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ISBRA 2012 Short Abstracts 1 ISBRA 20 2 SHORT ABSTRACTS 8TH INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS RESEARCH AND APPLICATIONS May 21-23, 2012 University of Texas at Dallas, Dallas, TX http://www.cs.gsu.edu/isbra12/ Symposium Organizers Steering Committee Dan Gusfield, University of California, Davis Ion Mandoiu, University of Connecticutt Yi Pan, Georgia State University Marie-France Sagot, INRIA Alex Zelikovsky, Georgia State University General Chairs Ovidiu Daesku, University of Texas at Dallas Raj Sunderraman, Georgia State University Program Chairs Leonidas Bleris, University of Texas at Dallas Ion Mandoiu, University of Connecticut Russell Schwartz, Carnegie Mellon University Jianxin Wang, Central South University Publicity Chair Sahar Al Seesi, University of Connecticut Finance Chairs Anu Bourgeois, Georgia State University Raj Sunderraman, Georgia State University Web Master, Web Design Piyaphol Phoungphol J. Steven Kirtzic Sponsors NATIONAL SCIENCE DEPARTMENT OF COMPUTER SCIENCE DEPARTMENT OF COMPUTER SCIENCE FOUNDATION GEORGIA STATE UNIVESITY UNIVERSITY OF TEXAS AT DALLAS i Program Committee Members Srinivas Aluru, Iowa State University Allen Holder, Rose-Hulman Istitute of S. Cenk Sahinalp, Simon Fraser Danny Barash, Ben-Gurion Technology University University Jinling Huang, Eastern Carolina David Sankoff, University of Ottawa Robert Beiko, Dalhousie University University Russell Schwartz, Carnegie Mellon Anne Bergeron, Universite du Lars Kaderali, University of University Quebec a Montreal Heidelberg Joao Setubal, Virginia Bioinformatics Iyad Kanj, DePaul University Daniel Berrar, University of Ulster Institute Ming-Yang Kao, Northwestern Paola Bonizzoni, Universita' Degli Mona Singh, Princeton University Ileana University Streinu, Smith College Studi di Milano-Bicocca Yury Khudyakov, CDC Wing-Kin Sung, Nuational University of Daniel Brown, University of Danny Krizanc, Wesleyan University Waterloo Singapore Jing Li, Case Western Reserve Sing-Hoi Sze, Texas A&M University Doina Caragea, Kansas State University University Ilias Tagkopoulos, University of Fenglou Mao, University of Georgia California Tien-Hao Chang, National Cheng Osamu Maruyama, Kyushu University Kung University Marcel Turcotte, University of Ottawa Li Min, Georgia State University Chien-Yu Chen, National Taiwan Gabriel Valiente, Technical University University Ion Moraru, University of of Catalonia Connecticut Health Center Matteo Comin, University of Padova Stéphane Vialette, Université Paris-Est Axel Mosig, University of Leipzig Marne-la-Vallée Bhaskar DasGupta, University of Illinois at Chicago Giri Narasimhan, Florida Li-San Wang, University of International University Pennsylvania Jorge Duitama, University of Connecticut Yi Pan, Georgia State University Lusheng Wang, City University of Hong Kong Oliver Eulenstein, Iowa State Laxmi Parida, IBM University Bogdan Pasaniuc, Harvard University Xiaowo Wang, Tsinghua University Guillaume Fertin, University of Andrei Paun, Louisiana Tech Fangxiang Wu, University of Nantes University Saskatchewan Vladimir Filkov, University of Itsik Pe'er, Columbia University Yufeng Wu, University of Connecticut California Davis Weiqun Peng, George Washington Zhen Xie, Massachusetts Institute of Jean Gao, University of Texas at University Technology Arlington Nadia Pisanti, University of Pisa Jinbo Xu, Toyota Technological Institute Katia Guimaraes, Federal University Maria Poptsova, University of at Chicago of Pernambuco Connecticut Zhenyu Xuan, University of Texas at Jiong Guo, Saarland University Teresa Przytycka, NCBI Dallas Robert Harrison, Georgia State Sven Rahmann, Technical University Alex Zelikovsky, Georgia State University Dortmund University Jieyue He, Southeast University Shoba Ranganathan, Macquarie Fa Zhang, Chinese Academy of Science Steffen Heber, North Carolina State University Yanqing Zhang, Georgia State University University Leming Zhou, University of Pittsburgh ii ISBRA 2012 Short Abstracts AutoPipe: A Toolbox for Systems Biology Workflow Query Synthesis, Hasan Jamil 1 A new method to predict linear B-cell epitope using support vector machine, Bo Yao, Lin Zhang and Chi Zhang 5 Asymptotic properties of a median tree under the coalescent model, Liang Liu 6 Comparison of RNA-Seq with Microarray Analysis of the Transcriptional Response in HT-29 Colon Cancer Cells to 5-aza-deoxycytidine, Xiao Xu, Erica Antinoiou, W. Richard McCombie, Jennie Williams, Asia Brown, Wei Zhu, Song Wu and Ellen Li 10 CPAM: Effective Composite Regulatory Pattern Miner for Genome Sequences, Dan He 14 Pattern Characterization and Functional Mapping for Biomedical Signal Sets, Anish Nair and Kamran Kiasaleh 18 MapBase: A Virtual Biological ID Map Database, Hasan Jamil 22 Investigations on Elastic Network