Table of Contents

• Keynote: A systems biology approach to integrative cancer genomicsAndrea Califano. 1 [doi]
• Keynote: High-resolution sequence and chromatin signatures predict transcription factor binding in the human genomeChristina S. Leslie. 2 [doi]
• Keynote: DNA-based molecular devicesJohn H. Reif. 3 [doi]
• Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent modelPaola Bonizzoni. 4 [doi]
• Invited: Fast and theoretically strong algorithms for kinship discoveryDaniel G. Brown 0001. 5 [doi]
• Invited: Reconciled gene trees and their applicationsOliver Eulenstein. 6 [doi]
• Invited: Searching massive epigenome data for evolutionarily conserved sequence motifsShinichi Morishita. 7 [doi]
• Invited: Comparative microbial genomicsGiri Narasimhan. 8 [doi]
• Invited: Challenges in metagenomic assemblyMihai Pop. 9 [doi]
• Invited: Multiclass RNA function classification using next-generation sequencingPaul Ryvkin, Yuk Yee Leung, Li-San Wang, Brian D. Gregory. 10 [doi]
• Invited: Going viral with biological sequence analysisDaniel Schwartz. 11 [doi]
• Bcl: : Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics SystemNathan Alexander, Nils Woetzel, Jens Meiler. 13-18 [doi]
• Identifying differentially regulated genesNirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci. 19-25 [doi]
• High-performance biocomputing for simulating the spread of contagion over large contact networksKeith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng. 26-32 [doi]
• PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a textPaola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi. 33-39 [doi]
• SIPPER: A flexible method to integrate heterogeneous data into a metabolic networkPhilippe Bordron, Damien Eveillard, Irena Rusu. 40-45 [doi]
• From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insectsPatricia Buendia, Shu-Ning Hsu, Akira Chiba, John Tyree, Robert Loredo. 46-51 [doi]
• Studying disorder-to-order transitions from structural analysisTien-Hao Chang, Chih-Yun Chiang, Fung-Wei Lin, Chen-Yu Fan. 52-56 [doi]
• Maximum likelihood parameter estimation in a stochastic resonate-and-fire neuronal modelJun Chen, Jose Suarez, Peter Molnar, Aman Behal. 57-62 [doi]
• An algorithm for mining frequent patterns in biological sequenceLing Chen, Wei Liu. 63-68 [doi]
• InfoBarcoding: Selection of non-contiguous sites in molecular biomarkerDavid K. Y. Chiu, Peter S. C. Xu. 69-74 [doi]
• Towards accelerating molecular modeling via multi-scale approximation on a GPUMayank Daga, Wu-chun Feng, Thomas Scogland. 75-80 [doi]
• Inferring serum proteolytic activity from LC-MS/MS dataPiotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin. 81-86 [doi]
• Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing dataJorge Duitama, Pramod K. Srivastava, Ion I. Mandoiu. 87-92 [doi]
• Extended correction model for retinal optical imagingMartin Ehler, J. Kainerstorfer, D. Cunningham, M. Bono, Brian P. Brooks, Robert F. Bonner. 93-98 [doi]
• Redundant interactions in protein rigid cluster analysisNaomi Fox, Ileana Streinu. 99-104 [doi]
• A new gene subset selection approach based on linearly separating gene pairsAmirali Jafarian, Alioune Ngom. 105-110 [doi]
• Exploring behaviors of SDE models of biological systems using change of measuresSumit Kumar Jha, Christopher James Langmead. 111-116 [doi]
• The analysis of ordered changes of gene expression and gene-gene co-expression patternsYinglei Lai. 117-122 [doi]
• Maximum expected accurate structural neighbors of an RNA secondary structureFeng Lou, Peter Clote. 123-128 [doi]
• A privacy-preserving framework for distributed clinical decision supportGeorge Mathew, Zoran Obradovic. 129-134 [doi]
• A grammar-based approach to RNA pseudoknotted structure prediction for aligned sequencesNobuyoshi Mizoguchi, Yuki Kato, Hiroyuki Seki. 135-140 [doi]
• Robust haplotype reconstruction of eukaryotic read data with HaplerShawn T. O Neil, Scott J. Emrich. 141-146 [doi]
• Parametric modeling of cellular state transitions as measured with flow cytometrySaumyadipta Pyne, Steven B. Haase, Hsiu J. Ho, Tsung I. Lin. 147-152 [doi]
• Model based clustering approach for identifying structural variation using next generation sequencing dataYoon Soo Pyon, Matthew Hayes, Jing Li. 153-158 [doi]
• Energy-based classification and structure prediction of transmembrane beta-barrel proteinsVan Du Tran, Philippe Chassignet, Saad Sheikh, Jean-Marc Steyaert. 159-164 [doi]
