ACM BCB 2011 Program

Sunday, July 31, 2011

1:00pm-5:00pm           Registration in Lakeshore Ballroom prefunct

 

 

Monday, Aug. 1, 2011

7:30am-8:30am          Registration and Continental Breakfast
Location: Lakeshore Ballroom prefunct

8:30am-5:00pm          WORKSHOPS & TUTORIALS

        Workshop 1 in Lakeshore Ballroom A
Workshop 2 in Lakeshore Ballroom B
Workshop 3 in Lakeshore Ballroom C

        LINCOLN PARK ROOM
Workshop 4, 8:30-Noon
Tutorial, 1:30-3:00pm
- Knowledge Discovery in Academic-Based Drug Design: New Opportunities and Challenges (Jun Luke Juan, Univ. of Kansas)

        Tutorial, 3:30-5:00pm
-Topological Indexing and Mining of Chemical Compounds (Sayan Ranu and Ambuj Singh, UC-Santa Barbara)

10:00am-10:30am      Morning Break

Noon-1:30pm             Lunch on your own

3:00pm-3:30pm         Afternoon Break

6:00pm-8:00pm         Workshop/Tutorial only poster session

 

 

Tuesday, Aug. 2, 2011

7:30am-8:45am          Registration and Continental Breakfast

    Location: Lakeshore Ballroom prefunct

8:45am-10:00am        Keynote talk
Michael Jordan from the University of California at Berkeley will give a keynote on “Statistical Inference of Protein Structure and Function”
Location: Lakeshore Ballroom

10:00am-10:30am      Morning Break

10:30am-Noon           PAPER SESSIONS
PAPER SESSION 1 Biological Networks (Regular papers; LAKESHORE A)
Session chair: Xinghuan Lu, University of Pittsburgh

  1. “Knowledge-Guided Differential Dependency Network Learning for Detecting Structural Changes in Biological Networks,” Ye Tian*, Virginia Tech; Bai Zhang, Virginia Tech; Ie-Ming Shih, Johns Hopkins University; Yue Wang, Virginia Tech
  2. “A Novel Framework for Large Scale Metabolic Network Alignments by Compression,” Michael Dang, University of Florida; Ferhat Ay*, University of Florida; Tamer Kahveci, University of Florida
  3. “Scalable Multiple Global Network Alignment for Biological Data,” Yu-Keng Shih*, Ohio State University; Srinivasan Parthasarathy, Ohio State University

PAPER SESSION 2 Proteins and gene expression (Short papers; LAKESHORE B)
Session chair: Chris Bailey-Kellogg, Dartmouth

  1. “An efficient algorithm for matching protein binding sites for protein function prediction,” Leif Ellingson, Florida State University; Jinfeng Zhang, Florida State University
  2. “Improving Protein Flexibility Predictions by Combining Statistical Sampling with a Mean-Field Virtual Pebble Game,” Luis Gonzalez, UNC-Charlotte; Dennis Livesay, UNC-Charlotte; Donald Jacobs, UNC-Charlotte
  3. “Kernel Methods for Calmodulin Binding and Binding Site Prediction,” Asa Ben-Hur, Colorado State University; Michael Hamilton, Colorado State University; Anireddy S.N. Reddy, Colorado State University
  4. “Inferring Conflict-Sensitive Phosphorylation Dynamics,” Qiong Cheng, University of Miami; Mitsunori Ogihara, University of Miami; Vineet Gupta, University of Miami
  5. “Changes in gene expression near evolutionary breakpoints,” David Sankoff, Department of Mathematics and Statistics University of Ottawa; Adriana Muñoz, University of Ottawa

PAPER SESSION 3 Proteins (Regular papers; LAKESHORE C)
Session chair: Gultekin Ozsoyoglu, Case Western Reserve University

