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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)

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)

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)

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)

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)

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)

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).

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)

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).

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)

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)

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)

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)

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.

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).

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

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

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

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

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

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

Identifying sigma70 promoters with novel pseudo nucleotide composition (Abstract)

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

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

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

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

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

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

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

Characteristics of Myosin V Processivity (Abstract)

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

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

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

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).

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)

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).

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)

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)

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

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

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)

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

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

Computing Minimum Reaction Modifications in a Boolean Metabolic Network (Abstract)

Takeyuki Tamura , Institute for Chemical Research, Kyoto University, Uji, Kyoto Japan 6110011 (e-mail: tamura@kuicr.kyoto-u.ac.jp)
Wei Lu , Kyoto University, Uji, Kyoto Japan (e-mail: rogi@nii.ac.jp)
Jiangning Song , Monash University, Melbourne, Victoria Australia (e-mail: jiangning.song@monash.edu)
Tatsuya Akutsu , Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto Japan (e-mail: takutsu@kuicr.kyoto-u.ac.jp)

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

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

The Robust Classification Model Based on Combinatorial Features (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

A sparse regression method for group-wise feature selection with false discovery rate control (Abstract)

Alexej Gossmann , Bioinnovation PhD Program, Tulane University, New Orleans, Louisiana United States (e-mail: agossman@tulane.edu)
Shaolong Cao , Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, 4002 Houston, Texas United States (e-mail: scao2@tulane.edu)
Damian Brzyski , Department of Epidemiology and Biostatistics, Indiana University Bloomington, 1771 Bloomington, Indiana United States (e-mail: damian.brzyski@uj.edu.pl)
Lan-Juan Zhao , Department of Global Biostatistics and Data Science, Tulane University, New Orleans, Louisiana United States (e-mail: lzhao2@tulane.edu)
Hong-Wen Deng , Department of Global Biostatistics and Data Science, Tulane University, New Orleans, Louisiana United States (e-mail: hdeng2@tulane.edu)
Yu-Ping Wang , Department of Biomedical Engineering, Tulane University, 5783 New Orleans, Louisiana United States (e-mail: wyp202002@yahoo.com)

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

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

SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter (PDF)

Osamu Hirose , Kanazawa University, Kanazawa, Ishikawa Japan 920-1192 (e-mail: ohirose.univ@gmail.com)
Shotaro Kawaguchi , Kanazawa University, Kanazawa, Ishikawa Japan (e-mail: zeb79637@gmail.com)
Terumasa Tokunaga , Kyushu Institute of Technology, Iizuka, Fukuoka Japan 820-8502 (e-mail: tokunaga@ces.kyutech.ac.jp)
Yu Toyoshima , The University of Tokyo, Bunkyo-ku, Tokyo Japan (e-mail: ytoyo@bs.s.u-tokyo.ac.jp)
Takayuki Teramoto , Department of Biology, Kyushu University, Fukuoka, Fukuoka Japan 819-0395 (e-mail: teramoto.takayuki.873@m.kyushu-u.ac.jp)
Sayuri Kuge , Biology, Kyushu University, Fukuoka, Fukuoka Japan 819-0395 (e-mail: kuge.sayuri.449@m.kyushu-u.ac.jp)
Takeshi Ishihara , Faculty of Sciences, Kyushu University, Fukuoka, Fukuoka Japan 810-0395 (e-mail: takeiscb@gmail.com)
Yuichi Iino , Biological Sciences, The University of Tokyo, Tokyo, Tokyo Japan 113-0032 (e-mail: iino@bs.s.u-tokyo.ac.jp)
Ryo Yoshida , Institute of Statistical Mathematics, Tachikawa, Tokyo Japan (e-mail: yoshidar@ism.ac.jp)

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

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

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

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

New Deep Learning Methods for Protein Loop Modeling (Abstract)

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

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

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

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

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

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

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

Credibility of Evolutionary Events in Gene Trees (Abstract)

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

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

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

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

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

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

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

Fast Algorithms for Computing Path-Difference Distances (Abstract)

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

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

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

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

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

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

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

Prediction of Hot Regions in PPIs Based on Improved Local Community Structure Detecting (Abstract)

Xiaoli Lin , Hubei Key Laboratory of Intelligent Information Processing and Real-time Industrial System, School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei China (e-mail: aneya@163.com)
Xiaolong Zhang , Hubei Key Laboratory of Intelligent Information Processing and Real-time Industrial System, School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei China (e-mail: xiaolong.zhang@wust.edu.cn)

