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publications

Our publications can also be found via PubMed or Google Scholar.

Copyrighted text is provided here only to permit fair use.

Current or former members of the Roth Lab are highlighted.


2020 | 2016 | 2012 | 2008 | 2004

2023

  • W van Loggerenberg*, S Sowlati-Hashjin*, J Weile, R Hamilton, A Chawla, D Sheykhkarimli, M Gebbia, N Kishore, L Fresard, S Mustajoki, E Pischik, E Di Pierro, M Barbaro, Y Floderus, C Schmitt, L Gouya, A Colavin, R Nussbaum, ECH Friesema, R Kauppinen, J To-Figueras, AK Aarsand, RJ Desnick†, M Garton†, FP Roth†. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. American Journal of Human Genetics 110(10):1769-1786 (2023). Full Text

  • J Weile, G Ferra, G Boyle, S Pendyala, C Amorosi, C-L Yeh, AG Cote, N Kishore, D Tabet, W van Loggerenberg, A Rayhan, DM Fowler, MJ Dunham, FP Roth†. Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries. bioRxiv https://doi.org/10.1101/2023.02.22.529427 (2023). Full Text

  • J Lacoste, M Haghighi, S Haider, ZY Lin, D Segal, C Reno, WW Qian, X Xiong, H Shafqat-Abbasi, PV Ryder, R Senft, BA Cimini, FP Roth, M Calderwood, D Hill, M Vidal, SS Yi, N Sahni, J Peng, AC Gingras, S Singh, AE Carpenter, M Taipale†. Pervasive mislocalization of pathogenic coding variants underlying human disorders. bioRxiv https://doi: 10.1101/2023.09.05.556368 (2023). Full Text

  • DM Fowler†, DJ Adams, AL Gloyn, WC Hahn, DS Marks, LA Muffley, JT Neal, FP Roth, AF Rubin, LM Starita, ME Hurles†. An Atlas of Variant Effects to understand the genome at nucleotide resolution. Genome Biology 24(1):147 (2023). Full Text

  • Y Zhao, D Tabet, D Rubio Contreras, L Lao, AN Kousholt, J Weile, H Melo, L Hoeg, S Feng, AG Coté, ZY Lin, D Setiaputra, J Jonkers, AC Gingras, F Gómez Herreros, FP Roth, D Durocher†. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Molecular Cell 83(15):2792-2809.e9 (2023). Full Text

  • M Claussnitzer*, VN Parikh*, AH Wagner*, JA Arbesfeld, CJ Bult, HV Firth, LA Muffley, ANN Ba, K Riehle, FP Roth, D Tabet, B Bolognesi†, AM Glazer†, AF Rubin†. Minimum information and guidelines for reporting a multiplexed assay of variant effect. ArXiv arXiv:2306.15113v1 (2023). Full Text

  • S Gersing, TK Schulze, M Cagiada, A Stein, FP Roth, K Lindorff-Larsen†, R Hartmann-Petersen†. Characterizing glucokinase variant mechanisms using a multiplexed abundance assay. bioRxiv https://doi.org/10.1101/2023.05.24.542036 (2023). Full Text

  • S Gersing, M Cagiada, M Gebbia, AP Gjesing, AG Cote, G Seesankar, R Li, D Tabet, J Weile, A Stein, AL Gloyn, T Hansen, FP Roth†, K Lindorff-Larsen†, R Hartmann-Petersen†. A comprehensive map of human glucokinase variant activity. Genome Biology 24(1):97 (2023). Full Text

  • H-W Tang*, K Spirohn*, Y Hu, T Hao, IA Kovács, Y Gao, R Binari, D Yang-Zhou, KH Wan, JS Bader, D Balcha, W Bian, BW Booth, AG Cote, S de Rouck, A Desbuleux, KY Goh, D-K Kim, JJ Knapp, WX Lee, I Lemmens, C Li, M Li, R Li, HJ Lim, Y Liu, K Luck, D Markey, C Pollis, S Rangarajan, J Rodiger, S Schlabach, Y Shen, D Sheykhkarimli, B TeeKing, FP Roth, J Tavernier, MA Calderwood, DE Hill, SE Celniker†, M Vidal†, N Perrimon†, SE Mohr†. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nature Communications 14(1):2162 (2023). Full Text

  • B Weller†, CW Lin, Pogoutse O, M Sauer, N Marin-de la Rosa, A Strobel, V Young, JJ Knapp, A Rayhan, Falter C, D-K Kim, FP Roth†, P Falter-Braun†. A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection. G3: Genes|Genomes|Genetics Online ahead of print (2023). Full Text

  • I Hoskins, S Sun, A Cote, FP Roth, C Cenik†. satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect. Genome Biology 24(1):82 (2023). Full Text

  • B Floyd*, J Weile*, P Kannankeril, A Glazer, C Reuter, C MacRae, E Ashley, D Roden, FP Roth, V Parikh†. Proactive variant effect mapping aids diagnosis in pediatric cardiac arrest. Circulation:Genomic and Precision Medicine 16(1):e003792 (2023). Full Text