  1. “Probabilistic Ensembles for Improved Inference in Protein-Structure Determination,” Ameet Soni*, University of Wisconsin-Madison; Jude Shavlik , University of Wisconsin-Madison
  2. “Parallel Simulation of Multiple Proteins Through a Bioreactor Coupled with Biochemical Reactions,” Changjiang Zhang*, University of Kentucky; Kimberly Forsten-Williams, Virginia Tech; Michael Fannon, University of Kentucky; Wensheng Shen, SUNY Brockport; Jun Zhang, University of Kentucky
  3. “Multi-view prediction of protein function,” Artem Sokolov*, Colorado State University; Asa Ben-Hur, Colorado State University

POSTER PAPER SESSION I (LINCOLN PARK)                
Session chair: Sun Kim, Indiana University

Noon-1:30pm             Lunch on your own

1:30pm-3:00pm         PAPER SESSIONS


PAPER SESSION 4 Interactions and Pathways (Regular papers; LAKESHORE A)
Session chair: Tamer Kahveci, University of Florida

  1. “FUSE: Towards Multi-Level Functional Summarization of Protein Interaction Networks,” Boon-Siew Seah, Nanyang Technological Univ; Sourav S Bhowmick*, Nanyang Technological Univ; C Forbes Dewey, Jr, MIT, USA; Hanry Yu, National University of Singapore
  2. “Similarity Boosting for Label Noise Tolerance in Protein-Chemical Interaction Prediction,” Aaron Smalter Hall*, University of Kansas; Jun Huan, University of Kansas; Gerald Lushington, University of Kansas
  3. “Sensitive Detection of Pathway Perturbations in Cancers,” Corban Rivera, Johns Hopkins University; Brett Tyler, Virginia Tech; T. M. Murali*, Virginia Tech

PAPER SESSION 5 Sequence Analysis (Short papers; LAKESHORE B)
Session chair: Chandan Reddy, Wayne State University

  1. “Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking,” Shilpa Nadimpalli, Tufts University; Noah Daniels, Tufts University; Lenore Cowen, Tufts University
  2. “DynMap : mapping short reads to multiple related genomes,” Solon Pissis, King’s College London; Tomas Flouri, CTU; Costas Iliopoulos, King’s College London
  3. “Detection of Novel Tandem Duplication with Next-Generation Sequencing,” Thomas K.F. Wong, The University of Hong Kong; Xuan Liu, The University of Hong Kong; Shing-Wan Choi, The University of Hong Kong; Tak-Wah Lam, The University of Hong Kong; Siu Ming Yiu, The University of Hong Kong
  4. “Mapping Short Sequencing Reads to Distant Relatives,” Vinicio Reynoso, Loyola University Chicago; Catherine Putonti, Loyola University Chicago
  5. “TreeLign: Simultaneous Stepwise Alignment and Phylogenetic Positioning, with its Application to Automatic Phylogenetic Assignment of 16S rRNAs,” Shaojie Zhang , University of Central Florida; Yuan Li, University of Central Florida; Aaron Halpern, Complete Genomics

PAPER SESSION 6 Computational Structural Biology (Regular papers; LAKESHORE C)
Session chair: Luke Huan, University of Kansas

  1. “Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks,” Shaojie Zhang *, University of Central Florida; Yuan Li, University of Central Florida
  2. “Improved Machine Learning Models for Predicting Selective Compounds,” Xia Ning*, UMN; George Karypis, University of Minnesota
  3.  “Combining Ambiguous Chemical Shift Mapping with Structure-Based Backbone and NOE Assignment from 15N-NOESY,” Richard Jang*, University of Waterloo; Xin Gao, King Abdullah University of Science and Technology; Ming Li, University of Waterloo

POSTER PAPER SESSION II (LINCOLN PARK)
Session chair: Jie Liang, University of Illinois at Chicago

 

3:00pm-3:30pm         Afternoon Break

3:30pm -5:00pm        PAPER SESSIONS


PAPER SESSION 7 Network Analysis (Regular papers; LAKESHORE A)
Session chair:  Osmar Zaiane, Simon Fraser University

