Genomic Sciences Program Seminars
(Chem 923, Section 157)
Thursdays, 4:45 p.m., Rm. 1360 Biotech Center
(unless listed otherwise)

Fall 2017

    • Sept. 14
      Introductory Session
    • Sept. 18
      Presentation by Adam Hughes, PhD (Assistant Professor, Dept. of Biochemistry, University of Utah School of Medicin
      Dissecting Organelle Relationships that Drive Aging, 
    • Sept. 27, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
      Presentation by Daven Presgraves, PhD (Associate Professor, Department of Biology, University of RochesteSex Chromosomes, Conflict, and Complex Speciation in Drosophila
    • Oct. 2
      Presentation by Nevan Krogan, PhD (Professor, Dept. of Cellular & Molecular Pharmacology, UCSF School of Medicine)
      Cancelled
    • Oct. 12
      Presentation by Amy Dapper, PhD (GSTP postdoctoral fellow, Department of Genetics),
      Molecular Phylogenetic Analysis of the Recombination Pathway
    • Oct. 18
      Presentation by David Pagliarini, PhD (Professor, Department of Biochemistry; Morgridge Institute for Research), Mitochondrial Proteins, Pathways and Pathogenesis
    • Oct. 26
      Presentation by Michael Engstrom, PhD, GSTP postdoctoral fellow (Chemical & Biological Engineering)
      Title TBA
    • Nov. 2  Presentation by Tim James, PhD (U. Michigan) – moved to May 3, 2018
    • Nov. 9
      Presentation by Kelly Schwartz, PhD, GSTP postdoctoral fellow (Biochemistry)
      Title TBA
    • Nov. 16
      Presentation by Katie Buxton, GSTP predoctoral fellow (Chemistry)
      Title TBA
    • Nov. 20
      Presentation by  Jeff Gelles, PhD (Aron and Imre Tauber Professor of Biochemistry and Molecular Pharmacology, Brandeis U.)
      Non-equilibrium Regulation of DNA Transcription, 3:30 pm, Room 1211 Hector DeLuca Biochemical Sciences Building
    • Nov. 29
      Presentation by Christian Landry, PhD (Associate Professor, Canada Research Chair in Evolutionary Cell and Systems Biology, Dept. of Biology, University Laval)
      Title TBA
    • Dec. 6
      Presentation by Erica Larschan, PhD (Richard and Edna Salomon Assistant Professor of Molecular Biology, Cell Biology and Biochemistry, Assistant Professor of Biology, Brown University)
      Title TBA, 3:30 pm, Biotechnology Center Auditorium
    • Dec. 11
      Presentation by Steve Block, (Ascherman Professor and Professor of Applied Physics and Biology, Stanford U.)
      Optical Tweezers: Gene Regulation, Studied One Molecule at a Time, 3:30 pm Room 1211 Hector DeLuca Biochem. Sci. Building

Spring 2017

  • Jan. 23
    Nancy Thornberry, CEO, Kallyope
    Discovery of Gut-Based Therapies for the Treatment of Type 2 Diabetes and Related Disorders – Cancelled
  • Feb. 2
    Jeff Nelson, PhD, GSTP postdoctoral fellow (Morgridge Institute for Research),
    Investigating Axolotl Limb Regeneration via Single Cell Transcriptomics
  • Feb. 9
    Ed Huttlin, PhD (Instructor, Harvard Medical School)
    A Systematic Survey of the Human Protein Interaction Landscape
  • Feb. 16
    Jesse Dabney, PhD, GSTP postdoctoral fellow (Molecular Archeology Group)
    Genetic Diversity in Mycobacterium tuberculosis Populations Isolated from Paired Sputum and Culture Samples
  • Feb. 23
    Drew Doering, GSTP predoctoral fellow (CMB Graduate Program),UW-Madison)
    An Approach to Track and Predict Evolutionary Paths Through Fitness Landscapes
  • March 2
    Sid Kiblawi, GSTP predoctoral fellow (Computer Sciences)
    Augmenting Subnetwork Inference with Information Extracted from the Scientific Literature
  • March 9
    Alejandra Canales, GSTP predoctoral fellow (Biochemistry),
    Uncovering Roles for the VPS10 Family in the Secretory Pathway
  • March 16
    Matthew MacGilvray, GSTP predoctoral fellow (Microbiology Doctoral Program)
    The Inferred NaCl-stress Network in Yeast Reveals Novel Pathway Connections
  • March 23
    No seminar, spring break (recommend optional seminar: Mona Singh, Princeton U.)
  • March 30
    Katie Buxton, GSTP predoctoral fellow (Chemistry),
    Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometr
  • April 6
    Taylor Scott, GSTP predoctoral fellow (Cellular & Molecular Biology Graduate Program)
    Single-cell Experiments in Yeast Showcase the Power of a Modular Approach to Modeling Signal Transduction
  • April 13
    No seminar – NHGRI Trainees’ National Meeting, St. Louis, MO
  • April 20
    Elizabeth Waters, GSTP predoctoral fellow (Chemical and Biological Engineering),
    Discovery of Variable Lymphocyte Receptors to Cross the Human Blood-brain Barrier
  • April 27
    Presentations by Anji Trujillo (Chemistry) and Eamon Winden (Genetics), GSTP predoctoral fellows
    Metabolite Profiling of Plasma and Cecum Elucidates the Impacts of Host Genetics and Environment on the Gut (AT)
    Genome Synthesis: Fabricating Large DNA Constructs (EW)

