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Items: 1 to 50 of 135

1.

Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas.

Weile J, Roth FP.

Hum Genet. 2018 Aug 2. doi: 10.1007/s00439-018-1916-x. [Epub ahead of print] Review.

PMID:
30073413
2.

The impact of oncogenic EGFRvIII on the proteome of extracellular vesicles released from glioblastoma cells.

Choi D, Montermini L, Kim DK, Meehan B, Roth FP, Rak J.

Mol Cell Proteomics. 2018 Jul 13. pii: mcp.RA118.000644. doi: 10.1074/mcp.RA118.000644. [Epub ahead of print]

3.

Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.

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, Prendergast D, Gupta G, Öztürk S, Durocher D, Brown GW, Roth FP.

Mol Syst Biol. 2018 May 28;14(5):e7985. doi: 10.15252/msb.20177985.

4.

A framework for exhaustively mapping functional missense variants.

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, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP.

Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908.

5.

CRISPR/Cas9 System as a Valuable Genome Editing Tool for Wine Yeasts with Application to Decrease Urea Production.

Vigentini I, Gebbia M, Belotti A, Foschino R, Roth FP.

Front Microbiol. 2017 Nov 9;8:2194. doi: 10.3389/fmicb.2017.02194. eCollection 2017.

6.

Variant Interpretation: Functional Assays to the Rescue.

Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM.

Am J Hum Genet. 2017 Sep 7;101(3):315-325. doi: 10.1016/j.ajhg.2017.07.014.

7.

Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.

Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV.

Hum Mutat. 2017 Sep;38(9):1051-1063. doi: 10.1002/humu.23293.

PMID:
28817247
8.

Quantitative analysis of protein interaction network dynamics in yeast.

Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, St Onge RP.

Mol Syst Biol. 2017 Jul 13;13(7):934. doi: 10.15252/msb.20177532.

9.

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target.

Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC, Roth FP, Suk K.

Genome Res. 2017 Sep;27(9):1487-1500. doi: 10.1101/gr.211649.116. Epub 2017 Jun 8.

10.

Identifying pathogenicity of human variants via paralog-based yeast complementation.

Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, Roth FP.

PLoS Genet. 2017 May 25;13(5):e1006779. doi: 10.1371/journal.pgen.1006779. eCollection 2017 May.

11.

Systematic identification of phosphorylation-mediated protein interaction switches.

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB.

PLoS Comput Biol. 2017 Mar 27;13(3):e1005462. doi: 10.1371/journal.pcbi.1005462. eCollection 2017 Mar.

12.

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP.

RNA. 2017 Mar;23(3):270-283. doi: 10.1261/rna.059105.116. Epub 2016 Dec 19.

13.

Exploring genetic suppression interactions on a global scale.

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, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C.

Science. 2016 Nov 4;354(6312). pii: aag0839.

14.

Taking Exception to Human Eugenics.

Roth FP, Wakeley J.

Genetics. 2016 Oct;204(2):821-823. No abstract available.

15.

Dual action antifungal small molecule modulates multidrug efflux and TOR signaling.

Shekhar-Guturja T, Gunaherath GM, Wijeratne EM, Lambert JP, Averette AF, Lee SC, Kim T, Bahn YS, Tripodi F, Ammar R, Döhl K, Niewola-Staszkowska K, Schmitt L, Loewith RJ, Roth FP, Sanglard D, Andes D, Nislow C, Coccetti P, Gingras AC, Heitman J, Gunatilaka AA, Cowen LE.

Nat Chem Biol. 2016 Oct;12(10):867-75. doi: 10.1038/nchembio.2165. Epub 2016 Aug 29.

16.

An inter-species protein-protein interaction network across vast evolutionary distance.

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, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

17.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

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, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP.

Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

18.

An extended set of yeast-based functional assays accurately identifies human disease mutations.

Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP.

Genome Res. 2016 May;26(5):670-80. doi: 10.1101/gr.192526.115. Epub 2016 Mar 14.

19.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

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, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

20.

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

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, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H.

Cell. 2016 Jan 14;164(1-2):310-323. doi: 10.1016/j.cell.2015.11.037.

21.

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

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, Durocher D, Angers S, Moffat J.

Cell. 2015 Dec 3;163(6):1515-26. doi: 10.1016/j.cell.2015.11.015. Epub 2015 Nov 25.

22.

SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets.

Petsalaki E, Helbig AO, Gopal A, Pasculescu A, Roth FP, Pawson T.

Nucleic Acids Res. 2015 Jul 1;43(W1):W276-82. doi: 10.1093/nar/gkv459. Epub 2015 May 6.

23.

Widespread macromolecular interaction perturbations in human genetic disorders.

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, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

24.

Protein domain-level landscape of cancer-type-specific somatic mutations.

Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP.

PLoS Comput Biol. 2015 Mar 20;11(3):e1004147. doi: 10.1371/journal.pcbi.1004147. eCollection 2015 Mar.

25.

Prioritizing causal disease genes using unbiased genomic features.

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.

Genome Biol. 2014 Dec 3;15(12):534. doi: 10.1186/s13059-014-0534-8.

26.

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.