  1. “Neural System Modeling and Simulation using Hybrid Functional Petri Net,” Yin Tang*, Fudan University; Fei Wang, Fudan University
  2. “Mathematical Network Model for Bone Mineral Density (BMD) and Bone Quality Assessment,” Taehyong Kim*, SUNY at Buffalo
  3. “An integrative approach to infer regulation programs in a transcription regulatory module network,” Jianlong Qi*, Concordia University; Tom Michoel, Freiburg Institute for Advanced Studies; Gregory Butler, Concordia University

PAPER SESSION 8 Protein Interaction Networks (Short papers; LAKESHORE B)
Session chair: Asa Ben-Hur, Colorado State University

  1. “Modeling of Multi Domain Contribution to Protein Interaction,” Woo-Hyuk Jang, KAIST; Suk-Hoon Jung, KAIST; Bo-Ra Hyun, KAIST ; Dong-Soo Han , KAIST
  2. “A fuzzy entropy based approach for development of Gene Prediction Networks (GPNs): Detecting altered dependency in carcinogenic state,” Anupam Ghosh, Netaji Subhash Engineering Col; Rajat De, Indian Statistical Institute
  3. “An ACO Based Functional Module Detection Algorithm For Protein Interaction Network,” Lei Shi, SUNY at Buffalo
  4. “A Statistical Approach for Extracting Protein-Protein Interactions,” Lindsey Bell, Florida State University; Jinfeng Zhang, Florida State University; Xufeng Niu, Florida State University
  5. “Sequence Based Partner-Specific Prediction of Protein- Protein Interfaces and its Application in Ranking Docked Models,” Li Xue, Iowa State University; Rafael Jordan, Iowa State University; Yasser EL-Manzalawy , Iowa State University; Drena Dobbs, Iowa State University; Vasant Honavar, Iowa State University

PAPER SESSION 9 Evolution and Phylogeny (Regular papers; LAKESHORE C)
Session chair: Dannie Durand, CMU

  1. “Inference of tumor phylogenies from genomic assays on heterogeneous samples,” Ayshwarya Subramanian, Carnegie Mellon University; Russell Schwartz*, Carnegie Mellon University; Stanley Shackney, Carnegie Mellon University
  2. “Using Compact Encodings for Path-based Computations on Pedigree Graphs,” Lei Yang, Case Western Reserve University; En Cheng, ; Meral Ozsoyoglu*, CWRU
  3. “A Two-Way Multi-dimensional Mixture Model for Clustering Metagenomic Sequences,” Shruthi Prabhakara*, Pennsylvania State University; Raj Acharya, Pennsylvania State University

PAPER SESSION 10 Computational Systems Biology (Short papers; LINCOLN PARK)
Session chair:  Vasant Honavar, Iowa State University

  1. “PANI: A Novel Algorithm for Fast Discovery of Putative Target Nodes in Signaling Networks,” Huey-Eng Chua, Nanyang Technological Univ; Sourav S Bhowmick, Nanyang Technological Univ; Qing Zhao, Nanyang Technological Univ; Lisa Tucker-Kellogg, National University of Singapore; C Forbes Dewey, Jr, MIT, USA; Hanry Yu, National University of Singapore
  2. “A scalable Approach for Inferring Transcriptional Regulation in the Yeast Cell Cycle,” Akther Shermin, Macquarie University; Hasan Jamil, Wayne State University; Mehmet Orgun, Macquarie University
  3. “Ranking Differential Genes in Co-expression Networks,” Omar Odibat, Wayne State University; Chandan Reddy, Wayne State University
  4. “A graph model and an exact algorithm to find transcription factor modules,” Songjian Lu, University of Pittsburgh; Xinghua Lu, University of Pittsburgh
  5. “An ACO Based Functional Module Detection Algorithm For Protein Interaction Network,” Lei Shi, SUNY at Buffalo

 

