The Community for Technology Leaders
2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) (2012)
Las Vegas, NV, USA
Feb. 23, 2012 to Feb. 25, 2012
ISBN: 978-1-4673-1320-9
TABLE OF CONTENTS
Papers

Keynote: De novo sequencing of novel peptide antibiotics by tandem mass spectrometry (Abstract)

Pavel Pevzner , Computer Science and Engineering, University of California at San Diego, USA
pp. 1

Keynote: Aspects of fractionation (Abstract)

David Sankoff , Department of Mathematics and Statistics, University of Ottawa, Canada
pp. 1

Invited: Reverse engineering whole-genome networks (Abstract)

Srinivas Aluru , Dept. of Electrical and Computer Engineering, Bioinformatics and Computational Biology Program, Iowa State University, Ames, USA
pp. 1

Invited: Computational behavioral ecology (Abstract)

Tanya Berger-Wolf , Department of Computer Science, University of Illinois at Chicago, USA
pp. 1

Invited: Identifying mutations from TILLING experiments (Abstract)

Vladimir Filkov , Department of Computer Science, UC Davis, CA, USA
pp. 1

Invited: Algorithmic challenges in DNA sequencing and disease association (Abstract)

Bjarni V. Halldorsson , School of Science and Engineering, Reykjavík University, Iceland
pp. 1

Invited: A protein domain-centric approach to translational bioinformatics (Abstract)

Maricel G. Kann , Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, USA
pp. 1

Invited: Discovering combinatorial biomarkers (Abstract)

Gowtham Atluri , Department of Computer Science, University of Minnesota, Minneapolis, USA
Vipin Kumar , Department of Computer Science, University of Minnesota, Minneapolis, USA
Vanja Paunic , Department of Computer Science, University of Minnesota, Minneapolis, USA
Sean Landman , Department of Computer Science, University of Minnesota, Minneapolis, USA
Gang Fang , Department of Computer Science, University of Minnesota, Minneapolis, USA
Wen Wang , Department of Computer Science, University of Minnesota, Minneapolis, USA
Sanjoy Dey , Department of Computer Science, University of Minnesota, Minneapolis, USA
Michael Steinbach , Department of Computer Science, University of Minnesota, Minneapolis, USA
pp. 1-2

Invited: From protein networks to disease mechanisms (Abstract)

Roded Sharan , Blavatnik School of Computer Science, Tel Aviv University, Israel
pp. 1

Invited: Using novel small RNAs to understand genome structure and function (Abstract)

Sarah Trusiak , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Judy Brown , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Laura Hall , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Craig Obergfell , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Mark Longo , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Rachel O'Neill , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
Chu Zhang , Dept of Molecular and Cellular Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, 06269 USA
pp. 1

Effects of rooting via outgroups on ingroup topology in phylogeny (Abstract)

Dan Brown , Cheriton School of Computer Science, University of Waterloo, Canada
David Loker , Cheriton School of Computer Science, University of Waterloo, Canada
Margareta Ackerman , Cheriton School of Computer Science, University of Waterloo, Canada
pp. 1-7

PMS6: A fast algorithm for motif discovery (Abstract)

Sartaj Sahni , Department of CISE, University of Florida, Gainesville, 32611, USA
Shibdas Bandyopadhyay , Department of CISE, University of Florida, Gainesville, 32611, USA
Sanguthevar Rajasekaran , Department of CSE, University of Connecticut, Storrs, 06269, USA
pp. 1-6

Accelerating gene regulatory networks inference through GPU/CUDA programming (Abstract)

Raphael Y. Camargo , Universidade Federal do ABC, Santo André-SP, Brazil
Beatriz Stransky , Universidade Federal do ABC, Santo André-SP, Brazil
Luiz C. S. Rozante , Universidade Federal do ABC, Santo André-SP, Brazil
Fabrizio F. Borelli , Universidade Federal do ABC, Santo André-SP, Brazil
David C. Martins , Universidade Federal do ABC, Santo André-SP, Brazil
pp. 1-6

A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma (Abstract)

