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This meeting took place in 2005
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Proteomics and Bioinformatics (X3)
Organizer(s) Matthias Mann and Catherine E. Costello
April 8—13, 2005
Keystone Resort • Keystone, Colorado USA
Abstract Deadline: Dec 7, 2004
Late Abstract Deadline:
Scholarship Deadline:
Early Registration Deadline: Feb 8, 2005
Supported by The Director's Fund
Joint Meeting:
Systems and Biology (X4)
Summary of Meeting:
Proteomics has emerged as a key discipline in the post-genomic 'tool chest' and over the last few years, proteomics technology has become extraordinarily powerful. Mass spectrometry, array based protein methods and single cell imaging methods have combined to give us rich data of all the expressed proteins of the cell, 'its proteome'. While the technology is still developing rapidly, and 'data collection' efforts are just gathering steam, the focus of this meeting will be on applications of proteomics to problem solving in molecular cell biology as well as in molecular medicine. Bioinformatics methods to keep track of the wealth of data and beginning efforts to integrate disparate large-scale data sets will also be highlighted. Another emerging area in bioinformatics and systems biology is the building of models of whole cells.
View Scholarships/Awards
Proteomics has emerged as a key discipline in the post-genomic 'tool chest' and over the last few years, proteomics technology has become extraordinarily powerful. Mass spectrometry, array based protein methods and single cell imaging methods have combined to give us rich data of all the expressed proteins of the cell, 'its proteome'. While the technology is still developing rapidly, and 'data collection' efforts are just gathering steam, the focus of this meeting will be on applications of proteomics to problem solving in molecular cell biology as well as in molecular medicine. Bioinformatics methods to keep track of the wealth of data and beginning efforts to integrate disparate large-scale data sets will also be highlighted. Another emerging area in bioinformatics and systems biology is the building of models of whole cells.
View Scholarships/Awards
No registration fees are used to fund entertainment or alcohol at this conference
FRIDAY, APRIL 8
SATURDAY, APRIL 9
SUNDAY, APRIL 10
MONDAY, APRIL 11
TUESDAY, APRIL 12
WEDNESDAY, APRIL 13
Conference Program Print | View meeting in 12 hr (am/pm) time
FRIDAY, APRIL 8
19:30—20:30
Keynote Address (Joint)
Meeting has ended...abstracts no longer viewable online.
Marc W. Kirschner,
Harvard Medical School, USA
Specificity and Timing in the Cell Cycle: A Kinetic and Proteomic Exploration
Specificity and Timing in the Cell Cycle: A Kinetic and Proteomic Exploration
08:00—11:15
Mapping and Analyzing Networks I (Joint)
Meeting has ended...abstracts no longer viewable online.
*
Anne-Claude Gavin,
European Molecular Biology Laboratory, Germany
Global Interaction Networks Probed by Mass Spectrometry
Global Interaction Networks Probed by Mass Spectrometry
Matthias Mann,
Max Planck Institute of Biochemistry, Germany
Global Elucidation of Phosphorylation Dependent Protein-Protein Interactions
Global Elucidation of Phosphorylation Dependent Protein-Protein Interactions
Michael Tyers,
University of Montreal, Canada
Integration of Interaction Networks
Integration of Interaction Networks
Igor Stagljar,
University of Toronto, Canada
Short Talk: Large-Scale Analysis of Yeast and Human Integral Membrane Protein Interactions
Short Talk: Large-Scale Analysis of Yeast and Human Integral Membrane Protein Interactions
Ariel Jaimovich,
Hebrew University of Jerusalem, Israel
Short Talk: Towards an Integrated Probabilistic Protein-Protein Interaction Map
Short Talk: Towards an Integrated Probabilistic Protein-Protein Interaction Map
15:00—16:30
Workshop 1: Location, Location, Location: Mapping Phosphorylation
*
Forest M. White,
Massachusetts Institute of Technology, USA
Alejandro Wolf-Yadlin,
University of Washington, USA
Comparative Phosphotyrosine Proteomics of the EGFR, HER2 and HER3 Pathways
Comparative Phosphotyrosine Proteomics of the EGFR, HER2 and HER3 Pathways
Steen Gammeltoft,
Glostrup Hospital, University of Copenhagen, Denmark
Neural Network and Mass Spectrometry for Identification of Protein Kinase A Substrates Involved in Apoptosis
Neural Network and Mass Spectrometry for Identification of Protein Kinase A Substrates Involved in Apoptosis
Irina H. Kratchmarova,
University of Southern Denmark, Denmark
Quantitative Proteomics of EGF and PDGF Signaling Networks Reveals Controlling Mechanism of Mesenchymal Stem Cell Differentiation
Quantitative Proteomics of EGF and PDGF Signaling Networks Reveals Controlling Mechanism of Mesenchymal Stem Cell Differentiation
Hanno Steen,
Harvard Medical School, USA
Stable Isotope-Free Relative and Absolute Quantitation of Protein Phosphorylation Stoichiometry by Mass Spectrometry
Stable Isotope-Free Relative and Absolute Quantitation of Protein Phosphorylation Stoichiometry by Mass Spectrometry
17:00—19:00
Proteomics in an Array Format
Meeting has ended...abstracts no longer viewable online.
