Sciences, Southwest University, Beibei, Chongqing China (e-mail: ywzhao@email.swu.edu.cn)

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)

Gene Tree Construction and Correction using SuperTree and Reconciliation (Abstract)

Manuel Lafond , DIRO, University of Montreal, Montreal, Quebec Canada (e-mail: lafonman@iro.umontreal.ca)
Cedric Chauve , Mathematics, Simon Fraser University, Burnaby, British Columbia Canada V5A1S6 (e-mail: cedric.chauve@sfu.ca)
Nadia El-Mabrouk , Computer Science (DIRO), U. of Montreal, Montreal, Quebec Canada (e-mail: mabrouk@iro.umontreal.ca)
Aida Ouangraoua , Computer Science, Universite de Sherbrooke, 7321 Sherbrooke, Quebec Canada (e-mail: aida.ouangraoua@usherbrooke.ca)

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)

Modeling Methylation Patterns with Long Read Sequencing Data (Abstract)

Karlene Nicole Meyer , Mathematics, Georgetown University, 8368 Washington, District of Columbia United States (e-mail: knm6@georgetown.edu)
Michelle Lacey , Mathematics, Tulane University, 5783 New Orleans, Louisiana United States 70118-5665 (e-mail: mlacey1@tulane.edu)

NGS-FC: A Next-Generation Sequencing Data Format Converter (Abstract)

Chunjiang YU , Center for Systems Biology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: yucj@siso.edu.cn)
Wentao WU , Center for Systems Biology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: wwtg99@126.com)
Jing Wang , Center for Systems Biology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: 774660640@qq.com)
Yuxin Lin , Center for Systems Biology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: yxlin1990@163.com)
Yang Yang , Soochow University, 12582 Suzhou, Jiangsu China (e-mail: yyang@suda.edu.cn)
Jiajia Chen , School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, 66339 Suzhou, Jiangsu China (e-mail: njucjj@126.com)
Fei Zhu , School of Computer Science and Technology, Soochow University, School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu China 215006 (e-mail: zhufei@suda.edu.cn)
Bairong Shen , Center for Systems Biology, Soochow University, Suzhou, Jiangsu China 215006 (e-mail: bairong.shen@suda.edu.cn)

A Study of Cell-free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification (Abstract)

Shifu Chen , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 12381 Shenzhen, Guangdong China (e-mail: sf.chen@siat.ac.cn)
Ming Liu , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: liuming@haplox.com)
Xiaoni Zhang , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: xn.zhang@haplox.com)
Renwen Long , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: longrw@haplox.com)
Yixing Wang , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: wangyx@haplox.com)
Yue Han , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: hanyue@haplox.com)
Shiwei Zhang , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: zhangsw@haplox.com)
Mingyan Xu , HaploX BioTechnology, Shenzhen, Guangdong China (e-mail: ming@haplox.com)
Jia Gu , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 12381 Shenzhen, Guangdong China (e-mail: jia.gu@siat.ac.cn)

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)

Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram for Detecting DNA Copy Number Aberrations (Abstract)

Nha Nguyen , Philadelphia, Pennsylvania United States (e-mail: nhnguyen@mail.med.upenn.edu)
An Vo , New York, New York United States (e-mail: avo@nshs.edu)
Haibin Sun , College of Information Science and Engineering, Shandong University of Science and Technology, 74789 Qingdao, Shandong China (e-mail: sdustsun@163.com)
Heng Huang , Computer Science and Engineering, UTA, Arlington, Texas United States (e-mail: heng@uta.edu)

Combination of Supervised and Unsupervised Approaches for miRNA Target Prediction (Abstract)

Nafiseh Sedaghat , Computer Engineering, Iran University of Science and Technology, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: nf_sedaghat@yahoo.com)
Mahmood Fathy , Computer Engineering School, Iran University of Science and Technology, 56944 Tehran, Tehran Iran (the Islamic Republic of) (e-mail: mafathy@iust.ac.ir)
Mohammad hossein Modarressi , Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Tehran Iran (the Islamic Republic of) (e-mail: modaresi@tums.ac.ir)
Ali Shojaie , Department of Biostatistics, University of Washington School of Public Health, 49462 Seattle, Washington United States (e-mail: ashojaie@uw.edu)

