Genomic Sciences Program Seminar
(Chem 923, Section 157)
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), Title TBA

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

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 SEMINAR SERIES

Genomic Sciences Program Seminar
(Chem 923, Section 157)
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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