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.

Fall 2016

        • Sept. 8
          Schahram Akbarian, MD, PhD (Professor, Psychiatry, Neuroscience, Mt. Sinai School of Medicine),
          Higher Order Chromatin Affecting Cognition and Behavior in Human and Mouse Brain
        • Sept. 15
          Introductory Session
          Discussion of events and training activities in the upcoming year; introduction of all GSTP trainees
        • Sept. 22
          Shirley Liu, PhD (Professor, Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Harvard School of Public Health),
          Translational Cancer Research for Personal Genomics
        • Sept. 28
          Stanley Fields, PhD (Professor, Genome Sciences, University of Washington)
          Deep Mutational Scanning: Proteins, RNA and DNA
        • Oct. 5
          Mary-Claire King, PhD (Professor, Genome Sciences and of Medicine, Univ. of Washington),
          Genomic Analysis of Inherited Breast and Ovarian Cancer: from Gene Discovery to Precision Medicine and Public Health
        • Oct. 27
          Bill Noble, PhD (Professor, Department of Genome Sciences; Department of Computer Science and Engineering, University of Washington)
          Machine Learning Methods for Annotating and Extending Big, Heterogeneous Genomic Data
        • Nov. 3
          Amy Dapper, PhD, GSTP postdoctoral fellow (Genetics))
          The Effect of Demography on the Detection of Recombination Hotspots
        • Nov. 17
          Brian McLoone, PhD, GSTP postdoctoral fellow (Wisconsin Institute for Discovery)
          Cooperation in Nature and Evolutionary Biology: How Stochasticity and Group Structure Promote the Fixation
        • Dec. 1
          Neil Kelleher, PhD (Professor, Chemistry, Northwestern University)
          On the Value of Top Down Proteomics in Basic and Translational Research

    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.

Spring 2016

  • Jan. 21, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    **Note different time and room**
    Presentation by Jack Gilbert, PhD (Principal Investigator, Biosciences Division, Argonne National Laboratory)
    The Built Environment Microbiome: Health and Disease
  • Jan. 28
    Presentation by Jesse Dabney, PhD, GSTP postdoctoral fellow (Molecular Archeology Group)
    Long-term and Intra-Host Diversity of Mycobacterium tuberculosis
  • Feb. 4, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    **Note different time and room**
    Presentation by Tom Gingeras, PhD (Professor and Head, Functional Genomics, Cold Spring Harbor Laboratory)
    Selective Recruitment and Processing of RNAs in Extracellular Vesicles Contribute to the Shaping Cancer Cell Environments
  • Feb. 11
    Presentation by Jeff Nelson, PhD, GSTP postdoctoral fellow (Morgridge Institute for Research)
    Analysis of Embryonic Development in the Unsequenced Axolotl: Waves of Transcriptional Upheaval and Stability
  • Feb. 18
    Presentation by Christopher Trimbly, PhD (Director of Teaching Fellows Programs & Exploring Biology, WISCIENCE – Wisconsin Institute for Science Education and Community Engagement)
    Making Time for Teaching Professional Development: Thinking about Thinking and Thinking about Teaching
  • Feb. 25
    Presentation by Drew Doering, GSTP predoctoral fellow (CMB Graduate Program)
    Title TBA
  • March 3
    Presentation by Ted de Groot, GSTP predoctoral fellow (Biomedical Engineering)
    Title TBA
  • March 10Presentation by Mark Nolte, PhD, GSTP postdoctoral fellow (Genetics)
    Title TBA
  • March 17
    Presentation by Mark Politz, GSTP predoctoral fellow (Chemical & Biological Engineering)
    Title TBA
  • March 24
    No seminar-Spring break
  • March 31
    Presentation by Matthew MacGilvray, GSTP Predoctoral Fellow (Microbiology Doctoral Training Program)
    Title TBA
  • April 7
    No seminar (NHGRI Trainees’ National Meeting, Bethesda MA)
  • April 14
    Presentations by Katie Buxton and Ben Steyer, GSTP predoctoral fellows (Chemistry [KB} CMB [BS])
    Titles TBA
  • April 21
    Presentation by Sam Krerowicz, GSTP predoctoral fellow (Chemistry)
    Title TBA
  • April 28
    Presentation by Alejandra Canales and Sid Kiblawi, GSTP predoctoral fellows (Biochemistry [AC]; Computer Sciences [SK])
    Titles TBA