Hardware Accelerator for the Multifractal Analysis of DNA Sequences (Abstract)

Jorge E. Duarte-Sanchez , Universidad del Valle, Cali, Valle del Cauca Colombia (e-mail: jorge.enrique.duarte@correounivalle.edu.co)
Jaime Velasco-Medina , School of Electrical and Electronics Eng., Universidad del Valle, Cali, Valle Colombia (e-mail: jaime.velasco@correounivalle.edu.co)
Pedro A. Moreno , Universidad del Valle, Cali, Valle del Cauca Colombia (e-mail: pedro.moreno@correounivalle.edu.co)

Improving Alzheimeres Disease Classification by Combining Multiple Measures (Abstract)

Jin Liu , Computer Science, Central South University, ChangSha, Hunan China (e-mail: liujin06@csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Zhenjun Tang , School of Computer Science and Information Technology, Guangxi Normal University, 12388 Guilin, Guangxi China (e-mail: zjtang@gxnu.edu.cn)
Bin Hu , School of Information Science and Engineering, Lanzhou Uiversity, Lanzhou, Gansu Province China 730000 (e-mail: bh@lzu.edu.cn)
Fang-xiang 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)

Continuous Petri Nets and microRNA analysis in melanoma (Abstract)

Giulia Russo , Dipartimento di Scienze Biomediche e Biotecnlogiche, University of Catania, Catania, Sicily Italy (e-mail: giulia.russo@unict.it)
Marzio Pennisi , Universita degli Studi di Catania, 9298 Catania, Catania Italy (e-mail: mpennisi@dmi.unict.it)
Roberta Boscarino , Universita degli Studi di Catania, 9298 Catania, Catania Italy (e-mail: roberta.boscarino@hotmail.it)
Francesco Pappalardo , Universita degli Studi di Catania, 9298 Catania, Catania Italy 95124 (e-mail: francesco.pappalardo@unict.it)

Bijective Diameters of Gene Tree Parsimony Costs (Abstract)

Pawel Gorecki , Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, mazowieckie Poland 02-097 (e-mail: gorecki@mimuw.edu.pl)
Oliver Eulenstein , Computer Science, Iowa State University, Ames, Iowa United States (e-mail: oeulenst@iastate.edu)

Influence of secretion on airflow dynamics of mechanical ventilated respiratory system (Abstract)

Shuai Ren , School of Automation Science and Electrical Engineering, Beihang University, Beijing, Beijing China (e-mail: yesoyou@gmail.com)
Yan Shi , School of Automation Science and Electrical Engineering, Beihang University, Beijing, Beijing China (e-mail: renshuainemo@163.com)
Maolin Cai , School of Automation Science and Electrical Engineering, Beihang University, Beijing, Beijing China (e-mail: caimaolin@buaa.edu.cn)
Weiqing Xu , School of Automation Science and Electrical Engineering, Beihang University, Beijing, Beijing China (e-mail: weiqing.xu@buaa.edu.cn)

Multiple network alignment via multiMAGNA++ (Abstract)

Vipin Vijayan , Computer Science and Engineering, University of Notre Dame, South Bend, Indiana United States 46556 (e-mail: vvijayan@nd.edu)
Tijana Milenkovic , Computer Science and Engineering, University of Notre Dame, South Bend, Indiana United States 46617 (e-mail: tmilenko@nd.edu)

Optimizing Phylogenetic Queries for Performance (Abstract)

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

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)

Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimization (Abstract)