• An improved maximum likelihood formulation for accurate genome assemblyAditya Varma, Abhiram Ranade, Srinivas Aluru. 165-170 [doi]
• Identifying interacting SNPs with parallel fish-agent based logic regressionJiayin Wang, Jin Zhang, Yufeng Wu. 171-177 [doi]
• Using deliberate-delay decentralized controllers to stop spread dynamics in canonical network modelsXu Wang, Sandip Roy, Yan Wan. 178-183 [doi]
• Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgroundsYingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying Wai Li, Russell L. Malmberg, Liming Cai. 184-189 [doi]
• Comparative genetic pathway analysis using structural equation ModelingXiao Wu, Kathryn Sharpe, Tianyi Zhang, Hongyan Chen, Wei Zhu, Ellen Li, Safiyh Taghavi, Daniel Van Der Lelie. 190-195 [doi]
• Symmetry-based presentation for stem-cell image segmentationYi Xiao, Tuan D. Pham, Jeff Chang, Xiaobo Zhou. 196-201 [doi]
• CloG: A pipeline for closing gaps in a draft assembly using short readsXing Yang, Daniel Medvin, Giri Narasimhan, Deborah Yoder-Himes, Stephen Lory. 202-207 [doi]
• Parallelizing Peptide-Spectrum scoring using modern graphics processing unitsJian Zhang, Ian McQuillan, FangXiang Wu. 208-213 [doi]
• Network model and efficient method for detecting relative duplications or horizontal gene transfersLouxin Zhang, Yen Kaow Ng, Taoyang Wu, Yu Zheng. 214-219 [doi]
• Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseasesTianyi Zhang, Robert A. DeSimone, Hongyan Chen, Christina M. Hamm, Jeffrey Yuan, Qing Qing Gong, Steven R. Hunt, Themistocles Dassopoulos, Rodney D. Newberry, Daniel N. Frank, Charles E. Robertson, Norman R. Pace, Erica Sodergren, George Weinstock, Xiangmin Jiao, Wei Zhu, Ellen Li. 220-225 [doi]
• Efficient pairwise statistical significance estimation for local sequence alignment using GPUYuhong Zhang, Sanchit Misra, Daniel Honbo, Ankit Agrawal, Wei-keng Liao, Alok N. Choudhary. 226-231 [doi]
• Poster: Risk prediction for post-operative adverse outcomes in colorectal cancer surgeryAnkit Agrawal, Sanchit Misra, Alok N. Choudhary, Karl Bilimoria. 232 [doi]
• Poster: A lung cancer mortality risk calculator based on SEER dataAnkit Agrawal, Sanchit Misra, Ramanathan Narayanan, Lalith Polepeddi, Alok N. Choudhary. 233 [doi]
• Poster: ViSpA: Viral spectrum assembling methodIrina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky. 234 [doi]
• Poster: Development of dynamic leg joint model for paraplegic with Functional Electrical StimulationM. Bijanzadeh, Rozita Jailani. 235 [doi]
• Poster: Gene regulatory network inference using time lagged context likelihood of relatednessVijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins. 236 [doi]
• Poster: Quasi-Monte Carlo method in population genetics parameter estimationHongmei Chi, Peter Beerli. 237 [doi]
• Poster: MRMPath: A web-based tool that identifies peptide transitions for LCMRM- MS analysis and its application to biological pathwaysChiquito J. Crasto, Chandrahas Narne, Mikako Kawai, Landon Wilson, Stephen Barnes. 238 [doi]
• Poster: Issues in functional characterization and clustering of genes by literature miningVenu Dasigi, Orlando Karam, Sailaja Pydimarri. 239 [doi]
• Poster: Designing reusable user-interfaces for browsing a collection of neuroscience ontologiesAkshaye Dhawan, Alison Nolan. 240 [doi]
• Poster: Assessing the content of active endogenous LINE1 retrotransposons in human colorectal cancer samples using high-throughput pyrosequencingDanhua Fan, Eric P. Rahrmann, Kevin A. T. Silverstein, David A. Largaespada. 241 [doi]
• Poster: De novo protein identification by dynamic programmingJason Gallia, Anna Tan-Wilson, Patrick H. Madden. 242-243 [doi]
• Poster: In silico hypotheses of the Ass42 peptide aggregation process in Alzheimer s diseasePreetam Ghosh, Bhaswati Datta, Vijayaraghavan Rangachari. 244 [doi]
• Poster: A comparison of local shape descriptors for biological applicationsCindy Grimm, Ruosi Li, Paul Heider, Alain Pierre-Pierre, Rolf Mueller. 245 [doi]
• Poster: Comprehensive pharmacogenomic pathway screening by data assimilationTakanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano. 246 [doi]
• Poster: A neighbor-weighted K-nearest neighbor method for predicting protein subnuclear localizationsJing Hu, Marc Schilder, Xianghe Yan. 247 [doi]
