ABRF : 2010 Presentations

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.

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