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Computational Biology Seminar

The Computational Biology Seminar is a weekly series of seminars on topics in computational biology presented by invited speakers, Duke faculty and CBB doctoral and certificate graduate students.

Spring 2008 Schedule

Time:11 am - Noon
Place:MSRBI, room 001

Date Speaker Institution Title of Presentation
1/14 Jeff Hoch University of Connecticut Health Center Maximum Entropy Unmasked
1/28 Katia Koelle Dept. of Biology The Role of Antigenic Neutrality in the Evolutionary Dynamics of Influenza
2/4 Jason Haugh North Carolina State University Systematic Analysis of Crosstalk in Signal Transduction Networks
2/11 Joshua Socolar Dept. of Physics Dynamics of Complex Regulatory Networks
2/18 Jeff Headd CBB PhD Student Dave & Jane Richardson Group Escaping Eclipsed-chi Local Minima with Real-Space Refinement and Rotamer Selection
2/25 Joel Bader Johns Hopkins University Understanding Gene Function from Network Context
3/3 Gunjan Verma CBB PhD Student Sayan Mukherjee and Terry Furey Groups TBD
3/17 Mathieu Blanchette McGill University TBD
3/24 Angel Garcia Rensselaer Polytechnic Institute TBD
3/31 Daniel Mace CBB PhD Student Uwe Ohler Group Through the looking glass: Quantification and analysis of spatiotemporal gene expression patterns from high throughput microscopy images
4/7 Karen Hayden CBB Certificate Student Hunt Willard Group Designing a path through a hall of mirrors: Facing human centromere sequence organization and assembly
4/14 Stoyan Georgiev CBB PhD Student Uwe Ohler Group TBD
4/12 Josh Robinson CBB Certificate Student Alex Hartemink Group TBD

Fall 2007 Schedule

Time: 11 am
Place: 147 Nanaline Duke

Date Speaker Institution Title of Presentation
9/3 Elena Edelman CBB PhD Student, Sayan Mukherjee Group Modeling Cancer Progression via Pathway Dependencies
9/10 Anand Asthagiri Division of Chemistry and Chemical Engineering, California Institute of Technology Quantitative Variations in Molecular Networks and the Emergence of Multicellular Phenotypic Diversity
9/17 David Orlando CBB PhD Student, Philip Benfey Group Approaches to Analyzing Whole Genome Expression Data from the Yeast Cell Cycle and Arabidopsis Root
9/24 Justin Guinney CBB PhD Student, Sayan Mukherjee and Philip Febbo Groups Multi-task Gradient Learning: Structure and Dependence in Cancer Genomics
10/1 Raluca Gordon Computer Science PhD Student, Alex Hartemink Group Informative Positional Priors Improve DNA Motif Discovery
10/15 Florian Markowetz Lewis-Siegler Institute for Integrative Genomics, Princeton University Nested Effects Models for High-dimensional Phenotyping Screens
10/22 Spencer Muse Dept. of Statistics, North Carolina State University Site-to-site Variability of Silent Substitution Rates
10/29 Philip Febbo Dept. of Medicine Searching for the Expression Signature of mTOR Activity
11/5 Jeanette McCarthy Dept. of Community and Family Medicine Making the Most of Public Data to Map a Diabetes Locus
11/12 Andrej Sali Dept. of Biopharmaceutical Sciences,
University of California, San Francisco		 Integrating Diverse Data for Structure Determination of Macromolecular Assemblies
11/19 Joseph Volpe CBB PhD Student, Thomas Kepler Group Statistical Signatures of Molecular Mechanisms in Immunoglobulin Development
11/26 Jen-Tsan Ashley Chi Depts. Molecular Genetics and Microbiology The Gene Expression Program of Lactic Acidosis Response in Human Cancers
12/3 Alan Boyle CBB PhD Student, Terry Furey Group Whole Genome Identification and Analysis of DNaseI Hypersensitive Sites

