ABRF 2011 Presentations

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ABRF Award for Outstanding Contributions to Biomolecular Technologies - Sponsored by Agilent Technologies

Sir Alec John Jeffreys - DNA Fingerprinting and the Turbulent Genome

Plenary Sessions

Personalized Medicine: Opportunities and Challenges

Raju Kucherlapati, Paul C. Cabot Professor, Harvard Medical School Department of Genetics and Professor, Department of Medicine, Brigham and Women?s Hospital

Unlocking Biomarker Discovery: Unbiased Human Proteomics at High Scale, Sensitivity, and Accuracy

Larry Gold, Chairman, Founder, & CEO of SomaLogic, Inc.

En Route to the Era of Genomic Medicine (63 mB)

Eric Green, Director, National Human Genome Research Institute

Development by Selventa of a Therapeutic Diagnostic^TM Stratification Biomarker for Drug Response in Ulcerative Colitis

David de Graaf, President & CEO, Selventa

Scientific Sessions

(S1) Improving Human Health from the Ground Up
Session Organizer: Theodore W. ThannhauserUnited States Department of Agriculture/Agricultural Research Service
- (S1-1) Vaccine and Therapeutic Protein Manufacture in Plants
  
  Terence E. Ryan, iBio, Inc.
  
  (S1-2) Improving Human Nutrition from the Ground Up: Linking Agriculture to Human Health
  
  Ross M. Welch, Department of Food Science, Cornell University
  
  (S1-3) A Food Systems Approach to Address Poor Nutritional Health in Both Advanced and Developing Economies
  
  Robin D. Graham, Flinders University of South Australia
(S2) Integration of Bioinformatics for Genomics and Proteomics Data
Session Organizer: Cathy Wu, Center for Bioinformatics & Computational Biology, University of Delaware
- (S2-1) Integrative Bioinformatics for Genomics and Proteomics
  
  Cathy Wu, Center for Bioinformatics & Computational Biology, University of Delaware
  
  (S2-2) Integrated Bioinformatics for MS-Based Proteomics
  
  Eric Deutsch, Institute for Systems Biology
  
  (S2-3) Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration
  
  James Vincent, University of Vermont
(S3) Single-Cell Environmental Genomics
Session Organizer: Rob Knight, University of Colorado
- (S3-1) Early Elements of a Pipeline for Single Bacterial Cell Genomics
  
  Dave Relman, Departments of Microbiology & Immunology, and of Medicine, Stanford University
  
  (S3-2) Assembling Complete Genomes from Complex Mixtures
  
  Folker Meyer, Argonne National Laboratory, Mathematics and Computer Science Division
  
  (S3-3) Dining in with Trillions of Fascinating Friends: Exploring our Human Gut Microbiome in Health and Disease
  
  Jeff Gordon, Center for Genome Sciences and Systems Biology, Washington University School of Medicine
(S4) Epigenetics
Session Organizer: Benjamin A. Garcia, Princeton University
- (S4-1) Next Generation Quantitative Proteomic Tools for Analyzing Histone Modifications
  
  Benjamin A. Garcia, Princeton University
  
  (S4-2) Chromatin Dynamics in Melanoma: A Role for MacroH2A
  
  Avnish Kapoor, Department of Oncological Sciences, Mount Sinai School of Medicine
  
  (S4-3) Using Protein Domain Microarrays to Read the Histone Code
  
  Mark Bedford, Department of Carcinogenesis, Science Park, Research Division, The University of Texas MD Anderson Cancer Center
(S5) High-Throughput Genome Centers
Session Organizer: George Grills, Cornell University
- (S5-1) Overview of the Illumina Sequencing Platform at the Broad Institute
  
  Kristen Connolly, Process & Technology Development, Genome Sequencing Platform, The Broad Institute of MIT and Harvard
  
  (S5-2) Science and Technology at a High-Throughput Genome Center
  
  Lucinda Fulton, The Genome Center at Washington University School of Medicine
  
  (S5-3) High-Throughput Next Generation Sequencing Methods and Applications
  
  Donna Muzny, Baylor College of Medicine, Human Genome Sequencing Center
(S6) Strategies for Deep Mining of Complex Protein Mixtures
Session Organizer: David Speicher, The Wistar Institute
- (S6-1) Coverage and Recovery of Upstream Protein Fractionation Methods in LC-MS/MS Workflows
  
  Leonard J. Foster, Centre for High-Throughput Biology, The University of British Columbia
  
