1. ICCABS 2011: Orlando, Florida, USA

Keynote Talk Abstracts

• Andrea Califano:
  Keynote: A systems biology approach to integrative cancer genomics. 1
  
• Christina S. Leslie:
  Keynote: High-resolution sequence and chromatin signatures predict transcription factor binding in the human genome. 2
  
• John H. Reif:
  Keynote: DNA-based molecular devices. 3
  

Invited Talk Abstracts

• Paola Bonizzoni:
  Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model. 4
  
• Daniel G. Brown:
  Invited: Fast and theoretically strong algorithms for kinship discovery. 5
  
• Oliver Eulenstein:
  Invited: Reconciled gene trees and their applications. 6
  
• Shinichi Morishita:
  Invited: Searching massive epigenome data for evolutionarily conserved sequence motifs. 7
  
• Giri Narasimhan:
  Invited: Comparative microbial genomics. 8
  
• Mihai Pop:
  Invited: Challenges in metagenomic assembly. 9
  
• Paul Ryvkin, Yuk Yee Leung, Li-San Wang, Brian D. Gregory:
  Invited: Multiclass RNA function classification using next-generation sequencing. 10
  
• Daniel Schwartz:
  Invited: "Going viral" with biological sequence analysis. 11
  
• Alexander Zelikovsky:
  Invited: Metabolic network alignments. 12
  

Extended Abstracts

• Nathan Alexander, Nils Woetzel, Jens Meiler:
  Bcl: : Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System. 13-18
  
• Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci:
  Identifying differentially regulated genes. 19-25
  
• Keith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng:
  High-performance biocomputing for simulating the spread of contagion over large contact networks. 26-32
  
• Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi:
  PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text. 33-39
  
• Philippe Bordron, Damien Eveillard, Irena Rusu:
  SIPPER: A flexible method to integrate heterogeneous data into a metabolic network. 40-45
  
• Patricia Buendia, Shu-Ning Hsu, Akira Chiba, John Tyree, Robert Loredo:
  From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects. 46-51
  
• Tien-Hao Chang, Chih-Yun Chiang, Fung-Wei Lin, Chen-Yu Fan:
  Studying disorder-to-order transitions from structural analysis. 52-56
  
• Jun Chen, Jose Suarez, Peter Molnar, Aman Behal:
  Maximum likelihood parameter estimation in a stochastic resonate-and-fire neuronal model. 57-62
  
• Ling Chen, Wei Liu:
  An algorithm for mining frequent patterns in biological sequence. 63-68
  
• David K. Y. Chiu, Peter S. C. Xu:
  InfoBarcoding: Selection of non-contiguous sites in molecular biomarker. 69-74
  
• Mayank Daga, Wu-chun Feng, Thomas Scogland:
  Towards accelerating molecular modeling via multi-scale approximation on a GPU. 75-80
  
• Piotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin:
  Inferring serum proteolytic activity from LC-MS/MS data. 81-86
  
• Jorge Duitama, Pramod K. Srivastava, Ion I. Mandoiu:
  Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. 87-92
  
• Martin Ehler, J. Kainerstorfer, D. Cunningham, M. Bono, Brian P. Brooks, Robert F. Bonner:
  Extended correction model for retinal optical imaging. 93-98
  
• Naomi Fox, Ileana Streinu:
  Redundant interactions in protein rigid cluster analysis. 99-104
  
• Amirali Jafarian, Alioune Ngom:
  A new gene subset selection approach based on linearly separating gene pairs. 105-110
  
• Sumit Kumar Jha, Christopher James Langmead:
  Exploring behaviors of SDE models of biological systems using change of measures. 111-116
  
• Yinglei Lai:
  The analysis of ordered changes of gene expression and gene-gene co-expression patterns. 117-122
  
• Feng Lou, Peter Clote:
  Maximum expected accurate structural neighbors of an RNA secondary structure. 123-128
  
• George Mathew, Zoran Obradovic:
  A privacy-preserving framework for distributed clinical decision support. 129-134
  
• Nobuyoshi Mizoguchi, Yuki Kato, Hiroyuki Seki:
  A grammar-based approach to RNA pseudoknotted structure prediction for aligned sequences. 135-140
  
• Shawn T. O'Neil, Scott J. Emrich:
  Robust haplotype reconstruction of eukaryotic read data with Hapler. 141-146
  
• Saumyadipta Pyne, Steven B. Haase, Hsiu J. Ho, Tsung I. Lin:
  Parametric modeling of cellular state transitions as measured with flow cytometry. 147-152
  
• Yoon Soo Pyon, Matthew Hayes, Jing Li:
  Model based clustering approach for identifying structural variation using next generation sequencing data. 153-158
  
• Van Du Tran, Philippe Chassignet, Saad Sheikh, Jean-Marc Steyaert:
  Energy-based classification and structure prediction of transmembrane beta-barrel proteins. 159-164
  
