SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis
Primary Organizer: Nalini Raghavachari
Supported by:
NuGEN – Giga Sponsor
Rubicon – Giga Sponsor
Illumina – Mega Sponsor

SW2: Mass Spectrometry of Glycoproteins and their Glycans
Primary Organizer: Ron Orlando
New England Biolabs – Deca Sponsor
 

4:00pm – 5:00pm

First-Time Attendee Welcome & Orientation Session

Keynote Session: Turning Cancer on its Side: Convergence of Physical Sciences Perspectives in Oncology
Dr. Larry Nagahara, Director, Office of Physical Sciences-Oncology, National Cancer Institute
 

9:00am – 10:30am       

Parallel Scientific and Core Administration Tracks

(S1) Super–Resolution Microscopy
Session Organizer: Alison North, The Rockefeller University

Emerging Fluorescence Technology to Study the Spatial and Temporal Dynamics of Molecules and Organelles Within Cells
Jennifer Lippincott-Schwartz, Cell Biology and Metabolism Branch, NIH

Stimulated Emission Depletion Microscopy
Carlo Alonso, Leica Microsystems

3D Structured Illumination Microscopy
Paul Goodwin, Applied Precision, Inc.

(S2) Biomarkers
Session Organizer: Robert Gerszten, Massachusetts General Hospital, Center for Immunology and Inflammatory Diseases

Metabolite Profiles of Diabetes Risk
Robert Gerszten, Massachusetts General Hospital

Metabolite Profiles of Cardiovascular Risk
Svati Shah, Duke University

SOMAmers and  SOMAscan -Protein Biomarker Discovery to Clinical Assay
Preston Hensley, Somalogic

(S3) Mendelian Genomics
Session Organizer: Shrikant Mane, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University

Recent Advances in Mendelian Genomics at the Yale Center for Genome Analysis
Shrikant Mane, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University

Whole Exome Sequencing in Nervous System Disorders
Kaya Bilguvar, Yale University

An Integrated Approach for Prioritizing Causal Variants in Whole Exome and Whole Genome Sequencing
Martin Kircher, University of Washington

(A1) Research Compliance – What Core Directors Need To Know
Session Organizers: Phil Hockberger, Northwestern University; Susan Meyn, Vanderbilt University
Presenters:
Steve Eisner, Stanford University
Donna DePasquale, Vanderbilt University
Sujna Raval-Fernandes, University of California, Los Angeles

10:30am – 11:00am

Morning Break
Exhibit Hall

11:00am – 12:00pm

Research Group Presentations
(RG1) ABRF Next-Generation Sequencing Study (ABRF-NGS)
Session Organizer: George Grills, Cornell University
Presenters:
Don Baldwin, University of Pennsylvania
Scott Tighe, University of Vermont
Chris Mason, Weill Cornell Medical College
George Grills, Cornell University

(RG2) Proteome Informatics Research Group (iPRG)
Session Organizer: Robert Chalkley, University of California, San Francisco
Presenters:
Robert Chalkley, University of California, San Francisco
Eric Deutsch, Institute for Systems Biology

(RG3) Antibody Technology Research Group (ARG)
Session Organizer: Frances Weis-Garcia, Memorial Sloan Kettering Cancer Center

Role of Immune Modulators in Generating a Robust Humoral Immune Response
Robert Carnahan, Vanderbilt University

Evaluating Options for Hard to Label Antibodies
Brian Agnew, Life Technologies

ARG Protocol Repository
Frances Weis-Garcia, Memorial Sloan Kettering Cancer Center

Administration Session
(A2) Career Opportunities For Core Directors
Sponsored by Northwestern University

Session Organizer: Phil Hockberger, Northwestern University
Presenters:
Claire Brown, McGill University
Sheenah Mische, New York University
Sangeeta Vohra, Northwestern University

1:30pm – 3:00pm

Parallel Scientific Workshop and Administration Tracks

(W1) Lessons Learned for Super-Resolution Microscopy
Session Organizer: Alison North, The Rockefeller University

Stochastic Optical Reconstruction Microscopy (STORM)
Christopher O’Connell, Nikon Instruments Inc.

