UW Genome Sciences: News & Events: Past Combi Seminars

There is increasing interest in understanding the molecular basis of complex traits. Initially, the genetic dissection of quantitative traits involved measurements of gross phenotypes. Most recently, the underlying mechanisms of inheritance have been studied through various approaches that are supported by modern technological and methodological advances, namely quantitative trait locus/loci (QTL) analysis and mutant analysis in genetics; genome sequencing and gene expression analysis in genomics; and protein structure analysis and protein assay in proteomics. Since each technology and approach focuses on specific pieces of the larger, poorly understood systems biology, the challenge is to integrate these different types of information to elucidate the genetic architecture of complex traits. To address one of these challenges we have combined QTL analysis with microarray analysis to characterize the genomic architecture that controls quantitative traits. Using Affymetrix technology and 211 individuals from a segregating Arabidopsis population, the transcript variation (i.e., expression level polymorphisms, ELPs) of 22,810 genes, in both control and treatment conditions, provide data for mapping expression QTL (eQTL). Results from our statistical analysis of the entire genome reveal both cis- and trans-eQTL under both control and treatment conditions. The statistical methodology developed for this type of experiment will be presented for a directed analysis of SA-inducible secretory genes controlled by NPR1.

***This work is funded by NSF Arabidopsis 2010 in collaboration with Drs. Marilyn West, Hans van Leeuwen, Richard Michelmore, and Dina St.Clair University of California, Plant Sciences Dept, Davis CA, and Dr. Kyunga Kim, Purdue University, West Lafayette, IN, and Seoul National University, Seoul, Korea.

Spring 2008

Thursday, May 15 - Dr. Harmen Bussemaker
Columbia University
“Predicting expression from sequence: Data-driven biophysical models of (post-) transcriptional networks”
1:00 - 2:00, Foege Auditorium

Winter 2008

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

March 5 - Dr. Adam Siepel
“Comparative genomics of animals and plants”
Cornell University

Abstract:
I will describe three recent comparative genomics projects, including two of mammals and one of plants. The first is a large-scale effort, carried out as part of the Mammalian Gene Collection (MGC) project, to identify human genes not yet in the gene catalogs. Our approach was to produce gene predictions by algorithms that rely on comparative sequence data but do not require direct cDNA evidence, then to test predicted novel genes by RT-PCR. This work led to the identification of more than 2000 novel exons corresponding to an estimated ~500 genes, including >160 that were completely absent from the gene catalogs. The second project is a comprehensive analysis of positively selected genes (PSGs) in mammals based on the six high-coverage eutherian mammalian genome assemblies now available. Compared with previous genome-wide scans for PSGs, the increased phylogenetic depth of this data set results in substantially improved statistical power, and permits several new lineage- and clade-specific tests to be applied. Several hundred apparent PSGs were identified, and a detailed analysis was performed of their selection histories (evolutionary patterns of selection and nonselection), the functional categories and pathways to which they belong, and their expression patterns. The third project is an attempt to apply tools and techniques developed for comparative genomics of mammals to a group of plants showing similar levels of genomic divergence. This project involved the generation and analysis of sequences for a ~100kb conserved syntenic segment (CSS) in the genomes of five members of the agriculturally important plant family Solanaceae. Our analysis suggests that, as in mammals, a large fraction of noncoding bases in these genes is under selection, and it sheds light on the dates of divergence if these species. Together, these three projects illustrate the power of comparative genomics in characterizing evolutionary dynamics, selection pressures, and genomic function.

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

February 20 - Dr. Chung-I Wu
“The birth and death of miRNAs in Drosophila and their evolving relationships with targets"

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

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 Genome Sciences seminar

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

January 16 - Dr. William Noble
University of Washington
"Consistent probabilistic outputs for protein function prediction"

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 Genome Sciences seminar

Autumn 2007

December 5 - Dr. David Baker
University of Washington
“Rapid structure determination, novel enzymes, and a multiplayer computer game”

November 28 - Dr. Robert Gentleman
Fred Hutchinson Cancer Research Center
“Modeling Interactions”

November 14 - Zizhen Yao
Ruzzo Lab, University of Washington
"Genome scale search of noncoding RNAs, Bacteria to Vertebrates"

November 7 - Dr. Wenying Shou
Fred Hutchinson Cancer Research Center
"Collapse or Collaborate: Experimental and Mathematical Analyses of a Synthetic Cooperative System”

