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Fostering new paradigms for the biological sciences

Genomic Sciences Program Seminars
(Chem 923, Section 157)
Spring 2015

Thursdays, 4:45 p.m., Rm. 1360 Biotech Center

(unless listed otherwise)

Sept. 16 3:30 pm, Biotechnology Center Auditoium

Presentation by Allen Moore, PhD (Department Head of Genetics, University of Georgia), Sex Differences in Parenting

Sept. 30, 3:30 pm, Biotechnology Center Auditorium

James Ntambi, PhD (Professor of Biochemistry, UW-Madison)

Lipogenesis and Metabolic Signaling in Obesity and Diabetes

- or -

Oct. 1 1:30 pm, Biotechnology Center Auditorium,

Gabriel Renaud (Dept. of Evolutionary Genetics, Max Planck Inst.), Computational Analysis of Ancient DNA from Ancient Human Samples

Oct. 7, 3:30 pm, Biotechnology Center Auditorium,
Michael Puragganan, PhD (Professor of Biology, Dean for Sciene, New York University), The Evolutionary Genomics of Plant Domestication

Oct. 13, 3:30 pm, Biotechnology Center Auditorium

Matt Harris, PhD (Assistant Professor, Department of Genetics, Harvard Medical School), What Lies Beneath: Latency of Developmental Potential

Oct. 22, Introductory session, GSTP

Oct. 29, 1:30 pm, Biotechnology Center Auditorium,

Tom Tullius, PhD (Professor, Depts. of Chemistry, Pharmaology, Experimental Therapeutics, Boston University), Nucleotide Resolution Structural lMaps of DNA, in vitro and in vivo


Nov. 5 Jason Lajoie, GSTP predoctoral fellow (Chemical & Biological Engineering), The Lamprey Antibodies and the Blood-brain Barrier

Nov. 11, 3:30 pm Biotechnology Center Auditorium, Garret Suen, PhD (Assistant Professor, Bacteriology), Cellulose Degradation by the Bactrium Celulomonas gilvus

Nov. 19, Amy Dapper, PhD, GSTP postdoctoral fellow (Genome Center of Wisconsin), Title TBA

Dec.  3 Sam Krerowicz, GSTP predoctoral fellow (Chemistry), Title TBA

 

Past Genomic Sciences Program Seminars

Spring 2015

Jan. 22 David Hibbett, PhD (Warren Litsky Endowed Chair in Biology, Clark Univ.), The Roots of Rot: Phylogenomics of Wood-Decaying Fungi and the "End of Carboniferous"

Jan. 29 Presentation by Jeffrey Nelson, PhD, GSTP postdoctoral fellow (Morgridge Institute for Research), Investigating Axolotl Regeneration via Single Cell Transcriptomics

Feb. 5, 1:30 pm, Biotechnology Center Auditorium,

Presentation by David Liu, PhD (HHMI Investigator; Prof. of Chemistry and Chemical Biology; Harvard University), Integrating Chemistry and Evolution to Illuminate and Program Biology

Feb. 11, 3:30 pm, Biotechnology Center Auditorium,
Thomas Hammond, PhD (Assistant Professor of Biology, Illinois State University), A Search for Party Crashers: Unpaired DNA Detection in the Model Eukaryote Neurospora crassa

Feb. 19, Presentation by Ted de Groot, GSTP predoctoral fellow (Department of Biomedical Engineering),How to Build and Use Microfluidic Devices Without Frustration, Panic, Mountains of Money, or an Engineering Degree

Feb. 26, Presentation by Drew Doering, GSTP predoctoral fellow (Cellular & Molecular Biology Graduate Program), A High-Throughput Approach for Testing Human Rare Variants and the Functional Divergence of Orthologs

March 5, Presentation by Anna Kropornicka, GSTP predoctoral fellow (Genetics), A Dynamic Framework for Metabolic Engineering of the Branched-Chain Amino Acid Biosynthesis Pathway in Escherichia coli


March 12 Presentation by Gene Tsvid, PhD, GSTP postdoctoral fellow (Biotechnology Center), DNA Analysis and Control in Microfluidic and Electromechanical Systems

March 19, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Joshua Akey, PhD (Associate Professor of Genome Sciences, University of Washington), Characteristics of Functional Genomic Variation in Yeast and Humans

March 26, Presentation by Matthew MacGilvray, GSTP predoctoral fellow (Microbiology Doctoral Program)), Inferring the Stress-Activated Signaling Network of S. cerevisiae Using a Computational and Experimental Pipeline

April 9, 1:30 pm, Biotechnology Center Auditorium

Presentation by Kevin Shokat, PhD (Professor and Chair, Department Cellular and Molecular Pharmacology, University of California San Francisco; Investigator, Howard Hughes Medical Institute), The Use of Chemical Genomics to Study mRNA Splicing


April 16, Presentation by Mark Nolte, PhD, GSTP postdoctoral fellow (Department of Genetics), Gene Expression Evolution in Giant Island Mice

 
April 24, Presentation by Saurabh Sinha, PhD (Associate Professor, Computer Science and Institute of Genomic Biology, U. Illinois Urbana-Champaign), Modeling the Function and Evolution of Regulatory Sequences in Drosophila, 12:00 pm, Biotechnology Center Auditorium,

Sept. 11 Introductory Session, Rm. 1360 Biotechnology Center

Wed., Sept. 17 3:30 pm Biotechnology Center Auditorium

Dudley Lamming, PhD (Assistant Professor, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, UW-Madison School of Medicine and Public Health), Modulating the mTOR Signaling Pathway for the Treatment of Age-related Diseases

Fall 2014

Week of Sept. 22nd:

Wed., Sept. 24 3:30 pm, Biotechnology Center Auditorium
Greg Wray, PhD (Professor, Department of Biology, Duke University), We Became What We Ate: Genetic Bases for the Interdependent Evolution of Human Brain Size and Diet

-OR-

Th., Sept. 25 3:30 pm, 1220 Microbial Sciences Building
Deborah Blum (Assoc. Professor, Journalism, UW-Madison), The (Sometimes Poisonous) Chemistry of Communication

Th., Oct. 2, Presentation by Matt Copeland, PhD, GSTP postdoctoral fellow (Department of Chemical & Biological Engineering), A TALE Repressor-Induction System Medicated by Proteolytic Degradation

Th., Oct. 9, Presentation by Alicia Richards, GSTP predoctoral fellow (Department of Chemistry), SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching

Mo., Oct. 13, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
Gerry Shadel, PhD (Professor of Pathology and Genetics, Yale University)
Mitochondrial Stress Signaling in Disease and Aging


Th., Oct. 23, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Nurten Akarsu, MD, PhD (Professor of Medical Genetics, Hacetepe University, Ankara Turkey) Researching the Rare: Genetics of Facial Malformations

Wed, Oct. 29, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Antonis Rokas, PhD (Associate Professor of Biological Sciences, Associate Professor of Biomedical Informatics, and Cornelius Vanderbilt Chair in Biological Sciences, Vanderbilt University), The Evolution of Fungal Chemodiversity

Th., Nov. 6, Presentation by Sam Krerowicz, GSTP predoctoral fellow (Department of Chemistry), Self-Assembly of Genomic  DNA into Microscale Objects

Th., Nov. 13, 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Ctr)
Laurie Comstock (Associate Professor of Medicine, Harvard Medical School), Ecological Interactions among Bacteria of the Human Intestinal Microbiome


Th., Nov. 20, Presentation by Jason Lajoie, GSTP predoctoral fellow (Chemical and Biological Engineering, UW-Madison), Interrogation of the Blood-Brain Barrier Membrane Proteome and Glycoproteome via Creation And Screening of an Immunized Lamprey VLR Library

 
Th., Dec. 4, 1:30 pm Biotechnology Center Auditorium 425 Henry Mall
Joshua Akey, PhD, Associate Professor of Genome Sciences, University of Washington, Characteristics of Functional Genomic Variation in Yeast and Humans

Spring 2014


Jan. 29 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Matt Hahn, PhD, Associate Professor of Biology and Informatics (University of Indiana), How I Learned to Stop Worrying and Love Bad Genomes


Feb. 6 Presentation by Anna Merrill, GSTP Predoctoral Fellow (Department of Chemistry), NeuCode Labeling for Multiplexed, Global Protein Quantification


Feb. 13 Presentation by Mark Nolte, PhD, GSTP Postdoctoral Fellow (Department of Genetics), Dissecting the Genetic Architecture of Island Gigantism: Into One Large Mouse Add Functional, Quantitative and Population Genetics and Stir Together


Feb. 20 Presentation by Gene Tsvid, PhD, GSTP Postdoctoral Fellow (Biotechnology Center)


Feb. 27 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Michael Shapiro, PhD (Univ. of Utah)


March 6 Presentation by Ashley Baltes, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering)


March 13 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Dan Gibson, Craig Venter Institute


March 20 No seminar – Spring Break


March 27 Presentation by Sam Krerowicz, GSTP Predoctoral Fellow (Department of Chemistry)


April 3 Presentation by Deborah Muganda-Rippchen, GSTP Predoctoral Fellow (Department of Computer Sciences)


April 10 Presentation by Teddy de Groot, GSTP Predoctoral Fellow (Department of Biomedical Engineering)


April 17 Presentation by Joe Ollar, GSTP Predoctoral fellow (Cellular & Molecular Pathology Graduate Program)


April 24 Presentation by Anna Kropornicka, GSTP Predoctoral Fellow (Department of Genetics)


Wed., April 30 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Marlene Rabinovitch, M.D. Dwight and Vera Dunlevie Professor of Pediatrics (Stanford University School of Medicine)
Genetics, Genomics, and Gene Regulation in Pulmonary Hypertension

Fall 2013

Sept. 11 3:30 pm, Biotechnology Center Auditorium
Corinne Engelman, PhD, Assistant Professor, Population Health Sciences, UW-Madison),
The Genetic Architecture of Alzheimer's Disease

