Past Genome Sciences Seminars

Summer 2014

Thursday, August 28 - Dr. Wenxiu Ma
Noble Lab, University of Washington
1:00, Foege Auditorium

Monday, August 18 - Dr. Sarah Zanders
"Genetic conflict and the evolution of infertility"
Malik Lab, Fred Hutchinson Cancer Research Center
1:00, Foege Auditorium

Monday, August 11 - Dr. Kiersten Henderson
"Mother-Daughter Asymmetry of pH Underlies Aging and Rejuvenation"
Gottschling Lab, Fred Hutchinson Cancer Research Center
1:00, Foege Auditorium

Monday, July 21 - Dr. Julie Ahringer
The Gurdon Institute, University of Cambridge
"Genome organization, boundaries, and the landscape of RNA polymerase II transcription in C. elegans"
3:30, Foege Auditorium

Spring 2014

June 4 - Dr. Sarah Otto
University of British Columbia
“Genomic scope of adaptive mutations to different environments”

May 28 - Dr. Michael Fischbach
UC San Francisco
“Insights from a global view of secondary metabolism: Small molecules from the human microbiota”

May 21 - Dr. Michael Boehnke
University of Michigan
"Identifying and Correcting for Sample Contamination in DNA Sequencing Studies"

May 14 - Dr. Lior Pachter
UC Berkeley
"Quantifying the Extent of Geographic Signature in the Human Genome"

May 7 - Dr. Andrew Goodman
Yale University
"Causes and consequences of interpersonal microbial variation"

April 30 - Dr. Brook Nunn
University of Washington
"Using proteomics to understand the fate of carbon and nitrogen in the ocean: From Bloom to Burial"

April 30 - Dr. Steven Carr
Broad Institute
"Quantitative Proteomics in Biology, Chemistry and Medicine"

April 23 - Dr. David Goldstein
Duke University
"Toward precision medicine in neuropsychiatric disease"

April 16 - Dr. Alla Grishok
Columbia University
"Insights into gene regulation by RNAi, chromatin and Forkhead transcription factors"

April 9 - Dr. Cliff Tabin
Harvard University

Winter 2014

March 19 (finals week) - Dr. Oliver Rando
University of Massachusetts
"Structural biology of the yeast genome"

March 12 - Dr. William Greenleaf
Stanford University
"'Off-label' uses of high-throughput sequencing: from assaying chromatin structure with transposes to hijacking sequencers for massively parallel, quantitative biophysics"

March 5 - Dr. Katherine Pollard
UC San Francisco
WiGS invited speaker

February 26 - Dr. Elaine Ostrander
NHGRI
"Good Dogs with Bad Genes Informing Human Health"

February 19 - Dr. Gavin Sherlock
Stanford University
"Attack of the Clones: tracking adaptive evolution in real time and at high resolution"

February 12 - Dr. Lisa Stubbs
University of Illinois
"Rapidly evolving transcription factors and developmental diversity"

February 5 - Dr. Virginia Zakian
Princeton University
"Pif1 DNA helicases promote fork progression past hard-to-replicate sites"

January 29 - Dr. John Novembre
University of Chicago
"Addressing challenges for population genetic inference from next-generation sequencing"
postdoc invited speaker

January 22 - Two Seminars:

1:30: Dr. Cole Trapnell
Harvard University
"Mapping Regulatory Networks with Single-Cell Transcriptomics in Cell Differentiation and Disease"
Foege Auditorium

3:30: Dr. Asher Cutter
University of Toronto
"Hyperdiversity and hypodiversity in genome evolution of Caenorhabditis nematodes"
Foege Auditorium

January 15 - Two Seminars:

1:30: Dr. Dengke Ma
MIT
"Understanding the Genome for the Control of Animal Physiology and Behavior"
Foege Auditorium

3:30: Dr. Marc Vidal
Harvard University
"Interactome Networks and Human Disease"
Foege Auditorium

Monday, January 13 - Dr. Prashant Mali
Harvard University
"Cas9 as a versatile tool for engineering biology"
2:00, Foege Auditorium

January 8 - Dr. Polly Fordyce
UC San Francisco
"High-throughput Mapping of Protein Energy Landscapes Using Novel Microfluidic Tools"

Autumn 2013

December 4 - Dr. Stanley Prusiner
UC San Francisco
"How and why prions cause many different neurodegenerative diseases"

November 20 - Dr. Matthew State
UC San Francisco
"The Tipping Point: Rare Mutations, Gene Discovery and the Emerging Biology of Autism Spectrum Disorders"

November 13 - Dr. Daniel Bolon
University of Massachusetts
"Systematic exploration of relationships between genotype, phenotype, and experimental fitness"

November 6 - Dr. Cisca Wijmenga
University Medical Center Groningen
"A genomics approach to celiac disease"

October 30 - Dr. Arjun Raj
University of Pennsylvania
"Non-local cis gene regulation at the single cell, single chromosome, single molecule, and single base level"

October 23 - Dr. Jonathan Eisen
UC Davis
"Phylogeny-Driven Approaches to Genomics and Metagenomics"
grad student invited speaker

October 16 - Dr. Wenying Shou
Fred Hutchinson Cancer Research Center
"The Survival of the Most Cooperative"

October 9 - Dr. Jason Bielas
Fred Hutchinson Cancer Research Center
"DNA Mutagenesis: Insights into Human Aging, Carcinogenesis, and Novel Anticancer Therapies"

October 2 - Dr. Jonathan Weissman
UC San Francisco
"Monitoring protein synthesis one codon at a time through ribosome profiling"

September 25 - Dr. Richard Gibbs
Baylor College of Medicine
“Genomic Futurism”

 

Summer 2013

Monday, July 29 - Dr. Maulik Patel
Malik Lab, Fred Hutchinson Cancer Research Center
"Genetic conflicts shape mitochondrial function"

 

Spring 2013

June 5 - Dr. Richard Youle
NIH
"Role of Pink1 and Parkin in mitochondrial quality control and Parkinson's disease"

May 29 - Dr. Harmit Malik
Fred Hutchinson Cancer Research Center

May 22 - Dr. Alea Mills
Cold Spring Harbor Laboratory

May 15 - Dr. Cori Bargmann
Rockefeller University

May 1 - Dr. Beth Shapiro
UC Santa Cruz
"Ligers, tigons and bears (Oh my!): The genomic consequences of inter-species hybridization"

April 24 - Dr. James Noonan
Yale University

April 17 - Dr. Stephen Quake
Stanford University
"Dissecting Genome Mixtures"

April 3 - Dr. Charles Rotimi
NHGRI
"Genome Science and Health Disparities: A Growing Success Story?"

Winter 2013

February 27 - Two Seminars:

The More-or-Less 10th Anniversary of the Human Genome Sequence
with a Discussion and Q & A among
Mary-Claire King
Maynard Olson
Robert Waterston
1:30, Foege Auditorium

Dr. Justin Fay
Washington University
"When does change in gene expression matter?"
3:30, Foege Auditorium

February 20 - Genome Sciences Symposium
all day, Foege Auditorium

February 13 - Dr. Silvere van der Maarel
Leiden University Medical Center
"Macrosatellite Repeats in Health and Disease"

February 6 - Dr. Audrey Gasch
University of Wisconsin
"Functional Genomics of Stress Defense in Yeast"

January 30 - Dr. Bing Ren
UC San Diego
"The 3D Genome Landscape and Transcriptional Control in Mammalian Cells"

January 23 - Dr. Ileana Cristea
Princeton University
"Emerging roles for acetylation in regulating host defense mechanisms against viral infection"

January 16 - Dr. Angelika Amon
MIT
"Consequences of Aneuploidy"

Monday, January 14 - Dr. Charles Kurland
"Genome Content Phylogeny of the Three Superkingdoms: Phylogenetic reconstruction for genomicists and consenting adults"

January 9 - Dr. Jennifer Van Eyk
Johns Hopkins University
"A protein centric road to individualizing medicine: brain and myocardial injury biomarkers"

Autumn 2012

December 5 - Dr. Andrew Clark
Cornell University
“Analysis of X chromosome inactivation by RNA-sequencing in mouse, horse and opossum”

November 28 - Dr. Becket Feierbach
Genentech
"CMV: The Most Dangerous Pregnancy Complication You're Never Heard Of"

November 14 - Dr. Susan Biggins
Fred Hutchinson Cancer Research Center
“How do cells get the right chromosomes?”

November 7 - Dr. Steve Altschuler
UT Southwestern Medical Center
“Phenotypic variation in cellular models of disease and differentiation: which differences make a difference?”

October 24 - Dr. Molly Przeworski
University of Chicago
"Learning about modes of adaptation from genetic variation data in apes"

October 17 - Dr. Howard Chang
Stanford University
"Genome regulation by long noncoding RNAs"

October 10 - Dr. Edward Marcotte
University of Texas
"Deeply conserved gene modules and disease"

October 3 - Dr. Leonid Kruglyak
Princeton University
"Causes and Consequences of Natural Genetic Variation"

Summer 2012

Public Lecture Series: July 11 - August 1

Monday, July 9 - Dr. Ewan Birney
European Bioinformatics Institute
"ENCODE: Understanding our genome"
10:30, Foege Auditorium

Spring 2012

May 30 - Dr. Anne-Claude Gingras
University of Toronto
"Navigating signaling interactomes"

May 23 - Dr. John Moran
University of Michigan
"Studies of a Human Retrotransposon"

May 16 - Dr. Amy Caudy
Princeton University
"Riboneogenesis - A New Pathway to Convert Glucose to Ribose that Preserves Redox Balance"

May 9 - Dr. Bret Payseur
University of Wisconsin
"Microsatellites as Targets of Natural Selection"

May 7 - Panel Discussion: The Future of Genome Sciences
7:00 pm, Kane Hall 120
no registration required

The speakers were:

Dr. Bruce Alberts who President Obama has appointed as one of his first Science Envoys.  Dr. Alberts is editor of Science magazine, author of The Cell, and former President of the National Academy of Sciences.

Dr. Natalie Angier who is a science writer for The New York Times and the Andrew D. White Professor-at-Large at Cornell University.  In 1991 she received the Pulitzer Prize for Beat Reporting.

Dr. James Evans who is the Bryson Distinguished Professor of Genetics and Medicine at University of North Carolina and directs the Clinical Cancer Genetics Services at UNC.

