ABRF 2010 Presentations

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ABRF Award  Sponsored by Agilent Technologies

• The Dark Matter of Biological Regulation
• 
  Awardee and Speaker: Dr. Pat Brown, Stanford University, California.

Quick Links

• Satellite Workshop (you must have been registered for the workshop to gain access)
• Plenary Sessions
• Scientific Sessions
• Workshops
• Expert's Tables
• Research Group Presentations
• ABRF Poster Awards
• Member Meeting

Plenary Sessions

• (p1) Research Cores - Their Crucial Role in Translational Science
• • Lars Berglund, University of California Davis

• (p2) Proteomic Applications to Translational Research
  • John Yates III, The Scripps Research Institute

• (p3) Next-Generation Applications to Translational Research
• • Elaine Mardis, Washington University

Scientific Sessions

• (s1) Quantitative Interactomics – Session Organizer: Michael Doyle, Bristol–Myers Squibb
  • 
    (s1-1) Interaction Networks as Scaffolds for Organizing and Interpreting Proteomes
    • John Parkinson, Hospital for Sick Children, and University of Toronto
  • (s1-2) Development of a Tagless Strategy for the Structural Characterization of Native Protein Complexes
    • Ming Dong, Genomics Division, Lawrence Berkeley National Laboratory
  • (s1-3) The First Draft of the Endostatin Interaction Network
    • Sylvie Ricard-Blum, Institut de Biologie et Chimie des Protéines, Université de Lyon
• 
  (s2) Opportunities and Hurdles for Personalized Medicine – Session Organizer: Preston Hensley, Lotus Translational Medicine, LLC
  • 
    (s2-1) Personalized Medicine – Future Impact, Pharma Industry Perspective
    • Alison Ayers, Pfizer Oncology Worldwide Commercial Development
  • (s2-2) Proteomics for Enabled Clinical Development and Personalized Medicine
    • Stephen A. Williams, Somalogic
  • (s2-3) From Bench-Top to Bedside: Speeding Personalized Medicine's Translation
    • Paul Billings, Genomic Medicine Institute, El Camino Hospital
• 
  (s3) Cell-based Assays – Session Organizer: Scott Tighe, University of Vermont
  • 
    (s3-1) Recent Trends in Cell-based Assays
    • Scott Tighe, University of Vermont
  • (s3-2) Miniaturized Systems for Cell-based Assays
    • David Lawrence, Wadsworth Center
  • (s3-3) Live-cell Microarrays for High Throughput Screening Applications
    • Nathan Cady, College of Nanoscale Science and Engineering University of Albany SUNY
• 
  (s4) Metagenomics: What we Really Should be Doing with these Massive Parallel Sequencers – Session Organizer: Paul Morrison, Dana Farber Cancer Institute
  • 
    (s4-1) Approaches to Metagenomics Using Pyrosequencing: The Metagenome of the Mouth
    • Roger Bumgarner, University of Washington
  • (s4-2) Microbial Metagenomes and the Flux of Greenhouse Gases from Soil
    • Thomas Schmidt, Michigan State University
  • (s4-3) From Sequences to Insights in Microbial Ecology
    • Rob Knight, HHMI and Department of Chemistry & Biochemistry, University of Colorado at Boulder
• 
  (s5) Metabolomics – Session Organizer: Bill Wikoff, The Scripps Research Institute
  • 
    (s5-1) Managing Complexity - How Many Platforms Do We Need for Metabolomics?
    • Oliver Fiehn, University of California Davis
  • (s5-2) Trends in Quantitative Metabolomics
    • David Wishart, University of Alberta
  • (s5-3) Metabolomics Techniques and Applications
    • Chris Beecher, University of Michigan