  • DK Kim*, B Weller*, CW Lin*, D Sheykhkarimli*, JJ Knapp*, G Dugied, A Zanzoni, C Pons, MJ Tofaute, SB Maseko, K Spirohn, F Laval, L Lambourne, N Kishore, A Rayhan, M Sauer, V Young, H Halder, N Marin-de la Rosa, O Pogoutse, A Strobel, P Schwehn, R Li, S Rothballer, M Altmann, P Cassonnet, G Dugied, AG Cote, LE Vergara, I Hazelwood, BB Liu, M Nguyen, R Pandiarajan, B Dohai, PAR Coloma, J Poirson, P Giuliana, L Willems, M Taipale, Yves Jacob, Tong Hao, DE Hill, C Brun, JC Twizere, D Krapmann, M Heinig, C Falter, P Aloy, C Demeret†, M Vidal†, MA Calderwood†, FP Roth†, P Falter-Braun†. A proteome-scale map of the SARS-CoV-2—human contactome. Nature Biotechnology 41(1):140-149 (2023). Full Text


    2022

  • Y Zhao, D Tabet, DR Contreras, AN Kousholt, J Weile, H Melo, L Hoeg, AG Cote, ZY Lin, D Setiaputra, J Jonkers, AC Gingras, FG Herreros, FP Roth, D Durocher†. Genome-scale mapping of DNA damage suppressors identifies GNB1L as essential for ATM and ATR biogenesis. bioRxiv https://doi.org/10.1101/2022.09.23.508845 (2022). Full Text

  • RA Silverstein, S Sun, M Verby, J Weile, Y Wu, M Gebbia, I Fotiadou, J Kitaygorodsky, FP Roth†. A systematic genotype-phenotype map for missense variants in the human intellectual disability-associated gene GDI1. bioRxiv https://doi.org/10.1101/2021.10.06.463360 (2022). Full Text

  • D Kuang, R Li, Y Wu, J Weile, RA Hegele, FP Roth†. Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choice. bioRxiv https://doi.org/10.1101/2021.09.20.459182 (2022). Full Text

  • D Tabet, V Parikh, P Mali, FP Roth†, M Claussnitzer†. Scalable functional assays for the interpretation of human genetic variation. Annual Review of Genetics (2022). PDF

  • D Choi, N Khan, L Montermini, N Tawil, B Meehan, D-K Kim, FP Roth, M Divangahi, J Rak†. Quantitative proteomics and biological activity of extracellular vesicles engineered to express SARS-CoV-2 spike protein. Journal of Extracelluar Biology 2022;1:e58 (2022). Full Text

  • L Lambourne, A Yadav, Y Wang, A Desbuleux, DK Kim, T Cafarelli, C Pons, IA Kovács, N Jailkhani, S Schlabach, D De Ridder, K Luck, W Bian, Y Shen, Z Yang, M Mee, M Helmy, Y Jacob, I Lemmens, T Rolland, A Cote, M Gebbia, J Knapp, J Mellor, J Reimand, J Tavernier, ME Cusick, P Falter-Braun, K Spirohn, Q Zhong, P Aloy, T Hao, B Charloteaux, FP Roth, DE Hill†, MA Calderwood†,JC Twizere†, M Vidal†. Binary interactome models of inner- versus outer-complexome organization. bioRxiv (doi:10.1101/2021.03.16.435663) (2022). Full Text


    2021

  • Y Wu, R Li, S Sun, J Weile, FP Roth†. Improved pathogenicity prediction for rare human missense variants. American Journal of Human Genetics 108(10):1891-1906 (2021). Full Text

  • J Weile, N Kishore, S Sun, R Maaieh, M Verby, R Li, I Fotiadou, J Kitaygorodsky, Y Wu, A Holenstein, C Bürer, L Blomgren, S Yang, R Nussbaum, R Rozen, D Watkins, M Gebbia, V Kozich, M Garton, DS Froese, FP Roth†. Shifting landscapes of human MTHFR missense-variant effects. American Journal of Human Genetics 108(7):1283-1300 (2021). Full Text

  • A Savinov†, FP Roth†. Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads. Cell Systems 12(7):691-693 (2021). Full Text

  • D Kuang, J Weile, N Kishore, AF Rubin, S Fields, DM Fowler, FP Roth†. MaveRegistry: a collaboration platform for multiplexed assays of variant effect. Bioinformatics (2021). Full Text


    2020

  • D Kuang, R Truty, J Weile, B Johnson, K Nykamp, C Araya, RL Nussbaum, FP Roth†. Prioritizing genes for systematic variant effect mapping. Bioinformatics 36(22-23):5448-5455 (2020). Full Text

  • J-H Kim, Y Seo, M Jo, H Jeon, Y-S Kim, E-J Kim, D Seo, W-H Lee, SR Kim, N Yachie, Q Zhong, M Vidal, FP Roth, K Suk†. A genetic interaction screen in yeast identifies genes relevant to human PAK1 function in glioma. Journal of Biological Chemistry 295(50):16906-16919 (2020). Full Text