B. Niu , Shenzhen University, Shenzhen, Guangdong China (e-mail: drniuben@gmail.com)
J. Liu , Shenzhen University, 47890 Shenzhen, Guangdong China (e-mail: liujing_1993@foxmail.com)
T. Wu , Arizona State University, 7864 Tempe, Arizona United States (e-mail: teresa.wu@asu.edu)
X.H. Chu , Shenzhen University, 47890 Shenzhen, Guangdong China (e-mail: x.chu@szu.edu.cn)
Z.X. Wang , THE HK POLYTECHNIC UNIVERSITY, Hong Kong, Hong Kong Hong Kong (e-mail: jeremy.wang@connect.polyu.hk)
Y.M. Liu , Zunyi Normal College, 230955 Zunyi, Guizhou China (e-mail: yanmin7813@163.com)

Integrating Imaging Genomic Data in the Quest for Biomarkers for Schizophrenia Disease (Abstract)

Su-Ping Deng , Biomedical Engineering, Tulane University, 5783 New Orleans, Louisiana United States (e-mail: dsptk2003@126.com)
Wenxing Hu , Biomedical Engineering, Tulane University, 5783 New Orleans, Louisiana United States (e-mail: whu@tulane.edu)
Vince D. Calhoun , the Mind Research Network, 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)

Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis (Abstract)

Loic Pauleve , Laboratoire de Recherche en Informatique, 72830 Orsay, FR France 91405 (e-mail: loic.pauleve@lri.fr)

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)

DNA watermarking using Codon Postfix technique (Abstract)

Safwat Hamad , Centro de Investigao em Sistemas Computacionais Avancados, Universidade do Porto, 26706 Porto, Porto Portugal 4169-007 (e-mail: ahmed.elhadad@fc.up.pt)
Ahmed Elhadad , Department of Scientific Computing, Ain Shams University Faculty of Computer and Information Science, 451909 Cairo, Cairo Egypt (e-mail: shamad@cis.asu.edu.eg)
Amal Khalifa , Department of Scientific Computing, Ain Shams University Faculty of Computer and Information Science, 451909 Cairo, Cairo Egypt (e-mail: amal@fcis.asu.edu.eg)

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)

Mutli-features Predction of Protein Translational Modification Sites (PDF)

Wenzheng Bao , tongji university, shanghai, shanghai China (e-mail: baowz55555@126.com)
Chuan-An Yuan , Nanning, Guangxi China (e-mail: yca@gxtc.edu.cn)
Younhua Zhang , Hefei, Anhui China (e-mail: zhangyh@ahau.edu.cn)
Kyungsook Han , Computer Science & Engineering, Inha University, Incheon, Inchon Korea (the Republic of) 402-751 (e-mail: khan@inha.ac.kr)
Asoke K. Nandi , Electronic and Computer Engineering, Brunel University, Uxbridge, Middlesex United Kingdom of Great Britain and Northern Ireland UB8 3PH (e-mail: Asoke.Nandi@brunel.ac.uk)
Barry Honig , Nicholas Avenue, New York United States (e-mail: bh6@columbia.edu)
De-shuang Huang , Computer Science Department, Tongji University, Shanghai, ShangHai China (e-mail: dshuang@tongji.edu.cn)

Species tree estimation using ASTRAL: how many genes are enough? (Abstract)

Shubhanshu Shekhar , Electrical and Computer Science, University of California San Diego, 8784 La Jolla, California United States 92093 (e-mail: shshekha@eng.ucsd.edu)
Sebastien Roch , Department of Mathematics, University of Wisconsin Madison, 5228 Madison, Wisconsin United States (e-mail: roch@wisc.edu)
Siavash Mirarab , Department of Electrical and Computer Engineering, University of California San Diego, 8784 La Jolla, California United States (e-mail: smirarab@ucsd.edu)

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)

PREMER: a Tool to Infer Biological Networks (Abstract)

Alejandro F. Villaverde , BioProcess Engineering, CSIC, Vigo, Galiza Spain (e-mail: afvillaverde@iim.csic.es)
Kolja Becker , Modelling of Biological Networks, Institute of Molecular Biology gGmbH, Mainz, Rhineland-Palatinate Germany (e-mail: kobecker@uni-mainz.de)
Julio R. Banga , BioProcess Engineering, CSIC, Vigo, Galiza Spain (e-mail: julio@iim.csic.es)

