Registration Information

Location: Atkinson Hall (Calit2 building)
FRIDAY, August 17, 2007
7:00–8:30 AM Breakfast and On-site Registration
10:15–10:30 AM Snacks
12:00–1:30 PM Lunch
3:15–3:30 PM Snacks
WS1 Alternative Splicing
WS2 Metagenomics
WS3 Systems Biology for Microbial Genomes
Understanding microbes through multifaceted functional genomics


WS1: Alternative Splicing

Alternative splicing (AS) generates multiple transcripts and protein products from a single eukaryotic gene. Genome-wide analyses have established the prevalence of alternative splicing in higher eukaryotes. Alternative splicing provides a major mechanism for regulation of gene function and has been implicated in a number of human diseases.

The study of alternative splicing has benefited tremendously from computational analyses of genomic data. The purpose of this CSB workshop is to cover latest results and challenges in genomic and bioinformatic analyses of alternative splicing. We hope to bring computational biologists and experimentalists together to this exciting field. This one-day workshop will consist of 8 talks (approximately 30 minutes each).

• Bafna, Vineet Ph.D.
Department of Computer Science, University of California, San Diego (UCSD)
"Proteogenomic annotation"

• Clark, Tyson, Ph.D.
"Discovery of tissue-specific exons using comprehensive human exon microarrays"

• Fu, Xiang-dong, Ph.D.
Department of Cellular & Molecular Medicine, University of California, San Diego (UCSD)
"Co-transcriptional regulation of alternative splicing in mammalian cells"

• Lee, Christopher, Ph.D.
Department of Biochemistry & Molecular Biology Institute, University of California, Los Angeles (UCLA)
"Alternative splicing and the evolution of exon duplications in insect DSCAM genes"

• Lee, Ji-Ann
Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles (UCLA)
"Genome-wide identification of splicing changes in response to neuronal depolarization"

• Xing, Yi, Ph.D.
Department of Internal Medicine, Carver College of Medicine & Department of Biomedical Engineering, University of Iowa
"Exon array analysis of gene expression"

• Xu, Ying, Ph.D.
Department of Biochemistry and Molecular Biology/Institute of Bioinformatics, University of Georgia
"Structural studies of alternatively spliced protein isoforms"

• Yeo, Gene, Ph.D.
Crick-Jacobs Center for Computational and Theoretical Biology, Salk Institute
"Discovery of intronic splicing regulatory elements"

Jun-tao Guo, University of Georgia, GA, USA
Yi Xing, University of Iowa, IA, USA

To register for this workshop, please go to CSB 2007 registration site

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WS2: Metagenomics

9:00-9:30 AM An Introduction to Metagenomics and CAMERA
Weizhong Li and Kayo Arima
9:30-10:00 AM CAMERA Architecture and OptlPortal
Mason Katz
10:00-10:30 AM Cave Demo, in Vis Lab
Jurgen Shulze
10:30-11:00 AM Coffee Break
11:00 AM-12:00 PM CAMERA website, Gemstone, CAMERA Labs Overview
Karan Bhatia and Sriram Krishnan
12:00-1:30 PM Lunch
1:30-2:15 PM Protein Family Clustering and GOS Data
Weizhong Li
2:15-3:15 PM Function Based Target Selection; SGeno - Mgeno Connections
Iddo Friedberg
3:15-3:30 PM Break
3:30-4:00 PM Community Collaborations via Wiki Technology: TOPSAN
Sri Krishna Subramaniam
4:00-4:30 PM TOPSAN, CAMERA - Continuing Dialogue
John Wooley, all speakers, attendees

Weizhong Li, University of California, San Diego
Iddo Friedberg, University of California, San Diego

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WS3: Systems Biology for Microbial Genomes
Understanding microbes through multifaceted functional genomics

As the world-wide efforts continue to make available a large amount of omics data, system biology has been gradually shaped as a field to study the interactions among components of biological systems, to address the causes and effects in biological networks through simultaneously measuring multiple components and rigorous data integration with mathematical models, and to integrate computational modeling, hypotheses formulation, experimental validation, and computational model refining.

We have invited scientists from leading research centers/laboratories to present their work in system biology, particularly for microbial genomes, which cover different aspects (reconstruction, modeling, analysis and simulation) of biological network studies using both experimental and computational techniques.

The workshop will also provide a platform for researchers from different disciplines to exchange visions, insights, ideas, and discoveries about the challenges and opportunities in the field of system biology, to share and appreciate research efforts that have been devoted to the field, to provide and seek advice/suggestion/solutions to some problems in the field, and to establish face-to-face collaboration.

Invited Speakers:
• Nitin S. Baliga
Institute for System Biology
Title: "A Predictive Model of Adaptive Responses to Environment"

All organisms routinely sense and process complex changes in their environment through a web of intricate information processing networks to adapt their behavior. Any attempt to predict these responses or re-engineer new ones would require a sophisticated and quantitative understanding of this entire process. Using a systems approach we have constructed a predictive model of the complete gene regulatory program in Halobacterium salinarum NRC-1, an archaeal microbe that thrives in a saturated salt environment that is lethal to most life forms. The architecture of this model reflects how diverse physiological processes are inter-coordinated during environmental responses and as such can now be used as a framework for characterizing and reengineering environmental response sub-circuits. This study promotes the idea that a systems approach can help to quickly unlock the potential of the already vast and increasing numbers of organisms with fully sequenced genomes.