October 31 - Dr. Michael Hawrylycz
Allen Institute for Brain Science
"AGEA: An Anatomic Gene Expression Atlas for the C57BL/6J mouse brain"

October 24 - Dr. Hong Qian
University of Washington
"From Biochemical Reaction Networks to Cellular States: A Computational Approach"

October 17 - Dr. James Mullins
University of Washington
"The evolution of HIV and its battle with host cellular immune responses during asymptomatic infection"

October 10 - Dr. Serafim Batzoglou
Stanford University
“Algorithms for Sequences, Networks, and Populations"

October 3 - Dr. Bernhard Palsson
University of California, San Diego
“Reconstruction of the genome-scale transcriptional regulatory network in e. coli”

October 1 - Dr. Chris Ponting
University of Oxford
“Recombination and rapid evolution of genes and chromosomes”
1:30, Foege Auditorium
sponsored jointly with Genome Sciences seminar

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”
sponsored jointly with Genome Sciences seminar

Summer 2007

July 25 - Dr. Gil Ast
"Alternative splicing and human genomic complexity"
1:30, Foege Auditorium

June 27 - Dr. Dahlia Nielsen
North Carolina State University
"Examining the dirt underneath the association mapping carpet: what kind of genes do we expect these methods to find?"
sponsored by WiGS

Winter 2007

March 7 - Dr. Joshua Akey
University of Washington
“Gene expression variation within and among human populations”

February 28 - Dr. Eric Siggia
The Rockefeller University
sponsored jointly with the Genome Sciences Seminar series

February 21 - Dr. Paul Pavlidis
University of British Columbia
"Large-scale mining of expression patterns in public microarray datasets"

February 14 - Tobias Mann
University of Washington
"A thermodynamic approach to PCR primer design"

February 7 - Dr. John Mittler
University of Washington
“Dynamical modeling of HIV-1 drug resistance"

January 31 - Dr. Martin Tompa
University of Washington
"Which Portions of Whole-Genome Multiple Alignments Are Reliable?"

January 24 - Dr. Martha Bulyk
Harvard University
sponsored jointly with the Genome Sciences Seminar series

January 17 - Dr. William Noble
University of Washington
“Machine Learning Analyses of Tandem Mass Spectra”

January 10 - Genome Sciences / Combi Seminar
Dr. Jonathan Pritchard
University of Chicago
“Genetic Variation and Natural Selection in the Human Genome”
sponsored jointly with the Genome Sciences Seminar series

Autumn 2006

December 6 - Genomic Medicine / Combi Seminar
Dr. Eric Schadt
Rosetta Inpharmatics
sponsored jointly with the Genome Sciences Seminar series

November 15 - Dr. Bradley Till
“TILLING and Ecotilling from Arabidopsis to Humans"
University of Washington

November 8 - Dr. Harlan Robins
Fred Hutchinson Cancer Research Center
“Isochores and symmetry breaking in the human genome”

November 1 - Dr. Jared Roach
Institute for Systems Biology
"Genetic Mapping at 3-kb Resolution"

October 18 - Dr. Daniel Zilberman
Fred Hutchinson Cancer Research Center
"Genome-wide analysis of DNA methylation and demethylation in Arabidopsis"

October 11 - Dr. Lon Cardon
Fred Hutchinson Cancer Research Center
"Finding Human Disease Genes by Whole Genome Association"
sponsored jointly with the Genome Sciences Seminar series

Wednesday, August 16
Dr. Chip Lawrence
Center for Computational Molecular Biology, Division of
Applied Mathematics, Brown University
“Abuse of the Mode and an Ensemble Alternative”

