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TABLE OF CONTENTS
Issue No. 06 - Nov.-Dec. (vol. 11)
ISSN: 1545-5963

Table of Contents (PDF)

pp. C1

Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012) (Abstract)

Yufei Huang , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX 78249
Yidong Chen , Department of Epidemiology & Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
Xiaoning Qian , Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 78743
pp. 981-983

Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data (Abstract)

Karl B. Gregory , Department of Statistics, Texas A&M University, College Station, TX
Amin A. Momin , Department of Clinical Cancer Prevention, the University of Texas MD Anderson Cancer Center, Houston, TX
Kevin R. Coombes , Department of Biomedical Informatics, the Ohio State University Wexner Medical Center, Columbus, OH
Veerabhadran Baladandayuthapani , Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX
pp. 984-994

An Integrated Approach to Anti-Cancer Drug Sensitivity Prediction (Abstract)

Noah Berlow , Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX
Saad Haider , Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX
Qian Wan , Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX
Mathew Geltzeiler , Department of Pediatrics, Oregon Health & Science University, Portland, OR
Lara E. Davis , Department of Pediatrics, Oregon Health & Science University, Portland, OR
Charles Keller , Department of Pediatrics, Oregon Health & Science University, Portland, OR
Ranadip Pal , Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX
pp. 995-1008

Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses (Abstract)

Ye Tian , Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA
Sean S. Wang , Department of Electrical and Computer Engineering, University of Maryland, College Park, MD
Zhen Zhang , Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
Olga C. Rodriguez , Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
Emanuel Petricoin III , Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
Ie-Ming Shih , Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
Daniel Chan , Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
Maria Avantaggiati , Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
Guoqiang Yu , Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA
Shaozhen Ye , College of Mathematics and Computer Science, Fuzhou University, Fuzhou, P.R., China
Robert Clarke , Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
Chao Wang , Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL
Bai Zhang , Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
Yue Wang , Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA
Chris Albanese , Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
pp. 1009-1019

Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis (Abstract)

Meng Lu , Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX
Hye-Seung Lee , Department of Pediatrics, College of Medicine, University of South Florida, Tampa, FL
David Hadley , Department of Pediatrics, College of Medicine, University of South Florida, Tampa, FL
Jianhua Z. Huang , Department of Statistics, Texas A&M University, College Station, TX
Xiaoning Qian , Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX
pp. 1020-1028

Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers (Abstract)

Seyed Javad Sajjadi , Department of Industrial and Management Systems Engineering, University of South Florida, Tampa
Xiaoning Qian , Department of Electrical & Computer Engineering, Texas A&M University, College Station
Bo Zeng , Department of Industrial and Management Systems Engineering, University of South Florida, Tampa
Amin Ahmadi Adl , Department of Computer Science and Engineering, University of South Florida, Tampa
pp. 1029-1037

BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data (Abstract)

Yanxun Xu , Division of Statistics and Scientific Computing, the University of Texas at Austin, Austin, TX
Xiaofeng Zheng , University of Texas MD Anderson Cancer Center, Houston, TX
Yuan Yuan , Baylor College of Medicine, Houston, TX
Marcos R Estecio , University of Texas MD Anderson Cancer Center, Houston, TX
Jean-Pierre Issa , , Temple University, Philadelphia, PA
Peng Qiu , , Georgia Institute of Technology and Emory University, Atlanta, GA
Yuan Ji , , University of Chicago, Chicago, IL
Shoudan Liang , University of Texas MD Anderson Cancer Center, Houston, TX
pp. 1038-1044

Unfold High-Dimensional Clouds for Exhaustive Gating of Flow Cytometry Data (Abstract)

Peng Qiu , Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA
pp. 1045-1051

A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice (Abstract)

Maina Bitar , Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte CEP, Minas Gerais, Brazil
Gloria Regina Franco , Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte CEP, Minas Gerais, Brazil
pp. 1052-1065

A Parameter Estimation Method for Biological Systems modelled by ODE/DDE Models Using Spline Approximation and Differential Evolution Algorithm (Abstract)

Choujun Zhan , Department of Electronics Communication and Software Engineering, Nanfang College of Sun Yat-Sen University, China
Wuchao Situ , Department of Electronic Engineering, City University of Hong Kong, Hong Kong, China
Lam Fat Yeung , Department of Electronic Engineering, City University of Hong Kong, Hong Kong, China
Peter Wai-Ming Tsang , Department of Electronic Engineering, City University of Hong Kong, Hong Kong, China
Genke Yang , Department of Automation, Shanghai Jiao Tong University
pp. 1066-1076

An Efficient and Very Accurate Method for Calculating Steady-State Sensitivities in Metabolic Reaction Systems (Abstract)

Fumihide Shiraishi , Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1, Hakozaki, Higashi-Ku, Fukuoka, Japan
Erika Yoshida , Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1, Hakozaki, Higashi-Ku, Fukuoka, Japan
Eberhard O. Voit , Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Suite 4103, Atlanta, GA
pp. 1077-1086

Computing Elementary Flux Modes Involving a Set of Target Reactions (Abstract)

Laszlo David , Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
Alexander Bockmayr , Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
pp. 1099-1107

Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures (Abstract)