Sept. 19 Introductory Session

Mo., Sept. 23  3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
**Note different time and room**
Presentation by Marc Riedel, PhD, Associate Professor, Electrical and Computer Engineering, University of Minnesota, Towards a Computer Engineering Discipline Based on DNA

Mo., Sept. 30th, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
Presentation by Kris Saha, PhD (Ass’t. Professor, Biomedical Engineering; Wisconsin Institute for Discovery, UW-Madison), Towards Synthetic Biology with Human Stem Cells


Week of Oct. 7th

Wed., Oct. 9, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Galina Petukhova, PhD, Uniformed Services, Univ. of Health Science, Recombination Hotspots: Molecular Causes and Consequences for Human Health

  -Or

Fri., Oct. 11th, 12:00 pm, 140 Bardeen, Jeffrey Leek, PhD, Ass’t Professor, Johns Hopkins Bloomberg School of Public Health, Research area - development of quantitative tools for summarizing and understanding high-dimensional genomic data


Mo., Oct. 14th, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
Presentation by George Church, Professor of Genetics, Harvard University

Wed, Oct. 23, Hugo Bellen, PhD, Professor, Depts. of Molecular and Human Genetics; Neuroscience; Program in Developmental Biology, Bayor College of Medicine; HHMI Investigator, Molecular Mechanisms of Amyotropic Lateral Schlerosis

Th., Oct. 31, Matt Copeland, PhD, CIBM predoctoral fellow (Chemical & Biological Engineering, UW-Madison)

Th., Nov. 7, Alicia Richards, CIBM predoctoral fellow (Chemistry, UW-Madison)

Week of Nov. 11th
Mo., Nov. 11th, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
Presentation by Bernard Palsson, Professor of Bioengineering, UC San Diego

 -Or

Wed., Nov 13th , 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall, Presentation by Murray Brilliant, Marshfield Clinic Research Foundation, Personalized Medicine: Research and Implementation


Th., Nov. 21, 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Center), Presentation by Patrick Schloss, PhD, Assoc. Professor, Dept. of Microbiology & Immunology, Univ. of Michigan Medical School, Dynamics of the Human Microbiome

Th., Dec. 5, Gene Tsvid, PhD, CIBM postdoctoral fellow (Biotechnology Center)

 

Spring 2013

Jan. 31   ** Note different time and room**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

Presentation by John Novembre, Associate Professor (Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California - Los Angeles), An Abundance of Rare Variants as a Major Feature of Human Genetic Diversity

Feb. 4 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
** Note different time and room**
Presentation by Richard Vallee, Professor (Pathology; Anatomy and Cell Biology. Columbia University Medical Center), Role of Microtubule Motor Proteins in Brain Developmental Disease

Feb. 14 Presentation by Jonathan Whitmer, GSTP Postdoctoral Fellow (Department of Chemical & Biological Engineering), Multiscale Modeling of the Genome


Feb. 21 Presentation by Jose Rodriguez-Martinez, GSTP Postdoctoral Fellow (Department of Biochemistry), Exploring the intrinsic DNA-binding preferences of human transcription factors using Cognate Site Identification and Sequence Specificity Landscapes


Feb. 27 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
** Note different time and room **
Presentation by Ellen Roy Elias, MD, Professor (General Peds, University of Colorado Denver – Anschutz Medical Campus), Smith-Lemli-Opitz Syndrome (SLOS): a Genetic Journey of Discovery


March 7 Presentation by Deborah Muganda-Rippchen, GSTP Predoctoral Fellow (Department of Computer Sciences), Computing Multi-Level Clustered Alignments of Gene-Expression Time Series


March 14 Presentation by Tyler Roberts, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering), Liquid Crystals in Genomic Applications


March 21 Presentation by Julia Kennedy-Darling, GSTP Predoctoral Fellow (Department of Chemistry), Title TBA


March 28 No seminar – Spring Break


April 4 Presentation by Chris Tervo, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering), Title TBA


April 11 Presentation by Anna Merrill, GSTP Predoctoral Fellow (Department of Chemistry), Title TBA


April 18 Presentation by Gloria Sheynkman, GSTP Predoctoral Fellow (Department of Chemistry), Title TBA


April 25 Presentation by Ashley Baltes GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering), Title TBA


Fall 2012

Sept. 6 CANCELLED ** Note different time and room**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

Presentation by Deborah Nickerson, PhD (Professor of Genome Sciences,
Adjunct Professor of Bioengineering, University of Washington)

Sept. 13 Introductory Session


Week of September 17th - Choose either seminar:

Tu., Sept. 18 4:00 pm, Wisconsin Inst. for Discovery, 330 N. Orchard St.

John C. Doyle, PhD (Professor of Control & Dynamical Systems; Electrical Engineering; Bioengineering, Caltech), Universal Laws and Architectures

Wed., Sept. 19 3:30 pm, Biotechnology Center Auditorium
Dana Wohlbach, PhD (Assistant Scientist, Laboratory of Genetics, UW-Madison), Comparative Multiomics Approaches to Understanding and Improving Bioenergy Production in Saccharomyces cerevisiae


Sept. 27
Presentation by John Zaborske, PhD, GSTP Postdoctoral Fellow (Department of Genetics), More to NMD than Meets the Eye: Examining the Role of NMD in Stress Response and a Novel Model for mRNA 3’UTR Mediated Degradation


Mo., Oct. 1 3:30 pm, Ebling Symposoium Center

**Note different time and room**
Presentation by Chip Asbury University of WA-Seattle, New Strategies for Uncovering How Chromosomes Are Segregated During Mitosis

Week of Oct. 8th – Choose either seminar:
Mo., Oct. 8 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
**Note different time and room**
Presentation by Terry Orr-Weaver, Professor of Biology, MIT; Member, Whitehead Institute, Changes in Genome Copy Number and Stability in Development
   OR


Wed., Oct. 10 3:30 pm, Biotechnology Center, 425 Henry Mall
**Note different time and room**
Presentation by James Faeder, Associate Professor, Department of Computational and Systems Biology, University of Pittsburgh, Rule-Based Modeling for Systems Biology

Oct. 18 Presentation by David Vereide, PhD, GSTP Postdoctoral Fellow (Morgridge Institute for Research), You Can Run But You Can’t Hide:
Applying Genomics to Make the Elusive Hematopoietic Stem Cell

Oct. 25 Presentation by Justin Lack, PhD, GSTP Postdoctoral Fellow (Department of Genetics), Sifting through the Pile: Ancient Guano Contains 10,000-Year DNA Record of Bats and Their Insect Prey

Nov. 1 Presentation by Ben Minkoff, GSTP Predoctoral Fellow (Department of Biochemistry), Abscisic Acid, Drought, and Phosphorylation: Progress toward Understanding Abscisic Acid’s Cellular Phosphosignaling Network

Wed., Nov. 7   ** Note different time and room**

3:30 pm, Biotechnology Center, 425 Henry Mall
Presentation by Josep Comeron, Associate Professor (Department of Biology, University of Iowa), Evolutionary Consequences of Variable Recombination across the D. Melanogaster Genome

Nov. 15 Presentation by Alicia Richards, GSTP Predoctoral Fellow (Department of Chemistry), Mass Spectrometry-based Identification of ATM Targets Following Exposure to Oxidative Stress

Week of Nov. 26th: Choose either seminar


Mo., Nov. 26 ** Note different time and room**

3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
Presentation by Emmanuel Skordalakes, Associate Professor (Gene Expression and Regulation Program, Wistar Institute), Telomerase Structure, Function, and Cancer Therapies

Th., Nov. 29 **Note different time and room**

3:30 pm Ebling Symposium Center, Microbial Sciences Bldg.

Presentation by Seth Darst, Jack Fishman Professor (Laboratory of Molecular Biophysics, The Rockefeller University), Structural Studies of Bacterial Transcription

Tu., Dec. 4 ** Note different time and room**

4:00 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Murray H. Brilliant (Director, Center for Human Genetics, James Weber Endowed Chair Awardee, Marshfield Clinic Research Foundation), Personalized Medicine at the Marshfield Clinic: Research and Implementation


Wed., Dec. 12
**Note different day and room**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Wade Harper (Harvard University, Proteomic Exploration of the Ubiquitin System


Spring 2012

Jan. 26 Presentation by Jonathan Whitmer, GSTP Postdoctoral Fellow (Department of Chemical & Biological Engineering), DNA Electrohydrodynamics


Feb. 2  Presentation by Jose Rodriguez-Martinez, GSTP Postdoctoral Fellow (Department of Biochemistry), Exploring DNA-binding Preferences of Transcription Factors using Cognate Site Identification and Sequence Specificity Landscapes


Feb. 9
Presentation by Chris Tervo, GSTP Predoctoral Fellow (Department of Chemical & Biological Engineering), Interrogating Genome-Scale Models: Algorithms for Experimental Design and Curation of Functional Annotations

Feb. 16 Presentation by Gloria Kreitinger, GSTP Predoctoral Fellow (Department of Chemistry), Comprehensive Analysis of the Transcriptome and Proteome of Human Cells Undergoing Apoptosis

Feb. 23 Presentation by Katie Clowers, GSTP Predoctoral Fellow (Department of Genetics), Determining the Genetic Basis of Niche-Specific Survival in Complex Environments

March 1 **Note different time and room**
1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by David Nelson, Professor, Department of Molecular and Human Genetics (Baylor College of Medicine), Lessons from the Fragile X Locus: Unstable DNA, Toxic RNA and Neuronal Function

March 8 Presentation by Presentation by Juan Rodriguez-Molina, GSTP Predoctoral Fellow (Department of Biochemistry), Global Nrd1 Distribution Is Regulated by Dynamic Phosphorylation States of the C-Terminal Domain of RNA Polymerase II