Abstract:
Advances in data collection technologies have rendered increasingly large data sets available for analysis. While the emergence of such large data sets would seem to lead to increasingly more precise estimates of parameters, paradoxically just the opposite seems to becoming increasingly common. This paradoxical circumstance has emerged because these technologies have simultaneously opened opportunities to draw inferences on previously unanswerable high dimensional questions. For decades optimization procedures such as maximum likelihood, minimum free energy, and MAP estimators, have been employed as the major tool of most inference procedures. It has been clearly recognized for some time now that the favorable properties of optimization based inferences rest on an asymptotic foundation that requires the data to grow in comparison with the number of unknowns. Nevertheless, optimization very often continues as the method of choice even when these supporting conditions are not present and even when the most probable solution has a probability of 10-10 or less. Genomics and computational molecular biology are among the more predominate fields experiencing the duality of the growth in data resources and inference expectations. In fact, prediction and inference of high dimensional objects are now arguably the most important activities in these allied new biological fields, and the inspiration for this paper. RNA secondary structure prediction offers a very special lens to examine the untoward consequences of the reliance on the mode in high dimensional inferences because polynomial time algorithms are available to comprehensively characterize the space of solutions, and a references set of structures is available for the comparison of alternative prediction methods. Through this lens we will examine these untoward effects, consider their boarder implications, and present alternative "ensemble based" centroid estimators. Using a model identical to the well know Mfold model, we find that centroid estimators both better represent the posterior space and improve positive predictive values of the reference set predictions by 30% while improving sensitivity by 3% compared to Mfold predictions that minimize free energy.

7/26/06
Dr. Eleazar Eskin
University of California, San Diego
“Whole genome association in inbred mouse strains”

Spring 2006:

4/19 - Dr. Sagi Snir
UC Berkeley
"Graphs, Colorings and Beyond in Comparative Genomics"

Abstract:
Comparative genomics seeks to explore characteristic patterns of a set of
organisms by comparing common features of the given organisms. Computational
methods are a significant part in this type of discipline. In this talk I will
describe the use of colored graphs to solve two problems in comparative
genomics:

1. Micro-indels are small insertion or deletion events (indels) that occur
during genome evolution. The study of micro-indels is important, both in order
to better understand the underlying biological mechanisms, and also for
improving the evolutionary models used in sequence alignment and phylogenetic
analysis. The inference of micro-indels poses a difficult computational
problem, and is far more complicated than the related task of inferring the
history of point mutations. We introduce the concept of indel history, a tree
alignment based approach that is suitable for working with multiple genomes,
which enables us to arrive at some interesting computational and biological
findings.

2. Horizontal gene transfer (HGT) is the transfer of genetic material from one
lineage to another. HGT plays a major role in bacteria's genome diversification
as well as their ability to develop resistance to antibiotics. This mechanism
cannot be represented by the traditional tree-like evolution rather as a
network. We show new results, both combinatorial and statistical, improving
significantly over current approaches and enable us to analyze real biological
data sets.

4/12 - Dr. William Atchley
North Carolina State University
"Computational Biology, Molecular Architecture and Transcription"

Abstract:
Elucidating the underlying causes of sequence variability in proteins is an important goal in modern biology. Sophisticated statistical analyses geared toward partitioning sequence variation into its underlying causal components are difficult because of the so-called “sequence metric problem.” That is, biosequences are comprised of alphabetic codes that have no underlying natural metric. Recently, we offered a solution to this problem (PNAS 102:6395-6400, 2005) that permits these alphabetic codes to be transformed into highly interpretable numerical values. These new values were derived from multivariate statistical analysis of a large suite of amino acid physiochemical attributes. I will briefly describe this new approach and then introduce some applications using the basic helix-loop-helix (bHLH) proteins as exemplars. As time permits, I will discuss this approach and partitioning amino acid covariation, elucidating the molecular architecture of DNA binding and dimerization, and understanding those amino acids involved in enhanced binding specificity.

Winter 2006:

3/1 - Bert Tanner
Graduate Student, Department of Bioengineering, University of Washington
"force production in muscle modeled as a coupled network of motor proteins"

2/22 - Dr. Willie Swanson
University of Washington
“Adaptive evolution and co-evolution of sperm - egg recognition molecules”

2/15 - Dr. Joshua Akey
University of Washington

2/8 - Dr. John Storey
University of Washington
“PCA for Variance Decomposition and Linkage Analysis of Genome-wide Expression”

2/1 - Dr. James Thomas
University of Washington
"Evolution of gene families in Caenorhabditis"

1/25 - Dr. Michael Hawrylycz
The Allen Institute for Brain Science
"Data Mining of in situ Hybridization Expression Data in
the Adult Mouse Brain"

1/18 - Dr. Larry Ruzzo & Dr. Martin Tompa
University of Washington
“Computational prediction of non-coding RNA motifs in bacteria”

1/11 - Dr. Pavel Pevzner
UC San Diego
“Identification of post-translational modifications by blind search of mass spectra”

1/4 - Dr. Diane Genereux
University of Washington
"using empirical and mathematical approaches to understand the dynamics of DNA methylation in the human genome"

Autumn 2005:

12/7 - Dr. Hong Hung
University of Washington
"Clean structures from dirty data"

11/30 - Dr. John Mittler
University of Washington
"Modeling evolution of HIV-1 in vivo."