6:00pm-8:00pm         POSTER RECEPTION

 

Wednesday, Aug. 3, 2011

7:30am-8:45am          Registration and Continental Breakfast

    Location: Lakeshore Ballroom prefunct

8:45am-10:00am        Keynote talk
Nancy Cox from the University of Chicago will give a keynote on “Transitions: GWAS to Sequencing, Discovery to Understanding, and Bench to Bedside.”
Location: Lakeshore Ballroom

10:00am-10:30am      Morning Break

10:30am-Noon           PAPER SESSIONS


PAPER SESSION 11 Alignment and Assembly (Regular papers; LAKESHORE A)
Session chair:  Yufeng Wu, University of Connecticut

  1. “NcRNA Homology Search Using Hamming Distance Seeds,” Osama Aljawad, Michigan State University; Yanni Sun*, Michigan State University; Jikai Lei, Michigan State University; Alex Liu, Michigan State University
  2. “Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences,” Marco Pellegrini*, IIT – CNR; M. Elena Renda, IIT – CNR; Alessio Vecchio, Dip. Ing. Inf. – Università di Pisa
  3. “MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads,” Toshiaki Namiki, Keio University; Tsuyoshi Hachiya, Keio University; Hideaki Tanaka, Keio University; Yasubumi Sakakibara*, Keio University

PAPER SESSION 12 Visualization and Image Analysis (Short papers; LAKESHORE B)
Session chair: Rajat Kumar De, Indian Statistical Institute

  1. “Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data,” Jeremy Wang, UNC; Leonard McMillan, University of North Carolina; Fernando Pardo-Manuel de Villena, University of North Carolina at Chapel Hill
  2. “Topology aware coloring of gene regulatory networks,” Gunhan Gulsoy, University of Florida; Bhavik Gandhi, University of Florida; Tamer Kahveci, University of Florida
  3. “Geometric Visualization of Transcription Factor Binding Sites in Context,” Chih Lee, University of Connecticut; Chun-Hsi Huang, University of Connecticut
  4. “Counting Cells in 3D Confocal Image for Fruitfly based on Discriminative Models,” Jie Zhou, Northern Illinois University
  5. “Classification and Interest Region Localization on Craniosynostosis Skulls,” Shulin Yang, Univ. of Washington; Linda Shapiro, Univ. of Washington ; Su-In Lee, Univ. of Washington; Michael Cunningham, Univ. of Washington; Matthew Speltz, Univ. of Washington

PAPER SESSION 13 Classification Models (Regular papers; LAKESHORE C)
Session chair: Aidong Zhang, State University of New York at Buffalo

  1. “Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages,” Minoo Aminian*, Rensselaer Polytechnic Institute; Kristin Bennett, Renesselaer Polytechnic Institute; Amina Shabbeer, Renesselaer Polytechnic Institute; Kane Hadley, Renesselaer Polytechnic Institute
  2. “Win Percentage for Comparing Classifiers under the Uncertainty of Feature Selection,” R. Mitchell Parry*, Georgia Tech / Emory; John Phan, Georgia Tech / Emory; May Wang, Georgia Tech
  3. “Classification of Breast Cancer Grades through Quantitative Characterization of Ductal Structure Morphology in Three-Dimensional Cultures,” Basak Oztan*, Rensselaer Polytechnic Inst.; Lindsey Polizzotti, Rensselaer Polytechnic Institute; Cemal Bilgin, RPI; Kira Henderson, Rensselaer Polytechnic Institute; George Plopper, Rensselaer Polytechnic Institute; Bulent Yener, Rensselaer Polytechnic Institute

PAPER SESSION 17 (Short papers; LINCOLN PARK)
Session chair: Jing Li, Case Western Reserve University

