ABRF 2009 Presentations
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ABRF Award
(Sponsored by Agilent Technologies
The Creation of a Human Protein Atlas (17MB)
Awardee and Speaker: Mathias Uhlen, Royal Institute of Technology (KTH), Sweden
Scientific Sessions Workshops Research Group Presentations
(s1) Personalized Medicine — Ballroom A
Eric Wieben, Mayo Clinic (session organizer)
(s1-a) Moving Genomics from Research to Clinical Care in Childhood Leukemia
Mary Relling, St. Jude Children’s Research Hospital
(s1-b) DNA Sequencing: The Next Generatiion - The Road to the Clinical Laboratory
W. Edward Highsmith, Mayo Clinic
(s1-c) Array Based Platforms in Clinical Diagnostics
Ulrich Broeckel, Medical College of Wisconsin
(s2) Biofuels — Ballroom C
Towards a Biofuels Economy: Technologies and Infrastructure Associated with Developing New Bioenergy Crops
Jocelyn Rose, Cornell University (session organizer)
(s2-a) Instrumentation and Methods for the High Throughput Analysis of Plant Materials as a Resource for
Biofuels
Markus Pauly, Michigan State University
(s2-b) From Single Molecules Spectroscopy to Process Batch Fermentation: Methods and
Instrumentation Implemented in the Biofuel Research Laboratory at Cornell University
Stephane Corgie, Cornell University
(s2-c) Identify Molecular Features of Biomass Recalcitrance Using Non-Destructive Microscopy and
Spectroscopy
Shi-You Ding, National Renewable Energy Laboratory (NREL)
(s3) Optical Imaging — Ballroom D
(s3-a) Developments in Microscopic Imaging of Intravital Dynamics
Sam Wells, Vanderbilt University School of Medicine (session organizer)
(s3-b) Intravital Multiphoton Microscopy in a Microscopy Core Resource
Kenneth Dunn, Indiana University School of Medicine
(s4) Next Generation Nucleic Acid Quantitation — Ballroom C
Kevin Knudtson, University of Iowa (session organizer)
(s4-a) “Gene Expression Measurements Using the nCounter Technology”
Roger Bumgarner, University of Washington
(s4-b) “On-Chip PCR and Microfluidic Biochips for High Throughput Screening of Genetic Markers”
Syed Hasham, Michigan State University
(s4-a) Profiling Circulating Tumor Cells as Prognostic Biomarkers in Patients with Metastatic Prostate Cancer
Daniel Danila, Memorial Sloan-Kettering Cancer Center
(s5) Biotech in Forensics and Clinical Diagnostics — Ballroom D
Lessons in Optimizing Specialty Facilities: Forensics, Systematics and Clinical
Howard Cash, Genecodes (session organizer)
(s5-a) Assay Development: From Proof-of-Concept to CLIA-validation of Assays for Patient Testing
Ellen Paxinos, Monogram Biosciences
(s5-b) Biodiversity Documentation via DNA Barcoding at the Smithsonian Institution’s L.A.B. (25MB)
Lee Weigt, Smithsonian Institution, National Museum of Natural History, Laboratories of Analytical Biology
(s5-c) Existing and Emerging Biotechnologies for Forensic DNA Applications
Mitch Holland, Pennsylvania State University
(s6) Quantitative Proteomics — Ballroom A
Reproducibility in Quantitative Proteomics
Kathryn Lilley, University of Cambridge, UK (session organizer)
(s6-a) Reproducibility of 2D Gel-based Proteomics Experiments
Jules Westbrook, University College Dublin, Ireland
(s6-b) Reproducibility of Protein MRM-Based Assays: Towards Verification of Candidate Biomarkers in
Human Plasma
Steven Hall, University of California at San Francisco
(s7) Metagenomics — Ballroom A
Computational Approaches for Metagenomic and Supragenomic Data Sets
(s7-a) Development and Application of a Global Comparative Genomics Pipeline for Performing Inter-isolate
Analyses within Microbial Species
Garth Ehrlich, Allegheny Singer Research Institute and Drexel University College of Medicine (session organizer)
(s7-b) Massively Parallel Barcoded Pyrosequencing Reveals Unexpected Diversity in the Human Microbiome
Rob Knight, University of Colorado at Boulder
(s7-c) MG-RAST: a Web-based Tool for the Analysis of Metagenomic Data Sets
Dionysios Antonopoulos, Institute For Genomics &Systems Biology, Biosciences Division, Dept of Medicine, University of Chicago
(s8) Label Free Detection — Ballroom C
(s8-a) Label-Free Characterization of Protein-Peptide and Protein-Drug Interactions
Gil Privé, University of Toronto and Ontario Cancer Institute (session organizer)
(s8-b) Application of Differential Static Light Scattering and Isothermal Denaturation to Investigate
Thermostability and Binding Specificity of Protein Families
Masoud Vedadi, Structural Genomics Consortium, University of Toronto
