DIMACS Workshop on Clustering Problems in Biological Networks

May 9 - 11, 2006
DIMACS Center, CoRE Building, Rutgers University, Piscataway, NJ

Sergiy Butenko, Texas A&M, butenko@tamu.edu
W. Art Chaovalitwongse, Rutgers University, wchaoval@rci.rutgers.edu
Panos Pardalos, University of Florida, pardalos@ufl.edu
Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology.

This special focus is jointly sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), the Biological, Mathematical, and Physical Sciences Interfaces Institute for Quantitative Biology (BioMaPS), and the Rutgers Center for Molecular Biophysics and Biophysical Chemistry (MB Center).

Workshop Program:

Program in pdf format
Tuesday, May 9, 2006

 8:00 -  8:30  Breakfast and Registration
               Conference Registration Desk

 8:30 -  8:45  Opening Remarks
               Mel Janowitz, DIMACS Associate Director and Conference Organizers

Session T1 Analyzing Metabolic and Protein Networks
Chair: Panos Pardalos

 8:45  - 9:15  Using Mathematical Programming for the Analysis and Redesign of
               Metabolic and Signaling Networks
               Costas Maranas, Pennsylvania State University

 9:15 -  9:45  Dynamic Modules in Metabolic Networks
               Eivind Almaas, Lawrence Livermore National Laboratory

 9:45 - 10:15  Analysis of Interaction Networks from Clusters of Co-
               Expressed Genes:  A Case Study on Inflammation
               Ioannis Androulakis, Rutgers University

10:15 - 10:45  Break

Session T2 Graph-Based Clustering Techniques
Chair: Art Chaovalitwongse

10:45 - 11:15  Clique Relaxation Models of Clusters in Biological Networks
               Sergiy Butenko, Texas A&M University

11:15 - 11:45  Maximal Hyperclique Pattern in Gene Profiles
               Weili Wu, The University of Texas at Dallas

11:45 - 12:15  Practical Fixed-Parameter Algorithms for Graph-Modeled Data Clustering
               Sebastian Wernicke, Friedrich-Schiller-University, Germany

12:15 -  1:45  Lunch

Session T3 Optimization Techniques for Biological Data Comparison
Chair: Sergiy Butenko

 1:45 -  2:15  Mathematical Programming Methods for Comparison Problems in Biocomputing
               Carlos Oliveira, Oklahoma State University

 2:15 -  2:45  Using Formal Concept Analysis for Microarray Data Comparison
               Vicky Choi, Virginia Tech  

 2:45 -  3:15  Stereotyped Activity Flow in Auditory Neocortical Microcircuits
               Kenneth Harris, Rutgers University 

 3:15 -  3:45  Break

Session T4 Clusters and Dynamics of Biological Networks 
Chair: Carlos Oliveira

 3:45 -  4:15  The Pure Parsimony Problem
               Allen Holder, Trinity University

 4:15 -  4:45  A Time Series Clustering Algorithm for Brain Network Analysis
               W. Art Chaovalitwongse, Rutgers University

 4:45 -  5:15  Fast and Effective Clustering Very Large Networks Using Density-
               Based Clustering Algorithm
               Xiaowei Xu, University of Arkansas

Wednesday, May 10, 2006

 8:00 -  8:45  Registration and Registration
               Conference Registration Desk

Session W1 Models and Algorithms for Genetic Expression Data 
Chair: Sergiy Butenko

 8:45 -  9:15  Mining High-Throughput Biological Data:
               Methods, Algorithms and Applications
               Eytan Domany, Weizmann Institute of Science, Israel

 9:15 -  9:45  Clustering Algorithms for the Analysis of Type 1 Diabetes Data
               Michael Langston, University of Tennessee 

 9:45 - 10:15  A Projected Clustering Algorithm for Biological Data Analysis
               Ping Deng, The University of Texas at Dallas

10:15 - 10:45  Break

Session W2 Coregulation in Metabolic Networks
Chair: Sungchul Ji

10:45 - 11:15  Sequence-Based Predictive Modeling of Posttranscriptional Regulatory Networks
               Harmen Bussemaker, Columbia University

11:15 - 11:45  Posttranscriptional Regulation within the Transcriptome of Human Tissues
               Gary Brewer, University of Medicine & Dentistry of New Jersey -
               Robert Wood Johnson Medical School

11:45 - 12:15  Five Levels of Molecular Networks Underlying the
               Structure and Function of the Living Cell
               Sungchul Ji, Rutgers University

