Frederick P. Roth, Ph.D. - Publications

Affiliations: 
2011- Molecular Genetics University of Toronto, Toronto, ON, Canada 
Area:
Computational Biology, Genomics
Website:
http://llama.mshri.on.ca/

106 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, ... ... Roth FP, et al. A framework for exhaustively mapping functional missense variants. Molecular Systems Biology. 13: 957. PMID 29269382  0.32
2017 Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. American Journal of Human Genetics. 101: 315-325. PMID 28886340 DOI: 10.1016/j.ajhg.2017.07.014  0.32
2017 Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N(1)-methyladenosine modification. Rna (New York, N.Y.). 23: 270-283. PMID 27994090 DOI: 10.1261/rna.059105.116  0.6
2016 Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, ... ... Roth FP, et al. An inter-species protein-protein interaction network across vast evolutionary distance. Molecular Systems Biology. 12: 865. PMID 27107014 DOI: 10.15252/msb.20156484  0.88
2016 Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld C, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, ... ... Roth FP, et al. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Research. PMID 26975778 DOI: 10.1101/gr.192526.115  0.88
2015 Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, et al. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell. PMID 26627737 DOI: 10.1016/j.cell.2015.11.015  0.88
2015 Petsalaki E, Helbig AO, Gopal A, Pasculescu A, Roth FP, Pawson T. SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. Nucleic Acids Research. PMID 25948583 DOI: 10.1093/nar/gkv459  0.88
2015 Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP. Protein domain-level landscape of cancer-type-specific somatic mutations. Plos Computational Biology. 11: e1004147. PMID 25794154 DOI: 10.1371/journal.pcbi.1004147  0.88
2015 Ta?an M, Musso G, Hao T, Vidal M, MacRae CA, Roth FP. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nature Methods. 12: 154-9. PMID 25532137 DOI: 10.1038/nmeth.3215  0.88
2014 Deo RC, Musso G, Tasan M, Tang P, Poon A, Yuan C, Felix JF, Vasan RS, Beroukhim R, De Marco T, Kwok PY, MacRae CA, Roth FP. Prioritizing causal disease genes using unbiased genomic features. Genome Biology. 15: 534. PMID 25633252 DOI: 10.1186/s13059-014-0534-8  0.88
2014 Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 159: 1511-23. PMID 25525873 DOI: 10.1016/j.cell.2014.11.035  0.88
2014 Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP, Cokol M. Target-independent prediction of drug synergies using only drug lipophilicity. Journal of Chemical Information and Modeling. 54: 2286-93. PMID 25026390 DOI: 10.1021/ci500276x  0.88
2014 Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, ... ... Roth FP, et al. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nature Communications. 5: 3650. PMID 24722188 DOI: 10.1038/ncomms4650  0.88
2014 Cokol M, Weinstein ZB, Yilancioglu K, Tasan M, Doak A, Cansever D, Mutlu B, Li S, Rodriguez-Esteban R, Akhmedov M, Guvenek A, Cokol M, Cetiner S, Giaever G, Iossifov I, ... ... Roth FP, et al. Large-scale identification and analysis of suppressive drug interactions. Chemistry & Biology. 21: 541-51. PMID 24704506 DOI: 10.1016/j.chembiol.2014.02.012  0.88
2014 Musso G, Tasan M, Mosimann C, Beaver JE, Plovie E, Carr LA, Chua HN, Dunham J, Zuberi K, Rodriguez H, Morris Q, Zon L, Roth FP, MacRae CA. Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development (Cambridge, England). 141: 224-35. PMID 24346703 DOI: 10.1242/dev.099796  0.88
2013 Sunyaev SR, Roth FP. Systems biology and the analysis of genetic variation. Current Opinion in Genetics & Development. 23: 599-601. PMID 24291212 DOI: 10.1016/j.gde.2013.11.010  0.88
2013 Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, et al. Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Science Signaling. 6: ra38. PMID 23695164 DOI: 10.1126/scisignal.2003350  0.88
2013 Mahadevan K, Zhang H, Akef A, Cui XA, Gueroussov S, Cenik C, Roth FP, Palazzo AF. RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins. Plos Biology. 11: e1001545. PMID 23630457 DOI: 10.1371/journal.pbio.1001545  0.88
2013 Pak TR, Roth FP. ChromoZoom: a flexible, fluid, web-based genome browser. Bioinformatics (Oxford, England). 29: 384-6. PMID 23220575 DOI: 10.1093/bioinformatics/bts695  0.88