  1. “A tripartite clustering analysis on microRNA, gene and disease model,” Chengcheng Shen, Univ. of Texas at Dallas; Ying Liu, Univ. of North Texas at Dallas
  2. “A Bayesian Integration Model of Heterogeneous Data Sources for Improved Gene Functional Inference,” Noor Al Aydie, Wayne State University; Chandan Reddy, Wayne State University; Farshad Fotouhi, Wayne State University
  3. “Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors,” Emmett Sprecher, Yale Univ.; Steven Kleinstein, Yale University School of Medicine; Lyndsay Harris, Yale Univ.; David Tuck, Yale Univ.
  4. “A Novel K-mer Mixture Logistic Regression for Methylation Susceptibility Modeling of CpG Dinucleotides in Human Gene Promoters,” Youngik Yang, J. Craig Venter Institute
  5. “Resolving Observation Conflicts in Steady State Metabolic Network Dynamics Analysis ,” Ercument Cicek, Case Western Reserve Univ.; Tekin Ozsoyoglu, Case Western Reserve Univ.

 

Noon-1:30pm             Lunch on your own

1:30pm-3:00pm         PAPER SESSIONS


PAPER SESSION 14 Sequence Analysis (Regular papers; LAKESHORE A)
Session chair:  Leonard McMillan, UNC Chapel Hill

  1. “Algorithms for optimizing cross-overs in DNA shuffling,” Lu He, Dartmouth Computer Science; Alan Friedman, Purdue Biological Sciences; Chris Bailey-Kellogg*, Dartmouth
  2. “Using Inversion Signatures to Generate Draft Genome Sequence Scaffolds,” Zanoni Dias*, UNICAMP and Virginia Tech; Ulisses Dias, Unicamp; João Setuba, Virginia Tech
  3. “A Fast Method for Large-scale Multichromosomal Breakpoint Median Problems,” Maryam Haghighi*, University of Ottawa; Sylvia Boyd, University of Ottawa

PAPER SESSION 15 Simulation and Data Analysis (Short papers; LAKESHORE B)
Session chair: Keun Ryu, Chungbuk National University

  1. “Sequence-Based Prediction of HIV-1 Coreceptor Usage: Utility of n-Grams for Representing gp120 V3 Loops,” Majid Masso, George Mason University
  2. “Generation of Synthetic Data and Design of Simulations in Evaluating Interactions for Association Studies,” Jing Li, Case Western Reserve University, Computer Science; Yixuan Chen, Case Western Reserve University
  3. “Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis,” Xinjian Qi, Case Western Reserve Univ.; Tekin Ozsoyoglu, Case Western Reserve Univ.; Ali Cakmak, Case Western Reserve Univ.; Ercument Cicek, Case Western Reserve Univ.
  4. “ISO: Numeric Representation of Nucleic Acid Forms,” M. Fanning, University of New Mexico; Joanne Macdonald, Columbia University; Darko Stefanovic, University of New Mexico
  5. “Erlang-Delayed Stochastic Chemical Kinetic Formalism for Efficient Analysis of Biological Systems with Non-elementary Reaction Effects,” Hiroyuki Kuwahara, Carnegie Mellon University; Chris Myers, University of Utah

PAPER SESSION 16 Microarrays and Beyond (Regular papers; LAKESHORE C)
Session chair: May Wang, Georgia Institute of Technology

  1. “Biological Assessment of Grid and Spot Detection in cDNA Microarray Images,” Iman Rezaeian, University of Windsor; Luis Rueda*, University of Windsor
  2. “Identifying pair-wise gene functional similarity by multiplex gene expression maps and supervised learning,” Li An*, Temple University; Haibin Ling, Center for Information Science and Technology, Temple University; Zoran Obradovic, Center for Information Science and Technology, Temple University; Desmond Smith, UCLA; Vasileios Megalooikonomou, Center for Information Science and Technology, Temple University

3:00pm-3:30pm         Afternoon Break

3:30pm-4:15pm         Annual SIG Business Meeting

4:15pm-5:00pm         ACM Tech Pack Initiative

6:00pm-8:00pm         ACM-BCB11 Conference & Award Ceremony Banquet