| Year |
Citation |
Score |
| 2023 |
van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Sheykhkarimli D, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, ... ... Roth FP, et al. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. American Journal of Human Genetics. PMID 37729906 DOI: 10.1016/j.ajhg.2023.08.012 |
0.765 |
|
| 2023 |
Tang HW, Spirohn K, Hu Y, Hao T, Kovács IA, Gao Y, Binari R, Yang-Zhou D, Wan KH, Bader JS, Balcha D, Bian W, Booth BW, Coté AG, de Rouck S, ... ... Roth FP, et al. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nature Communications. 14: 2162. PMID 37061542 DOI: 10.1038/s41467-023-37876-0 |
0.786 |
|
| 2022 |
Kim DK, Weller B, Lin CW, Sheykhkarimli D, Knapp JJ, Dugied G, Zanzoni A, Pons C, Tofaute MJ, Maseko SB, Spirohn K, Laval F, Lambourne L, Kishore N, Rayhan A, ... ... Roth FP, et al. A proteome-scale map of the SARS-CoV-2-human contactome. Nature Biotechnology. PMID 36217029 DOI: 10.1038/s41587-022-01475-z |
0.768 |
|
| 2022 |
Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annual Review of Genetics. PMID 36055970 DOI: 10.1146/annurev-genet-072920-032107 |
0.607 |
|
| 2020 |
van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, ... Roth FP, et al. Systematic analysis of bypass suppression of essential genes. Molecular Systems Biology. 16: e9828. PMID 32939983 DOI: 10.15252/Msb.20209828 |
0.388 |
|
| 2020 |
Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. Elife. 9. PMID 32870157 DOI: 10.7554/Elife.58026 |
0.305 |
|
| 2020 |
Kim DK, Knapp JJ, Kuang D, Chawla A, Cassonnet P, Lee H, Sheykhkarimli D, Samavarchi-Tehrani P, Abdouni H, Rayhan A, Li R, Pogoutse O, Coyaud É, van der Werf S, Demeret C, ... ... Roth FP, et al. A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions. G3 (Bethesda, Md.). PMID 32763951 DOI: 10.1534/G3.120.401554 |
0.751 |
|
| 2020 |
Kim JH, Seo Y, Jo M, Jeon H, Lee WH, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Yeast-Based Genetic Interaction Analysis of Human Kinome. Cells. 9. PMID 32392905 DOI: 10.3390/Cells9051156 |
0.363 |
|
| 2020 |
Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, ... ... Roth FP, et al. A reference map of the human binary protein interactome. Nature. 580: 402-408. PMID 32296183 DOI: 10.1038/S41586-020-2188-X |
0.791 |
|
| 2020 |
Kuang D, Weile J, Li R, Ouellette TW, Barber JA, Roth FP. MaveQuest: a web resource for planning experimental tests of human variant effects. Bioinformatics (Oxford, England). PMID 32251504 DOI: 10.1093/Bioinformatics/Btaa228 |
0.37 |
|
| 2020 |
Müller PM, Rademacher J, Bagshaw RD, Wortmann C, Barth C, van Unen J, Alp KM, Giudice G, Eccles RL, Heinrich LE, Pascual-Vargas P, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, ... ... Roth FP, et al. Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nature Cell Biology. PMID 32203420 DOI: 10.1038/S41556-020-0488-X |
0.313 |
|
| 2019 |
Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biology. 20: 223. PMID 31679514 DOI: 10.1186/S13059-019-1845-6 |
0.522 |
|
| 2019 |
Celaj A, Gebbia M, Musa L, Cote AG, Snider J, Wong V, Ko M, Fong T, Bansal P, Mellor JC, Seesankar G, Nguyen M, Zhou S, Wang L, Kishore N, ... ... Roth FP, et al. Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network. Cell Systems. PMID 31668799 DOI: 10.1016/J.Cels.2019.09.009 |
0.351 |
|
| 2019 |
Yang F, Kim DK, Nakagawa H, Hayashi S, Imoto S, Stein L, Roth FP. Quantifying immune-based counterselection of somatic mutations. Plos Genetics. 15: e1008227. PMID 31344031 DOI: 10.1371/Journal.Pgen.1008227 |
0.328 |
|
| 2019 |
Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, ... Roth FP, et al. Assessing predictions on fitness effects of missense variants in calmodulin. Human Mutation. PMID 31283071 DOI: 10.1002/Humu.23857 |
0.33 |
|
| 2019 |
Yingzhou W, Weile J, Cote A, Sun S, Knapp J, Verby M, Roth FP. A web application and service for imputing and visualizing missense variant effect maps. Bioinformatics (Oxford, England). PMID 30649215 DOI: 10.1093/Bioinformatics/Btz012 |
0.347 |
|
| 2018 |
Weile J, Roth FP. Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Human Genetics. PMID 30073413 DOI: 10.1007/S00439-018-1916-X |
0.376 |
|
| 2018 |
Díaz-Mejía JJ, Celaj A, Mellor JC, Coté A, Balint A, Ho B, Bansal P, Shaeri F, Gebbia M, Weile J, Verby M, Karkhanina A, Zhang Y, Wong C, Rich J, ... ... Roth FP, et al. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Molecular Systems Biology. 14: e7985. PMID 29807908 DOI: 10.15252/Msb.20177985 |
0.39 |
|
