Previous presentations

Tuesday, September 10
Dr. Golan Yona (Computer Science)

Title: Modeling regulatory networks in cells using Bayesian networks
(based partially on the paper "Using Bayesian networks to analyze expression data" abstract, paper)

presentation files: file1


Tuesday, September 17
Bill Dirks (Applied Math)

Title: Inferring subnetworks from perturbed expression profiles abstract, paper

presentation files: file1


Tuesday, September 24
Dr. Marty Wells(Biological Statistics and Computational Biology)

(1) Inferring a System of Differential Equations for a Gene Regulatory Network by using Genetic Programming. paper,
(2) Modeling Gene Expression With Differential Equations. paper


Tuesday, October 1
Bart Sautois (Computer Science)

Reverse engineering gene networks using singular value decomposition and robust regression abstract, paper

presentation files: file1


Tuesday, October 8
Dr. Michael Shuler (Chemical Engineering)

Minimal Cell Models:From Cell to Genome?


Tuesday, October 22
Chris Chau (Electrical engineering)

(1) Organizing and computing metabolic pathway data in terms of binary relations. abstract, paper (2) Nutrition-Related Analysis of Pathway/Genome Databases abstract, paper

presentation files: file1


Tuesday, October 29
Dr. Susan McCouch (Plant Breeding)

(1) Enrichment of regulatory signals in conserved non-coding genomic sequence abstract, paper (2) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. abstract, paper (3) Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. abstract, paper


Tuesday, November 5
Dr. Susan Henry (Molecular Biology and Genetics)

A Genetic Dissection of a Complex Metabolic Pathway in Baker's Yeast.
abstract


Tuesday, November 12
Cara Haney (Plant Biology)

(1) E-CELL: software environment for whole-cell simulation. abstract, paper (2) Mathematical simulation and analysis of cellular metabolism and regulation. abstract, paper

presentation files: file1


Tuesday, November 19
Jian Qiu (Computer Science) and Xin Zhao (Nutrition)

(1) Generalized neighbor-joining: more reliable phylogenetic tree reconstruction. abstract, paper (2) A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny abstract, paper


Tuesday, November 26
Rasmus Nielsen (Biological Statistics and Computational Biology)

Detecting positive Darwinian selection in coding and non-coding regions of DNA sequences
paper1, paper2


Spring 2002

Wednesday January 30
Dr. Ron Elber (Computer Science)

Threading algorithms


Wednesday February 6
Jian Qiu (Computer Science)

(1) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. abstract (2) Protein fold recognition by prediction-based threading. abstract

presentation files: file1


Wednesday February 13
Cat Lautenschlager (Chemistry)

(1) Fold prediction by a hierarchy of sequence, threading, and modeling methods. abstract (2) Protein structure prediction by threading. Why it works and why it does not. abstract, paper


Wednesday February 20
Leonid Meyerguz (Computer Science) and Nick DeNunzio (Biology)

(1) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. abstract, paper (2) Protein Structure Comparison by Alignment of Distance Matrices. abstract, paper

presentation files: file1, file2


Wednesday February 27
Arkendra De (Math)

(1) A Unified Statistical Framework for Sequence Comparison and Structure Comparison. abstract, paper (2) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. abstract, paper

presentation files: file1


Wednesday March 6
Bill Dirks (Math)

(1) Parser for protein folding units. abstract (2) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. abstract

presentation files: file1


Wednesday March 13
Niranjan Nagarajan (Computer Science)

(1) Protein structural domain identification. abstract, paper (2) Protein domain decomposition using a graph-theoretic approach. abstract, paper

presentation files: file1


Wednesday March 27
Catherine S. Grasso (Math)

(1) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. abstract, paper (2) Localizing proteins in the cell from their phylogenetic profiles. abstract, paper

presentation files: file1


Wednesday April 3
Chris Chau (Electrical Engineering)

(1) Detecting protein function and protein-protein interactions from genome sequences. abstract, paper (2) Protein interaction maps for complete genomes based on gene fusion events. abstract, paper

presentation files: file1


Wednesday April 10,17
Sharmistha Majumdar (Molecular Medicine) and Sushma Naithanii (Molecular Biology and Genetics)

(1) A network of protein-protein interactions in yeast. abstract, paper (2) A fast method to predict protein interaction sites from sequences. abstract, paper (3) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. abstract, paper (4) A combined algorithm for genome-wide prediction of protein function. abstract, paper

presentation files: file1, file2, file3


Wednesday May 1
Edward Choi (Electrical Engineering)

(1) Correlated mutations contain information about protein-protein interaction. abstract, paper (2) Coevolving Protein Residues: Maximum Likelihood Identification and Relationship to Structure. abstract, paper (3) Co-evolution of Proteins with their Interaction Partners. abstract, paper

presentation files: file1


Fall 2001

Monday September 17
Niranjan Nagarajan(Computer Science) and Garmay Leung (Computer Science/Biology)

(1) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. abstract (2) Optimization of a new score function for the detection of remote homologs. abstract

presentation files: file1, file2


Monday September 24
Rommel Regis(Operations Research) and Wendy Wong (Biometrics)

(1) Twilight zone of protein sequence alignments abstract (2) Statistical alignment: computational properties, homology testing and goodness-of-fit abstract

presentation files: file1, file2, file3, file4


Monday October 1
Catherine Grasso (Applied Math)

(1) Multiple Sequence Alignment Using Partial Order Graphs abstract, paper, figures (2) T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment. abstract

presentation files: file1


Monday October 15
Bill Pottle (Computer Science)

(1) Searching the Protein Structure Databank with Weak Sequence Patterns and Structural Constraints. abstract

presentation files: file1


Monday October 22
Mauricio La Rota (Plant Biology)

(1) A homology identification method that combines protein sequence and structure information. abstract

presentation files: file1


Monday October 29
Christopher Chau (Electrical Engineering)

(1) Analysis and prediction of functional sub-types from protein sequence alignments. abstract, paper (2) A method to predict functional residues in proteins. abstract

presentation files: file1, file2


Monday November 5
Dr. David Lin (Dept. of Biomedical Sciences)

Introduction to Microarray Technology and Analysis

presentation files: file1


Monday November 12
Jing Qiu (Statistics)

(1) Comparison of methods for image analysis on cDNA microarray data. paper (2) Normalization for cDNA Microarray Data. paper


Monday November 19
John Pool (Genetics)

(1) Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations abstract, paper (2) Design and Analysis of Gene Expression Microarray Experiments. paper

presentation files: file1


Monday November 26
Daniel Korenblum (Biophysics)

(1) Cluster analysis and display of genome-wide expression patterns. abstract, paper (2) Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. abstract, paper

presentation files: file1


Monday December 3
Dr. Marty Wells (Biometrics) and Steve Ayers (Genetics)

(1) Singular value decomposition for genome-wide expression data processing and modeling. abstract, paper (2) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. abstract, paper

presentation files: file1


Monday December 10
Dr. Mike Stillman and Dr. Harry Tsai (Math)

(1) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. abstract (2) Supervised harvesting of expression trees. abstract

presentation files: file1