Workshops

• (w1) Operating a Quantitative Molecular Interactions Facility – Session Organizer: Michael Doyle, Bristol–Myers Squibb
  • 
    (w1-1) Technology Arena: Protein Production, Quality Assessment and Interaction Analysis
    • Michael Doyle, Bristol-Myers Squibb
  • (w1-2) Collaborations, Instrumentation and Funding in a Nonprofit Shared Facility
    • Satya Yadav, Lerner Research Institute, Cleveland Clinic
  • (w1-3) Impact of Biophysical Techniques on the Small Molecule Discovery Process
    • Simon Berqqvist, Pfizer
• 
  (w2) LIMS - One Abbreviation, Many Meanings – Session Organizer: Jan Kieleczawa, Global Biological Technologies, Pfizer
  • 
    (w2-1) LIMS Primer
    • Jan Kieleczawa, Global Biological Technologies, Pfizer
  • (w2-2) Keeping Your DNA Sequencing, Genotyping, and Microarray Laboratory Competitive in a New Era of Genomics
    • Todd Smith, Geospiza, Inc.
  • (w2-3) From Project-to-Peptides: Customizing a Commercial LIMS for LC-MS Proteomics
    • Tom Frederick, Bioinformatics Analysis Solutions, Global Biological Technologies, Pfizer
• 
  (w3) In-vivo Imaging - Cells to Animals – Session Organizer: Richard Cole, Wadsworth Center, New YorkState Department of Health
  • 
    (w3-1) A Novel Method to Quantify Angiogenesis in vivo Using Multiphoton Confocal Imaging
    • Richard Cole, Wadsworth Center, New YorkState Department of Health
  • (w3-2) Live Cell Imaging and Measurements of Molecular Dynamics
    • Claire M. Brown, McGill University
• 
  (w4) Proteomics I: MS-Based Workflows and Sample Preparation – Session Organizer: Tom Neubert, New York University School of Medicine
  • 
    (w4-1) Overview
    • Tom Neubert, New York University School of Medicine
  • (w4-2) Quantitation Strategies
    • David Fenyo, Rockefeller University
  • (w4-3) Sample Prep for Protein Expression and Posttranslational Modification Studies
    • Roland Annan, GlaxoSmithKline
• 
  (w5) Next-Generation Sequencing I - Sample Prep/Workflow – Session Organizer: Sushmita Singh, Pennsylvania State University
  • 
    (w5-1) SOLiD Sequencing RNA Applications Sample Prep and Workflow
    • Deb Grove, Pennsylvania State University
  • (w5-2) Next Generation Sequencing Illumina GA Workflow Sample Prep Details
    • Robert Steen, Harvard Medical School
• 
  (w6) Proteomics II - Applications – Session Organizer: Kathryn Lilley, University of Cambridge & David Friedman, Vanderbilt University
  • 
    (w6-1) Leveraging technologies: DIGE and MudPIT
    • David Friedman, Vanderbilt University
  • (w6-2) Differential Protein Expression to the Hepatic Response From a High Fat Diet Using Complementary Quantitative Approaches: 2D-DIGE, Label-Free and iTRAQ Labeling
    • Angel Aponte, National Heart Lung and Blood Insititute, NIH
  • (w6-3) Discovery-Driven Targeted Analysis of Integral Membrane Proteins
    • Christine Wu, University of Colorado School of Medicine
    • presented by Breandan MacLean, University of Colorado School of Medicine
• 
  (w7) Next-Generation Sequencing II - Applications – Session Organizer: George Grills, Cornell University
  • 
    (w7-1) Efficient Variant Discovery from Nanogram amounts of RNA by RNASeq
    • Shawn Levy, Hudson Alpha Institute for Biotechnology
  • (w7-2) A Wiki based LIMS to Automate Next Generation Sequencing Data Analysis and Annotation for Epigenomics and Genomics Applications
    • Andrew McLellan, Albert Einstein College of Medicine
  • (w7-3) BioHPC for Next Generation Sequencing Data and Analysis Applications
    • Jaroslaw Pillardy, Cornell University
• 
  (w8) Proteomics III - Data/Informatics: Introduction to Proteome Informatics Data Analysis – Session Organizer: Brian Searle, Proteome Software & Lennart Martens, Ghent University
  • 
    (w8-1) Peptide Identification by Database Search
    • John Cottrell, Matrix Science
  • (w8-2) Identifying Post-translational Modifications
    • Nuno Bandeira, University of California, San Diego
  • (w8-3) Assessing and Interpreting Protein Identifications
    • Sean Seymour, AB SCIEX
• 
  (w9) Next-Generation Sequencing III : Tools to Facilitate Management, Analysis and Visialization of 2nd Generation Sequencing Data – Session Organizer: Helaman Escobar, EurofinsMWG Operon
  • 
    (w9-1) Brief Survey Report: Current Trends on NGS Data Management and Analysis
    • Helaman Escobar, Eurofins MWG Operon
  • (w9-2) The Microsoft Biology Foundation - Applications for High-Throughput Sequencing
    • Simon Mercer, Microsoft Research
  • (w9-3) Next Generation Tools for Genomic Data Generation, Distribution, and Visualization
    • David A. Nix, Huntsman Cancer Institute, University of Utah
  • (w9-4) GMOD, Visualization Tools for nextgen Sequence Data
    • Mitchell Skinner, UC Berkeley
• 
  (w10) What to do when Protein Expression Goes Wrong – Session Organizer: Richard Heath, St. Jude Children's Research Hospital
  • 
    (w10-1) Baculovirus Expression: Over Expression or Over Expectation
    • Muralidhar Reddivari, St. Jude Children's Research Hospital
  • (w10-2) Rescue Strategies for Protein Production in E. coli
    • Cynthia Kinsland, Cornell University
• 
  (w11) Publishing Standards for Proteomics – Session Organizer: Ralph Bradshaw, University of California, San Francisco
  • 
    (w11-1) Publishing Standards for Proteomics
    • Robert Chalkley, UCSF
  • (w11-2) Publishing Standards for Proteomics
    • Karl Clauser, Broad Institute

