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Biological Language Conference

In cooperation with the AAAI

Integration of Language Technologies in Bioinformatics/Computational Biology Research

November 20-21, 2003

2M/2P Wesley W. Posvar Hall,
230 South Bouquet Street.
University of Pittsburgh

November 20, 2003

8:30 9:00 Breakfast

I. Introduction

9:00 9:05 Raj Reddy Welcome

9:05 9:25 Judith Klein-Seetharaman and Roni Rosenfeld Overview of Biological Language Conference

9:25 9:35 Jim Lyons-Weiler Editorial

II. Sequence structure mapping

9:35 10:20 Chris Bystroff, Yu Shao and Xin Yuan Five hierachical levels of sequence structure correlations in proteins

10:20 10:45 Maria Kurnikova and Kirill Speranskiy Composite approaches to modeling of ion channels and receptors. What we can and can not do

10:45 11:00 Coffee break

11:00 11:30 Igor B. Kuznetsov and S. Rackovsky Varieties of Meaning in Protein Sequences: The Nature of the Folding Code

11:30 12:00 Yan Liu, Jaime Carbonell et al. Secondary structure and supersecondary structure prediction

12:00 1:00 Lunch

III. Microarray

1:00 1:30 Ziv Bar-Joseph Computational Challenges in the Analysis of Time Series Expression Data

1:30 1:50 Fan Li and Yiming Yang Learning gene regulatory network from micro-array data

1:50 2:00 Deepika Jagan and Gautam B. Singh Word Similarity Based Phylogenetic Reconstruction for Validating Micro-arrays Reuse in Closely Related Species

2:00 2:15 Coffee break

IV. Function prediction

2:15 2:30 Betty Cheng, Jaime Carbonell and Judith Klein-Seetharaman GPCR ligand and G protein coupling prediction

2:30 2:45 John Vries, Rajan Munshi, Dror Tobi, Judith Klein-Seetharaman, Takis Benos and Ivet Bahar Protein family classification

2:45 3:05 Tao Tao, ChengXiang Zhai, Xinghua Lu and Hui Fang A study of statistical methods for function prediction of protein motifs

3:05 3:25 Vijay Ilavarasan , Jay Wren and Gautam B. Singh Functional Inference Properties of Protein N-grams

3:25 3:55 M. Couch, M. Paterson and M.B. Swindells Annotating the proteome

3:55 4:25 Stephanie Seneff, Chao Wang and Chris Burge Improved Gene Prediction through Human/Mouse Ortholog Similarity Constraints

4:25 5:00 Coffee break

V. Protein dynamics and folding

5:00 5:10 Tejasvini Prasad , Tamilselvi Subramanian, Sridhar Hariharaputran, Chaitra H.S. and Nagasuma Chandra Extracting hydrogen-bond signature patterns from protein structure data

5:10 5:20 Ravindranath S. Rathore and T. Narasimhamurthy Structural features in the model of a thermostable and stress-resistant protein, SP1 from aspen

5:20 5:30 Jiangbo Miao, Judith Klein-Seetharaman and Hagai Meirovitch Percolation and hydrophobic clusters

5:30 5:40 Seung-Yeon Kim, Julian Lee and Jooyoung Lee Folding dynamics of small proteins with different types of structures

5:40 5:50 AJ Rader, Gulsum Anderson, Basak Isin, Judith Klein-Seetharaman and Ivet Bahar The folding core of rhodopsin

5:50 6:00 Peter Weigele, Eben Scanlon and Jonathan King Amino acid sequences encoding the triple beta-helical repeat

6:00 6:30 Pedro Romero, Zoran Obradovic, & A.Keith Dunker Natively Disordered Protein: Functions and Predictions

7:00 Dinner

November 21, 2003

8:30 9:00 Breakfast

VI. Best idea competition

9:00 10:30 All students and postdocs

10:30 11:00 Coffee break

VII. Generation and analysis of multiple sequence alignments

11:00 11:20 Fern Y. Hunt, Anthony J. Kearsley and Agnes O'Gallagher Constructing Sequence Alignments from a Markov Decision model with estimated parameter values