March 15 Presentation by Julia Kennedy-Darling, GSTP Predoctoral Fellow (Department of Chemistry), Elucidating Protein-DNA Interactions at the E. coli rrn Operon

March 22 Presentation by Ashley Baltes GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering), Multiscale Virus-Host Interactions in Model Systems

March 29 Presentation by Anna Larson GSTP Predoctoral Fellow (Department of Chemistry), Multiplexed Quantification of Signaling in Yeast as Induced by Osmotic Stress

April 5 No seminar – Spring Break

April 12 **Note different time and room**
1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Pamela Silver, (Department of Systems Biology, Harvard Medical School), Designing Biological Systems

April 19 Presentation by Tyler Roberts, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering), Simulations of Colloidal-Liquid Crystal Systems

April 26 **Note different time and room**
1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Ron Weiss, Associate Professor (Department of Biological Engineering, MIT), Synthetic Biology: From Parts to Modules to Therapeutic Systems

PAST SEMINAR SERIES

Genomic Sciences Program Seminar

Fall 2011

Sept. 15 Introductory Session


Sept. 22 ** Note different time and room**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

Presentation by John Yates III, PhD (Professor, Chemical Biology, Scripps Research Institute), Using Mass Spectrometry to Understand Protein Misfolding Diseases


Sept. 29 Presentation by Leslie Turner, PhD, GSTP Postdoctoral Fellow (Dept. of Genetics, UW-Madison)
, Genetic Mapping of Testis Expression Traits Associated with Hybrid Male Sterility in House Mice (Mus musculus)

Fri., Oct. 7th   ** Note different time and room**

1:15 pm, Pyle Center, 702 Langdon Street, Room 313
Presentation by Atul Butte, MD, PhD (Chief and Associate Professor of Systems Medicine and Pediatrics, Stanford University), Systems and Personalized Medicine

Week of Oct. 10th: Choose either seminar


Th., Oct. 13 ** Note different time and room**

12:15 pm, 1315 Chemistry, 1101 University Avenue
Presentation by J. Michael Ramsey, PhD (Professor, Department of Chemistry, University of North Carolina-Chapel Hill), Micro- and Nanofabricated Devices for Elucidating Chemical and Biochemical Information

Fri., Oct. 14 **Note different time and room**

1:00 pm Ebling Symposium Center, Microbial Sciences Bldg.

Presentation by Steven Turner, PhD (Founder and Chief Technology Officer,
Pacific Biosciences), PacBio RS: Capabilities of Third Generation Genome Sequencing


Wed., Oct. 19
**Note different day and room**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by David B. Goldstein, PhD (Professor of Molecular Genetics & Microbiology, Professor of Biology and Director of the Center for Human Genome Variation, Duke University), Sequencing and Genetics of Human Disease


Wed., Oct. 26
**Note different time and room**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Matthew Dean, PhD (Assistant Professor of Biological Science, Univ. of Southern California), Proteomics of Male Seminal Fluid: The Evolutionary Dynamics of Sexual Conflict


Nov. 3 Presentation by John Zaborske, PhD (GSTP Postdoctoral Fellow, Department of Genetics, UW-Madison), Examining NMD’s (Nonsense mediated mRNA Decay) Role in Cellular Adaptation to Stresses and Identifying New NMD 3’ UTR Targets In Yeast

Week of Nov. 7th: Choose either seminar


Nov. 10 **Note different time**

12:00 pm, 1360 Biotechnology Center
Presentation by Tandy Warnow PhD (Professor, Computer Sciences, University of Texas, Austin), Fast Methods for Estimating Species Trees from Gene Trees

Nov. 11 **Note different time and room**

12:00 pm, 140 Bardeen, 1215 Linden Dr.
Presentation by Tandy Warnow PhD (Professor, Computer Sciences, University of Texas, Austin), SEPP: SATe-enabled Phylogenetic Placement


Nov. 17
** Note different time and room**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Tim Hughes, PhD (University of Toronto), Exploring the Eukaryotic Protein-Nucleic Acid Interactome


Dec. 1
Presentation by David Vereide, PhD (GSTP postdoctoral fellow; Biotechnology Center; The Morgridge Inst. for Research), Mutations, mRNAs, and miRNAs: Making Clinically useful Cells Safely

Dec. 8 Presentation by Jennifer Apodaca (GSTP predoctoral trainee, Microbiology Doctoral Program), Evolution of the Anaerobic Stimulon in Closely Related Enterobacteria


Spring 2011

Jan. 20 CANCELLED
1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Pamela Silver (Department of Systems Biology, Harvard Medical School), Title TBA


Jan. 27 **Note different time and room**
12:15 pm, Rm. 1315 Chemistry Building, Ben Garcia (Assistant Professor, Dept. of Molecular Biology, Princeton University), Understanding the Histone Code through Quantitative Proteomics


Tu., Feb. 1st  **NOTE DIFFERENT TIME AND ROOM
3:30 pm Ebling Symposium Center, Microbial Sciences Bldg., 1550 Linden Dr.
Ben Cravatt (Department of Chemical Physiology, Scripps Research Institute), Activity-based Proteomics: Applications for Enzyme and Inhibitor Discovery


Feb. 10 Presentation by Mary Kate Bonner, GSTP Predoctoral Fellow (Department of Genetics)
, Proteomic Analysis of CHO Cell Mitotic Spindles Reveals Key Cell Division Factors

Feb. 17 Presentation by Jose Rodriguez-Martinez, GSTP Postdoctoral Fellow (Department of Biochemistry), Expanding the Cognate Site Identification (CSI) Platform to Study the DNA-Binding Preferences of Transcription Factor Complexes


Feb. 24 Presentation by Dan Hinckley, GSTP Predoctoral Fellow (Department of Chemical & Biological Engineering)
, Coarse Grain Modeling of Nucleic Acids: A Case Study and Future Prospects


March 3 Presentation by Chris  Tervo, GSTP Predoctoral Fellow (Department of Chemical & Biological Engineering)
, Genome Annotation Validation, GPR Association Discovery and Microbial Strain Design Via the Forced Coupling Algorithm


March 10 Presentation by Juan Rodriguez-Molina, GSTP Predoctoral Fellow (Department of Biochemistry)
, Chemical-Genomic Analysis Reveals Bur1 as an Unexpected Ser7 CTD Kinase


March 24 **NOTE DIFFERENT TIME AND ROOM**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Gary Stormo (Professor, Genetics, Washington University School of Medicine)
, Specificity of Protein-DNA Interactions: Experimental and Computational Approaches


March 31 Presentation by Gloria Kreitinger, GSTP Predoctoral Fellow (Department of Chemistry)
, Sequence-specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification


April 5 **NOTE DIFFERENT TIME AND DAY**

11:45, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by
Leo Pallanck (Dept. of Genome Sciences, University of Washington), Using Drosophila to Study the Influence of Mitochondrial Quality Control in Parkinson's Disease


Mo., April 11
**NOTE DIFFERENT TIME AND ROOM**

3:30 pm, Ebling Symposium Center, Microbial Sciences Center

Presentation by James Chen (Department of Chemical and Systems Biology, Stanford University), Spatiotemporal Resolution of the Embryonic Transcriptome Using Caged Morpholinos

Week of April 18th: choose either seminar


Wed., April 20th 3:30 pm, Biotechnology Center Auditorium
[Laurie Jackson-Grusby (Ass’t. Prof., Pathology, Harvard Medical School), Developmental Field Cancerization and Origins of Medulloblastoma Stem Cells

April 21 **NOTE DIFFERENT TIME AND ROOM**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by
Charles Boone (Univ. of Toronto), The Genetic Landscape of a Cell

April 28 Presentation by Julia Kennedy-Darling, GSTP Predoctoral Fellow (Department of Chemistry), Development of a Tool to Identify Protein:Protein and Glycan:Protein Interactions at Cell:Cell Interfaces


Fall 2010

Wed., Sept. 8 **NOTE DIFFERENT TIME AND ROOM**
3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Bret Payseur (Assistant Professor, Department of Genetics, UW-Madison), Of Mice and People: Evolutionary Genetics in Two Familiar Species


Sept. 16 Introductory Session


Wed., Sept. 22  **NOTE DIFFERENT TIME AND ROOM**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Audrey Gasch (Assistant Professor, Department of Genetics, UW-Madison), Comparative and Functional Genomics of Fungal Environmental Responses


Sept. 30 Presentation by Kelli Kline, GSTP Postdoctoral Fellow (Department of Biochemistry)
, Quantitative Arabidopsis Phosphoproteomics using Mass Spectrometry

Week of Oct. 4th: Choose either seminar – Oct. 6th or Oct. 7th:


Wed., Oct. 6th **NOTE DIFFERENT TIME AND ROOM**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Patricia (Trisha) Wittkopp (Assistant Professor, Ecology and Evolutionary Biology, University of Michigan), Genomic Sources of Regulatory Variation

Th., Oct. 7th   ** Note different time and room**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Frank Rozenzweig (Associate Professor, Biological Sciences, University of Montana), E unibus plurum: Evolution of Biodiversity in a Simple Constant Environment


Oct. 14 Presentation by Jessica Fautch, GSTP Postdoctoral Fellow (Department of Oncology)
, Non-coding Risk SNP Variants and Gene Expression in Breast Cancer Susceptibility


Oct. 21 Presentation by Leslie Turner, GSTP Postdoctoral Fellow (Department of Genetics)
, Using Systems Genetics to Uncover Causes of Hybrid Male Sterility in House Mice


Oct. 28 Presentation by John Zaborske, GSTP Postdoctoral Fellow (Department of Genetics)
, Charged tRNAs as Regulators of Metabolic State in Saccharomyces cerevisiae


Nov. 4 **NOTE DIFFERENT TIME AND ROOM**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by Michael Washburn (Associate Professor, Director of Proteomics Center, Stowers Institute for Medical Research)
, Probing the Dynamics of Transcriptional Regulatory Complexes with Quantitative Proteomics