  • J van Leeuwen†, C Pons, G Tan, JZ Wang, J Hou, J Weile, M Gebbia, W Liang, E Shuteriqi, Z Li, M Lopes, M Ušaj, A Dos Santos Lopes, N van Lieshout, CL Myers, FP Roth, P Aloy, BJ Andrews† & C Boone†. Systematic analysis of bypass suppression of essential genes. Molecular Systems Biology 16(9):e9828 (2020). Full Text

  • P Samavarchi-Tehrani, H Abdouni, JDR Knight, A Astori, R Samson, Z-Y Lin, D-K Kim, JJ Knapp, J St-Germain, CD Go, B Larsen, CJ Wong, P Cassonnet, C Demeret, Y Jacob, FP Roth, B Raught†, A-C Gingras†. A SARS-CoV-2-host proximity interactome. bioRxiv (2020). Full Text

  • JR St-Germain, A Astori, P Samavarchi-Tehrani, H Abdouni, V Macwan, D-K Kim, JJ Knapp, FP Roth, A-C Gingras†, B Raught†. A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research. bioRxiv (2020). Full Text

  • EMN Laurent, Y Sofianatos, A Komarova, J-P Gimeno, P Samavarchi-Tehrani, D-K Kim, H Abdouni, M Duhamel, P Cassonnet, JJ Knapp, D Kuang, A Chawla, D Sheykhkarimli, A Rayhan, R Li, O Pogoutse, DE Hill, MA Calderwood, P Falter-Braun, P Aloy, U Stelzl, M Vidal, A-C Gingras, GA Pavlopoulos, S Van Der Werf, I Fournier, FP Roth, M Salzet†, C Demeret†, Y Jacob†, E Coyaud†. Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms. bioRxiv (2020). Full Text

  • D-K Kim, JJ Knapp, D Kuang, P Cassonnet, P Samavarchi-Tehrani, H Abdouni, A Rayhan, D Sheykhkarimli, E Coyaud, S van der Werf, C Demeret, A-C Gingras, B Raught, Y Jacob†, FP Roth†. A flexible genome-scale resource of SARS-CoV-2 coding sequence clones. G3: Genes|Genomes|Genetics 10(9):3399-3402 (2020). Full Text

  • D Kuang, J Weile, R Li, TW Ouellette, JA Barber, FP Roth†. MaveQuest: a web resource for planning experimental tests of human variant effects. Bioinformatics 36(12):3938-3940 (2020). Full Text

  • MA Chiasson, NJ Rollins, JJ Stephany, KA Sitko, KA Matreyek, M Verby, S Sun, FP Roth, D DeSloover, D Marks, AE Rettie, DM Fowler† Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020;9:e58026 (2020). Full Text

  • K Luck*, D-K Kim*, L Lambourne*, K Spirohn*, BE Begg, W Bian, R Brignall, T Cafarelli, FJ Campos-Laborie, B Charloteaux, D Choi, AG Cote, M Daley, S Deimling, A Desbuleux, A Dricot, M Gebbia, MF Hardy, N Kishore, JJ Knapp, IA Kovács, I Lemmens, MW Mee, JC Mellor, C Pollis, C Pons, AD Richardson, S Schlabach, B Teeking, A Yadav, M Babor, D Balcha, O Basha, S-F Chin, SG Choi, C Colabella, G Coppin, C D'Amata, D De Ridder, S De Rouck, M Duran-Frigola, H Ennajdaoui, F Goebels, A Gopal, G Haddad, M Helmy, Y Jacob, Y Kassa, R Li, N van Lieshout, A MacWilliams, D Markey, JN Paulson, S Rangarajan, J Rasla, A Rayhan, T Rolland, A San Miguel, Y Shen, D Sheykhkarimli, GM Sheynkman, E Simonovsky, M Tasan, A Tejeda, J-C Twizere, Y Wang, R Weatheritt, J Weile, Y Xia, X Yang, E Yeger-Lotem, Q Zhong, P Aloy, GD Bader, J De Las Rivas, S Gaudet, T Hao, J Rak, J Tavernier, V Tropepe, DE Hill†, M Vidal†, FP Roth†, MA Calderwood†. A reference map of the human protein interactome. Nature 580(7803):402-408 (2020). Full Text

  • AO Helbig†, M Kofler, G Gish, K Lorenzen, M Tucholska, C Zhang, FP Roth, T Pawson, K Colwill & E Petsalaki†. Decoding the functional Fes kinase signaling network topology in a lymphocyte model. bioRxiv 125088 (2020). Full Text

  • PM Muller*, J Rademacher*, RD Bagshaw*, C Wortmann, C Barth, J van Unen, KM Alp, G Giudice, RL Eccles, LE Heinrich, P Pascual-Vargas, M Sanchez-Castro, L Brandenburg, G Mbamalu, M Tucholska, L Spatt, MT Czajkowski, RW Welke, S Zhang, V Nguyen, T Rrustemi, P Trnka, K Freitag, B Larsen, O Popp, P Mertins, A-C Gingras, 121. PM Muller*, J Rademacher*, RD Bagshaw*, C Wortmann, C Barth, J van Unen, KM Alp, G Giudice, RL Eccles, LE Heinrich, P Pascual-Vargas, M Sanchez-Castro, L Brandenburg, G Mbamalu, M Tucholska, L Spatt, MT Czajkowski, RW Welke, S Zhang, V Nguyen, T Rrustemi, P Trnka, K Freitag, B Larsen, O Popp, P Mertins, A-C Gingras, FP Roth, K Colwill, C Bakal, O Pertz, T Pawson, E Petsalaki†, O Rocks†. Systems-analysis of RhoGEF/RhoGAP regulatory proteins reveals spatially organized Rac1 signaling from integrin adhesions. Nature Cell Biology 22(4):498-511 (2020). PDF