| 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 DOI: 10.15252/Msb.20177908 |
0.432 |
|
| 2017 |
Vigentini I, Gebbia M, Belotti A, Foschino R, Roth FP. CRISPR/Cas9 System as a Valuable Genome Editing Tool for Wine Yeasts with Application to Decrease Urea Production. Frontiers in Microbiology. 8: 2194. PMID 29163459 DOI: 10.3389/Fmicb.2017.02194 |
0.331 |
|
| 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 |
0.542 |
|
| 2017 |
Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV. Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. Human Mutation. 38: 1051-1063. PMID 28817247 DOI: 10.1002/Humu.23293 |
0.322 |
|
| 2017 |
Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, St Onge RP. Quantitative analysis of protein interaction network dynamics in yeast. Molecular Systems Biology. 13: 934. PMID 28705884 DOI: 10.15252/Msb.20177532 |
0.394 |
|
| 2017 |
Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC, Roth F, Suk K. Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target. Genome Research. PMID 28596290 DOI: 10.1101/Gr.211649.116 |
0.397 |
|
| 2017 |
Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, Roth FP. Identifying pathogenicity of human variants via paralog-based yeast complementation. Plos Genetics. 13: e1006779. PMID 28542158 DOI: 10.1371/Journal.Pgen.1006779 |
0.401 |
|
| 2017 |
Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB. Systematic identification of phosphorylation-mediated protein interaction switches. Plos Computational Biology. 13: e1005462. PMID 28346509 DOI: 10.1371/Journal.Pcbi.1005462 |
0.335 |
|
| 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 |
0.662 |
|
| 2016 |
van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, ... ... Roth FP, et al. Exploring genetic suppression interactions on a global scale. Science (New York, N.Y.). 354. PMID 27811238 DOI: 10.1126/Science.Aag0839 |
0.387 |
|
| 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 |
0.372 |
|
| 2016 |
Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, ... ... Roth FP, et al. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Molecular Systems Biology. 12: 863. PMID 27107012 DOI: 10.15252/Msb.20156660 |
0.784 |
|
| 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 |
0.386 |
|
| 2016 |
Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, ... ... Roth FP, et al. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 164: 805-817. PMID 26871637 DOI: 10.1016/J.Cell.2016.01.029 |
0.448 |
|
| 2016 |
Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, ... ... Roth FP, et al. A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell. 164: 310-323. PMID 26771498 DOI: 10.1016/J.Cell.2015.11.037 |
0.44 |
|
| 2016 |
Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, ... ... Roth FP, et al. Pooled-matrix protein interaction screens using Barcode Fusion Genetics Molecular Systems Biology. 12. DOI: 10.15252/msb.20156660 |
0.786 |
|
| 2016 |
Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, Macleod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Driks P, Sidhu S, Roth FP, Rissland OS, Durocher D, et al. Abstract PR03: High-resolution detection of fitness genes and genotype-specific cancer vulnerabilities with CRISPR-Cas9 screens Cancer Research. 76. DOI: 10.1158/1538-7445.Fbcr15-Pr03 |
0.387 |
|
| 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 |
0.37 |
|
| 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 |
0.304 |
|
| 2015 |
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, ... ... Roth FP, et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161: 647-60. PMID 25910212 DOI: 10.1016/J.Cell.2015.04.013 |
0.396 |
|
| 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 |
0.37 |
|
| 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 |
0.375 |
|
| 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 |
0.327 |
|
| 2014 |
Rolland T, TaÅŸan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, ... ... Roth FP, et al. A proteome-scale map of the human interactome network. Cell. 159: 1212-26. PMID 25416956 DOI: 10.1016/J.Cell.2014.10.050 |
0.402 |
|
| 2014 |
Labunskyy VM, Suzuki Y, Hanly TJ, Murao A, Roth FP, Gladyshev VN. The insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast. G3 (Bethesda, Md.). 4: 1183-91. PMID 24776987 DOI: 10.1534/G3.114.010868 |
0.378 |
|
| 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 |
0.392 |
|
| 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 |
0.376 |
|
| 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 |
0.419 |
|
| 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 |
