Keystone Symposia | Scientific Conferences on Biomedical and Life Science Topics

Biomolecular Interaction Networks: Function and Disease (C1)

Organizer(s): Anna Panchenko, Teresa Przytycka and Andrea Califano
March 7 - 12, 2010
Fairmont Le Château Frontenac · Québec, QC
Abstract Deadline: November 9, 2009
Late Abstract Deadline: December 7, 2009
Scholarship Deadline: November 9, 2009
Early Registration Deadline: January 7, 2010

Supported by The Directors' Fund

This meeting took place in the 2010 season.

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see our meeting list, or search for a meeting.

Summary of Meeting
The aim of this symposium is to bring together researchers from different fields of computational and experimental biology, to discuss the use of biomolecular interaction networks to study cell function in both physiological and pathological contexts. These interaction maps, also known as interactomes, model protein-protein, protein-DNA and protein-small molecule interaction networks either within an organism or within specific cellular contexts. The function of proteins, nucleic acids, and other biomolecules can only be defined through their interactions in vivo. Such biochemical interactions – including those involved in signal transduction, transcriptional and translational regulation, as well as in the assembly of large molecular complexes – are astonishing in their magnitude and diversity. For instance, it has been shown that most proteins interact with multiple partners, forming intricate interaction networks. Similarly, individual transcription factor can bind to tens of thousands of genomic sites and regulate the expression of thousands of genes, both in isolation and in combinatorial fashion. Regulatory interactions play a key role in determining cellular differentiation, in maintaining cellular and organism homeostasis, and in triggering abnormal differentiation events leading to human disease including cancer. Not surprisingly, even slight genetic and epigenetic perturbations of these regulatory pathways can trigger macroscopic changes in normal cell physiology and lead to disease. Due to the abundance of experimental data, researchers are starting to uncover some general rules and principles underlying molecular interaction networks: their topological properties, the relationships between their components, evolutionary conservation and divergence, and their role in maintaining specific cellular functions and processes. Despite significant advances, however, knowledge about the distinct functional roles of many proteins is still elusive. Thus, interaction networks have emerged as exceedingly useful tools in predicting context-specific molecular function based on knowledge of upstream regulators, cognate binding partners, and downstream regulated targets. Furthermore, molecular interaction networks are starting to provide a unique integrative context to study additional disease-related genetic and epigenetic data, including single nucleotide mutations and polymorphisms, gene copy number alterations and complex, polygenic diseases.

Sunday, March 7
3:00 - 7:30 PM	Registration	Vercheres
3:00 - 7:30 PM	Refreshments	Vercheres
Monday, March 8
7:00 - 8:00 AM	Breakfast	Frontenac
8:00 - 11:15 AM	Experimental Identification, Characterization and Verification of Interaction Data This session will describe different experimental techniques of biomolecular interaction identification, will discuss the main promises and pitfalls of different methods and present several approaches to verify and validate the diverse experimental data.	Salle de Bal
	* Ruth Nussinov, National Cancer Institute and Tel Aviv University
	Anne-Claude Gavin, European Molecular Biology Laboratory Biomolecular Networks from Proteins to Small Molecules
	Nevan J. Krogan, University of California, San Francisco Functional Insights from Protein-Protein and Genetic Interaction Maps
	Douglas A. Lauffenburger, Massachusetts Institute of Technology Integrated Experimental and Computational Approaches to Dissect Cell Response to Stimuli
	Aimee Dudley, Institute for Systems Biology Systems Genetics Approaches to Complex Traits and Non-linear Interactions
	Sebastian Kühner, European Molecular Biology Laboratory - EMBL Short Talk: Proteome Organization in a Genome-Reduced Bacterium
	Curtis Huttenhower, Harvard School of Public Health Short Talk: Computational Methodology for Microbial and Metagenomic Characterization using Large Scale Functional Genomic Data Integration
9:20 - 9:40 AM	Coffee Break	Salle de Bal Foyer
11:15 AM -	On Own for Lunch and Recreation
11:15 AM - 1:00 PM	Poster Setup	Salle de Bal
1:00 - 10:00 PM	Poster Viewing	Salle de Bal
4:30 - 5:00 PM	Coffee Available	Vercheres
5:00 - 7:00 PM	Biomolecular Network Architecture and Biological Function of the Cell This session will focus on the characterization of dynamic and functional properties of regulatory and signaling networks. In particular, speakers will discuss genomic and genetic components of transcriptional networks in yeast and human, with a particular emphasis on the perturbations of regulatory networks leading to disease phenotypes.	Salle de Bal
	* Ivan Ovcharenko, National Institutes of Health
	Edward M. Marcotte, University of Texas at Austin Linking Genes to Traits Using Network-Guided Genetics
	Shoshana Wodak, Hospital for Sick Children, Research Institute Modularity of the Transcriptional Regulation of Protein Complexes in Yeast
	Hunter B. Fraser, Stanford University Widespread Adaptive Evolution of Gene Expression