2013 Carvunis AR, Roth FP, Calderwood MA, Cusick ME, Superti-Furga G, Vidal M. Interactome Networks Handbook of Systems Biology. 45-63. DOI: 10.1016/B978-0-12-385944-0.00003-4  0.88
2012 Suzuki Y, Stam J, Novotny M, Yachie N, Lasken RS, Roth FP. The green monster process for the generation of yeast strains carrying multiple gene deletions. Journal of Visualized Experiments : Jove. e4072. PMID 23271437 DOI: 10.3791/4072  0.88
2012 Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ. Introns in UTRs: why we should stop ignoring them. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 34: 1025-34. PMID 23108796 DOI: 10.1002/bies.201200073  0.6
2012 Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, ... ... Roth FP, et al. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 487: 491-5. PMID 22810586 DOI: 10.1038/nature11288  0.32
2012 Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, ... ... Roth FP, et al. Viral perturbations of host networks reflect disease etiology. Plos Computational Biology. 8: e1002531. PMID 22761553 DOI: 10.1371/journal.pcbi.1002531  0.88
2012 Cheng E, Vaisica JA, Ou J, Baryshnikova A, Lu Y, Roth FP, Brown GW. Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae. Genetics. 192: 147-60. PMID 22673806 DOI: 10.1534/genetics.112.141051  0.88
2012 Derti A, Roth FP. 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. 34: 576-7. PMID 22467222 DOI: 10.1002/bies.201200023  0.88
2012 Ta?an M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP. A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda, Md.). 2: 223-33. PMID 22384401 DOI: 10.1534/g3.111.000828  0.88
2011 Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP. Systematic exploration of synergistic drug pairs. Molecular Systems Biology. 7: 544. PMID 22068327 DOI: 10.1038/msb.2011.71  0.88
2011 Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, ... ... Roth FP, et al. Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science (New York, N.Y.). 333: 596-601. PMID 21798943 DOI: 10.1126/science.1203659  0.88
2011 Chua HN, Roth FP. Discovering the targets of drugs via computational systems biology. The Journal of Biological Chemistry. 286: 23653-8. PMID 21566122 DOI: 10.1074/jbc.R110.174797  0.88
2011 Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP. Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. Plos Genetics. 7: e1001366. PMID 21533221 DOI: 10.1371/journal.pgen.1001366  0.6
2011 Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, ... Roth FP, et al. Next-generation sequencing to generate interactome datasets. Nature Methods. 8: 478-80. PMID 21516116 DOI: 10.1038/nmeth.1597  0.88
2011 Suk K, Choi J, Suzuki Y, Ozturk SB, Mellor JC, Wong KH, MacKay JL, Gregory RI, Roth FP. Reconstitution of human RNA interference in budding yeast. Nucleic Acids Research. 39: e43. PMID 21252293 DOI: 10.1093/nar/gkq1321  0.88
2011 Suzuki Y, St Onge RP, Mani R, King OD, Heilbut A, Labunskyy VM, Chen W, Pham L, Zhang LV, Tong AH, Nislow C, Giaever G, Gladyshev VN, Vidal M, Schow P, ... ... Roth FP, et al. Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nature Methods. 8: 159-64. PMID 21217751 DOI: 10.1038/nmeth.1550  0.88
2011 Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. The Journal of Biological Chemistry. 286: 1204-15. PMID 21051541 DOI: 10.1074/jbc.M110.190884  0.6
2010 Yan H, Venkatesan K, Beaver JE, Klitgord N, Yildirim MA, Hao T, Hill DE, Cusick ME, Perrimon N, Roth FP, Vidal M. A genome-wide gene function prediction resource for Drosophila melanogaster. Plos One. 5: e12139. PMID 20711346 DOI: 10.1371/journal.pone.0012139  0.88
2010 Lewis GD, Farrell L, Wood MJ, Martinovic M, Arany Z, Rowe GC, Souza A, Cheng S, McCabe EL, Yang E, Shi X, Deo R, Roth FP, Asnani A, Rhee EP, et al. Metabolic signatures of exercise in human plasma. Science Translational Medicine. 2: 33ra37. PMID 20505214 DOI: 10.1126/scitranslmed.3001006  0.88
2010 Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP. FuncBase: a resource for quantitative gene function annotation. Bioinformatics (Oxford, England). 26: 1806-7. PMID 20495000 DOI: 10.1093/bioinformatics/btq265  0.88