Tsz-Kwong Man , Texas Children's Cancer Center, Baylor College of Medicine, Houston, USA 77030
Stephen T.-C. Wong , Dept. Sys. Med. and Bioeng. (SMAB), The Methodist Hospital Research Institute, Houston, USA 77030
Peikai Chen , Department of Electrical, and Electronic Engineering, The University of Hong Kong, China
Y. S. Hung , Department of Electrical, and Electronic Engineering, The University of Hong Kong, China
Ching C. Lau , Texas Children's Cancer Center, Baylor College of Medicine, Houston, USA 77030
Yubo Fan , Dept. Sys. Med. and Bioeng. (SMAB), The Methodist Hospital Research Institute, Houston, USA 77030
pp. 1-6

Volume matching with application in medical treatment planning (Abstract)

Steven Kirtzic , Department of Computer Science, The University of Texas at Dallas, Richardson, USA
Lech Papiez , Graduate School of Biomedical Sciences, The University of Texas Southwestern Medical Center at Dallas, USA
Ovidiu Daescu , Department of Computer Science, The University of Texas at Dallas, Richardson, USA
Yam Ki Cheung , Department of Computer Science, The University of Texas at Dallas, Richardson, USA
pp. 1-6

Periodic rigidity of protein crystal structures (Abstract)

Filip Jagodzinski , Department of Computer Science, University of Massachusetts, Amherst, 01003, USA
Jessica Grant , Dept. of Mathematics, Dept. of Biological Sciences, Dept. of Computer Science, Smith College, Northampton, Massachusetts 01060, USA
Pamela Clark , Dept. of Mathematics, Dept. of Biological Sciences, Dept. of Computer Science, Smith College, Northampton, Massachusetts 01060, USA
Ileana Streinu , Dept. of Mathematics, Dept. of Biological Sciences, Dept. of Computer Science, Smith College, Northampton, Massachusetts 01060, USA
Samantha Monastra , Dept. of Mathematics, Dept. of Biological Sciences, Dept. of Computer Science, Smith College, Northampton, Massachusetts 01060, USA
pp. 1-6

Towards accurate modeling for protein rigidity analysis (Abstract)

Naomi Fox , Department of Computer Science, University of Massachusetts, Amherst, USA
Ileana Streinu , Department of Computer Science, Smith College, Northampton, MA, USA
pp. 1-6

Demarcation of bacterial ecotypes from DNA sequence data: A comparative analysis of four algorithms (Abstract)

Danny Krizanc , Department of Mathematics and Computer Science, Wesleyan University, Middletown, Connecticut, USA
Frederick M. Cohan , Department of Biology, Wesleyan University, Middletown, Connecticut, USA
Juan Carlos Francisco , Department of Mathematics and Computer Science, Wesleyan University, Middletown, Connecticut, USA
pp. 1-6

Filtering of MS/MS data for peptide identification (Abstract)

Katelyn Lavrich , Biological Sciences Department, State University of New York at Binghamton, 13850, USA
Patrick H. Madden , Computer Science Department, State University of New York at Binghamton, 13850, USA
Anna Tan-Wilson , Biological Sciences Department, State University of New York at Binghamton, 13850, USA
Jason Gallia , Computer Science Department, State University of New York at Binghamton, 13850, USA
Rachel McGough , Computer Science Department, State University of New York at Binghamton, 13850, USA
pp. 1-6

Decision procedure based discovery of rare behaviors in Stochastic Differential Equation models of biological systems (Abstract)

Sumit K. Jha , EECS Department, University of Central Florida, Orlando, USA
Susmit Jha , EECS Department, UC Berkeley, CA 94709, USA
Arup K. Ghosh , EECS Department, University of Central Florida, Orlando, USA
Christopher J. Langmead , Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
Faraz Hussain , EECS Department, University of Central Florida, Orlando, USA
pp. 1-6

A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support system (Abstract)

Eren Gultepe , Dept. of Biomedical Engineering, University of California - Davis, United States of America
Ilias Tagkopoulos , Computer Science, University of California - Davis, United States of America
Hien Nguyen , Internal Medicine, University of California - Davis, United States of America
Timothy Albertson , Internal Medicine, University of California - Davis, United States of America
pp. 1-5

The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics (Abstract)