Super-Resolution and Correlative Light Electron Microscopy (CLEM)
Joseph Huff, Zeiss

Challenges for Super-Resolution
Alison North, The Rockefeller University

How Super Is My Resolution?
Jonas Ries, EMBL

Additional Presenters
Judith Lacoste, McGill University

(W2) Biostatistical Analysis of Large-Scale Proteomics Datasets
Session Organizer: Christopher Colangelo, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University

Statistics in the Design and Planning of Proteomic Experiments
David Cairns, University of Leeds

Quantitative Analysis of Discovery-Based MS/MS Results
Brian C. Searle, Proteome Software, Inc.

Biostatical Tools for Targeted and Data-Independent Proteomics Results
Christopher Colangelo, Yale University

(W3) Advances in Targeted Gene Modifications
Session Organizer: Kym Delventhal, Stowers Institute

Starting a TALEN Core Facility Service
Kym Delventhal, Stowers Institute

University of Wisconsin-Madison TALEN Facility
Fang Wan, University of Wisconsin

Using TALEN Technology as a Core Facility Resource
Timothy Dahlem, University of Utah

(A3) Regional Resource Sharing/Collaboration/Consolidation: Models of Effective Resource Access and Utilization
Session Organizer: Jay Fox, University of Virginia School of Medicine

VA Research Resource Consortium: Statewide Partnerships Between Research Intensive Institutional Cores, Non-Research Intensive Institutions and the Biotech Industry
Jay Fox, University of Virginia School of Medicine

Multiple Institutional Core Networks
Philip Hockberger, Northwestern University
Rand Haley, Huron Education

Organization of a Regional NCI Cancer Center Core Network
Nicholas Ambulos, University of Maryland School of Medicine

IT for Life Science Research: Trends, Tips and Tricks
Chris Dagdigian, BioTeam

Core Lab Navigation of Rough Seas at NIH in Uncertain Economic Times
Franziska Grieder, acting Director of the Office of Research Infrastructure Programs, National Institutes of Health
Mark Lively, Wake Forest University

4:45pm – 6:00pm

Convergence Science: Models of Success
Session Organizer: Nathaniel Cady, University at Albany, State University of New York
Presenters:
Nathaniel Cady, University at Albany, State University of New York
Amy Herr, University of California, Berkeley

7:30pm – 10:00pm

Evening Networking Events

Award Presentations:
ABRF Outstanding Scientist/Technologist Award
Waters Poster Awards, presented by Roy Martin, Waters Corporation

Plenary Session: Activity-Based Proteomics – Applications for Enzyme and Inhibitor Discovery
Dr. Benjamin Cravatt, Department of Chemical Physiology,The Scripps Research Institute

9:00am – 10:30am       

Parallel Scientific and Core Administration Tracks

(S4) New Developments in Fluorescent Probes – Not Your Dad’s Fluorochromes
Session Organizer: Richard Cole, New York State Department of Health, Wadsworth Center

Engineered Fluorescent Proteins For Visualizing Biochemistry In Situ
Robert Campbell, University of Alberta

Nanobodies and Binding-Activated Probes For Localization Microscopy
Jonas Ries, EMBL

(S5) Molecular Interactions /Interactomics
Session Organizer: Anne-Claude Gingras, Samuel Lunenfeld Research Institute at Mount Sinai Hospital

How to Generate High Quality Protein Interaction Maps
Alexey Nesvizhskii, University of Michigan

Mapping Cancer Interactomes Using Mass Spectrometry
Anne-Claude Gingras, Samuel Lunenfeld Research Institute at Mount Sinai Hospital

Identifying Specific Protein-DNA Interactions Using Quantitative Mass Spectrometry-Based Proteomics
Michiel Vermeulen, University Medical Center Utrecht, The Netherlands

(S6) Epigenomics
Session Organizer: Rob Mitra, Washington University School of Medicine
Presenters:
Peter Jones, USC Epigenome Center
John Stamatoyannopoulos, University of Washington
Rob Mitra, Washington University School of Medicine

(A4) Metrics of Success for Core Facilities
Session Organizer: Julie Auger, University of California, San Francisco
Presenters:
Valerie Scott, The Jackson Laboratory Cancer Center
Andrew Chitty, Oregon Health and Sciences University
James Schilling, University of Chicago

10:30am – 11:00am

Morning Break
Exhibit Hall

11:00am – 12:30pm

Research Group Presentations
(RG4 and RG5) Nucleic Acids Research Group (NARG) and Genomics Research Group (GRG) Joint Session

