((roth fp[Author]OR roth fp[IR]) AND (1998[PDAT] : 3000[PDAT])) NOT speech[AFFL] NOT child[AFFL] NOT "J Speech Lang Hear Res"[Journal] - Search Results

Year	Number of Results
1998	1
2001	1
2002	2
2003	8
2004	9
2005	8
2006	4
2007	5
2008	15
2009	9
2010	10
2011	9
2012	8
2013	4
2014	9
2015	5
2016	9
2017	9
2018	4
2019	7
2020	10
2021	6
2022	3
2023	15
2024	6

1

Guidelines for releasing a variant effect predictor.

Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA. Livesey BJ, et al. Among authors: roth fp. ArXiv [Preprint]. 2024 Apr 16:arXiv:2404.10807v1. ArXiv. 2024. PMID: 38699161 Free PMC article. Preprint.

2

Minimum information and guidelines for reporting a multiplexed assay of variant effect.

Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Claussnitzer M, et al. Among authors: roth fp. Genome Biol. 2024 Apr 19;25(1):100. doi: 10.1186/s13059-024-03223-9. Genome Biol. 2024. PMID: 38641812 Free PMC article.

3

Characterizing glucokinase variant mechanisms using a multiplexed abundance assay.

Gersing S, Schulze TK, Cagiada M, Stein A, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. Gersing S, et al. Among authors: roth fp. Genome Biol. 2024 Apr 16;25(1):98. doi: 10.1186/s13059-024-03238-2. Genome Biol. 2024. PMID: 38627865 Free PMC article.

4

Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries.

Weile J, Ferra G, Boyle G, Pendyala S, Amorosi C, Yeh CL, Cote AG, Kishore N, Tabet D, van Loggerenberg W, Rayhan A, Fowler DM, Dunham MJ, Roth FP. Weile J, et al. Among authors: roth fp. Bioinformatics. 2024 Mar 29;40(4):btae182. doi: 10.1093/bioinformatics/btae182. Bioinformatics. 2024. PMID: 38569896 Free PMC article.

5

Workshop report: the clinical application of data from multiplex assays of variant effect (MAVEs), 12 July 2023.

Allen S, Garrett A, Muffley L, Fayer S, Foreman J, Adams DJ, Hurles M, Rubin AF, Roth FP, Starita LM, Biesecker LG, Turnbull C. Allen S, et al. Among authors: roth fp. Eur J Hum Genet. 2024 May;32(5):593-600. doi: 10.1038/s41431-024-01566-2. Epub 2024 Mar 4. Eur J Hum Genet. 2024. PMID: 38433264 Free PMC article.

6

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.

Critical Assessment of Genome Interpretation Consortium. Critical Assessment of Genome Interpretation Consortium. Genome Biol. 2024 Feb 22;25(1):53. doi: 10.1186/s13059-023-03113-6. Genome Biol. 2024. PMID: 38389099 Free PMC article.

7

Pervasive mislocalization of pathogenic coding variants underlying human disorders.

Lacoste J, Haghighi M, Haider S, Lin ZY, Segal D, Reno C, Qian WW, Xiong X, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Roth FP, Calderwood M, Hill D, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M. Lacoste J, et al. Among authors: roth fp. bioRxiv [Preprint]. 2023 Sep 5:2023.09.05.556368. doi: 10.1101/2023.09.05.556368. bioRxiv. 2023. PMID: 37732209 Free PMC article. Preprint.

8

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation.

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, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. van Loggerenberg W, et al. Among authors: roth fp. Am J Hum Genet. 2023 Oct 5;110(10):1769-1786. doi: 10.1016/j.ajhg.2023.08.012. Epub 2023 Sep 19. Am J Hum Genet. 2023. PMID: 37729906 Free PMC article.

9

Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens.

Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D. Zhao Y, et al. Among authors: roth fp. Mol Cell. 2023 Aug 3;83(15):2792-2809.e9. doi: 10.1016/j.molcel.2023.06.025. Epub 2023 Jul 20. Mol Cell. 2023. PMID: 37478847 Free article.

10

Minimum information and guidelines for reporting a Multiplexed Assay of Variant Effect.

Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Claussnitzer M, et al. Among authors: roth fp. ArXiv [Preprint]. 2023 Jun 26:arXiv:2306.15113v1. ArXiv. 2023. PMID: 37426450 Free PMC article. Updated. Preprint.

11

An Atlas of Variant Effects to understand the genome at nucleotide resolution.

Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME. Fowler DM, et al. Among authors: roth fp. Genome Biol. 2023 Jul 3;24(1):147. doi: 10.1186/s13059-023-02986-x. Genome Biol. 2023. PMID: 37394429 Free PMC article.

12

Characterizing glucokinase variant mechanisms using a multiplexed abundance assay.

Gersing S, Schulze TK, Cagiada M, Stein A, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. Gersing S, et al. Among authors: roth fp. bioRxiv [Preprint]. 2023 May 24:2023.05.24.542036. doi: 10.1101/2023.05.24.542036. bioRxiv. 2023. PMID: 37292969 Free PMC article. Updated. Preprint.

13

A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection.

Weller B, Lin CW, Pogoutse O, Sauer M, Marin-de la Rosa N, Strobel A, Young V, Knapp JJ, Rayhan A, Falter C, Kim DK, Roth FP, Falter-Braun P. Weller B, et al. Among authors: roth fp. G3 (Bethesda). 2023 Jul 5;13(7):jkad105. doi: 10.1093/g3journal/jkad105. G3 (Bethesda). 2023. PMID: 37267226 Free PMC article.

14

A comprehensive map of human glucokinase variant activity.

Gersing S, Cagiada M, Gebbia M, Gjesing AP, Coté AG, Seesankar G, Li R, Tabet D, Weile J, Stein A, Gloyn AL, Hansen T, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. Gersing S, et al. Among authors: roth fp. Genome Biol. 2023 Apr 26;24(1):97. doi: 10.1186/s13059-023-02935-8. Genome Biol. 2023. PMID: 37101203 Free PMC article.

15

satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect.

Hoskins I, Sun S, Cote A, Roth FP, Cenik C. Hoskins I, et al. Among authors: roth fp. Genome Biol. 2023 Apr 20;24(1):82. doi: 10.1186/s13059-023-02922-z. Genome Biol. 2023. PMID: 37081510 Free PMC article.

16

Next-generation large-scale binary protein interaction network for Drosophila melanogaster.

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, Desbuleux A, Goh KY, Kim DK, Knapp JJ, Lee WX, Lemmens I, Li C, Li M, Li R, Lim HJ, Liu Y, Luck K, Markey D, Pollis C, Rangarajan S, Rodiger J, Schlabach S, Shen Y, Sheykhkarimli D, TeeKing B, Roth FP, Tavernier J, Calderwood MA, Hill DE, Celniker SE, Vidal M, Perrimon N, Mohr SE. Tang HW, et al. Among authors: roth fp. Nat Commun. 2023 Apr 15;14(1):2162. doi: 10.1038/s41467-023-37876-0. Nat Commun. 2023. PMID: 37061542 Free PMC article.

