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2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) (2014)
Miami, FL, USA
June 2, 2014 to June 4, 2014
ISBN: 978-1-4799-5786-6
TABLE OF CONTENTS

[Title page] (PDF)

pp. 1

Characterization of probabilistic signaling networks through signal propagation (Abstract)

Haitham Gabr , Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA
Tamer Kahveci , Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA
pp. 1-2

An integrated model of human Biomedical and Clinical Data structures (Abstract)

Egidijus Paliulis , Department of Information Technology, Šiauliai University, 76353, Lithuania
Hesham H. Ali , College of Information Science and Technology, University of Nebraska at Omaha, 68182, USA
pp. 1-6

A new multi-level thresholding algorithm for finding peaks in ChIP-Seq data (Abstract)

Iman Rezaeian , School of Computer Science, University of Windsor, Canada
Luis Rueda , School of Computer Science, University of Windsor, Canada
pp. 1-6

Breast cancer subtype identification using machine learning techniques (Abstract)

Forough Firoozbakht , School of Computer Science, University of Windsor, Canada
Iman Rezaeian , School of Computer Science, University of Windsor, Canada
Lisa Porter , Department of Biological Sciences, University of Windsor, Canada
Luis Rueda , School of Computer Science, University of Windsor, Canada
pp. 1-2

A weighted classification model for peptide identification (Abstract)

Xijun Liang , College of Science, China University of Petroleum, Qingdao, China 266555
Zhonghang Xia , Department of Computer Science, Western Kentucky University, Bowling Green, 42101, USA
Xinnan Niu , Dept. of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Andrew Link , Dept. of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
pp. 1-2

Putting humpty-dumpty together: Mining causal mechanistic biochemical models from big data (Abstract)

Faraz Hussain , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
Alvaro Velasquez , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
Emily Sassano , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
Sumit Kumar Jha , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
pp. 1-6

Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling (Abstract)

David Sankoff , Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, ON, Canada, K1N 6N5
Baoyong Wang , Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, ON, Canada, K1N 6N5
Chunfang Zheng , Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, ON, Canada, K1N 6N5
Carlos Fernando Buen Abad Najar , Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Distrito Federal, México
pp. 1-2

How genome complexity can explain the hardness of aligning reads to genomes (Abstract)

Vinhthuy Phan , Department of Computer Science, the University of Memphis, Tennessee 38152, USA
Shanshan Gao , Department of Computer Science, the University of Memphis, Tennessee 38152, USA
Quang Tran , Department of Computer Science, the University of Memphis, Tennessee 38152, USA
Nam S. Vo , Department of Computer Science, the University of Memphis, Tennessee 38152, USA
pp. 1-2

SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction (Abstract)

Nataliya Timoshevskaya , Department of Computer Science, Virginia Tech, Blacksburg, USA
Wu-chun Feng , Department of Computer Science, Virginia Tech, Blacksburg, USA
pp. 1-6

Comparison of data discretization methods for cross platform transfer of gene-expression based tumor subtyping classifier (Abstract)

Segun Jung , Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
Yingtao Bi , Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
Ramana V. Davuluri , Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
pp. 1-2

In search of perfect reads (Abstract)

Soumitra Pal , Dept. of Comput. Sci. & Eng., Indian Inst. of Technol. Bombay, Mumbai, India
Srinivas Aluru , Sch. of Comput. Sci. & Eng., Georgia Inst. of Technol., Atlanta, GA, USA
pp. 1-2

Improving bisulfite short-read mapping efficiency with hairpin-bisulfite data (Abstract)

Jacob Porter , Computer Science, Virginia Tech, Blacksburg, USA
Ming-an Sun , Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, USA
Hehuang Xie , Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, USA
Liqing Zhang , Computer Science, Virginia Tech, Blacksburg, USA
pp. 1-2

Optimization of IMRT treatment plan with Kinetic Data Structures (Abstract)

David Allen , The University of Texas at Dallas, Richardson, USA
Ovidiu Daescu , The University of Texas at Dallas, Richardson, USA
pp. 1-6

A systems biology analysis for the whole genome sequencing data (Abstract)

Deepali Jhamb , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Meeta P. Pradhan , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Akshay Desai , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Mathew J. Palakal , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Premkumar Duraiswamy , Department of Computer Science and Engineering, Indiana University Purdue University Indianapolis, USA 46202
pp. 1-6

Identification of protein interaction methods from biomedical literature (Abstract)

Deepali Jhamb , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Anand Krishnan , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Meelia Palakal , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Yogesh Pandit , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Mathew J. Palakal , School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA 46202
Premkumar Duraiswamy , Department of Computer Science and Engineering, Indiana University Purdue University Indianapolis, USA 46202
pp. 1-6