Nov. 11 Presentation by Gordon Freeman, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering)
, Exploring DNA Biophysics via Mesoscale Simulation


Nov. 18 **NOTE DIFFERENT TIME AND ROOM**

1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
Presentation by James Ferrell (Professor and Chair, Chemical & Systems Biology, Stanford University)
, Dissecting the Mitotic Oscillator


Wed., Dec. 1
**NOTE DIFFERENT TIME AND ROOM**

3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

Presentation by Sue Jinks-Robertson (Professor, Department of Molecular Genetics and Microbiology, Duke University Medical Center), Transcription and Genome Instability in Yeast

Spring 2010

Feb. 4 **NOTE DIFFERENT TIME AND ROOM** 1:30 Biotech Ctr Aud.
Alan Marshall, PhD (Professor, Dept. of Chemistry, Florida State University), Ultrahigh Mass Resolution and Mass Accuracy for Biomolecules: What's Possible, What's Not, and What It's Good For


Feb. 11 Presentation by Tim Schramm, GSTP Predoctoral Fellow (Department of Chemistry), Flash Sequencing: Structure and Sequencing Information from Single Molecules


Feb. 18 Presentation by Mary Kate Bonner, GSTP Predoctoral Fellow (Department of Genetics)
, Metaphase Spindle Proteome Reveals Potential Furrow Initiation Factors


Feb. 25 Presentation by Douglas Phanstiel, GSTP Predoctoral Fellow (Department of Chemistry)
, Global Proteomic and Phosphoproteomic Comparison of Human ES, IPS, and Fibroblast Cells


March 4 **NOTE DIFFERENT TIME AND ROOM** 1:30 Biotech Ctr Aud.
Presentation by John Stamatoyannopoulos, MD (Assistant Professor of Genome Sciences, University of Washington)
, Mapping the Human Regulatory Genome


March 11 Presentation by Juan Rodriguez-Molina, GSTP Predoctoral Fellow (Department of Biochemistry)
, Chemical Genomic Dissection of the RNA Polymerase II CTD Code


March 18 **NOTE DIFFERENT TIME AND ROOM** 1:30 Biotech Ctr Aud.
Presentation by Noah Rosenberg, (Associate Professor, Departments of Human Genetics, Biostatistics, and Ecology and Evolutionary Biology, U. Mich), Worldwide Human Genetic Variation: Implications for Disease-Association Studies in Diverse Populations


March 25 Presentation by Scott Topper, GSTP Predoctoral Fellow (Department of Genetics)
, Global Analysis of RNA and Protein Changes in Response to Osmotic Stress


April 1 spring break, no seminar


April 8 **NOTE DIFFERENT TIME AND ROOM** 1:30 Biotech Ctr Aud.
Presentation by Peggy Farnham, PhD (Professor, University of California-Davis Genome Center), Using Genomic Technologies to Investigate Transcriptional Regulation of Normal and Cancer Genomes


April 15 Presentation by Jennifer Apodaca, GSTP Predoctoral Fellow (Microbiology Doctoral Training Program)
, Regulation of the Transcriptional Response to Oxygen Limitation in Enterobacteria


Mo., Apr. 19 **CANCELLED**
3:30 pm - Ebling Symposium Center, Microbial Sciences Bldg., 1550 Linden Dr.
Presentation by Todd Michael, PhD (Assistant Professor, Plant Biology & Pathology, Rutgers University), Exploring Plant Genomes with High-throughput Sequencing

April 29 Presentation by Jamison Wolfer, PhD, GSTP Postdoctoral Fellow (Department of Biochemistry)
, Oligonucleotide Microarrays on One Square Millimeter Glass Chips: Development and Applications of the ‘Millichip’

Genomic Sciences Program Seminars
Fall 2009

Thursdays, 4:45 p.m., Rm. 1360 Biotech Center

Sept. 10 Introductory Session


Week of Sept. 14th: Choose either seminar:

Sept. 16 **Note different time and room**

    3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    John Petrini (Sloan-Kettering Institute), Genetic Analysis of

    Chromosome Break Metabolism

Th., Sept. 17 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
   ** Note different time and room**
     Presentation by Job Dekker (Associate Professor, Biochemistry and

      Molecular Pharmacology, University of Massachusetts Medical School),

     Long Range Gene Regulatory Architecture of the Human Genome


Week of Sept. 28th: Choose either seminar – Sept. 30th or Oct. 1st:

Wed., Sept. 30 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

  ** Note different time and room**
   James Womack (Texas A&M), Salient Messages from the Bovine

   Genome Sequence

Th., Oct. 1 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

    ** Note different time and room**
   Presentation by Rachel Brem (Assistant Professor of Genetics, Genomics

    and Development, Department of Molecular and Cell Biology, University

    of California – Berkeley), Transcriptional Variation and Regulatory Feedback

    in Saccharomyces

Th., Oct. 8 Presentation by Yongku Cho, GSTP predoctoral fellow

    (Department of Chemical and Biological Chemistry, UW-Madison),

    Antibody-Based Membrane Proteomics

Week of Oct. 12th: Choose one seminar – Oct. 14th or either on Oct. 15th:

Wed., Oct. 14 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
   ** Note different date and room**
    Jonathan Pritchard (Professor, Dept. of Human Genetics, University of

    Chicago), High Resolution Mapping of Expression-QTLs Yields Insight

    into Human Gene Regulation

Th., Oct. 15 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
   ** Note different time and room**
   Presentation by Gavin Sherlock (Assistant Professor of Genetics, School

    of Medicine, Stanford University), Watching Yeast Change: Using Genomics

   to View the Adaptivge Landscape

Th., Oct. 15 3:30 pm, 1220 Microbial Sciences Building (Ebling

    Symposium Center)
   ** Note different time and room**
   Presentation by David Lipman, MD (Director, National Center for

  Biotechnology Information), Evolution in Computational Biology

Th., Oct. 22 Presentation by Gordon Freeman, GSTP predoctoral fellow

    (Department of Chemical and Biological Chemistry, UW-Madison),

    A Coarse-Grained Model for a Capsid-Genome System

Th., Oct. 29 Presentation by Jessica Fautch, GSTP postdoctoral fellow

    (Department of Oncology, UW School of Medicine & Public Health),

    Characterization of Candidate Genes Near the Rat Mammary Carcinoma

    Susceptibility Locus Mcs1c

Th., Nov. 5 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    ** Note different time and room**
    Michael Snyder, Ph.D. (Professor, Genetics, Stanford University), Analyzing

    Genomes and Regulatory Informating Using Omics Technologies

Th., Nov. 12 Presentation by Suzanne Kulevich, GSTP predoctoral fellow

    (Department of Chemistry, UW-Madison), Hydrophobic Chemical Modification

    of Peptides to Improve Mass Spectrometry-Based Proteomics

Week of November 16th: Choose either seminar:

Th., Nov. 19th 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
   ** Note different time and room**
   Presentation by Aviv Regev (Broad Institute; Assistant Professor,

    Department of Biology, MIT), Modular Biology: The Function and Evolution

    of Regulatory Networks

Th., Nov. 19 3:30 pm, 1220 Microbial Sciences Building (Ebling

    Symposium Center)
    ** Note different date and room**
    Presentation by George Weinstock, PhD (Professor, Department of

     Genetics, Washington University; Assoc. Director, Genome Center),

    Adventures in the Human Microbiome

Th., Dec. 3 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Center)
   ** Note different time and room**
   Presentation by Tanja Woyke (Postdoctoral fellow, DOE Joint Genome 

  Institute), Microbial Single Cell Genomics

 

Genomic Sciences Program Seminars
Spring 2008

Thursdays, 4:45 p.m., Rm. 1360 Biotech Center

Jan. 29 Presentation by Jamison Wolfer, GSTP Postdoctoral Fellow (Department

    of Biochemistry), Development of New Methodology Employing the Maskless

    Array Synthesizer: 'Millichips' and 'Sugar-Chips'


Feb. 5 Presentation by Jennifer Apodoca, GSTP Predoctoral Fellow

    (Microbiology Doctoral Training Program , UW-Madison), Evolution of the

    Transcriptional Response to Oxygen Limitation in the Enterobacteria


Feb. 12 Presentation by Edward Huttlin, GSTP Postdoctoral Fellow

   (Departments of Oncology and Biochemistry),  Quantitative Proteomic

  Characterization of the ApcMin Mouse via 15N Metabolic Labeling


Feb. 19 No seminar


Feb. 26 Presentation by Danielle Swaney, GSTP Predoctoral Fellow

    (Department of Chemistry, UW-Madison), Innovative Technology for the

    Large-scale Study of Proteins and their Post-translational Modifications


March 5 Presentation by Irene Ong, GSTP Postdoctoral Fellow (Dept. of

    Biostatistics and Medical Informatics, UW-Madison), Ensemble Dynamic Bayesian Networks for Inferring Gene Regulation from Time-Series Data


March 12 Presentation by Mary Kate Bonner, GSTP Predoctoral Trainee

    (Department of Genetics, UW-Madison), Metaphase Spindle Proteome

    Reveals Potential Furrow Initiation Factors

March 19 Spring Break, no seminar

March 26 Presentation by Jeremy Lavine, GSTP Predoctoral Fellow

    (Department of Biochemistry, UW-Madison), FoxM1 is Sufficient to Stimulate

    Islet Cell Proliferation  in Isolated Mouse and Human Islets

April 2  Presentation by Josh Tietjen, GSTP Predoctoral Fellow (Microbiology

   Doctoral Training Program, UW-Madison), Chemical-genomic Dissection of

   the CTD Code

  
April 9 Presentation by Douglas Phanstiel, GSTP Predoctoral Fellow

   (Department of Chemistry, UW-Madison), Large-Scale Quantitative Proteomic

   Comparison of Human ES, IPS, and Somatic Cells

April 16 Presentation by Scott Topper, GSTP Predoctoral Fellow (Department

    of Genetics, UW-Madison), A Genetic Screen to Identify Regulators of the

    Environmental Stress Response


April 23 Presentation by Ed Sambriski, GSTP Postdoctoral Fellow (Department

   of Chemical and Biological Engineering, UW-Madison), Uncovering Pathways

   in DNA Oligonucleotide Hybridization via Transition State Analysis


April 30 Presentation by Juan Rodriguez-Molina, GSTP Predoctoral Fellow

    (Department of Biochemistry, UW-Madison)