0.391 |
|
| 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 |
0.656 |
|
| 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 |
0.321 |
|
| 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 |
0.368 |
|
| 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 |
0.371 |
|
| 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 |
0.382 |
|
| 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 |
0.331 |
|
| 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 |
0.364 |
|
| 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 |
0.394 |
|
| 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 |
0.336 |
|
| 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 |
0.667 |
|
| 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 |
0.399 |
|
| 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 |
0.34 |
|
| 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 |
0.375 |
|
| 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 |
0.343 |
|
| 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 |
0.301 |
|
| 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 |
0.38 |
|
| 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 |
0.401 |
|
| 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 |
0.412 |
|
| 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 |
0.351 |
|
| 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 |
0.365 |
|
| 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 |
0.439 |
|
| 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 |
0.385 |
|
| 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 |
0.388 |
|
| 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 |
0.404 |
|
| 2009 |
Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis A, Simonis N, Rual J, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, ... Roth FP, et al. Addendum: Literature-curated protein interaction datasets Nature Methods. 6: 934-935. DOI: 10.1038/Nmeth1209-934 |
0.356 |
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| 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 |
0.396 |
|
| 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 |
0.377 |
|
| 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 |
0.366 |
|
| 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 |
0.363 |
|
| 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 |
0.366 |
|
| 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 |
0.422 |
|
| 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 |
0.339 |
|
| 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 |
0.324 |
|
| 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 |
0.372 |
|
| 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 |
0.406 |
|
| 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 |
0.325 |
|
| 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 |
0.407 |
|
| 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 |
0.373 |
|
| 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 |
0.498 |
|
| 2006 |
Suzuki Y, Roth FP. Systematic genetics swims forward elegantly. Molecular Systems Biology. 2: 48. PMID 16969340 DOI: 10.1038/Msb4100092 |
0.393 |
|
| 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 |
0.309 |
|
| 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 |
0.431 |
|
| 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 |
0.398 |
|
| 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 |
0.346 |
|
| 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 |
0.339 |
|
| 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 |
0.414 |
|
| 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 |
0.352 |
|
| 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 |
0.437 |
|
| 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 |
0.41 |
|
| 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 |
0.65 |
|
| 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 |
0.345 |
|
| 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 |
0.411 |
|
| 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 |
0.554 |
|
| 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 |
0.41 |
|
| 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 |
0.502 |
|
| 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 DOI: 10.1093/Bioinformatics/Btg1024 |
0.706 |
|
| 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 |
0.356 |
|
| 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 |
0.36 |
|
| 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 |
0.319 |
|
| 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 |
0.765 |
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