Plant Cell Population Tracking in a Honeycomb Structure Using an IMM Filter Based 3D Local Graph Matching Model (Abstract)

Min Liu , College of Electrical and Information Engineering, Hunan University, Changsha, Hunan China (e-mail: liu_min@hnu.edu.cn)
Yue He , College of Electrical and Information Engineering, Hunan University, Changsha, Hunan China (e-mail: yueh@hnu.edu.cn)
Weili Qian , Changsha, Hunan China (e-mail: weiliqian@hnu.edu.cn)
Yangliu Wei , College of Electrical and Information Engineering, Hunan University, Changsha, Hunan China (e-mail: yangliuw@hnu.edu.cn)
Xiaoyan Liu , Changsha, Hunan China (e-mail: xyliu_hnu@163.com)

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)

Novel Consensus Gene Selection Criteria for Distributed GPU Partial Least Squares-based Gene Microarray Analysis in Diffused Large B Cell Lymphoma (DLBCL) and related findings (Abstract)

Ho-Chun Wu , Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: andrewhcwu@eee.hku.hk)
Xi-Guang Wei , Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: xgwei@eee.hku.hk)
Shing-Chow Chan , Electrical and Electronic Engineering, The University of Hong Kong, HKSAR, HKSAR Hong Kong (e-mail: scchan@eee.hku.hk)

Unified Deep Learning Architecture for Modeling Biology Sequence (Abstract)

Hongjie WU , School of Computer Science and Technology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: hongjie.wu@qq.com)
Chengyuan CAO , School of Computer Science and Technology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: 495851267@qq.com)
Xiaoyan XIA , School of Computer Science and Technology, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: xyxia@suda.edu.cn)
Qiang LU , School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu China (e-mail: qiang@suda.edu.cn)

MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters (Abstract)

Jorge Gonzalez-Dominguez , Universidade da Coruna, A Coruna, Galicia Spain (e-mail: jgonzalezd@udc.es)
Maria J. Martin , Universidade da Coruna, 16737 A Coruna, Galicia Spain (e-mail: mariam@udc.es)

Identifying condition-specific modules by clustering multiple networks (Abstract)

Xiaoke Ma , School of Computer Science and Technology, Xidian University, 47905 Xian, Shaanxi China 710071 (e-mail: xkma@xidian.edu.cn)
Penggang Sun , School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi China (e-mail: sun198268@163.com)
Guimin Qin , School of Software, Xidian University, Xi'an, Shaanxi China (e-mail: gmqin@mail.xidian.edu.cn)

Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Based on Conditional Mutual Information (Abstract)

Juntao Li , Henan Normal University, Xinxiang, Henan China 453007 (e-mail: juntaolimail@126.com)
Wenpeng Dong , Henan Normal University, Xinxiang, Henan China (e-mail: wenpengdongmail@126.com)
Deyuan Meng , Beihang University (BUAA), Beijing, Beijing China 100191 (e-mail: dymeng23@126.com)

Clustering-based Compression for Population DNA Sequences (Abstract)

Kin On Cheng , Electronic and Information Engineering, The Hong Kong Polytechnic University, Nil, Nil Hong Kong (e-mail: ramchi_ece-work@yahoo.com.hk)
Ngai Fong Law , Electronic and Information Engineering, The Hong Kong Polytechnic University, Nil, Nil Hong Kong (e-mail: ennflaw@polyu.edu.hk)
W.-C. Siu , Electronic & Information Engg, Hong Kong Polytechnic Unviersity, Hong Kong, Kln Hong Kong Kln (e-mail: enwcsiu@polyu.edu.hk)

fmpRPMF: A Web Implementation for Protein Identification by Robust Peptide Mass Fingerprinting (Abstract)