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

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

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

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

Altering indispensable proteins in controlling directed human protein interaction network (Abstract)

Xizhe Zhang , Noreastern Univerisity, Shenyang, Liaoning China (e-mail: zhangxizhe@mail.neu.edu.cn)

Structural Target Controllability of Linear Networks (Abstract)

Eugen Czeizler , Computer Science, Abo Akademi Institutionen for naturvetenskaper, 278232 Abo, Länsi-Suomen lääni Finland 20500 (e-mail: eugen.czeizler@abo.fi)
Kai Chiu Wu , Abo Akademi Institutionen for naturvetenskaper, 278232 Turku, Länsi-Suomen lääni Finland (e-mail: kai.wu@abo.fi)
Cristian Gratie , Information Technologies, Åbo Akademi University, Turku, Finland Proper Finland 20520 (e-mail: cgratie@abo.fi)
Krishna Kanhaiya , Abo Akademi Institutionen for naturvetenskaper, 278232 Turku, Länsi-Suomen lääni Finland (e-mail: kkanhaiy@abo.fi)
Ion Petre , Department of Information Technologies, Abo Akademi, Turku, Turku Finland (e-mail: ipetre@abo.fi)

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

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

Organisation-Oriented Coarse Graining and Refinement of Stochastic Reaction Networks (Abstract)

Chunyan Mu , Computer Science, Teesside University, 5462 Middlesbrough, Tees Valley United Kingdom of Great Britain and Northern Ireland (e-mail: c.mu@tees.ac.uk)
Peter Dittrich , Friedrich-Schiller-University Jena, Jena, Jena Germany (e-mail: peter.dittrich@uni-jena.de)
David Parker , Computer Science, University of Birmingham, Birmingham, West Midlands United Kingdom of Great Britain and Northern Ireland B15 2TT (e-mail: d.a.parker@cs.bham.ac.uk)
Jonathan E. Rowe , University of Birmingham, 1724 Birmingham, West Midlands United Kingdom of Great Britain and Northern Ireland (e-mail: j.e.rowe@cs.bham.ac.uk)

A Simplified Description of Child Tables for Sequence Similarity Search (PDF)

Martin Frith , Artificial Intelligence Research Center, Sangyo Gijutsu Sogo Kenkyujo Rinkai Fukutoshin Center, 73463 Koto-ku, Tokyo Japan (e-mail: mcfrith@edu.k.u-tokyo.ac.jp)
Anish Shrestha , Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba Japan (e-mail: anish@edu.k.u-tokyo.ac.jp)

A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of Shewanella (Abstract)

dewu ding , State Key Laboratory of Bioelectronics, 127382 Nanjing, Jiangsu China 210096 (e-mail: dwding2008@aliyun.com)
xiao Sun , Southeast university, Nanjing, Jiangsu China (e-mail: xsun@seu.edu.cn)

Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors (Abstract)

Francois Fages , Inria Centre de Recherche Saclay Ile-de-France, 202552 Palaiseau, Île-de-France France (e-mail: francois.fages@inria.fr)
Thierry Martinez , INRIA Paris 75012, Paris, Paris France (e-mail: Thierry.Martinez@inria.fr)
David Rosenblueth , Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, 7180 Coyoacan, Ciudad de Mexico Mexico 04510 (e-mail: drosenbl@unam.mx)
Sylvain Soliman , Inria Centre de Recherche Saclay Ile-de-France, 202552 Palaiseau, Île-de-France France (e-mail: Sylvain.Soliman@inria.fr)

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

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

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

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

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

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

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

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

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

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

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

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

A robust simulator for physiologically structured population models (Abstract)

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

Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients (Abstract)