Dr. Keith Yamamoto who is Vice Chancellor for Research, Executive Vice Dean of the School of Medicine, and Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco. 

discussion moderator:

Dr. Maynard Olson who is a Professor in the Departments of Genome Sciences and Medicine at the University of Washington and is one of the founders of the Human Genome Project.

panel discussion poster

May 2 - Dr. Arend Sidow
Stanford University
invited by postdoctoral trainees

April 25 - Dr. Nicole Soranzo
Wellcome Trust Sanger Institute
"From GWAS to function and beyond"

April 18 - Dr. Maria Barna
University of California, San Francisco
"Decoding the genomic template into morphology: specialized ribosomes and cell signaling conduits"

April 11 - Dr. Joseph Thornton
University of Oregon
invited by graduate students & postdoctoral trainees

April 4 - Dr. Gerald Rubin
Howard Hughes Medical Institute
"Studying the Drosophila Brain with Single Cell-Type Resolution"

March 28 - Dr. Michael Lynch
Indiana University
“Mutation, Drift, and Evolution at the Subcellular Level”

Winter 2012

March 14 - Pathology & Genome Sciences Seminar
Dr. Jenny Graves

March 7 - Dr. Alan Shuldiner
University of Maryland

February 29 - Two Seminars:

1:30, Foege Auditorium - Dr. Sylvia Fischer

3:30, Foege Auditorium - Dr. Ed Lein
Allen Institute for Brain Science
“Spatiotemporal mapping of the developing brain transcriptome from mice to humans”

February 22 - Dr. R. Scott Hawley
The Stowers Institute
“The Molecular Genetics of Meiosis”

Thursday, February 16 - Dr. Felicity Jones
“The Genomics of Adaption and Parallel Evolution in Sticklebacks”
11:30, Foege Auditorium

February 15 - Dr. Alan Aderem
Seattle Biomedical Research Institute
"A Systems Approach to Dissecting Immunity"

Thursday, February 9 - Dr. Douglas Fowler
“Deep Mutational Scanning to Analyze Protein Function”
11:30, Foege Auditorium

February 8 - Dr. Helen Blau
Stanford University
"Regulating Regeneration: Stem Cells, Newts, and Niches"

Monday, February 6 - Dr. Susan Lott
2:00, Foege Auditorium

February 1 - Dr. Rick Myers
Hudson Alpha Institute
"Genetics and epigenetics of human gene regulation"

Thursday, January 12 - Dr. Chaolin Zhang
"Global RNA Regulatory Networks in the Mammalian Brain: Insights from an Integrative Systems Biology Approach"
11:00, Foege Auditorium

January 11 - Dr. Christina Smolke
Stanford University
"Designing synthetic regulatory RNAs: new tools for temporal and spatial control in biological systems"
sponsored jointly with WiGS

Monday, January 9 - Dr. Koen Venken
“Genome Engineering Approaches to Manipulate Fruit Flies”
2:00, Foege Auditorium

January 4 - Dr. Carolyn Brown
University of British Columbia
"Spreading the Silence: X-Chromosome Inactivation in Humans"

Autumn 2011

December 7 - Dr. Judit Villen
University of Washington
"Food, trash and phosphorylation: a proteomic view"

November 30 - Dr. Matt Kaeberlein
University of Washington

November 16 - Dr. Michael Eisen
UC Berkeley
"Embryos start your engines: Transcription activation and regulation at the beginning of Drosophila development"
sponsored jointly with the Combi seminar series

November 9 - Dr. Nicholas Katsanis
Duke University
"Modeling the Morbid Human Genome"

November 2 - Dr. Matthew Farrer
University of British Columbia
“Parkinson's genetics: an embarrassment of riches”

Genome Sciences Symposium: October 18 & 19

October 12 - Dr. Roger Brent
Fred Hutchinson Cancer Research Center

October 5 - The Larry Sandler Lecture: Dr. Michael Levine
University of California, Berkeley
"Transcriptional precision in the Drosophila embryo"

 

Spring 2011

June 1 - Dr. Lorraine Symington
Columbia University
"Mechanisms of homologous recombination"

May 25 - Dr. Trisha Wittkopp
University of Michigan
"The evolution of gene expression: from mutation to polymorphism to divergence"

May 18 - Dr. David Relman
Stanford University
"Our extended self: the human microbial ecosystem"

May 11 - Dr. Saeed Tavazoie
Princeton University
"Reverse engineering mammalian transcriptional regulatory networks"

May 4 - Dr. Rasmus Nielsen
University of California, Berkeley
"Evolutionary analyses of new-generation sequencing data"
invited by GS graduate students

April 27 - Dr. Lynn Cooley
Yale University
“Intercellular communication through ring canals”

April 20 - The Larry Sandler Lecture: Dr. Barbara Wakimoto
University of Washington
"Our Privileged Inheritance: The Scientific Legacy of Larry Sandler"

April 13 - Dr. Joachim Li
University of California, San Francisco
"From Regulation to Deregulation of Eukaryotic DNA Replication: Potential Genetic Variability in Evolution and Disease"

April 6 - Dr. Daphne Koller
Stanford University
"Uncovering Regulatory Mechanisms in Transcription and Translation using Statistical Analysis"

March 30 - Dr. Hua Tang
Stanford University

Winter 2011

March 9 - Dr. Tim Hughes
University of Toronto
"Mapping the eukaryotic protein-nucleic acid interactome"
invited by GS graduate students

March 2 - Dr. Eric Klavins
University of Washington
"Engineering Noise in Genetic Regulatory Networks"

February 23 - Dr. Donald Hunt
University of Virginia
"Innovative Mass Spectrometry Technology for the Identification of Protein Post-Translational Modifications and Cancer Immunotherapeutics"

February 16 - Dr. Michael Snyder
Stanford University
"Personal and Non-personal Genomes: Their Analysis and Variation"

February 9 - Dr. Kevin White
University of Chicago
"Mining genomes: flies, cancer and rare alleles"

February 2 - Dr. Mark Ptashne
Sloan-Kettering Institute
lecture video

Friday, January 28 - Dr. Maynard Olson
"Stan Gartler: A Scientific Appreciation"
lecture flier

January 19 - Dr. Nancy Cox
University of Chicago
"New Features of Genetic Architecture in Complex Disease"
sponsored jointly with WiGS

January 12 - Dr. Trey Ideker
University of California, San Diego
"Biomarkers based on networks, not individual loci"

January 5 - Dr. Carolyn Bertozzi
Director, The Molecular Foundry
Lawrence Berkeley National Laboratory
“Chemical Approaches for Imaging and Profiling Protein Glycosylation”

Autumn 2010

December 8 - Dr. Axel Visel
Lawrence Berkeley National Laboratory
“Large-scale Identification of Tissue-Specific Enhancers”

December 1 - Dr. Vivian Cheung
University of Pennsylvania
“Human Genetic Variation and Gene Expression”

November 17 - Dr. Sarah Tishkoff
University of Pennsylvania
“African Integrative Genomics: Implications for Human Origins and Disease”
sponsored jointly with WiGS

November 10 - Dr. Forest White
MIT
“Biological Insights from Quantitative Analysis of Receptor Tyrosine Kinase Signaling Networks”

November 3 - Dr. Keith Dunker
“Protein Intrinsic Disorder and Cell Signaling”
Indiana University - Purdue University Indianapolis

October 27 - Dr. Anna Di Rienzo
University of Chicago
“Genetic adaptations to novel environments in humans”
invited by GS graduate students

October 20 - Dr. Brian Browning
University of Washington
“Fast detection of identity-by-descent in ‘unrelated’ individuals”
sponsored jointly with Combi seminars

October 13 - Dr. David Hawkins
University of Washington
“Epigenomic Landscapes in Human Pluripotent and Differentiated Cells”

October 6 - Dr. Olga Troyanskaya
Princeton University
“From Data to Networks to Understanding Complexity of Human Disease”
sponsored jointly with Combi seminars

Summer 2010

August 25 - Dr. Mirela Andronescu
Noble Lab, University of Washington

Thursday, July 15 - Dr. Gill Bejerano
Assistant Professor of Developmental Biology and Computer Science, Stanford University
“Seeing the wood for the trees: Interpreting ChIP-Seq peaks and similar glimpses of human cis-regulation”

Thursday, June 24 - Dr. Quaid Morris
Assistant Professor of Cellular and Biomedical Research, University of Toronto
"Predicting the targets of mRNA-binding proteins"

Wednesday, June 23 - Dr. Alison Motsinger-Reif
North Carolina State University
“The Impact of Retrospective Sampling on Multifactor Dimensionality Reduction”
sponsored by Women in Genome Sciences

Spring 2010

May 26 - Dr. Ruth Ley  
Cornell University
“Host-microbiome interactions in the gut and metabolic diseases”

May 19 -  Two Seminars:

Dr. Jenny Graves

Dr. Elhanan Borenstein
University of Washington
“Systems Biology of Microbes and Microbiomes: Reverse Ecology, Super-Metabolism, and Metagenomic Analysis”

April 28 - Dr. Jay Parrish
Assistant Professor of Biology
University of Washington
"Genetic and genomic analysis of developmental transitions in Drosophila neurons"

April 21 - Dr. Drew Endy
Assistant Professor of Bioengineering
Stanford University
“Work towards an 8-bit Engineered Genetic Combinatorial Counter”

April 14 - Dr. Anne Bowcock
Washington University

April 7 - Genome Sciences Symposium and Panel Discussion

March 31 - Dr. Catherine Peichel
Fred Hutchinson Cancer Research Center
“Genetics of speciation in sticklebacks”

Winter 2010

March 10 -  Dr. Sean Eddy
HHMI Janelia Farm Research Campus
“HMMER3: A New Generation of Sequence Homology Search Software”
sponsored jointly with Combi Seminar

March 5 - Dr. Joan Bennett
"From Hurricane Katrina and its moldy aftermath to 'sick building syndrome' and its elusive etiology"
sponsored jointly with WiGS

March 4 - Dr. Joan Bennett
"Doing science with two X chromosomes"
sponsored jointly with WiGS

March 3 - Dr. Ken Wolfe
Smurfit Institute of Genetics, Trinity College
“Yeast Comparative Genomics and the Aftermath of Ancient Polyploidization”
sponsored jointly with Combi Seminar

March 1 - Dr. Shao-En Ong
Broad Institute of MIT and Harvard
"Hitting the Target with Quantitative Proteomics: Applications in
Discovering Small Molecule-Protein Interactions with SILAC”

February 24 - Dr. Andrew Clark
Cornell University
sponsored jointly with Combi Seminar

February 24 - Dr. Mathew Sowa
Department of Pathology, Harvard Medical School
"Tools and Techniques for Proteomic-based Discovery and Analysis of
Protein Interactions and Signaling Pathways”

Thursday, February 18 - Dr. Sharon Pitteri
Fred Hutchinson Cancer Research Center
"Molecular Profiling of Breast Cancer from a Proteomics Perspective”

February 17 - Dr. Manolis Kellis
Associate Professor of Computer Science
MIT Computer Science and Artificial Intelligence Laboratory

February 10 -  Dr. David Stahl
UW Civil & Environmental Engineering
“Microbial Transformations of Nitrogen: from Genomes to Global Processes”

February 10 - Dr. Alejandro Wolf-Yadlin
Department of Chemical Biology, Harvard University
"Deciphering Receptor Tyrosine Kinase Signaling Networks Conservation and Diversification Using Lysate Microarrays”

February 3 -  Dr. David Reich
Harvard University
“Learning about Population History from Genomic Data”
sponsored jointly with Combi Seminar

January 27 - Dr. Eric Green
Director, NHGRI
sponsored jointly with Combi Seminar

January 20 - Dr. Chris Burge
MIT
“Global Analysis of RNA Processing in Health and Disease”
sponsored jointly with Combi Seminar

January 13 -  Dr. Greg Gibson
Professor and Director of the Center for Integrative Genomics, Department of Biology, Georgia Tech
“Geographical Genomics, Human Transitions, and the Origins of Chronic Disease”

January 6 -   Dr. John Stamatoyannopoulos
“Mapping and Footprinting the Human Regulatory Genome”

Autumn 2009

December 9 - Dr. David C. Schwartz
Professor of Chemistry and Genetics
University of Wisconsin 
“A Singular View of the Genome”

December 2 -  Dr. Aviv Regev
Broad Institute / MIT
“Modular Biology: The Function and Evolution of Regulatory Networks”
sponsored jointly with Combi Seminar

November 18 - Dr. Thomas Schwarz
Harvard Medical School / Children's Hospital
"Two Problems for a Neuron: Moving Mitochondria and Building Synapses"

Monday, November 16
Roundtable Discussion:
Personal Genomes: Promise or Hype?