 

Genomic Sciences Program Seminar
(Chem 923, Section 157)
Fall 2008

Sept. 11 Introductory Session


Sept. 18 **Note different time and room**

  1:30 pm, Bioechnology Center Auditorium, 425 Henry Mall

  Alan Moses, PhD (Dept. of Cell & Systems Biology, University of Toronto),

  Selection and Function in Population Genetics


Wed., Sept. 24th **Note different time and day**

   3:30 pm, Biotechnology Center Auditorium

   Cliff Tabin, PhD (Professor, Dept. of Genetics, Harvard Medical School),

   Evolution and Development of Vertebrate Morphology


Oct. 2
Suzanne Kulevich, GSTP predoctoral fellow (Department of Chemistry,

  UW-Madison), Improved Mass Spectrometric Analysis of Mixtures of Intact

  Proteins"


Tu., Oct. 7 **Note different day and room**

   4:00 p.m., 1800 Engineering Hall

   Anand Asthagiri, PhD (Assistant Professor, Chemical Engineering, California

   Institute of Technology), Tuning Biological Signals and Multicellular Dynamics


Oct. 16  Omar Negrete, GSTP predoctoral fellow (Department of Electrical &

   Computer Engineering, UW-Madison), Sequence Specific Immobilization of

   DNA Nanostructures

Week of Oct. 20th: Choose either seminar – Oct. 22nd or Oct. 23rd:
Wed., Oct. 22 **Note different day and room**

    3:30 pm, Biotech Center Auditorium
    Joe Thornton (Assoc. Prof., Center for Ecology & Evol. Biol., Univ. of

    Oregon-Eugene), The Origins of Complexity: Molecular Evolution of

     Steroid Hormone Receptors


Oct. 23 **Note different time and room**

     3:30 pm, 1520 Microbial Sciences Building

     Clay Wang, PhD (Assistant Professor of Pharmaceutical Sciences and

     Chemistry, University of Southern California), Natural Product Drug

     Discovery in the Genomic Era: Molecular Genetic Mining of the

     Aspergillus Secondary Metabolome


Oct. 30  Tim Schramm, GSTP predoctoral fellow (Department of Chemistry,      UW-Madison), A Single Molecule System for Discovery of Structural Alteration

     and Sequence Information

Week of Nov. 3rd: Choose either seminar – Nov. 5th or Nov. 6th
Wed., Nov. 5, **Note different day and room**

   3:30 pm Biotech Center Auditorium

   Alexander D. (Sandy) Johnson (Prof., Dept. of Microbiology & Immunology,

   Biochemistry; Biophysics; Univ. Calif.-San Francisco) Evolution of Transcription

   Networks

Nov. 6 **Note different time and room**

   1:30 p.m. in the Biotechnology Center Auditorium

   Alan Attie, PhD (Professor, Dept. of Biochemistry, UW-Madison),

   Genes, Gene Networks and Type 2 Diabetes

Nov. 13
Yongku Cho, GSTP predoctoral fellow (Department of Chemical and

    Biological Chemistry, UW-Madison), Antibody Library Selection and

    Characterization in Detergent-Solubilized Whole-Cell Lysates Using

    Yeast Display

Week of Nov. 17th: Choose any one seminar – Nov. 17th, 19th, or 20th:
Mo., Nov. 17 **Note different day and room**

   3:30 p.m. in Ebling Symposium Center, MSB, 1550 Linden Drive

    Jay Keasling, PhD (Professor, Departments of Chemical Engineering;

   Bioengineering, UC-Berkeley), Synthetic Biology for Synthetic Chemistry

Wed., Nov. 19, **Note different day and room**

   3:30 pm, Biotech Center Auditorium

   Sarah Tishkoff, PhD (Assoc. Prof., Dept. of Biology, U. Penn), Genotypic and

   Phenotypic Variation in Africa: Implications for Human Evolution and Disease

Th., Nov. 20 **Note different time and room**

   1:30 p.m., Biotechnology Center Auditorium, 425 Henry Mall

   Michael Olivier, PhD (Assistant Professor, Human & Molecular Genetics

   Center, Medical College of Wisconsin), Title TBA

Mo., Nov. 24 **Note different day and room**

   3:30 p.m. in Ebling Symposium Center, MSB, 1550 Linden Drive

   Roger Brent, PhD (President and Research Director, The Molecular Sciences

   Institute), Single Cell Experiments that Define and Quantify Physiological

   Variables that Measure Key Cell States, and How These Might Impact Microbial

   Biosynthetic Production

Th., Dec. 4   Kaveh Jorabchi, PhD, GSTP postdoctoral fellow (Department of

   Chemistry, UW-Madison), Mass Spectrometry of Levitated Droplets by Charge

   Assisted Laser Desorption/Ionization

Optional Seminar:
Wed., Dec. 10, 3:30 pm, Biotech Center Auditorium

   Greg Wray, PhD (Prof. of Biology, Duke Univ.) Ganglia, Guts, and Gonads:

   Evolutionary Changes in Gene Expression During Human Origins

 

Genomic Sciences Program Seminar
(Chem 923, Section 157)
Spring 2008

 

Jan. 24 Presentation by Jill Herschleb, (Cellular and Molecular Biology

    Graduate Program; GSTP Alum), Using Single-Molecule Technology

    to Uncover High-Resolution Gene Rearrangements and Novel Breast

    Cancer Candidate Genes


Jan. 31 Presentation by Ryan Hilger, GSTP Predoctoral Fellow (Department of

    Chemistry, UW-Madison), Modifying a Triple Quadrupole Mass Spectrometer

     in Order to Perform Ion-Molecule Reactions


Feb. 7 Presentation by Ed Sambriski, GSTP Postdoctoral Fellow (Department

    of Chemical and Biological Engineering), Toward a Comprehensive Coarse-

    Graining Scheme for DNA: Caturing the Single-to-Double Stranded Transition

    and the Encasidation of Genomes in Bacteriophage


Feb. 14 Presentation by Irene Ong, GSTP Postdoctoral Fellow (Dept. of

    Biostatistics and Medical Informatics, UW-Madison), Inferring Regulatory

    Networks from Time Series Data

Feb. 21 Presentation by Scott Topper, GSTP Predoctoral Fellow (Department

    of Genetics), Genomic Analysis of the Role of PKC1 in Regulating the

    Environmental Stress Response


Feb. 28 Presentation by Danielle Swaney, GSTP Predoctoral Fellow

    (Department of Chemistry, UW-Madison), Decision Tree-Driven Tandem Mass

    Spectrometry for Shotgun Proteomics


March 6 **Note different time and room**

   1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

     Presentation by Sunduz Keles, PhD (Assistant Professor, Departments of

     Statistics and Biostatistics and Medical Informatics), Statistical and

     Computational Issues in the Analysis of ChIP-chip Experiments for

     Chromatin Modifications


March 13 Presentation by Josh Tietjen, GSTP Predoctoral Fellow (Microbiology

    Graduate Program, UW-Madison), Challenging the Dogma of RNA Polymerase

    II CTD Phosphorylation

March 20 Spring Break, no seminar

March 27 Presentation by Leslie Donato, GSTP Postdoctoral Fellow

    (Department of Biochemistry, UW-Madison), Binding Site Specificity in

    Genomes: The Role of Allosteric DNA Modulaton in Protein-DNA Assembly

April 3
**Note different time and room**

   1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall

   Presentation by Erin O'Shea, PhD (Professor, Department of Molecular

   and Cellular Biology, Harvard University), Structure and Function of

   Transcriptional Networks

  
April 10 Presentation by Steven Giles, GSTP Postdoctoral Fellow (Department

    of Biomol. Chemistry, UW-Madison), Elucidating Determinants of Sexual

    Identity in Cryptococcus neoformans


April 17 Presentation by Jeremy Lavine, GSTP Predoctoral Fellow (CMB

    Program, UW-Madison), Overexpresson of Cholecystokinin in Isolated

    Human Islets Stimultes Beta-cell Proliferation


April 24 Presentation by Doug Phanstiel, GSTP Predoctoral Fellow

    (Department of Chemistry), The Development and Application of Proteomic

    Strategies for the Analysis of Human Embryonic Stem Cells: From Histones

    to Whole Cell Lysates


May 1 **Note different time and room**
      1:30 pm, Biotechnology Center Auditorium
      David Botstein (Princeton University), Coordination of Growth Rate, Cell