(s8-c) Biochemical and Cell-based Detection by Epic System
Meng Wu, Department of Neuroscience and High Throughput Biology Center, School of Medicine, Johns Hopkins
University
(s9) Stem Cell Applications — Ballroom D
(s9-a) Adult Stem Cell Cores and Regenerative Medicine (16MB)
Jeffrey Spees, University of Vermont (session organizer)
(s9-b) Probing Human Embryonic Stem Cell Proliferation with Arrayed Cellular Microenvironment
Technology
Karl Willert, University of California at San Diego
(s9-c) The Ellison Stem Cell Core
Carol Ware, University of Washington
(s10) Next Generation Sequencing — Ballroom A
(Session sponsored by Applied Biosystems)
(s10-a) Toward the $1000 Genome: Molecular Engineering Approaches for DNA Sequencing by Synthesis
Jingyue Ju, Columbia University College of Physicians and Surgeons (session organizer)
(s10-b) Nearly Complete Genomic Profiling of Individual Identified Neurons: SOLiD Approach
Leonid Moroz, University of Florida
(s10-c) Using the SOLiD System for Genomic Solutions
Robert C. Nutter, Applied Biosystems
(s11) Phosphoproteomics — Ballroom C
(s11-a) A New Acid Mix Enhances Phosphopeptide Enrichment on Titanium and Zirconium Dioxide for
Mapping of Phosphorylation Sites on Protein Complexes
Karl Mechtler, University of Vienna, Austria (session organizer)
(s11-b) Current Methods in Phospho-Proteomics
Albert Sickmann, University of Wurzburg, Germany
(s11-c) Analysis of the Yeast Protein Kinase - Substrate Networks by Quantitative Phosphoproteomics
Bernd Bodenmiller, Swiss Federal Institute of Technology Zurich (ETH Zurich), Switzerland
(s12) microRNA — Ballroom D
MicroRNA Profiling in Medical Practice
Non-coding RNAs: from scientist benchside to patient bedside
George Calin, M.D. Anderson Cancer Center, Univ. of Texas (session organizer)
(s12-a) Real-time PCR Expression Profiling of microRNA
Thomas Schmittgen, Ohio State University
(s12-b) microRNA: Regulation, Development and Disease
Michael Thomson, University of North Carolina
(s13) Epigenomics — Ballroom A
(s13-a) Techniques for Cytosine Methylation Patterns
Masako Suzuki, Albert Einstein College of Medicine
(s13-b) Deciphering the Methylome
Bill Caldwell, University of Missouri School of Medicine
s13-c) High Throughput Chromatin Immunoprecipitations, Integrative Epigenomics, and Personalized
Medicine
Ari Melnick, Weill Cornell Medical College (session organizer)
(s14) Targeted Proteomics — Ballroom C
Practical Targeted Proteomics
Brett Phinney, University of California at Davis (session organizer)
(s14-a) Establishing SRM as a Robust and Reliable Technique for Targeted Proteomics
Daneila Tomazela, University of Washington
(s14-b) Targeted Proteomics as a Translational Tool in Drug Discovery
Weixun Wang, Merck Research Laboratories (MRL)
(s14-c) Practical Aspects of Quantitation with Triple-quadrupole Mass Spectrometers
Benjamin Moeller, University of California at Davis
(s15) Bioinformatics — Ballroom D
Gil Alterovitz, Harvard Medical School and MIT (session organizer) and Gail Rosen, Drexel University (session co-organizer)
(s15-a) Informatic Challenges in Metaproteomics
Patricia Carey, University of Tennessee at Knoxville
(s15-b) An Agua-Silico Algorithm for Genome Assembly Validation and DNA Biomarker Discovery, and its
Potential as a Mass-Market Application for Microfluidic Platforms
Robert Boissy, Allegheny Singer Research Institute, Center for Genomic Sciences
(s15-c) Bioinformatics for Metagenomic Taxonomic Classification
Gail Rosen, Drexel University
(s16) Disruptive Life Sciences Technologies — Ballroom A
New Integrated Analytical Systems Based on Miniaturized Optics and Fluidics
Harold Craighead, Cornell University (session organizer)
(s16-a) Optical Biosensors: Future Trends and Perspectives
Chris Taitt, U.S. Naval Research Laboratory
(s16-b) Lithographically Printed Optical, Fluidic, and Electronic Systems
Axel Scherer, California Institute of Technology
(s16-c) Real-Time DNA Sequencing from Single Polymerase Molecules
David Rank, Pacific Biosciences
Ari Melnick, Weill Cornell Medical College (session organizer)
Workshops Scientific Sessions Research Group Presentations
(w1) Core Facility Management Models: Development and Culture — Ballroom A
Valerie Scott, Jackson Laboratory (session organizer)
(w1-a)
Julie Auger, University of Chicago
(w1-b)
Kelvin Lee, University of Delaware
(w1-c) Enhancing Core Research Facility Management, Strategy, and Investment
Rand Haley, Huron Consulting Group
(w2) Women in Science and Core Laboratories — Ballroom C
