Frederick P. Roth Donnelly Centre & Department of Molecular Genetics University of Toronto Biography Publications Institution JoVE Articles Frederick P. Roth has not added a biography. If you are Frederick P. Roth and would like to personalize this page please email our Author Liaison for assistance. Publications ChromoZoom: a Flexible, Fluid, Web-based Genome Browser Bioinformatics (Oxford, England). Dec, 2012 | Pubmed ID: 23220575 Introns in UTRs: Why We Should Stop Ignoring Them BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Dec, 2012 | Pubmed ID: 23108796 Interpreting Cancer Genomes Using Systematic Host Network Perturbations by Tumour Virus Proteins Nature. Jul, 2012 | Pubmed ID: 22810586 Viral Perturbations of Host Networks Reflect Disease Etiology PLoS Computational Biology. 2012 | Pubmed ID: 22761553 Genome Rearrangements Caused by Depletion of Essential DNA Replication Proteins in Saccharomyces Cerevisiae Genetics. Sep, 2012 | Pubmed ID: 22673806 Response to "MHC-dependent Mate Choice in Humans: Why Genomic Patterns from the HapMap European American Data Set Support the Hypothesis". HapMap Genotypes Do Not Confidently Support a Role for the MHC Locus in Human Mate Selection BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Jul, 2012 | Pubmed ID: 22467222 A Resource of Quantitative Functional Annotation for Homo Sapiens Genes G3 (Bethesda, Md.). Feb, 2012 | Pubmed ID: 22384401 Personalized Medicine: from Genotypes and Molecular Phenotypes Towards Computed Therapy Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2012 | Pubmed ID: 22174287 Systematic Exploration of Synergistic Drug Pairs Molecular Systems Biology. 2011 | Pubmed ID: 22068327 Independently Evolved Virulence Effectors Converge Onto Hubs in a Plant Immune System Network Science (New York, N.Y.). Jul, 2011 | Pubmed ID: 21798943 Discovering the Targets of Drugs Via Computational Systems Biology The Journal of Biological Chemistry. Jul, 2011 | Pubmed ID: 21566122 Genome Analysis Reveals Interplay Between 5'UTR Introns and Nuclear MRNA Export for Secretory and Mitochondrial Genes PLoS Genetics. Apr, 2011 | Pubmed ID: 21533221 Next-generation Sequencing to Generate Interactome Datasets Nature Methods. Jun, 2011 | Pubmed ID: 21516116 Reconstitution of Human RNA Interference in Budding Yeast Nucleic Acids Research. Apr, 2011 | Pubmed ID: 21252293 Knocking out Multigene Redundancies Via Cycles of Sexual Assortment and Fluorescence Selection Nature Methods. Feb, 2011 | Pubmed ID: 21217751 Identification of Neuronal RNA Targets of TDP-43-containing Ribonucleoprotein Complexes The Journal of Biological Chemistry. Jan, 2011 | Pubmed ID: 21051541 A Genome-wide Gene Function Prediction Resource for Drosophila Melanogaster PloS One. 2010 | Pubmed ID: 20711346 Metabolic Signatures of Exercise in Human Plasma Science Translational Medicine. May, 2010 | Pubmed ID: 20505214 FuncBase: a Resource for Quantitative Gene Function Annotation Bioinformatics (Oxford, England). Jul, 2010 | Pubmed ID: 20495000 Absence of Evidence for MHC-dependent Mate Selection Within HapMap Populations PLoS Genetics. Apr, 2010 | Pubmed ID: 20442868 Genome-wide Functional Analysis of Human 5' Untranslated Region Introns Genome Biology. 2010 | Pubmed ID: 20222956 The Tandem Inversion Duplication in Salmonella Enterica: Selection Drives Unstable Precursors to Final Mutation Types Genetics. May, 2010 | Pubmed ID: 20215473 Interpreting Metabolomic Profiles Using Unbiased Pathway Models PLoS Computational Biology. Feb, 2010 | Pubmed ID: 20195502 Numerous Conserved and Divergent MicroRNAs Expressed by Herpes Simplex Viruses 1 and 2 Journal of Virology. May, 2010 | Pubmed ID: 20181707 The Genetic Landscape of a Cell Science (New York, N.Y.). Jan, 2010 | Pubmed ID: 20093466 Pathways of the Heart Circulation. Cardiovascular Genetics. Aug, 2009 | Pubmed ID: 20031600 Large-scale RACE Approach for Proactive Experimental Definition of C. Elegans ORFeome Genome Research. Dec, 2009 | Pubmed ID: 19801531 Next Generation Software for Functional Trend Analysis Bioinformatics (Oxford, England). Nov, 2009 | Pubmed ID: 19717575 Quantitative Phenotyping Via Deep Barcode Sequencing Genome Research. Oct, 2009 | Pubmed ID: 19622793 Q&A: Epistasis Journal of Biology. 