     Cycle, Stress Response and Metabolic Activity in Yeast

Genomic Sciences Program Seminar
(Chem 923, Section 157)
Fall 2007

Thursdays, 4:45 p.m., Rm. 1360 Biotech Center

Sept. 6  1:30 pm, Biotechnology Center Auditorium

     **Note different time and room**
      Bing Ren, PhD (Assoc. Prof., Cellular & Molecular Medicine, UC San

      Diego), Global Analysis of the Gene Regulatory Networks and

      Epigenome in Human Cells

Sept. 13 Introductory Session

Sept. 20 1:30 pm, Biotechnology Center Auditorium

    **Note different time and room**
     Josh Rabinowitz, PhD (Ass't. Professor, Chemistry and Integrative

     Genomics, Princeton), Towards a Comprehensive Understanding of

     Cellular Metabolism

Sep. 27 Jennifer Apodaca, GSTP Predoctoral Fellow (Comparative

     Biomedical Sciences Graduate Program), Evolution of the

     Transcriptional Response to Oxygen Limitation in the Enterobacteria

Oct. 4   1:30 pm, Biotechnology Center Auditorium

    **Note different time and room**
    John Ryals, PhD (President and CEO, Metabolon, Inc.), Metabolomics

    as a Tool to Understand Drug Action and Safety in Perclinical Models

Oct. 11 No seminar

Mo., Oct. 15  3:30 pm in B1118 Biochemistry, 420 Henry Mall

    ** Note different day and room**

    Tom Misteli (Head, Cell Biology of Genomes Group, National Cancer

    Institute) The Surprising Role of Nuclear Architecture in Human Aging

Oct. 25 Dan Abras, GSTP Predoctoral Fellow (Department of Chemical and

    Biological Engineering), Effect of Severe Confinement on DNA Relaxation

    Behavior: Application to High Throughpu Genome Analysis

Nov. 1 Jason McCoy, GSTP Postdoctoral Fellow (Department of

    Biochemistry), Functional Characterization of Structural Genomics

    Targets

Mo., Nov. 5   3:30 pm in B1118 Biochemistry, 420 Henry Mall

    **Note different day and room**

    Bruce Stillman (President, Cold Spring Harbor Labortories), Control of

    the Chromosome Cycle in Human Cells by the Origin Recognition

    Complex

Nov. 15 Yongku Cho, GSTP Predoctoral Fellow (Department of Chemical

    and Biological Engineering), Yeast Antibody Display Technology for

    Efficient Targeting and Characterization of Cell-surface Biomarkers

Mo., Nov. 19  3:30 pm in B1118 Biochemistry, 420 Henry Mall

      **Note different day and room**

      Jonathan Widom (William Deering Professor, BMBCB and Chemistry,

      Northwestern University), The Genomic Code for Nucleosome

      Positioning


Nov. 29 Nicholas C. Shera, GSTP Predoctoral Fellow (Department of

     Genetics), Cancer Genomics: Discovery of Characterization of

     Complex Alterations in the Solid Tumor Oligodendroglioma via

     Single Molecule Analysis

Dec. 6    3:30 pm in Rm. 1220 Microbial Sciences Bldg., 1550 Linden Dr.

      **Note different time and room**

       Cameron Currie (Assistant Professor, Department of Bacteriology,

       UW-Madison), Cooperaton, Conflict and Coevolution: Exploring Ancient

       Agriculture in Ants

Genomic Sciences Program Seminar
(Chem 923, Section 157)
Spring 2007

Thursdays, 4:45 p.m., Rm. 1360 Biotech Center

 

Jan. 25   2:30 pm, Biotech. Center Audit. - **Note different time and room**

     Annelise Barron (Professor of Chemical and Biological Engineering,

      Northwestern University), DNA Sequencing by Free-Solution Microchannel

      Electrophoresis of DNA-Polyamide Conjugates

Feb. 1 - Presentation by Michael Benton, GSTP Predoctoral Fellow (Department

      of Chemical and Biological Engineering, UW-Madison), A Green Approach to

      DNA Damage Detection

Feb. 8 - Presentation by Josh Mandir, GSTP Predoctoral Fellow (Department of

      Chemistry, UW-Madison), Applying the Invasive Cleavage Reaction to

      miRNA analysis

Feb. 15 - Presentation by Edward Sambriski, GSTP Postdoctoral Fellow

      (Department of Chemical and Biological Engineering, UW-Madison),

      Analytical Coarse-Grained Description of Polymer Liquids: Extending

      Computer Simulations of Polymers to Larger Length Scales

Feb. 22 - Presentation by Michael Toepke GSTP Postdoctoral Fellow

      (Department of Biomedical Engineering, UW-Madison), Microfluidic Platforms

      for High-Throughput Cellular Assays

March 1 - Presentation by Josh Tietjen, GSTP Predoctoral Fellow (Microbiology

     Graduate Program, UW-Madison), Determining the DNA Binding Profile of

     Proteins and Small Molecules Using the Cognate Site Identifier (CSI)

March 8 - CANCELLED - will be rescheduled

      Presentation by Michael Elowitz, (Assistant Professor of Biology and

      Applied Physics, Caltech), Noise and Differentiation in Bacteria

March 15 - Presentation by Ryan Hilger, GSTP Predoctoral Fellow (Department

    of Chemistry, UW-Madison), Detection of High Mass Ions in Time of Flight

    Spectrometry

March 22 - Presentation by Omar Negrete, GSTP Predoctoral Fellow (Dept. of

     Elect. & Comp. Eng., UW-Madison), High-Throughput In-Situ Synthesis of

     Ultra-Large Scale DNA Microarrays with Maskless Scanning System

March 29 - Presentation by Leslie Donato, GSTP Postdoctoral Fellow

     (Department of Biochemistry, UW-Madison), A Tale of Two Projects: Probing

     the Mechanism of Retinoic Acid Mediated Growth Inhibition in Mammary

     Carcinoma Cells, and Probing the Function of Embryonic Stem Cell Specific

     Transcription Factors

April 5 - Spring Break, no class

April 12- Presentation by Steve Giles, GSTP Postdoctoral Fellow (Department of

     Biomol. Chemistry, UW-Madison), Elucidating How Sxi1 and Sxi2 Control

     Sexual Development in C. neoformans

April 19- Presentation by Jeremy Levine, GSTP Predoctoral Fellow (CMB

     Program, UW-Madison), Cholecystokinin Overexpression in Isolated Islets

      Promotes Beta-cell Proliferation in a CCK1R- and CCK2R-independent Manner

April 26- Presentation by Danielle Swaney, GSTP Predoctoral Fellow

       (Department of Chemistry, UW-Madison), Discovery and Quantitation of the

        Phosphorylation Events that Trigger Human Embryonic Stem Cells to Exit

        the Pluripotent State

May 3 - 1:30 pm, Biotech Center Audit. - **Note different time and room**

        Presentation by Eddie Rubin, PhD, Joint Genome Institute,

        Genomic Approaches to Bioenergy and Gene Regulation

 

                                                   * * * * * *

Genomic Sciences Program Seminar
(Chem 923, Section 157)
Fall 2006

Thursdays, 5:00 p.m., Rm. 1360 Biotech Center

Sept. 28, Introductory Session

Oct. 5, 1:30 pm, Biotech Center Auditorium

      Simon N. Twigger, PhD (Assistant Professor, Medical College of Wisconsin)

       Taming the Gene List- Bioinformatic Approaches to Annotating 'Omics Data

Fri., Oct. 13, **Note different time and room**

       9:45 am, 313 Pyle Center, 702 Langdon St.

      Presentation by Jill Mesirov, PhD (Director, Computational Biology and

      Bioinformatics, Broad Institute; Adjunct Professor of Bioinformatics, Boston

      University)

      Gene Expression Analysis: A Knowledge-based Approach


Oct. 19,  **Note different time and room **
      1:30 p.m., Biotech Center Auditorium, 425 Henry Mall
      Presentation by Angela Koehler (Broad Institute, Chemical Biology

      Program)
       Building a Platform for High-Throughput Ligand Discovery Using Small

      Molecule Microarrays

Oct. 26, Presentation by Jill Herschleb, GSTP Predoctoral Fellow (Cellular and

     Molecular PhD Program, UW-Madison)

     Using Single-Molecule Technology to Uncover Recurrent Mutations and High-

     Resolution Gene Rearrangements In Breast Cancer

Nov. 2, **Note different time and room

     3:30 pm, B1118 Biochemistry, 420 Henry Mall

     Presentation by Mike Adams (University of Georgia)  

     The Metabolism of Hydrogen Gas by the Hyperthermophilic Archaeon,

     Pyrococcus furiosus

     
Fri., Nov. 10, 12:00 noon, Room 5275 MSC, 1300 University Avenue    

     Presentation by Hongyu Zhao, PhD (Associate Professor of Public Health,

     Yale University)

     Protein Interaction Predictions Through Integrating High-Throughput Data

     from Diverse Organisms
     
Nov. 16, Presentation by Adriana Alejandro-Osorio, GSTP Predoctoral Fellow

    (Biomolecular Chemistry, UW-Madison)

     The histone deacetylase Rpd3p plays a role in coordinating stress related gene       expression changes in the Environmental Stress Response program in

     S. cerevisiae

Tu., Nov. 21, **Note different time and room **

     4:00 pm, Biotech Center Auditorium, 425 Henry Mall

     Robert D. Nowak, PhD (McFarland-Bascom Professor of Electrical and

     Computer Engineering, UW-Madison), Genome Network Tomography

   
Dec 7, Presentation by Ian Lewis, GSTP Predoctoral Fellow (Biochemistry,

     UW-Madison), Metabolomics by Multidimensional Dimensional NMR: A Story of

     two Membrane Proteins and a Magnet

Instructor:
     David C. Schwartz (Departments of Chemistry and Genetics;

     Biotechnology Center); dcschwartz@wisc.edu

Grading:
      Students who don’t present: Those students who don’t give a presentation will be assigned an S/U letter grade based on participation and attendance. Each student will be required to evaluate the seminar speakers for sufficiency of background, presentation of the problem, understandability, explanation of methodology, suitability of the scope of the presentation for the audience, and to comment on the presentation and on insights learned. Grading will be done by the instructor.
      Students who present: Students will present a seminar on their own research or on a relevant article from the scientific literature. The articles chosen for presentations must be approved in advance by the instructors. The students that give a presentation will be assigned a letter grade A-F based on their presentation, in addition to attendance and participation. Their presentation will be evaluated jointly by the instructors, and the grade for the presentation will be based on the quality and clarity of their presentation, taking into account their oral delivery as well as use of visual aids, their ability to explain the research problem, results and its impact to a multi-disciplinary audience and on their ability to answer questions.

Reading List:
      A list of articles recommended by presenters will be distributed prior to their seminars.