  • S Sun†, J Weile†, M Verby, Y Wu, Y Wang, AG Cote, I Fotiadou, J Kitaygorodsky, M Vidal, J Rine, P Jesina, V Kozich†, FP Roth†. A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Genome Medicine 12(1):13 (2020). Full Text

  • A Celaj, M Gebbia, L Musa, AG Cote, J Snider, V Wong, M Ko, T Fong, P Bansal, JC Mellor, G Seesankar, M Nguyen, S Zhou, L Wang, N Kishore, I Stagljar, Y Suzuki, N Yachie† & FP Roth†. Highly combinatorial genetic interaction analysis reveals a multi-drug transporter influence network.. Cell Systems 9: 1–14 (2020) Full Text


    2019

  • D Esposito*, J Weile*, J Shendure, LM Starita, AT Papenfuss, FP Roth†, DM Fowler† & AF Rubin†. MaveDB: An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biology 20(1):223 (2019). Full Text

  • F Yang, D-K Kim, H Nakagawa, S Hayashi, S Imoto, L Stein, FP Roth†. Quantifying immune-based counterselection of somatic mutations.. PLoS Genetics 15(7): e1008227 (2019) Full Text

  • J Zhang, LN Kinch, Q Cong, P Katsonis, O Lichtarge, C Savojardo, G Babbi, PL Martelli, E Capriotti, R Casadio, A Garg, D Pal, J Weile, S Sun, M Verby, FP Roth & NV Grishin†. Assessing predictions on fitness effects of missense variants in calmodulin. Human Mutation 40(9):1463-1473 (2019). PDF

  • Y Wu, J Weile, AG Cote, S Sun, J Knapp, M Verby, FP Roth†. A web application and service for imputing and visualizing missense variant effect maps. Bioinformatics 35(17):3191-3193 (2019). Full Text

  • A Sokolov, S Ashenden, N Sahin, R Lewis, N Erdem, E Ozaltan, A Bender, FP Roth, M Cokol†. Characterizing ABC-transporter substrate-likeness using a clean-slate genetic background. Frontiers in Pharmacology 10:448 (2019). PDF

  • E Deneault, M Faheem, SH White, DC Rodrigues, S Sun, W Wei, A Piekna, T Thompson, JL Howe, L Chalil, V Kwan, S Walker, P Pasceri, FP Roth, RKC Yuen, KK Singh, J Ellis†, SW Scherer†. CNTN5-/+ or EHMT2-/+ human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks. eLife 12(8):pii;e40092 (2019). Full Text


    2018

  • J Weile† & FP Roth†. Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Human Genetics 137(9):665–678 (2018). Full Text

  • ZB Weinstein, N Kuru, S Kiriakov, AC Palmer, AS Khalil, PA Clemons, MH Zaman, FP Roth, M Cokol†. Modeling the impact of drug interactions on therapeutic selectivity. Nature Communications 9(1):3452 (2018). Full Text

  • D Choi, L Montermini, D-K Kim, B Meehan, FP Roth, J Rak†. The impact of oncogenic EGFRvIII on the proteome of extracellular vesicles released from glioblastoma cells. Molecular and Cellular Proteomics. 17(10):1948-1964 (2018). Full Text

  • JJ Diaz-Mejia, A Celaj, JC Mellor, A Cote, A Balint, B Ho, P Bansal, F Shaeri, M Gebbia, J Weile, M Verby, A Karkhanina, Y Zhang, C Wong, J Rich, D Prendergast, G Gupta, S Ozturk, D Durocher, GW Brown, FP Roth†. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Molecular Systems Biology 14(5):e7985 (2018). Full Text


    2017

  • J Weile*, S Sun*, AG Cote, J Knapp, M Verby, JC Mellor, Y Wu, C Pons, C Wong, N van Lieshout, F Yang, M Tasan, G Tan, S Yang, DM Fowler, R Nussbaum, JD Bloom, M Vidal, DE Hill, P Aloy & FP Roth†. A framework for exhaustively mapping functional missense variants. Molecular Systems Biology 13:157 (2017) Full Text

  • I Vigentini†, M Gebbia, A Belotti, R Foschino, FP Roth. CRISPR/Cas9 system as a valuable genome editing tool for wine yeasts with application to decrease urea production. Frontiers in Microbiology 8:2194 (2017) Full Text

  • LM Starita†, N Ahituv, MJ Dunham, JO Kitzman, FP Roth, G Seelig, J Shendure, DM Fowler†. Variant interpretation: functional assays to the rescue. American Journal of Human Genetics 101(3):315-325 (2017). Full Text