	Raja Jothi, NIEHS, National Institutes of Health Short Talk: Genomic Analysis Reveals a Tight Link between Transcription Factor Dynamics and Regulatory Network Architecture
7:00 - 8:00 PM	Social Hour w/ Lite Bites	Salle de Bal Foyer
7:30 - 10:00 PM	Poster Session 1	Salle de Bal
Tuesday, March 9
7:00 - 8:00 AM	Breakfast	Frontenac
8:00 - 11:15 AM	General Principles of Molecular Recognition and Binding Specificity This session will highlight the principles of protein recognition, the properties of interaction interfaces in relation to diseases. In particular, it will highlight the recent analyses on specific sequence and structural features of interaction interfaces and discuss the mechanisms of regulation of protein activity and binding selectivity through conformational selection and intrinsic disorder.	Salle de Bal
	* Anna Panchenko, National Center for Biotechnology Information, NIH
	Ruth Nussinov, National Cancer Institute and Tel Aviv University Protein-Protein Interactions: What is the Preferred Way for Proteins to Interact?
	Barry Honig, Columbia University / HHMI On the Nature of Protein Fold Space: Extracting Functional Information from Apparently Remote Structural Neighbors
	Madan Babu Mohan, University of Cambridge Intrinsically Unstructured Proteins: Regulation and Disease
	Anna Tramontano, University of Rome, La Sapienza Antibody Structure Prediction: Implications and Applications
	Brian Joughin, Massachusetts Institute of Technology Short Talk: Examination of the Interpositional Dependence of Kinase Specificity on Substrate Sequence
	Maricel G. Kann, University of Maryland Short Talk: Using Correlated Evolution of Interacting Protein Domains to Predict their Interactions
9:20 - 9:40 AM	Coffee Break	Vercheres
11:15 AM -	On Own for Lunch and Recreation
11:15 AM - 1:00 PM	Poster Setup	Salle de Bal
1:00 - 10:00 PM	Poster Viewing	Salle de Bal
4:30 - 5:00 PM	Coffee Available	Vercheres
5:00 - 7:00 PM	From Molecular Interaction Networks to Function Prediction This session will focus on inferring and characterizing cellular functions and functional moonlighting within the context of different types of interactions, and will underline computational methods to predict protein interactions and protein function.	Salle de Bal
	* Edward M. Marcotte, University of Texas at Austin
	Mona Singh, Princeton University Analyzing and Interrogating Protein Interaction Maps via Network Schemas
	Alfonso Valencia, Spanish National Cancer Research Centre Coevolutionary Information in the Prediction of Global Interactomes and Interaction Regions

	Michael Cusick, Dana-Farber Cancer Institute Interactome Networks: The Next Decade
	Saikat Chakrabarti, Indian Institute of Chemical Biology Short Talk: Connecting the Functional Dots in Coevolutionary Networks
7:00 - 8:00 PM	Social Hour w/ Lite Bites	Salle de Bal Foyer
7:30 - 10:00 PM	Poster Session 2	Salle de Bal
Wednesday, March 10
7:00 - 8:00 AM	Breakfast	Frontenac
8:00 - 11:15 AM	Disease Interactome: Disease-Associated Genes, Disease Mutations and Protein Interactions This session will highlight the approach to link disease networks with the experimental biomolecular interaction networks, predict disease associated genes, and elucidate the role of polymorphisms in the manifestation of different diseases.	Salle de Bal
	* Dana Pe'er, Columbia University
	Andrea Califano, Columbia University A Molecular Interaction Networks Elucidates Master Regulators of the Mesenchymal Transformation of High-Grade Glioma
	Aviv Bergman, Albert Einstein College of Medicine Evolutionary Capacitance as a General Feature of Complex Gene Networks