      (RG4) Nucleic Acids Research Group (NARG)
      Session Organizer: Jennifer Holbrook, AI Dupont Hospital for Children

      Role of DNA Extraction in Metagenomic Sample Identification
      Jennifer Holbrook, AI Dupont Hospital for Children
      Russ Carmical, The University of Texas Medical Branch at Galveston

      (RG5) Genomics Research Group (GRG)
      Session Organizer: Nalini Raghavachari, Genetics and Development Biology Center, NHLBI

      Evaluation of Technologies for miRNA Analysis Using Synthetic miRNA Standards
      Nalini Raghavachari, Genetics and Development Biology Center, NHLBI

      Oyster Transcriptome Analysis by Next Gen Sequencing
      Natalia Reyero, The Interdisciplinary Center for Nanotoxicity

      Research Activities of the Genomics Research Group
      Sridar Chittur, State University of New York at Albany

(RG6 and RG7) Proteomics Research Group (PRG) and Proteomics Standards Research Group (sPRG) Joint Session

      (RG6) Proteomics Research Group (PRG)
      Session Organizer: Maureen Bunger, Proteovations, LLC

      The PRG2012 Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis (Part 1)
      Maureen Bunger, Proteovations, LLC

      The PRG2012 Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis (Part 2)
      David Tabb, Vanderbilt University

      (RG7) Proteomics Standards Research Group (sPRG)
      Session Organizer: Craig Dufresne, Thermo Fisher Scientific

      Qualitative Analysis of the Degradation Pathways of Selected Peptides from the ABRF 2011-2012 Study
      Craig Dufresne, Thermo Fisher Scientific

      Development and Initial Evaluation of a Quantitative Peptide Standard
      Scott A. Shaffer, University of Massachusetts Medical School

(RG8 and RG9) Metabolomics Research Group (MRG) and Molecular Interactions Research Group (MIRG) Joint Session

      (RG8) Metabolomics Research Group (MRG)
      Session Organizer: Amrita Cheema, Georgetown University
      Applications of Metabolomics to Biomedical Research

      (RG9) Molecular Interactions Research Group (MIRG)
      Session Organizer: Aaron Yamniuk, Bristol-Myers Squibb

      Introduction to a Protein Interaction System used for Quantitative Evaluation of Biomolecular Interactions
      Aaron Yamniuk, Bristol-Myers Squibb

      Results of the MIRG 2012 Benchmark Study on Quantitative Evaluation of a Protein-Protein Interaction
      Satya Yadav, Cleveland Clinic Lerner Research Institute

(RG10) Flow Cytometry Research Group and New Advances in Cytometry Instrumentation
Session Organizer: Peter Lopez, New York University

Overview of the New Flow Cytometry RG and Proposed Cell Sorting (FACS) Microarray Study
Scott Tighe, Vermont Cancer Center at the University of Vermont

Comparing Dendritic Cell Function After Enrichment Using Different Fluorescence Activated Cell Sorters (FACS)
Monica DeLay, Cincinnati Children’s Hospital Medical Center

New Advances in Cytometry Instrumentation
Peter Lopez, New York University

2:00pm – 3:30pm

Parallel Scientific Workshop and Administration Tracks

(W4) Choosing the Right Fluorescent Probe
Session Organizer: Rich Cole, New York State Department of Health, Wadsworth Center

Choosing Duolink ® for Localizing and Quantifying Protein Interactions and Their Modifications at Physiological Cellular Levels
Itxaso Apraiz, Olink Bioscience

Engineered Fluorescent Proteins For Visualizing Biochemistry In Situ
Robert Campbell, University of Alberta

Nanobodies and Binding-Activated Probes For Localization Microscopy
Jonas Ries, EMBL

Flow Cytometry challenges: Detecting Fluorescent Proteins
Andy Riddell, Wellcome Trust MRC Stem Cell Institute Centre for Stem Cell Research

(W5) Data-Independent Acquisition Mass Spectrometry
Session Organizer: Nathalie Selevsek, ETH Zurich Institute of Molecular Systems Biology
Presenters:
Nathalie Selevsek, ETH Zurich Institute of Molecular Systems Biology
Christopher Colangelo, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University

(W6) Community Resource Solutions to Analyzing Large Genomic Data Sets
Session Organizer: James Vincent, University of Vermont

Analysis of Shotgun Metagenomes with MG-RAST
Folker Meyer, Argonne National Laboratory