• Poster: Synthesis of biochemical modelsSumit Kumar Jha, Christopher James Langmead. 248 [doi]
• Poster: Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from PubMed publicationsSimon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun-ichi Tsujii. 249 [doi]
• Poster: H3N2 influenza vaccine: A historical perspectiveHam Ching Lam, Daniel Boley, Srinand Sreevatsan. 250 [doi]
• Poster: Modelling the tumor shrinkage pharmacodynamics with BlenXPaola Lecca, Ozan Kahramanogullari, Daniele Morpurgo, Corrado Priami, Ross A. Soo. 251 [doi]
• Poster: Scaffolding draft genomes using paired sequencing dataJames Lindsay, J. Zhang, T. Farnham, Y. Wu, Ion I. Mandoiu, Rachel J. O Neill, H. Salooti, E. Bullwinkel, Alexander Zelikovsky. 252 [doi]
• Poster: Distinguishing scientific abbreviations and genes in bio-medical literature miningGuozhen Liu, Han Zhang, George Quellhorst. 253 [doi]
• Poster: GPU-accelerated artificial neural network for QSAR modelingEdward W. Lowe, Nils Woetzel, Jens Meiler. 254 [doi]
• Poster: Haplotype discovery from high-throughput sequencing dataSerghei Mangul, Alexander Zelikovsky. 255 [doi]
• Poster: Empirical comparison of protocols for sequencing-based gene and isoform expression profilingMarius Nicolae, Ion I. Mandoiu. 256 [doi]
• Poster: Biochemical signaling: A discrete simulation with memory enhancementAndrei Paun, Mihaela Paun, Alfonso Rodríguez-Patón, John Jack. 257 [doi]
• Poster: Chronic disease prevention: A Translational Bioinformatics approachJuliana Tarossi Pollettini, Alessandra Alaniz Macedo. 258 [doi]
• Poster: Robust estimation of DNA methylation with local regressionAtsushi Sasaki, Shinichi Morishita. 259 [doi]
• Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing dataYufeng Shen, Yiwei Gu, Itsik Pe er. 260 [doi]
• Poster: PRDDs: A Protein Residue Distance & Angle Distribution Database for Secondary StructuresXiaoyong Sun, Ajith Gunaratne, Zhijun Wu. 261 [doi]
• Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognitionPandurangan Sundaramurthy, Raashi Sreenivasan, Khader Shameer, Sunita Gakkhar, Ramanathan Sowdhamini. 262 [doi]
• Poster: High-performance computing for mapping disease-related genesWilliam Valentine-Cooper, Yungui Huang, Sang-Cheol Seok, Veronica J. Vieland. 263 [doi]
• Poster: Linear B-cell epitope prediction based on Support Vector Machine and propensity scalesHsien-Wei Wang, Ya-Chi Lin, Tun-Wen Pai, Hao-Teng Chang. 264 [doi]
• Poster: GPU-accelerated rigid body fitting of atomic structures into electron density mapsEdward W. Lowe, Nils Woetzel, Jens Meiler. 265 [doi]
• Poster: Identification and classification of internal repeats in proteinsCing-Han Yang, Hsin-Wei Wang, Tsan-Huang Shih, Tun-Wen Pai. 266 [doi]
• Workshop: Inferring viral population from ultra-deep sequencing dataIrina Astrovskaya. 267 [doi]
• Workshop: Error correction methods in next generation sequencingDumitru Brinza, Fiona Hyland. 268 [doi]
• Workshop: Bioinformatics pipeline for fosmid based molecular haplotype sequencingJorge Duitama, Eun-Kyung Suk, Sabrina Schulz, Gayle McEwen, Thomas Huebsch, Margret R. Hoehe. 269 [doi]
• Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicingBrian E. Howard, Xiaoping Tan, Paola Veronese, Steffen Heber. 270 [doi]
• Workshop: Transcriptome assembly from RNA-Seq data: Objectives, algorithms and challengesWei Li, Jianxing Feng, Tao Jiang. 271 [doi]
• Workshop: The utility of next generation sequencing for genome scale studiesRachel J. O Neill, James Lindsay, Dawn Carone, Sahar Al Seesi, Thomas Heider, Ion I. Mandoiu, Andrew Pask. 272 [doi]
• Workshop: Can you assemble whole genomes from next generation sequencing data?Mihai Pop. 273 [doi]
• Workshop: Efficient sequential and parallel algorithms for sequence assemblySanguthevar Rajasekaran, Hieu Dinh, Vamsi Kundeti. 274 [doi]
• Workshop: Characterization of structural variants with next generation DNA sequencingBenjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir. 275 [doi]
• Workshop: Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting associationYufeng Shen, Ruijie Song, Itsik Pe er. 276 [doi]
• Workshop: Flexible read decomposition for improved short read error correctionXiao Yang, Karin S. Dorman, Srinivas Aluru. 277 [doi]
• Workshop: Targeting mechanism of epigenetic factorsGuo-Cheng Yuan. 278 [doi]
• Workshop: Transcript assembly through a dY. Zhang, D. M. Rao, J. Mueller, M. Ozden, C. Liang, J. E. Karro. 279 [doi]