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 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.

Reading List:

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

Fall 2015

  • Sept. 11
    Introductory Session
  • 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. 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
  • Week of Sept. 28th
    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

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, 12:00 pm, Biotechnology Center Auditorium
    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

Fall 2014

  • Week of Sept. 22nd
    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-
    Sept. 25, 3:30 pm, 1220 Microbial Sciences Building
    Deborah Blum (Assoc. Professor, Journalism, UW-Madison),
    The (Sometimes Poisonous) Chemistry of Communication
  • Oct. 2
    Presentation by Matt Copeland, PhD, GSTP postdoctoral fellow (Department of Chemical & Biological Engineering)
    A TALE Repressor-Induction System Medicated by Proteolytic Degradation
  • Oct. 9
    Presentation by Alicia Richards, GSTP predoctoral fellow (Department of Chemistry)
    SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching
  • 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
  • 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
  • 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
  • Nov. 6
    Presentation by Sam Krerowicz, GSTP predoctoral fellow (Department of Chemistry)
    Self-Assembly of Genomic  DNA into Microscale Objects
  • 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
  • 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
  •  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)
  • 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
  • Sept. 23, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
    Presentation by Marc Riedel, PhD, Associate Professor, Electrical and Computer Engineering, University of Minnesota
    Towards a Computer Engineering Discipline Based on DNA
  • Sept. 30, 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
    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-
    Oct. 11, 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
  • Oct. 14, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
    Presentation by George Church, Professor of Genetics, Harvard University
  • 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
  • Oct. 31
    Matt Copeland, PhD, CIBM predoctoral fellow (Chemical & Biological Engineering, UW-Madison)
  • Nov. 7
    Alicia Richards, CIBM predoctoral fellow (Chemistry, UW-Madison)
  • Week of Nov. 11th
    Nov. 11, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
    Presentation by Bernard Palsson, Professor of Bioengineering, UC San Diego
    -or-
    Nov 13 , 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall, Presentation by Murray Brilliant, Marshfield Clinic Research Foundation, Personalized Medicine: Research and Implementation
  • 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
  • Dec. 5
    Gene Tsvid, PhD, CIBM postdoctoral fellow (Biotechnology Center)

Spring 2013

  • Jan. 31, 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
    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
    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, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall (CANCELLED)
    Presentation by Deborah Nickerson, PhD (Professor of Genome Sciences, Adjunct Professor of Bioengineering, University of Washington)
  • Sept. 13
    Introductory Session
  • Week of September 17th
    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
    -or-
    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
  • Oct. 1, 3:30 pm, Ebling Symposoium Center
    Presentation by Chip Asbury University of WA-Seattle
    New Strategies for Uncovering How Chromosomes Are Segregated During Mitosis
  • Week of Oct. 8th
    Oct. 8, 3:30 pm, 1211 Biochemical Sciences Building, 440 Henry Mall
    Presentation by Terry Orr-Weaver, Professor of Biology, MIT; Member, Whitehead Institute
    Changes in Genome Copy Number and Stability in Development
    -or-
    Oct. 10, 3:30 pm, Biotechnology Center, 425 Henry Mall
    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
  • Nov. 7, 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
    Nov. 26 , 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
    -or-
    Nov. 29, 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
  • Dec. 4 , 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
  • Dec. 12 , 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, 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, 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, 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

