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TABLE OF CONTENTS
Issue No. 02 - March-April (vol. 14)
ISSN: 1545-5963

Guest Editorial for Special Section on BIBM 2014 (HTML)

Illhoi Yoo , Department of Health Management and Informatics, University of Missouri School of Medicine CE718 Clinical Support and Education Building (DC006.00), Five Hospital Dr., Columbia
Amarda Shehu , Department of Computer Science, George Mason University, 4400 University Drive, MSN 4A5, Fairfax
pp. 252-253

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

En-Shiun Annie Lee , Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada
Ho-Yin Antonio Sze-To , Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada
Man-Hon Wong , Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, Hong Kong
Kwong-Sak Leung , Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, Hong Kong
Terrence Chi-Kong Lau , Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
Andrew K. C. Wong , Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada
pp. 254-263

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

Yong Zhang , College of Computer Science, Central China Normal University, Wuhan, China
Xiaohua Hu , College of Computer Science, Central China Normal University, Wuhan, China
Xingpeng Jiang , College of Computing & InformaticsDrexel University Philadelphia
pp. 264-271

Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics (HTML)

Ilona Kifer , Agilent Laboratories, Tel Aviv, Israel
Rui M. Branca , Karolinska Institute, Stockholm, Sweden
Amir Ben-Dor , Agilent Laboratories, Tel Aviv, Israel
Linhui Zhai , BPRC, Beijing Institute of Radiation Medicine, Beijing, P.R. China
Ping Xu , BPRC, Beijing Institute of Radiation Medicine, Beijing, P.R. China
Janne Lehtio , Karolinska Institute, Stockholm, Sweden
Zohar Yakhini , Agilent Laboratories, Tel Aviv, Israel
pp. 272-281

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

Huiru Zheng , Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, BT37 0QB, Northern Ireland, United Kingdom
Chaoyang Wang , College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
Haiying Wang , Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, BT37 0QB, Northern Ireland, United Kingdom
pp. 282-289

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

Matthias Becker , MIRALab, University of Geneva, Battelle, Building A, 7 route de Drize, Carouge, Geneva, Switzerland
Nadia Magnenat-Thalmann , MIRALab, University of Geneva, Battelle, Building A, 7 route de Drize, Carouge, Geneva, Switzerland
pp. 290-299

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

Daniel Veltri , School of Systems Biology, George Mason University, Fairfax, VA
Uday Kamath , OntoLabs, 20929 Ivymount Terrace, Ashburn, VA
Amarda Shehu , Department of Computer Science, George Mason University, Fairfax, VA
pp. 300-313

Guest Editors Introduction to the Special Section on ISBRA 2014 (HTML)

Mitra Basu , Computer & Information Science & Engineering Directorate, National Science Foundation, 4201 Wilson Blvd, Arlington, VA
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, GA
Jianxin Wang , School of Information Science and Engineering, Central South University, Changsha, China
pp. 314-315

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

Fa Zhang , Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
Yu Chen , Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
Fei Ren , Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
Xuan Wang , Yanshan University, Qinhuangdao, China
Zhiyong Liu , State Key Laboratory for Computer Architecture Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
Xiaohua Wan , Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
pp. 316-325

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

Yi Liu , Department of Computer Science, The University of Western Ontario, London
Bin Ma , David R. Cheriton School of Computer Science, University of Waterloo, Waterloo
Kaizhong Zhang , Department of Computer Science, The University of Western Ontario, London
Gilles Lajoie , Department of Biochemistry, The University of Western Ontario, London
pp. 326-336

NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra (Abstract)

Yan Yan , Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
Anthony J. Kusalik , Division of Biomedical Engineering and the Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
Fang-Xiang Wu , Division of Biomedical Engineering and the Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
pp. 337-344

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

Lin Zhu , Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Caoan Road 4800, Shanghai, China
Su-Ping Deng , Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Caoan Road 4800, Shanghai, China
Zhu-Hong You , College of Computer Sciences and Software Engineering, Shenzhen University, Shenzhen, Guangzhou, China
De-Shuang Huang , Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Caoan Road 4800, Shanghai, China
pp. 345-352

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

Xingpeng Jiang , Central China Normal University, Wuhan, Hubei, China
Xiaohua Hu , Drexel University, Philadelphia, PA
Weiwei Xu , Wuhan University, Wuhan, Hubei, China
pp. 353-359

Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks (Abstract)

Wei Peng , School of Information Science and Engineering, Central South University, Changsha, P. R. China
Min Li , School of Information Science and Engineering, Central South University, Changsha, P. R. China
Lu Chen , School of Information Science and Engineering, Central South University, Changsha, P. R. China
Lusheng Wang , Department of Computer Science, City University of Hong Kong, Kowloon
pp. 360-369

United Complex Centrality for Identification of Essential Proteins from PPI Networks (Abstract)

Min Li , School of Information Science and Engineering, Central South University, Changsha, China
Yu Lu , School of Information Science and Engineering, Central South University, Changsha, China
Zhibei Niu , School of Information Science and Engineering, Central South University, Changsha, China
Fang-Xiang Wu , Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
pp. 370-380

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits (Abstract)

Behrang Mahjani , Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden
Salman Toor , Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden
Carl Nettelblad , Science for Life Laboratory, Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden
Sverker Holmgren , Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden
pp. 381-392

A New Scheme to Characterize and Identify Protein Ubiquitination Sites (Abstract)

