PTools '13
E&J Gallo Sponsored by E & J Gallo Winery

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Please note that schedule is subject to change. Check back for updates

Mar 4th - Phenotype MicroArray Analysis

9:00Peter KarpSRI[PPT] Welcome to the Conference
9:05Barry BochnerBiolog, Inc[PDF] Overview of issues of cell phenotyping and cell modeling
9:50Michael ZimanBiolog, Inc[PPT] Collection and analysis of phenotypic data using PM Software
10:00Suzanne PaleySRI[PDF] Support for Phenotype Microarray Data in Pathway Tools
10:20Coffee Break
10:50Markus GokerDSMZ[PDF] OPM software: An R package for analyzing PM data
11:20Joe SturinoTexas A&M[PDF] Adding power to metabolic studies: Novel statistical approaches for PM Phenotypic data
11:40Marco GalardiniDepartment of Biology, University of Florence, Florence, Italy[PDF] DuctApe: a tool for the analysis and correlation of genomic and high throughput phenotypic Biolog data
12:00Lunch Break
Genome Analysis & Annotation
1:00Marc HarperUCLA[PDF] Phenotype Sequencing: Identifying the Genes and Pathways That Cause a Phenotype using EcoCyc
1:20Jim TrippJGI[PPT] Automated gene annotation and assignment of function
1:50Bas E. DutilhRadboud University Medical Centre[PPT] Genome-wide association studies for microbial genomes
2:10Eyal AkivaUCSF[PDF] Unraveling new protein functions and pathways using sequence similarity networks and genomic context information
2:40Coffee Break
3:10Marcin JoachimiakLBNLDeep surveys of biological modules: K-biclustering gene expression and phenotype data
3:40Rob EdwardsSan Diego StateViral Dark Matter: Predicting the functions of unknown proteins
4:00Francois Le FevreGenoscopeMicroScope, an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
4:20Steven HallamU British Columbia[PPT] Pathway analysis of environmental metagenomes
4:50Ado Van AsscheScientia TerraeComparison of four Cupriavidus metallidurans strains using Phenotype MicroArray analysis
5:10End of 1st Day
6:30Conference Dinner

Mar 5th - Analysis of Microbes

8:30Rachel BremUC BerkeleyGenetic Dissection of Trait Variation in Fungal Populations
9:00Jeremy ZuckerBroad Institute[PPT] Mechanistic insights from the reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa
9:30Corrado NaiBAM, Berlin[PDF] Characterization of a Rock-Inhabiting Microcolonial (Black) Fungus with the Biolog™: Restrictions, Solutions, Results
9:40Markus CovertStanford UniversityA whole cell model of Mycoplasma genitalium
10:10Coffee Break
10:40Joy ScariaCornell UniversityMulti-Omics driven analysis of metabolic pathways in Clostridium difficile
11:10Jonathan MonkUCSD[PDF] Comparison of multiple E. coli models reveals unique metabolic phenotypes
11:40Matthew OberhardtTel Aviv UniversityTowards culturing the unculturables
12:00Lunch Break
Pathway Tools
1:00Peter KarpSRI[PDF] Of MODS and Models: Predicting and Validating Phenotypes from Pathway Tools Metabolic Models
1:30Suzanne PaleySRI[PPT] Expanded Representation of EC Numbers in Pathway Tools
1:50Markus KrummenackerSRI[PDF] Glycans in Pathway Tools
2:10Mario LatendresseSRI[PDF] Atom Mapping in MetaCyc and Pathway Tools
2:30Amit GhoshLBNLA peptide-based method for 13C metabolic flux analysis in microbial communities.
2:50Coffee Break
3:20Peter KremplACIB - Austrian Centre of Industrial Biotechnology[PDF] A sequence comparison and gene expression data integration add-on for the Pathway Tools software
3:40Tomer AltmanStanford University[PDF] Statistical Computing with Pathway Tools using RCyc
4:00Tomer AltmanStanford University[PDF] Data Mining the Human Microbiome using Pathway Tools
4:20Peter KarpSRI[PDF] Web Groups -- Enhancements and Applications
4:40End of 2nd Day
5:00 - 6:30Reception

Mar 6th - Human Metabolism & Global Metabolism

8:30Barry BochnerBiolog, inc.Additional complexities of analyzing human cells
8:50Luigi BoccutoGreenwood Genetics[PDF] Utilization of the Biolog Platform to Understand Neurodevelopmental Disorders
9:20George I. MiasDepartment of Genetics, StanfordIntegrative Personal Omics Profiling and Personalized Medicine
9:50Leonid ChindelevitchMITMONGOOSE - a new approach to metabolic network analysis
10:20Coffee Break
10:50Sriram ChandrasekaranUIUC, UrbanaPredicting Cellular Phenotypes through Integrative Modeling of Genome scale Metabolic and Regulatory Networks
11:10Bill CannonPacific Northwest LabModeling metabolism with simulations of state
11:40Richard BaranLBNL[PDF] Mapping Microbial Metabolism using Metabolomics
12:00Lunch Break
Yeast and Biofuels
1:00Pablo MeyerIBM Computational Biology Center, Yorktown Heights, NY, USALocalized enzymes reflect cellular metabolic state
1:30David DillStanford UniversityQualitative Analysis of the Yeast Metabolic Network
2:00Kevin CorreiaUniversity of Toronto[PPT] Elucidating the xylose metabolising properties of Scheffersomyces stipitis using a genome scale metabolic model
2:30Ado Van AsscheScientia Terrae[PDF] Comparison of four Cupriavidus metallidurans strains using Phenotype MicroArray analysis
2:50Coffee Break
3:20Pablo MeyerIBMOpen discussion: Pathway competition
3:50Hector Garcia MartinLBNLQuantitative metabolic modeling for biofuel production at the Joint BioEnergy Institute
4:20Kourosh Salehi-AshtianiNew York University Abu DhabiDynamic and Static Long-range Evolutionary Couplings in Chlamydomonas Metabolic Network
4:50End of Conference

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