Dr. Sydney Brenner

November 4 -  Dr. Sharad Ramanathan
FAS Center for Systems Biology, Harvard University
“Evolution of Protein Kinase Pathways”

October 28 - Dr. Victoria Prince
Department of Organismal Biology and Anatomy
University of Chicago
“Using Zebrafish to Learn How to Build a Pancreas”

October 21 - Dr. Dmitri Petrov 
Stanford University
"Adaptation in Drosophila"

October 14 -  Dr. Kun Zhang
UC San Diego
“Targeted Methylome Analysis of Human Pluripotent and Adult Cells”

October 7 - Dr. Barak Cohen  
Washington University Medical School
“Analysis of Natural Variation in Yeast”

Thursday, October 1 - Dr. Edward Ramos
Science Policy Analyst and Research Fellow
Center for Research on Genomics and Global Health at NHGRI
"From Bench to Bills (and back): the intersection of science and policy"

Summer 2009

8/19 - Dr. Greg Cooper
Acting Assistant Professor of Genome Sciences
"High-throughput analysis of large copy-number variants and hotspots of human genetic disease"

Spring 2009

June 3 - Dr. Jonathan Ewbank
Group Leader, Centre d'Immunologie de Marseille-Luminy, INSERM-CNRS, France
"Genetics and genomics to dissect innate immunity in C. elegans"

May 27 - Dr. Rob Mitra
Assistant Professor, Department of Genetics, Washington University School of Medicine
"New technologies for the analysis of gene regulatory networks"

Thursday, May 21 - Dr. Su-In Lee
Visiting Assistant Professor
Machine Learning Department, Lane Center for Computational Biology
Carnegie Mellon University
"Gene Regulation and Individual Genetic Variation: From Networks to Mechanism”

May 20 - Dr. Pui-Yan Kwok
Professor of Dermatology, Henry Bachrach Distinguished Professor and Investigator Cardiovascular Research Institute, University of California, San Francisco
"Genetic Analysis of Complex Traits"

May 13 - Dr. John Carlson
Eugene Higgins Professor of Molecular, Cellular, and Developmental Biology, Yale University
"Olfaction in Drosophila and Anopheles"

May 6 - Dr. Paul Nurse
President, Rockefeller University
"Controlling the Cell Cycle"
seminar video

Thursday, April 30 – Genome Sciences Symposium

April 22 - Dr. Arlene Blum
"Breaking Trail: Molecules and Mountains"

April 15 - Dr. Len A. Pennacchio
Senior Staff Scientist, Genomics Division, Head, Genomic Technologies Department
Joint Genome Institute, Lawrence Berkeley National Laboratory
"Large-Scale Identification of Tissue-Specific Enhancers In Vivo"

April 8 - Dr. David Page
Director, Whitehead Institute
Professor of Biology, Massachusetts Institute of Technology Investigator, Howard Hughes Medical Institute
"What do sex chromosomes have to do with sex?"

April 1 - Dr. Aimee Dudley
Institute for Systems Biology
“Integrating spatial dynamics and genetic variation into systems biology"

Winter 2009

March 18 - Dr. Barbara Wold
Bren Professor of Molecular Biology; Director, Beckman Institute Division of Biology, Cal Tech
"Building genome-wide networks for myogenesis"

Thursday, March 12 - Dr. Nadia Singh
"The Importance of Scale in Drosophila Evolutionary Genomics”

March 11 - Dr. Trudy Mackay
William Neal Reynolds and Distinguished University Professor of Genetics North Carolina State University
"Systems Genetics of Complex Traits in Drosophila"
sponsored jointly with Combi Seminar

Monday, March 9 - Dr. Sherry Yen
"GPS: A Genomic Approach for Measuring Regulated Protein Turnover”

March 4 - Dr. Judit Villen
"Elucidating Signaling Events through Mass Spectrometry-Based Proteomics”

Thursday, February 26 - Dr. Alon Keinan
"Evolutionary History of Modern Humans: A Genomic Perspective”

February 11 - Dr. Steven McCarroll
Broad Institute
"Structural and Regulatory Variation in Human Genomes”

February 4 - Dr. Elhanan Borenstein
Stanford University
"Reverse Ecology: From Large-Scale Analysis of Metabolic Networks, Growth Environments and Seeds Sets to Species Interaction and Metagenomics”

Monday, February 2 - Dr. Andrew Grimson
"Animal MicroRNAs: Their Ancient Origins and Contemporary Targets”

Thursday, January 29 - Dr. Bret Pearson
University of Utah
"Adult Stem Cells, Tumor Suppressors and Regeneration in Planarians”

January 28 - Dr. Michael Ferdig
Associate Professor, Eck Institute for Global Health, Department of Biology, University of Notre Dame
"Dissecting the complexity of malaria drug resistance: integrating gene expression levels and chromosome structural variation"

January 21 - Dr. Leonie Moyle
Assistant Professor, Department of Biology, Indiana University
“Genetics, genomics,and the origin of species”

Tuesday, January 20 - Dr. Gautam Dantas
Department of Genetics, Harvard Medical School
"Functional Microbiomics: Harnessing the Chemical Potential of the Microbial World”

January 14 - Dr. Andrew Fire
Stanford University
"Structure-based genome surveillance mechanisms (or 'How the genome got its stripes')"

Autumn 2008

December 10 - Dr. Leigh Anderson
"Protein Quantitation through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory"

November 19 - Dr. John Roth
UC Davis
"Positive selection for deleterious chromosome rearrangements"

November 12 - Dr. Maitreya Dunham
"Genomic analysis of experimental evolution in yeast"

November 5 - Dr. David Chan
"Mitochondrial dynamics in development and disease"

October 29 - Dr. Daniel Gottschling
Fred Hutchinson Cancer Research Center
"How do cellular sub-systems breakdown with age?"

October 22 - Dr. Jeff Long
University of Michigan
"Natural Selection for an Allele (ALDH2-2) that Blocks Ethanol Metabolism”

October 15 - Dr. Jon Beckwith
American Cancer Society Professor
Department of Microbiology and Molecular Genetics
Harvard Medical School
“Evolution and Diversity of Pathways for Protein Disulfide Bond Formation and Reduction in Bacteria”

October 8 - Dr. Kevin Hiom
MRC Laboratory of Molecular Biology
"Genomic instability and cancer : Lessons from the analysis of BRCA1"

October 1 - Dr. Harmit Malik
Fred Hutchinson Cancer Research Center
sponsored jointly with Combi Seminar

Summer 2008

September 11 - Dr. Joshua Coon
"Characterizing the Human Embryonic Stem Cell Proteome with an ETD-Enabled Orbitrap Mass Spectrometer"

June 30 - Dr. Anne Donaldson
“Telomere replication and positioning: molecules and mechanisms”

Spring 2008

May 28 - Dr. Anne Yoder
"Using genetic signatures of Madagascar's vertebrates as a method for time travel into the past "
Duke University

May 22 (Thursday)
The 4th Annual Genome Training Grant Symposium
Dr. Joseph Felsenstein
Dr. William Rice
Dr. Mohamed Noor
Dr. Hopi Hoekstra
Foege Auditorium
8:30 - 11:20 a.m.

May 21 - Dr. David Goldstein
Duke University
“Host determinants of response to HIV-1”

May 19 - Dr. Katherine Friedman
Vanderbilt University
"Finding the right balance: Mechanisms of telomere length homeostasis in yeast"

May 14 - Dr. Gerald Rubin
Howard Hughes Medical Institute
“Using Genomics to Develop New Tools for Neuroanatomy and Neurogenetics in Drosophila

May 7 - Dr. June Nasrallah
Cornell University
“Recognition and Rejection of Self in Plant Reproduction: Mechanism and Evolution”

April 30 - Dr. Joseph Ecker
“1,001 Genomes: Genetic and Epigenetic Variation in Arabidopsis
The Salk Institute for Biological Studies

April 24 - The 7th Annual Genome Sciences Symposium

April 23 - Genome Sciences Community Panel Discussion

April 16 - Dr. Kimmen Sjolander
University of California, Berkeley
“Phylogenomic analysis on a pan-genome scale”

April 16 - Dr. Richard Lewontin
Harvard University
Joint talk for Genome Sciences, Medical Genetics, and Public Health Genetics
"Frequency and Population Context Dependent Fitness"
1:30-2:30 pm

April 9 - Two Seminars:

Dr. David Han
"Large-scale Quantitative Phosphoproteomic Analysis of T-Cell Receptor
Signaling: System-wide Modulation of Protein-Protein Interaction
Mediated by Site-Specific Phosphorylation "
1:30, Foege Auditorium

Dr. David Botstein
Princeton University
“Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast”
3:30, Foege Auditorium

April 2 - Dr. Joshua Akey
University of Washington
“Genome Wide Scans for Selection: It Was the Best of Times, It Was the Worst of Times”

Winter 2008

March 12 - Dr. Joanne Chory
The Salk Institute
“Dissection of Growth Control Networks in Plants”

March 12 - Dr. Qianjun Wang
“Proteomics on the brain – The role of autophagy (self-eating) in axons”

March 10 - Dr. James Bruce
“Chemistry and Mass Spectrometry: New Tools for Protein Interaction Network Identification"

March 5 - Dr. Pardis Sabeti
“Natural selection in humans and pathogen”
Broad Institute of MIT and Harvard

February 27 - Dr. John Stamatoyannopoulos
University of Washington
“Multi-lineage programming of human regulatory DNA”
sponsored jointly with Combi

February 27 - Dr. Jonathan Trinidad
“Understanding the Function of Synapses in Health and Disease”

February 20 - Dr. Elaine Ostrander
National Human Genome Research Institute
“Dog Genes Tell Surprising Tales: Finding Genes for Complex Traits"

February 13 - Dr. Steven Henikoff
Fred Hutchinson Cancer Research Center
“Histone variants and epigenetic inheritance”
sponsored jointly with Combi

February 6 - Dr. Goncalo Abecasis
University of Michigan
“Adventures in Genome Scanning: Meta-Analysis and Genotype Imputation Identify New Loci Influencing Lipid Levels and Coronary Artery Disease”
sponsored jointly with Combi

January 30 - Dr. Job Dekker
University of Massachusetts Medical School
“Towards spatial maps of the human genome”

January 23 - Dr. Joel Hirschhorn
Broad Institute of MIT and Harvard
“Genetics of body size and other complex traits”
sponsored jointly with Combi

January 17 - Dr. Charles Kurland
Professor Emeritus of Molecular Biology, University of Uppsala, Uppsala, Sweden
"Are Archaea and Bacteria pre-Karyotes or post-Karyotes?"