• Aditya Varma, Abhiram Ranade, Srinivas Aluru:
  An improved maximum likelihood formulation for accurate genome assembly. 165-170
  
• Jiayin Wang, Jin Zhang, Yufeng Wu:
  Identifying interacting SNPs with parallel fish-agent based logic regression. 171-177
  
• Xu Wang, Sandip Roy, Yan Wan:
  Using deliberate-delay decentralized controllers to stop spread dynamics in canonical network models. 178-183
  
• Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, Liming Cai:
  Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds. 184-189
  
• Xiao Wu, Kathryn Sharpe, Tianyi Zhang, Hongyan Chen, Wei Zhu, Ellen Li, Safiyh Taghavi, Daniel Van Der Lelie:
  Comparative genetic pathway analysis using structural equation Modeling. 190-195
  
• Yi Xiao, Tuan D. Pham, Jeff Chang, Xiaobo Zhou:
  Symmetry-based presentation for stem-cell image segmentation. 196-201
  
• Xing Yang, Daniel Medvin, Giri Narasimhan, Deborah Yoder-Himes, Stephen Lory:
  CloG: A pipeline for closing gaps in a draft assembly using short reads. 202-207
  
• Jian Zhang, Ian McQuillan, FangXiang Wu:
  Parallelizing Peptide-Spectrum scoring using modern graphics processing units. 208-213
  
• Louxin Zhang, Yen Kaow Ng, Taoyang Wu, Yu Zheng:
  Network model and efficient method for detecting relative duplications or horizontal gene transfers. 214-219
  
• Tianyi 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:
  Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. 220-225
  
• Yuhong Zhang, Sanchit Misra, Daniel Honbo, Ankit Agrawal, Wei-keng Liao, Alok N. Choudhary:
  Efficient pairwise statistical significance estimation for local sequence alignment using GPU. 226-231
  

Poster Abstracts

• Ankit Agrawal, Sanchit Misra, Alok N. Choudhary, Karl Bilimoria:
  Poster: Risk prediction for post-operative adverse outcomes in colorectal cancer surgery. 232
  
• Ankit Agrawal, Sanchit Misra, Ramanathan Narayanan, Lalith Polepeddi, Alok N. Choudhary:
  Poster: A lung cancer mortality risk calculator based on SEER data. 233
  
• Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky:
  Poster: ViSpA: Viral spectrum assembling method. 234
  
• M. Bijanzadeh, Rozita Jailani:
  Poster: Development of dynamic leg joint model for paraplegic with Functional Electrical Stimulation. 235
  
• Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins:
  Poster: Gene regulatory network inference using time lagged context likelihood of relatedness. 236
  
• Hongmei Chi, Peter Beerli:
  Poster: Quasi-Monte Carlo method in population genetics parameter estimation. 237
  
• Chiquito J. Crasto, Chandrahas Narne, Mikako Kawai, Landon Wilson, Stephen Barnes:
  Poster: MRMPath: A web-based tool that identifies peptide transitions for LCMRM- MS analysis and its application to biological pathways. 238
  
• Venu Dasigi, Orlando Karam, Sailaja Pydimarri:
  Poster: Issues in functional characterization and clustering of genes by literature mining. 239
  
• Akshaye Dhawan, Alison Nolan:
  Poster: Designing reusable user-interfaces for browsing a collection of neuroscience ontologies. 240
  
• Danhua Fan, Eric P. Rahrmann, Kevin A. T. Silverstein, David A. Largaespada:
  Poster: Assessing the content of active endogenous LINE1 retrotransposons in human colorectal cancer samples using high-throughput pyrosequencing. 241
  
• Jason Gallia, Anna Tan-Wilson, Patrick H. Madden:
  Poster: De novo protein identification by dynamic programming. 242-243
  
• Preetam Ghosh, Bhaswati Datta, Vijayaraghavan Rangachari:
  Poster: In silico hypotheses of the Ass42 peptide aggregation process in Alzheimer's disease. 244
  
• Cindy Grimm, Ruosi Li, Paul Heider, Alain Pierre-Pierre, Rolf Mueller:
  Poster: A comparison of local shape descriptors for biological applications. 245
  
• Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
  Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. 246
  
• Jing Hu, Marc Schilder, Xianghe Yan:
  Poster: A neighbor-weighted K-nearest neighbor method for predicting protein subnuclear localizations. 247
  
• Sumit Kumar Jha, Christopher James Langmead:
  Poster: Synthesis of biochemical models. 248
  
• Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun-ichi Tsujii:
  Poster: Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from PubMed publications. 249
  
• Ham Ching Lam, Daniel Boley, Srinand Sreevatsan:
  Poster: H3N2 influenza vaccine: A historical perspective. 250
  