Youyuan Li , State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 47860 Shanghai, Shanghai China (e-mail: yyli@ecust.edu.cn)
Yingping Zhuang , State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 47860 Shanghai, Shanghai China (e-mail: ypzhuang@ecust.edu.cn)

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)

Classification of Single-cell Gene Expression Trajectories from Incomplete and Noisy Data (Abstract)

Alireza Karbalayghareh , Department of Electrical and Computer Engineering, Texas A&M University, 14736 College Station, Texas United States (e-mail: karbalayghareh@gmail.com)
Ulisses Braga-Neto , Texas A&M University, College Station, Texas United States 77843-3128 (e-mail: ulisses@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)

Co-expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A (Abstract)

Kavitha Mukund , Bioengineering, University of California San Diego, 8784 La Jolla, California United States (e-mail: k1mukund@eng.ucsd.edu)
Samuel R. Ward , Bioengineering, University of California San Diego, 8784 La Jolla, California United States (e-mail: srward@ucsd.edu)
Richard L. Lieber , Bioengineering, University of California San Diego, 8784 La Jolla, California United States (e-mail: rlieber@ric.org)
Shankar Subramaniam , Bioengineering, University of California San Diego, 8784 La Jolla, California United States 92093 (e-mail: shankar@ucsd.edu)

Switched latent force models for reverse-engineering transcriptional regulation in gene expression data (Abstract)

Andres F. Lopez-Lopera , Department of Mathematics and Industrial Engineering, Ecoles des Mines de Saint-Etienne, Saint-Etienne, Saint-Etienne France (e-mail: andres-felipe.lopez@emse.fr)
Mauricio A. Alvarez , Department of Computer Science, University of Sheffield, Sheffield, Sheffield United Kingdom of Great Britain and Northern Ireland (e-mail: mauricio.alvarez@sheffield.ac.uk)

Protein remote homology detection and fold recognition based on Sequence-Order Frequency Matrix (Abstract)

Bin Liu , Harbin Institute of Technology, Harbin, Heilongjiang China (e-mail: bliu@insun.hit.edu.cn)
Junjie Chen , shenzhen campus, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: junjie.chen.hit@gmail.com)
Mingyue Guo , shenzhen campus, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: gmy362717784@126.com)
Xiaolong Wang , shenzhen campus, Harbin Institute of Technology, Shenzhen, Guangdong China (e-mail: wangxl@insun.hit.edu.cn)

An Integrated Approach for Identification of Functionally Similar MicroRNAs in Colorectal Cancer (Abstract)

Sushmita Paul , Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, 231955 Jodhpur, Rajasthan India (e-mail: sushmitapaul@iitj.ac.in)
Dhanajit Brahma , Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, 231955 Jodhpur, Rajasthan India (e-mail: dbrahma.in@gmail.com)

Structured Penalized Logistic Regression for Gene Selection in Gene Expression Data Analysis (Abstract)

Cheng Liu , Computer science, City University of Hong Kong, 53025 Kowloon, Hong Kong Hong Kong (e-mail: cliu272-c@my.cityu.edu.hk)
Hau San Wong , Computer Science, City University of Hong Kong, Hong Kong, Hong Kong Hong Kong - (e-mail: cshswong@cityu.edu.hk)

A Mixed-norm Laplacian Regularized Low-Rank Representation Method for Tumor Samples Clustering (Abstract)

Juan Wang , School of Information Science and Engineering, Qufu Normal University, 56650 Rizhao, Shandong China (e-mail: wangjuansdu@163.com)
Jin-Xing Liu , School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong China (e-mail: sdcavell@126.com)
Chun-Hou Zheng , College of Electrical Engineering and Automation, Anhui University, Hefei, Anhui China (e-mail: zhengch99@126.com)
Ya-Xuan Wang , School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong China (e-mail: yxwsfz@126.com)
Xiong-Zhen Kong , School of Information Science and Engineering, Qufu Normal University, 56650 Rizhao, Shandong China (e-mail: kongxzhen@163.com)
Chang-Gang Weng , School of Information Science and Engineering, Qufu Normal University, 56650 Rizhao, Shandong China (e-mail: chgwenqrnu@126.com)

