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This meeting took place in 2005



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Systems and Biology (X4)


Organizer(s) Marc Vidal, Albert-László Barabási and David M. Sabatini
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

Sponsored by Iconix Pharmaceuticals, Inc. and The Director's Fund


Summary of Meeting:
Biological processes can be considered as complex networks of interconnected components. Thus, to understand network properties involved in development and diseases, one should consider a "systems approach" that integrates global functional and imaging analyses, modeling and synthetic biology. The goal of this meeting is to integrate functional genomics, proteomics, and computational and systems biology to foster a "modular" understanding of biology.

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No registration fees are used to fund entertainment or alcohol at this conference

Conference Program    Print  |   View meeting in 12 hr (am/pm) time


FRIDAY, APRIL 8

15:00—19:30
Registration

Grays Peak Foyer
18:30—19:30
Refreshments

Longs Peak Foyer
19:30—20:30
Keynote Address (Joint)
Meeting has ended...abstracts no longer viewable online.

Longs Peak
Marc W. Kirschner, Harvard Medical School, USA
Specificity and Timing in the Cell Cycle: A Kinetic and Proteomic Exploration


SATURDAY, APRIL 9

07:00—08:00
Breakfast

Grays Peak
08:00—11:15
Mapping and Analyzing Networks I (Joint)
Meeting has ended...abstracts no longer viewable online.

Longs Peak
* Anne-Claude Gavin, European Molecular Biology Laboratory, Germany
Global Interaction Networks Probed by Mass Spectrometry

Marc Vidal, Dana-Farber Cancer Institute, USA
Interactome Networks

Matthias Mann, Max Planck Institute of Biochemistry, Germany
Global Elucidation of Phosphorylation Dependent Protein-Protein Interactions

Michael Tyers, University of Montreal, Canada
Integration of Interaction Networks

Igor Stagljar, University of Toronto, Canada
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

09:20—09:40
Coffee Break

Longs Peak Foyer
11:15—13:00
Poster Setup

Grays Peak
13:00—22:00
Poster Viewing

Grays Peak

Following Session is for Proteomics and Bioinformatics (X3)

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

Steen Gammeltoft, Glostrup Hospital, University of Copenhagen, Denmark
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

Hanno Steen, Harvard Medical School, USA
Stable Isotope-Free Relative and Absolute Quantitation of Protein Phosphorylation Stoichiometry by Mass Spectrometry

16:30—17:00
Coffee & Snacks Available

Longs Peak Foyer
17:00—19:00
Networks and Biology
Meeting has ended...abstracts no longer viewable online.

Longs Peak
Debra S. Goldberg, Harvard Medical School, USA
Short Talk: Topology Classification for Biological Networks

Réka Albert, Pennsylvania State University, USA
Connecting Regulatory Network Topology and Dynamics

Albert-László Barabási, Northeastern University, USA
Network Biology: From the Metabolism to Protein Interactions

* Pamela A. Silver, Harvard Medical School, USA
Spatial Organizatin and Network Optimization in Eukaryotic Cells


Following Session is for Proteomics and Bioinformatics (X3)

17:00—19:00
Proteomics in an Array Format
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* John J.M. Bergeron, McGill University, Canada

Michael P. Snyder, Stanford University School of Medicine, USA
Global Activity Mapping of Yeast Proteins

Dolores J. Cahill, Pfizer Inc., Ireland
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

Viorica Lopez-Avila, Agilent Technologies, Inc., USA
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

19:00—20:00
Social Hour

Grays Peak
19:30—22:00
Poster Session 1

Grays Peak

SUNDAY, APRIL 10

07:00—08:00
Breakfast

Grays Peak
08:00—11:15
Mapping and Analyzing Networks II (Joint)
Meeting has ended...abstracts no longer viewable online.

Longs Peak
Dalia Cohen, RNA Medicines Company, USA
Functional Genomics to New Drug Targets

Catherine E. Costello, Boston University School of Medicine, USA
Glycoproteomics

* Richard A. Young, Whitehead Institute for Biomedical Research, USA
Yeast Transcriptional Networks

Leroy E. Hood, Institute for Systems Biology, USA
Systems Approaches to Biology and Disease

Andrew Emili, University of Toronto, Canada
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

09:20—09:40
Coffee Break

Longs Peak Foyer
11:15—13:00
Poster Setup

Grays Peak
13:00—22:00
Poster Viewing

Grays Peak
16:30—17:00
Coffee & Snacks Available

Longs Peak Foyer
17:00—19:00
Modeling Networks
Meeting has ended...abstracts no longer viewable online.

Longs Peak
* Ravi Iyengar, Mount Sinai Medical Center, USA
Modeling Signal Transduction Pathways

Luis Serrano, European Molecular Biology Laboratory, Germany
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

Patrick McGrath, Stanford University, USA
Short Talk: Bioinformatic Screen Identifies Two Regulatory Genes Controlling the Caulobacter Cell-Cycle


Following Session is for Proteomics and Bioinformatics (X3)

17:00—19:00
Visualizing the Proteome
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* 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

Wolfgang P. Baumeister, Max Planck Institute of Biochemistry, Germany
Exploring the Cellular Proteome by Cryo Electron Tomography

Carol V. Robinson, University of Oxford, UK
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

19:00—20:00
Social Hour

Grays Peak
19:30—22:00
Poster Session 2

Grays Peak

MONDAY, APRIL 11

07:00—08:00
Breakfast

Grays Peak
08:00—11:00
Mapping and Analyzing Networks III
Meeting has ended...abstracts no longer viewable online.