17

Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.

Weile J, Ferra G, Boyle G, Pendyala S, Amorosi C, Yeh CL, Cote AG, Kishore N, Tabet D, van Loggerenberg W, Rayhan A, Fowler DM, Dunham MJ, Roth FP. Weile J, et al. Among authors: roth fp. bioRxiv [Preprint]. 2023 Dec 7:2023.02.22.529427. doi: 10.1101/2023.02.22.529427. bioRxiv. 2023. PMID: 36865234 Free PMC article. Updated. Preprint.

18

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation.

van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. van Loggerenberg W, et al. Among authors: roth fp. bioRxiv [Preprint]. 2023 Feb 6:2023.02.06.527353. doi: 10.1101/2023.02.06.527353. bioRxiv. 2023. PMID: 36798224 Free PMC article. Updated. Preprint.

19

Author Correction: 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, Wanamaker 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. Corominas R, et al. Among authors: roth fp. Nat Commun. 2023 Feb 2;14(1):569. doi: 10.1038/s41467-023-36264-y. Nat Commun. 2023. PMID: 36732511 Free PMC article. No abstract available.

20

Proactive Variant Effect Mapping Aids Diagnosis in Pediatric Cardiac Arrest.

Floyd BJ, Weile J, Kannankeril PJ, Glazer AM, Reuter CM, MacRae CA, Ashley EA, Roden DM, Roth FP, Parikh VN. Floyd BJ, et al. Among authors: roth fp. Circ Genom Precis Med. 2023 Feb;16(1):e003792. doi: 10.1161/CIRCGEN.122.003792. Epub 2023 Jan 30. Circ Genom Precis Med. 2023. PMID: 36716194 Free PMC article. Review. No abstract available.

21

Quantitative proteomics and biological activity of extracellular vesicles engineered to express SARS-CoV-2 spike protein.

Choi D, Khan N, Montermini L, Tawil N, Meehan B, Kim DK, Roth FP, Divangahi M, Rak J. Choi D, et al. Among authors: roth fp. J Extracell Biol. 2022 Oct;1(10):e58. doi: 10.1002/jex2.58. Epub 2022 Oct 13. J Extracell Biol. 2022. PMID: 36710959 Free PMC article.

22

A proteome-scale map of the SARS-CoV-2-human contactome.

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, Sauer M, Young V, Halder H, la Rosa NM, Pogoutse O, Strobel A, Schwehn P, Li R, Rothballer ST, Altmann M, Cassonnet P, Coté AG, Vergara LE, Hazelwood I, Liu BB, Nguyen M, Pandiarajan R, Dohai B, Coloma PAR, Poirson J, Giuliana P, Willems L, Taipale M, Jacob Y, Hao T, Hill DE, Brun C, Twizere JC, Krappmann D, Heinig M, Falter C, Aloy P, Demeret C, Vidal M, Calderwood MA, Roth FP, Falter-Braun P. Kim DK, et al. Among authors: roth fp. Nat Biotechnol. 2023 Jan;41(1):140-149. doi: 10.1038/s41587-022-01475-z. Epub 2022 Oct 10. Nat Biotechnol. 2023. PMID: 36217029 Free PMC article.

23

Scalable Functional Assays for the Interpretation of Human Genetic Variation.

Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Tabet D, et al. Among authors: roth fp. Annu Rev Genet. 2022 Nov 30;56:441-465. doi: 10.1146/annurev-genet-072920-032107. Epub 2022 Sep 2. Annu Rev Genet. 2022. PMID: 36055970 Review.

24

Improved pathogenicity prediction for rare human missense variants.

Wu Y, Liu H, Li R, Sun S, Weile J, Roth FP. Wu Y, et al. Among authors: roth fp. Am J Hum Genet. 2021 Dec 2;108(12):2389. doi: 10.1016/j.ajhg.2021.11.010. Am J Hum Genet. 2021. PMID: 34861178 Free PMC article. No abstract available.

25

Improved pathogenicity prediction for rare human missense variants.

Wu Y, Li R, Sun S, Weile J, Roth FP. Wu Y, et al. Among authors: roth fp. Am J Hum Genet. 2021 Oct 7;108(10):1891-1906. doi: 10.1016/j.ajhg.2021.08.012. Epub 2021 Sep 21. Am J Hum Genet. 2021. PMID: 34551312 Free PMC article.

26

Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads.

Savinov A, Roth FP. Savinov A, et al. Among authors: roth fp. Cell Syst. 2021 Jul 21;12(7):691-693. doi: 10.1016/j.cels.2021.06.003. Cell Syst. 2021. PMID: 34293323 Free article.

27

Shifting landscapes of human MTHFR missense-variant effects.

Weile J, Kishore N, Sun S, Maaieh R, Verby M, Li R, Fotiadou I, Kitaygorodsky J, Wu Y, Holenstein A, Bürer C, Blomgren L, Yang S, Nussbaum R, Rozen R, Watkins D, Gebbia M, Kozich V, Garton M, Froese DS, Roth FP. Weile J, et al. Among authors: roth fp. Am J Hum Genet. 2021 Jul 1;108(7):1283-1300. doi: 10.1016/j.ajhg.2021.05.009. Am J Hum Genet. 2021. PMID: 34214447 Free PMC article.

28

MaveRegistry: a collaboration platform for multiplexed assays of variant effect.

Kuang D, Weile J, Kishore N, Nguyen M, Rubin AF, Fields S, Fowler DM, Roth FP. Kuang D, et al. Among authors: roth fp. Bioinformatics. 2021 Oct 11;37(19):3382-3383. doi: 10.1093/bioinformatics/btab215. Bioinformatics. 2021. PMID: 33774657 Free PMC article.

29

Prioritizing genes for systematic variant effect mapping.

Kuang D, Truty R, Weile J, Johnson B, Nykamp K, Araya C, Nussbaum RL, Roth FP. Kuang D, et al. Among authors: roth fp. Bioinformatics. 2021 Apr 1;36(22-23):5448-5455. doi: 10.1093/bioinformatics/btaa1008. Bioinformatics. 2021. PMID: 33300982 Free PMC article.

30

Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways.

Kim JH, Seo Y, Jo M, Jeon H, Kim YS, Kim EJ, Seo D, Lee WH, Kim SR, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Kim JH, et al. Among authors: roth fp. J Biol Chem. 2020 Dec 11;295(50):16906-16919. doi: 10.1074/jbc.RA120.014831. Epub 2020 Oct 15. J Biol Chem. 2020. PMID: 33060198 Free PMC article.

31

Systematic analysis of bypass suppression of essential genes.