  (S6-2) Improving the Comprehensiveness of Large-Scale Proteomics Experiments Using Advanced Computational Tools and Accurate Multiple Hypothesis Testing Statistics
  
  Michael J. MacCoss, Department of Genome Sciences, University of Washington
  
  (S6-3) In-Depth Analysis of Human and Mouse Plasma Using 3-D and 4-D Fractionation Strategies
  
  David Speicher, The Wistar Institute
(S7) Next Generation Sequencing Technologies on the Horizon
Session Organizer: Katia Sol-Church, Nemours Biomedical Research, A.I. duPont Hospital for Children
- (S7-1) Towards Optical DNA Sequencing Using Nanopore Arrays
  
  Amit Meller, Department of Biomedical Engineering & Department of Physics, Boston University
  
  (S7-2) Single Molecule Real-Time DNA Sequencing on the Surface of a Quantum-Dot Nanocrystal
  
  Peter B. Vander Horn, Genetic Systems, Life Technologies
  
  (S7-3) Sequencing with Semiconductor Chips
  
  Glenn Powell, Ion Torrent
(S9) Proteomics Standardization
Session Organizer: David B. Friedman, Proteomics Laboratory Mass Spectrometry Research Center, Vanderbilt University
- (S9-1) A Multi-Laboratory Study Assessing Robustness and Reproducibility of Plasma Reference Sample for Benchmarking LC-MS Platform Performance
  
  Juan-Pablo Albar, ProteoRed, National Center for Biotechnology-CSIC
  
  (S9-2) Clinical Proteomic Technologies for Cancer: NIH-Funded Measurement Science
  
  Christopher Kinsinger, National Cancer Institute, Center for Strategic Scientific Initiatives, Office of Cancer Clinical Proteomics Research
  
  (S9-3) Why Reproducible Outcomes are Essential in Proteomic Research and Why Standardization of Processes is Essential for Achieving Reproducibility
  
  Andy Borthwick, Nonlinear Dynamics Limited

Workshops

(W1) The Diagnostics Core Facility: Harvesting the Promise of Personalized Medicine
Session Organizer: Katia Sol-Church, Nemours Biomedical Research, A.I. duPont Hospital for Children
- (W1-1) Win on Sunday, Sell on Monday: From the Exome Sequencing of One Boy to the Delivery of Clinical Diagnostics
  
  Michael R. Tschannen, Human and Molecular Genetics Center, Department of Physiology, Medical College of Wisconsin
  
  (W1-2) Chromosomal Microarray Analysis in the Clinic
  
  Lisa D. White, Microarray Core, Baylor College of Medicine
  
  (W1-3) Whole Genome Sequencing in the Clinical Laboratory
  
  Tina Hambuch, Illumina Clinical Services Laboratory, Illumina, Inc.
(W2) Spectral and Sequence Database Searching in Proteomics
Session Organizer: Lennart Martens, Ghent University
- (W2-1) ETD Performance and Complementarity to Other Fragmentation Methods for Proteomic Analysis
  
  Robert Chalkley, University of California San Francisco
  
  (W2-2) Discovery, Identification and Localization of Post-Translational Modifications
  
  Nuno Bandeira, Center for Computational Mass Spectrometry, Department of Computer Science and Engineering Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
  
  (W2-3) Building and Using MS/MS Spectral Libraries for Peptide Identifications in Proteomics
  
  Henry Lam, The Hong Kong University of Science and Technology
(W3) Quantifying Protein Turnover by In Vivo Metabolic Labeling
Session Organizer: Kieran Geoghegan, Pfizer, Inc.
- (W3-1) Stable Isotope Tracers Applied to Measuring Rates of Protein Synthesis and Breakdown in Muscle: Principles and Applications
  
  Robert R. Wolfe, University of Arkansas Medical Sciences
  
  (W3-2) In Vivo Stable Isotope Labeling for Quantifying Amyloid-Beta Kinetics in Alzheimer?s Disease: Is it All in our Head?
  