ToBio: Global Pathway Similarity Search based on Topological and Biological Features (Abstract)

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)
Sam Kwong , Computer Science, City University of Hong Kong, Kowloon, kowloon Hong Kong qwww (e-mail: cssamk@cityu.edu.hk)
Ka-Chun Wong , City University of hong Kong, Kowloon Tong, Kowloon Hong Kong (e-mail: kc.w@cityu.edu.hk)

Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data (Abstract)

Ping Luo , University of Saskatchewan, 7235 Saskatoon, Saskatchewan Canada (e-mail: pil562@mail.usask.ca)
Li-Ping Tian , Beijing Wuzi University, 71227 Tongzhou, Beijing China (e-mail: bmitian@163.com)
Jishou Ruan , Informatics and Probability, Naikai University, Tianjin, Tianjin China 300071 (e-mail: jsruan@nankai.edu.cn)
Fangxiang Wu , Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan Canada S7N 5A9 (e-mail: faw341@mail.usask.ca)

A Bi-objective RNN Model to Reconstruct Gene Regulatory Network: A Modified Multi-objective Simulated Annealing Approach (Abstract)

Surama Biswas , Maulana Abul Kalam Azad University of Technology, West Bengal, Kolkata, West Bengal India (e-mail: surama.biswas@gmail.com)
Sriyankar Acharyya , Maulana Abul Kalam Azad University of Technology, West Bengal, Kolkata, West Bengal India (e-mail: srikalpa8@gmail.com)

Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle (Abstract)

Minghan Chen , Computer Science, Virginia Polytechnic Institute and State University, 1757 Blacksburg, Virginia United States (e-mail: cmhshirl@vt.edu)
Brandon Amos , Computer Science, Virginia Polytechnic Institute and State University, 1757 Blacksburg, Virginia United States (e-mail: bamos@cs.cmu.edu)
Layne T. Watson , Computer Science, VPI & SU, Blacksburg, Virginia United States (e-mail: ltw@cs.vt.edu)
John Tyson , Biological Science, Virginia Polytechnic Institute and State University, 1757 Blacksburg, Virginia United States (e-mail: tyson@vt.edu)
Yang Cao , Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia United States (e-mail: ycao@cs.vt.edu)
Cliff Shaffer , Computer Science, Virginia Polytechnic Inst. & State Univ., Blacksburg, Virginia United States (e-mail: shaffer@cs.vt.edu)
Michael Trosset , Indiana University Bloomington, 1771 Bloomington, Indiana United States (e-mail: mtrosset@indiana.edu)
Cihan Oguz , Computer Science, Virginia Polytechnic Institute and State University, 1757 Blacksburg, Virginia United States (e-mail: cihanoguzvt@gmail.com)
Gisella Kakoti , Computer Science, Virginia Polytechnic Institute and State University, 1757 Blacksburg, Virginia United States (e-mail: kemikakoti@gmail.com)

RF-NR: Random forest based approach for improved classification of Nuclear Receptors (Abstract)

Hamid Ismail , NC A&T State University, Greensboro, North Carolina United States (e-mail: hdismail@ncat.edu)
Hiroto Saigo , Bioscience and Bioinformatics, Kyushu Institute of Dechnology, Iijuka-shi, Fukuoka Japan (e-mail: saigo@bio.kyutech.ac.jp)
Dukka KC , Computational Science and Engineering, North Carolina A&T State University, Greensboro, North Carolina United States (e-mail: dbkc@ncat.edu)

ASSA-PBN: A Toolbox for Probabilistic Boolean Networks (Abstract)

