| Time | Speaker | Org | Title |
|---|
| 8:30 | Registration | | |
| 9:00 | Peter Karp | SRI | [PPT] Welcome to the Conference |
| 9:05 | Barry Bochner | Biolog, Inc | [PDF] Overview of issues of cell phenotyping and cell modeling |
| 9:50 | Michael Ziman | Biolog, Inc | [PPT] Collection and analysis of phenotypic data using PM Software |
| 10:00 | Suzanne Paley | SRI | [PDF] Support for Phenotype Microarray Data in Pathway Tools |
| 10:20 | Coffee Break | | |
| 10:50 | Markus Goker | DSMZ | [PDF] OPM software: An R package for analyzing PM data |
| 11:20 | Joe Sturino | Texas A&M | [PDF] Adding power to metabolic studies: Novel statistical approaches for PM Phenotypic data |
| 11:40 | Marco Galardini | Department of Biology, University of Florence, Florence, Italy | [PDF] DuctApe: a tool for the analysis and correlation of genomic and high throughput phenotypic Biolog data |
| 12:00 | Lunch Break | | |
| Genome Analysis & Annotation | | |
| 1:00 | Marc Harper | UCLA | [PDF] Phenotype Sequencing: Identifying the Genes and Pathways That Cause a Phenotype using EcoCyc |
| 1:20 | Jim Tripp | JGI | [PPT] Automated gene annotation and assignment of function |
| 1:50 | Bas E. Dutilh | Radboud University Medical Centre | [PPT] Genome-wide association studies for microbial genomes |
| 2:10 | Eyal Akiva | UCSF | [PDF] Unraveling new protein functions and pathways using sequence similarity networks and genomic context information |
| 2:40 | Coffee Break | | |
| 3:10 | Marcin Joachimiak | LBNL | Deep surveys of biological modules: K-biclustering gene expression and phenotype data |
| 3:40 | Rob Edwards | San Diego State | Viral Dark Matter: Predicting the functions of unknown proteins |
| 4:00 | Francois Le Fevre | Genoscope | MicroScope, an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data |
| 4:20 | Steven Hallam | U British Columbia | [PPT] Pathway analysis of environmental metagenomes |
| 4:50 | Ado Van Assche | Scientia Terrae | Comparison of four Cupriavidus metallidurans strains using Phenotype MicroArray analysis |
| 5:10 | End of 1st Day |
| 6:30 | Conference Dinner | | |
| Time | Speaker | Org | Title |
|---|
| 8:30 | Rachel Brem | UC Berkeley | Genetic Dissection of Trait Variation in Fungal Populations |
| 9:00 | Jeremy Zucker | Broad Institute | [PPT] Mechanistic insights from the reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa |
| 9:30 | Corrado Nai | BAM, Berlin | [PDF] Characterization of a Rock-Inhabiting Microcolonial (Black) Fungus with the Biolog™: Restrictions, Solutions, Results |
| 9:40 | Markus Covert | Stanford University | A whole cell model of Mycoplasma genitalium |
| 10:10 | Coffee Break | | |
| 10:40 | Joy Scaria | Cornell University | Multi-Omics driven analysis of metabolic pathways in Clostridium difficile |
| 11:10 | Jonathan Monk | UCSD | [PDF] Comparison of multiple E. coli models reveals unique metabolic phenotypes |
| 11:40 | Matthew Oberhardt | Tel Aviv University | Towards culturing the unculturables |
| 12:00 | Lunch Break | | |
| Pathway Tools | | |
| 1:00 | Peter Karp | SRI | [PDF] Of MODS and Models: Predicting and Validating Phenotypes from Pathway Tools Metabolic Models |
| 1:30 | Suzanne Paley | SRI | [PPT] Expanded Representation of EC Numbers in Pathway Tools |
| 1:50 | Markus Krummenacker | SRI | [PDF] Glycans in Pathway Tools |
| 2:10 | Mario Latendresse | SRI | [PDF] Atom Mapping in MetaCyc and Pathway Tools |
| 2:30 | Amit Ghosh | LBNL | A peptide-based method for 13C metabolic flux analysis in microbial communities. |
| 2:50 | Coffee Break | | |
| 3:20 | Peter Krempl | ACIB - Austrian Centre of Industrial Biotechnology | [PDF] A sequence comparison and gene expression data integration add-on for the Pathway Tools software |
| 3:40 | Tomer Altman | Stanford University | [PDF] Statistical Computing with Pathway Tools using RCyc |
| 4:00 | Tomer Altman | Stanford University | [PDF] Data Mining the Human Microbiome using Pathway Tools |
| 4:20 | Peter Karp | SRI | [PDF] Web Groups -- Enhancements and Applications |
| 4:40 | End of 2nd Day |
| 5:00 - 6:30 | Reception |
| Time | Speaker | Org | Title |
|---|
| 8:30 | Barry Bochner | Biolog, inc. | Additional complexities of analyzing human cells |
| 8:50 | Luigi Boccuto | Greenwood Genetics | [PDF] Utilization of the Biolog Platform to Understand Neurodevelopmental Disorders |
| 9:20 | George I. Mias | Department of Genetics, Stanford | Integrative Personal Omics Profiling and Personalized Medicine |
| 9:50 | Leonid Chindelevitch | MIT | MONGOOSE - a new approach to metabolic network analysis |
| 10:20 | Coffee Break | | |
| 10:50 | Sriram Chandrasekaran | UIUC, Urbana | Predicting Cellular Phenotypes through Integrative Modeling of Genome scale Metabolic and Regulatory Networks |
| 11:10 | Bill Cannon | Pacific Northwest Lab | Modeling metabolism with simulations of state |
| 11:40 | Richard Baran | LBNL | [PDF] Mapping Microbial Metabolism using Metabolomics |
| 12:00 | Lunch Break | | |
| Yeast and Biofuels | | |
| 1:00 | Pablo Meyer | IBM Computational Biology Center, Yorktown Heights, NY, USA | Localized enzymes reflect cellular metabolic state |
| 1:30 | David Dill | Stanford University | Qualitative Analysis of the Yeast Metabolic Network |
| 2:00 | Kevin Correia | University of Toronto | [PPT] Elucidating the xylose metabolising properties of Scheffersomyces stipitis using a genome scale metabolic model |
| 2:30 | Ado Van Assche | Scientia Terrae | [PDF] Comparison of four Cupriavidus metallidurans strains using Phenotype MicroArray analysis |
| 2:50 | Coffee Break | | |
| 3:20 | Pablo Meyer | IBM | Open discussion: Pathway competition |
| 3:50 | Hector Garcia Martin | LBNL | Quantitative metabolic modeling for biofuel production at the Joint BioEnergy Institute |
| 4:20 | Kourosh Salehi-Ashtiani | New York University Abu Dhabi | Dynamic and Static Long-range Evolutionary Couplings in Chlamydomonas Metabolic Network |
| 4:50 | End of Conference |
Sponsored by E & J Gallo Winery
R&D Divisions