Michelle Cilia-Reeve, USDA-ARS (session organizer) and Michelle Detwiler, Roswell Park Cancer Institute (session coorganizer)
(w2-a) From Proteins to DNA and Back Again
Kathryn Lilley, University of Cambridge, UK
(w2-b) One Step at a Time: Directing a Core Facility
Nancy Denslow, University of Florida
(w2-c) Sustaining Women in Science, Lessons from the American Society for Cell Biology
Joan Goldberg, American Society for Cell Biology
(w3) Educational Outreach — Ballroom D
Panel: Janet Murray, University of Vermont (session organizer), Cherilynn Shadding, Washington University, Laurel Southard,
Cornell University and Virginia Shepherd, Vanderbilt University
(w4) Implementing Next Generation Sequencing Technologies — Ballroom A
Hit the Ground Running with Next Gen!
(w4-a) Implementing and Running the Illumina GA and Roche 454 at a DNA Sequencing Core Lab
Robert H. Lyons, University of Michigan
(w4-b) Implementing and Running SOLiD Services at a Microarray Core Facility
Jeff Palatini, Comprehensive Cancer Center
(w4-c) Platform Cross-Comparison and Core Facility Next Gen Survey Data
Helaman Escobar, University of Utah (session organizer)
(w5) Implementing Mass Spectrometry Technologies — Ballroom C
Challenges of Implementing New Mass Spectrometry Technologies in Shared Resource Facilities
Joseph Loo, University of California at Los Angeles (session organizer)
(w5-a) Application of Advanced Mass Spectrometry Technologies at the University of Tennessee Health
Science Center
Sarka Beranova-Giorgianni, University of Tennessee Health Science Center
(w5-b) Center for Mass Spectrometry and Proteomics at the University of Minnesota: Organization and
Policies
Gary Nelsestuen, University of Minnesota
(w5-c) The NIH National Center for Research Resources Mass Spectrometry at Washington University
Michael Gross, Washington University
(w6) Implementing Optical Imaging Technologies — Ballroom D
(w6-a) Implementing Optical Imaging Technologies
Simon Watkins, University of Pittsburgh School of Medicine (session organizer), Scott Henderson, Virginia
Commonwealth University, Victoria Frohlich, University of Texas Health Science Center
(w7) Core Support and Instrumentation Funding — Ballroom A
Structure and Function of Cores: New is Old and Old is New
(w7-a) Structure, Function and Funding of Shared Research Resources
Jay Fox, University of Virginia (session organizer)
(w7-b) Evolving Role of Shared Resource Cores and Their Support in the Future
Louise Ramm, NIH National Center for Research Resources (NCRR)
(w7-c) Instrumentation for Core Facilities: The NIH SIG and HEI Programs
Marjorie Tingle, NIH National Center for Research Resources (NCRR)
(w8) Bio-Information Technology (Bio-IT) — Ballroom C
Custom Software Development in Support of Core Facilities
(w8-a) Removing Data Silos with ISIS
Michael McFarland, Jackson Laboratory
(w8-b) Internal Software Development and Integration Experiences at the Cornell University Life Sciences
Core Laboratories Center
James VanEe, Cornell University
(w8-c) SRM 2.0: Building the Next Generation of Core Facility Management Systems
Matthew Stine, St. Jude Children’s Research Hospital (session organizer)
(w9) Protein Expression — Ballroom D
John Hawes, Miami University (session organizer)
(w10) Next Generation Sequencing Instruments — Ballroom A
Massively Parallel Sequencing Instrumentation Panel Session
Ken Dewar, McGill University and Genome Innovation Centre (session organizer), Robert Nutter, Applied Biosystems, and
Avak Khavejian, Helicos Biosciences
(w11) Proteomics Data Publication — Ballroom C
Searching and Sorting: Preparing Protein Identification Data for Publication
Ralph Bradshaw, University of California at San Francisco (session organizer)
(w11-a) From Results to Publication: Journal Guidelines and Protein Prospector
Robert Chalkley, University of California at San Francisco
(w11-b) Providing Mascot Search Results in a Format Suitable for Submission as Supplementary Data
David Creasy, Matrix Sciences
(w11-c) Organizing MS/MS Proteomic Data for Publication
Brian Searle, Proteome Software
(w12) Molecular Interactions Instruments — Ballroom D
(w12-a) Technical Workshop on Real-Time Biophysical Technologies Used for Characterization of
Biomolecular Interactions
Satya Yadav, Cleveland Clinic Lerner Research Institute (session organizer) and Aaron Yamniuk, Bristol-Myers Squibb
Co. (session co-organizer) Panel: Yasmina N. Abdiche, BBC Rinat Laboratories-Pfizer, Inc. (Bio-Rad), Anthony G.