EpiSpec: A formal specification language for parameterized agent-based models against epidemiological ground truth (Abstract)

Faraz Hussain , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, 32816, USA
Arvind Ramanathan , Computational Analytics Group, Oak Ridge National Lab, TN 37830, USA
Laura L. Pullum , Computational Analytics Group, Oak Ridge National Lab, TN 37830, USA
Sumit K. Jha , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, 32816, USA
pp. 1-6

Parameter discovery for stochastic computational models in systems biology using Bayesian model checking (Abstract)

Faraz Hussain , Dept. of Electrical Engineering and Computer Science, University of Central Florida, USA
Christopher J. Langmead , School of Computer Science, Carnegie Mellon University, USA
Qi Mi , Dept. of Sports Medicine and Nutrition, University of Pittsburgh, USA
Joyeeta Dutta-Moscato , Dept. of Biomedical Informatics, University of Pittsburgh, USA
Yoram Vodovotz , Dept. of Surgery and McGowan Institute of Regenerative Medicine, University of Pittsburgh, USA
Sumit K. Jha , Dept. of Electrical Engineering and Computer Science, University of Central Florida, USA
pp. 1-2

A computational method for drug repositioning using publicly available gene expression data (Abstract)

K M Shabana , Department of Computer Science and Engineering, National Institute of Technology, Calicut, India
K A Abdul Nazeer , Department of Computer Science and Engineering, National Institute of Technology, Calicut, India
Meeta Pradhan , IU School of Informatics and Computing, Indiana University Purdue, University Indianapolis, US
Mathew J Palakal , IU School of Informatics and Computing, Indiana University Purdue, University Indianapolis, US
pp. 1-2

Constructing regulatory gene set networks to reveal novel insights into biological systems (Abstract)

Chayaporn Suphavilai , Purdue University School of Science Department of Computer & Information Science, Indianapolis, IN, USA
Liugen Zhu , Indiana University School of Informatics and Computing, Indianapolis, USA
Jake Y. Chen , Purdue University School of Science Department of Computer & Information Science, Indianapolis, IN, USA
pp. 1-2

Multi-scale modeling of microvascular reactivity (Abstract)

Jaimit Parikh , Department of Biomedical Engineering at Florida International University, Miami, 33174 USA
Adam Kapela , Department of Biomedical Engineering at Florida International University, Miami, 33174 USA
Daniel Rodriguez , Department of Biomedical Engineering at Florida International University, Miami, 33174 USA
Nikolaos Tsoukias , Department of Biomedical Engineering at Florida International University, Miami, 33174 USA
pp. 1-2

Poster: Context-sensitive use of bioinformatics tools with complementary functionalities for hypothesis generation (Abstract)

Vida Abedi , Department of Electrical and Computer Engineering, University of Memphis, TN, 38152, USA
Mohammed Yeasin , Department of Electrical and Computer Engineering, University of Memphis, TN, 38152, USA
Ramin Zand , Department of Neurology, University of Tennessee Health Science Center, Memphis, 38163, USA
pp. 1-2

Poster: Efficient record linkage techniques (Abstract)

Abdullah-Al Mamun , Department of Computer Science and Engineering, University of Connecticut, Storrs, 06269-2155, USA
Robert Aseltine , Institute for Public Health Research, University of Connecticut, East Hartford, USA
Sanguthevar Rajasekaran , Department of Computer Science and Engineering, University of Connecticut, Storrs, 06269-2155, USA
pp. 1

Viral quasispecies assembly from paired-end reads (Abstract)

Armin Topfer , Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
Niko Beerenwinkel , Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
pp. 1

VGA: A method for viral quasispecies assembly from ultra-deep sequencing data (Abstract)

Serghei Mangul , Computer Science Department, University of California, Los Angeles, 90095, USA
Nicholas C. Wu , Department of Molecular and Medical Pharmacology, University of California, Los Angeles, 90095, USA
Nicholas Mancuso , Department of Computer Science, Georgia State University, Atlanta, 30303, USA
Alex Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, 30303, USA
Ren Sun , Department of Molecular and Medical Pharmacology, University of California, Los Angeles, 90095, USA
Eleazar Eskin , Computer Science Department, University of California, Los Angeles, 90095, USA
pp. 1

Oak Ridge Biosurveillance Toolkit: Scalable machine learning for public health surveillance (Abstract)

Laura L. Pullum , Computational Science and Engineering Division, Oak Ridge National Laboratory, USA
Arvind Ramanathan , Computational Science and Engineering Division, Oak Ridge National Laboratory, USA
pp. 1

Identifying representative drug resistant mutants of HIV reverse transcriptase (Abstract)