  • J Zhang, LN Kinch, Q Cong, J Weile, S Sun, AG Cote, FP Roth, NV Grishin†. Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. Human Mutation 38(9):1051-1063 (2017). PDF

  • M Jo, AY Chung, N Yachie, M Seo, H Jeon, Y Nam, Y Seo, E Kim, Q Zhong, M Vidal, HC Park†, FP Roth†, K Suk†. Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target. Genome Research 27(9):1487-1500 (2017). Full Text

  • A Celaj*, U Schlecht*, JD Smith, W Xu, S Suresh, M Miranda, AM Aparicio, M Proctor, RW Davis, FP Roth†, RP St Onge†. Quantitative analysis of protein interaction network dynamics in yeast. Molecular Systems Biology 13(7):934 (2017). Full Text

  • F Yang, S Sun, G Tan, M Costanzo, DE Hill, M Vidal, BJ Andrews, C Boone, FP Roth†. Identifying pathogenicity of human variants via paralog-based yeast complementation. PLOS Genetics 13(5):e1006779 (2017). Full Text

  • MJ Betts, O Wichmann, M Utz, T Andre, E Petsalaki, P Minguez, L Parca, FP Roth, AC Gavin, P Bork, RB Russell†. Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Computational Biology 13(3):e1005462 (2017). Full Text

  • C Cenik, HN Chua, G Singh, A Akef, MP Snyder, AF Palazzo, MJ Moore† & FP Roth†. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA 23(3):270-283 (2017). Full Text


    2016

  • J van Leeuwen*, C Pons*, JC Mellor, TN Yamaguchi, H Friesen, J Koschwanez, MM Usaj, M Pechlaner, M Takar, M Usaj, B VanderSluis, Kerry Andrusiak, P Bansal, A Baryshnikova, CE Boone, J Cao, A Cote, M Gebbia, G Horecka, I Horecka, E Kuzmin, N Legro, W Liang, N van Lieshout, M McNee, B-J San Luis, F Shaeri, E Shuteriqi, S Sun, L Yang, J-Y Youn, M Yuen, M Costanzo, A-C Gingras, P Aloy, C Oostenbrink, A Murray, TR Graham, CL Myers†, BJ Andrews†, FP Roth† & C Boone†. Exploring genetic suppression interactions on a global scale. Science 354(6312):599,aag0839-1-11 (2016). PDF

  • FP Roth† & J Wakeley†. Taking exception to human eugenics. Genetics 206(2):821-823 (2016). Full Text

  • T Shekhar-Guturja, GM Gunaherath, EM Wijeratne, JP Lambert, AF Averette, SC Lee, T Kim, YS Bahn, F Tripodi, R Ammar, K Dohl, K Niewola-Staszkowska, L Schmitt, RJ Loewith, FP Roth, D Sanglard, D Andes, C Nislow, P Coccetti, AC Gingras, J Heitman, AA Gunatilaka & LE Cowen†. Dual action antifungal small molecule modulates multidrug efflux and TOR signaling. Nature Chemical Biology 12(10):867-875 (2016). Full Text

  • Q Zhong*†, SJ Pevzner*, T Hao, Y Wang, R Mosca, J Menche, M Taipale, M Tasan, C Fan, X Yang, P Haley, RR Murray, F Mer, F Gebreab, S Tam, A MacWilliams, A Dricot, P Reichert, B Santhanam, L Ghamsari, MA Calderwood, T Rolland, B Charloteaux, S Lindquist, AL Barabási, DE Hill, P Aloy, ME Cusick, Y Xia, FP Roth† & M Vidal†. An inter-species protein-protein interaction network across vast evolutionary distance. Molecular Systems Biology 12(4):865 (2016). Full Text

  • N Yachie*†, E Petsalaki*, JC Mellor, J Weile, Y Jacob, M Verby, SB Ozturk, S Li, AG Cote, R Mosca, JJ Knapp, M Ko, A Yu, M Gebbia, N Sahni, S Yi, T Tyagi, D Sheykhkarimli, JF Roth, C Wong, L Musa, J Snider, Y-C Liu, H Yu, P Braun, I Stagljar, T Hao, MA Calderwood, L Pelletier, P Aloy, DE Hill, M Vidal & FP Roth†. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Molecular Systems Biology 12(4):863 (2016). Full Text

  • S Sun, F Yang, G Tan, M Costanzo, R Oughtred, J Hirschman, C Theesfeld, P Bansal, N Sahni, S Yi, A Yu, T Tyagi, C Tie, DE Hill, M Vidal, BJ Andrews, C Boone, K Dolinski & FP Roth†. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Research 26(5):670-80 (2016). Full Text

  • X Yang, J Coulombe-Huntington, S Kang, GM Sheynkman, T Hao, A Richardson, S Sun, F Yang, YA Shen, RR Murray, K Spirohn, BE Begg, M Duran-Frigola, A MacWilliams, SJ Pevzner, Q Zhong, SA Trigg, S Tam, L Ghamsari, N Sahni, S Yi, MD Rodriguez, D Balcha, G Tan, M Costanzo, B Andrews, C Boone, XJ Zhou, K Salehi-Ashtiani, B Charloteaux, AA Chen, MA Calderwood, P Aloy, FP Roth, DE Hill, LM Iakoucheva†, Y Xia† & M Vidal†. Widespread expansion of protein interaction capabilities by alternative splicing. Cell 164(4):805-817 (2016). PDF