Miguel Aires Barros Monteiro , Universidade de Lisboa Instituto Superior Tecnico, 72971 Lisboa, Lisboa Portugal (e-mail: mab.mtr@gmail.com)
Ana Catarina Fonseca , Neurology, Hospital de Santa Maria, Lisboa, NA Portugal 1640-035 (e-mail: catarinagfonseca@gmail.com)
Ana Teresa Freitas , CSE, Universidade de Lisboa Instituto Superior Tecnico, 72971 Lisboa, Lisboa Portugal 1049-001 (e-mail: ana.freitas@tecnico.ulisboa.pt)
Teresa Pinho e Melo , Neurology, Hospital de Santa Maria, 70899 Lisboa, Lisboa Portugal 1649-035 (e-mail: tmelo@fm.ul.pt)
Alexandre P. Francisco , CSE Dept, Universidade de Lisboa Instituto Superior Tecnico, 72971 Lisboa, Lx Portugal 1049-001 (e-mail: aplf@ist.utl.pt)
Jose M. Ferro , Neurology, Hospital de Santa Maria, 70899 Lisboa, Lisboa Portugal 1649-035 (e-mail: jmferro@fm.ul.pt)
Arlindo Oliveira , INESC-ID / IST, Lisboa, Portugal Portugal (e-mail: aml@inesc-id.pt)

Local traces: an over-approximation of the behaviour of the proteins in rule-based models (Abstract)

Jerome FERET , DI - ENS, INRIA Paris, Paris, Ile de France France 75005 (e-mail: feret@ens.fr)
Kim Quyen Quyen Ly , DI - ENS, INRIA Paris, Paris, Ile de France France (e-mail: quyen@di.ens.fr)

Comorbidity Scoring with Causal Disease Networks (Abstract)

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

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

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

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

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

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

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

A Novel Computational Approach for Global Alignment for Multiple Biological Networks (Abstract)

Warith Eddine Djeddi , Computer Science, Universite de Tunis El Manar Faculte des Sciences de Tunis, 155529 Tunis, Tunis Tunisia 2092 (e-mail: waritheddine@yahoo.fr)
Sadok Ben Yahia , departement of computer science, faculty of science of tunis, tunis, Tunis Tunisia (e-mail: sadok.benyahia@fst.rnu.tn)
Engelbert Mephu Nguifo , Mathematics and Computer Science, Blaise Pascal University, Aubiere, Auvergne France 63173 (e-mail: engelbert.mephu_nguifo@uca.fr)

Designing optimal experiments to discriminate interaction graph models (PDF)

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

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework (Abstract)

Nina Luhmann , International Research Training Group GRK 1906/1, Bielefeld University, Bielefeld, NRW Germany (e-mail: nluhmann@techfak.uni-bielefeld.de)
Cedric Chauve , Mathematics, Simon Fraser University, Burnaby, British Columbia Canada V5A1S6 (e-mail: cedric.chauve@sfu.ca)
Jens Stoye , Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, NRW Germany (e-mail: jens.stoye@uni-bielefeld.de)
Roland Wittler , International Research Training Group GRK 1906/1, Bielefeld University, Bielefeld, NRW Germany (e-mail: roland.wittler@uni-bielefeld.de)

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

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

ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy (PDF)

Annie Wang , Bronx High School of Science, 246983 Bronx, New York United States (e-mail: wangan@bxscience.edu)
Hansaim Lim , Computer Science, Hunter College, 5924 New York, New York United States 10065-5024 (e-mail: hlim1@gradcenter.cuny.edu)
Shu-Yuan Cheng , Sciences, John Jay College of Criminal Justice, 14775 New York, New York United States (e-mail: shcheng@jjay.cuny.edu)
Lei Xie , Hunter College, CUNY, New York City, New York United States (e-mail: lei.xie@hunter.cuny.edu)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bioimage Classification with Handcrafted and Learned Features (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

Machine Vision System for 3D Plant Phenotyping (Abstract)

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

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

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

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

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

Robust Gene Circuit Control Design for Time-delayed Genetic Regulatory Networks without SUM Regulatory Logic (Abstract)

Hongmei Jiao , Medical Academy, Yangzhou University, Yangzhou, Jiangsu China (e-mail: hmjiao@yzu.edu.cn)
Liping Zhang , School of Electrical and Electronic Engineering, Shanghai University of Engineering Science, 66323 Shanghai, Shanghai China (e-mail: zhangliping@sues.edu.cn)
Qikun Shen , Department of Automatica, the College of Information Engineering, Yangzhou University, Yangzhou, Jiangsu China 225127 (e-mail: qkshen@yzu.edu.cn)
Junwu Zhu , Medical Academy, Yangzhou University, Yangzhou, Jiangsu China (e-mail: jwzhu@yzu.edu.cn)
Peng Shi , the School of Electrical and Electronic Engineering, The University of Adelaide, Adelaide, SA 5005, South Australia Australia (e-mail: peng.shi@adelaide.edu.au)