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, Aloy P, Andrews BJ, Boone C. van Leeuwen J, et al. Among authors: roth fp. Mol Syst Biol. 2020 Sep;16(9):e9828. doi: 10.15252/msb.20209828. Mol Syst Biol. 2020. PMID: 32939983 Free PMC article.

32

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact.

Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Chiasson MA, et al. Among authors: roth fp. Elife. 2020 Sep 1;9:e58026. doi: 10.7554/eLife.58026. Elife. 2020. PMID: 32870157 Free PMC article.

33

A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions.

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, Gingras AC, Taipale M, Raught B, Jacob Y, Roth FP. Kim DK, et al. Among authors: roth fp. G3 (Bethesda). 2020 Sep 2;10(9):3399-3402. doi: 10.1534/g3.120.401554. G3 (Bethesda). 2020. PMID: 32763951 Free PMC article.

34

Yeast-Based Genetic Interaction Analysis of Human Kinome.

Kim JH, Seo Y, Jo M, Jeon H, Lee WH, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Kim JH, et al. Among authors: roth fp. Cells. 2020 May 7;9(5):1156. doi: 10.3390/cells9051156. Cells. 2020. PMID: 32392905 Free PMC article.

35

A reference map of the human binary protein interactome.

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, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. Luck K, et al. Among authors: roth fp. Nature. 2020 Apr;580(7803):402-408. doi: 10.1038/s41586-020-2188-x. Epub 2020 Apr 8. Nature. 2020. PMID: 32296183 Free PMC article.

36

MaveQuest: a web resource for planning experimental tests of human variant effects.

Kuang D, Weile J, Li R, Ouellette TW, Barber JA, Roth FP. Kuang D, et al. Among authors: roth fp. Bioinformatics. 2020 Jun 1;36(12):3938-3940. doi: 10.1093/bioinformatics/btaa228. Bioinformatics. 2020. PMID: 32251504 Free PMC article.

37

Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions.

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, Spatt L, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Gingras AC, Roth FP, Colwill K, Bakal C, Pertz O, Pawson T, Petsalaki E, Rocks O. Müller PM, et al. Among authors: roth fp. Nat Cell Biol. 2020 Apr;22(4):498-511. doi: 10.1038/s41556-020-0488-x. Epub 2020 Mar 23. Nat Cell Biol. 2020. PMID: 32203420

38

A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase.

Sun S, Weile J, Verby M, Wu Y, Wang Y, Cote AG, Fotiadou I, Kitaygorodsky J, Vidal M, Rine J, Ješina P, Kožich V, Roth FP. Sun S, et al. Among authors: roth fp. Genome Med. 2020 Jan 30;12(1):13. doi: 10.1186/s13073-020-0711-1. Genome Med. 2020. PMID: 32000841 Free PMC article.

39

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.

Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. Esposito D, et al. Among authors: roth fp. Genome Biol. 2019 Nov 4;20(1):223. doi: 10.1186/s13059-019-1845-6. Genome Biol. 2019. PMID: 31679514 Free PMC article.

40

Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network.

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, Stagljar I, Suzuki Y, Yachie N, Roth FP. Celaj A, et al. Among authors: roth fp. Cell Syst. 2020 Jan 22;10(1):25-38.e10. doi: 10.1016/j.cels.2019.09.009. Epub 2019 Oct 23. Cell Syst. 2020. PMID: 31668799 Free PMC article.

41

Quantifying immune-based counterselection of somatic mutations.

Yang F, Kim DK, Nakagawa H, Hayashi S, Imoto S, Stein L, Roth FP. Yang F, et al. Among authors: roth fp. PLoS Genet. 2019 Jul 25;15(7):e1008227. doi: 10.1371/journal.pgen.1008227. eCollection 2019 Jul. PLoS Genet. 2019. PMID: 31344031 Free PMC article.

42

Assessing predictions on fitness effects of missense variants in calmodulin.

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, Grishin NV. Zhang J, et al. Among authors: roth fp. Hum Mutat. 2019 Sep;40(9):1463-1473. doi: 10.1002/humu.23857. Epub 2019 Sep 3. Hum Mutat. 2019. PMID: 31283071 Free PMC article.

43

Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background.

Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M. Sokolov A, et al. Among authors: roth fp. Front Pharmacol. 2019 Apr 25;10:448. doi: 10.3389/fphar.2019.00448. eCollection 2019. Front Pharmacol. 2019. PMID: 31105571 Free PMC article.

44

CNTN5^-^/+or EHMT2^-^/+human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks.

Deneault E, Faheem M, White SH, Rodrigues DC, Sun S, Wei W, Piekna A, Thompson T, Howe JL, Chalil L, Kwan V, Walker S, Pasceri P, Roth FP, Yuen RK, Singh KK, Ellis J, Scherer SW. Deneault E, et al. Among authors: roth fp. Elife. 2019 Feb 12;8:e40092. doi: 10.7554/eLife.40092. Elife. 2019. PMID: 30747104 Free PMC article.

45

A web application and service for imputing and visualizing missense variant effect maps.

Wu Y, Weile J, Cote AG, Sun S, Knapp J, Verby M, Roth FP. Wu Y, et al. Among authors: roth fp. Bioinformatics. 2019 Sep 1;35(17):3191-3193. doi: 10.1093/bioinformatics/btz012. Bioinformatics. 2019. PMID: 30649215 Free PMC article.

46

Modeling the impact of drug interactions on therapeutic selectivity.

Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M. Weinstein ZB, et al. Among authors: roth fp. Nat Commun. 2018 Aug 27;9(1):3452. doi: 10.1038/s41467-018-05954-3. Nat Commun. 2018. PMID: 30150706 Free PMC article.

47

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

Weile J, Roth FP. Weile J, et al. Among authors: roth fp. Hum Genet. 2018 Sep;137(9):665-678. doi: 10.1007/s00439-018-1916-x. Epub 2018 Aug 2. Hum Genet. 2018. PMID: 30073413 Free PMC article. Review.

48

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. Choi D, et al. Among authors: roth fp. Mol Cell Proteomics. 2018 Oct;17(10):1948-1964. doi: 10.1074/mcp.RA118.000644. Epub 2018 Jul 13. Mol Cell Proteomics. 2018. PMID: 30006486 Free PMC article.

49

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. Díaz-Mejía JJ, et al. Among authors: roth fp. Mol Syst Biol. 2018 May 28;14(5):e7985. doi: 10.15252/msb.20177985. Mol Syst Biol. 2018. PMID: 29807908 Free PMC article.

50

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. Weile J, et al. Among authors: roth fp. Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908. Mol Syst Biol. 2017. PMID: 29269382 Free PMC article.

51

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. Vigentini I, et al. Among authors: roth fp. Front Microbiol. 2017 Nov 9;8:2194. doi: 10.3389/fmicb.2017.02194. eCollection 2017. Front Microbiol. 2017. PMID: 29163459 Free PMC article.