11/16 - Dr. William Noble
University of Washington
"Identifying remote protein homologs by network propagation"

11/9 - Dr. Zhirong Bao
University of Washington
"Mobilomics: RECON in the Genome's Junk Yard"

11/2 - Dr. Matthew Stephens
University of Washington
"Automatically detecting and genotyping SNPs by sequencing of diploid
samples"

10/26 - Amol Prakash
Graduate Student, Department of Computer Science & Engineering, University of Washington
"Comparative Genomics in Vertebrates and Multiple Alignments"

10/19 - Dr. David Baker
University of Washington
"Progress in high resolution modeling of protein structures and
interactions"

10/5 - Dr. Daniel Miranker
University of Texas
“MoBIoS: A Specialized Database Management System for Biological Discovery”

9/28 - Dr. Hamid Bolouri
Institute For Systems Biology
"Pointillist: an open source tool for high throughput data integration"

Winter 2005:

Wednesday, March 9 - Dr. Ram Samudrala, University of Washington
"Modelling proteomes"

Wednesday, March 2 - Dr. Evan Eichler, University of Washington
“Segmental Duplications and Human Genome Evolution”
website

Wednesday, February 23 - Dr. William Noble, University of Washington
"Predicting the in vivo signature of human gene regulatory sequences"
website

Wednesday, February 16 - Dr. John Storey, Unversity of Washington
“Multiple Locus Linkage Analysis of High-throughput Phenotypes Applied to Genome-wide Expression in Yeast”
website

Wednesday, February 9 - Dr. Jon McAuliffe
"Statistical Methods for Genome Comparison"

Wednesday, February 2 - Dr. Michael MacCoss, University of Washington
"Computational Analysis of Shotgun Proteomics Data"
website

Wednesday, January 26 - Dr. Adam Siepel, University of California, Santa Cruz
"Comparative mammalian genomics: models of evolution and detection of functional elements"

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%).

Wednesday, January 19 - Dr. Michael Katze, University of Washington
“Virology Meets Computational Biology: Is This Enough To Stop The Next Pandemic?”
website

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

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 Genome Sciences
3:30, Hitchcock 132

Autumn 2004:

Wed, December 8 - Dr. Emily Rocke, postdoctoral researcher, Thomas Lab, University of Washington
"Evidence for chromatin-interacting function of a GAGA motif in C. elegans"

Wednesday, December 1 - Dr. Rick Myers
"Genome-wide analysis of human transcriptional regulatory elements"
sponsored jointly with Genome Sciences
3:30, Hitchcock 132

Wed, November 17 - Dr. James Thomas, University of Washington
"Gene Clusters in C. elegans"
website

Wed, November 10 - Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center
"Profiling DNA Methylation in the Arabidopsis Genome"
website

Wed, November 3 - Dr. David Baker, University of Washington
"Prediction and design of macromolecular structures and interactions"
website

Wed, October 27 - Zasha Weinberg, graduate student, UW Computer Science & Engineering
"Accurate annotation of non-coding RNA in practical time"

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 Genome Sciences

Wed, October 13 - Dr. Phil Green, University of Washington
"Signal and Noise in Genome Sequences"
website

Wed, October 6 - Dr. Martin Tompa, University of Washington
"Tools for Prediction of Regulatory Elements in Microbial Genes"
website

Abstract:
I will describe and demonstrate the course project tackled by undergraduate students in last spring's inaugural Computational Biology Capstone Course, CSE 490MT. The goal of the project was to write software that starts from a single microbial gene of interest, finds a large collection of orthologous genes from multiple microbes, and uses this collection to identify evolutionarily conserved motifs in their regulatory regions. These motifs are good candidates to be functional regulatory elements. Such a tool, if done well, could be very useful for working microbiologists.

(For more detail on the project, see http://www.cs.washington.edu/education/courses/cse490mt/04sp/project.html .)