January 16 - Dr. Steven Carr
Broad Institute of MIT and Harvard
“Progress Toward a Biomarker Discover-to-Verification Pipeline in Clinical Proteomics"

January 9 - Dr. Carlos Bustamante
Cornell University
"Whole Genome Association Mapping and Population Genomics of Domesticated Species: Promises, Potential Pitfalls, and Preliminary results"
sponsored jointly with Combi

Autumn 2007

December 5 - Dr. Thomas Petes
Duke University
"Genetic regulation of genome stability in yeast"

Tuesday, November 27
Biology Seminar; Co-sponsored by Genome Sciences
Dr. Morris Goodman

Department of Anatomy and Cell Biology; Wayne State University
“Phylogenomics of Primates and Other Mammals: Deep Roots of the Adaptive Evolution Behind Human Uniqueness”

November 14 - Dr. Jake Lusis
UCLA
"Integrating genetics and genomics to understand complex cardiovascular traits"

November 7 - Dr. Huda Zoghbi
Baylor College of Medicine
"Genetic and Biochemical Approaches to Polyglutamine Neurodegenerative Disorders"

October 24 - Dr. Michael MacCoss
University of Washington
“Finding Protein Needles Amongst Cellular Haystacks”

October 17 - Dr. Bing Ren
University of California, San Diego
“Global analysis of gene regulatory networks and epigenome in mammalian cells”

October 10 - Dr. Lucy Shapiro
Stanford University
“An integrated Genetic System Controls the Tempotal and Spacial Architecture of the Bacterial Cell Cycle”

October 3 - Dr. Virginia Zakian
Princeton University
“Maintaining the end: regulation of telomerase in yeast”

October 1 - Dr. Chris Ponting
University of Oxford
“Recombination and rapid evolution of genes and chromosomes”

September 26 - Dr. Michael Nachman
University of Arizona
“Population genetics of wild and inbred house mice: insights into speciation and the use of mice as models for biomedical research”

Spring 2007

June 6 - Dr. Debra Schwinn
University of Washington
"Perioperative Genomics: Defining the Vulnerable Patient"

May 29 (Tuesday) - Dr. Susan Lindquist
MIT
“The Surprising Biology of Protein Misfolding”

May 23 - Dr. Scott Edwards
Harvard University
“Genome evolution in Reptilia, the sister group of mammals”

May 16 - Dr. Andrew Chisholm
University of California, San Diego
“Regeneration and repair of C. elegans neurons and skin"

May 15 - Dr. Robert Cook-Deegan
Duke University
"Intellectual Property and Genomic Innovation: DNA Science, Patents and Money"

May 9 - Dr. Amy Pasquinelli
University of California, San Diego
“MicroRNAs: A Small Contribution from Worms”

May 2 - Genomic Medicine Seminar
Dr. Carole Ober
University of Chicago
"Genome-Wide Association Studies in a Founder Population"

April 25 - Genome Sciences Symposium: "Pests, Plagues and Plants: Genomics and Global Health"

April 11 - Dr. Susan Mango
“Making and shaping the digestive tract”
University of Utah

April 4 - Genomic Medicine Seminar
Dr. David Altshuler
Broad Institute
“Genome sequence variation and the inherited basis of common disease”

March 28 - Dr. Maggie Werner-Washburne
University of New Mexico
“Differentiation of quiescent and non-quiescent yeast cells: Novel model systems for critical eukaryotic processes”

March 26 - Dr. Donald Kirkpatrick
Department of Cell Biology
, Harvard Medical School
“Decoding Signals of the Ubiquitin-Proteasome Pathway using Quantitative Mass Spectrometry”

Winter 2007

March 7 - Dr. Matthew Saunders
“Human Nucleotide Variability and Signatures of Natural Selection”

March 5 - Dr. Lin He
“MicroRNAs in Cancer Biology: Small Regulators with a Big Impact”

March 1 - Dr. Zhiping Weng
“Computational Analysis of Transcription Regulation in the Human Genome and Protein
-protein Docking”

February 28 - Dr. Eric Siggia
The Rockefeller University
“Fluctuations and the cell cycle in budding yeasts”

February 27 - Dr. Benjamin Garcia
“Reshaping the Chromatin Landscape with Mass Spectrometry Based Proteomics”

February 21 - Dr. Sara Sawyer
“Tracking the Evolutionary Footprints of Viruses”

February 14 - Dr. Maitreya Dunham
“Genome-scale molecular analysis of experimental evolution in yeasts”

February 7 - Dr. Christine Queitsch
Harvard
University
“Phenotypic robustness and variance: molecular mechanisms and evolutionary impact”

February 5 - Dr. Jay Shendure
Harvard
Medical School
“Technologies & Tools for the Next Generation of DNA Sequencing”

January 31 - Dr. Patrick Brown
Stanford University
“The ‘dark matter’ of biological regulation?  Diversity and specificity of RNA-binding proteins in yeast”

January 29 - Dr. Jenny Graves
Professor, Comparative Genomics, Australian National University
"Genome of Weird Australian Mammals"

January 24 - Dr. Martha Bulyk
Harvard University
"DNA Regulatory Codes:  Genomic Analyses of Transcription Factors and Cis Regulatory Elements"

Abstract:
The interactions between transcription factors (TFs) and their DNA binding sites are an integral part of the cellular regulatory networks that control gene expression. We have developed in vitro protein binding microarray (PBM) technologies that allow the rapid, high-throughput characterization of the DNA binding site sequence specificities of TFs in a single day. We are currently performing PBM experiments on a large number of yeast and mouse TFs, as well as TFs from other organisms. We plan to use PBM data on the DNA binding specificities of metazoan TFs for more accurate prediction of cis regulatory modules within the vast noncoding portions of those organisms' genomes. Specifically, we are inferring co-regulation by sets of TFs through an integrated analysis of gene expression data, TF binding site motif data, and prediction of cis regulatory modules.

January 22 - Dr. Paul DeBakker
“Genetic variation and human disease”

January 17 - Dr. Daniel Pinkel
UC San Francisco
“Confronting the Genome with Array CGH”

January 10 - Dr. Jonathan Pritchard
University of Chicago
“Genetic Variation and Natural Selection in the Human Genome”

January 3 - Genomic Medicine Seminar
Dr. Huntington Willard
Duke University

Autumn 2006

December 6 - Genomic Medicine Seminar
Dr. Eric Schadt
Rosetta Inpharmatics
“A systems genetics approach to dissecting complex physiological traits associated with disease"
sponsored jointly with Combi

November 29 - Dr. Jonathan Sebat
Cold Spring Harbor Laboratories

November 15 - Dr. Edward Rubin
Lawrence Berkeley National Laboratory
“Extreme Comparative Genomics: Microbes to Neanderthals”

November 8 - Dr. Patrick Griffin
Scripps Florida
“Probing the mechanism of partial agonist activation of PPARy”

November 1 - Genomic Medicine Seminar
Dr. Terry Hassold
Washington State University
"Aneuploidy in humans: where we've been, where we're going"

October 25 - Dr. David Muddiman
North Carolina State University
“Novel Chemical and Instrumental Approaches Coupled to ESI-FT-ICR Mass Spectrometry to Effectively Address Proteomics Questions”

October 18 - Dr. Richard Smith
Pacific Northwest National Laboratory
“Biological Variation and Proteome Biomarker Discovery”

October 11
- Dr. Lon Cardon
Fred Hutchinson Cancer Research Center
sponsored jointly with Combi

10/4
- Genomic Medicine Seminar
Dr. Janis Abkowitz
University of Washington
"The genetic regulation of heme trafficking: lessons from cat and mouse"

Spring 2006

6/13 - Dr. Joseph Loo
"Mass Spectrometry for Characterizing Proteins and Proteomes"

6/1 - Dr. Andrew Emili
“Cracking the Proteome Code: Squaring the Circle”

5/31 - Dr. Claire Fraser
The Institute for Genome Research

5/24 - The 5th Annual Genome Sciences Symposium
"Insights From Model Organisms"
all day, Hogness Auditorium

5/17 - Dr. Oliver Hobert
Columbia University
“MicroRNAs and the neuronal cell fate determination in C. elegans

5/10 - Genome Sciences / Developmental Biology Training Grant Joint Seminar:
Dr. Trudi Schüpbach

Princeton University
“Regulation of EGF receptor activation in Drosophila oogenesis”

5/3 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Buddy Ratner
UW Bioengineering
“Biomaterials: A Platform Technology for Diagnostics, Therapeutics and Medical Devices"
Dr. Cecilia Giachelli
UW Bioengineering
“Genetic Control of Vascular Calcification: Implications for Therapy and Biomaterial Development"

4/26 - Dr. Mark Gerstein
Yale University
“Understanding Protein Function on a Genome-scale using Networks”

4/19
- Dr. David Sabatini
Whitehead Institute for Biomedical Research
“New Approaches to the Study of Growth Control”

4/12 - Dr. Rasmus Nielsen
Cornell University
“Detecting positing selection from DNA sequence data”

4/5 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Joan Sanders
“Prosthetic Engineering”

Dr. Jay Rubinstein
"Engineering cochlear implants: from channel kinetics to sound perception"

UW Bioengineering

4/4
Dr. Anton Valouev
University of Southern California
“Optical Mapping: Technology, data, and application to finding structural genomic variants”
1-2
, K-069

3/29 - Dr. Vivian Cheung
University of Pennsylvania
“Genetics of variation in human gene expression”

Winter 2006

3/15 - Dr. Bruce Weir
University of Washington
“Genomic heterogeneity of measures of human population structure”

3/1 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Patrick Stayton
UW Bioengineering
“Smart” Biomaterials

2/22 - Dr. Timothy Hughes
University of Toronto
“The functional landscape of gene expression in yeast and vertebrates”

2/15 - Dr. Helen Hobbs
University of Texas Southwestern Medical Center
“Genetic Architecture of Plasma Lipoprotein Levels: Impact on Atherosclerosis”

2/8 - Dr. David Parichy
University of Washington
“Zebrafish pigment pattern and somatic metamorphosis: models for development and evolution of adult form”

2/3 - Genome Sciences / Microbiology Joint Seminar
Dr. Charles Kurland
“Evolution of the Eukaryotic cell”

2/1 - Genome Sciences / Bioengineering Joint Seminar
Dr. Suzie Pun
“Nanoparticles for targeted drug delivery”

Dr. Thomas Horbett
“Biological Activity of Absorbed Proteins: A Basis for Improved Design of Biocompatible Biomaterials”

Dr. David Castner
“Surface Science Studies of DNA Microarrays”

UW Bioengineering

1/25 - Dr. Christopher J. O'Donnell
NHLBI/Framingham Heart Study
“Evolving Genomic Approaches to the Study of Complex Cardiovascular Diseases in Human Populations”

1/18 - Dr. Benjaman Cravatt
Scripps Research Institute
“Activity-based proteomics”

1/11 - Dr. Pavel Pevzner
UC San Diego
“The Fragile Breakage versus Random Breakage Models of Chromosome Evolution”

1/4 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Gerald Pollack
"Unexpectedly central role of water in cell function"

Dr. Shahram Vaezy
"Ultrasound for Therapy: Hemorrhage Control, Tumor Treatment, and Gene/Drug Delivery"

Dr. Xingde Li
“Translational Optical Imaging Techniques” 

UW Bioengineering

Autumn 2005

12/14 - Dr. Susan Lolle
NSF
"Evidence for non-Mendelian inheritance of ancestral sequences in plants”
Genome Sciences / Developmental Biology Training Grant Joint Seminar

12/7 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Paolo Vicini
"From Biomarkers to Surrogate Endpoints: Regression Models for Disease Quantification"

Dr. Henry Lai
"Electromagnetic Fields and Artemisinin"

Dr. Allan Hoffman
"Having Fun Combining Smart Polymers With Biomolecules"

11/30 - Dr. David Schwartz
University of Wisconsin
“Single Molecule Analysis of Mammalian Genomes”

11/16 - Dr. Yishi Jin
UC Santa Cruz
“Molecular Mechanisms of Synapse Assembly in C. elegans Nervous System”

11/9 - Dr. Kelly Frazer
Perlegen Sciences
“Human Genetic Variation”

11/2 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Albert Folch
UW Bioengineering
"Life on a chip: microfluidic devices for cell biology studies"

Dr. James Bassingthwaite
UW Bioengineering
"The Physiome Project: Genes to Human Function"

Dr. James Bryers
UW Bioengineering
"Bacterial Biofilms"

10/19 - Dr. Rick Kittles
Ohio State University
“Genetic Ancestry and Prostate Cancer Risk”

10/12 - Dr. Neil Kelleher
University of Illinois
“Chromatin and Beyond: Detecting Post-translational Switches in the Human Nucleus by Next-Generation Mass Spectrometry”

10/5 - Genome Sciences / Bioengineering Joint Seminar:
Dr. Paul Yager
UW Bioengineering
"Microfluidics for Point-of-Care Bioassays"
Dr. Wendy Thomas
UW Bioengineering
"Beyond Protein Structure: How Mechanical Force Regulates
Function"
Dr. Narendra Singh
UW Bioengineering
"DNA damage, aging and cancer treatment"

9/28 - Dr. Melissa Moore
Brandeis University
"The Exon Junction Complex and Spliced mRNA Metabolism"
&
"Functional Proofreading of Eukaryotic Ribosomes"

Summer 2005

8/24 - Dr. Robin Holliday
"Aging is no longer an unsolved problem in biology"

8/19 - Dr. Shobhit Gupta
Max Planck Institute for Molecular Genetics
"EST-based detection and analysis of mammalian transcripts"
1:30, Health Sciences K-350

Abstract:

Alternative splicing generates multiple products from a single gene
and partly explains the diversity in eukaryotic transcriptomes.
Expressed Sequence Tag (EST) data is a major resource that enables
identification of exon-intron structure of transcripts, including the
alternative ones. However, technical artifacts like contamination of
the EST data with unspliced mRNA, gaps in the alignment, etc. lead to
incorrect predictions of exon-intron boundaries. Therefore, this
thesis aims to separate potentially reliable splice sites from the
frequent data-/method-related artifacts. Once the gene structure has
been efficiently delineated, the more complicated derivation of
tissue-/tumor-specific transcripts could be addressed with increased
reliability.