52

Variant Interpretation: Functional Assays to the Rescue.

Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Starita LM, et al. Among authors: roth fp. Am J Hum Genet. 2017 Sep 7;101(3):315-325. doi: 10.1016/j.ajhg.2017.07.014. Am J Hum Genet. 2017. PMID: 28886340 Free PMC article.

53

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. Zhang J, et al. Among authors: roth fp. Hum Mutat. 2017 Sep;38(9):1051-1063. doi: 10.1002/humu.23293. Hum Mutat. 2017. PMID: 28817247 Free PMC article.

54

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. Celaj A, et al. Among authors: roth fp. Mol Syst Biol. 2017 Jul 13;13(7):934. doi: 10.15252/msb.20177532. Mol Syst Biol. 2017. PMID: 28705884 Free PMC article.

55

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. Jo M, et al. Among authors: roth fp. Genome Res. 2017 Sep;27(9):1487-1500. doi: 10.1101/gr.211649.116. Epub 2017 Jun 8. Genome Res. 2017. PMID: 28596290 Free PMC article.

56

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. Yang F, et al. Among authors: roth fp. PLoS Genet. 2017 May 25;13(5):e1006779. doi: 10.1371/journal.pgen.1006779. eCollection 2017 May. PLoS Genet. 2017. PMID: 28542158 Free PMC article.

57

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. Betts MJ, et al. Among authors: roth fp. PLoS Comput Biol. 2017 Mar 27;13(3):e1005462. doi: 10.1371/journal.pcbi.1005462. eCollection 2017 Mar. PLoS Comput Biol. 2017. PMID: 28346509 Free PMC article.

58

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. Cenik C, et al. Among authors: roth fp. RNA. 2017 Mar;23(3):270-283. doi: 10.1261/rna.059105.116. Epub 2016 Dec 19. RNA. 2017. PMID: 27994090 Free PMC article.

59

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. van Leeuwen J, et al. Among authors: roth fp. Science. 2016 Nov 4;354(6312):aag0839. doi: 10.1126/science.aag0839. Science. 2016. PMID: 27811238 Free PMC article.

60

Taking Exception to Human Eugenics.

Roth FP, Wakeley J. Roth FP, et al. Genetics. 2016 Oct;204(2):821-823. doi: 10.1534/genetics.116.192096. Genetics. 2016. PMID: 27729496 Free PMC article. No abstract available.

61

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. Shekhar-Guturja T, et al. Among authors: roth fp. Nat Chem Biol. 2016 Oct;12(10):867-75. doi: 10.1038/nchembio.2165. Epub 2016 Aug 29. Nat Chem Biol. 2016. PMID: 27571477 Free PMC article.

62

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. Zhong Q, et al. Among authors: roth fp. Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484. Mol Syst Biol. 2016. PMID: 27107014 Free PMC article.

63

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. Yachie N, et al. Among authors: roth fp. Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660. Mol Syst Biol. 2016. PMID: 27107012 Free PMC article.

64

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. Sun S, et al. Among authors: roth fp. Genome Res. 2016 May;26(5):670-80. doi: 10.1101/gr.192526.115. Epub 2016 Mar 14. Genome Res. 2016. PMID: 26975778 Free PMC article.

65

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, Wanamaker 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. Yang X, et al. Among authors: roth fp. Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029. Cell. 2016. PMID: 26871637 Free PMC article.

66

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. Vo TV, et al. Among authors: roth fp. Cell. 2016 Jan 14;164(1-2):310-323. doi: 10.1016/j.cell.2015.11.037. Cell. 2016. PMID: 26771498 Free PMC article.

67

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. Hart T, et al. Among authors: roth fp. Cell. 2015 Dec 3;163(6):1515-26. doi: 10.1016/j.cell.2015.11.015. Epub 2015 Nov 25. Cell. 2015. PMID: 26627737 Free article.

68

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. Petsalaki E, et al. Among authors: roth fp. Nucleic Acids Res. 2015 Jul 1;43(W1):W276-82. doi: 10.1093/nar/gkv459. Epub 2015 May 6. Nucleic Acids Res. 2015. PMID: 25948583 Free PMC article.

69

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. Sahni N, et al. Among authors: roth fp. Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013. Cell. 2015. PMID: 25910212 Free PMC article.

70

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

Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP. Yang F, et al. Among authors: roth fp. PLoS Comput Biol. 2015 Mar 20;11(3):e1004147. doi: 10.1371/journal.pcbi.1004147. eCollection 2015 Mar. PLoS Comput Biol. 2015. PMID: 25794154 Free PMC article.

71

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. Deo RC, et al. Among authors: roth fp. Genome Biol. 2014 Dec 3;15(12):534. doi: 10.1186/s13059-014-0534-8. Genome Biol. 2014. PMID: 25633252 Free PMC article.

72

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

Taşan M, Musso G, Hao T, Vidal M, MacRae CA, Roth FP. Taşan M, et al. Among authors: roth fp. Nat Methods. 2015 Feb;12(2):154-9. doi: 10.1038/nmeth.3215. Epub 2014 Dec 22. Nat Methods. 2015. PMID: 25532137 Free PMC article.

73

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. Irimia M, et al. Among authors: roth fp. Cell. 2014 Dec 18;159(7):1511-23. doi: 10.1016/j.cell.2014.11.035. Cell. 2014. PMID: 25525873 Free PMC article.

74

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, Wanamaker 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. Rolland T, et al. Among authors: roth fp. Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050. Cell. 2014. PMID: 25416956 Free PMC article.

75

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. Yilancioglu K, et al. Among authors: roth fp. J Chem Inf Model. 2014 Aug 25;54(8):2286-93. doi: 10.1021/ci500276x. Epub 2014 Aug 1. J Chem Inf Model. 2014. PMID: 25026390 Free PMC article.

76

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. Labunskyy VM, et al. Among authors: roth fp. G3 (Bethesda). 2014 Apr 28;4(7):1183-91. doi: 10.1534/g3.114.010868. G3 (Bethesda). 2014. PMID: 24776987 Free PMC article.

77

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, Wanamaker 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. Corominas R, et al. Among authors: roth fp. Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650. Nat Commun. 2014. PMID: 24722188 Free PMC article.

78

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. Cokol M, et al. Among authors: roth fp. Chem Biol. 2014 Apr 24;21(4):541-551. doi: 10.1016/j.chembiol.2014.02.012. Epub 2014 Apr 3. Chem Biol. 2014. PMID: 24704506 Free PMC article.

79

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. Musso G, et al. Among authors: roth fp. Development. 2014 Jan;141(1):224-35. doi: 10.1242/dev.099796. Development. 2014. PMID: 24346703 Free PMC article.

80

Systems biology and the analysis of genetic variation.