Frutos, Corning, Theres Jägerbrink, Attana AB, Sriram Kumarswamy, ForteBio, and Eric Rhous, GE Healthcare,
Advanced Systems – Biacore
Research Group Presentations Scientific Sessions Workshops
(also available on specific Research Group page at http://www.abrf.org)
(r1) Joint Research Group Presentation on Proteomics
Evaluating the State of the Art in Quantitative Proteomics
Proteomics Research Group (PRG)
(r1-a) PRG 2009 Study: Relative Protein Quantification in a Clinical Matrix
Michael MacCoss, University of Washington (session organizer)
Proteomics Standards Research Group (sPRG)
(r1-b) ABRF-sPRG09: Development of a Quantitative Proteomics Standards
James Farmar, Albert Einstein College of Medicine (session organizer) and Jeffrey Kowalak, National Institute of Mental
Health (NIMH)
(r1-b2) sPRG2009 Prototype Sample @HSPH
Alexander R. Ivanov, HSPH Proteomics Resource, Harvard School of Public Health
Proteome Informatics Research Group (iPRG)
(r1-c) iPRG 2009 Study: Testing for Qualitative Differences Between Samples in MS/MS Proteomics Datasets
Brian Searle, Proteome Software (session organizer)
(r2) Nucleic Acids Research Group (NARG)
(r2-a) NARG 2008-2009 Study: A Comparison of Different Priming Strategies for cDNA Synthesis by Reverse Transcriptase,
as Evaluated by Real-Time qPCR
Kevin Knudtson, University of Iowa (session organizer)
(r2-b) Common Practices for Routine RNA handling
Scott Tighe, University of Vermont
(r3) Joint Research Group Presentation on Genomics
Detection of Human microRNAs across miRNA Arrays and Next Generation DNA Sequencing Platforms
DNA Sequencing Research Group (DSRG)
(r3-a) ABRF 2009 — Application and Optimization of Existing and Emerging Biotechnologies
Peter Schweitzer, Cornell University (session organizer)
Microarrays Research Group (MARG)
(r3-b) 2008-09 Joint Research Group Project: Detection of Human microRNAs Across miRNA Array and Next
Generation DNA Sequencing Platforms
Susan Hester, U.S. Environmental Protection Agency (session organizer)
Genomic Variation Research Group (GVRG)
(r3-c) GVRG 2009 Study
Christian Lytle, Dartmouth Medical School (session organizer) and Brewster Kingham, University of Delaware
(r4) Joint Research Group Presentation on Proteins
Edman Sequencing Research Group (ESRG)
(r4-a) ESRG Study 2009: Comparison of Edman and Mass Spectrometry Techniques for N-terminal Sequencing
Peter Hunziker, University of Zürich, Switzerland (session organizer) and Wendy Sandoval, Genentech, Inc.
Protein Expression Research Group (PERG)
(r4-b) Recombinant Protein Expression and Purification Study
John Hawes, Miami University (session organizer)
(r5) Light Microscopy Research Group (LMRG)
Light Microscopy Research Group (LMRG)
Performance Testing and Standard Good Operating Practice in Light Microscopy
Richard Cole, Wadsworth Center / NY State Dept. of Health (session organizer) and Carol Bayles, Cornell University