Genomic Sciences Program Seminar
(Chem 923, Section 157)

Spring 2006

Thursdays, 5:00 p.m., Rm. 1360 Biotech Center

 

Jan. 26, Presentation by Matthew Robison, GSTP Predoctoral Fellow

       (Department of Biochemistry, UW-Madison)

       Tiling Expression Aarray Analysis of Silica Limited Growth in the

       Diatom Thalassiosira pseudonana

Feb. 2, 3:30 p.m., Biochemistry B1118, 420 Henry Mall

      Presentation by Jo Handelsman (Dept. of Plant Pathology, UW-Madison)

      A Vision of Microbiology: from Genes to Communities

Feb. 9, Presentation by Ian Lewis, GSTP Predoctora Fellow (Department of

      Biochemistry, UW-Madison)

      Isotope-Assisted Differential Metabolomics: A New Strategy for

      Investigating Global Metabolic Profiles

Feb. 16, Presentation by Gene Ananiev, GSTP Predoctoral Fellow (Cellular and

      Molecular Biology Ph.D. Program, UW-Madison): (Cancelled due to snow)

      Whole Genome Methylomic Profiling via Single Molecule Analysis

Feb. 23, Presentation by Michael Benton, GSTP Predoctoral Fellow (Department

      of Chemical and Biological Engineering, UW-Madison)

      The Utilization of Saccharomyces cerevisiae as Living Biosensors

Mo., Feb. 27 – **Note different time and room **
      3:30 p.m., Biochemistry B1118, 420 Henry Mall
      Presentation by Stephen Buratowski (Biological Chemistry and Molecular
      Pharmacology, Harvard):
      Connecting transcription with chromatin and mRNA processing

March 2, Presentation by Elenita Kanin, GSTP Predoctoral Fellow (Department

      of Biochemistry, UW-Madison)
      Chemical Genomics Offers Unexpected Insight Into Mechanisms of
      Global Transcription Control


March 9, Presentation by Joshua Mandir, GSTP Predoctoral Fellow  

       (Department of Chemistry, UW-Madison)
       Enzyme Cycling and SNP Detection on a Surface

March 16 Spring Break

March 23, Presentation by Michael J. Bassetti, GSTP Predoctoral Fellow 

      (Department of Electrical and Computer Engineering, UW-Madison)
      Automated Gene Synthesis from Microarray Oligos

March 30, Presentation by Thomas Knotts, GSTP Predoctoral Fellow

     (Department of Chemical and Biological Engineering, UW-Madison)

April 6th **Note different time and room!**
    3:30 pm., Biochem B1118, 420 Henry Mall
    Presentation by Carol Gross (Dept. of Microbiology and Immunology,
    UCSF)

    Design Principles of a Stress-Signaling Pathway: Relationship Between

    Regulation and Function

April 13, Presentation by Ryan Hilger, GSTP Predoctoral Fellow (Department of

     Chemistry, UW-Madison)

April 20, Presentation by Gene Ananiev, GSTP Predoctoral Fellow (Cellular and

      Molecular Biology Ph.D. Program, UW-Madison)

      Whole Genome Methylomic Profiling via Single Molecule Analysis


April 27 Presentation by Jennifer Apodaca, GSTP Predoctoral Fellow (Comparative Biomedical Sciences Graduate Program, UW-Madison)


Fall 2005

 

Th., Sept. 8, **NOTE DIFFERENT TIME AND ROOM**

      3:30 p.m., B1118 Biochemistry

      Bonnie Bassler (Professor, Dept. of Molecular Biology, Princeton University),

      Tiny Conspiracies: Cell-to-Cell Communication in Bacteria

Tu., Sept. 12, **NOTE DIFFERENT TIME AND ROOM**

      9:00 - 9:30 a.m., Room BIA/BIB, Lowell Conference Ctr, 610 Langdon St.

      Maithreyan Srinivasan (454 Life Sciences, Branford CT),

       A Novel, Picoliter Scale Technology for Genome-scale Sequencing

Th., Sept. 22  Presentation by Changhan Kim (Electrical and Computing

       Engineering, UW-Madison)

       Light directed DNA Synthesis Error Study for Gene Assembly from

       Microarrays: Modeling and Experiment

Either of the following 2 seminars can be attended  (9/26 or 9/28):

Mon., Sept. 26th **Note different time and room**

       Genetics/Biotechnology Center Auditorium, 1:30 p.m.

       Ollie Rando, M.D., Ph.D. (Bauer Center for Genomics Research, Harvard        University), Genome-scale Characterization of Chromatin Structure

Wed., Sept. 28 **Note different time and room!**

       Genetics/Biotechnology Center Auditorium, 3:30 p.m.

       Presentation by John White (Professor of Anatomy and Molecular

       Biology, UW-Madison),          

       Cytokinesis in C. elegans

 

Either of the following 2 seminars can be attended (10/5 or 10/6):

Wed., Oct. 5   **Note different time and room**

        Genetics/Biotechnology Center Auditorium, 3:30 p.m.

        Presentation by Bret Payseur (Assistant Professor, Department of

        Genetics, UW-Madison)

        Genetics of Speciation in House Mouse   

       

             OR

Th., Oct. 6 **Note different time and room**

       3:30 p.m. Biochemistry B1118

       Molly Schmid (Keck Graduate Institute - Jacobs Visiting Professor)

       Where Are all the New Antibiotics? Assessment of the Impact of Genomics

       on the Drug Discovery Process and Pipeline

 

Wed., Oct. 12        **Note different time and room**

       Josh Kaplan (Dept. of Mol. Biology, Mass. General Hospital [Harvard

       Medical School])

       Mechanisms regulating synaptic transmission in C. elegans

 

Wed.., Oct. 19  **Note different time and room**

       Marc Vidal (Associate Professor, Dept. of Cancer Biology, Dana-Farbar

        Institute)

       Interactome Network

 

Mon., Oct. 24 **Note different time and room**           

         Stephen D. Levene (Assistant Professor, Molecular and Cell Biology,

         UT Dallas)

         Topology in Biology: From DNA Mechanics to Enzymology

          

Th., Nov. 3     Presentation by Jill Herschleb (Cellular and Molecular Biology

         Program), GSTP Predoctoral Trainee

         Fine Scale Genomic Structure and Variation in the MCF-7 Breast Cancer

         Cell Line (pdf)

Th., Nov. 10  Presentation by Adriana Alejandro-Osorio (Department of 

      Biomolecular Chemistry), GSTP Predoctoral Trainee

 

Mon., Nov. 14 **Note different time and room**

         3:30 p.m., B1118 Biochemistry

         Charles Brooks (Professor, Departmnt of Molecular Biology, Scripps

         Research Institute

         General Features and Methanisms of Functionally Relevant Large-Scale

          Reorganization of Molecular Machines

 

Th., Nov. 24 – Thanksgiving, no seminar

 

Fri., Dec. 2 **Note different time and day**

         12:00 p.m., Biotechnology Center Auditorium, 425 Henry Mall

         James E. Rothman (Director, Columbia Genome Center; Professor,

         Dept. of Physiology and Cellular Biophysics, Columia Univ.)

         Principles of Intracellular Membrane Fusion

          

Mon., Dec. 12 th   **Note different time and date**

         3:30 p.m. Biochemistry B1118

         George Rose (Professor, Department of Biophysics, Johns Hopkins

         University)

         Proteins, The Unfolding Story

Grading

Students who don’t present: Those students who don’t give a presentation will be assigned an S/U letter grade based on participation and attendance. Each student will be required to evaluate the seminar speakers for sufficiency of background, presentation of the problem, understandability, explanation of methodology, suitability of the scope of the presentation for the audience, and to comment on the presentation and on insights learned. Grading will be done by the instructors.

Students who present: Students will present a seminar on their own research or on a relevant article from the scientific literature. The articles chosen for presentations must be approved in advance by the instructors. The students that give a presentation will be assigned a letter grade A-F based on their presentation, in addition to attendance and participation. Their presentation will be evaluated jointly by the instructors, and the grade for the presentation will be based on the quality and clarity of their presentation, taking into account their oral delivery as well as use of visual aids, their ability to explain the research problem, results and its impact to a multi-disciplinary audience and on their ability to answer questions.

Instructor

David C. Schwartz (Departments of Chemistry and Genetics and Biotechnology Center);
dcschwartz@wisc.edu

Reading List

A list of articles recommended by presenters will be distributed prior to their seminars.

                                                   * * * * * *

Past Genomic Sciences Program Seminars
(Chem 923)
Spring 2005

Thursdays, 5:00 p.m., Rm. 1360 Biotech Center

Jan. 20 **NOTE DIFFERENT TIME AND ROOM** B1118 Biochem., 3:30 p.m.

            Richard M. Losick, Ph.D. (Professor, Dept. of Molecular and Cellular

            Biology, Harvard University): Commitment and Cannibalism in a 

            Bacterium

Jan. 27  Presentation by Mark Berres, Ph.D., GSTP Postdoctoral Fellow

            (Department of Genetics, UW-Madison): Luminescent Quantum Dot

            Bioconjugates and Microarray Assays (pdf)

Feb. 3   Presentation by Thomas Knotts, GSTP Predoctoral Fellow (Department                of Chemical and Biological Engineering, UW-Madison): Proteins,  

             Nucleic Acids, and Surfaces - Understanding Interactons at Interfaces

             (pdf)

Wed., Feb. 9 **NOTE DIFFERENT TIME AND ROOM

            Genetics/Biotechnology Center Auditorium, 3:30 p.m.