2009 | Pubmed ID: 19486505 Empirically Controlled Mapping of the Caenorhabditis Elegans Protein-protein Interactome Network Nature Methods. Jan, 2009 | Pubmed ID: 19123269 Literature-curated Protein Interaction Datasets Nature Methods. Jan, 2009 | Pubmed ID: 19116613 An Empirical Framework for Binary Interactome Mapping Nature Methods. Jan, 2009 | Pubmed ID: 19060904 An Experimentally Derived Confidence Score for Binary Protein-protein Interactions Nature Methods. Jan, 2009 | Pubmed ID: 19060903 A C. Elegans Genome-scale MicroRNA Network Contains Composite Feedback Motifs with High Flux Capacity Genes & Development. Sep, 2008 | Pubmed ID: 18794350 Chemical Substructures That Enrich for Biological Activity Bioinformatics (Oxford, England). Nov, 2008 | Pubmed ID: 18784118 Metabolite Profiling of Blood from Individuals Undergoing Planned Myocardial Infarction Reveals Early Markers of Myocardial Injury The Journal of Clinical Investigation. Oct, 2008 | Pubmed ID: 18769631 High-quality Binary Protein Interaction Map of the Yeast Interactome Network Science (New York, N.Y.). Oct, 2008 | Pubmed ID: 18719252 The Synergizer Service for Translating Gene, Protein and Other Biological Identifiers Bioinformatics (Oxford, England). Oct, 2008 | Pubmed ID: 18697767 A Protein Domain-based Interactome Network for C. Elegans Early Embryogenesis Cell. Aug, 2008 | Pubmed ID: 18692475 An En Masse Phenotype and Function Prediction System for Mus Musculus Genome Biology. 2008 | Pubmed ID: 18613952 Combining Guilt-by-association and Guilt-by-profiling to Predict Saccharomyces Cerevisiae Gene Function Genome Biology. 2008 | Pubmed ID: 18613951 A Critical Assessment of Mus Musculus Gene Function Prediction Using Integrated Genomic Evidence Genome Biology. 2008 | Pubmed ID: 18613946 A Race Through the Maze of Genomic Evidence Genome Biology. 2008 | Pubmed ID: 18613945 Isoform Discovery by Targeted Cloning, 'deep-well' Pooling and Parallel Sequencing Nature Methods. Jul, 2008 | Pubmed ID: 18552854 Challenges in Translating Plasma Proteomics from Bench to Bedside: Update from the NHLBI Clinical Proteomics Programs American Journal of Physiology. Lung Cellular and Molecular Physiology. Jul, 2008 | Pubmed ID: 18456800 Defining Genetic Interaction Proceedings of the National Academy of Sciences of the United States of America. Mar, 2008 | Pubmed ID: 18305163 Functional Specificity Among Ribosomal Proteins Regulates Gene Expression Cell. Nov, 2007 | Pubmed ID: 17981122 Confirmation of Organized Modularity in the Yeast Interactome PLoS Biology. Jun, 2007 | Pubmed ID: 17564493 Genome-scale Analysis of in Vivo Spatiotemporal Promoter Activity in Caenorhabditis Elegans Nature Biotechnology. Jun, 2007 | Pubmed ID: 17486083 Genetic Interaction Screens Advance in Reverse Genes & Development. Jan, 2007 | Pubmed ID: 17234880 Systematic Pathway Analysis Using High-resolution Fitness Profiling of Combinatorial Gene Deletions Nature Genetics. Feb, 2007 | Pubmed ID: 17206143 Mammalian Ultraconserved Elements Are Strongly Depleted Among Segmental Duplications and Copy Number Variants Nature Genetics. Oct, 2006 | Pubmed ID: 16998490 Systematic Genetics Swims Forward Elegantly Molecular Systems Biology. 2006 | Pubmed ID: 16969340 Using High-throughput Screening Data to Discriminate Compounds with Single-target Effects from Those with Side Effects Journal of Chemical Information and Modeling. Jul-Aug, 2006 | Pubmed ID: 16859287 Query Chem: a Google-powered Web Search Combining Text and Chemical Structures Bioinformatics (Oxford, England). Jul, 2006 | Pubmed ID: 16672261 Metabolomic Identification of Novel Biomarkers of Myocardial Ischemia Circulation. Dec, 2005 | Pubmed ID: 16344383 Chipper: Discovering Transcription-factor Targets from Chromatin Immunoprecipitation Microarrays Using Variance Stabilization Genome Biology. 