  • TV Vo, J Das, MJ Meyer, NA Cordero, N Akturk, X Wei, BJ Fair, AG Degatano, R Fragoza, LG. Liu, A Matsuyama, M Trickey, S Horibata, A Grimson, H Yamano, M Yoshida, FP Roth, JA Pleiss, Y Xia & H Yu†. A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human. Cell 164(1-2):310-323 (2016). PDF


    2015

  • T Hart*, MC Chandrashekhar*, M Aregger*, Z Steinhart, KR Brown, G MacLeod, M Mis, M Zimmermann, A Fradet-Turcotte, S Sun, P Mero, P Dirks, S Sidhu, FP Roth, OS Rissland, D Durocher, S Angers & J Moffat† High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163(6):1515-1526 (2015). PDF

  • E Petsalaki†, AO Helbig, A Gopal, A Pasculescu, FP Roth† & T Pawson Correlation-based identification of kinase-associated networks from global phospho-proteomics datasets. Nucleic Acids Research 43(W1): W276-W282 (2015). Full Text

  • N Sahni, S Yi, M Taipale, JI Fuxman Bass, J Coulombe-Huntington, F Yang, J Peng, J Weile, GI Karras, Y Wang, IA Kovacs, A Kamburov, I Krykbaeva, MH Lam, G Tucker, V Khurana, A Sharma, Y-Y Liu, N Yachie, Q Zhong, Y Shen, A Palagi, A San-Miguel, C Fan, D Balcha, A Dricot, DM Jordan, JM Walsh, AA Shah, X Yang, A Stoyanova, A Leighton, MA Calderwood, Y Jacob, ME Cusick, K Salehi-Ashtiani, LJ Whitesell, S Sunyaev, B Berger, A-L Barabasi, B Charloteaux, DE Hill, T Hao, FP Roth, Y Xia, AJM Walhout, S Lindquist† & M Vidal† Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161(3):647-660 (2015). PDF

  • F Yang, E Petsalaki E, T Rolland, DE Hill, M Vidal & Roth FP†. Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Computational Biology 11(3):e1004147 (2015). Full Text

  • TR Pak, M Rodriguez & FP Roth†. Why clinical trials are terminated. bioRxiv DOI 10.1101/021543 (2015). Full Text

  • M Tasan*, G Musso*, T Hao, M Vidal, CA MacRae & FP Roth†. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nature Methods 12(2):154-159 (2015). PDF


    2014

  • RC Deo†, G Musso, M Tasan, P Tang, A Poon, C Yuan, JF Felix, RS Vasan, R Beroukhim, T De Marco, P-Y Kwok, CA MacRae & FP Roth†. Prioritizing causal disease genes using unbiased genomic features. Genome Biology 15:3274 (2014). PDF

  • M Irimia, RJ Weatheritt, JD Ellis, NN Parikshak, T Gonatopoulos-Pournatzis, M Babor, M Quesnel-Vallieres, J Tapial, B Raj, D O'Hanlon, M Barrios-Rodiles, MJE Sternberg, SP Cordes, FP Roth, JL Wrana, DH Geschwind & BJ Blencowe†. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159(7): 1511-1523 (2014). PDF

  • T Rolland*, M Tasan*, B Charloteaux*, SJ Pevzner*, Q Zhong*, N Sahni*, S Yi*, I Lemmens, C Fontanillo, R Mosca, A Kamburov, SD Ghiassian, X Yang, L Ghamsari, D Balcha, BE Begg, P Braun, M Brehme, MP Broly, A-R Carvunis, D Convery-Zupan, R Corominas, J Coulombe-Huntington, E Dann, M Dreze, A Dricot, C Fan, E Franzosa, F Gebreab, BJ Gutierrez, MF Hardy, M Jin, S Kang, R Kiros, GN Lin, K Luck, A MacWilliams, J Menche, RR Murray, A Palagi, MM Poulin, X Rambout, J Rasla, P Reichert, V Romero, E Ruyssinck, JM Sahalie, A Scholz, AA Shah, A Sharma, Y Shen, K Spirohn, S Tam, AO Tejeda, SA Trigg, J-C Twizere, K Vega, J Walsh, ME Cusick, Y Xia, A-L Barabasi, L Iakoucheva, P Aloy, J De Las Rivas, J Tavernier, MA Calderwood, DE Hill, T Hao, FP Roth† & M Vidal†. A proteome-scale map of the human interactome network. Cell 159(5):1212-1226 (2014). PDF

  • K Yilancioglu, ZB Weinstein, C Meydan, A Akhmetov, I Toprak, A Durmaz, I Iossifov, H Kazan, FP Roth & M Cokol† Target-independent prediction of drug synergies using only drug lipophilicity. Journal of Chemical Information and Modeling 54(8): 2286-2293 (2014). PDF