Mai Hamdalla , Computer Science and Engineering Department, University of Connecticut, USA
Dennis Hill , Pharmaceutical Sciences Department, University of Connecticut, USA
Sanguthevar Rajasekaran , Computer Science and Engineering Department, University of Connecticut, USA
Reda Ammar , Computer Science and Engineering Department, University of Connecticut, USA
Ion Mandoiu , Computer Science and Engineering Department, University of Connecticut, USA
David Grant , Pharmaceutical Sciences Department, University of Connecticut, USA
pp. 1-6

Hierarchical factor modeling of proteomics data (Abstract)

J. Will Thompson , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
Lawrence Carin , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
Joseph E. Lucas , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
Ricardo Henao , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
M. Arthur Moseley , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
Geoffrey S. Ginsburg , Duke Institute for Genome Science & Policy, Duke University, Durham, USA
pp. 1-6

A robust, library-based, optimization-driven method for automatic gene circuit design (Abstract)

Linh Hunyh , Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA
Ilias Tagkopoulos , Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA
pp. 1-6

Parameter discovery for stochastic biological models against temporal behavioral specifications using an SPRT based Metric for simulated annealing (Abstract)

Christopher James Langmead , Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
Sumit Kumar Jha , Electrical Engineering and Computer Science Department, University of Central Florida, Orlando, USA
Faraz Hussain , Electrical Engineering and Computer Science Department, University of Central Florida, Orlando, USA
Susmit Jha , EECS Department, UC Berkeley, CA, USA
Raj Gautam Dutta , Electrical Engineering and Computer Science Department, University of Central Florida, Orlando, USA
pp. 1-6

Pairwise sequence alignment for very long sequences on GPUs (Abstract)

Sanjay Ranka , Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, USA
Sartaj Sahni , Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, USA
Junjie Li , Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, USA
pp. 1-6

Finding consensus stable local optimal structures for aligned RNA sequences (Abstract)

Shaojie Zhang , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA, 32816-2362
Yuan Li , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA, 32816-2362
pp. 1-6

A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information (Abstract)

Yuri Pirola , DISCo, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Stefano Biffani , CeRSA, Parco Tecnologico Padano, Lodi, Italy
Alessandra Stella , CeRSA, Parco Tecnologico Padano, Lodi, Italy
Gianluca Della Vedova , Dip. Statistica, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Paola Bonizzoni , DISCo, Univ. degli Studi di Milano-Bicocca, Milan, Italy
pp. 1-6

Automatic B cell lymphoma detection using flow cytometry data (Abstract)

Rachel Donohue , Department of Pathology, Methodist Hospital, Houston, TX, USA
Ming-Chih Shih , Department of Computer Science, University of Houston, TX, USA
Youli Zu , Department of Pathology, Methodist Hospital, Houston, TX, USA
Shou-Hsuan Stephen Huang , Department of Computer Science, University of Houston, TX, USA
Chun-Che Jeff Chang , Department of Pathology, University of Central Florida, Orlando, USA
pp. 1-6

The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice (Abstract)

John L. Spouge , Computational Biology Branch, National Center for Biotechnology Information, Bethesda MD 20894 USA
Leonardo Marino-Ramirez , Computational Biology Branch, National Center for Biotechnology Information, Bethesda MD 20894 USA
Sergey L. Sheetlin , Computational Biology Branch, National Center for Biotechnology Information, Bethesda MD 20894 USA
pp. 1-6

Signal extraction from movies of honeybee brain activity by convex analysis. (Abstract)

Julia Rein , Neurobiology, University of Konstanz, 78457 Germany
C. Giovanni Galizia , Neurobiology, University of Konstanz, 78457 Germany
Martin Strauch , Bioinformatics and Information Mining, University of Konstanz, 78457 Germany
pp. 1-6

Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work Queue (Abstract)

Scott Emrich , Department of Computer Science and Engineering, University of Notre Dame, IN, USA
Andrew Thrasher , Department of Computer Science and Engineering, University of Notre Dame, IN, USA
Zachary Musgrave , Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, USA
Douglas Thain , Department of Computer Science and Engineering, University of Notre Dame, IN, USA
pp. 1-6

A machine learning framework for trait based genomics (Abstract)