In this work the EST data has been employed to reliably identify
(alternative) transcripts. Subsequent evaluation of the expression
patterns using RT-PCR experiments confirmed the tissues in which the
transcripts were predicted to be expressed, but often revealed
expression in additional tissues. Therefore, such predictions of
expression patterns of transcripts need to be supported by large scale
validation experiments, for example using cutting edge microarray
technology (Johnson et. al., 2004, Science). Such an integration is
facilitated by our comprehensive database, T-STAG. Advanced features
of the T-STAG web-interface enable several biological applications
like the detection of tumor markers and the evolution of
tissue-specific expression of transcripts.

Dr. Gupta is interviewing for a postdoctoral position in the Noble
lab. If you are interested in meeting with him during his visit,
please contact Bill Noble (noble@gs.washington.edu)

Spring 2005

Wednesday, June 1

Dr. Timothy Anderson, Southwest Foundation for Biomedical Research
“Genomic Impact of Strong Recent Selection in Malaria Parasites”

Friday, May 27

Dr. Ulrich Muller, Postdoctoral Fellow, Whitehead Institute for Biomedical Research
"Towards a Self-Replicating System from Catalytic RNA"

Thursday, May 26

"Genes, chromosomes and cells, then and now: some historical perspective"

with a panel consisting of:

James F. Crow, Emeritus Professor of Genetics and Medical Genetics,
University of Wisconsin, Madison

Stan Gartler, Professor, Genome Sciences and Medical Genetics, UW,
Seattle

Arno Motulsky, Professor, Medical Genetics and Genome Sciences, UW,
Seattle

Iris Sandler, Affiliate Instructor, Genome Sciences, UW, Seattle

David Stadler, Professor, Genome Sciences, UW, Seattle

 

Wednesday, May 25
Dr. Erin O' Shea
, UC San Francisco
“Analysis of the Budding Yeast Proteome”

Tuesday, May 24
Dr. Jiang Gui
, UC Davis
"Statistical Learning Methods for Censored Regression in the
High-Dimension and Low-Sample Size Settings, With Applications to
Genomic Data"

Abstract:
"
New high-throughput technologies are generating many types of very
high-dimensional genomic and proteomic data. These data can
potentially be used for predicting clinical outcomes and for studying
interindividual differences in responses to drugs. In practice,
however, the number of independent samples is usually very small as
compared to these high-dimensional genomic data. As a result, many
standard statistical methods cannot be applied directly or perform
poorly in such high-dimension and low-sample size settings. In this
talk, I will present several learning methods for relating microarray
gene expression data to censored survival outcomes. I will demonstrate
and evaluate these methods using both simulations and applications to
real data sets."

Monday, May 23
Frontiers in Biomedical Research Symposium

Wednesday, May 18
GENOME SCIENCES SYMPOSIUM

Wednesday, May 11
Dr. Augustine Kong
, Decode Genetics
“Studying Recombination Rate as a Phenotype” 

Wednesday, May 4
Dr. Jo Handelsman
, University of Wisconsin
“Conversions with the Silent Majority: Signaling and Robustness in Microbial Communities”

Wednesday, April 27
Dr. Arend Sidow
, Departments of Pathology and Genetics, Stanford University
"Functional and Comparative Dissection of Gene Regulation in Ciona"

Wednesday, April 20
Dr. Zhiping Weng
, Boston University

Wednesday, April 13
Dr. Ulf Landegren
, Department of Genetics and Pathology/Molecular Medicine, Rudbeck Laboratory, Uppsala, Sweden
“New Tools to Probe Molecular Composition and Architecture”

Wednesday, April 6
Dr. Edward Marcotte
, Dept of Chemistry and Biochemistry, University of Texas
“Organization and Dynamics of the Yeast Proteome”

Tuesday, April 5
GENOME TRAINING GRANT SYMPOSIUM

Hogness Auditorium (Health Sciences A-420)

Wednesday, March 30
Dr. Marco Marra, University of British Columbia
"A strategy for cloning genome rearrangements in follicular lymphoma"

Winter 2005

Wednesday, March 9 - Dr. Zhenglong Gu
"Evolution of Duplicate Genes and Evolution of Laboratory Yeast"

Monday, March 7 - Dr. Matt Kaeberlein
“Putting the ‘omics’ in Aging Research: A Genome-Wide Hunt for Conserved Regulators of Longevity”

Friday, March 4 - Dr. Richard Bonneau
“The Human Proteome Folding Project and the Inferelator: Two Examples of Computational Systems Biology”

Thursday, March 3 - Dr. Jing Yang
“Molecular Dissection of Multi-Step Tumor Metastasis”

Tuesday, March 1 - Dr. John Stamatoyannopoulos
“Using Chromatin Structure to Map the Cis-regulatory Genome”

Wednesday, February 16 - Dr. Duncan Odom
"Control of Liver and Pancreas Gene Expression by Transcriptional Master Regulators"

Wednesday, February 9 - Dr. Paul Sternberg, California Institute of Technology
“Signaling and Transcriptional Networks Controlling C. elegans Vulva Development”

Monday, February 7 - Dr. Dee Denver
"Spontaneous Mutation and Genome Evolution in Caenorhabditis elegans"

Wednesday, February 2 - Dr. Sebastian Zoellner
"Mapping Complex Disease Genes"

Wednesday, January 26 -

Two Seminars:

Dr. Adam Siepel, University of California, Santa Cruz
"Comparative mammalian genomics: models of evolution and detection of functional elements"
sponsored jointly with Combi

Abstract:
Having the complete genomes of multiple species is causing sweeping changes in biology. Comparative sequence analysis is leading to new insights about the evolutionary forces that have shaped present-day genomes and is enabling previously unknown functional sequences to be identified and characterized. Comparative methods hold particular promise for mammalian and other vertebrate genomes, which--because of their size and complexity, and because of other obstacles to experimental study--have been more difficult to approach experimentally than the genomes of simpler organisms such as flies and nematodes.

In this talk, I will discuss both recent methodological advances in comparative sequence analysis and scientific insights gained from genome-wide surveys conducted with these methods. The main theme of the talk will be using evolutionary models to help shed light on sequence function. Three particular problems will be discussed: the identification of evolutionarily conserved elements, modeling context- or neighbor-dependent substitution, and the identification of evolutionarily conserved protein-coding exons. These problems have been addressed using phylogenetic hidden Markov models (phylo-HMMs), statistical models that describe both the process of nucleotide substitution at individual sites in a genome and how this process changes from one site to the next. Using a phylo-HMM-based program called phastCons, we have conducted a comprehensive search for conserved elements in vertebrate genomes. I will discuss the results of this search and of parallel searches in Drosophila, Caenorhabditis, and Saccharomyces genomes. Particular attention will devoted to the most highly conserved of the elements identified in vertebrates, which appear to be associated with both transcriptional and post-transcriptional regulation and which show significant statistical evidence of an enrichment for RNA secondary structure. In separate work, another phylo-HMM-based program called ExoniPhy has been used to predict about 170,000 protein-coding exons conserved in the human, mouse, and rat genomes, corresponding to an expected 20,400 genes. Of these, about 23,000 predicted exons (2,800 genes) are not represented in sets of known genes. Preliminary experimental (RT-PCR) results indicate that the false positive rate of these predictions is quite low (<30%).

and:

Dr. Thomas Hudson
"Mapping Regulatory Variants in the Human and Mouse Genomes"

Wednesday, January 19 - Dr. Mark Johnston, Washington University
"Feasting, Fasting, and Fermenting: Glucose Sensing and Signaling in Yeast"
website

Wednesday, January 12 - Dr. Michael Lynch, Indiana University
“The Origins of Gene and Genome Complexity”
website
sponsored jointly with Combi

Wednesday, January 5 - Dr. Martin Kreitman, University of Chicago
"Deciphering rules governing enhancer functional evolution"

Abstract:
Lack of knowledge about how regulatory regions evolve in relation to their structure-function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out the first functional genetic complementation analysis of a eukaryotic cis-regulatory module - the even-skipped stripe 2 enhancer - from four Drosophila species. The functional evolution of this enhancer is non-clocklike: important functional differences have evolved between closely related species that are not found between distantly related species. We can attribute the functional conservation between distantly related species to evolutionary convergence rather than evolutionary stasis. Functional divergence of the stripe2 enhancer between closely related species is attributable to differences in activation levels rather than spatio-temporal control of gene expression. Our findings have implications for understanding enhancer structure-function, mechanisms of speciation, and computational identification of regulatory modules.

sponsored jointly with Combi

Autumn 2004

Wednesday, December 8 - Dr. Mariana Wolfner, Cornell University
"Seminal Influences: How Proteins Donated by Males During Mating Females-a Genetic/Genomic Analysis in Drosophila"
website

Wednesday, December 1 - Dr. Rick Myers
"Genome-wide analysis of human transcriptional regulatory elements"
sponsored jointly with Combi

Wednesday, November 17 - Dr. Jennifer Graves, Australian National University
"Exploring Kangaroo and Platypus Genomes"

Wednesday, November 10 - Dr. Edward Kravitz, Harvard University
"Genetic manipulations in the fruit fly fight club"
lab website
related website

Wednesday, November 3 - Dr. Marc Van Gilst, Dept of Cellular and Molecular Pharmacology, UC San Francisco
"Function and Evolution of Dietary Sensing Nuclear Receptors in Nematodes: Fat Regulation, Gene Duplication, and More… "

Wednesday, October 27 - Dr. Catherine Peichel, Fred Hutchinson Cancer Research Center
"Fishing for the Secrets of Speciation: Genetic Analysis of Reproductive Isolation in Sticklebacks"
website

Wednesday, October 20 - Dr. Thomas Gingeras, Affymetrix Inc.
"Empirical Analysis of Sites of RNA Transcription for 30% of the Human Genome: The Changing Landscape of the Human Genome Annotations"
sponsored jointly with Combi