Wednesday, September 29 - Dr. Charles Aquadro, Cornell University
website
sponsored jointly with Genome Sciences
3:30, Hitchcock 132

Summer 2004:

Wed, September 1 - Dr. Daniel Barker, School of Animal and Microbial Sciences, University of Reading, U.K.
"Phylogeny, pathways and protein complexes"
website

Spring 2004:

Wed, June 2 - Dr. Willie Swanson, University of Washington
"Adaptive Evolution of Reproductive Proteins"
website

Wed, May 19 - Genome Sciences Symposium

Wed, May 12 - Dr. Ping Ao, Institute for Systems Biology, UW Mechanical Engineering
"Calculating Biological Behaviors in Phage Lambda Life Cycle"

Wed, May 5 - Dr. Charles Langley, Professor of Genetics, UC Davis
website
sponsored jointly with Genome Sciences

Wed, April 28 - Dr. Harmit Malik, Assistant Member, Basic Sciences, Fred Hutchinson Cancer Research Center & Affiliate Assistant Professor, University of Washington
"Molecular Investigations of Genetic Conflict"
website

Wed, April 21 - Dr. Ira Kalet, University of Washington
Associate Professor, Radiation Oncology and Medical Education and Biomedical Informatics (joint)

"Anatomy, Biomedicine and Computing: the ABC's of Informatics in Cancer Treatment"

Abstract:
The explosive growth in the application of computing to medical and health care research and practice has been most visible in computerized medical record systems, web based medical knowledge resources and biomolecular data such as GENBANK. By contrast, the field of radiation therapy for cancer has had computing as an integral part of research and practice since the mid-1960's. Designing radiation treatments is typically done with an interactive graphic software system called a "radiation therapy planning", or RTP, system. The design of RTP systems requires solving difficult graphic visualization problems, careful attention to user interface design, efficient numerical computation, and advanced networking. In addition, as these systems can grow to large size (from 75,000 up to a million lines of code), they provide an industrial strength trial opportunity for new ideas in software engineering. Finally, the design process itself, largely done by human experts, may be automated by creating computational models of human anatomy, tumor biology and radiation machinery. The talk will include an interactive demonstration of the Prism RTP system developed at the University of Washington, and will conclude with a short summary of the UW Biomedical and Health Informatics program, a larger context for such biocomputing research.

website

Wed, April 14 - Dr. Carl Bergstrom , University of Washington
"Mathematical Models of RNA Silencing: How an Intracellular Immune System Avoids Autoimmune Reactions"

Wed, April 7 - Dr. Martin Tompa, University of Washington
"An Assessment of Algorithms for the Discovery of Transcription Factor Binding Sites"
website

Winter 2004:

Thursday, March 4 - Dr. Mary Kuhner, Research Associate Professor of Genome Sciences, University of Washington
"Coalescent Likelihood Estimators in Theory and Practice"
website

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"
sponsored jointly with Genome Sciences

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 Genome Sciences

Wed, February 18 - Dr. Liqing Zhang, Department of Ecology and Evolution, University of Chicago
"The Distribution and Evolution of Duplications in the Genomes of Arabidopsis thaliana and Human"
website

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

Wed, February 4 - Dr. Eran Segal, Computer Science Department, Stanford University
"Rich Probabilistic Models for Genomic Data"

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

Wed, January 21 - Dr. Elizabeth Thompson, Professor of Statistics and of Biostatistics, University of Washington
"Inferring Relationships Among Individuals and Populations"
website

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

Wed, January 7 - Dr. Eric Green, 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

Wed, December 3 - Dr. Larry Ruzzo, Professor of Computer Science and Engineering, University of Washington
"Improved Gene Selection For Classification Using Microarrays"
website

Wed, November 19 - Dr. Thomas Daniel, Joan and Richard Komen Professor of Zoology, Dept. of Biology, UW
"Modeling Molecular Motors: Monte-Carlo Meets Mechanics"
website

Wed, November 12 - Dr. Simon Tavare, Professor of Biological Sciences, University of Southern California
website

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

Wed, October 29 - Dr. James Thomas, Professor of Genome Sciences, University of Washington
"Rapidly Evolving Domains in the C. elegans Genome"
website

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

Wed, October 15 - Dr. William Noble, Assistant Professor of Genome Sciences, University of Washington
"A Statistical Framework for Genomic Data Fusion"
website

Wed, October 8 - Dr. Chao Tang, Sr. Research Staff Member, NEC Research Institute, Princeton, NJ
"Finding Transcriptional Modules From Large Scale Gene Expression Data"