  • M Cokol†, ZB Weinstein, K Yilancioglu, M Tasan, A Doak, D Cansever, B Mutlu, S Li, R Rodriguez-Esteban, M Akhmedov, A Guvenek, M Cokol, S Cetiner, G Giaever, I Iossifov, C Nislow, B Shoichet & FP Roth†. Large-scale identification and analysis of suppressive drug interactions. Chemistry & Biology 21:541-551 (2014). PDF

  • VM Labunskyy, Y Suzuki, TJ Hanly, A Murao, FP Roth† & VN Gladyshev†. The Insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast. G3: Genes|Genomes|Genetics 4(7):1183-1191 (2014). PDF

  • R Corominas, X Yang, GN Lin, S Kang, Y Shen, L Ghamsari, M Broly, M Rodriguez, S Tam, SA Trigg, C Fan, S Yi, M Tasan, I Lemmens, X Kuang, N Zhao, D Malhotra, JJ Michaelson, V Vacic, MA Calderwood, FP Roth, J Tavernier, S Horvath, K Salehi-Ashtiani, D Korkin, J Sebat, DE Hill, T Hao†, M Vidal†, LM Iakoucheva†. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nature Communications 5:3650 (2014). PDF

  • G Musso, M Tasan, C Mosimann, JE Beaver, E Plovie, LA Carr, HN Chua, J Dunham, K Zuberi, H Rodriguez, Q Morris, L Zon, FP Roth†, and CA MacRae†. Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development 141:224-235 (2014). PDF


    2013

  • SR Sunyaev† & Roth FP†. Systems biology and the analysis of genetic variation. Current Opinion in Genetics & Development 23(6):599-601 (2013). PDF

  • J Das, TV Vo, X Wei, JC Mellor, V Tong, AG Degatano, X Wang, L Wang, NA Cordero, N Kruer-Zerhusen, A Matsuyama, JA Pleiss, SM Lipkin, M Yoshida, FP Roth & H Yu†. Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Science Signaling 6(276):ra38 (2013). PDF

  • TR Pak & FP Roth†. ChromoZoom: a flexible, fluid, web-based genome browser. Bioinformatics 29(3):384-6 (2013). Full Text

  • K Mahadevan, H Zhang, A Akef, XA Cui, S Gueroussov, C Cenik, FP Roth & AF Palazzo†. RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins. PLOS Biology 11(4):e1001545 (2013). Full Text


    2012

  • Y Suzuki, J Stam, M Novotny, N Yachie, RS Lasken & FP Roth. The Green Monster process for the generation of yeast strains carrying multiple gene deletions. Journal of Visualized Experiments 70, e4072 (2012). Full Text

  • A Bicknell, C Cenik, FP Roth & M Moore†. Introns in UTRs: Why we should stop ignoring them. BioEssays 34(12):1025-1034 (2012). PDF

  • O Rozenblatt-Rosen*, RC Deo*, M Padi*, G Adelmant*, MA Calderwood, T Rolland, M Grace, A Dricot, M Askenazi, M Tavares, SJ Pevzner, F Abderazzaq, D Byrdsong, AR Carvunis, AA Chen, J Cheng, M Correll, M Duarte, C Fan, MC Feltkamp, SB Ficarro, R Franchi, BK Garg, N Gulbahce, T Hao, AM Holthaus, R James, A Korkhin, L Litovchick, JC Mar, TR Pak, S Rabello, R Rubio, Y Shen, S Singh, JM Spangle, M Tasan, S Wanamaker, JT Webber, J Roecklein-Canfield, E Johannsen, AL Barabasi, R Beroukhim, E Kieff, ME Cusick, DE Hill†, K Munger†, JA Marto†, J Quackenbush†, FP Roth†, JA DeCaprio† & M Vidal†. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 487(7408):491-495 (2012). PDF Supplementary Materials

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    Research Watch: Tumor Virus-Induced Host Network Perturbations Identify Cancer Genes. Cancer Discovery Full Text

    Research Highlights: Identifying driver mutations with the help of viruses. Nature Reviews Clinical Oncology Full Text

  • N Gulbahce*, H Yan*, A Dricot, M Padi, D Byrdsong, R Franchi, DS Lee, O Rozenblatt-Rosen, JC Mar, MA Calderwood, A Baldwin, B Zhao, B Santhanam, P Braun, N Simonis, KW Huh, K Hellner, M Grace, A Chen, R Rubio, JA Marto, NA Christakis, E Kieff, FP Roth, J Roecklein-Canfield, JA Decaprio, ME Cusick, J Quackenbush, DE Hill, K Munger, M Vidal† & AL Barabasi†. Viral perturbations of host networks reflect disease etiology. PLoS Computational Biology 8(6):e1002531 (2012). Full Text

  • E Cheng, JA Vaisica, J Ou, A Baryshnikova, Y Lu, FP Roth, GW Brown†. Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae. Genetics 192(1):147-160 (2012). Full Text

  • M Tasan, HJ Drabkin, JE Beaver, HN Chua, J Dunham, W Tian, JA Blake & FP Roth†. A resource of quantitative functional annotation for Homo sapiens genes. G3: Genes, Genomes, Genetics 2(2):223-233 (2012). Full Text