2005 | Pubmed ID: 16277751 Towards a Proteome-scale Map of the Human Protein-protein Interaction Network Nature. Oct, 2005 | Pubmed ID: 16189514 Predictive Models of Molecular Machines Involved in Caenorhabditis Elegans Early Embryogenesis Nature. Aug, 2005 | Pubmed ID: 16094371 Genomewide Identification of Sko1 Target Promoters Reveals a Regulatory Network That Operates in Response to Osmotic Stress in Saccharomyces Cerevisiae Eukaryotic Cell. Aug, 2005 | Pubmed ID: 16087739 Transcriptional Compensation for Gene Loss Plays a Minor Role in Maintaining Genetic Robustness in Saccharomyces Cerevisiae Genetics. Oct, 2005 | Pubmed ID: 15998714 Discovering Functional Relationships: Biochemistry Versus Genetics Trends in Genetics : TIG. Aug, 2005 | Pubmed ID: 15982781 Motifs, Themes and Thematic Maps of an Integrated Saccharomyces Cerevisiae Interaction Network Journal of Biology. 2005 | Pubmed ID: 15982408 Combining Biological Networks to Predict Genetic Interactions Proceedings of the National Academy of Sciences of the United States of America. Nov, 2004 | Pubmed ID: 15496468 Evidence for Dynamically Organized Modularity in the Yeast Protein-protein Interaction Network Nature. Jul, 2004 | Pubmed ID: 15190252 Prediction of Similarly Acting Cis-regulatory Modules by Subsequence Profiling and Comparative Genomics in Drosophila Melanogaster and D.pseudoobscura Bioinformatics (Oxford, England). Nov, 2004 | Pubmed ID: 15145800 SILVER Helps Assign Peptides to Tandem Mass Spectra Using Intensity-based Scoring Journal of the American Society for Mass Spectrometry. Jun, 2004 | Pubmed ID: 15144981 Predicting Protein Complex Membership Using Probabilistic Network Reliability Genome Research. Jun, 2004 | Pubmed ID: 15140827 Predicting Co-complexed Protein Pairs Using Genomic and Proteomic Data Integration BMC Bioinformatics. Apr, 2004 | Pubmed ID: 15090078 Global Mapping of the Yeast Genetic Interaction Network Science (New York, N.Y.). Feb, 2004 | Pubmed ID: 14764870 Intensity-based Protein Identification by Machine Learning from a Library of Tandem Mass Spectra Nature Biotechnology. Feb, 2004 | Pubmed ID: 14730315 A Map of the Interactome Network of the Metazoan C. Elegans Science (New York, N.Y.). Jan, 2004 | Pubmed ID: 14704431 Characterizing Gene Sets with FuncAssociate Bioinformatics (Oxford, England). Dec, 2003 | Pubmed ID: 14668247 A Non-parametric Model for Transcription Factor Binding Sites Nucleic Acids Research. Oct, 2003 | Pubmed ID: 14500844 Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression Journal of Virology. Sep, 2003 | Pubmed ID: 12915567 Predicting Phenotype from Patterns of Annotation Bioinformatics (Oxford, England). 2003 | Pubmed ID: 12855456 Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation Genetics. Apr, 2003 | Pubmed ID: 12702691 Predicting Gene Function from Patterns of Annotation Genome Research. May, 2003 | Pubmed ID: 12695322 GoFish Finds Genes with Combinations of Gene Ontology Attributes Bioinformatics (Oxford, England). Apr, 2003 | Pubmed ID: 12691998 Assessing Experimentally Derived Interactions in a Small World Proceedings of the National Academy of Sciences of the United States of America. Apr, 2003 | Pubmed ID: 12676999 Judging the Quality of Gene Expression-based Clustering Methods Using Gene Annotation Genome Research. Oct, 2002 | Pubmed ID: 12368250 The Genome-wide Localization of Rsc9, a Component of the RSC Chromatin-remodeling Complex, Changes in Response to Stress Molecular Cell. Mar, 2002 | Pubmed ID: 11931764 The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions Yo Suzuki1, Jason Stam1, Mark Novotny2, Nozomu Yachie3, Roger S. Lasken2, Frederick P. Roth3,4 1Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, 2Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 3Donnelly Centre & Department of Molecular Genetics, University of Toronto, 4Lunenfeld Research Institute, Mt Sinai Hospital JoVE 4072 Biology
The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions Yo Suzuki1, Jason Stam1, Mark Novotny2, Nozomu Yachie3, Roger S. Lasken2, Frederick P. Roth3,4 1Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, 2Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 3Donnelly Centre & Department of Molecular Genetics, University of Toronto, 4Lunenfeld Research Institute, Mt Sinai Hospital JoVE 4072 Biology