2010 Derti A, Cenik C, Kraft P, Roth FP. Absence of evidence for MHC-dependent mate selection within HapMap populations. Plos Genetics. 6: e1000925. PMID 20442868 DOI: 10.1371/journal.pgen.1000925  0.88
2010 Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5' untranslated region introns. Genome Biology. 11: R29. PMID 20222956 DOI: 10.1186/gb-2010-11-3-r29  0.88
2010 Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth JR. The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics. 185: 65-80. PMID 20215473 DOI: 10.1534/genetics.110.114074  0.88
2010 Deo RC, Hunter L, Lewis GD, Pare G, Vasan RS, Chasman D, Wang TJ, Gerszten RE, Roth FP. Interpreting metabolomic profiles using unbiased pathway models. Plos Computational Biology. 6: e1000692. PMID 20195502 DOI: 10.1371/journal.pcbi.1000692  0.88
2010 Jurak I, Kramer MF, Mellor JC, van Lint AL, Roth FP, Knipe DM, Coen DM. Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. Journal of Virology. 84: 4659-72. PMID 20181707 DOI: 10.1128/JVI.02725-09  0.88
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Roth FP, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/science.1180823  0.88
2009 Deo RC, Roth FP. Pathways of the heart. Circulation. Cardiovascular Genetics. 2: 303-5. PMID 20031600 DOI: 10.1161/CIRCGENETICS.109.892588  0.88
2009 Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, et al. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Research. 19: 2334-42. PMID 19801531 DOI: 10.1101/gr.098640.109  0.88
2009 Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics (Oxford, England). 25: 3043-4. PMID 19717575 DOI: 10.1093/bioinformatics/btp498  0.88
2009 Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, Nislow C. Quantitative phenotyping via deep barcode sequencing. Genome Research. 19: 1836-42. PMID 19622793 DOI: 10.1101/gr.093955.109  0.88
2009 Roth FP, Lipshitz HD, Andrews BJ. Q&A: epistasis. Journal of Biology. 8: 35. PMID 19486505 DOI: 10.1186/jbiol144  0.88
2009 Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, ... ... Roth FP, et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods. 6: 47-54. PMID 19123269 DOI: 10.1038/nmeth.1279  0.88
2009 Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, ... Roth FP, et al. Literature-curated protein interaction datasets. Nature Methods. 6: 39-46. PMID 19116613 DOI: 10.1038/nmeth.1284  0.88
2009 Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, ... ... Roth FP, et al. An empirical framework for binary interactome mapping. Nature Methods. 6: 83-90. PMID 19060904 DOI: 10.1038/nmeth.1280  0.88
2009 Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, ... ... Roth FP, et al. An experimentally derived confidence score for binary protein-protein interactions. Nature Methods. 6: 91-7. PMID 19060903 DOI: 10.1038/nmeth.1281  0.88
2008 Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJ. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes & Development. 22: 2535-49. PMID 18794350 DOI: 10.1101/gad.1678608  0.88
2008 Klekota J, Roth FP. Chemical substructures that enrich for biological activity. Bioinformatics (Oxford, England). 24: 2518-25. PMID 18784118 DOI: 10.1093/bioinformatics/btn479  0.88
2008 Lewis GD, Wei R, Liu E, Yang E, Shi X, Martinovic M, Farrell L, Asnani A, Cyrille M, Ramanathan A, Shaham O, Berriz G, Lowry PA, Palacios IF, Ta?an M, ... Roth FP, et al. Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. The Journal of Clinical Investigation. 118: 3503-12. PMID 18769631 DOI: 10.1172/JCI35111  0.88
2008 Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, ... ... Roth FP, et al. High-quality binary protein interaction map of the yeast interactome network. Science (New York, N.Y.). 322: 104-10. PMID 18719252 DOI: 10.1126/science.1158684  0.88
2008 Berriz GF, Roth FP. The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics (Oxford, England). 24: 2272-3. PMID 18697767 DOI: 10.1093/bioinformatics/btn424  0.88
2008 Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, ... ... Roth FP, et al. A protein domain-based interactome network for C. elegans early embryogenesis. Cell. 134: 534-45. PMID 18692475 DOI: 10.1016/j.cell.2008.07.009  0.88
2008 TaÅŸan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP. An en masse phenotype and function prediction system for Mus musculus. Genome Biology. 9: S8. PMID 18613952 DOI: 10.1186/gb-2008-9-s1-s8  0.88