*
John J.M. Bergeron,
McGill University, Canada
Michael P. Snyder,
Stanford University School of Medicine, USA
Global Activity Mapping of Yeast Proteins
Global Activity Mapping of Yeast Proteins
Dolores J. Cahill,
Pfizer Inc., Ireland
Generation and Recent Applications of Protein and Antibody Arrays
Generation and Recent Applications of Protein and Antibody Arrays
Amy E. Keating,
Massachusetts Institute of Technology, USA
Short Talk: Combinatorial Associations of the Human bZIP Transcription Factors: Microarray Measurements and Computational Predictions
Short Talk: Combinatorial Associations of the Human bZIP Transcription Factors: Microarray Measurements and Computational Predictions
Viorica Lopez-Avila,
Agilent Technologies, Inc., USA
Short Talk: Focused-Proteomics Using Protein Microarrays
Short Talk: Focused-Proteomics Using Protein Microarrays
Erin N. Warren,
University of North Carolina at Chapel Hill, USA
Short Talk: A Novel MS-Based Peptide Chip Approach for Quantitating Expression and Modification Levels of Cancer-Related Proteins
Short Talk: A Novel MS-Based Peptide Chip Approach for Quantitating Expression and Modification Levels of Cancer-Related Proteins
17:00—19:00
Networks and Biology
Meeting has ended...abstracts no longer viewable online.
Debra S. Goldberg,
Harvard Medical School, USA
Short Talk: Topology Classification for Biological Networks
Short Talk: Topology Classification for Biological Networks
Réka Albert,
Pennsylvania State University, USA
Connecting Regulatory Network Topology and Dynamics
Connecting Regulatory Network Topology and Dynamics
Albert-László Barabási,
Northeastern University, USA
Network Biology: From the Metabolism to Protein Interactions
Network Biology: From the Metabolism to Protein Interactions
*
Pamela A. Silver,
Harvard Medical School, USA
Spatial Organizatin and Network Optimization in Eukaryotic Cells
Spatial Organizatin and Network Optimization in Eukaryotic Cells
08:00—11:15
Mapping and Analyzing Networks II (Joint)
Meeting has ended...abstracts no longer viewable online.
Catherine E. Costello,
Boston University School of Medicine, USA
Glycoproteomics
Glycoproteomics
Andrew Emili,
University of Toronto, Canada
Short Talk: Interaction Network of Conserved and Essential Protein Complexes in Escherichia coli
Short Talk: Interaction Network of Conserved and Essential Protein Complexes in Escherichia coli
Alan M. Moses,
University of Toronto, Canada
Short Talk: Models for Evolution of Simple Transcription Networks
Short Talk: Models for Evolution of Simple Transcription Networks
17:00—19:00
Visualizing the Proteome
Meeting has ended...abstracts no longer viewable online.