Galaxy for Core Facilities
Dave Clements, Emory University

CloVR: An Automated Genomic Analysis Tool Using Virtual Machine and Cloud Computing
Mahesh Vangala, Norwich University

(A5) Core Facility Financial Essentials
Session Organizer: Susanna Perkins, University of Massachusetts Medical School

Constructing a Business Plan
Natalie Nguyen, Partners Research Management

Core Rate Setting/Cost Allocations
Jennifer Wei, Northwestern University

Reporting on Core Facilities – Who Needs to Know What Information?
Susanna Perkins, University of Massachusetts Medical School

3:30pm – 5:00pm

Ice Cream Social Poster Session II
Exhibit Hall
*Poster presenters will be available at their posters during these hours, but posters will be available for viewing throughout the entire conference.

5:00pm – 6:00pm

ABRF Award Lecture – Dr. Leonard Herzenberg, Stanford University

6:30pm – 10:00pm

Evening Networking Events

Plenary Session: The Expanding Scope of Next-Generation DNA Sequencing
Dr. Jay Shendure, Department of Genome Sciences, University of Washington

9:00am – 10:30am       

Parallel Scientific and Core Administration Tracks

(S7) Fundamentals of Image Processing and Analysis
Session Organizer: Phil Hockberger, Northwestern University

Optical Illusions: Why You Should NOT Trust Your Eyes
Philip Hockberger, Northwestern University

Why Do We Need Image Processing? 
Glen MacDonald, University of Washington

You Call That Quantitative?
James Jonkman, Ontario Cancer Institute

(S8) Epigenetic Mechanisms: Protein and DNA Covalent Modifications
Session Organizer: Benjamin Garcia, University of Pennsylvania

Epigenomic Analysis of Multi-Lineage Differentiation of the Human Embyronic Stem Cells
Bing Ren, University of California, San Diego

De Novo Sequencing of Small Non-coding RNA Using Bottom-Up MALDI Spiral TOF Mass Spectrometry
Norman Chiu, University of North Carolina at Greensboro

Quantitative Proteomics for Understanding the Histone Code
Benjamin Garcia, University of Pennsylvania

(S9) Advances in Single Cell Genomics and Transcriptomics
Session Organizer: Herbert Auer, Institute for Research in Biomedicine

20 Years of Single Cell Transcriptomics (Publications)
Herbert Auer, Institute for Research in Biomedicine

Analysis of Human Colon Tissue Cell Composition Using Single-Cell Gene-Expression PCR
Piero Dalerba, Stanford University

Microarray Comparative Genomic Hybridization and Comprehensive Chromosomal Screening in Reproductive Medicine: In Vitro Fertilization Applications to Reduce Multiple Gestation and Preterm Birth Rate
Scott Sills, Pacific Reproductive Center

(A6) Embracing Lab Biocontainment and Biosafety – From Policy to Best Practice
Session Organizer: Peter Lopez, New York University

Laboratory Biological Safety Principles and Practices
Erik A. Talley, Weill Cornell Medical College

The Integration of Biosafety in Core Research Facilities
Benjamin Fontes, Yale University Environmental Health & Safety

Biosafety Best Practices in the Flow Cytometry Laboratory
Peter Lopez, New York University Langone Medical Center

10:30am – 11:00am

Morning Break
Exhibit Hall

11:00am – 12:30pm

Research Group Presentations

(RG11 and RG12) DNA Sequencing Research Group (DSRG) and Genomic Bioinformatics Research Group (GBIRG) Joint Session

      (RG11) DNA Sequencing Research Group (DSRG)
      Session Organizer: Deb Grove, Penn State University

       Update on DSRG Projects
       Deb Grove, Penn State University

       Evaluation of Commercially Available RNA Amplification Kits at Sub-Nanogram Input Amounts of Total RNA for RNA-Seq: Study Design and          Workflow
       Savita Shankar, University of Florida

       Evaluation of Commercially Available RNA Amplification Kits at Sub-Nanogram Input Amounts of Total RNA for RNA-Seq: Analysis
       Charles Nicolet, University of Southern California

      (RG12) Genomic Bioinformatics Research Group (GBIRG)
      Session Organizer: Nadereh Jafari, Northwestern University