Dan Liu , Department of Biological Science, University of Notre Dame, South Bend, Indiana 46556, USA
Erliang Zeng , Department of Computer Science and Engineering, University of Notre Dame, South Bend, Indiana 46556, USA
Scott Emrich , Department of Computer Science and Engineering, University of Notre Dame, South Bend, Indiana 46556, USA
Stuart Jones , Department of Biological Science, University of Notre Dame, South Bend, Indiana 46556, USA
Wei Zhang , Department of Computer Science and Engineering, University of Notre Dame, South Bend, Indiana 46556, USA
pp. 1-6

Ancient angiosperm hexaploidy meets ancestral eudicot gene order (Abstract)

Eric Lyons , IPlant, Department of Plant Sciences, University of Arizona, Tucson, USA
David Sankoff , Department of Mathematics and Statistics, University of Ottawa, Canada
Chunfang Zheng , Department of Mathematics and Statistics, University of Ottawa, Canada
Victor A. Albert , Department of Biology, University at Buffalo, New York, USA
pp. 1-6

Discovering non-coding RNA elements in drosophila 3' untranslated regions (Abstract)

Justen Andrews , Department of Biology, Indiana University, Bloomington, 47405, USA
Shaojie Zhang , Department of EECS, University of Central Florida, Orlando, 32816, USA
Cuncong Zhong , Department of EECS, University of Central Florida, Orlando, 32816, USA
pp. 1-6

Identifying cancer biomarkers by knowledge discovery from medical literature (Abstract)

Reda Alhajj , Department of Computer Science, University of Calgary, Alberta, Canada
Ala Qabaja , Department of Computer Science, University of Calgary, Alberta, Canada
Shang Gao , Department of Computer Science, University of Calgary, Alberta, Canada
Khaled Dawoud , Department of Computer Science, University of Calgary, Alberta, Canada
Jon Rokne , Department of Computer Science, University of Calgary, Alberta, Canada
pp. 1

Poster title (mass spectrometric protein profiling analyses of pathological and physiological hypertrophy cardiac muscle tissues) (Abstract)

Dong-Yu Kim , School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Korea (R.O.K.)
Hyekyeong Kwon , School of Life Sciences, Gwangju Institute of Science and Technology, Korea (R.O.K.)
Jang-Soo Chun , School of Life Sciences, Gwangju Institute of Science and Technology, Korea (R.O.K.)
Zee-Yong Park , School of Life Sciences, Gwangju Institute of Science and Technology, Korea (R.O.K.)
pp. 1

Poster: Accurate scaffolding of large genomes using integer programming and Non-Serial Dynamic Programming (Abstract)

I. Mandoiu , Computer Science & Engineering Dept., University of Connecticut, Storrs, USA
H. Salooti , Computer Science Dept., Georgia State University, Atlanta, USA
J. Lindsay , Computer Science & Engineering Dept., University of Connecticut, Storrs, USA
A. Zelikovsky , Computer Science Dept., Georgia State University, Atlanta, USA
pp. 1

Poster: Randomized algorithms for planted Motif Search (Abstract)

Jerlin C Merlin , Department of Computer Science, University of Connecticut, Storrs, USA
Hieu Dinh , Department of Computer Science, University of Connecticut, Storrs, USA
pp. 1

Poster: Sequence classification of homopolymer emissions (SCOPE) (Abstract)

John E. Karro , Departments of Comp. Sci., Botany, and Statistics, Miami University, Oxford, Ohio, USA
Chun Liang , Departments of Comp. Sci., Botany, and Statistics, Miami University, Oxford, Ohio, USA
James T. Morton , Departments of Comp. Sci., Botany, and Statistics, Miami University, Oxford, Ohio, USA
Patricia Abrudan , Departments of Comp. Sci., Botany, and Statistics, Miami University, Oxford, Ohio, USA
pp. 1

Poster: Applying data mining algorithms to early detection of liver cancer (Abstract)

Fabiola M. R. Pinheiro , School of Health Information Science, University of Victoria, B.C., Canada
Mu-Hsing Kuo , School of Health Information Science, University of Victoria, B.C., Canada
pp. 1

Poster evaluation of the level set method by using similarity criterion (KCC) for clustering and analysis of functional MRI data (Abstract)

Maryam Rahimi , Department of Biomedical Engineering at Tehran University of Medical Sciences, Iran
Mohamadali Oghabiyan , Department of Biomedical Engineering at Tehran University of Medical Sciences, Iran
pp. 1