Abstract: The current status of the functional annotations associated with the human genome is in a rudimentary state. The majority of current genome annotations is heavily protein coding gene centric. This focus on protein coding genes intrinsically influences current perceptions of how the genome is structured and is regulated. This view of the genome also has an underlying supposition that transcripts with very little coding potential are not biologically important. However, recent unbiased experiments analyzing the sites of transcription across large sections of the human genome have led to the conclusion that the current human genome annotations can not account for the amounts of empirically detected transcription. (Kapranov, et al. 2002; Rinn, et al., 2003, Kampa, et al., 2004, Martone, et al., 2003, Cawley et al., 2004). Most of the detected unannotated transcription is composed of RNAs with very little coding capacity (<100 aa). These transcripts of unknown function (TUFs) share many properties with well characterized coding genes. Using high density oligonucleotide arrays which interrogate the non-repetitive sequences of human chromosomes 21 and 22 at 35 base pair resolution and a collection of arrays interrogating 30% of the human genome along 10 chromosomes (6,7,13,14,19,20,21,22,X and Y) at a 5 bp resolution, the sites of transcription and transcriptional regulation have been analyzed in 8 developmentally diverse cell lines. Both polyadenylated and non-polyadenylated transcripts have been mapped along the 10 chromosomes and their distribution between cytoplasm and nucleus determined for one of the eight cell lines (HepG2). In previous studies, sites of binding for three transcription factors, cMyc, Sp-1 and p53 along these chromosomes have been mapped along chromosomes 21 and 22 indicating a potential novel strategy for the regulation of some of these detected TUFs. For Sp-1 and c-Myc a total of 866 high confidence binding sites have been mapped in a single cell line. Approximately 23% of these sites are located at least 5 kb away from the nearest annotation ( exon or EST) and many (24%) are proximal to novel non-coding transcripts discovered using these arrays to map the sites of RNA transcription along these two chromosomes. Half of the Sp-1 binding sites are co-localized with a c-Myc binding site and at least 37% of the binding sites of these factors have been mapped within the introns and exons of well characterized genes (Cawley, et al 2004). These data describe unannotated populations of poly A+ and A- transcripts as well as the association of transcription factor binding sites that is strongly suggestive of novel architecture for the transcribed regions of the genome and strategies for transcriptional regulation.

1. Kapranov, P., S. Cawley, J. Drenkow, S. Bekironov, R. L. Strausberg, S. P. A. Fodor and T. R. Gingeras (2002) Large-scale transcriptional activity of the human genome revealed in chromosomes 21 and 22 Science 296: 916-919. 2. Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. , Wheeler, R. , Wong, B. , Drenkow, J., Yamanaka, M.1, Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K. and Gingeras, T. R. (2004) Mapping of transcription factor binding sites points to wide-spread antisense transcription along human chromosomes 21 and 22. Cell 116: 499-510. 3. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S. Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., and T. R. Gingeras (2004) Novel RNAs identified from a comprehensive analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14: 331-342. 4. Martone, R., Euskirchen, G., Hartman, S., Royce, T.E., Luscombe, N.M., Rinn, J.L., Nelson, F.K., Miller, P., Gerstein, M., Weissman, S., and Snyder, M. (2003) Distribution of NF-kappaB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100:12247-12252.

5. Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N. M., Hartman, S. Harrison, M.P., Nelson, F. K., Miller, P., Gerstein, M., Weissman, S. and Snyder, M. (2003) The transcriptional activity of human Chromosome 22. Genes Dev. 17:529-540.

Wednesday, October 13 - Dr. Mark Shriver, Pennsylvania State University
"Ancestry and admixture mapping methods in the search for genes affecting complex disease risks"

Wednesday, October 6 - Dr. Marc Vidal, Harvard University
“Interactome Networks”
website

Abstract:

Despite the considerable success of molecular biology to understand diseases such as cancer, many fundamental questions remain unanswered. Most importantly, since the majority of gene products in the cell mediate their function together with other gene products, biological processes should be considered as complex networks of interconnected components. In other words, for any normal biological process, or any disease mechanism, such as cancer, one might consider a “systems approach” in which the behavior and function of such networks are studied as a whole, in addition to studying some of its components individually. The draft of the human genome sequence is likely to help such a transition from molecular biology to systems biology. Our laboratory uses a model organism, the nematode C. elegans, to study the role of protein networks in development and, doing so, develop the concepts and technologies needed for a transition to systems biology. Our goals are to: i) generate protein-protein interaction, or 'interactome', maps for C. elegans networks involved in development,

ii) develop new concepts to integrate such interactome maps with other functional maps such as expression profiles (transcriptome), global phenotypic analysis (phenome), localization of expression projects (localizome), etc…. and

iii) use such integrated information to discover novel network properties.

Wednesday, September 29 - Dr. Charles Aquadro, Cornell University
"Genome Scans for Footprints of Selection in Drosophila: Lessons, Challenges, and Opportunities for Revealing the Functional Basis of Adaptation"
website
sponsored jointly with Combi

Monday, September 20 - Dr. Jianming Zhang, Department of Ecology and Evolution, University of Chicago
"The Origin And Evolution Of A New Chimerical Drosophila Gene, jingwei"

Summer 2004

Friday, September 3 - Symposium: 40 Years of the Yeast Genome
9 a.m. - 6 p.m.
Physics-Astronomy Auditorium A-118

Monday, August 9 - Dr. Oliver King, Dept of Biological Chemistry and Molecular Pharmacology, Harvard University
"Binding Sites and Barcodes"

Abstract:
I'll talk about models of transcription factor binding sites that relax the assumption of independence between positions.

I'll also talk about designing large sets of DNA segments that don't hybridize to one another, to use for example as barcodes in yeast knockout strains.

Thursday, July 29 - Dr. Robin Dowell, Dept of Biomedical Engineering, Washington University
"Feasible structural alignment of RNAs"

Abstract:
Many non-coding RNAs conserve secondary structure more than sequence. Therefore, to properly align structural RNAs requires simultaneous consideration of both alignment and folding. We utilize a pairwise stochastic context-free grammar (pairSCFG) to model the structural alignment between two RNA sequences. In general, calculating the structural alignment is computationally demanding. Consequently, special care is taken when designing our pairSCFG to minimize resource requirements while retaining solid performance. In addition, we developed a constrained version of the algorithm to further reduce the computational requirements.

Monday, June 28 - Dr. Ting Wu, Department of Genetics, Harvard Medical School
"Transvection: A Pairing-Mediated Homology Effect"

Wednesday, June 23 - Two Seminars:

Informal Seminar:
Dr. Charles Sugnet, Department of of Computer Science, University of California, Santa Cruz
"Discovery and Detection of Alternative Splicing in Humans and Mice"

Abstract:
ESTs and mRNAs have illustrated the prevalence of alternative splicing in both the human and mouse transcriptomes. However, the quality of the EST databases is quite poor, and it is difficult to distinguish between faulty ESTs, aberrant spicing, and alternative splicing events that are functional in normal cells. Using alignments between the human and mouse genomes allows us to translate between the two transcriptomes and find alternative splicing events that are present in both organisms. Because these events have been conserved through evolution, they are likely to provide a functional advantage to the organisms. In addition to being conserved in the transcriptome, the intronic regions proximal to these alternative splicing events are conserved at the genomic level, indicating the presence of possible cis-regulatory elements. Recently, we have also employed splicing sensitive microarrays to detect alternative splicing events in a variety of normal mouse tissues. This approach allows us to explore the regulation of alternative splicing and the importance of alternative splicing to tissue identity and function.

Dr. John Yates, Dept. of Cell Biology, Scripps Research Institute
"Towards Comprehensive Proteomics of Cells"
website

Spring 2004

Wednesday, June 2 - Dr. Matthew Bogyo, Dept. of Pathology, Stanford University School of Medicine
"Small Molecule Probes of Protease Function: Applications from Cancer to Malaria"

Wednesday, May 26 - Dr. Scott Fraser, Professor of Biology, California Institute of Technology
"Imaging Developmental Mechanics and Mechanical Influences on Development in the Vertebrate Embryo"
website
sponsored jointly with the Department of Biology

Monday, May 24 - Dr. George Church, Professor of Genetics, Harvard Medical School and Director of the Lipper Center for Computational Genetics
"New Technologies for Analyzing, Constructing, and Regulating Biological 'Operating Systems' "

Friday, May 21 - Dr. Tim Ting Chen, Assistant Professor, Departments of Biological Sciences, Computer Science, and Mathematics, USC
"De Novo Peptide Sequencing and Peptide Identification via Tandem Mass Spectrometry" (revised title)
website

Wed, May 19 - Genome Sciences Symposium

Wednesday, May 12 - Dr. Thomas Muir, Professor, Rockefeller University
"The Chemical Biology of Protein Splicing"
website

Tuesday, May 11 - Dr. Zemer Gitai, Dept. of Developmental Biology, Shapiro Lab, Stanford University
"Understanding the Mechanisms that Determine Cell Polarity"

Wed, May 5 - Dr. Charles Langley, Professor of Genetics, UC Davis
"The Impact of Strong Selection on Population Genomic Variation"
website
sponsored jointly with Combi

Wed, April 28 - Dr. Andrew Fire, Departments of Pathology and Genetics, Stanford School of Medicine
"Ratcheted DNA and Maintenance of Genetic Activity in the C. elegans Germline"
website

Wed, April 21 - Dr. William Talbot, Associate Professor of Developmental Biology, Stanford University
"Genetic Analysis of Gastrulation in the Zebrafish"
website

Wed, April 14 - Dr. Jay Hirsh, Professor of Biology, University of Virginia
"Flies (& Mice) as Models for Studying Cocaine Response Pathways"
website

Wed, April 7 - Dr. Howard Jacob, Professor and Director, Human and Molecular Genetics Center, Medical College of Wisconsin
"Application of Comparative Genomics to Common Complex Disease"
website

Monday, April 5 - Dr. Christine Wu, The Scripps Research Institute, Department of Cell Biology
"Proteomic Tools for the Cell Biologist"

Friday, April 2 - Dr. Paul Horton, Center for Computational Biology, Tokyo, Japan
"WoLF+PSORT system for protein localization prediction"

visitor to Noble Lab, Informal Seminar
website

Abstract: The prediction of protein subcellular localization sites from amino acid sequence is a problem which has literally produced hundreds of scientific papers. Yet current solutions are black boxish or inaccurate

Several systems employing classifiers such as support vector machines, applied to the amino acid content or simple generalizations of the amino acid content of proteins have shown relatively high accuracy. In contrast, the older PSORT and PSORTII programs mainly rely on features which have been shown to exert causal influence on localization. Unfortunately (tests used by this author at least) show that the accuracy of the PSORT and PSORTII programs is not competitive with the state of the art, although the detailed analysis of sorting signals output by the PSORT programs is still useful to biologists.

In this talk we introduce a classification program which utilizes both PSORT features and amino acid content to produce a prediction accuracy which is competitive with state of the art SVM + generalized amino acid content approaches. Like PSORTII, the program is example based and shows the user what examples the classification is based on. This has two advantages 1) biologically sophisticated users can decide if the examples upon which the decision is based are plausible, and 2) ad hoc localization annotation associated with the examples (such as multiple or conditional localization), which are important but don't easily fit into a classification problem formulation, can be shown to the user.