*
Catherine E. Costello,
Boston University School of Medicine, USA
Philippe Bastiaens,
European Molecular Biology Laboratory, Germany
Identification of Novel Proteins in Growth Factor Signaling by Functional Imaging on Cell Arrays
Identification of Novel Proteins in Growth Factor Signaling by Functional Imaging on Cell Arrays
Wolfgang P. Baumeister,
Max Planck Institute of Biochemistry, Germany
Exploring the Cellular Proteome by Cryo Electron Tomography
Exploring the Cellular Proteome by Cryo Electron Tomography
Carol V. Robinson,
University of Oxford, UK
Deciphering Multiprotein Complexes from the Cellular Environment
Deciphering Multiprotein Complexes from the Cellular Environment
Leonard J. Foster,
University of British Columbia, Canada
Short Talk: A Mammalian Organelle Map by Protein Correlation Profiling
Short Talk: A Mammalian Organelle Map by Protein Correlation Profiling
17:00—19:00
Modeling Networks
Meeting has ended...abstracts no longer viewable online.
*
Ravi Iyengar,
Mount Sinai Medical Center, USA
Modeling Signal Transduction Pathways
Modeling Signal Transduction Pathways
Luis Serrano,
European Molecular Biology Laboratory, Germany
Prediction of Protein-Protein Interaction Networks using Structural Information
Prediction of Protein-Protein Interaction Networks using Structural Information
Dana Pe'er,
Memorial Sloan Kettering Cancer Center, USA
Inferring Mammalian Signaling Pathways: A Multi-Level Approach
Inferring Mammalian Signaling Pathways: A Multi-Level Approach
Patrick McGrath,
Stanford University, USA
Short Talk: Bioinformatic Screen Identifies Two Regulatory Genes Controlling the Caulobacter Cell-Cycle
Short Talk: Bioinformatic Screen Identifies Two Regulatory Genes Controlling the Caulobacter Cell-Cycle
08:00—11:00
Proteomic Databases
Meeting has ended...abstracts no longer viewable online.
*
Leonard J. Foster,
University of British Columbia, Canada
Cathy H. Wu,
Georgetown University Medical Center, USA
UniProt and PIR Databases for Proteomic Bioinformatics
UniProt and PIR Databases for Proteomic Bioinformatics
Gianni Cesareni,
University of Rome Tor Vergata, Italy
Protein Interaction Domain Network in the MINT Database
Protein Interaction Domain Network in the MINT Database
Christopher Hogue,
University of Toronto, Canada
The Roadmap for the Biomolecular Interaction Network Database and its Related Tools to Enable Proteomics Research
The Roadmap for the Biomolecular Interaction Network Database and its Related Tools to Enable Proteomics Research
Kara Dolinski,
Princeton University, USA
Short Talk: Utilizing Bioinformatics Methods and Open Source Packages to Create Useful Functional Genomics Tools for the Research Community
Short Talk: Utilizing Bioinformatics Methods and Open Source Packages to Create Useful Functional Genomics Tools for the Research Community
Michael Hippler,
Plant Science Institute, USA
Short Talk: Digging into the Proteome of Chlamydomonas by Optimizing the Search of Mass Spectrometric Data in Genomic Databases
Short Talk: Digging into the Proteome of Chlamydomonas by Optimizing the Search of Mass Spectrometric Data in Genomic Databases
David P. Leader,
University of Glasgow, UK
Short Talk: The Protein Motif Database
Short Talk: The Protein Motif Database
08:00—11:00
Mapping and Analyzing Networks III
Meeting has ended...abstracts no longer viewable online.
Elizabeth A. Winzeler,
University of California, San Diego, USA
Systems Biology of Malaria
Systems Biology of Malaria
*
David K. Gifford,
Massachusetts Institute of Technology, USA
High Resolution Models of Genome Function
High Resolution Models of Genome Function
Peer Bork,
European Molecular Biology Laboratory, Germany
Comparative Genomics of Microbial Communities Reveals Environmental Features
Comparative Genomics of Microbial Communities Reveals Environmental Features
Maya R. Said,
Massachusetts Institute of Technology, USA
Short Talk: Global Network Analysis of Phenotypic Effects: Protein Networks and Toxicity Modulation in the Yeast Saccharomyces cerevisiae
Short Talk: Global Network Analysis of Phenotypic Effects: Protein Networks and Toxicity Modulation in the Yeast Saccharomyces cerevisiae
Kristin C. Gunsalus,
New York University, USA
Short Talk: Predictive Models of Molecular Machines Involved in C. elegans early embryogenesis
Short Talk: Predictive Models of Molecular Machines Involved in C. elegans early embryogenesis
15:00—16:30
Workshop 2: Protein IDS: How Certain do the Results Need to Be?