2008 Tian W, Zhang LV, TaÅŸan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology. 9: S7. PMID 18613951 DOI: 10.1186/gb-2008-9-s1-s7  0.88
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Roth FP, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/gb-2008-9-s1-s2  0.88
2008 Hughes TR, Roth FP. A race through the maze of genomic evidence. Genome Biology. 9: S1. PMID 18613945 DOI: 10.1186/gb-2008-9-s1-s1  0.88
2008 Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D, Tusneem N, Smith DR, Cusick ME, Hill DE, Roth FP, et al. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature Methods. 5: 597-600. PMID 18552854 DOI: 10.1038/nmeth.1224  0.88
2008 Gerszten RE, Accurso F, Bernard GR, Caprioli RM, Klee EW, Klee GG, Kullo I, Laguna TA, Roth FP, Sabatine M, Srinivas P, Wang TJ, Ware LB. 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. 295: L16-22. PMID 18456800 DOI: 10.1152/ajplung.00044.2008  0.88
2008 Mani R, St Onge RP, Hartman JL, Giaever G, Roth FP. Defining genetic interaction. Proceedings of the National Academy of Sciences of the United States of America. 105: 3461-6. PMID 18305163 DOI: 10.1073/pnas.0712255105  0.88
2007 Komili S, Farny NG, Roth FP, Silver PA. Functional specificity among ribosomal proteins regulates gene expression. Cell. 131: 557-71. PMID 17981122 DOI: 10.1016/j.cell.2007.08.037  0.88
2007 Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, Vidal M. Confirmation of organized modularity in the yeast interactome. Plos Biology. 5: e153. PMID 17564493 DOI: 10.1371/journal.pbio.0050153  0.88
2007 Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, ... ... Roth FP, et al. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nature Biotechnology. 25: 663-8. PMID 17486083 DOI: 10.1038/nbt1305  0.88
2007 Komili S, Roth FP. Genetic interaction screens advance in reverse. Genes & Development. 21: 137-42. PMID 17234880 DOI: 10.1101/gad.1512707  0.88
2007 St Onge RP, Mani R, Oh J, Proctor M, Fung E, Davis RW, Nislow C, Roth FP, Giaever G. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nature Genetics. 39: 199-206. PMID 17206143 DOI: 10.1038/ng1948  0.88
2007 Huang H, Zhang LV, Roth FP, Bader JS. Probabilistic paths for protein complex inference Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4532: 14-28.  0.88
2006 Derti A, Roth FP, Church GM, Wu CT. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nature Genetics. 38: 1216-20. PMID 16998490 DOI: 10.1038/ng1888  0.88
2006 Suzuki Y, Roth FP. Systematic genetics swims forward elegantly. Molecular Systems Biology. 2: 48. PMID 16969340 DOI: 10.1038/msb4100092  0.88
2006 Klekota J, Brauner E, Roth FP, Schreiber SL. Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects. Journal of Chemical Information and Modeling. 46: 1549-62. PMID 16859287 DOI: 10.1021/ci050495h  0.88
2006 Klekota J, Roth FP, Schreiber SL. Query Chem: a Google-powered web search combining text and chemical structures. Bioinformatics (Oxford, England). 22: 1670-3. PMID 16672261 DOI: 10.1093/bioinformatics/btl155  0.88
2005 Sabatine MS, Liu E, Morrow DA, Heller E, McCarroll R, Wiegand R, Berriz GF, Roth FP, Gerszten RE. Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation. 112: 3868-75. PMID 16344383 DOI: 10.1161/CIRCULATIONAHA.105.569137  0.88
2005 Gibbons FD, Proft M, Struhl K, Roth FP. Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biology. 6: R96. PMID 16277751 DOI: 10.1186/gb-2005-6-11-r96  0.88
2005 Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, ... ... Roth FP, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature. 437: 1173-8. PMID 16189514 DOI: 10.1038/nature04209  0.88
2005 Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sönnichsen B, Echeverri CJ, ... Roth FP, et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature. 436: 861-5. PMID 16094371 DOI: 10.1038/nature03876  0.88
2005 Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K. Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryotic Cell. 4: 1343-52. PMID 16087739 DOI: 10.1128/EC.4.8.1343-1352.2005  0.88
2005 Wong SL, Roth FP. Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae. Genetics. 171: 829-33. PMID 15998714 DOI: 10.1534/genetics.105.046060  0.88