Sunyaev SR, Roth FP. Sunyaev SR, et al. Among authors: roth fp. Curr Opin Genet Dev. 2013 Dec;23(6):599-601. doi: 10.1016/j.gde.2013.11.010. Epub 2013 Nov 28. Curr Opin Genet Dev. 2013. PMID: 24291212 Free PMC article. No abstract available.

81

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. Das J, et al. Among authors: roth fp. Sci Signal. 2013 May 21;6(276):ra38. doi: 10.1126/scisignal.2003350. Sci Signal. 2013. PMID: 23695164 Free PMC article.

82

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. Mahadevan K, et al. Among authors: roth fp. PLoS Biol. 2013;11(4):e1001545. doi: 10.1371/journal.pbio.1001545. Epub 2013 Apr 23. PLoS Biol. 2013. PMID: 23630457 Free PMC article.

83

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. Suzuki Y, et al. Among authors: roth fp. J Vis Exp. 2012 Dec 15;(70):e4072. doi: 10.3791/4072. J Vis Exp. 2012. PMID: 23271437 Free PMC article.

84

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

Pak TR, Roth FP. Pak TR, et al. Among authors: roth fp. Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6. Bioinformatics. 2013. PMID: 23220575 Free PMC article.

85

Introns in UTRs: why we should stop ignoring them.

Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ. Bicknell AA, et al. Among authors: roth fp. Bioessays. 2012 Dec;34(12):1025-34. doi: 10.1002/bies.201200073. Epub 2012 Oct 26. Bioessays. 2012. PMID: 23108796

86

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. Rozenblatt-Rosen O, et al. Among authors: roth fp. Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288. Nature. 2012. PMID: 22810586 Free PMC article.

87

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. Gulbahce N, et al. Among authors: roth fp. PLoS Comput Biol. 2012;8(6):e1002531. doi: 10.1371/journal.pcbi.1002531. Epub 2012 Jun 28. PLoS Comput Biol. 2012. PMID: 22761553 Free PMC article.

88

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. Cheng E, et al. Among authors: roth fp. Genetics. 2012 Sep;192(1):147-60. doi: 10.1534/genetics.112.141051. Epub 2012 Jun 5. Genetics. 2012. PMID: 22673806 Free PMC article.

89

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.

Derti A, Roth FP. Derti A, et al. Among authors: roth fp. Bioessays. 2012 Jul;34(7):576-7. doi: 10.1002/bies.201200023. Epub 2012 Mar 29. Bioessays. 2012. PMID: 22467222 Free PMC article.

90

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. Taşan M, et al. Among authors: roth fp. G3 (Bethesda). 2012 Feb;2(2):223-33. doi: 10.1534/g3.111.000828. Epub 2012 Feb 1. G3 (Bethesda). 2012. PMID: 22384401 Free PMC article.

91

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. Cokol M, et al. Among authors: roth fp. Mol Syst Biol. 2011 Nov 8;7:544. doi: 10.1038/msb.2011.71. Mol Syst Biol. 2011. PMID: 22068327 Free PMC article.

92

Evidence for network evolution in an Arabidopsis interactome map.

Arabidopsis Interactome Mapping Consortium. Arabidopsis Interactome Mapping Consortium. Science. 2011 Jul 29;333(6042):601-7. doi: 10.1126/science.1203877. Science. 2011. PMID: 21798944 Free PMC article.

93

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. Mukhtar MS, et al. Among authors: roth fp. Science. 2011 Jul 29;333(6042):596-601. doi: 10.1126/science.1203659. Science. 2011. PMID: 21798943 Free PMC article.

94

Discovering the targets of drugs via computational systems biology.

Chua HN, Roth FP. Chua HN, et al. Among authors: roth fp. J Biol Chem. 2011 Jul 8;286(27):23653-8. doi: 10.1074/jbc.R110.174797. Epub 2011 May 12. J Biol Chem. 2011. PMID: 21566122 Free PMC article. Review.

95

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. Cenik C, et al. Among authors: roth fp. PLoS Genet. 2011 Apr;7(4):e1001366. doi: 10.1371/journal.pgen.1001366. Epub 2011 Apr 14. PLoS Genet. 2011. PMID: 21533221 Free PMC article.

96

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. Yu H, et al. Among authors: roth fp. Nat Methods. 2011 Jun;8(6):478-80. doi: 10.1038/nmeth.1597. Epub 2011 Apr 24. Nat Methods. 2011. PMID: 21516116 Free PMC article.

97

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. Suk K, et al. Among authors: roth fp. Nucleic Acids Res. 2011 Apr;39(7):e43. doi: 10.1093/nar/gkq1321. Epub 2011 Jan 19. Nucleic Acids Res. 2011. PMID: 21252293 Free PMC article.

98

Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection.

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, Lehár J, Roth FP. Suzuki Y, et al. Among authors: roth fp. Nat Methods. 2011 Feb;8(2):159-64. doi: 10.1038/nmeth.1550. Epub 2011 Jan 9. Nat Methods. 2011. PMID: 21217751 Free PMC article.

99

Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes.

Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G. Sephton CF, et al. Among authors: roth fp. J Biol Chem. 2011 Jan 14;286(2):1204-15. doi: 10.1074/jbc.M110.190884. Epub 2010 Nov 4. J Biol Chem. 2011. PMID: 21051541 Free PMC article.

100

A genome-wide gene function prediction resource for Drosophila melanogaster.

Yan H, Venkatesan K, Beaver JE, Klitgord N, Yildirim MA, Hao T, Hill DE, Cusick ME, Perrimon N, Roth FP, Vidal M. Yan H, et al. Among authors: roth fp. PLoS One. 2010 Aug 12;5(8):e12139. doi: 10.1371/journal.pone.0012139. PLoS One. 2010. PMID: 20711346 Free PMC article.

101

Metabolic signatures of exercise in human plasma.

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, Systrom DM, Semigran MJ, Vasan RS, Carr SA, Wang TJ, Sabatine MS, Clish CB, Gerszten RE. Lewis GD, et al. Among authors: roth fp. Sci Transl Med. 2010 May 26;2(33):33ra37. doi: 10.1126/scitranslmed.3001006. Sci Transl Med. 2010. PMID: 20505214 Free PMC article.

102

FuncBase: a resource for quantitative gene function annotation.

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP. Beaver JE, et al. Among authors: roth fp. Bioinformatics. 2010 Jul 15;26(14):1806-7. doi: 10.1093/bioinformatics/btq265. Epub 2010 May 21. Bioinformatics. 2010. PMID: 20495000 Free PMC article.

103

Absence of evidence for MHC-dependent mate selection within HapMap populations.

Derti A, Cenik C, Kraft P, Roth FP. Derti A, et al. Among authors: roth fp. PLoS Genet. 2010 Apr 29;6(4):e1000925. doi: 10.1371/journal.pgen.1000925. PLoS Genet. 2010. PMID: 20442868 Free PMC article.