Research Group Presentations

• 
  (r1) Optimal Priming Strategies for cDNA Synthesis in Real-Time RT-qPCR – Session Organizer: Katia Sol-Church (sub. for Sridar Chittur) A.I.DuPont Hospital for Children
  • 
    (r1-1) Nucleic Acid Research Group (NARG)2009-2010 Study : Optimal Priming Strategies for cDNA Synthesis in Real-Time RT-qPCR
    • Katia Sol-Church, Alfred I. duPont Hospital for Children
  • (r1-2) Preparation of RNA for the 2009-2010 NARG Study
    • Scott Tighe, University of Vermont
• 
  (r2) Molecular Interactions Research Group (MIRG) Session Chair: Michael Doyle, Bristol-Myers Squibb
  • 
    (r2-1) Overview of MIRG Study on a Ternary Interaction
    • Michael Doyle, Bristol-Myers Squibb
  • (r2-2) Update on MIRG Study on a Ternary Interaction
    • Aaron Yamniuk, Bristol-Myers Squibb
  • (r2-3) Update on MIRG Study on a Ternary Interaction
    • Ed Eisenstein, Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute
• 
  (r3) Metabolomics Research Group (MRG) – Session Organizer: Chris Turck, Max Planck Institute of Psychiatry
  • 
    (r3-1) An Introduction to NMR-based Metabolomics
    • Thomas O'Connell, University of North Carolina, Chapel Hill
  • (r3-2) Mass Spectrometry Based Metabolomics
    • Pavel Aronov, Stanford University
  • (r3-3) Metabolomics Core at UC Davis: Evolution
    • Vladimir Tolstikov, University of California, Davis
• 
  (r4) xPRG Studies: Proteomics, Proteomics Standards and Proteome Informatics Research Groups – Session Organizer: Chris Turck, Max Planck Institute of Psychiatry
  • 
    (r4-1) PRG2010 Study: Identifying Unforeseen Problems in a 'Simple' Analysis
    • David Friedman, Vanderbilt University
  • (r4-2) iPRG2010 Study: Phosphopeptide Identification
    • Paul Rudnick, National Institute of Standards and Technology
    • presented by Karl Clauser, Broad Institute)
  • (r4-3) sPRG2010 Study: Phosphopeptide Standard
    • Jim Farmar, University of Virginia
• 
  (r5) Joint Presentation: DNA Sequencing Research Group (DSRG) & Genomic Variation Research Group (GVRG)
  • 
    (r5a) DSRG – Session Organizer: Jan Kieleczawa, Global Biological Technologies, Pfizer
              (r5a-1) Multi-Center Genome Sequencing and Analysis of the Dutch Elm Disease Fungus using the Roche/454 Titanium System
    • Ken Dewar, McGill University
    • (r5a-2) Comparison of Commercially Available Target Enrichment Methods for Next Generation Sequencing-Illumina Platform
    • Anoja Perera, Stowers Institute
  • 
    (r5b) GVRG: Analysis of Copy Number Variation in C. elegans Using Next Generation Sequencing
    • Session Organizer: Brian Sanderson, Stowers Institute
    • Presenters: Brian Sanderson, Stowers Institute, Sean Blake, University of Missouri & Aaron Noll, StowersInstitute
• 
  (r6) Glyco Proteomics Research Group (gPRG): Results of the 2010 Glycoprotein Research Group's (gPRG) Study on Quantitative Glycoprotein Analysis
  • Session Organizer: Ron Orlando
  • 
    (r6-1) gPRG Glycoprotein Sample Analysis-Genetech
    • Rod Keck, University of Georgia, Complex Carbohydrate Research Center
  • (r6-2) Differential Quantification of N-Glycans: a Strategy using HILIC LC LC-MS negative mode
    • Nancy Leymarie, Boston University School of Medicine
• 
  (r7) Microarray Research Group (MARG): New Directions and Update on MicroRNA Profiling Study –
  • Session Organizers: Don Baldwin, University of Pennsylvania & Christina Harrington, Oregon Health & Science University
• • 
    (r7-1) MARG Activities and MicroRNA Profiling and (r7-2) Launch of MARG Webforum for Genomic Profiling Technology and Assays
    • Christina Harrington, Oregon Health & Science University and Natalia G. Reyero, JacksonState University
  • (r7-3) Performance Evaluation of Microarray and Next Generation Sequencing Platforms for MicroRNA Profiling and (r7-4) Synthetic MicroRNA Standards for Benchmarking Core Lab MicroRNA Profiling Platforms
    • Don Baldwin, University of Pennsylvania
• 
  (r8) Protein Expression Research Group (PERG) HIV Protease Refolding Study
  • Session Organizer & Presenter: Richard Heath, St. Jude Children's Research Hospital