Poster: Image registration and visualization tool for in-situ gene expression images (Abstract)

Eric Rouchka , Department of Computer Engineering & Computer Science, University of Louisville, KY, USA
Ernur Saka , Department of Computer Engineering & Computer Science, University of Louisville, KY, USA
pp. 1

Poster: Public health applications of metagenomic data using publicly available computing framework (Abstract)

Jesse Port , Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, USA
Elaine Faustman , Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, USA
Marissa Smith , Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, USA
Jame C. Wallace , Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, USA
pp. 1

Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences (Abstract)

Tomoya Tagami , Biosciences and Informatics, Keio University, Yokohama, 223-8522, Japan
Tsuyoshi Hachiya , Biosciences and Informatics, Keio University, Yokohama, 223-8522, Japan
Yasubumi Sakakibara , Biosciences and Informatics, Keio University, Yokohama, 223-8522, Japan
pp. 1

Poster: MIGL - a database for identifying the mechanisms of intron gain and loss (Abstract)

Paul Yenerall , Department of Biological Sciences, University of Pittsburgh, PA 15260, USA
Yuanyuan Jiang , School of Information Sciences, University of Pittsburgh, PA 15260, USA
Leming Zhou , Department of Health Information Management, University of Pittsburgh, PA 15260, USA
pp. 1

Poster: De novo expression fragment assembly from Spanning Trees (EAST) (Abstract)

Jens Mueller , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
Dhananjai Rao , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
Yuan Zhang , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
Mufit Ozden , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
Chun Liang , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
Praveen Raj Kumar , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
John E. Karro , Departments of Comp. Sci., Botany, Tech. Services, and Statistics, Miami University, Oxford, Ohio, USA
pp. 1

Poster: Parameter estimation for a reduced order spiking neuron model with relevance to in vitro embryonic rat motoneuronal data (Abstract)

Aman Behal , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
Zhao Wang , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
Lingfei Zhi , Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, USA
pp. 1

Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination (Abstract)

Italo Zoppis , Department of Informatics, System and Communication, University of Milano Bicocca, Italy
Giancarlo Albo , Department of Specialistic Surgical Sciences, "Ospedale Maggiore Policlinico" Foundation, Milano, Italy
Clizia Chinello , Department of Experimental Medicine, University of Milano Bicocca, Italy
Fulvio Magni , Department of Experimental Medicine, University of Milano Bicocca, Italy
Erica Gianazza , Department of Experimental Medicine, University of Milano Bicocca, Italy
Francesco Rocco , Department of Specialistic Surgical Sciences, "Ospedale Maggiore Policlinico" Foundation, Milano, Italy
Marco Antoniotti , Department of Informatics, System and Communication, University of Milano Bicocca, Italy
Massimiliano Borsani , Department of Informatics, System and Communication, University of Milano Bicocca, Italy
Yuri E. M. van der Burgt , Department of Parasitology, Leiden University Medical Center, The Netherlands
Giancarlo Mauri , Department of Informatics, System and Communication, University of Milano Bicocca, Italy
Andre M. Deelder , Department of Parasitology, Leiden University Medical Center, The Netherlands
pp. 1

Workshop: Robust algorithms for inferring haplotype phase and deletion polymorphism from high-throughput whole genome sequence data (Abstract)

Derek Aguiar , Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
Sorin Istrail , Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
pp. 1

Workshop: Inference of allele specific expression levels from RNA-Seq data (Abstract)

Ion Mandoiu , Computer Science and Engineering, University of Connecticut, Storrs, USA
Sahar Al Seesi , Computer Science and Engineering, University of Connecticut, Storrs, USA
pp. 1

Workshop: Taxonomic clustering of large-scale metagnomic data (Abstract)

Srinivas Aluru , Dept. of Electrical and Computer Engineering, Iowa State University, Ames, USA
pp. 1

Workshop: An efficient data structure for exact-match overlap graphs and next generation sequence assembly (Abstract)

Hieu Dinh , Computer Science and Engineering Department, University of Connecticut, Storrs, 06269, USA
Sanguthevar Rajasekaran , Computer Science and Engineering Department, University of Connecticut, Storrs, 06269, USA
pp. 1