Ahsan Z. Rizvi , Indian Institute of Technology, Indore, India
C. Bhattacharya , Department of Electronics Engineering, Defence Institute of Advanced Technology, Pune, India
pp. 1108-1118

Determining Semantically Related Significant Genes (Abstract)

Kamal Taha , Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE
pp. 1119-1130

GECC: Gene Expression Based Ensemble Classification of Colon Samples (Abstract)

Saima Rathore , Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
Mutawarra Hussain , Department of Computer Science and Information Technology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
Asifullah Khan , Department of Computer Science and Information Technology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
pp. 1131-1145

Gene Selection Using Locality Sensitive Laplacian Score (Abstract)

Bo Liao , Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha, Hunan, China
Yan Jiang , Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha, Hunan, China
Wei Liang , School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, Hunan, China
Wen Zhu , Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha, Hunan, China
Lijun Cai , Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha, Hunan, China
Zhi Cao , Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha, Hunan, China
pp. 1146-1156

Identification of Functionally Related Enzymes by Learning-to-Rank Methods (Abstract)

Michiel Stock , Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Ghent, Belgium
Thomas Fober , Department of Mathematics and Computer Science, Philipps-Universität of Marburg, Hans-Meerwein-Straße 6, D-35032 Marburg, Germany
Eyke Hullermeier , Department of Mathematics and Computer Science, Philipps-Universität of Marburg, Hans-Meerwein-Straße 6, D-35032 Marburg, Germany
Serghei Glinca , Department of Pharmacy, Philipps-Universität of Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany
Gerhard Klebe , Department of Pharmacy, Philipps-Universität of Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany
Tapio Pahikkala , Department of Information Technology and the Turku Centre for Computer Science, University of Turku, Joukahaisenkatu 3-5 B, 20520 Turku, Finland
Antti Airola , Department of Information Technology and the Turku Centre for Computer Science, University of Turku, Joukahaisenkatu 3-5 B, 20520 Turku, Finland
Bernard De Baets , Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Ghent, Belgium
Willem Waegeman , Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Ghent, Belgium
pp. 1157-1169

Identifying Non-Redundant Gene Markers from Microarray Data: A Multiobjective Variable Length PSO-Based Approach (Abstract)

Anirban Mukhopadhyay , Department of Computer Science and Engineering, University of Kalyani, Kalyani-741235, West Bengal, India
Monalisa Mandal , Department of Computer Science and Engineering, University of Kalyani, Kalyani-741235, West Bengal, India
pp. 1170-1183

Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case (Abstract)

Yoram Zarai , School of Electrical Engineering, Tel-Aviv University, Tel-Aviv, Israel
Michael Margaliot , School of Electrical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
Tamir Tuller , Department of Biomedical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
pp. 1184-1195

Molecular Modeling and Evaluation of Novel Dibenzopyrrole Derivatives as Telomerase Inhibitors and Potential Drug for Cancer Therapy (Abstract)

Umesh Kalathiya , Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza, Gdansk, Poland
Monikaben Padariya , Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza, Gdansk, Poland
Maciej Baginski , Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza, Gdansk, Poland
pp. 1196-1207

Nonparametric Tikhonov Regularized NMF and Its Application in Cancer Clustering (Abstract)

Andri Mirzal , Computer Science Department, College of Arts and Applied Sciences, Dhofar University, Salalah, Oman
pp. 1208-1217

On Representing Protein Folding Patterns Using Non-Linear Parametric Curves (Abstract)

Parthan Kasarapu , Clayton School of Information Technology, Monash University, VIC, Australia
Maria Garcia de la Banda , Clayton School of Information Technology, Monash University, VIC, Australia
Arun S. Konagurthu , Clayton School of Information Technology, Monash University, VIC, Australia
pp. 1218-1228

On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees (Abstract)

Filippo Disanto , Department of Biology, Stanford University, Stanford, CA
Noah A. Rosenberg , Department of Biology, Stanford University, Stanford, CA
pp. 1229-1238

Shifting-and-Scaling Correlation Based Biclustering Algorithm (Abstract)

Hasin Afzal Ahmed , Department of Computer Science and Engineering, Tezpur University, Assam, India
Priyakshi Mahanta , Department of Computer Science and Engineering, Tezpur University, Assam, India
Dhruba Kumar Bhattacharyya , Department of Computer Science and Engineering, Tezpur University, Assam, India
Jugal Kumar Kalita , Department of Computer Science, University of Colorado, Colorado Springs, CO
pp. 1239-1252

ILP/SMT-Based Method for Design of Boolean Networks Based on Singleton Attractors (Abstract)

Koichi Kobayashi , School of Information Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
Kunihiko Hiraishi , School of Information Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
pp. 1253-1259

Improving Detection of Driver Genes: Power-Law Null Model of Copy Number Variation in Cancer (Abstract)

Loes Olde Loohuis , Center for Neurobehavioral Genetics, University of California Los Angeles, CA, USA
Andreas Witzel , , Google Inc, 76 Ninth Avenue, New York, NY
Bud Mishra , NYU Courant Institute, New York, NY, USA
pp. 1260-1263

Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle (Abstract)

Haiying Wang , Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, Jordanstown Campus, Shore Road, Newtownabbey, United Kingdom
Huiru Zheng , Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, Jordanstown Campus, Shore Road, Newtownabbey, United Kingdom
pp. 1264-1270

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