Van-Nui Nguyen , Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, Taiwan
Kai-Yao Huang , Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, Taiwan
Chien-Hsun Huang , Department of Computer Science and EngineeringYuan Ze University
K. Robert Lai , Department of Computer Science and EngineeringYuan Ze University
Tzong-Yi Lee , Department of Computer Science and EngineeringYuan Ze University
pp. 393-403

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

Julia Matsieva , Department of Computer Science, University of California at Davis, Davis, CA
Steven Kelk , Department of Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
Celine Scornavacca , Institut des Sciences de l'Evolution de Montpellier (ISE-M), Montpellier, France
Chris Whidden , Fred Hutchinson Cancer Research Center, Seattle, WA
Dan Gusfield , Department of Computer Science, University of California at Davis, Davis, CA
pp. 404-417

Algorithms and Complexity Results for Genome Mapping Problems (Abstract)

Ashok Rajaraman , Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
Joao Paulo Pereira Zanetti , Institute of Computing, Unicamp, Campinas SP, Brazil
Jan Manuch , Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
Cedric Chauve , Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
pp. 418-430

Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models (HTML)

Kieran Alden , York Computational Immunology Lab, the Centre for Immunology and Infection at the Department of Biology and Hull York Medical School, Department of Electronics, University of York, Heslington, York, United Kingdom
Jon Timmis , York Computational Immunology Lab and Department of Electronics, University of York, Heslington, York, United Kingdom
Paul S. Andrews , York Computational Immunology Lab and Department of Electronics, University of York, Heslington, York, United Kingdom
Henrique Veiga-Fernandes , Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisboa, Portugal
Mark Coles , York Computational Immunology Lab, the Centre for Immunology and Infection at the Department of Biology and Hull York Medical School, University of York, Heslington, York, United Kingdom
pp. 431-442

Genome-Wide Semi-Automated Annotation of Transporter Systems (Abstract)

Oscar Dias , Centre of Biological Enginnering, University of Minho, Campus de Gualtar, Braga, Portugal
Daniel Gomes , Centre of Biological Enginnering, University of Minho, Campus de Gualtar, Braga, Portugal
Paulo Vilaca , SilicoLife Lda., Rua do Canastreiro 15, Braga, Portugal
Joao Cardoso , SilicoLife Lda., Rua do Canastreiro 15, Braga, Portugal
Miguel Rocha , Centre of Biological Enginnering, University of Minho, Campus de Gualtar, Braga, Portugal
Eugenio C. Ferreira , Centre of Biological Enginnering, University of Minho, Campus de Gualtar, Braga, Portugal
Isabel Rocha , Centre of Biological Enginnering, University of Minho, Campus de Gualtar, Braga, Portugal
pp. 443-456

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

Katya Mkrtchyan , Department of Computer Science and Engineering, University of California at Riverside, Riverside, CA
Anirban Chakraborty , Department of Electrical and Computer Engineering, University of California at Riverside, Riverside, CA
Amit K. Roy-Chowdhury , Department of Electrical and Computer Engineering, University of California at Riverside, Riverside, CA
pp. 457-467

A Characterization of Minimum Spanning Tree-Like Metric Spaces (HTML)

Momoko Hayamizu , Department of Statistical Science, SOKENDAI (The Graduate University for Advanced Studies), Tokyo, Japan
Hiroshi Endo , Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
Kenji Fukumizu , Institute of Statistical Mathematics, Tokyo, Japan
pp. 468-471

A Linear Bound on the Number of States in Optimal Convex Characters for Maximum Parsimony Distance (Abstract)

Olivier Boes , Deparment of Knowledge Engineering, Maastricht University, P.O. Box 616, Maastricht, MD, The Netherlands
Mareike Fischer , Institut für Mathematik und Informatik, Walther-Rathenau-Straße 47, Greifswald, Germany
Steven Kelk , Deparment of Knowledge Engineering, Maastricht University, P.O. Box 616, Maastricht, MD, The Netherlands
pp. 472-477

Building Ancestral Recombination Graphs for Whole Genomes (Abstract)

Thao Thi Phuong Nguyen , Institute of Information Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
Vinh Sy Le , VNU University of Technology and Engineering, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam
Hai Bich Ho , Institute of Information Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
Quang Si Le , School of Pharmacy and Biomedical Sciences, University of Portsmouth, Winston Churchill Avenue Portsmouth, United Kingdom
pp. 478-483

D-Map: Random Walking on Gene Network Inference Maps Towards differential Avenue Discovery (Abstract)

Emmanouil Athanasiadis , Systems Biology Center, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens, Greece
Marilena Bourdakou , Department of Informatics and Telecommunications, University of Athens, Ilissia, Greece
George Spyrou , Systems Biology Center, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens, Greece
pp. 484-490

Metabolic Flux Analysis in Isotope Labeling Experiments Using the Adjoint Approach (Abstract)

Stephane Mottelet , Department EA4297 TIMR, Sorbonne University, Université de technologie de Compiègne, rue du docteur Schweitzer, Compiègne, France
Gil Gaullier , Department EA2222 LMAC, Sorbonne University, Université de technologie de Compiègne, France
Georges Sadaka , Department CNRS, UMR7352 LAMFA, Université de Picardie Jules Verne, France
pp. 491-497

Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices (Abstract)

Scott Goldweber , Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC
Jamal Theodore , Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC
John Torcivia-Rodriguez , The Institute for Biomedical Sciences, George Washington University Medical Center, Washington, DC
Vahan Simonyan , Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue Northeast, Silver Spring, MD
Raja Mazumder , Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC
pp. 498-500
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