  Kevin E. Yarasheski, Biomedical Mass Spectrometry Research Laboratory, Washington University School of Medicine
(W4) Insights for Expression of Recombinant Proteins for Drug Target Validation
Session Organizer: Francis Rajamohan, Pfizer, Inc.
- (W4-1) New Developments in BacMam Vectors
  
  Frederick M. Boyce, Massachusetts General Hospital, Department of Neurology
  
  (W4-2) Strategies for Optimized High-Throughput Cloning, Expression, and Purification of Recombinant Proteins
  
  Rebecca Page, Brown University, Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genetics, Genomics and Proteomics
(W5) Proteomics Tips and Tricks: From Discovery to Protein-Protein Interactions
Session Organizer: Michelle Cilia, United States Department of Agriculture/Agricultural Research Service, Robert W. Holley Center for Agriculture and Health
- (W5-1) Proteomics Tips and Tricks: From Discovery to Protein-Protein Interactions
  
  Michelle Cilia, United States Department of Agriculture/Agricultural Research Service, Robert W. Holley Center for Agriculture and Health
  
  (W5-2) Protein Interactions and Topologies in Cells
  
  James Bruce, University of Washington, Department of Genome Sciences
  
  (W5-3) The Virus-Host Interface: Exploring Dynamic Protein Interactions via Targeted Proteomics
  
  Ileana Cristea, Princeton University, Department of Molecular Biology
  
  (W5-4) Towards the Development of Proteomics Workflows for the Analysis of Samples Derived from Refractory Plant Tissues
  
  Theodore W. Thannhauser, United States Department of Agriculture/Agricultural Research Service
(W6) Current State and Future of Capillary Electrophoresis and Sanger Sequencing
Session Organizer: Jan Kieleczawa, Pfizer, Inc.
- Presenters:
  
  Prolonged Storage of Plasmid DNAs under Different Conditions: Effect on Sequence Quality, Spectral Characteristics, Plasmid Integrity and Transformation Efficiency
  
  Jan Kieleczawa, Pfizer, Inc.
  
  Capillary Electrophoresis Update
  
  Eric Vennemeyer, LifeTechnologies
  
  Apollo100: a robotic, microcycler for Sanger Sequencing
  
  Michael Zianni, Plant-Microbe Genomics Facility, Ohio State University
- Panelists: Debbie Adam, NAPS Unit, Michael Smith Laboratories, University of British Columbia
  
  Peter Schweitzer, Cornell University
(W7) Cellular 3D Imaging
Session Organizer: Richard Cole, Wadsworth Center, New York State Department of Health
- (W7-1) 3D Cellular Imaging: Beyond the Simple Imaging Paradigm
  
  Richard Cole, Wadsworth Center, New York State Department of Health
  
  (W7-2) Basics of Colocalization Analyses
  
  Judith Lacoste, Cell Imaging and Analysis Network, Department of Biology, McGill University
(W8) Successful Production of Functional Proteins
Session Organizer: Jeff Culp, Pfizer, Inc.
- (W8-1) Successful Protein Production
  
  Jeff Culp, Pfizer, Inc.
  
  (W8-2) Overcoming Problems in Protein Expression and Purification
  
  Bill Gillette, SAIC-Frederick, Inc., National Cancer Institute at Frederick
  
  (W8-3) When Proteins Misbehave, Try Adding a Little Pressure
  
  Robert M. Petrovich, National Institute of Environmental Health Sciences Laboratory of Structural Biology
(W9) Therapeutic Antibodies: Over-Hyped "Magic Bullet", or Under-Explored Technology?
Session Organizer: Dan L. Crimmins, Washington University School of Medicine
- Presenters:
  
  Dan L. Crimmins, Washington University School of Medicine
  
  John Harlan, Abbott Laboratories
  
  Therapeutic Antibodies: Over-Hyped "Magic Bullet", or Under-Explored Technology?
  
  Frances Weis-Garcia, Memorial Sloan-Kettering Cancer Center
(W10) Identification of Mechanism-Based Biomarkers and Drug Targets Using Pathway Analysis
Session Organizer: Alexander Kel, geneXplain GmbH
- (W10-1) GeneXplain - Identification of Causal Biomarkers and Drug Targets in Personalized Cancer Pathways
  
  Alexander Kel, geneXplain GmbH
  
  (W10-2) Pathway Analysis in Expression Proteomics
  
  Roman Zubarev, Chemistry I Division, Department of Medical Biochemistry and Biophysics, Karolinska Institute
  
  (W10-3) Metabolic Biomarkers, Metabolic Networks, and Pathway Analysis
  
  Vladimir Tolstikov, University of California Davis Genome Center
(W11) The Business of Running a Core Facility
Session Organizer: Nicholas Ambulos, University of Maryland School of Medicine
- Presenters:
  