Wed, March 31 - Dr. Coleen Murphy, Department of Biochemistry and Biophysics School of Medicine, UCSF, Mission Bay
"Genes That Act Downstream of the DAF-16 FOXO Transcription Factor to Influence the Lifespan of C. elegans"

Winter 2004

Wed, March 17 - Two Seminars:

Dr. Benjamin Turk, Research Assoc., Dept. of Systems Biology, Harvard Medical School & Division of Signal Transduction at Beth Israel Deaconess Medical Center
"Novel Peptide Library Approaches for Functional Profiling of Proteases and Protein Kinases"

and

Dr. Asa Ben-Hur, Department of Biochemistry, Stanford University
"Protein sequence motifs: predicting protein function, remote homology, and protein-protein interactions"
website

visitor to Noble Lab, Informal Seminar

Wed, March 10 - Dr. Amy Kiger, Department of Genetics, Harvard Medical School
"Inside-Out: Investigating Cell Shape Using Genome-Wide RNAi"

Monday, March 1 - Dr. Siavash Kurdistani , Department of Biological Chemistry, UCLA
"Mapping Global Acetylation Patterns to Gene Expression"

Wed, March 3 - Dr. Joshua Akey, Affiliate Postdoctoral Fellow, Kruglyak Lab, Human Biology, Fred Hutchinson Cancer Research Center
"Computational Studies of Genetic Variation: Searching For Signatures of Selection in Humans and Mapping Gene Expression QTL in Yeast"

Wed, February 25 - Dr. Noah Rosenberg, Research Associate, Program in Molecular and Computational Biology, University of Southern Calfornia
"Genome-wide Analysis of Human Variation and Population Structure"
website
sponsored jointly with Combi

Wed, February 18 - Dr. Steve Warren, Professor and Chair, Dept of Human Genetics, Emory University
"The FMR1 Gene: Two Diseases and Two Mechanisms"
website

Wed, February 11 - Dr. Sean Eddy, Associate Professor of Genetics, Washington University
"Computational Analysis of Noncoding RNA Genes"
website
sponsored jointly with Combi

Thursday, February 12 - Dr. Stephen Proulx, Center for Ecology & Evolutionary Biology, University of Oregon
"The Evolution of Genome Complexity: The Rise and Proliferation of Genetic Interactions"
website
3:30 - 4:30, T-739 Health Sciences

Wed, February 4 - Dr. Jane Gitschier , Professor of Genetics, UC San Francisco
"Absolute Pitch: Genetics and Perception"
website

Wed, January 28 - Dr. Marcus Feldman, Professor, Stanford University
"Some Perspectives on the Genetic Structure of Human Populations"
website
sponsored jointly with Combi

Wed, January 21 - Dr. Brian Chait, Professor, Rockefeller University
"Proteomic Tools for Dissecting Cellular Function"
website

Wed, January 14 - Dr. Terry Speed, Professor of Statistics, UC Berkeley
"Incorporating Dependence Into Models for Biomolecular Motifs"
website
sponsored jointly with Combi

Wed, January 7 - Dr. Eric Green, M.D., Ph.D., Senior Investigator and Chief, Genome Technology Branch, NHGRI
"Multi Species Comparative Sequencing: Using Evolution to Decode the Human Genome"
website

Autumn 2003

Wed, December 10 - Dr. Jonathan Pritchard, Assistant Professor of Human Genetics, University of Chicago
"Linkage Disequilibrium in the Human Genome, and Implications for Complex Trait Mapping"
website
sponsored jointly with Combi

Wed, December 3 - Dr. Victor Ambros, Professor of Genetics, Dartmouth College
"Small Noncoding RNA's and Animal Development"
website

Wed, November 19 - Dr. Gisela Storz , NICHD
"Regulating With Noncoding RNAs"
website

Wed, November 12 - Dr. Simon Tavare, Professor of Biological Sciences, University of Southern California
"Approximate Bayesian Computation in Population Genetics"
website
sponsored jointly with Combi

Wed, November 5 - Dr. James Kent, UC Santa Cruz
"The Gene Family Browser and other Recent Research at genome.ucsc.edu"
website
sponsored jointly with Combi

Wed, October 29 - Dr. Mario Capecchi, Professor of Biology and Human Genetics, University of Utah
"Gene Targeting Into the 21st Century: Mouse Models of Human Disease from Cancer to Psychiatric Disorders"
website

Wed, October 22 - Dr. Terry Hwa, Professor of Physics, UC San Diego
"Complex Transcriptional Logics From Simple Molecular Interactions"
website
sponsored jointly with Combi

Wed, October 15 - Dr. Eric Selker, University of Oregon
"Genome Defense and DNA Methylation in Neurospora"
website

Wed, October 8 - Dr. Ajit Varki, Professor of Medicine, UC San Diego
"Multiple Differences in Sialic Acid Biology Between Humans and Great Apes"
website

Wed, October 1 - Dr. Mark Chee, Vice President of Genomics, Illumina, Inc.
"Accessing Genetic Information: Technology for Large Scale SNP Genotyping"
website

Summer 2003

Monday, July 14 - Dr. Shozo Yokoyama, Asa Griggs Candler Professor Department of Biology, Emory University
"Molecular Genetics and the Evolution of Color Vision in Vertebrates."

Spring 2003

Wed, June 4 - Dr. Deirdre Meldrum, Prof., Dept. of Electrical Engineering, University of Washington
"Microsystems and Applications for Life-on-a-Chip"
website
sponsored jointly with COMBI

Wed, May 28 - Dr. Martin Yanofsky, Dept. of Biology, University of California-San Diego
"Flower and Fruit Development in Arabidopsis"
website

Wed, May 21 - Dr. Gabriel Guarneros, Dept. de Genetica y Biologia Molecular, Centro de Investigacion y de Estudios Avanzados, Mexico City, Mexico.
"Minigenes as Models for the Effect of Early Codon Composition on Protein Synthesis"

Wed, May 14 - Genome Sciences Symposium: "Human - Mouse Comparative Biology"

Wed, May 7 - Dr. Jay Heinecke, Dept. of Medicine, UW
"Oxidants Restrain Matrix Metalloproteinase Activity by Making Kinky Proteins"
website

Wed, April 30 - Dr. John Carlson, Dept. of Molecular, Cellular & Developmental Biology, Yale University
"Odor and Taste Receptors in Drosophila: Genetics and E-genetics"
website

Wed, April 23 - Dr. Robert Darnell, Laboratory of Molecular Neuro-Oncology, Rockefeller University
"Paraneoplastic Neurologic Disorders: Windows Into Neuron-Specific Regulatory Systems and Tumor Immunity"
website

Wed, April 16 - Dr. Randy Schekman, University of California, Berkeley; HHMI & Prof. of Cell & Developmental Biology, and Affiliate, Div. of Biochemistry & Molecular Biology
"Mechanism of Cargo Sorting in the Secretory Pathway"
website

Wed, April 9 - Dr. Phil Benfey, Dept. of Biology, Duke University
"Identifying Transcriptional Networks Using Cell-type Specific Expression Profiling"
website

Wed, April 2 - Two Speakers:

Dr. Karen Mohlke, Genome Technology Branch, National Human Genome Research Institute
"Evaluating a Complex Trait: Evidence for Type 2 Diabetes Susceptibility Genes in Finns"
1:30, K-069

and

Dr. Terry Gaasterland, Rockefeller University, Laboratory of Computational Genomics
"Computational Analysis of Splicing in Mouse and Trypanosomes"
website
Jointly sponsored with COMBI.

Mon, March 31 - Dr. Bradley Bernstein, Dept. of Chemistry & Chemical Biology, Harvard University
"Global Approaches for the Study of Chromatin"
1:30, K-069

Winter 2003

Mon, March 24 - Dr. Scott Seiwert, Ribozyme Pharmaceuticals Inc.
"Molecular Engineering of Nucleic Acids for Biosensor Applications"
1:30, J-280

Wed, March 19 - Two Speakers:

Dr. Robin Allshire, Wellcome Trust Centre for Cell Biology, ICMB The University of Edinburgh, Scotland
"Silencing In and Out of Fission Yeast Centromeres"
11:30, J-280 and

Dr. Kara Koehler, Department of Genetics, Case Western Reserve University
"The Incredible Egg: Modeling Human Aneuploidy in the Mouse"
K-069, 1:30
sponsored jointly with COMBI

Mon, March 17 - Two Speakers:

Dr. David Wang, Department of Biochemistry & Biophysics, University of California, San Francisco
"A Viral Genomics Approach to Pathogen Detection"
1:30, J-280

Dr. Kerry Kim, Physics Dept., St. Lawrence University, NY
"Characterization and Analysis of Temporal Contrast Adaptation in the Salamander Retina"
website
2:30, K-069

Wed, March 12 - Two Speakers

Dr. Evan Eichler, Department of Genetics, Case Western Reserve University
"Recent Duplication, Disease and the Evolution of the Human Genome"
1:30, K-069
Jointly sponsored with COMBI.

Dr. Joanne Chory, Plant Molecular & Cellular Biology, Salk Institute
"Light, Brassinosteroids, and Arabidopsis Development"
website

Wed, March 5 - Two Speakers:

Dr. Len Pennachio, Department of Genome Sciences, Lawrence Berkeley National Laboratory
"Expoiting Vertebrate Sequence for Insights into Human Biology"
1:30, K-069
Jointly sponsored with COMBI.

Dr. Richard Losick, Dept. of MCB-Biochemical Sciences, Harvard University
"Generating and Exploiting Asymmetry in a Simple Organism"
website

Mon, March 3 - Dr. Lars Steinmetz, Dept. of Biochemistry, Stanford University
"Functional Genomics of Complex Traits and Pathways"
1:30, J-280

Mon, Feb 24 - Dr. Michael J. MacCoss Dept. of Cell Biology, Scripps Research Inst.
"Technological Advances in the Measurement of Proteins and Protein Modifications in Complex Mixtures by Mass Spectrometry"
1:30 p.m., K-069

Tues, February 25 - Dr. Fotis Kafatos Director-General, European Molecular Biology Laboratory Heidelberg, Germany
"Malaria and the Mosquito: Innate Immunity and Plasmodium Transmission"
3:00 - 4:00 p.m. Rm. K-069
sponsored jointly with Medical Genetics

Wed, February 26 - Mel Feany, M.D. & Ph.D., Asst. Prof. of Pathology, Brigham & Women's Hospital, Harvard University
"Modeling Human Neurodegenerative Disease in Drosophila"

Wed, February 19 - Dr. Ian Hickson, University of Oxford
"Bloom's Syndrome: A Chromosomal Instability Disorder Associated with Cancer Predisposition"
website

Wed, February 12 - Dr. Andrew Feinberg, School of Medicine, Institute of Genetic Medicine, Johns Hopkins University
"Cancer, Epigenomics, and Life in a Dish"

Wed, February 5 - Dr. Joel Richter, Prof. in Molecular Medicine, University of Massachusetts.
"From a Frog's Egg to a Mouse's Brain: Translational Control by CPEB"
website

Wed, January 29 - Dr. Peter Nelson, Fred Hutchinson Cancer Research Center, Human Biology Div., Adj. Asst. Prof. in Genome Sciences and Pathology & Asst. Prof. in Medical Oncology, UW
"Of Mice and Men: Comparative Studies of Gene Expression Alterations in Mouse and Human Prostate Carcinogenesis"
website

Fri, January 24 - Dr. Charles Kurland, Prof. Emeritus, Dept. of Molecular Biology Uppsala University, Sweden
"Origins of Eukaryotes and the Vanished Role of HGT"
2:30-3:30 K-069

Wed, January 22 - Dr. John Storey, Dept of Statistics, University of California, Berkeley
"Exploratory Detection of Differential Gene Expression in DNA Microarray Experiments"
Jointly sponsored with COMBI.
website

Wed, January 15 - Dr. Bradley D. Preston, Pathology Department, UW
"Mutator Mice: When DNA Replication Fidelity Fails"

Wed, January 8 - Dr. Richard Mathies, Prof. of Chemistry, University of California, Berkeley
"Microfabricated Biochemical Analysis Systems: From the Human Genome to Mars"
website

Autumn 2002

Wed, December 11 - Dr. Andrew Clark, Dept of Molecular Biology & Genetics, Cornell University
"Comparative Genomics and Molecular Population Genetics of the Drosophila Y Chromosome"
website
Jointly sponsored with COMBI.