2005 Wong SL, Zhang LV, Roth FP. Discovering functional relationships: biochemistry versus genetics. Trends in Genetics : Tig. 21: 424-7. PMID 15982781 DOI: 10.1016/j.tig.2005.06.006  0.88
2005 Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. Journal of Biology. 4: 6. PMID 15982408 DOI: 10.1186/jbiol23  0.88
2004 Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth FP. Combining biological networks to predict genetic interactions. Proceedings of the National Academy of Sciences of the United States of America. 101: 15682-7. PMID 15496468 DOI: 10.1073/pnas.0406614101  0.88
2004 Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 430: 88-93. PMID 15190252 DOI: 10.1038/nature02555  0.88
2004 Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics (Oxford, England). 20: 2738-50. PMID 15145800 DOI: 10.1093/bioinformatics/bth320  0.88
2004 Gibbons FD, Elias JE, Gygi SP, Roth FP. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Journal of the American Society For Mass Spectrometry. 15: 910-2. PMID 15144981 DOI: 10.1016/j.jasms.2004.02.011  0.88
2004 Asthana S, King OD, Gibbons FD, Roth FP. Predicting protein complex membership using probabilistic network reliability. Genome Research. 14: 1170-5. PMID 15140827 DOI: 10.1101/gr.2203804  0.88
2004 Zhang LV, Wong SL, King OD, Roth FP. Predicting co-complexed protein pairs using genomic and proteomic data integration. Bmc Bioinformatics. 5: 38. PMID 15090078 DOI: 10.1186/1471-2105-5-38  0.88
2004 Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, ... ... Roth FP, et al. Global mapping of the yeast genetic interaction network. Science (New York, N.Y.). 303: 808-13. PMID 14764870 DOI: 10.1126/science.1091317  0.88
2004 Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology. 22: 214-9. PMID 14730315 DOI: 10.1038/nbt930  0.88
2004 Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, ... ... Roth FP, et al. A map of the interactome network of the metazoan C. elegans. Science (New York, N.Y.). 303: 540-3. PMID 14704431 DOI: 10.1126/science.1091403  0.88
2003 Cairns J, Foster PL. The risk of lethals for hypermutating bacteria in stationary phase. Genetics. 165: 2317-8; author reply. PMID 14738105  0.88
2003 Berriz GF, King OD, Bryant B, Sander C, Roth FP. Characterizing gene sets with FuncAssociate. Bioinformatics (Oxford, England). 19: 2502-4. PMID 14668247 DOI: 10.1093/bioinformatics/btg363  0.88
2003 King OD, Roth FP. A non-parametric model for transcription factor binding sites. Nucleic Acids Research. 31: e116. PMID 14500844  0.88
2003 Kramer MF, Cook WJ, Roth FP, Zhu J, Holman H, Knipe DM, Coen DM. Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression. Journal of Virology. 77: 9533-41. PMID 12915567 DOI: 10.1128/JVI.77.17.9533-9541.2003  0.88
2003 King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP. Predicting phenotype from patterns of annotation. Bioinformatics (Oxford, England). 19: i183-9. PMID 12855456  0.88
2003 Roth JR, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI. Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics. 163: 1483-96. PMID 12702691  0.88
2003 King OD, Foulger RE, Dwight SS, White JV, Roth FP. Predicting gene function from patterns of annotation. Genome Research. 13: 896-904. PMID 12695322 DOI: 10.1101/gr.440803  0.88
2003 Berriz GF, White JV, King OD, Roth FP. GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics (Oxford, England). 19: 788-9. PMID 12691998 DOI: 10.1093/bioinformatics/btg088  0.88
2003 Goldberg DS, Roth FP. Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences of the United States of America. 100: 4372-6. PMID 12676999 DOI: 10.1073/pnas.0735871100  0.88
2002 Gibbons FD, Roth FP. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Research. 12: 1574-81. PMID 12368250 DOI: 10.1101/gr.397002  0.88
2002 Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Molecular Cell. 9: 563-73. PMID 11931764 DOI: 10.1016/S1097-2765(02)00475-6  0.88
2001 Roth FP. Bringing out the best features of expression data. Genome Research. 11: 1801-2. PMID 11691842 DOI: 10.1101/gr.215501  0.88
1998 Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology. 16: 939-45. PMID 9788350 DOI: 10.1038/nbt1098-939  0.88
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