11:20 11:40 Rose Hoberman, Roni Rosenfeld and Judith Klein-Seetharaman Inferring property selection pressure from positional residue conservation

11:40 12:00 Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert MSAT – a Multiple Sequence Alignment tool based on TOPS

12:00 12:20 Bernardo Barbiellini, Alexandra Portnova , Anna Chetoukhina and Chia-Hsin Lu, Robert Grothe and Matteo Pellegrini Computing Evolutionary Distances Between Proteins

12:20 1:15 Lunch

VIII. DNA sequence analysis

1:15 1:45 Alexander Bolshoy DNA Sequence Analysis Linguistic Tools: Words and Patterns

1:45 2:15 Russell Schwartz Haplotype Parsing: Methods for Extracting Information from Human Genetic Variations

2:15 2:30 Eric P. Xing Profile Hidden Markov Dirichlet-Multinomial Models for Motif Families

2:30 2:45 Coffee break

IX.Toolkits

2:45 2:55 Sivaraman Balakrishnan, Madhavi Ganapathiraju, Judith Klein-Seetharaman, N. Balakrishnan and Raj Reddy Extensions to the Biological Language Modeling Toolkit (BLMT)

2:55 3:05 Viji Manoharan and Judith Klein-Seetharaman Biological Language Modeling Interface

3:05 3:15 Naveena V.K. Yanamala, Harikrishna V. Rekapalli, Sri Jyothsna Yeleswarapu, Ram Sateesh Talari and Abhijit Mitra IPSVAC – Integrated Platform for Sequence Visualization, Analysis and Comparison

3:15 3:25 Lucio Cetto and Rob Henson The Matlab Bioinformatics Toolkit

X. Interdisciplinary Education

3:25 3:40 Gautam B. Singh and Christine Hansen Cognitive Assessment Driven Strategy for Integrating Bioinformatics Concepts in Computer Science Curricula

3:40 3:55 Yang Cai, Ingo Snel, Clementine Klein, Suman Bharathi Balasubramaniam, Betty Cheng and Judith Klein-Seetharaman Biomedical Problem Solving Environment