12:15 -  1:45  Lunch

Session W3 Optimization-Based Clustering Techniques
Chair: Panos Pardalos

 1:45 -  2:15  A Novel Mixed-Integer Nonlinear Optimization-Based Clustering Approach:
               Global Optimum Search in Clustering with Enhanced Positioning
               Christodoulos Floudas, Princeton University

 2:15 -  2:45  Nonlinear Skeletons of Data Sets and Kernel Fuzzy Hyperplane
               Clustering Algorithm
               Pando Georgiev, University of Cincinnati

 2:45 -  3:15  Consistent Biclustering via Fractional 0-1 Programming
               Stas Busygin, University of Florida

 3:15 -  3:45  Break

Session W4 Clustering Microarray Data
Chair: Dhammika Amaratunga and Javier Cabrera

 3:45 -  4:15  Generalizations of the Topological Overlap Matrix for Module
               Detection in Gene and Protein Networks
               Steve Horvath, University of California

 4:15 -  4:45  Clustering as a Means of Identifying Co-Regulated Genes
               Jyotsna Kasturi, Johnson & Johnson Pharmaceutical Research & Development

 4:45 -  5:15  Tuned Two-Way Bagging for Clustering Microarrays
               Vladimir Kovtun, Johnson & Johnson Pharmaceutical Research & Development

 5:15 -  5:45  Data Analysis in Immune Response Profiling using Human Protein Microarrays
               Mariusz Lubomirski, Johnson & Johnson Pharmaceutical Research & Development

 6:30 -  8:30  Reception at Holiday Inn

Thursday, May 11, 2006 (JOINT WITH CSNA)

 8:00 -  8:45  Breakfast and Registration
               Conference Registration Desk

Session H1 CSNA Invited Talks
Chair: Mel Janowitz - 1st Floor Lecture Hall

 8:45 -  9:30  Data Mining and Network Models of Massive Datasets
               Panos Pardalos, University of Florida

 9:30 - 10:15  Multi-Class Protein Classification Using String Kernels and Adaptive Codes
               Christina Leslie, Columbia University 

10:15 - 10:45  Break

Session H2-1 Classification and Anomaly Detection in Biological Processes 	
Chair: Bernie Harris - Room 431

10:45 - 11:15  Comparison of Classification Methods to Predict Complications to Liver Surgery
               Leah Ben-Porat, Memorial Sloan-Kettering Cancer Center

11:15 - 11:45  Self-Organizing Maps for Brain Electrical Activity Classification
               Wei Zeng, Rutgers University

11:45 - 12:15  Using Scan Statistics for Anomaly Detection in Genetic Networks
               Christopher Overall, George Mason University

Session H2-2  Author Identification  - 1st Floor Lecture Hall
Chair: Paul Kantor, Rutgers University

10:45 - 11:15  Identifying Authors and Authors' Styles
               David Hoover, NYU

11:15 - 11:45  Simulated Entity Resolution: DIMACS Work on the 
               KDD Challenge of 2005
               Aynur Dayanik, Dmitriy Fradkin, Paul Kantor, David Lewis, 
               David Madigan,and Fred Roberts, Rutgers University
11:45 - 12:15  The Words of Our Lives: Analyzing Age-and Sex-Linked
               Language Variation in the Blogosphere
               Shlomo Argamon, Moshe Koppel, James W. Pennebaker, and Jonathan Schler, 
               Illinois Institute of Technology      

12:15 -  1:30  Lunch

Session H3 Classification vs Clustering, Analyzing Gene Functionality
Chair: Claudia Perlich - 1st Floor Lecture Hall

 1:30 -  2:00  Protein Cluster Analysis via Directed Diffusion
               Yosi Keller, Yale University

 2:00 -  2:30  Learning and Classification in Biological Data
               Sofus Macskassy, Fetch Technologies, Inc.

 2:30 -  3:00  Information-Based Clustering
               Gurinder Singh Atwal, Princeton University

 3:00 -  3:30  Classification vs Clustering, Analyzing Gene Functionality
               Claudia Perlich, IBM T.J. Watson Research Center

 3:30 -  3:45  Break

Session H4 Clustering and Sequencing Genomic Data 	
Chair: Panos Pardalos  - 1st Floor Lecture Hall

 3:45 -  4:15  Using Cluster Analysis to Relate Subjective and Objective
               Pharmacovigilance Association Measures
               Ronald Pearson, ProSanos Corporation

 4:15 -  4:45  Distance Based Probabilistic Clustering of Data
               Cem Iyigun, Rutgers University

 4:45 -  5:00  Closing Remarks from the Conference Organizers

 5:00 	       Adjourn

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Document last modified on May 10, 2006