Wed, October 1 - Dr. Phil Green, Professor of Genome Sciences, University of Washington
"Finishing the Gene-ome: Computationally Directed Gene Structure Verification in C. elegans"
website

Summer 2003:

Wednesday, August 20 - Dr. Michal Linial, Department of Biological Chemistry, Hebrew University
"Constructing the Protein Space: From Sequence to Functional Inference"
website
1:30 - 2:30, Health Sciences K-069

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
3:30, Hitchcock 132
sponsored jointly with Genome Sciences

Wed, May 28 - Dr. Chris Carlson, Dept of Genome Sciences, University of Washington
"Building a maximally informative SNP map using linkage disequilibrium"
website

Wed, May 21 - Dr. Barbara Trask, Dept of Genome Sciences, University of Washington, Fred Hutchinson Cancer Research Center
"Dynamic Duplications in the Human Genome"
website

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

Wed, May 7 - Dr. Scott Edwards, Dept of Zoology, University of Washington
"Genome and Transcriptome Evolution in Reptilia, Including Birds"
website

Wed, April 30 - Dr. Subramani Mani, Center for Biomedical Information, University of Pittsburgh
"Discovering Causal Relationships from Biomedical Data"
website

Wed, April 23 - Dr. Steve Henikoff, Fred Hutchinson Cancer Research Center
"Traditional Mutagenesis in the Post-Genomic Era"
website

Wed, April 16 - Dr. Wyeth Wasserman, University of British Columbia
"Discovery of Regulatory Sequences Directing Transcription of Co-expressed Genes"
website

Wed, April 9 - Dr. Gane Ka-Shu Wong , Genome Center, University of Washington
"Genome Structure in Plants and Animals"

Wed, April 2 - Dr. Terry Gaasterland, Rockefeller University, Laboratory of Computational Genomics
"Computational Analysis of Splicing in Mouse and Trypanosomes"
website
3:30, Hitchcock 132
Jointly sponsored with Genome Sciences.

Winter 2003:

Wed, March 12 - Dr. Evan Eichler, Department of Genetics, Case Western Reserve University
"Recent Duplication, Disease and the Evolution of the Human Genome"
Jointly sponsored with Genome Sciences

Wed, March 5 - Dr. Len Pennacchio, Department of Genome Sciences, Lawrence Berkeley National Laboratory
"Expoiting Vertebrate Sequence for Insights into Human Biology"
Jointly sponsored with Genome Sciences

Wed, February 26 - Dr. Wei Wu, Wadsworth Center, NYS Dept. of Health, David Axelrod Inst., SUNY-Albany
"Intein function and manipulation for protein purification."

Wed, February 19 - Dr. Matthew Stephens, Dept of Statistics, University of Washington
"Haplotypes, Hotspots, and a Multilocus Model for Linkage Disequilibrium"

Wed, February 12 - Dr. David Baker, Dept of Biochemistry, University of Washington
"Prediction and Design of Protein Structures and Protein-Protein Interactions"

Wed, January 29 - Dr. Ellen Wijsman, Dept of Medical Genetics, University of Washington
"Genetic Analysis of Complex Traits: From Case-Control to Large Pedigree Designs"

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 Genome Sciences. 3:30, Hitchcock 132
website

Wed, January 15 - Jared Roach, M.D., Ph.D., Institute for Systems Biology
"Evolutionary Algorithms for Multiobjective Optimization: Application to the SNP Selection Problem"

Wed, January 8 - Dr. Joe Felsenstein, University of Washington
"Using Wright's Quantitative Genetic Threshold Model to Analyze Discrete Traits"

Autumn 2002:

Wed, December 11 - Dr. Andrew Clark, Cornell University
"Comparative Genomics and Molecular Population Genetics of the Drosophila Y Chromosome"
website
Jointly sponsored with Genome Sciences. 3:30, Hitchcock 132

Wed, December 4 - Dr. Lincoln Stein, Cold Spring Harbor Laboratory
"How to Build a Model Organism System Database"
website
Jointly sponsored with Genome Sciences. 3:30, Hitchcock 132

Wed, November 20 - Dr. Willie Swanson, University of Washington
"Functional Inferences From Rapidly Evolving Reproductive Proteins"

Wed, November 13 - Dr. Martin Tompa, University of Washington
"Interdisciplinary Collaborations on Discovering Regulatory Elements."