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

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

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

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

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

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

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

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

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

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

A Distributed Classifier for MicroRNA Target Prediction with Validation through TCGA Expression Data (Abstract)

Asish Ghoshal , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States 47907-2050 (e-mail: aghoshal@purdue.edu)
Jinyi Zhang , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States (e-mail: zhang1182@purdue.edu)
Michael Roth , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States (e-mail: roth28@purdue.edu)
Kevin Xia , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States (e-mail: xia51@purdue.edu)
Ananth Grama , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States (e-mail: ayg@purdue.edu)
Somali Chaterji , Computer Science, Purdue University System, 8522 West Lafayette, Indiana United States (e-mail: schaterji@acm.org)

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

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

An efficient mixed-model for screening differentially expressed genes of breast cancer based on LR-RF (Abstract)

Mengmeng Sun , Wuxi, Jiangsu China (e-mail: sunmeng926@126.com)
Tao Ding , Wuxi, Jiangsu China (e-mail: dingtao_jnu@163.com)
Xu-Qing Tang , Jiangnan University, School of Science, Wuxi, Jiangsu China 214122 (e-mail: txq5139@jiangnan.edu.cn)
Keming Yu , London, London United Kingdom of Great Britain and Northern Ireland (e-mail: Keming.Yu@brunel.ac.uk)

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

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

SAFETY: Secure gwAs in Federated Environment Through a hYbrid solution (Abstract)

Md Nazmus Sadat , Computer Science, University of Manitoba, 8664 Winnipeg, Manitoba Canada (e-mail: sadat@cs.umanitoba.ca)
Md Momin Al Aziz , Computer Science, University of Manitoba, Winnipeg, Manitoba Canada R3T2H4 (e-mail: momin.aziz.cse@gmail.com)
Noman Mohammed , Department of Computer Science, University of Manitoba, 8664 Winnipeg, Manitoba Canada R3T 2N2 (e-mail: noman@cs.umanitoba.ca)
Feng Chen , Department of Biomedical Informatics, University of California, San Diego, San Diego, California United States (e-mail: f4chen@ucsd.edu)
Xiaoqian Jiang , Division of Biomedical Informatics, University of California, San Diego, California United States (e-mail: x1jiang@ucsd.edu)
Shuang Wang , Division of Biomedical Informatics, University of California, San Diego, San Diego, California United States 92093-0505 (e-mail: shw070@ucsd.edu)

Phylogenetic Reconstruction for Copy-Number Evolution Problems (Abstract)

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

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

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

MIMOSA: Algorithms for Microbial Profiling (Abstract)

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

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

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

DrPOCS: Drug repositioning based on projection onto convex sets (Abstract)

Yin-Ying Wang , Tongji University, 12476 Shanghai, Shanghai China 200092 (e-mail: yy_wang@tongji.edu.cn)
Chunfeng Cui , Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong Hong Kong (e-mail: chunfcui@cityu.edu.hk)
Liqun Qi , Hong Kong, Hong Kong China (e-mail: liqun.qi@polyu.edu.hk)
Hong Yan , Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong Hong Kong KLN (e-mail: h.yan@cityu.edu.hk)
Xingming Zhao , ISTBI, Fudan University, 12478 Shanghai, Shanghai China 200433 (e-mail: xmzhao@fudan.edu.cn)

Modelling Microbial Fuel Cells using lattice Boltzmann methods (Abstract)

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

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics (Abstract)

Romeo Rizzi , Department of Computer Science, University of Verona, Verona, Verona Italy (e-mail: romeo.rizzi@univr.it)
Massimo Cairo , Universita degli Studi di Trento Dipartimento di Matematica, 201805 Povo, - Italy (e-mail: massimo.cairo@unitn.it)
Veli Makinen , Department of Computer Science, University of Helsinki, Helsinki, - Finland (e-mail: vmakinen@cs.helsinki.fi)
Alexandru Ioan Tomescu , Department of Computer Science, University of Helsinki, Helsinki, Helsinki Finland (e-mail: tomescu@cs.helsinki.fi)
Daniel Valenzuela , Department of Computer Science, University of Helsinki, Helsinki, - Finland (e-mail: Daniel.Valenzuela@helsinki.fi)

An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements (Abstract)