*
Roman A. Zubarev,
Karolinska Institutet, Sweden
Vanathi Gopalakrishnan,
University of Pittsburgh, USA
Proteomic Data Mining identifies Potential Biomarkers of Amyotrophic Lateral Sclerosis
Proteomic Data Mining identifies Potential Biomarkers of Amyotrophic Lateral Sclerosis
Joshua E. Elias,
Harvard Medical School, USA
Comparative Evaluation of Complementary MS/MS Analysis and Instrumentation Platforms
Comparative Evaluation of Complementary MS/MS Analysis and Instrumentation Platforms
Michael L. Nielsen,
Uppsala University, Sweden
Doubling the Number of Identified Proteins using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry On-line with nanoLC
Doubling the Number of Identified Proteins using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry On-line with nanoLC
Maria E. Warren,
University of North Carolina at Chapel Hill, USA
In-gel Digestion from Unstained Gels for Increased Confidence in Protein Identification
In-gel Digestion from Unstained Gels for Increased Confidence in Protein Identification
17:00—19:00
Protein Mapping
Meeting has ended...abstracts no longer viewable online.
Roman A. Zubarev,
Karolinska Institutet, Sweden
ECD FTMS for Complete Protein Primary Structure Determination of Proteins
ECD FTMS for Complete Protein Primary Structure Determination of Proteins
Forest M. White,
Massachusetts Institute of Technology, USA
Phosphoproteomic Analysis of Cellular Signaling
Phosphoproteomic Analysis of Cellular Signaling
John J.M. Bergeron,
McGill University, Canada
Proteomics of the Early Secretory Pathway
Proteomics of the Early Secretory Pathway
Sean A. Beausoleil,
Harvard Medical School, USA
Short Talk: Large-Scale, Automated Analysis of HeLa Cell Phosphoproteins
Short Talk: Large-Scale, Automated Analysis of HeLa Cell Phosphoproteins
17:00—19:00
Modeling Networks
Meeting has ended...abstracts no longer viewable online.
Charlie M. Boone,
University of Toronto, Canada
Global Mapping of the Yeast Genetic Interaction Network
Global Mapping of the Yeast Genetic Interaction Network
Hamid Bolouri,
Institute for Systems Biology, USA
Modeling the Response of Macrophages to Pathogens
Modeling the Response of Macrophages to Pathogens
Amoolya H. Singh,
University of California, Berkeley, USA
Short Talk: Evolution and Modularity of Gene Regulatory Networks in Bacteria
Short Talk: Evolution and Modularity of Gene Regulatory Networks in Bacteria
Eduardo D. Sontag,
Rutgers University, USA
Qualitative/Quantitative Analysis of a Class of Biological Networks
Qualitative/Quantitative Analysis of a Class of Biological Networks
08:00—09:20
Function and Dynamics of Networks
Meeting has ended...abstracts no longer viewable online.
*
Jennifer A. Lippincott-Schwartz,
Howard Hughes Medical Institute - Janelia Farm, USA
The Golgi Apparatus as a Two-Phase System for Protein Sorting and Transport
The Golgi Apparatus as a Two-Phase System for Protein Sorting and Transport
David M. Sabatini,
Whitehead Institute for Biomedical Research, USA
Deciphering Mammalian Signaling Networks
Deciphering Mammalian Signaling Networks
09:40—11:00
Proteomics for Clinical Diagnostics
Meeting has ended...abstracts no longer viewable online.