	Teresa M. Przytycka, NCBI, NLM, National Institutes of Health Gene Regulation in the Context of Variations in DNA Sequence and Structure; Relation to Diseases
	Olga G. Troyanskaya, Princeton University From Integrated Functional Networks to Understanding Disease
	Christina S. Leslie, Memorial Sloan-Kettering Cancer Center Short Talk: Inferring Transcriptional and microRNA-mediated Regulatory Programs in Glioblastoma
	Richard Notebaart, Radboud University Nijmegen Medical Centre Short Talk: Function and Evolution of Asymmetric Protein Associations
9:20 - 9:40 AM	Coffee Break	Vercheres
11:15 AM -	On Own for Lunch and Recreation
4:30 - 5:00 PM	Coffee Available	Vercheres
5:00 - 7:00 PM	Evolution of Biomolecular Networks This session will give an overview of recent achievements in comparative analysis of protein-protein and protein-DNA interactions in different organisms, their evolutionary conservation (protein-protein interologs and protein-DNA regulogs), evolution of protein binding patterns.	Salle de Bal
	* Shoshana Wodak, Hospital for Sick Children, Research Institute
	Trey G. Ideker, University of California, San Diego Comparative Analysis of Protein Networks
	Anna Panchenko, National Center for Biotechnology Information, NIH Protein Complexes: Evolution and Intrinsic Disorder
	Sarah Teichmann, MRC Laboratory of Molecular Biology Evolution and Assembly of Homomeric Protein Complexes
	Emmanuel D. Levy, Universite de Montreal Short Talk: Are all Protein-Protein Interactions Functional? Lessons from Evolution
7:00 - 8:00 PM	Social Hour w/ Lite Bites	Salle de Bal Foyer
Thursday, March 11
7:00 - 8:00 AM	Breakfast	Frontenac
8:00 - 11:15 AM	Linking Regulatory Networks to Cellular Function This session focuses on systems approaches to indentify, predict and analyze signal transduction networks in general and posttranslational modification networks in particular.	Salle de Bal
	* Hunter B. Fraser, Stanford University
	Tony Pawson, Samuel Lunenfeld Research Institute Proteomic Analysis of Bidirectional Signaling Networks

	Gustavo Stolovitzky, IBM Systems Biology of Small and Large Scale Gene Regulatory Networks
	Eric H. Davidson, California Institute of Technology Evolutionary Plasticity of Developmental Gene Regulatory Network Architecture
	Yitzhak Pilpel, Weizmann Institute of Science Adaptive Prediction of Environmental Changes by Microorganisms
	Mark D. Biggin, Lawrence Berkeley National Laboratory Short Talk: Evidence for Quantitative Transcription Networks
	Sarath Chandra Janga, MRC Laboratory of Molecular Biology Short Talk: Dissecting the Expression Dynamics of RNA-Binding Proteins in Posttranscriptional Regulatory Networks
9:20 - 9:40 AM	Coffee Break	Vercheres
11:15 AM -	On Own for Lunch and Recreation
4:30 - 5:00 PM	Coffee Available	Vercheres
5:00 - 7:00 PM	Regulatory Networks and Genetic Polymorphism This session will focus on the use of transcript abundances as quantitative traits. In particular, the speakers will focus on study of expression polymorphism in combination with other system biology approaches to delineate transcriptional mechanism and elucidate the role of disease genes.	Salle de Bal
	* Teresa M. Przytycka, NCBI, NLM, National Institutes of Health

	Ivan Ovcharenko, National Institutes of Health Genome-Wide Discovery of Human Heart Enhancers
	Dana Pe'er, Columbia University Driving Mutations: Lessons from Yeast and Cancer
	Rachel B. Brem, University of California, Berkeley Models of Speciation and Adaptation in Fungi

	Gregory Hannum, University of California, San Diego Short Talk: Genome-Wide Association Data Reveal a Global Map of Genetic Interactions Amongst Protein Complexes
7:00 - 8:00 PM	Social Hour w/ Lite Bites	Jacques Cartier
8:00 - 11:00 PM	Entertainment	Jacques Cartier
Friday, March 12
	Departure

*Session Chair †Speaker invited, not yet responded.