  Nicholas Ambulos, University of Maryland School of Medicine
  
  Steve Bobin, Dartmouth School of Medicine
(W12) Microarrays: The Reports of My Death Have Been Greatly Exaggerated
Session Organizer: Don Baldwin, University of Pennsylvania, Penn Molecular Profiling Facility
- (W12-1) Chip or Seq: Helping Clients Choose
  
  Don Baldwin, University of Pennsylvania, Penn Molecular Profiling Facility, and Kevin Knudtson, University of Iowa
  
  (W12-2) Microarray Analysis of Fluorescence Activated Cell Sorter-Derived Cells: Creating Harmony between Technologies
  
  Scott Tighe, University of Vermont
  
  (W12-3) Microarray Futures: Don't Decommission Your Scanners Just Yet
  
  Seth Crosby, Department of Genetics, Washington University School of Medicine
(W13) Institutional Core Management
Session Organizers: Susan Meyn, Vanderbilt University Medical Center, and Paula Turpen, University of Nebraska Medical Center
- Presenters:
  
  Pam Alexander, Morehouse School of Medicine
  
  Julie Auger, University of California San Francisco
  
  Gregory Farber, National Center for Research Resources
  
  Sheenah Mische, New York University Langone Medical Center
(W14) Next Generation Sequencing Software for Data Management, Analysis, and Visualization
Session Organizer: Kip Bodi, Tufts University School of Medicine,
- (W14-1) Tools for Next Generation Sequencing Data Analysis
  
  Kip Bodi, Tufts University School of Medicine
  
  (W14-2) GenomeView: Visualizing the Next Generation of Data
  
  Thomas Abeel, Broad Institute of MIT and Harvard, and VIB Department of Plant Systems Biology, Ghent University
  
  (W14-3) Galaxy Next Generation Sequencing Functionality from Sample Tracking to SNP Calling
  
  Greg Von Kuster, Pennsylvania State University
(W15b) ETD Workshop Seminar Series PART II: Manual Interpretation of Electron Transfer Dissociation (ETD) Mass Spectra of Peptides
- Donald F. Hunt, Departments of Chemistry and Pathology, University of Virginia

Research Group Presentations

(R1) Joint Session: Proteome Informatics Research Group (iPRG) & Proteomics Standards Research Group (sPRG)
- (R1a) iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra
  
  Session Organizer & Presenter: Lennart Martens, Ghent University
- (R1b) ABRF-sPRG2011 Study: Development of a Comprehensive Standard for Analysis of Post- Translational Modifications
  
  Session Organizer & Presenter: Alexander R. Ivanov, Harvard School of Public Health
(R2) Antibody Technology Research Group (ARG): Antibodies - Moving Closer to Personalized Therapeutics and Diagnostics
Session Organizers: Robert Carnahan, Vanderbilt University Medical Center, and Frances Weis-Garcia, Memorial Sloan- Kettering Cancer Center
- Clinical Utility of Platelet Antigen Bead Arrays in the Laboratory Diagnosis of Immune Platelet Disorders
  
  Brian Curtis, Blood Center of Wisconsin
  
  Therapeutic Antibodies: Looking Back and Forward
  
  John Harlan, Abbott Laboratories
  
  Multiplex Biomarker Assays for Translational Research
  
  Robert Umek, Meso Scale Discovery
(R3) Joint Session: Genomic Variation Research Group (GVRG) & DNA Sequencing Research Group (DSRG)
- (R3a): Evaluation of DNA Whole Genome Amplification Technologies for Genotyping
- Session Organizers & Presenters: Casey Dagnall and Amy Hutchinson, Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick
- (R3b): DNA Sequencing Research Group (DSRG)
- Session Organizer: Deborah Grove, Pennsylvania State University
- (R3b-1) Comparison of Custom Target Enrichment Methods; Agilent vs. Nimblegen
  
  Anoja Perera, Stowers Institute for Medical Research Molecular Biology Facility
  
  (R3b-2) A Methodology Study for Metagenomics Using Next Generation Sequencers
  
  Sushmita Singh, BioMedical Genomics Center, University of Minnesota
(R4) Joint Session: Protein Sequencing Research Group (PSRG) & Glycoprotein Research Group (gPRG)
- (R4a) PSRG 2011 Study: Sensitivity Assessment for Terminal Sequencing Techniques Using an Unknown Protein
  