*
Ronald Hendrickson,
Memorial Sloan Kettering Cancer Center, USA
Catherine Fenselau,
, USA
Applications of Proteomics to Homeland Security: Rapid Analysis of Airborne Microorganisms
Applications of Proteomics to Homeland Security: Rapid Analysis of Airborne Microorganisms
Carol L. Nilsson,
Lund University, Sweden
Bacterial Proteomics and Vaccine Development
Bacterial Proteomics and Vaccine Development
Mahadevan Sethuraman,
Boston University School of Medicine, USA
Short Talk: Isotope-Coded Affinity Tag (ICAT) Approach to the Proteomic Identification and Quantitation of Oxidant-Sensitive Cysteine Thiols in Complex Protein Mixtures
Short Talk: Isotope-Coded Affinity Tag (ICAT) Approach to the Proteomic Identification and Quantitation of Oxidant-Sensitive Cysteine Thiols in Complex Protein Mixtures
Robert J. Cotter,
Johns Hopkins School of Medicine, USA
Short Talk: Special K: The Center for Networks and Pathways of Lysome Modification
Short Talk: Special K: The Center for Networks and Pathways of Lysome Modification
09:40—11:00
Function and Dynamics of Networks
Meeting has ended...abstracts no longer viewable online.
*
Jennifer A. Lippincott-Schwartz,
Howard Hughes Medical Institute - Janelia Farm, USA
Edward M. Marcotte,
University of Texas at Austin, USA
Dynamics of the Yeast Proteome and Metabolome
Dynamics of the Yeast Proteome and Metabolome
Mads Kaern,
Ottawa Institute of Systems Biology, University of Ottawa, Canada
Short Talk: Programming Cells by Interfacing Natural and Synthetic Gene Circuits
Short Talk: Programming Cells by Interfacing Natural and Synthetic Gene Circuits
A.J. Marian Walhout,
University of Massachusetts Medical School, USA
Short Talk: A C. elegans Transcription Regulatory Network of the Digestive Tract
Short Talk: A C. elegans Transcription Regulatory Network of the Digestive Tract
17:00—19:00
Quantitative Methods and Systems Biology
Meeting has ended...abstracts no longer viewable online.
Rudolf H. Aebersold,
Institute of Molecular Systems Biology, ETH Zürich, Switzerland
Quantitative Proteomics: An Essential Component of Systems Biology
Quantitative Proteomics: An Essential Component of Systems Biology
Dieter Oesterhelt,
Max Planck Institute of Biochemistry, Germany
A Quantitative Model of Archaeal Signal Transduction
A Quantitative Model of Archaeal Signal Transduction
Robert L. Hettich,
Oak Ridge National Laboratory, USA
Short Talk: Proteomics Measurements of a Natural Microbial Community Reveal Information about Community Structure and Metabolic Potential
Short Talk: Proteomics Measurements of a Natural Microbial Community Reveal Information about Community Structure and Metabolic Potential
Judith A. Jebanathirajah,
Harvard Medical School, USA
Short Talk: Directed Biomarkers: Phosphorylation Analysis of the Anaphase Promoting Complex in Response to Spindle Poisons and Cell Cycle Progression Using Mass Spectrometry
Short Talk: Directed Biomarkers: Phosphorylation Analysis of the Anaphase Promoting Complex in Response to Spindle Poisons and Cell Cycle Progression Using Mass Spectrometry
Cameron O. Scarlett,
University of North Carolina at Chapel Hill, USA
Short Talk: Modeling the In Vivo Subunit Assembly of a Multi-Component Protein Complex with Discrete Molecular Dynamics using Data from a Binary in Vitro Interaction Study and Crosslinking Combined with Mass Spectrometry
Short Talk: Modeling the In Vivo Subunit Assembly of a Multi-Component Protein Complex with Discrete Molecular Dynamics using Data from a Binary in Vitro Interaction Study and Crosslinking Combined with Mass Spectrometry
17:00—19:00
Cellular Networks
Meeting has ended...abstracts no longer viewable online.
*
Bernhard O. Palsson,
University of California, San Diego, USA
New 'Dimensions' in Genome Annotation
New 'Dimensions' in Genome Annotation
Ilya Shmulevich,
Institute for Systems Biology, USA
Are Eukaryotic Cells Dynamically Ordered, Critical, or Chaotic?
Are Eukaryotic Cells Dynamically Ordered, Critical, or Chaotic?
*Session Chair †Invited, not yet responded.
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