ABRF Poster Awards – Sponsored by Waters Corporation

• 
  An Instrumental and Software Platform for the Targeted Protein-Protein "Interact-ome" of Signalling Pathways from Drosophila to Human Cancer Cells
• John Asara, Beth Israel Deaconess Medical Center
• 
  Optimizing in-source decay as a high-throughput alternative to Edman degradation for the determination of protein termini
• Yutian Gan , Genentech, Inc. South San Francisco, CA
• 
  Influenza A H1N1: A Rapid Approach to Cloning and Protein Expression
• Jeremy Hasseman, J. Craig Venter Institute, Rockville, MD

Expert's Table

• (e1) Core Models and Management – Session Organizer: Jay Fox, University Virginia
  • 
    (e1-1) Trudeau Institute Molecular Biology Core Facility
    • Pamela Scott Adams, Trudeau Institute
  • (e1-2) UC Davis Clinical and Translational Science Center Translational Resources
    • Alice F. Tarantal, UC Davis
  • (e1-3) Management Models at the Bauer Core
    • Claire B. Reardon, FAS Center for Systems Biology, Harvard University
  • (e1-4 ) NCRR and Core Facilities
    • Gregory K. Farber, National Center for Research Resources
• 
  (e2) Proteomics: Getting the Best Data from your Proteomics Core: Facility Proteomics Strategies and Workflows - Session Organizer: Brett Phinney, University of California, Davis
  • 
    (e2-1) ABRF - Getting the Best Data from your Proteomics Core
    • Mike Myers, ICGEB
  • (e2-2) Proteomics and Mass Spectrometry @ SUMS
    • Chris Adams, Stanford University
  • (e2-3) Share 2 tricks that we use in our proteomics core facility
    • John Asara, Beth Israel Deaconess Medical Center, Boston, MA
  •  
• (e3) Next Generation Sequencing - Session Organizer: Paul Morrison, Dana Farber Cancer Institute
  • Panelists:
    • Charlie Nicolet, University of California at Davis
    • James VanEe, Cornell University
    • Deb Grove, Pennsylvania State University
    • Bob Steen, Harvard Mefical School
    • Ryan Kim, NCGR
• 
  (gs1) Disruptive and Evolving Technologies & Open Mic Discussion -Session Organizer: Susan Hardin, HCI GP, LLC
•  
• • Presentation: The Prospects for Sequencing a Single Molecule of Double-Stranded DNA in a Nanopore With a Diameter Smaller than the Double Helix
  • Gregory Timp, University of Illinois

ABRF Member Meeting

• President's Report - Michelle Detwiler, Roswell Park Memorial Institute
• 
  Treasurer's Report - Arnold Falick, HHMI-UC Berkeley
• 
  Membership Committee Report - Ronald Niece, Research Resources & Technologies