Past Genome Sciences Seminars
Summer 2008
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 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"
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