Fall 2011

  • Sept. 15
    Introductory Session
  • Sept. 22, 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, 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
    Oct. 13, 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
    -or-
    Oct. 14, 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
  • Oct. 19 , 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
  • Oct. 26, 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
    Nov. 10, 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
    -or-
    Nov. 11, 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, 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, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall (CANCELLED)
    Presentation by Pamela Silver (Department of Systems Biology, Harvard Medical School)
    Title TBA
  • Jan. 27, 12:15 pm, Rm. 1315 Chemistry Building
    Ben Garcia (Assistant Professor, Dept. of Molecular Biology, Princeton University)
    Understanding the Histone Code through Quantitative Proteomics
  • Feb. 1, 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, 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, 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
  • April 11, 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
    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
    -or-
    April 21, 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

  • Sept. 8, 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
  • Sept. 22, 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
    Oct. 6th, 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
    -or-
    Oct. 7th, 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 inSaccharomyces cerevisiae
  • Nov. 4, 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, 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
  • Dec. 1, 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, 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, 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, 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, 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
  • April 19, 3:30 pm, Ebling Symposium Center, Microbial Sciences Bldg., 1550 Linden Dr. (CANCELLED)
    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’

Fall 2009

  • Sept. 10
    Introductory Session
  • Week of Sept. 14th
    Sept. 16, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    John Petrini (Sloan-Kettering Institute)
    Genetic Analysis of Chromosome Break Metabolism
    -or-
    Sept. 17, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    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
    Sept. 30, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    James Womack (Texas A&M)
    Salient Messages from the Bovine Genome Sequence
    -or-
    Oct. 1, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    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
  • 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
    Oct. 14, 3:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    Jonathan Pritchard (Professor, Dept. of Human Genetics, University of Chicago)
    High Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation
    -or-
    Oct. 15, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    Presentation by Gavin Sherlock (Assistant Professor of Genetics, School of Medicine, Stanford University)
    Watching Yeast Change: Using Genomics to View the Adaptivge Landscape
  • Oct. 15, 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Center)
    Presentation by David Lipman, MD (Director, National Center for Biotechnology Information)
    Evolution in Computational Biology
  • 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
  • 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
  • Nov. 5, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    Michael Snyder, Ph.D. (Professor, Genetics, Stanford University)
    Analyzing Genomes and Regulatory Informating Using Omics Technologies
  • 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
    Nov. 19, 1:30 pm, Biotechnology Center Auditorium, 425 Henry Mall
    Presentation by Aviv Regev (Broad Institute; Assistant Professor, Department of Biology, MIT)
    Modular Biology: The Function and Evolution of Regulatory Networks
    -or-
    Nov. 19, 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Center)
    Presentation by George Weinstock, PhD (Professor, Department of Genetics, Washington University; Assoc. Director, Genome Center
    Adventures in the Human Microbiome
  • Dec. 3, 3:30 pm, 1220 Microbial Sciences Building (Ebling Symposium Center)
    Presentation by Tanja Woyke (Postdoctoral fellow, DOE Joint Genome Institute)
    Microbial Single Cell Genomics

Spring 2009

  • 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)

Fall 2008

  • Sept. 11
    Introductory Session
  • Sept. 18, 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
  • Sept. 24th, 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
  • Oct. 7, 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
    Oct. 22, 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
    -or-
    Oct. 23, 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
    Nov. 5, 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
    -or-
    Nov. 6, 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
    Nov. 17, 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
    -or-
    Nov. 19, 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
  • Nov. 20, 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
  • Nov. 24, 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
  • 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
    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

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, 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, 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, 1:30 pm, Biotechnology Center Auditorium
    David Botstein (Princeton University)
    Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast

Fall 2007

  • Sept. 6, 1:30 pm, Biotechnology Center Auditorium
    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
    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
    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
  • Oct. 15, 3:30 pm in B1118 Biochemistry, 420 Henry Mall
    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
  • Nov. 5, 3:30 pm in B1118 Biochemistry, 420 Henry Mall
    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
  • Nov. 19, 3:30 pm in B1118 Biochemistry, 420 Henry Mall
    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.
    Cameron Currie (Assistant Professor, Department of Bacteriology, UW-Madison)
    Cooperaton, Conflict and Coevolution: Exploring Ancient Agriculture in Ants

Spring 2007

  • Jan. 25, 2:30 pm, Biotech. Center Audit.
    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)
    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.
    Presentation by Eddie Rubin, PhD, Joint Genome Institute
    Genomic Approaches to Bioenergy and Gene Regulation

Fall 2006

    • 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
    • Oct. 13, 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, 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, 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
    • 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
    • Nov. 21, 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.

Spring 2006

  • 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 (CANCELLED)
    Presentation by Gene Ananiev, GSTP Predoctoral Fellow (Cellular and Molecular Biology Ph.D. Program, UW-Madison)
    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
  • Feb. 27, 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-No seminar
  • 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, 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

  • Sept. 8, 3:30 p.m., B1118 Biochemistry
    Bonnie Bassler (Professor, Dept. of Molecular Biology, Princeton University)
    Tiny Conspiracies: Cell-to-Cell Communication in Bacteria
  • Sept. 12, 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
  • 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
  • Week of Sept. 26th
    Sept. 26, 1:30 p.m., Genetics/Biotechnology Center Auditorium
    Ollie Rando, M.D., Ph.D. (Bauer Center for Genomics Research, Harvard University)
    Genome-scale Characterization of Chromatin Structure
    -or-
    Sept. 28, 3:30 p.m., Genetics/Biotechnology Center Auditorium
    Presentation by John White (Professor of Anatomy and Molecular Biology, UW-Madison)
    Cytokinesis in C. elegans
  • Week of Oct. 3rd
    Oct. 5, 3:30 p.m., Genetics/Biotechnology Center Auditorium
    Presentation by Bret Payseur (Assistant Professor, Department of Genetics, UW-Madison)
    Genetics of Speciation in House Mouse
    -or-
    Oct. 6, 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
  • Oct. 12
    Josh Kaplan (Dept. of Mol. Biology, Mass. General Hospital [Harvard Medical School])
    Mechanisms regulating synaptic transmission in C. elegans
  • Oct. 19
    Marc Vidal (Associate Professor, Dept. of Cancer Biology, Dana-Farbar Institute)
    Interactome Network
  • Oct. 24
    Stephen D. Levene (Assistant Professor, Molecular and Cell Biology, UT Dallas)
    Topology in Biology: From DNA Mechanics to Enzymology
  • 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)
  • Nov. 10
    Presentation by Adriana Alejandro-Osorio (Department of Biomolecular Chemistry), GSTP Predoctoral Trainee
  • Nov. 14, 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
  • Nov. 24
    Thanksgiving-No seminar
  • Dec. 2, 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
  • Dec. 12, 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.

Spring 2005

  • Jan. 20, 3:30 p.m., B1118 Biochem.
    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]
  • Feb. 9, 3:30 p.m., Genetics/Biotechnology Center Auditorium
    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, 5:00 p.m., 1408 Genetics/Biotechnology Center
    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-No seminar
  • 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]

Fall 2004

  • Sept. 8 , 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’
  • Sept. 15, 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
  • Sept. 22, 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
    Sept. 22, 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
  • Oct. 6, 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
  • Oct. 13, 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)
  • Oct. 28, 5:00 p.m., Rm. 1360 Genetics/Biotechnology Center
    GSTP Trainees
    Short Introductions on GSTP-Supported Research Projects
  • Nov. 3, 12:00 p.m., Genetics/Biotechnology Center Auditorium
    Richard A. Young, Ph.D. (Member, Whitehead Institute; Professor of Biology, MIT)
  • Nov. 11, 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
  • Nov. 17, 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
  • Dec. 1, 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
  • Dec. 13, 3:30 p.m., B1119 Biochemistry, 420 Henry Mall
    Gary Ruvkun, Ph.D. (Mass. General Hospital)
    Genetic and Genomic Analysis of RNA Interference

Spring 2004

  • 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, 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 seminar-Spring Break
  • March 23, 6:30 p.m., Room 1360 Genetics/ Biotechnology Center (NOT REQUIRED)
    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, 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, 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.