      Background and Overview
      Nadereh Jafari, Northwestern University

      The Cross-Platform ABRF-NGS Study Leads to Improved Genome and Transcriptome Standards
      Chris Mason, Weill Cornell Medical College of Cornell University

      RNA-Seq Algorithms and Evaluation with Simulated Datasets
      Yuan Gao, Johns Hopkins University

(RG13 and RG14) Protein Sequencing Research Group (PSRG) and Glycoproteomics Research Group (sPRG) Joint Session

      (RG13) Protein Sequencing Research Group (PSRG)
      Session Organizer: Henriette Remmer, University of Michigan Medical School

      Results from the PSRG 2013 Study: Terminal Sequencing of Standard Proteins in a Mixture
      Henriette Remmer, University of Michigan Medical School
      Sara McGrath, FDA Center for Food Safety and Nutrition
      Robert English, University of Texas Medical Branch

      (RG14) Glycoproteomics Research Group (gPRG)
      Session Organizer: Nancy Leymarie, Boston University School of Medicine

      gPRG 2013 Interlaboratory Study: Quantitative N-glycan Profiling of Prostate Specific Antigen
      Nancy Leymarie, Boston University School of Medicine

     Evaluation of Two Complementary Methods for Quantitative Profiling of PSA N-Glycans and N-Glycopeptides
     Morten Thaysen-Andersen, Macquarie University, Sydney, Australia

     Top-Down and Bottom-Up Assessment and Quantification of the Glycosylation Sites in 2 Batches of PSA as Contribution to the 2013                    ABRF-gPRG Study
     Detlev Suckau, Bruker Daltonik

(RG15) Light Microscopy Research Group (LMRG)
Session Organizer: Claire Brown, McGill University

LMRG Mandate, Goals and Overview of Past Studies
Claire Brown, McGill University

Development of a Standard 3D Sample and Protocol for Confocal Microscope Quality Control
Richard Cole, New York State Department of Health, Wadsworth Center

Scientific Session

Mass Cytometry: The Means and the End
Session Organizer: Frances Weis-Garcia, Memorial Sloan-Kettering Cancer Center

The Means: Cytometry and Mass Spectrometry Converge in a Single Cell Deep Profiling Platform
Scott Tanner, University of Toronto

The End: Revealing the Uniqueness of Individual Cells through the Lens of Mass Cytometry
Sean Bendall, Stanford University

2:00pm – 3:30pm

Parallel Scientific Workshop and Administration Tracks

(W7) Image Processing: Tricks of the Trade
Session Organizer: Philip Hockberger, Northwestern University

Deconvolution
Kevin Ryan, MediaCybernetics

3D & 4D Image Processing & Analysis
Meredith Price, Bitplane

Custom Analysis with MetaMorph NX
Edward Rader, Molecular Devices

The Ethics of Image Processing
Douglas Cromey, University of Arizona

(W8) Bad Data in Mass Spectrometry – Real-Life Examples, Common Sources, Practical Solutions
Session Organizer: Allis Chien, Stanford University
Presenters:
Allis Chien, Stanford University
Brett Phinney, University of California, Davis
David Quilici, University of Nevada, Reno

(W9) The Challenges and Successes of Establishing CLIA Certification for Modern Genomics Technologies
Session Organizer: Lisa White, Baylor College of Medicine

Don’t Jump Off the Building! Considerations to Ensure Your Core Lab to CLIA-Certified Lab Transition is Only Moderately Painful
Lisa White, Baylor College of Medicine

The Good, the Bad and the Ugly: Getting CLIA-Certification for a Basic Research Lab
Nicholas P. Ambulos, University of Maryland School of Medicine

Exome Sequencing: Applications from the Lab Bench to the Clinic
Donna M. Muzny, Baylor College of Medicine

(A7) Strategies for Managing Multi-Sponsored Core Facilities
Session Organizers: Susan Meyn, Vanderbilt University; Paula Turpen, University of Nebraska Medical Center
Presenters:
James B. Turpen, University of Nebraska Medical Center
Clemencia Colmenares, Cleveland Clinic, Lerner Research Institute and Case Western Reserve University
Kevin Weller, Vanderbilt University Medical Center

4:00pm – 5:15pm

Status Report: NIH A21 FAQ
Susan Meyn, Vanderbilt University
Julie Auger, University of California, San Francisco

Research Partnering

5:30pm – 6:30pm

ABRF Members Meeting

7:00pm – 10:00pm

Closing Social