  Session Organizer: Jim Walters, Sigma Aldrich Presenters: Kwasi Mawuenyega, Washington University School of Medicine, Wendy Sandoval, Genentech, Inc., Steve Smith, University of Texas, and Jim Walters, Sigma Aldrich
  
  (R4b) gPRG: Toward Consensus on Glycan Analysis: Reliable Methods and Reproducibility
  
  Session Organizer & Presenter: Joseph Zaia, Boston University
(R5) Joint Session: Nucleic Acids Research Group (NARG) & Microarray Research Group (MARG)
- (R5a) Determining miRNA Expression Levels in Degraded RNA Samples Using Real-Time RT-qPCR and Microarray Technologies
  
  Session Organizer: Sridar Chittur, State University of New York at Albany
  
  Presenters: Sridar Chittur, State University of New York at Albany, and Scott Tighe, University of Vermont
  
  (R5b) Microarray Research Group Projects, 2010-11
  
  Session Organizer: Don A. Baldwin, Molecular Profiling Facility, University of Pennsylvania
  
  Presenters: Nadereh Jafari, Northwestern University, and Natalia Reyero-Vinas, Jackson State University
(R6) Joint Session: Protein Expression Research Group (PERG) & Molecular Interactions Research Group (MIRG)
- (R6a) PERG Research Group Presentation:
  
  Session Organizer: Cynthia Kinsland, Cornell University
  
  Refolding as a Rescue Strategy for Protein Production
  
  Cynthia Kinsland, Cornell University
  (R6b) Conclusions from the MIRG 2010 Benchmark Study: Molecular Interactions in a Three Component System and Presentation of 2011 Survey Results on Label-Free Technologies
  Session Organizer: Aaron Yamiuk, Bristol-Myers Squibb,
  
  MIRG overview
  
  Aaron Yamiuk, Bristol-Myers Squibb
  
  Presentation of 2011 Survey Results on Label-Free Technologies
  
  Satya Yadav, Cleveland Clinic Foundation
(R7) Light Microscopy Research Group (LMRG)
Session Organizer: Robert Stack, Wadsworth Center, New York State Department of Health
- (R7-1) Point Spread Functions, Spectral Calibration, and Beyond
  
  Robert Stack, Wadsworth Center, New York State Department of Health
  
  (R7-2) Deconvolution: Core Concepts, Algorithms, and Advanced Issues
  
  Brian Northan, MediaCybernetics
(R8) Joint Session: Proteomics Research Group (PRG) & Metabolomics Research Group (MRG)
- (R8a) PRG-2011: Defining the Interaction Between Users and Suppliers of Proteomics Services
  
  Session Organizer: David Hawke, The University of Texas MD Anderson Cancer Center
  
  (R8b) Metabolomics Research Group 2011 Study
  
  Session Organizer: William R. Wikoff, University of California DavisPresenters: John M. Asara, Beth Israel Deaconess Medical Center, Vladimir Tolstikov and William R. Wikoff, University of California Davis

Poster Awards Sponsored by Waters Corporation

A new sequencing primer and workflow increase 5' resolution and throughput on HLA sequencing,
Jenny Chuu, Life Technologies, Foster City, CA, United States
Protein-binding assays in biological liquids using Microscale Thermophoresis,
Stefan Duhr, Center for Nanoscience, University Munich, Munich, Germany

Validation of an Ion Mobility Hydrogen/Deuterium Exchange Mass Spectrometry System
Keith Fadgen, Waters Corporation, Milford, MA, United States

Comprehensive Biomarker Discovery Platform Reveals Qualified MRM Assay for Prediction of INF/Riboflavirin Treatment Response in Hepatitis C Patient
J. Will Thompson, Duke Institute for Genome Sciences and Policy, Raleigh, NC, United States

Photo of ABRF 2011 Water Poster Award winners with Water's sponsor Roy Martin

ABRF Member Meeting

Treasurers Report
Arnold Falick, ABRF treasurer
Education Committee Report
Katia Sol-Church, Education Committee Chair
Core Administrators Network - Coordinating Committee Report
Paula Turpen, Core Administrators Network - Coordinating Committee Co-chair
Affiliates and Chapters Report
Steve Jennings, Affiliates and Chapters Member
Membership Committee Report
Leslie Hicks, Membership Committee Member
Farewell to Retiring Executive Board Members
Tony Yeung, Incoming ABRF President
Who's Who in the ABRF
Tony Yeung, Incoming ABRF President