• Frank Bergmann
Keck Graduate Institute / University of Washington
Title: The Systems Biology Workbench: A modular framework for Systems Biology

A large number of software packages are available to assist researchers in systems biology. In this talk, I describe the current state of the Systems Biology Workbench (SBW), a modular framework that connects modeling and analysis applications, enabling them to reuse each other’s capabilities. I describe how users and developers will perceive SBW and then focus on currently available SBW modules. There is a wide variety of SBW enabled applications available, such as modeling, bifurcation analysis, frequency analysis, deterministic and stochastic simulation, and 3D visualization.

The developer of a new software application can use these tools as a foundation instead of recreating existing functionality, which allows them to focus on novel tasks. An existing application written in any supported programming language (C/C++, Java, .NET, Python, Delphi/Kylix, Matlab and FORTRAN) can be modified to interact with SBW with minimal programming overhead. This enables other applications to use its functionality.

The software, tutorial manual, and test models are freely available from the Computational and Systems Biology group at University of Washington. Source code is available from Source Forge. The software is open source and licensed under BSD.

• Jason Chan
University of California - San Diego
Title: "Integrating genetic and physical relationships – our current understanding of the genetic model"

The rising influx of sequenced genomes and the need to understand how their functional components relate presents an interesting and unique logistic challenge. Increasing availability of data from large scale screens introduced both interesting systematic insights as well as increased levels of artifacts due to noise. Previously, we have applied homology across species to both filter protein-protein interactions as well as infer previously unreported protein-protein interactions. Work has also been done to reconcile our understanding of genetics with high throughput protein interaction data to form conceptualized "pathways." Here, we provide evidence for an interesting motif found between protein-protein interactions and synthetic lethal interactions within Saccharomyces cerevisiae. Unsurprisingly, interactions involving essential genes tend to be genetically antagonistic. I will describe our current efforts to predict physical protein interactions as well as our current efforts to understand how this "synthetic lethal" motif plays a role in our concept of 'pathways' within an organism, and its potential use for analysis across species.

• Eric Mjolsness
University of California - Irvine
Title: "A random steady state model for the activity of pyruvate dehydrogenase"

Pyruvate dehydrogenase is a key metabolic enzyme which occurs in a complex containing many copies of three enzymes E1, E2, and E3. These enzymes act in a reaction sequence. We hypothesized that an important function of their multiplicity in the complex is to mix E1, E2, and E3 in approximately the right proportions so as to maximize net flux through the sequence, despite the inevitable local imbalances in their number. To quantify this hypotheses we constructed a "random steady state" (RSS) model combining equilibrium statistical mechanics (at a slow time scale) with steady-state kinetics (at a faster time scale). This order inverts that of the more common "quasi-equilibrium" class of molecular complex activity models, in which equilibration happens on a fast time scale. We show results from the RSS model and compare to data on pyruvate dehydrogenase in E. coli.

• Bernhard O. Palsson
University of California - San Diego
Title: "Reconstruction of the genome-scale transcriptional regulatory network in E. coli"

High-density tiling arrays have been used to perform location analysis for three classes of DNA protein in E. coli and for high resolutions expression profiling. The protein examined are: 1) the RNA polymerase and sigma factors, 2) 12 broad acting transcription factors, and 3) 7 DNA bending protein. This data will be discussed and its representation in an R matrix form discussed. The computation of the functional state of the TRN are illustrated.

• Bruce E. Shapiro
Caltech and Cal State University
Title: "Designing Simulations for Portability and Reuse: The Systems Biology Markup Language"

The Systems Biology Markup Language (SBML) is a tool-neutral, computer-readable, text file (XML) format for representing models of biochemical reaction networks. It is especially applicable to descriptions of cell signaling pathways, metabolic networks, genomic regulatory networks, and other modeling problems in systems biology. SBML is based on XML (the eXtensible Markup Language), a standard medium for representing and transporting data that is widely supported on the Internet as well as in computational biology and bioinformatics. The central goal of SBML is model portability. By encoding models in SBML, they can be freely interchanged between users, regardless of which software tool, hardware platform, or operating system each uses. The benefits of this interoperability are enormous: models can be shared, standardized, and made survivable through databases. These benefits are enhanced through publication on the BioModels database, a peer-reviewed, curated database that utilizes SBML as one of its core file formats; the Systems Biology Ontology (SBO), a set of controlled vocabularies and ontologies for the kinds of problems faced by computational modelers in systems biology; and a number of open source tools provided by the website that facilitate incorporation of SBML into users' individual modeling software.

• Lingchong You
Duke University
Title: "Sensing and communication in natural and engineered bacteria"

Quorum sensing is a mechanism by which many bacteria sense and respond to changes in their density via production and detection of small, diffusible chemical signals. Since its initial discovery, quorum sensing has been found to be involved in regulating diverse cellular functions, including bioluminescence, antibiotic resistance, and biofilm formation. From an engineering perspective, quorum sensing provides an elegant strategy for bacteria to coordinate their behavior in a population. Here I will discuss our computational and experimental efforts to analyze dynamic properties of quorum sensing and its application for engineering gene circuits. Specifically, I will discuss how and to what extent quorum sensing may reduce noise in gene expression, how quorum sensing provides a means for a bacterium to "measure" the dimension of its microenvironment, and how, when coupled regulated cell killing, quorum sensing enables programming of roust population dynamics.

Jason Chan, University of California - San Diego
Hongwei Wu, University of Georgia
John Wooley, University of California - San Diego

To register for this workshop, please go to CSB 2007 registration site


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