Tom Hartmann , Department of Computer Science, University of Leipzig, Leipzig, Saxony Germany (e-mail: thartmann@informatik.uni-leipzig.de)
Matthias Bernt , Department of Computer Science, University of Leipzig, Leipzig, 04109 Leipzig Germany (e-mail: bernt@informatik.uni-leipzig.de)
Martin Middendorf , Department of Computer Science, University of Leipzig, Leipzig, Sachsen Germany D-04009 (e-mail: middendorf@informatik.uni-leipzig.de)

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

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

Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-like Chemical Graphs (Abstract)

Yuhei Nishiyama , Department of Applied Mathematics and Physics, Kyoto University, Kyoto, Kyoto Japan (e-mail: y.nishiyama@amp.i.kyoto-u.ac.jp)
Aleksandar Shurbevski , Department of Applied Mathematics and Physics, Kyoto University, Kyoto, Kyoto Japan (e-mail: shurbevski@amp.i.kyoto-u.ac.jp)
Hiroshi Nagamochi , Department of Applied Mathematics and Physics, Kyoto University, Kyoto, Kyoto Japan (e-mail: nag@amp.i.kyoto-u.ac.jp)
Tatsuya Akutsu , Institute for Chemical Research, Kyoto University, Uji, Kyoto Japan (e-mail: takutsu@kuicr.kyoto-u.ac.jp)

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

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

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

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

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

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

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

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

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

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

Low Rank Subspace Clustering via Discrete Constraint and Hypergraph Regularization for Tumor Molecular Pattern Discovery (Abstract)

Jian Liu , School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu China (e-mail: liujiansqjxt@126.com)
Yuhu Cheng , School of Information and Control Engineering, China University of Mining and Technology, xuzhou, Jiangsu China (e-mail: chengyuhu@163.com)
Xuesong Wang , School of Information and Control Engineering, China University of Mining and Technology, xuzhou, Jiangsu China (e-mail: wangxuesongcumt@163.com)
Xiaoluo Cui , Weihai Ocean Vocational College, WeiHai, Sandong China (e-mail: cui.xiaoluole@163.com)
Yi Kong , China University of Mining and Technology, 12392 Xuzhou, Jiangsu China (e-mail: kongyicumt@163.com)
Junping Du , School of Computer, BUPT, Beijing, Beijing China (e-mail: junpingdu@126.com)

Computational Models for Trapping Ebola Virus Using Engineered Bacteria (Abstract)

Daniel Perez Martins , Computing, Math & Physics, Waterford Institute of Technology, 8807 Waterford, Wateford Ireland (e-mail: dpmartins@tssg.org)
Michael Barros , TSSG, Waterford Institute of Technology, 8807 Waterford, Waterford Ireland (e-mail: mbarros@tssg.org)
Massimiliano Pierobon , Computer Science and Engineering, University of Nebraska-Lincoln, 14719 Lincoln, Nebraska United States (e-mail: maxp@unl.edu)
Meenakshisundaram Kandhavelu , Tampere University of Technology, Tampere, Tampere Finland (e-mail: meenakshisundaram.kandhavelu@tut.fi)
Pietro Lio , Computer Laboratory, University of Cambridge, Cambridge, GB-CAM United Kingdom of Great Britain and Northern Ireland (e-mail: pl219@cam.ac.uk)
Sasitharan Balasubramaniam , Department of Electronic and Communication Engineering, Tampere University of Technology, Tampere, Pirkanmaa Finland (e-mail: sasi.bala@tut.fi)

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

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

Parallel Computation of the Burrows-Wheeler Transform of Short Reads Using Prefix Parallelism (Abstract)

Kouichi Kimura , Center for Technology Innovation - Healthcare, Hitachi Ltd., Kokubunji, Tokyo Japan (e-mail: kouichi.kimura.hh@hitachi.com)
Asako Koike , Future Investment Division, Hitachi Ltd., Chiyoda-ku, Tokyo Japan (e-mail: asako.koike.ea@hitachi.com)

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

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

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

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

Identifying gene network rewiring by integrating gene expression and gene network data (Abstract)

Ting Xu , School of Mathematics and Statistics, Central China Normal University, Wuhan, Hubei China (e-mail: tingxu@mail.ccnu.edu.cn)
Le Ou-Yang , Shenzhen University, 47890 Shenzhen, Guangdong China 518060 (e-mail: leouyang@szu.edu.cn)
Xiaohua Hu , College of Information Science and Technology, Drexel University, Philadelphia, Pennsylvania United States 19104 (e-mail: xh29@drexel.edu)
Xiaofei Zhang , School of Mathematics and Statistics, central china normal univiserty, wuhan, hubei China (e-mail: zhangxf@mail.ccnu.edu.cn)