104

Genome-wide functional analysis of human 5' untranslated region introns.

Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Cenik C, et al. Among authors: roth fp. Genome Biol. 2010;11(3):R29. doi: 10.1186/gb-2010-11-3-r29. Epub 2010 Mar 11. Genome Biol. 2010. PMID: 20222956 Free PMC article.

105

The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types.

Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth JR. Kugelberg E, et al. Among authors: roth fp. Genetics. 2010 May;185(1):65-80. doi: 10.1534/genetics.110.114074. Epub 2010 Mar 9. Genetics. 2010. PMID: 20215473 Free PMC article.

106

Interpreting metabolomic profiles using unbiased pathway models.

Deo RC, Hunter L, Lewis GD, Pare G, Vasan RS, Chasman D, Wang TJ, Gerszten RE, Roth FP. Deo RC, et al. Among authors: roth fp. PLoS Comput Biol. 2010 Feb 26;6(2):e1000692. doi: 10.1371/journal.pcbi.1000692. PLoS Comput Biol. 2010. PMID: 20195502 Free PMC article.

107

Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2.

Jurak I, Kramer MF, Mellor JC, van Lint AL, Roth FP, Knipe DM, Coen DM. Jurak I, et al. Among authors: roth fp. J Virol. 2010 May;84(9):4659-72. doi: 10.1128/JVI.02725-09. Epub 2010 Feb 24. J Virol. 2010. PMID: 20181707 Free PMC article.

108

The genetic landscape of a cell.

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, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. Costanzo M, et al. Among authors: roth fp. Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823. Science. 2010. PMID: 20093466 Free PMC article.

109

Pathways of the heart.

Deo RC, Roth FP. Deo RC, et al. Among authors: roth fp. Circ Cardiovasc Genet. 2009 Aug;2(4):303-5. doi: 10.1161/CIRCGENETICS.109.892588. Circ Cardiovasc Genet. 2009. PMID: 20031600 Free PMC article. No abstract available.

110

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

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, Vidal M. Salehi-Ashtiani K, et al. Among authors: roth fp. Genome Res. 2009 Dec;19(12):2334-42. doi: 10.1101/gr.098640.109. Epub 2009 Oct 2. Genome Res. 2009. PMID: 19801531 Free PMC article.

111

Next generation software for functional trend analysis.

Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Berriz GF, et al. Among authors: roth fp. Bioinformatics. 2009 Nov 15;25(22):3043-4. doi: 10.1093/bioinformatics/btp498. Epub 2009 Aug 28. Bioinformatics. 2009. PMID: 19717575 Free PMC article.

112

Quantitative phenotyping via deep barcode sequencing.

Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, Nislow C. Smith AM, et al. Among authors: roth fp. Genome Res. 2009 Oct;19(10):1836-42. doi: 10.1101/gr.093955.109. Epub 2009 Jul 21. Genome Res. 2009. PMID: 19622793 Free PMC article.

113

Q&A: epistasis.

Roth FP, Lipshitz HD, Andrews BJ. Roth FP, et al. J Biol. 2009;8(4):35. doi: 10.1186/jbiol144. Epub 2009 May 22. J Biol. 2009. PMID: 19486505 Free PMC article. No abstract available.

114

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

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, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M. Simonis N, et al. Among authors: roth fp. Nat Methods. 2009 Jan;6(1):47-54. doi: 10.1038/nmeth.1279. Nat Methods. 2009. PMID: 19123269 Free PMC article.

115

Literature-curated protein interaction datasets.

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, Vidal M. Cusick ME, et al. Among authors: roth fp. Nat Methods. 2009 Jan;6(1):39-46. doi: 10.1038/nmeth.1284. Nat Methods. 2009. PMID: 19116613 Free PMC article.

116

An empirical framework for binary interactome mapping.

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, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M. Venkatesan K, et al. Among authors: roth fp. Nat Methods. 2009 Jan;6(1):83-90. doi: 10.1038/nmeth.1280. Epub 2008 Dec 7. Nat Methods. 2009. PMID: 19060904 Free PMC article.

117

An experimentally derived confidence score for binary protein-protein interactions.

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, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M. Braun P, et al. Among authors: roth fp. Nat Methods. 2009 Jan;6(1):91-7. doi: 10.1038/nmeth.1281. Epub 2008 Dec 7. Nat Methods. 2009. PMID: 19060903 Free PMC article.

118

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity.

Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJ. Martinez NJ, et al. Among authors: roth fp. Genes Dev. 2008 Sep 15;22(18):2535-49. doi: 10.1101/gad.1678608. Genes Dev. 2008. PMID: 18794350 Free PMC article.

119

Chemical substructures that enrich for biological activity.

Klekota J, Roth FP. Klekota J, et al. Among authors: roth fp. Bioinformatics. 2008 Nov 1;24(21):2518-25. doi: 10.1093/bioinformatics/btn479. Epub 2008 Sep 10. Bioinformatics. 2008. PMID: 18784118 Free PMC article.

120

Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.

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, Taşan M, Roth FP, Min J, Baumgartner C, Keshishian H, Addona T, Mootha VK, Rosenzweig A, Carr SA, Fifer MA, Sabatine MS, Gerszten RE. Lewis GD, et al. Among authors: roth fp. J Clin Invest. 2008 Oct;118(10):3503-12. doi: 10.1172/JCI35111. J Clin Invest. 2008. PMID: 18769631 Free PMC article. Clinical Trial.

121

High-quality binary protein interaction map of the yeast interactome network.

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, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M. Yu H, et al. Among authors: roth fp. Science. 2008 Oct 3;322(5898):104-10. doi: 10.1126/science.1158684. Epub 2008 Aug 21. Science. 2008. PMID: 18719252 Free PMC article.

122

The Synergizer service for translating gene, protein and other biological identifiers.

Berriz GF, Roth FP. Berriz GF, et al. Among authors: roth fp. Bioinformatics. 2008 Oct 1;24(19):2272-3. doi: 10.1093/bioinformatics/btn424. Epub 2008 Aug 12. Bioinformatics. 2008. PMID: 18697767 Free PMC article.

123

A protein domain-based interactome network for C. elegans early embryogenesis.

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, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M. Boxem M, et al. Among authors: roth fp. Cell. 2008 Aug 8;134(3):534-45. doi: 10.1016/j.cell.2008.07.009. Cell. 2008. PMID: 18692475 Free PMC article.

124

An en masse phenotype and function prediction system for Mus musculus.

Taşan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP. Taşan M, et al. Among authors: roth fp. Genome Biol. 2008;9 Suppl 1(Suppl 1):S8. doi: 10.1186/gb-2008-9-s1-s8. Epub 2008 Jun 27. Genome Biol. 2008. PMID: 18613952 Free PMC article.