Workshop: Opportunities and challenges of non-model ecoinformatics (Abstract)

Scott Emrich , Department of Computer Science and Engineering, University of Notre Dame, IN, USA
pp. 1

Workshop: Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads (Abstract)

Tao Jiang , Department of Computer Science and Engineering, University of California, Riverside, 92521, USA
Wei Li , Department of Computer Science and Engineering, University of California, Riverside, 92521, USA
pp. 1

Workshop: Comparative assembly of metagenomic sequences (Abstract)

Mihai Pop , Department of Computer Science, Center for Bioinformatics and Computational Biology, UMIACS, University of Maryland, College Park, USA
Bo Liu , Department of Computer Science, Center for Bioinformatics and Computational Biology, UMIACS, University of Maryland, College Park, USA
pp. 1

Workshop: A maximum likelihood method for quasispecies spectrum assembly (Abstract)

Bassam Tork , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
Pavel Skums , Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30322, USA
Alex Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
Ion Mandoiu , Department of Computer Science & Engineering, University of Connecticut, Storrs, 06269, USA
Lilia Ganova-Raeva , Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30322, USA
Nicholas Mancuso , Department of Computer Science, Georgia State University, Atlanta, 30302-3994, USA
pp. 1

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution (Abstract)

Alex Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, 30303, USA
Adrian Caciula , Department of Computer Science, Georgia State University, Atlanta, 30303, USA
Ion Mandoiu , Department of Computer Science & Engineering, University of Connecticut, Storrs, 06269, USA
Serghei Mangul , Department of Computer Science, Georgia State University, Atlanta, 30303, USA
pp. 1

Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data (Abstract)

Nicholas Mancuso , Computer Science Department, Georgia State University, Atlanta, 30303, USA
Rachel O'Neill , Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA
Hongjun Wang , Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA
Andrew Bligh , Biomedical Engineering Program, University of Connecticut, Storrs, 06269 USA
Mazhar I. Khan , Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA
Bassam Tork , Computer Science Department, Georgia State University, Atlanta, 30303, USA
Alexander Zelikovsky , Computer Science Department, Georgia State University, Atlanta, 30303, USA
Ion Mandoiu , Computer Science & Engineering Dept., University of Connecticut, Storrs, 06269 USA
Craig Obergfell , Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA
pp. 1

Workshop: Graph compression approaches in assembly (Abstract)

Jason Pell , Computer Science and Engineering, Michigan State University, East Lansing, United States
James M. Tiedje , Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
Rosangela Canino-Koning , Computer Science and Engineering, Michigan State University, East Lansing, United States
Arend Hintze , Computer Science and Engineering, Michigan State University, East Lansing, United States
Adina Howe , Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
C. Titus Brown , Computer Science and Engineering, Michigan State University, East Lansing, United States
pp. 1-2

Workshop: Gene fusion detection with short and medium length next generation sequencing (Abstract)

Onur Sakarya , Ion Torrent R&D, Life Technologies, Foster City, CA 94404 U.S.A
Heinz Breu , Ion Torrent R&D, Life Technologies, Foster City, CA 94404 U.S.A
pp. 1

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform (Abstract)

Douglas Richman , Department of Medicine, University of California, San Diego, USA
Martin D Smith , Department of Medicine, University of California, San Diego, USA
Art FY Poon , BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
Konrad Scheffler , Department of Medicine, University of California, San Diego, USA
Sergei L Kosakovsky Pond , Department of Medicine, University of California, San Diego, USA
N Lance Hepler , Department of Medicine, University of California, San Diego, USA
Wayne Delport , Prognosys Biosciences, La Jolla, CA, USA
pp. 1

Workshop: Algorithms for discovery of mutated pathways in cancer (Abstract)

Fabio Vandin , Department of Computer Science, and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
Eli Upfal , Department of Computer Science, and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
Benjamin J. Raphael , Department of Computer Science, and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
pp. 1

Workshop: Calling Structural Variation with low-coverage sequencing data by mapping to focal region (Abstract)

Jin Zhang , Computer Science and Engineering, University of Connecticut, Storrs, USA
Yufeng Wu , Computer Science and Engineering, University of Connecticut, Storrs, USA
pp. 1
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