Xiaxia Yu , Department of Computer Science, Georgia State University, Atlanta, USA
Robert W. Harrison , Department of Computer Science, Georgia State University, Atlanta, USA
Irene T. Weber , Department of Biology, Georgia State University, Atlanta, USA
pp. 1

Reconstruction of influenza a virus variants from PacBio reads (Abstract)

Alexander Artyomenko , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
Serghei Mangul , Computer Science Department, University of California, Los Angeles, 90095, USA
Nicholas C. Wu , Molecular and Medical Pharmacology, University of California, Los Angeles, 90095, USA
Eleazar Eskin , Computer Science Department, University of California, Los Angeles, 90095, USA
Ren Sun , Molecular and Medical Pharmacology, University of California, Los Angeles, 90095, USA
Alex Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
pp. 1

Modeling genetic heterogeneity in Hepatitis C Virus hyper-variable region 1 infers demographic characteristics of infected hosts (Abstract)

James Lara , Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA
Yury Kudhyakov , Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA
pp. 1

New computational methods for assessing the genetic relatedness of close viral variants (Abstract)

David S. Campo , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
Zoya Dimitrova , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
Guo-Liang Xia , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
Pavel Skums , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
Lilia Ganova-Raeva , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
Yury Khudyakov , Molecular Epidemiology and Bioinformatics Laboratory, Centers for Disease Control and Prevention, Atlanta, United States
pp. 1

Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data (Abstract)

Pavel Skums , Centers of Disease Control and Prevention, Atlanta, GA, USA
Alexander Artyomenko , Georgia State University, Atlanta, 30303, USA
Olga Glebova , Georgia State University, Atlanta, 30303, USA
Alex Zelikovsky , Georgia State University, Atlanta, 30303, USA
David S. Campo , Centers of Disease Control and Prevention, Atlanta, GA, USA
Zoya Dimitrova , Centers of Disease Control and Prevention, Atlanta, GA, USA
Yury Khudyakov , Centers of Disease Control and Prevention, Atlanta, GA, USA
pp. 1

Role of ADAR in determining the substitution pattern in sigma virus (Rhabdoviridae) in Drosophila melanogaster (Abstract)

Helen Piontkivska , Department of Biological Sciences, Kent State University, OH 44242 USA
Sinu Paul , La Jolla Institute for Allergy & Immunology, USA
Brian Scharfenberg , Ohio University, USA
Marta Wayne , Department of Biology, University of Florida, Gainesville, 32611, USA
Luis F. Matos , Eastern Washington University, USA
William G. Farmerie , Department of Biology, University of Florida, Gainesville, 32611, USA
Michael M Miyamoto , Department of Biology, University of Florida, Gainesville, 32611, USA
pp. 1

SILP3: Maximum likelihood approach to scaffolding (Abstract)

Igor Mandric , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
James Lindsay , Computer Science and Engineering Department, University of Connecticut, Storrs, 06269, USA
Alex Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
pp. 1

Efficient algorithms for error correction and compression of NGS data (Abstract)

Subrata Saha , Department of CSE, University of Connecticut, Storrs, USA
Sanguthevar Rajasekaran , Department of CSE, University of Connecticut, Storrs, USA
pp. 1

Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data (Abstract)

Shuhua Fu , Department of Biochemistry & Biophysics, Texas A&M University, College Station, 77843, USA
Aaron M. Tarone , Department of Entomology, Texas A&M University, College Station, 77843, USA
Sing-Hoi Sze , Department of Computer Science and Engineering, Department of Biochemistry & Biophysics, Texas A&M University, College Station, 77843, USA
pp. 1

An SVM-based approach for discovering splicing junctions with RNA-Seq (Abstract)

Chong Chu , Computer Science and Engineering, University of Connecticut, Storrs, 06269, USA
Yufeng Wu , Computer Science and Engineering, University of Connecticut, Storrs, 06269, USA
pp. 1

Reference-free inference of tumor phylogenies from single-cell sequencing data (Abstract)

Ayshwarya Subramanian , Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA USA
Russell Schwartz , Department of Biological Sciences, Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA USA
pp. 1

A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types (Abstract)

Hsin-Ta Wu , Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, USA
Iman Hajirasouliha , Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, USA
Benjamin J. Raphael , Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, USA
pp. 1

Deterministic regression algorithm for transcriptome frequency estimation (Abstract)

Adrian Caciula , Georgia State University, Atlanta, 30303, USA
Olga Glebova , Georgia State University, Atlanta, 30303, USA
Alexander Artyomenko , Georgia State University, Atlanta, 30303, USA
Serghei Mangul , University of California, Los Angeles, 90095, USA
James Lindsay , University of Connecticut, Storrs, 06269, USA
Ion I. Mandoiu , University of Connecticut, Storrs, 06269, USA
Alex Zelikovsky , Georgia State University, Atlanta, 30303, USA
pp. 1
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