Models of Coarse-Grained Membrane Proteins, Kannan Sankar, Michael T. Zimmermann and Robert L. Jernigan 26 De novo Genome and Transcriptome Sequencing of Social Paper Wasps: Application to Understanding Parasite Manipulation of Host Behavior, Ruolin Liu, Daniel Standage and Amy Toth 30 Genome sequencing, assembly, annotation and comparative analysis of Pseudomonas fluorescens NCIMB 11764 bacterium, Claudia Vilo, Michael Benedik, Daniel Kunz and Qunfeng Dong 31 Statistical Evaluation of Dynamic Brain Cell Calcium Activity, Kinsey Cotton, Mark Decoster, Katie Evans, Richard Idowu, and Mihaela Paun, 35 Lineage Specific Expansion of Protein Families in Malaria Parasites, Hong Cai, Jianying Gu and Yufeng Wang 39 A Mean Shift Clustering Based Algorithm for Multiple Alignment of LC-MS Data, Minh Nguyen and Jean X. Gao 43 A new algorithm for the molecular distance geometry problem with inaccurate distance data, Michael Souza, Carlile Lavor, Albert Muritiba and Nelson Maculan 47 Identification of highly synchronized regulatory subnetwork with gene expression and interaction dynamics, Shouguo Gao and Xujing Wang 51 MGC: Gene calling in metagenomic sequences, Achraf El Allali and John Rose 55 Structural Motif Discovery Algorithms: Classification and Benchmarks, Isra Al-Turaiki, Ghada Badr and Hassan Mathkour 59 Enumerating Maximal Frequent Subtrees, Akshay Deepak and David Fernández-Baca 65 iii Bioinformatics: Desktop Applications to Peta-Scale Architectures with Web-Based Portals, Bhanu Rekepalli, Paul Giblock and Christopher Reardon 69 A Web-based multi-Genome Synteny Viewer for Customized Data, Kashi Revanna, Chi-Chen Chiu, Daniel Munro, Alvin Gao and Qunfeng Dong 70 Subgingival plaque microbiota in patients with type 2 diabetes, Mi Zhou, Ruichen Rong, Daniel Munro, Qi Zhang and Qunfeng Dong 74 Automatic Analysis of Dendritic Territory for Neuronal Images, Santosh Lamichhane and Jie Zhou 78 A Neural Network Approach to Pre-filtering MS/MS spectra, James Cleveland and John Rose 82 Statistical software and business productivity applications: workflows for communication and efficiency, Marie Vendettuoli, Heike Hofmann and David Siev 85 Development of a Detailed Model for the FcRn-mediated IgG Homeostasis, Venkat Pannala, Dilip Kumar Challa, Sally Ward and Leonidas Bleris 89 Querying Evolutionary Relationships in Phylogenetic Databases, Grant Brammer and Tiffani Williams 101 Gene Expression Resources Available from MaizeGDB, Wimalanathan Kokulapalan, Jack Gardiner, Bremen Braun, Ethalinda Cannon, Mary Schaeffer, Lisa Harper, Carson Andorf, Darwin Campbell, Scott Birkett, Taner Sen, Nicholas Provart and Carolyn Lawrence 105 Nocardia spp. Identification Using a Bioinformatics Approach, Dhundy Kiran Bastola, Scott McGrath, Ishwor Thapa and Peter Iwen 106 An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads, Serghei Mangul, Adrian Caciula, Nicholas Mancuso, Olga Glebova, Ion Mandoiu and Alex Zelikovsky 110 Distributions of Palindromic Proportional Content in Bacteria, Oliver Bonham-Carter, Lotfollah Najjar, Ishwor Thapa and Dhundy Kiran Bastola 114 GREDSTAT: Genome-wide Restriction Enzyme Digestion STatistical Analysis Tool, Maga Rowicka and Norbert Dojer 118 Scaffolding Large Genomes using Integer Linear Programming, James Lindsay, Hamed Salooti, Alex Zelikovsky and Ion Mandoiu 122 Inference of allele specic expression levels from RNA-Seq data, Sahar Al Seesi and Ion Mandoiu 128 Monitoring of Human body tissues at Molecular Level using FOTI Systems, G.S. Uthayakumar and A. Sivasubramanian 133 Multi-Commodity Flow Methods for Quasispecies Spectrum Reconstruction Given Amplicon Reads, Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion Mandoiu and Alex Zelikovsky 148 Quasispecies frequency reconstruction using multicommmodity flows, Pavel Skums, Alexander Artyomenko, Alex Zelikovsky and Yury Khudyakov 153 iv ISBRA 2012 Short Abstracts AutoPipe: A Toolbox for Systems Biology Workflow Query Synthesis? Hasan M. Jamil Department of Computer Science Wayne State University, USA [email protected] Abstract. Prohibitive software implementation costs are a major bar- rier for biologists in testing potentially insightful hypotheses. An intrigu- ing issue then is still outstanding is if it is possible for a biologist to con- ceptually state an arbitrary computational biology process and map it to a workflow query over a network of distributed resources. The major hurdle is how to map the conceptual concepts into concrete and semanti- cally equivalent computational artifacts. In this paper, we propose a novel model for ad hoc systems biology workflow query synthesis from stored description of hierarchical computational components. We leverage on- tological concept structures and concept transformation relationships in our system AutoPipe,
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