Spring 2007 Schedule

Time: 11am - noon
Place: 125 Hudson Hall

Date Speaker Institution Title of Presentation
1/22 Curtis Layton CBB PhD Student, Homme Hellinga Group Computational Design of Protein-Protein Interactions
1/29 David MacAlpine Duke University Depts. of Pharmacology and Cancer Biology Identifying chromosomal features that direct and regulate DNA replication
2/5 David Crosslin CBB PhD Student, Beth Hauser Group Assessment of ALOX5AP in Two Independent Coronary Artery Disease Studies
2/12 Rui Wang CBB PhD Student, Erich Jarvis Group A Comparative Approach to Identify Vocal Learning Related Genes
2/19 Spencer Muse North Carolina State University Department of Statistics Site-to-site Varaibility of Silent Substitution Rates
2/23 George Weinstock* Co-Director, Human Genome Sequencing Center
Baylor College of Medicine		 Amazing Genomes: Challenges and Solutions
2/26 Supriya Munshaw CBB PhD Student, Thomas Kepler Group An Information-theoretic Treatment of Horizontal Transfer within Gene Families
3/5 Saeed Tavazoie Department of Molecular Biology
& The Lewis-Sigler Institute for Integrative Genomics
Princeton University		 A Post-genomic Approach to Understanding Biological Behavior
3/19 Haige Shen CBB Phd Student, Mike West Group Probabilistic Pathway Annotation: Bayesian Analysis of Gene Set Enrichment in Genome-wide Expression Profiles
3/26 Ana Paula Sales CBB PhD Student, Thomas Kepler Group Prediction of MHC-peptide Binding Using Tree-base Statistical Techniques
4/2 Mike Eisen Lawrence Berkeley National Lab and the University of California at Berkeley (UCB) Understanding and Exploiting the Evolution of Eukaryotic Regulatory Sequences
4/9 Jingdong Tian Duke University Department of Biomedical Engineering Design and Engineering of Synthetic Biological Systems
4/16 Faisal Reza CBB PhD Student, Jingdong Tian Group Exploring Protein-nucleic Acid Ensemble Fundamentals
4/23 Todd Wasson CBB PhD Student, Alexander Hartemink Group Modeling Transcriptional Regulation: The Interplay Between Transcription Factors, Nucleosomes, and Upstream Sequence
4/30 Elizabeth Rach CBB PhD Student, Uwe Ohler Group Condition Specific Associations to Transcription Initiation

Fall 2006 Schedule

Time: Mondays 11am - noon
Place: 147 Nanaline Duke

Date Speaker Institution Title of Presentation
9/4 Dave Orlando CBB PhD Student, Philip Benfey Group Probabilistic Population Modeling: Understanding the Dynamics of Cell-Cycle Distributions in Synchrony/Release Experiments
9/11 Dan Mace CBB PhD Student, Uwe Ohler Group Towards a Unified Root Model: Extracting Spatiotemporal Gene Expression Data from Arabidopsis Confocal Images
9/18 Elena Edelman CBB PhD Student, Sayan Mukherjee Group Analysis of Sample Set Enrichment Scores: Assaying the Enrichment of Sets of Genes for Individual Samples in Genome-wide Expression Profiles
9/25 Florence Tama University of Arizona Department of Biochemistry & Molecular Biophysics Multi-scales Modelling Approaches to Unveil Function of Large Biomolecules
10/2 Jeff Headd CBB PhD Student, Johannes Rudolph & Herbert Edelsbrunner Groups Molecular Dynamics Studies of Protein-Protein Interfaces
10/16 Mike Weale Duke Center for Population Genetics & Pharmacogenomics Whole Genome Association: Sizing Up the Challenge
10/23 Joseph Volpe CBB PhD Student, Duke Center for Computational Immunology Comprehensive Analysis of Productive Ig Rearrangements and Comparison to Autoreactive, Anti-DNA Ig, and Anti-HIV Sequences
10/30 Jun Zhu Duke University Department of Cell Biology A Post-genomic Approach to Understanding Biological Behavior
11/6 Bill Noble University of Washington Department of Genome Sciences Machine Learning Analyses of Tandem Mass Spectra
11/13 Greg Crawford DUMC Pediatrics Genome-wide Mapping of DNase I Hypersensitive Sites to Identify Active Gene Regulatory Elements
11/20 Nicole Johnson Center for Human Genetics The Characterization of Genomic Changes and Progression Factors associated with Oligodendroglioma, Astrocytoma, and Glioblastoma Using Comparative Genomic Hybridization
11/27 Marcy Uyenoyama Duke University Department of Biology The Post-Modern Synthesis: Forward Models and Backward Inference

Sponsored by IGSP & Program in Computational Biology & Bioinformatics