Taşan M, Musso G, Hao T, Vidal M, MacRae CA, Roth FP.

Nat Methods. 2015 Feb;12(2):154-9. doi: 10.1038/nmeth.3215. Epub 2014 Dec 22.

27.

A highly conserved program of neuronal microexons is misregulated in autistic brains.

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, Geschwind DH, Blencowe BJ.

Cell. 2014 Dec 18;159(7):1511-23. doi: 10.1016/j.cell.2014.11.035.

28.

A proteome-scale map of the human interactome network.

Rolland T, Taşan 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, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

29.

Target-independent prediction of drug synergies using only drug lipophilicity.

Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP, Cokol M.

J Chem Inf Model. 2014 Aug 25;54(8):2286-93. doi: 10.1021/ci500276x. Epub 2014 Aug 1.

30.

The insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast.

Labunskyy VM, Suzuki Y, Hanly TJ, Murao A, Roth FP, Gladyshev VN.

G3 (Bethesda). 2014 Apr 28;4(7):1183-91. doi: 10.1534/g3.114.010868.

31.

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

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, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.

Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650.

32.

Large-scale identification and analysis of suppressive drug interactions.

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, Nislow C, Shoichet B, Roth FP.

Chem Biol. 2014 Apr 24;21(4):541-551. doi: 10.1016/j.chembiol.2014.02.012. Epub 2014 Apr 3.

33.

Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish.

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.

Development. 2014 Jan;141(1):224-35. doi: 10.1242/dev.099796.

34.

Systems biology and the analysis of genetic variation.

Sunyaev SR, Roth FP.

Curr Opin Genet Dev. 2013 Dec;23(6):599-601. doi: 10.1016/j.gde.2013.11.010. Epub 2013 Nov 28. No abstract available.

35.

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways.

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, Yu H.

Sci Signal. 2013 May 21;6(276):ra38. doi: 10.1126/scisignal.2003350.

36.

RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins.

Mahadevan K, Zhang H, Akef A, Cui XA, Gueroussov S, Cenik C, Roth FP, Palazzo AF.

PLoS Biol. 2013;11(4):e1001545. doi: 10.1371/journal.pbio.1001545. Epub 2013 Apr 23.

37.

The green monster process for the generation of yeast strains carrying multiple gene deletions.

Suzuki Y, Stam J, Novotny M, Yachie N, Lasken RS, Roth FP.

J Vis Exp. 2012 Dec 15;(70):e4072. doi: 10.3791/4072.

38.

ChromoZoom: a flexible, fluid, web-based genome browser.

Pak TR, Roth FP.

Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6.

39.

Introns in UTRs: why we should stop ignoring them.

Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ.

Bioessays. 2012 Dec;34(12):1025-34. doi: 10.1002/bies.201200073. Epub 2012 Oct 26.

PMID:
23108796
40.

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

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, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M.

Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288.

41.

Viral perturbations of host networks reflect disease etiology.

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, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, Decaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL.

PLoS Comput Biol. 2012;8(6):e1002531. doi: 10.1371/journal.pcbi.1002531. Epub 2012 Jun 28.

42.

Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae.

Cheng E, Vaisica JA, Ou J, Baryshnikova A, Lu Y, Roth FP, Brown GW.

Genetics. 2012 Sep;192(1):147-60. doi: 10.1534/genetics.112.141051. Epub 2012 Jun 5.

44.

A Resource of Quantitative Functional Annotation for Homo sapiens Genes.

Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP.

G3 (Bethesda). 2012 Feb;2(2):223-33. doi: 10.1534/g3.111.000828. Epub 2012 Feb 1.

45.

Systematic exploration of synergistic drug pairs.

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.

Mol Syst Biol. 2011 Nov 8;7:544. doi: 10.1038/msb.2011.71.

46.

Independently evolved virulence effectors converge onto hubs in a plant immune system network.

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, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y; European Union Effectoromics Consortium, Vandenhaute J, Roth FP, Hill DE, Ecker JR, Vidal M, Beynon J, Braun P, Dangl JL.

Science. 2011 Jul 29;333(6042):596-601. doi: 10.1126/science.1203659.

47.

Discovering the targets of drugs via computational systems biology.

Chua HN, Roth FP.

J Biol Chem. 2011 Jul 8;286(27):23653-8. doi: 10.1074/jbc.R110.174797. Epub 2011 May 12. Review.

48.

Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes.

Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP.

PLoS Genet. 2011 Apr;7(4):e1001366. doi: 10.1371/journal.pgen.1001366. Epub 2011 Apr 14.

49.

Next-generation sequencing to generate interactome datasets.

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, Braun P, Vidal M.

Nat Methods. 2011 Jun;8(6):478-80. doi: 10.1038/nmeth.1597. Epub 2011 Apr 24.

50.

Reconstitution of human RNA interference in budding yeast.

Suk K, Choi J, Suzuki Y, Ozturk SB, Mellor JC, Wong KH, MacKay JL, Gregory RI, Roth FP.

Nucleic Acids Res. 2011 Apr;39(7):e43. doi: 10.1093/nar/gkq1321. Epub 2011 Jan 19.

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