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1st ICCABS 2011: Orlando, Florida, USA
- Ion I. Mandoiu, Satoru Miyano, Teresa M. Przytycka, Sanguthevar Rajasekaran:
IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, 2011. IEEE Computer Society 2011, ISBN 978-1-61284-851-8
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
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
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
PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text. 33-39 - Philippe Bordron, Damien Eveillard
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
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
Inferring serum proteolytic activity from LC-MS/MS data. 81-86 - Jorge Duitama, Pramod Kumar Srivastava, Ion I. Mandoiu
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. 87-92 - Martin Ehler
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
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
A grammar-based approach to RNA pseudoknotted structure prediction for aligned sequences. 135-140 - Shawn T. O'Neil
Robust haplotype reconstruction of eukaryotic read data with Hapler. 141-146 - Saumyadipta Pyne, Steven B. Haase
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 - T. Van Du Tran
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
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, Chung-Che Jeff Chang, Xiaobo Zhou:
Symmetry-based presentation for stem-cell image segmentation. 196-201 - Xing Yang, Daniel Medvin, Giri Narasimhan
CloG: A pipeline for closing gaps in a draft assembly using short reads. 202-207 - Jian Zhang, Ian McQuillan
Parallelizing Peptide-Spectrum scoring using modern graphics processing units. 208-213 - Louxin Zhang, Yen Kaow Ng
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
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
Efficient pairwise statistical significance estimation for local sequence alignment using GPU. 226-231
Poster Abstracts
- Ankit Agrawal
Poster: Risk prediction for post-operative adverse outcomes in colorectal cancer surgery. 232 - Ankit Agrawal
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
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
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
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
Poster: Modelling the tumor shrinkage pharmacodynamics with BlenX. 251 - James Lindsay, J. Zhang, T. Farnham, Y. Wu, Ion I. Mandoiu, Rachel J. O'Neill, Hamed 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
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
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
Workshop: Flexible read decomposition for improved short read error correction. 277 - Guo-Cheng Yuan:
Workshop: Targeting mechanism of epigenetic factors. 278 - Yuan Zhang, Dhananjai Madhava Rao, Jens Mueller, Mufit Ozden, Chun Liang, John E. Karro:
Workshop: Transcript assembly through a d2-based MST approach. 279
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