• Paola Lecca, Ozan Kahramanogullari, Daniele Morpurgo, Corrado Priami, Ross A. Soo:
  Poster: Modelling the tumor shrinkage pharmacodynamics with BlenX. 251
  
• James Lindsay, J. Zhang, T. Farnham, Y. Wu, Ion I. Mandoiu, Rachel J. O'Neill, H. Salooti, E. Bullwinkel, Alexander Zelikovsky:
  Poster: Scaffolding draft genomes using paired sequencing data. 252
  
• Guozhen Liu, Han Zhang, George Quellhorst:
  Poster: Distinguishing scientific abbreviations and genes in bio-medical literature mining. 253
  
• Edward W. Lowe, Nils Woetzel, Jens Meiler:
  Poster: GPU-accelerated artificial neural network for QSAR modeling. 254
  
• Serghei Mangul, Alexander Zelikovsky:
  Poster: Haplotype discovery from high-throughput sequencing data. 255
  
• Marius Nicolae, Ion I. Mandoiu:
  Poster: Empirical comparison of protocols for sequencing-based gene and isoform expression profiling. 256
  
• Andrei Paun, Mihaela Paun, Alfonso Rodríguez-Patón, John Jack:
  Poster: Biochemical signaling: A discrete simulation with memory enhancement. 257
  
• Juliana Tarossi Pollettini, Alessandra Alaniz Macedo:
  Poster: Chronic disease prevention: A Translational Bioinformatics approach. 258
  
• Atsushi Sasaki, Shinichi Morishita:
  Poster: Robust estimation of DNA methylation with local regression. 259
  
• Yufeng Shen, Yiwei Gu, Itsik Pe'er:
  Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing data. 260
  
• Xiaoyong Sun, Ajith Gunaratne, Zhijun Wu:
  Poster: PRDDs: A Protein Residue Distance & Angle Distribution Database for Secondary Structures. 261
  
• Pandurangan Sundaramurthy, Raashi Sreenivasan, Khader Shameer, Sunita Gakkhar, Ramanathan Sowdhamini:
  Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. 262
  
• William Valentine-Cooper, Yungui Huang, Sang-Cheol Seok, Veronica J. Vieland:
  Poster: High-performance computing for mapping disease-related genes. 263
  
• Hsien-Wei Wang, Ya-Chi Lin, Tun-Wen Pai, Hao-Teng Chang:
  Poster: Linear B-cell epitope prediction based on Support Vector Machine and propensity scales. 264
  
• Edward W. Lowe, Nils Woetzel, Jens Meiler:
  Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps. 265
  
• Cing-Han Yang, Hsin-Wei Wang, Tsan-Huang Shih, Tun-Wen Pai:
  Poster: Identification and classification of internal repeats in proteins. 266
  

CANGS Workshop Abstracts

• Irina Astrovskaya:
  Workshop: Inferring viral population from ultra-deep sequencing data. 267
  
• Dumitru Brinza, Fiona Hyland:
  Workshop: Error correction methods in next generation sequencing. 268
  
• Jorge Duitama, Eun-Kyung Suk, Sabrina Schulz, Gayle McEwen, Thomas Huebsch, Margret R. Hoehe:
  Workshop: Bioinformatics pipeline for fosmid based molecular haplotype sequencing. 269
  
• Brian E. Howard, Xiaoping Tan, Paola Veronese, Steffen Heber:
  Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing. 270
  
• Wei Li, Jianxing Feng, Tao Jiang:
  Workshop: Transcriptome assembly from RNA-Seq data: Objectives, algorithms and challenges. 271
  
• Rachel J. O'Neill, James Lindsay, Dawn Carone, Sahar Al Seesi, Thomas Heider, Ion I. Mandoiu, Andrew Pask:
  Workshop: The utility of next generation sequencing for genome scale studies. 272
  
• Mihai Pop:
  Workshop: Can you assemble whole genomes from next generation sequencing data? 273
  
• Sanguthevar Rajasekaran, Hieu Dinh, Vamsi Kundeti:
  Workshop: Efficient sequential and parallel algorithms for sequence assembly. 274
  
• Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir:
  Workshop: Characterization of structural variants with next generation DNA sequencing. 275
  
• Yufeng Shen, Ruijie Song, Itsik Pe'er:
  Workshop: Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. 276
  
• Xiao Yang, Karin S. Dorman, Srinivas Aluru:
  Workshop: Flexible read decomposition for improved short read error correction. 277
  
• Guo-Cheng Yuan:
  Workshop: Targeting mechanism of epigenetic factors. 278
  
• Yuan Zhang, D. M. Rao, Jens Mueller, Mufit Ozden, Chun Liang, John E. Karro:
  Workshop: Transcript assembly through a d. 279
  

Last update Fri May 25 08:17:12 2012 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page