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

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

3gClust: Human Protein Cluster Analysis (Abstract)

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

Identification and analysis of key residues in protein—RNA complexes (Abstract)

A. Kulandaisamy , Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu India (e-mail: kulandai28@gmail.com)
Ambuj Srivastava , Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu India (e-mail: ambuj.88.in@gmail.com)
Pradeep Kumar , Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu India (e-mail: i.pradeep92@gmail.com)
Nagarajan Raju , Vanderbilt University Medical Center, 12328 Nashville, Tennessee United States 37232-2102 (e-mail: nagabioinfostar@gmail.com)
Binny Priya , Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu India (e-mail: binny.bioinfo@gmail.com)
Dr. M. Michael Gromiha , Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu India 600036 (e-mail: gromiha@iitm.ac.in)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arrhythmia Recognition and Classification Using ECG Morphology and Segment Feature Analysis (Abstract)

Wenliang Zhu , School of Electronic and Infomation Enginering, Soochow University, 12582 Suzhou, Jiangsu China 215006 (e-mail: 20155228021@stu.suda.edu.cn)
Xiaohe Chen , Suzhou institute of biomedical engineering and technology Chinese academy of sciences, Suzhou, Jiangsu China (e-mail: chenxh@sibet.ac.cn)
Yan Wang , School of Electronic and Information Engineering, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: 20155228030@stu.suda.edu.cn)
Lirong Wang , School of Electronic and Information Engineering, Soochow University, 12582 Suzhou, Jiangsu China (e-mail: wanglirong@suda.edu.cn)

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

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

An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution (PDF)

Lei Li , CSE, University of Connecticut, Storrs, Connecticut United States (e-mail: lei.li@uconn.edu)
Mukul S. Bansal , CSE, University of Connecticut, Storrs, Connecticut United States (e-mail: mukul.bansal@uconn.edu)

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

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

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

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

Bioinformatic workflow extraction from scientific texts based on word sense disambiguation and relation extraction (Abstract)

Ahmed Halioui , Universite du Quebec a Montreal Departement d'informatique, 198126 Montreal, Quebec Canada H3C 3P8 (e-mail: ahlioui@gmail.com)
Petko Valtchev , Universite du Quebec a Montreal Departement d'informatique, 198126 Montreal, Quebec Canada (e-mail: valtchev.petko@uqam.ca)
Abdoulaye Banire Diallo , Universite du Quebec a Montreal Departement d'informatique, 198126 Montreal, Quebec Canada (e-mail: diallo.abdoulaye@uqam.ca)

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

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

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

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

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

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

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

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

Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model (Abstract)

Jordan Haack , Harvey Mudd College, Claremont, California United States (e-mail: jhaack@g.hmc.edu)
Eli Zupke , Computer Science, California Polytechnic State University, Pomona, Pomona, California United States (e-mail: ezpuke@cpp.edu)
Andrew Ramirez , Department of Computer Science, California Institute of Technology, 6469 Pasadena, California United States (e-mail: abramire@caltech.edu)
Yi-Chieh Wu , Department of Computer Science, Harvey Mudd College, Claremont, California United States (e-mail: yjw@cs.hmc.edu)
Ran Libeskind-Hadas , Harvey Mudd College, Claremont, California United States 91711 (e-mail: hadas@cs.hmc.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)

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

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

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

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

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

Biological Sequence Analysis with Multivariate String Kernels (Abstract)

Pavel P. Kuksa , NEC Laboratories America Inc, Princeton

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

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

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

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

Multivariate Hypergeometric Similarity Measure (Abstract)

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

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

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

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

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

Improved Multiple Sequence Alignments Using Coupled Pattern Mining (Abstract)

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

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

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

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

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

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

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

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

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

Operon Prediction using Chaos Embedded Particle Swarm Optimization (Abstract)

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

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

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

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

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

Reverse Engineering Molecular Hypergraphs (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

A Combinatorial Perspective of the Protein Inference Problem (Abstract)

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

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

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

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

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

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

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

Statistical Detection of Boolean Regulatory Relationships (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Quantifying Significance of MHC II Residues (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Protein Function Prediction with Incomplete Annotations (Abstract)

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

Maximizing Deep Coalescence Cost (Abstract)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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