Andrzej Mizera , Faculte des Sciences, de la Technologie et de la Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg Luxembourg L-4364 (e-mail: andrzej.mizera@uni.lu)
Jun Pang , Faculte des Sciences, de la Technologie et de la Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg Luxembourg (e-mail: jun.pang@uni.lu)
Cui Su , Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, Esch-sur-Alzette, Luxembourg Luxembourg (e-mail: cui.su@uni.lu)
Qixia Yuan , Faculte des Sciences, de la Technologie et de la Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg Luxembourg 4364 (e-mail: qixia.yuan@uni.lu)

Sequence-based prediction of putative transcription factor binding sites in DNA sequences of any length (Abstract)

Wook Lee , Incheon, Incheon Korea (the Republic of) (e-mail: wooklee720@gmail.com)
Byungkyu Park , Incheon, Incheon Korea (the Republic of) (e-mail: bpark@inha.ac.kr)
Kyungsook Han , Computer Science & Engineering, Inha University, Incheon, Inchon Korea (the Republic of) 402-751 (e-mail: khan@inha.ac.kr)

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)

Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium (Abstract)

Michael Backenkohler , Computer Science, Universitat des Saarlandes, 9379 Saarbrucken, Germany Germany 66123 (e-mail: michael.backenkoehler@uni-saarland.de)
Luca Bortolussi , Universita degli Studi di Trieste Dipartimento di Matematica e Geoscienze, 124240 Trieste, Friuli-Venezia Giulia Italy (e-mail: luca@dmi.units.it)
Verena Wolf , Computer Science, Universitat des Saarlandes, 9379 Saarbrucken, Germany Germany (e-mail: verena.wolf@uni-saarland.de)

DNRLMF-MDA:Predicting microRNA-disease associations based on similarities of microRNAs and diseases (Abstract)

Cheng Yan , Computer Science, Central South University, ChangSha, Hunan China (e-mail: yancheng01@mail.csu.edu.cn)
Jianxin Wang , Computer Science, Central South University, ChangSha, Hunan China 410083 (e-mail: jxwang@mail.csu.edu.cn)
Peng Ni , School of Information Science and Engineering, Central South University, Changsha, Hunan China (e-mail: nipeng@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)

Elucidating Genome-Wide Protein-RNA Interactions using Differential Evolution (Abstract)

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

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)

Meta-path methods for prioritizing candidate disease miRNAs (Abstract)

Xuan Zhang , xiamen, fujian China (e-mail: xuanzhang@foxmail.com)
Quan Zou , School of Computer Science and Technology, Tianjin University, Tianjin, Tianjin China (e-mail: zouquan@nclab.net)
Alfonso Rodruguez-Paton , madrid, madrid Spain (e-mail: arpaton@fi.upm.es)
xiangxiang zeng , xiamen university, xiamen, fujian China (e-mail: xzeng@xmu.edu.cn)

Efficient Detection of Communities in Biological Bipartite Networks (PDF)

Paola Gabriela Pesantez , Electrical Engineering and Computer Science, Washington State University, 6760 Pullman, Washington United States 99164-2752 (e-mail: p.pesantezcabrera@wsu.edu)
Ananth Kalyanaraman , School of EECS, Washington State University, Pullman, Washington United States 99164-2752 (e-mail: ananth@eecs.wsu.edu)

Early Diagnosis of Alzheimer's Disease Based on Resting-State Brain Networks and Deep Learning (Abstract)

Ronghui Ju , School of Electronic Information and Communications, Huazhong University of Science and Technology, 12443 Wuhan, Hubei China 430074 (e-mail: juronghui@hust.edu.cn)
Chenhui Hu , School of Engineering and Applied Sciences, Harvard University, 1812 Cambridge, Massachusetts United States (e-mail: hu4@seas.harvard.edu)
pan zhou , School of Electronic Information and Communications, Huazhong University of Science and Technology, wuhan, Hubei China (e-mail: panzhou@hust.edu.cn)
Quanzheng Li , Nuclear Medicine and Molecular Imaging Radiology Department, Harvard Medical School, 1811 Boston, Massachusetts United States (e-mail: li.quanzheng@mgh.harvard.edu)
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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