Longs Peak
Elizabeth A. Winzeler, University of California, San Diego, USA
Systems Biology of Malaria

* David K. Gifford, Massachusetts Institute of Technology, USA
High Resolution Models of Genome Function

* Daphne Koller, Stanford University, USA
Extracting Protein Interaction Networks from Genomic Data

Peer Bork, European Molecular Biology Laboratory, Germany
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

Kristin C. Gunsalus, New York University, USA
Short Talk: Predictive Models of Molecular Machines Involved in C. elegans early embryogenesis


Following Session is for Proteomics and Bioinformatics (X3)

08:00—11:00
Proteomic Databases
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* Leonard J. Foster, University of British Columbia, Canada

Cathy H. Wu, Georgetown University Medical Center, USA
UniProt and PIR Databases for Proteomic Bioinformatics

Gianni Cesareni, University of Rome Tor Vergata, Italy
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

Kara Dolinski, Princeton University, USA
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

David P. Leader, University of Glasgow, UK
Short Talk: The Protein Motif Database

09:20—09:40
Coffee Break

Longs Peak Foyer
11:00—13:00
Poster Setup

Grays Peak
13:00—22:00
Poster Viewing

Grays Peak

Following Session is for Proteomics and Bioinformatics (X3)

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

Joshua E. Elias, Harvard Medical School, USA
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

Maria E. Warren, University of North Carolina at Chapel Hill, USA
In-gel Digestion from Unstained Gels for Increased Confidence in Protein Identification

16:30—17:00
Coffee & Snacks Available

Longs Peak Foyer
17:00—19:00
Modeling Networks
Meeting has ended...abstracts no longer viewable online.

Longs Peak
Charlie M. Boone, University of Toronto, Canada
Global Mapping of the Yeast Genetic Interaction Network

Hamid Bolouri, Institute for Systems Biology, USA
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

Eduardo D. Sontag, Rutgers University, USA
Qualitative/Quantitative Analysis of a Class of Biological Networks


Following Session is for Proteomics and Bioinformatics (X3)

17:00—19:00
Protein Mapping
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* Matthias Mann, Max Planck Institute of Biochemistry, Germany

Roman A. Zubarev, Karolinska Institutet, Sweden
ECD FTMS for Complete Protein Primary Structure Determination of Proteins

Forest M. White, Massachusetts Institute of Technology, USA
Phosphoproteomic Analysis of Cellular Signaling

John J.M. Bergeron, McGill University, Canada
Proteomics of the Early Secretory Pathway

Sean A. Beausoleil, Harvard Medical School, USA
Short Talk: Large-Scale, Automated Analysis of HeLa Cell Phosphoproteins

19:00—20:00
Social Hour

Grays Peak
19:30—22:00
Poster Session 3

Grays Peak

TUESDAY, APRIL 12

07:00—08:00
Breakfast

Grays Peak
08:00—09:20
Function and Dynamics of Networks
Meeting has ended...abstracts no longer viewable online.

Quandry Peak
* Jennifer A. Lippincott-Schwartz, Howard Hughes Medical Institute - Janelia Farm, USA
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

09:40—11:00
Function and Dynamics of Networks
Meeting has ended...abstracts no longer viewable online.

Longs Peak
* 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

Mads Kaern, Ottawa Institute of Systems Biology, University of Ottawa, Canada
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


Following Session is for Proteomics and Bioinformatics (X3)

09:40—11:00
Proteomics for Clinical Diagnostics
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* Ronald Hendrickson, Memorial Sloan Kettering Cancer Center, USA

Catherine Fenselau, , USA
Applications of Proteomics to Homeland Security: Rapid Analysis of Airborne Microorganisms

Carol L. Nilsson, Lund University, Sweden
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

Robert J. Cotter, Johns Hopkins School of Medicine, USA
Short Talk: Special K: The Center for Networks and Pathways of Lysome Modification

09:20—09:40
Coffee Break

Longs Peak Foyer
16:30—17:00
Coffee & Snacks Available

Longs Peak Foyer
17:00—19:00
Cellular Networks
Meeting has ended...abstracts no longer viewable online.

Longs Peak
* Bernhard O. Palsson, University of California, San Diego, USA
New 'Dimensions' in Genome Annotation

Stuart K. Kim, Stanford University Medical Center, USA
Transcriptional Networks

Ilya Shmulevich, Institute for Systems Biology, USA
Are Eukaryotic Cells Dynamically Ordered, Critical, or Chaotic?


Following Session is for Proteomics and Bioinformatics (X3)

17:00—19:00
Quantitative Methods and Systems Biology
Meeting has ended...abstracts no longer viewable online.

Quandary Peak
* Matthias Mann, Max Planck Institute of Biochemistry, Germany

Rudolf H. Aebersold, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
Quantitative Proteomics: An Essential Component of Systems Biology

Dieter Oesterhelt, Max Planck Institute of Biochemistry, Germany
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

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

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

19:00—20:00
Social Hour

Grays Peak
20:00—23:00
Entertainment

Grays Peak

WEDNESDAY, APRIL 13

 
Departure


*Session Chair †Invited, not yet responded.



We gratefully acknowledge support for this conference from:


Directors' Fund


These generous unrestricted gifts allow our Directors to schedule meetings in a wide variety of important areas, many of which are in the early stages of research.

Click here to view all of the donors who support the Directors' Fund.



We gratefully acknowledge the generous grant for this conference provided by:


National Institutes of Health

Grant No. 1R13-GM073377-01




We gratefully acknowledge additional support for this conference from:

Iconix Biosciences, Inc.

We gratefully acknowledge additional in-kind support for this conference from those foregoing speaker expense reimbursements:



Cellzome AG


Novartis Institutes for BioMedical Research


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Special thanks to the following for their support of Keystone Symposia initiatives to increase participation at this meeting by scientists from underrepresented backgrounds:


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Phone:+1 970-262-2690

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Phone:+1 970-262-2676