La Jolla Cove  

In partnership with the International Society for Computational Biology(ISCB)

DECEMBER 1 - 3, 2006

University of California,
San Diego

 
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Systems Biology, Dec 1 - 2, 2006
Computational Proteomics, Dec 2-3, 2006

Friday, DEC 1, 2006
SYSTEMS BIOLOGY: REGULATORY NETWORKS

8:00a - 9:00a Registration & Continental Breakfast
9:00a - 9:15a Introductory remarks: Trey Ideker,  Bioengineering, UCSD
9:15a - 10:00a Invited Speaker: Eric Davidson, CalTech, "Experimental System Analysis of the Genomic Regulatory Code for Embryonic Development"
10:00a - 10:45a Invited Speaker: Martha Bulyk, Harvard Medical School, "Genomic Analyses of Transcription Factors and Cis Regulatory Elements"
10:45a - 11:15a Break/ Networking opportunities
11:15a - 11:35a Accepted paper: David Orlando, Charles Lin, Allister Bernard, Edwin S. Iversen, Alexander J. Hartemink, and Steven B. Haase, "A Probabilistic Model for Cell Cycle Distributions in Synchrony Experiments"
11:35a - 11:55a Accepted paper: Tomer Shlomi, Yariv Eisenberg, Roded Sharan, and Eytan Ruppin, "A Genome-Scale Computational Study of the Interplay between Transcriptional Regulation and Metabolism"
11:55a - 12:40p Invited Speaker: Daphne Koller, Stanford University, "Genetic Variation and Regulatory Networks: Mechanisms and Complexity"
12:40p - 2:00p Lunch/ Networking opportunities
2:00p - 2:05p Mona D. Lee, Research Development Officer, Industry-University Cooperative Research Program, UC Discovery, "Current and emerging grant opportunities through the UC Discovery program"
2:05p - 2:25p
Accepted paper: Celine Lefebvre, Wei K. Lim, Katia Basso, Riccardo D. Favera, and Andrea Califano, "A Context-specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells"
2.25p - 2:45p Accepted paper: Chun Ye, Matthew A. Zapala, Hyun Min Kang, Jennifer Wessel, Eleazar Eskin, and Nicholas Schork, "High-Density QTL Mapping to Identify Phenotypes and Loci Influencing Gene Expression Patterns in Entire Biochemical Pathways"
2:45p - 3:30p Invited Speaker: Bing Ren, UCSD, "Decoding the human genome - a chip-chip approach"
3:30p - 4:00p Break/ Networking opportunities
4:00p - 4:20p Accepted paper: Xuefeng Zhou, Guandong Wang, and Weixiong Zhang, "UV-B Responsive MicroRNA Genes in Arabidopsis thaliana"
4:20p - 4:40p Accepted paper: Rachel P. McCord, Michael F. Berger, Anthony A. Philippakis, and Martha L. Bulyk, "Inferring Condition-specific Transcription Factor Function"
4:40p - 5:25p Invited Speaker: Ron Shamir, Tel Aviv University, "Modeling and expansion of signaling pathways"
5:25p - 7:00p Poster session/ Reception

Saturday, DEC 2, 2006
PROTEIN INTERACTIONS

8:30a - 9:00a Continental Breakfast
9:00a - 9:15a Introductory remarks: Steven Briggs, UCSD
9:15a - 10:00a Invited Speaker: Mark Gerstein,  Yale University, "Understanding Protein Function on a Genome-scale using Networks"
10:00a - 10:20a Accepted paper: Jianhua Ruan and Weixiong Zhang, "Identification and Evaluation of Functional Modules in Gene Co-expression Networks"
10.20a - 10.40a Accepted paper: Xin Lu, UCSD, "Inverse correlation of connectivity and modulation"
10:40a - 11:15a Break/ Networking opportunities
11:15a - 11:35a
Accepted paper: Igor Ulitsky and Ron Shamir, "Pathway Redundancy and Protein Essentiality Revealed in the S. cerevisiae Interaction Networks"
11:35a - 11:55a
Accepted paper: Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, and Prahlad T. Ram, "De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis"
11:55p - 12:45p Invited Speaker: David Eisenberg, UCLA
12:45p - 2:20p Lunch/ Networking opportunities
2:20p - 3:05p Invited Speaker: Steven Briggs, UCSD, "Large-scale proteomics from plants to humans"
3:05p - 3:25p
Accepted paper: Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, and Cenk Sahinalp, "Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Netwok Emulation"
3:25p - 3:45p Accepted paper: Hailiang Huang, Lan V. Zhang, Frederick P. Roth, and Joel S. Bader "Probabilistic Paths in Protein Interaction Networks"
3:45p - 4:20p
Break/ Networking opportunities
4:20p - 4:40p
Accepted paper: Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, and Roded Sharan, "Structural Similarity is a Prominent Feature of Genetic Interactions"
4:45p - 5:30p Invited Speaker: Nevan Krogan, UCSF, "Genetic interactions reveal the functional relationships within and between protein complexes involved in chromosome biology"
6.30p Speaker and Program Committee only dinner

Sunday, DEC 3, 2006
MASS SPECTROMETRY

8:30a - 9:00a Continental Breakfast
9:00a - 9:15a Introductory remarks: Vineet Bafna, UCSD
9:15a - 10:00a Invited Speaker: Marshall Bern, Palo Alto Research Center, "Identification of Glycans and Glycopeptides using a mix of MS, MS/MS, and MS^n"
10:00a - 10:20a
Accepted paper: Nathan J Edwards, University of Maryland, "Novel Peptide Identification from Tandem Mass Spectra using Expressed Sequence Tags and Sequence Database Compression"
10:20a - 10.40a
Accepted paper: Anne-Katrin Emde, Lu-Yong Wang, Karin Noy, and Daniel Fasulo, "Alignment of Mass Spectrometry Data by Clique Finding and Optimization"
10:40a - 11:15a Break/ Networking opportunities
11:15a - 12:00p Invited Speaker: Forest White, MIT, "Quantitative Analysis of Cellular Signaling Network - Activity Relationships"
12:00p - 12:20p
Accepted paper: Mingzhou Song and Z. Lewis Liu, "A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast"
12:20p - 12:40p
Accepted paper: Jacob D. Feala, Laurence Coquin, Andrew D. McCulloch, and Giovanni Paternostro, "Flexibility in Energy Metabolism Supports Hypoxia Tolerance in Drosophila Flight Muscle: Metabolomic and Computational Systems Analysis"
12:40p - 2:00p Lunch/ Networking opportunities
2:00p - 2:20p
Accepted paper: Yin Wu, Yehia Mechref, Iveta Klouckova, Milos V. Novotny, and Haixu Tang, "A Computational Approach for the Identification of Site-specific Protein Glycosylations through Ion-Trap Mass Spectrometry"
2:20p - 2:40p
Accepted paper: Hans-Michael Kaltenbach, Sebastian Bocker, and Sven Rahmann, "Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting"
2:40p - 3:25p Invited Speaker: Richard Smith, Pacific Northwest National Laboratory
3:25p - 4:00p Break/ Networking opportunities
4:00p - 5:00p Panel Discussion, Chair: Parag Mallick, UCLA
5:00p - 5:30p Conference Closing Comments

 
 

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