Wed, December 4 - Dr. Lincoln Stein, Assoc. Prof., Cold Spring Harbor Laboratory
"How to Build a Model Organism System Database"
website
Jointly sponsored with COMBI.

Mon, December 2 - Richard D. Klausner, MD, Executive Director, Global Health Program, Bill & Melinda Gates Foundation
"One Gene and Cancer: Answers and Questions"
3:00, Turner Auditorium
Jointly sponsored with Medical Genetics

Dr. Klausner was recently featured in this Seattle Times article.

Wed, November 20 - Dr. David Allis, Dept of Biochemistry & Molecular Genetics, University of Virginia
"Deciphering and Translating the Histone Code: A Tale of Tails"
website

Wed, November 13 - Dr. David Roos, Dept of Biology, University of Pennsylvania
"Designing and Mining Pathogen Genome Databases"
website

Wed, November 6 - Dr. Anthony Blau, Medicine & Hematology, UW
"Pharmacologically Regulated Cell Therapy."

Mon, October 28 - Dr. John McPherson, Dept of Genetics, Washington University
"Post-genomic era? A perspective for the future."
1:30, Health Sciences J-280

Wed, October 30 - Dr. Richard Young, Dept of Biology, MIT
"Transcriptional Regulatory Circuitry: How Cells Coordinate Expression of Their Genomes"
website

Wed, October 23 - Dr. Richard Smith, Battelle, Pacific Northwest National Laboratory
Jointly sponsored with COMBI.
"Comprehensive Proteomics: Is it Possible, and is it Needed?"

Wed, October 16 - Dr. Stephen Altschul, National Center for Biotechnology Information, National Library of Medicine, NIH
Jointly sponsored with COMBI.
"Assessing the Accuracy of Database Search Methods, and Improving the Performance of PSI-BLAST"

Wed, October 9 - Dr. David Pollock, Dept of Biological Sciences, Louisiana State University
"Evolutionary Genetics and Biochemistry: Coevolution Among Protein Residues and Mutation Gradients in Vertebrate Mitochondria"
website

Wed, October 2 - Dr. Chris Burge, Dept of Biology, MIT
"Predictive Identification of Splicing Regulatory Sequences"
Jointly sponsored with COMBI.

Spring 2002

Wed., June 12
Chris T. Amemiya, Ph.D.
Virginia Mason Research Center, Benaroya Research Institute
http://vmresearch.org/research.htm
3:30 - 4:30, J-280
"Genomic Approaches to Problems in Evolution and Development"

Wed., June 5
Stanislas Leibler, Ph.D., Prof., Laboratory of Living Matter, Rockefeller University
http://www.rockefeller.edu/labheads/leibler/leibler.html
"Space, Time and Genetic Networks"
Jointly sponsored with COMBIWed., May 29
GENOME SCIENCES SYMPOSIUM: "Genetic Variation in Disease and Development"
Hogness Auditorium, 9:45 - 5:00

  • Cynthia Kenyon, University of California, San Francisco Leonid Kruglyak, HHMI, Fred Hutchinson Cancer Research Center Brad Merrill, University of Chicago Joseph Nadeau, Case Western Reserve University Svante Paabo, Max Planck Institute, Leipzig, Germany Leena Peltonen, University of California, Los Angeles
  • George Weinstock, University of Texas

Wed., May 22
Gary Ruvkun, Ph.D., Prof. of Genetics, Dept. of Molecular Biology, Harvard Medical, School Boston, MA
http://xanadu.mgh.harvard.edu/ruvkunweb/No17.html
"The Tiny RNA World"

Wed., May 15
Stuart Kim, M.D., Ph.D., Assoc. Prof. of Developmental Biology & Genetics, Stanford University, CA
http://cmgm.stanford.edu/devbio/
"Global Analysis of Gene Expression in C. elegans"

Wed., May 8
James Dahlberg, Ph.D., Prof. Biomolecular Chemistry, University of Wisconsin-Madison
http://www.medsch.wisc.edu/bmolchem/dahlberg/dahlberg.html
"Proofreading During Nuclear Export of tRNA and Ribosomes"

Wed., May 1
Daphne Preuss, Ph.D., HHMI, Dept. of Molecular Genetics & Cell Biology
University of Chicago, IL
http://preuss.bsd.uchicago.edu/index3.html?content=people.html
"Sexual Signaling on a Cellular Level: Lessons from Arabidopsis Reproduction"

Wed., April 24
Liqun Luo, Ph.D., Asst. Prof., Dept. of Biological Sciences, Stanford University, CA
http://www-med.stanford.edu/sbrc/faculty/sbrc_fac_list/luo.html
"From Single Neuron to Neural Circuits: Genetic Analysis of Brain Development in Drosophila"

Wed., April 10
Jack Szostak Ph.D., HHMI, Dept. of Molecular Biology, Massachusetts General Hospital & Dept. of Genetics
Harvard Medical School, Boston, MA
http://xanadu.mgh.harvard.edu/szostakweb/WEB.2
"Directed Evolution: From RNA to Protein to Cells"

Wed., April 3
David Eisenberg, Ph.D., Dept. of Biological Chemistry, Univ. of California-Los Angeles
http://www.chem.ucla.edu/dept/Faculty/eisenberg.html
Jointly sponsored with COMBI
"Protein Interactions"

Winter 2002

Wed., March 13
Ronald Davis, Ph.D., Prof. of Biochemistry & Genetics, Dir. Stanford DNA Sequencing & Technology Center,
Dept. of Biochemistry, Stanford, CA
http://cmgm.stanford.edu/biochem/davis.html
"Use of the Whole Genome Set of Yeast Deletion for Saturation Genetic Analysis and Multigenic Traits"

Wed., March 6
Harry Noller, Ph.D., Robert L. Sinsheimer Prof. of Molecular Biology, Dept.of Molecular, Cellular & Developmental Biology, Univ. of California, Santa Cruz
http://www.biology.ucsc.edu/faculty/noller.html
"Crystal Structure of the Ribosome, and its Interactions with mRNA and tRNA"

Mon., March 4
an informal lecture by Samuel Karlin, Ph.D., Robert Grimmett Prof. of Mathematics, Emeritus, Stanford University
"Overlapping Gene Groups in Human Chromosomes 21 and 22, and Disease Associations"
Changed to: 2:30 p.m., Health Sciences J-280
Sponsored by Genome Sciences and HHMI

Wed., February 27
Kathryn Anderson, Ph.D., Dept. of Molecular Biology, Sloan Kettering Inst., New York, NY
http://www.ski.edu/lab_homepage.cfm?lab=62
"Patterning the Mouse Spinal Cord: Perspectives from New Mutants"

Wed., February 20
Evan Eichler, Ph.D., Asst. Prof., Dept. of Genetics
School of Medicine, Case Western Reserve University,Cleveland, Ohio
http://genetics.cwru.edu/eichler.html
"Duplications, Disease, and the Evolution of the Human Genome"
Jointly sponsored with COMBI

Wed., February 13
Mitzi Kuroda, Ph.D., Prof., Dept. of Molecular & Human Genetics, Dept. of Molecular & Cell Biology, Investigator-HHMI
Baylor College of Medicine, Houston, TX
http://www.imgen.bcm.tmc.edu/molgen/facultyaz/kuroda.html
"Epigenetic Spreading of Chromatin Organization in Drosophila"

Wed., February 6
Andrew Link, Ph.D., Asst. Prof. Microbiology and Immunology; Ingram Assistant Professor of Cancer Research
Vanderbilt University Medical Center, Nashville, TN
http://www.mc.Vanderbilt.edu/microbio/link.html
"Systematic Analysis of Protein Complexes Using Mass Spectrometry"

Wed., January 30
Mark Boguski, M.D., Ph.D., Visiting Investigator, Fred Hutchinson Cancer Research Center
"Bioinformatics: Past, Present and Future"
Jointly sponsored with COMBI

Wed., January 23
Sean Eddy, Ph.D, Assoc. Prof., Dept. of Genetics, Washington University, St. Louis, MO
http://www.genetics.wustl.edu/eddy/
"The Modern RNA World: Computational Genomic Screens for Noncoding RNAs"
Jointly sponsored with COMBI

Wed., January 9
Edward M. Rubin, M.D., Ph.D., Laboratory Sr. Scientist Group Leader, Biology Group
Lawrence Berkeley Nat'l Laboratory, Berkeley, CA
http://www-hgc.lbl.gov/biology/members.html#Rubin
"Biological Jewels in Interspecies Sequence Data"
Jointly sponsored with COMBI

Autumn 2001

Wed., December 12
Michael Snyder, Ph.D., Prof. & Chair, Molecular, Cellular & Developmental Biology; Prof. of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT
http://www.yale.edu/snyder/
"Large Scale Analysis of Genome 2 Proteomes: A Tale of Two Chips"

Wed., December 5
Gerald Rubin, Ph.D., HHMI Vice President for Research & MacArthur Prof. of Genetics & Development, UC-Berkeley, CA
http://mcb.berkeley.edu/faculty/GEN/rubing.html
"Experimental and Computational Approaches for Interpreting the Drosophila Genome Sequence"

Wed., November 28
Matthew Stephens, Ph.D., Department of Statistics, UW
http://www.stat.washington.edu/stephens/
"Estimating Haplotypes from Population Genotype Data"

Wed., November 21
Gary Stormo, Ph.D., Prof., Dept. of Genetics, Washington University, St. Louis, MO
http://ural.wustl.edu/
"Experimental and Computational Studies of DNA-Protein Interactions"

Wed., November 14
Geoffrey Duyk, M.D., Ph.D., Exec. VP & Chief Scientific Officer, Exelexis, Inc., So. San Francisco, CA
http://www.exelixis.com/webpage_templates/general.php3?page_name=management
"Genetics in a Post-Genomics Era: Lessons from Model Systems"

Wed., November 7
K. Dane Wittrup, Ph.D., Joseph P. Mares Prof. of Chemical Engineering & Bioengineering, MIT, Boston, MA
http://web.mit.edu/cheme/www/People/Faculty/Wittrup_K_Dane.html
"Antibody Engineering by Yeast Surface Display"

Wed., October 31
Virginia Zakian, Ph.D., Dept. of Molecular Biology, Princeton University, Princeton, NJ
"Regulation of Telomere Replication in Yeast"

Wed., October 24
Seminar will be held in Kane Hall, Rm. 130
Leland Hartwell,
Ph.D., Nobel Prize winner, Pres. & Dir., Fred Hutchinson Cancer Research Center, Seattle, WA
http://www.fhcrc.org
"Accumulation and Expression of Natural Genetic Variation"

Wed., October 17
Joe Felsenstein, Genome Sciences, UW
"An Unintended Encounter: Molecular Biology Meets Population Biology"

Wed., October 10
John Yates, Scripps Institute
"Towards Comprehensive Analysis of Cells and Tissues"

Wed., October 3
Leroy Hood, Institute for Systems Biology
"Systems Approaches to Biology"