125

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Tian W, et al. Among authors: roth fp. Genome Biol. 2008;9 Suppl 1(Suppl 1):S7. doi: 10.1186/gb-2008-9-s1-s7. Epub 2008 Jun 27. Genome Biol. 2008. PMID: 18613951 Free PMC article.

126

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

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, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. Peña-Castillo L, et al. Among authors: roth fp. Genome Biol. 2008;9 Suppl 1(Suppl 1):S2. doi: 10.1186/gb-2008-9-s1-s2. Epub 2008 Jun 27. Genome Biol. 2008. PMID: 18613946 Free PMC article.

127

A race through the maze of genomic evidence.

Hughes TR, Roth FP. Hughes TR, et al. Among authors: roth fp. Genome Biol. 2008;9 Suppl 1(Suppl 1):S1. doi: 10.1186/gb-2008-9-s1-s1. Epub 2008 Jun 27. Genome Biol. 2008. PMID: 18613945 Free PMC article. No abstract available.

128

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.

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, Vidal M. Salehi-Ashtiani K, et al. Among authors: roth fp. Nat Methods. 2008 Jul;5(7):597-600. doi: 10.1038/nmeth.1224. Epub 2008 Jun 15. Nat Methods. 2008. PMID: 18552854 Free PMC article.

129

Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs.

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. Gerszten RE, et al. Among authors: roth fp. Am J Physiol Lung Cell Mol Physiol. 2008 Jul;295(1):L16-22. doi: 10.1152/ajplung.00044.2008. Epub 2008 May 2. Am J Physiol Lung Cell Mol Physiol. 2008. PMID: 18456800 Free PMC article. Review.

130

Defining genetic interaction.

Mani R, St Onge RP, Hartman JL 4th, Giaever G, Roth FP. Mani R, et al. Among authors: roth fp. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3461-6. doi: 10.1073/pnas.0712255105. Epub 2008 Feb 27. Proc Natl Acad Sci U S A. 2008. PMID: 18305163 Free PMC article.

131

Functional specificity among ribosomal proteins regulates gene expression.

Komili S, Farny NG, Roth FP, Silver PA. Komili S, et al. Among authors: roth fp. Cell. 2007 Nov 2;131(3):557-71. doi: 10.1016/j.cell.2007.08.037. Cell. 2007. PMID: 17981122 Free PMC article.

132

Confirmation of organized modularity in the yeast interactome.

Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, Vidal M. Bertin N, et al. Among authors: roth fp. PLoS Biol. 2007 Jun;5(6):e153. doi: 10.1371/journal.pbio.0050153. PLoS Biol. 2007. PMID: 17564493 Free PMC article. No abstract available.

133

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.

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, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Barabási AL, Baillie D, Vidal M. Dupuy D, et al. Among authors: roth fp. Nat Biotechnol. 2007 Jun;25(6):663-8. doi: 10.1038/nbt1305. Epub 2007 May 7. Nat Biotechnol. 2007. PMID: 17486083

134

Genetic interaction screens advance in reverse.

Komili S, Roth FP. Komili S, et al. Among authors: roth fp. Genes Dev. 2007 Jan 15;21(2):137-42. doi: 10.1101/gad.1512707. Genes Dev. 2007. PMID: 17234880 Free article. No abstract available.

135

Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

St Onge RP, Mani R, Oh J, Proctor M, Fung E, Davis RW, Nislow C, Roth FP, Giaever G. St Onge RP, et al. Among authors: roth fp. Nat Genet. 2007 Feb;39(2):199-206. doi: 10.1038/ng1948. Epub 2007 Jan 7. Nat Genet. 2007. PMID: 17206143 Free PMC article.

136

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.

Derti A, Roth FP, Church GM, Wu CT. Derti A, et al. Among authors: roth fp. Nat Genet. 2006 Oct;38(10):1216-20. doi: 10.1038/ng1888. Epub 2006 Sep 24. Nat Genet. 2006. PMID: 16998490

137

Systematic genetics swims forward elegantly.

Suzuki Y, Roth FP. Suzuki Y, et al. Among authors: roth fp. Mol Syst Biol. 2006;2:48. doi: 10.1038/msb4100092. Epub 2006 Sep 12. Mol Syst Biol. 2006. PMID: 16969340 Free PMC article. No abstract available.

138

Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects.

Klekota J, Brauner E, Roth FP, Schreiber SL. Klekota J, et al. Among authors: roth fp. J Chem Inf Model. 2006 Jul-Aug;46(4):1549-62. doi: 10.1021/ci050495h. J Chem Inf Model. 2006. PMID: 16859287

139

Query Chem: a Google-powered web search combining text and chemical structures.

Klekota J, Roth FP, Schreiber SL. Klekota J, et al. Among authors: roth fp. Bioinformatics. 2006 Jul 1;22(13):1670-3. doi: 10.1093/bioinformatics/btl155. Epub 2006 May 3. Bioinformatics. 2006. PMID: 16672261

140

Metabolomic identification of novel biomarkers of myocardial ischemia.

Sabatine MS, Liu E, Morrow DA, Heller E, McCarroll R, Wiegand R, Berriz GF, Roth FP, Gerszten RE. Sabatine MS, et al. Among authors: roth fp. Circulation. 2005 Dec 20;112(25):3868-75. doi: 10.1161/CIRCULATIONAHA.105.569137. Epub 2005 Dec 12. Circulation. 2005. PMID: 16344383

141

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Gibbons FD, Proft M, Struhl K, Roth FP. Gibbons FD, et al. Among authors: roth fp. Genome Biol. 2005;6(11):R96. doi: 10.1186/gb-2005-6-11-r96. Epub 2005 Nov 1. Genome Biol. 2005. PMID: 16277751 Free PMC article.

142

Towards a proteome-scale map of the human protein-protein interaction network.

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, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. Rual JF, et al. Among authors: roth fp. Nature. 2005 Oct 20;437(7062):1173-8. doi: 10.1038/nature04209. Epub 2005 Sep 28. Nature. 2005. PMID: 16189514

143

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.

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, Vidal M, Piano F. Gunsalus KC, et al. Among authors: roth fp. Nature. 2005 Aug 11;436(7052):861-5. doi: 10.1038/nature03876. Nature. 2005. PMID: 16094371

144

Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae.

Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K. Proft M, et al. Among authors: roth fp. Eukaryot Cell. 2005 Aug;4(8):1343-52. doi: 10.1128/EC.4.8.1343-1352.2005. Eukaryot Cell. 2005. PMID: 16087739 Free PMC article.

145

Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae.

Wong SL, Roth FP. Wong SL, et al. Among authors: roth fp. Genetics. 2005 Oct;171(2):829-33. doi: 10.1534/genetics.105.046060. Epub 2005 Jul 5. Genetics. 2005. PMID: 15998714 Free PMC article.

146

Discovering functional relationships: biochemistry versus genetics.