            Joseph Takahashi, Ph.D. (Professor, Dept. of Neurobiology and

            Physiology, Northwestern University):Genetic Analysis of Circadian

            Clocks in Mammals

Feb. 17  Presentation by Gene Ananiev GSTP Predoctoral Fellow (Cellular and

              Molecular Biology Ph.D. Program, UW-Madison): Discerning Genome

              Wide Methylation Profiles via Optical Mapping  (pdf)

Feb. 24   **Note room change: 1408 Genetics/Biotechnology Center. 5:00 pm

              Brad Anderson, Ph.D., GSTP Postdoctoral Fellow (Department of

              Animal Health and Biomedical Sciences, UW-Madison): CGHScan: A

              Novel Algorithm for Establishing Deletion Boundaries Using Comparative

              Genomic Hybridization Data (pdf)

March 3   Presentation by Elenita Kanin, GSTP Predoctoral Fellow (Dept/ of

               Biochemistry, UW-Madison): Chemical Genomics Offers Unexpected 

               Insight Into Mechanisms of Global Transcription Control

March 10 Presentation by Yeng-Long (Robert) Chen, Ph.D., GSTP Postdoctoral

               Fellow (Department of Chemical and Biological Engineering: Single

               DNA Simulation in Microchannel Confinement (pdf)

March 17  Presentation by Matthew Robison, GSTP Predoctoral Fellow

                (Department of Biochemistry, UW-Madison): DNA Microarray Analysis

                 of Diatom Cell Wall Synthesis (pdf)

March 24 Spring Break

March 31 Presentation by Joshua Mandir, GSTP Predoctoral Fellow (Department

               of Chemistry, UW-Madison): Single Nucleotide Polymorphism Detection

               using the Surface Invasive Cleavage Reaction (pdf)

April 7      Presentation by Ian Lewis GSTP Predoctoral Fellow (Department of

               Biochemistry, UW-Madison): Automated Filtering of NMR Spectra: A

               New Tool for the Discovery of Metabolites Associated with Type 2

               Diabetes (pdf)

April 14    No seminar - Open house for new Genetics/ Biotechnology Center

                Addition

April 21    Presentation by Michael Bassetti, GSTP Predoctoral Fellow

               (Department of Electrical and Computer Engineering, UW-Madison):                 Progress in the Development of an Automated Gene Synthesis

               Method (pdf)

April 28    Presentation by Michael Benton, GSTP Predoctoral Fellow

               (Department of Chemical and Biological Engineering, UW-Madison:

                S. cerevisiae-based Biosensors for the Detection of DNA Damage (pdf)

 

 

PREVIOUS SEMINARS

Genomic Sciences Program Seminar
(Chem 923)
Fall 2004

 

Wed., Sept. 8th , 12:00 p.m., Genetics/Biotechnology Center Auditorium, Mark Boguski, M.D., Ph.D. (University of Washington, Seattle WA), "There's No Place Like 'Ome'"

Wed., Sept. 15th , 3:30 p.m., Genetics/Biotechnology Center Auditorium, Philip Benfey, Ph.D. (Professor and Chair, Department of Biology, Duke University), "A Systems Approach to Understanding Root Development"

Wed., Sept. 22nd , 3:30 p.m., Genetics/Biotechnology Center Auditorium, Daniel Camerini-Otero, M.D., Ph.D. (Chief, Genetics and Biochemistry Branch, NIDDK, National Institutes of Health), "The Repair of Double-strand Breaks by Homologous Recombination in Bacteria and Mice"

[Recommended, not required]:

Wed., Sept. 22nd , 12:00 p.m., Genetics/Biotechnology Center Auditorium, Michael Eisen, Ph.D. (Member, Lawrence Berkeley Laboratory, Life Sciences Division), "Understanding and Exploiting the Evolution Eukaryotic cis-Regulatory Sequences"

 

Wed., Oct. 6th , 12:00 p.m., Genetics/Biotechnology Center Auditorium, George Church, Ph.D. (Professor, Director of Lipper Center of Genetics and Bioinformatics, Harvard Medical School), "Personal Genome & Synthetic Biology Projects"

Wed. Oct. 13th, 12:00 p.m., Genetics/Biotechnology Center Auditorium, Ross King, Ph.D. (Professor, Department of Computer Science, The University of Wales; Group Leader, Computational Biology Group)

Th., Oct. 28th , 5:00 p.m., Rm. 1360 Genetics/Biotechnology Center, GSTP Trainees: Short Introductions on GSTP-Supported Research Projects

 

Wed., Nov. 3rd , 12:00 p.m., Genetics/Biotechnology Center Auditorium, Richard A. Young, Ph.D. (Member, Whitehead Institute; Professor of Biology, MIT)

 

Th., Nov. 11th , 5:00 p.m ., Rm. 1360 Genetics/Biotechnology Center, Daniel McFarlin, GSTP Postdoctoral Fellow (Department of Biostatistics and Medical Informatics, UW-Madison), "Automated Kinetics Simulator (AKS) Freeware for Convenient Generation of Reaction Kinetics Simulations: with a Ras Activation Cycle Example"

Wed., Nov. 17 th , 3:30 p.m., Genetics/Biotechnology Center Auditorium, Fred Winston, Ph.D. (Professor, Department of Genetics, Harvard Medical School), "Analysis of Transcription and Chromatin Structure in Yeast"

Wed., Dec. 1st, 12:00 p.m., Genetics/Biotechnology Center Auditorium, Michael Snyder, Ph.D. ( Professor and Chair of Molecular, Cellular and Developmental Biology, Yale University), "Analyze This and That: Genomes and Proteomes"

Mon., Dec. 13th , 3:30 p.m., B1119 Biochemistry, 420 Henry Mall, Gary Ruvkun, Ph.D. (Mass. General Hospital), "Genetic and Genomic Analysis of RNA Interference"

Genomic Sciences Program Seminar
(Chem 923)
Spring 2004

Thursdays, 5:00 p.m.
Room 1360, Genetics/Biotechnology Center
425 Henry Mall

Printer-friendly version

Jan. 22 Presentation by Brad Anderson, Ph.D., GSTP Postdoctoral Fellow (Department of Animal Health and Biomedical Sciences, UW-Madison):

Genome Annotation and Genomic Analysis of Pathogenic E. coli

Jan. 29 Presentation by David Finton, Ph.D., GSTP Postdoctoral Fellow (Genetics/Biotechnology Center, UW-Madison): Detecting Breakpoints of Genomic Rearrangements via Optical Mapping

Feb. 5 Presentation by Mark Berres, Ph.D., GSTP Postdoctoral Fellow (Department of Genetics, UW-Madison): The Use of Luminescent Quantum Dot Bioconjugates as a Reporter in Microarray Assays

Feb. 12 Presentation by Elenita Kanin, GSTP Predoctoral Fellow (Department of Biochemistry, UW-Madison): Whole genome localization of the in vivo binding sites of the sigma subunits of E. coli RNA polymerase

Feb. 19 Presentation by Yeng-Long Chen, Ph.D., GSTP Postdoctoral Fellow (Department of Chemical and Biological Engineering, UW-Madison): Modeling Single DNA Molecules in a Microfluidic Channel

Feb. 23 **Note different time and day
6:30 p.m., Room 1360 Genetics/Biotechnology Center
Presentation by Tom Cech (President, Howard Hughes Medical Institute; Professor, University of Colorado, Boulder): RNA, RNA catalysis, and telomerase

March 4 Presentation by Matthew Robison, GSTP Predoctoral Fellow (Department of Biochemistry, UW-Madison): The Use of DNA Microarrays to Identify Genes Involved with Cell Wall Synthesis in the Marine Diatom, Thalassiosira pseudonana

March 11 No Seminar – RNA Maxi Group has room at 5:45 p.m.

March 18 No class; Spring Break

March 23 **Note different time and day– NOT REQUIRED
6:30 p.m., Room 1360 Genetics/ Biotechnology Center,
Presentation by Stan Fields (Professor, Dept. of Genome Sciences and Medicine, University of Washington): An RNA-Protein Idea: A Protein Functional Screen and Two-Hybrid Variation.

April 1 Presentation by Gene Ananiev, GSTP Predoctoral Fellow (Program in Cellular and Molecular Biology, UW-Madison): Analysis of Genome-Wide Methylation Patterns Using a Single Molecule Approach

April 8 No Seminar – RNA Maxi Group has room at 5:45 p.m.

April 15 **Note different time, 1:30 p.m., Genetics/Biotechnolgy Ctr Auditorium
Presentation by Eric Green, M.D., Ph.D. (Scientic Director, National Human Genome Research Institute): Comparative Genome Sequencing: Using Evolution to Decode the Human Genome

April 20 **Note different time and day,
4:00 p.m, CS/Stat. Building Room 1221, 1210 W. Dayton St.
Presentation by Audrey Gasch (Assistant Professor, Department of Genetics; Genome Center of Wisconsin): Conservation and Evolution of Cis-regulatory Elements in Diverse Fungi

April 22 Presentation by Thomas Knotts, GSTP Predoctoral Fellow (Department of Chemical and Biological Engineering): Advanced Molecular Simulation for Genomic Science

April 29 Presentation by Ian Lewis, GSTP Predoctoral Fellow (Department of Biochemistry): A Metabolomic Assessment of Susceptibility to Diabetes

Grading

Students who don’t present: Those students who don’t give a presentation will be assigned an S/U letter grade based on participation and attendance. Each student will be required to evaluate the seminar speakers for sufficiency of background, presentation of the problem, understandability, explanation of methodology, suitability of the scope of the presentation for the audience, and to comment on the presentation and on insights learned. Grading will be done by the instructors.

Students who present: Students will present a seminar on their own research or on a relevant article from the scientific literature. The articles chosen for presentations must be approved in advance by the instructors. The students that give a presentation will be assigned a letter grade A-F based on their presentation, in addition to attendance and participation. Their presentation will be evaluated jointly by the instructors, and the grade for the presentation will be based on the quality and clarity of their presentation, taking into account their oral delivery as well as use of visual aids, their ability to explain the research problem, results and its impact to a multi-disciplinary audience and on their ability to answer questions.

Instructor

David C. Schwartz (Departments of Chemistry and Genetics and Biotechnology Center);
dcschwartz@wisc.edu

Reading List

A list of articles recommended by presenters will be distributed prior to their seminars.

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