XI. Best idea competition award ceremony

3:55 4:00 Winners and selection committee

4:00 Adjourn

November 20, 2003
8:30	9:00	Breakfast
		I. Introduction
9:00	9:05	Raj Reddy	Welcome
9:05	9:25	Judith Klein-Seetharaman and Roni Rosenfeld	Overview of Biological Language Conference
9:25	9:35	Jim Lyons-Weiler	Editorial
		II. Sequence structure mapping
9:35	10:20	Chris Bystroff, Yu Shao and Xin Yuan	Five hierachical levels of sequence structure correlations in proteins
10:20	10:45	Maria Kurnikova and Kirill Speranskiy	Composite approaches to modeling of ion channels and receptors. What we can and can not do
10:45	11:00	Coffee break
11:00	11:30	Igor B. Kuznetsov and S. Rackovsky	Varieties of Meaning in Protein Sequences: The Nature of the Folding Code
11:30	12:00	Yan Liu, Jaime Carbonell et al.	Secondary structure and supersecondary structure prediction
12:00	1:00	Lunch
		III. Microarray
1:00	1:30	Ziv Bar-Joseph	Computational Challenges in the Analysis of Time Series Expression Data
1:30	1:50	Fan Li and Yiming Yang	Learning gene regulatory network from micro-array data
1:50	2:00	Deepika Jagan and Gautam B. Singh	Word Similarity Based Phylogenetic Reconstruction for Validating Micro-arrays Reuse in Closely Related Species
2:00	2:15	Coffee break
		IV. Function prediction
2:15	2:30	Betty Cheng, Jaime Carbonell and Judith Klein-Seetharaman	GPCR ligand and G protein coupling prediction
2:30	2:45	John Vries, Rajan Munshi, Dror Tobi, Judith Klein-Seetharaman, Takis Benos and Ivet Bahar	Protein family classification
2:45	3:05	Tao Tao, ChengXiang Zhai, Xinghua Lu and Hui Fang	A study of statistical methods for function prediction of protein motifs
3:05	3:25	Vijay Ilavarasan , Jay Wren and Gautam B. Singh	Functional Inference Properties of Protein N-grams
3:25	3:55	M. Couch, M. Paterson and M.B. Swindells	Annotating the proteome
3:55	4:25	Stephanie Seneff, Chao Wang and Chris Burge	Improved Gene Prediction through Human/Mouse Ortholog Similarity Constraints
4:25	5:00	Coffee break
		V. Protein dynamics and folding
5:00	5:10	Tejasvini Prasad , Tamilselvi Subramanian, Sridhar Hariharaputran, Chaitra H.S. and Nagasuma Chandra	Extracting hydrogen-bond signature patterns from protein structure data
5:10	5:20	Ravindranath S. Rathore and T. Narasimhamurthy	Structural features in the model of a thermostable and stress-resistant protein, SP1 from aspen
5:20	5:30	Jiangbo Miao, Judith Klein-Seetharaman and Hagai Meirovitch	Percolation and hydrophobic clusters
5:30	5:40	Seung-Yeon Kim, Julian Lee and Jooyoung Lee	Folding dynamics of small proteins with different types of structures
5:40	5:50	AJ Rader, Gulsum Anderson, Basak Isin, Judith Klein-Seetharaman and Ivet Bahar	The folding core of rhodopsin
5:50	6:00	Peter Weigele, Eben Scanlon and Jonathan King	Amino acid sequences encoding the triple beta-helical repeat
6:00	6:30	Pedro Romero, Zoran Obradovic, & A.Keith Dunker	Natively Disordered Protein: Functions and Predictions
7:00		Dinner
November 21, 2003
8:30	9:00	Breakfast
		VI. Best idea competition
9:00	10:30	All students and postdocs
10:30	11:00	Coffee break
		VII. Generation and analysis of multiple sequence alignments
11:00	11:20	Fern Y. Hunt, Anthony J. Kearsley and Agnes O'Gallagher	Constructing Sequence Alignments from a Markov Decision model with estimated parameter values
11:20	11:40	Rose Hoberman, Roni Rosenfeld and Judith Klein-Seetharaman	Inferring property selection pressure from positional residue conservation
11:40	12:00	Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert	MSAT – a Multiple Sequence Alignment tool based on TOPS
12:00	12:20	Bernardo Barbiellini, Alexandra Portnova , Anna Chetoukhina and Chia-Hsin Lu, Robert Grothe and Matteo Pellegrini	Computing Evolutionary Distances Between Proteins
12:20	1:15	Lunch
		VIII. DNA sequence analysis
1:15	1:45	Alexander Bolshoy	DNA Sequence Analysis Linguistic Tools: Words and Patterns
1:45	2:15	Russell Schwartz	Haplotype Parsing: Methods for Extracting Information from Human Genetic Variations
2:15	2:30	Eric P. Xing	Profile Hidden Markov Dirichlet-Multinomial Models for Motif Families
2:30	2:45	Coffee break
		IX.Toolkits
2:45	2:55	Sivaraman Balakrishnan, Madhavi Ganapathiraju, Judith Klein-Seetharaman, N. Balakrishnan and Raj Reddy	Extensions to the Biological Language Modeling Toolkit (BLMT)
2:55	3:05	Viji Manoharan and Judith Klein-Seetharaman	Biological Language Modeling Interface
3:05	3:15	Naveena V.K. Yanamala, Harikrishna V. Rekapalli, Sri Jyothsna Yeleswarapu, Ram Sateesh Talari and Abhijit Mitra	IPSVAC – Integrated Platform for Sequence Visualization, Analysis and Comparison
3:15	3:25	Lucio Cetto and Rob Henson	The Matlab Bioinformatics Toolkit
		X. Interdisciplinary Education
3:25	3:40	Gautam B. Singh and Christine Hansen	Cognitive Assessment Driven Strategy for Integrating Bioinformatics Concepts in Computer Science Curricula
3:40	3:55	Yang Cai, Ingo Snel, Clementine Klein, Suman Bharathi Balasubramaniam, Betty Cheng and Judith Klein-Seetharaman	Biomedical Problem Solving Environment
		XI. Best idea competition award ceremony
3:55	4:00	Winners and selection committee
4:00		Adjourn