Wong SL, Zhang LV, Roth FP. Wong SL, et al. Among authors: roth fp. Trends Genet. 2005 Aug;21(8):424-7. doi: 10.1016/j.tig.2005.06.006. Trends Genet. 2005. PMID: 15982781

147

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.

Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP. Zhang LV, et al. Among authors: roth fp. J Biol. 2005;4(2):6. doi: 10.1186/jbiol23. Epub 2005 Jun 1. J Biol. 2005. PMID: 15982408 Free PMC article.

148

Combining biological networks to predict genetic interactions.

Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth FP. Wong SL, et al. Among authors: roth fp. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15682-7. doi: 10.1073/pnas.0406614101. Epub 2004 Oct 20. Proc Natl Acad Sci U S A. 2004. PMID: 15496468 Free PMC article.

149

Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Han JD, et al. Among authors: roth fp. Nature. 2004 Jul 1;430(6995):88-93. doi: 10.1038/nature02555. Epub 2004 Jun 9. Nature. 2004. PMID: 15190252

150

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

Grad YH, Roth FP, Halfon MS, Church GM. Grad YH, et al. Among authors: roth fp. Bioinformatics. 2004 Nov 1;20(16):2738-50. doi: 10.1093/bioinformatics/bth320. Epub 2004 May 14. Bioinformatics. 2004. PMID: 15145800

151

SILVER helps assign peptides to tandem mass spectra using intensity-based scoring.

Gibbons FD, Elias JE, Gygi SP, Roth FP. Gibbons FD, et al. Among authors: roth fp. J Am Soc Mass Spectrom. 2004 Jun;15(6):910-2. doi: 10.1016/j.jasms.2004.02.011. J Am Soc Mass Spectrom. 2004. PMID: 15144981 Free article.

152

Predicting protein complex membership using probabilistic network reliability.

Asthana S, King OD, Gibbons FD, Roth FP. Asthana S, et al. Among authors: roth fp. Genome Res. 2004 Jun;14(6):1170-5. doi: 10.1101/gr.2203804. Epub 2004 May 12. Genome Res. 2004. PMID: 15140827 Free PMC article.

153

Predicting co-complexed protein pairs using genomic and proteomic data integration.

Zhang LV, Wong SL, King OD, Roth FP. Zhang LV, et al. Among authors: roth fp. BMC Bioinformatics. 2004 Apr 16;5:38. doi: 10.1186/1471-2105-5-38. BMC Bioinformatics. 2004. PMID: 15090078 Free PMC article.

154

Global mapping of the yeast genetic interaction network.

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, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. Tong AH, et al. Among authors: roth fp. Science. 2004 Feb 6;303(5659):808-13. doi: 10.1126/science.1091317. Science. 2004. PMID: 14764870

155

Intensity-based protein identification by machine learning from a library of tandem mass spectra.

Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Elias JE, et al. Among authors: roth fp. Nat Biotechnol. 2004 Feb;22(2):214-9. doi: 10.1038/nbt930. Epub 2004 Jan 18. Nat Biotechnol. 2004. PMID: 14730315

156

A map of the interactome network of the metazoan C. elegans.

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, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. Li S, et al. Among authors: roth fp. Science. 2004 Jan 23;303(5657):540-3. doi: 10.1126/science.1091403. Epub 2004 Jan 2. Science. 2004. PMID: 14704431 Free PMC article.

157

Characterizing gene sets with FuncAssociate.

Berriz GF, King OD, Bryant B, Sander C, Roth FP. Berriz GF, et al. Among authors: roth fp. Bioinformatics. 2003 Dec 12;19(18):2502-4. doi: 10.1093/bioinformatics/btg363. Bioinformatics. 2003. PMID: 14668247

158

A non-parametric model for transcription factor binding sites.

King OD, Roth FP. King OD, et al. Among authors: roth fp. Nucleic Acids Res. 2003 Oct 1;31(19):e116. doi: 10.1093/nar/gng117. Nucleic Acids Res. 2003. PMID: 14500844 Free PMC article.

159

Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression.

Kramer MF, Cook WJ, Roth FP, Zhu J, Holman H, Knipe DM, Coen DM. Kramer MF, et al. Among authors: roth fp. J Virol. 2003 Sep;77(17):9533-41. doi: 10.1128/jvi.77.17.9533-9541.2003. J Virol. 2003. PMID: 12915567 Free PMC article.

160

Predicting phenotype from patterns of annotation.

King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP. King OD, et al. Among authors: roth fp. Bioinformatics. 2003;19 Suppl 1:i183-9. doi: 10.1093/bioinformatics/btg1024. Bioinformatics. 2003. PMID: 12855456

161

Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation.

Roth JR, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI. Roth JR, et al. Among authors: roth fp. Genetics. 2003 Apr;163(4):1483-96. doi: 10.1093/genetics/163.4.1483. Genetics. 2003. PMID: 12702691 Free PMC article.

162

Predicting gene function from patterns of annotation.

King OD, Foulger RE, Dwight SS, White JV, Roth FP. King OD, et al. Among authors: roth fp. Genome Res. 2003 May;13(5):896-904. doi: 10.1101/gr.440803. Epub 2003 Apr 14. Genome Res. 2003. PMID: 12695322 Free PMC article.

163

GoFish finds genes with combinations of Gene Ontology attributes.

Berriz GF, White JV, King OD, Roth FP. Berriz GF, et al. Among authors: roth fp. Bioinformatics. 2003 Apr 12;19(6):788-9. doi: 10.1093/bioinformatics/btg088. Bioinformatics. 2003. PMID: 12691998

164

Assessing experimentally derived interactions in a small world.

Goldberg DS, Roth FP. Goldberg DS, et al. Among authors: roth fp. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4372-6. doi: 10.1073/pnas.0735871100. Epub 2003 Apr 3. Proc Natl Acad Sci U S A. 2003. PMID: 12676999 Free PMC article.

165

Judging the quality of gene expression-based clustering methods using gene annotation.

Gibbons FD, Roth FP. Gibbons FD, et al. Among authors: roth fp. Genome Res. 2002 Oct;12(10):1574-81. doi: 10.1101/gr.397002. Genome Res. 2002. PMID: 12368250 Free PMC article.

166

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress.

Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA. Damelin M, et al. Among authors: roth fp. Mol Cell. 2002 Mar;9(3):563-73. doi: 10.1016/s1097-2765(02)00475-6. Mol Cell. 2002. PMID: 11931764 Free article.

167

Bringing out the best features of expression data.

Roth FP. Roth FP. Genome Res. 2001 Nov;11(11):1801-2. doi: 10.1101/gr.215501. Genome Res. 2001. PMID: 11691842 Free article. No abstract available.

168

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.

Roth FP, Hughes JD, Estep PW, Church GM. Roth FP, et al. Nat Biotechnol. 1998 Oct;16(10):939-45. doi: 10.1038/nbt1098-939. Nat Biotechnol. 1998. PMID: 9788350

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