  • A Derti & FP Roth†. Response to "MHC-dependent mate choice in humans: Why genomic patterns from the HapMap European American data set support the hypothesis" (DOI: 10.1002/bies.201100150): HapMap genotypes do not confidently support a role for the MHC locus in human mate selection.. BioEssays 6(4):e1000925 (2012). PDF

  • O Stegle, FP Roth, Q Morris, J Listgarten. Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. Proceedings of the Pacific Symposium on Biocomputing 2012:323-326 (2012). PDF


    2011

  • M Cokol, HN Chua, M Tasan, B Mutlu, ZB Weinstein, Y Suzuki, ME Nergiz, M Costanzo, A Baryshnikova, G Giaever, C Nislow, CL Myers, BJ Andrews, C Boone & FP Roth†. Systematic exploration of synergistic drug pairs. Molecular Systems Biology 7(544):1-9 (2011). PDF

  • Arabidopsis Interactome Mapping Consortium [ M Dreze, A-R Carvunis, B Charloteaux, M Galli, SJ Pevzner & M Tasan contributed equally to this work and should be considered 'co-first' authors]. Evidence for network evolution in an Arabidopsis interactome map. Science 333(6042):601-7 (2011). PDF

  • MS Mukhtar, A-R Carvunis, M Dreze, P Epple, J Steinbrenner, J Moore, M Tasan, M Galli, T Hao, MT Nishimura, SJ Pevzner, SE Donovan, L Ghamsari, B Santhanam, V Romero, MM Poulin, F Gebreab, BJ Gutierrez, S Tam, D Monachello, M Boxem, CJ Harbort, N McDonald, L Gai, H Chen, Y He, EU Effectoromics Consortium, J Vandenhaute, FP Roth, DE Hill, JR Ecker, M Vidal†, J Beynon†, P Braun†, JL Dangl†. Independently evolved virulence effectors converge onto cellular hubs in a plant immune system network. Science 333(6042):596-601 (2011). PDF

  • HN Chua & FP Roth†. Discovering the targets of drugs via computational systems biology. Journal of Biological Chemistry 286(27):23653-23658 (2011). Full Text

  • H Yu, L Tardivo, S Tam, E Weiner, F Gebreab, C Fan, N Svrzikapa, T Hirozane-Kishikawa, E Rietman, X Yang, J Sahalie, K Salehi-Ashtiani, T Hao, ME Cusick, DE Hill, FP Roth, P Braun & M Vidal†. Next-generation sequencing to generate interactome datasets. Nature Methods 8(6):478-80 (2011). PDF

  • C Cenik, HN Chua, H Zhang, S Tarnawsky, A Akef, A Derti, M Tasan, MJ Moore, AF Palazzo† & FP Roth† Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS Genetics 7(4):e1001366 (2011). Full Text

  • K Suk, J Choi, Y Suzuki, SB Ozturk, JC Mellor, KH Wong, JL MacKay, RI Gregory & FP Roth† Reconstitution of human RNA interference in budding yeast. Nucleic Acids Research 39(7):e43 (2011). Full Text

    Research Highlight: Lab Times 4:46 (2011). PDF

  • Y Suzuki, RP St Onge, R Mani, OD King, A Heilbut, VM Labunskyy, W Chen, L Pham, LV Zhang, AH Tong, C Nislow, G Giaever, VN Gladyshev, M Vidal, P Schow, J Lehar & FP Roth†. Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nature Methods 8(2):159-64 (2011). PDF

  • CF Sephton, C Cenik, A Kucukural, EB Dammer, B Cenik, Y Han, CM Dewey, FP Roth, J Herz, J Peng, MJ Moore & Yu G† Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. Journal of Biological Chemistry 286(2):1204-15. (2011) Full Text


    2010

  • GD Lewis, L Farrell, MJ Wood, M Martinovic, Z Arany, GC Rowe, A Souza, S Cheng, EL McCabe, E Yang, X Shi, R Deo, FP Roth, A Asnani, EP Rhee, DM Systrom, MJ Semigran, RS Vasan, SA Carr, TJ Wang, MS Sabatine, CB Clish & RE Gerszten†. Metabolic signatures of exercise in human plasma. Science Translational Medicine 2(33):33ra37 (2010). PDF

  • JE Beaver, M Tasan, F Gibbons, W Tian, TR Hughes & FP Roth†. FuncBase: A resource for quantitative gene function annotation. Bioinformatics 26(14):1806-7 (2010). Full Text Software

  • A Derti, C Cenik, P Kraft & FP Roth† Absence of evidence for MHC-dependent mate selection within HapMap populations. PLoS Genetics 6(4):e1000925 (2010). Full Text

  • C Cenik, A Derti, JC Mellor, GF Berriz & FP Roth†. Genome-wide functional analysis of human 5' untranslated region introns. Genome Biology 11(3):R29 (2010). PDF

  • E Kugelberg†, E Kofoid, DI Andersson, Y Lu, J Mellor, FP Roth & JR Roth The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types.. Genetics 185(1):65-80. (2010). Full Text

  • H Yan, K Venkatesan, JE Beaver, N Klitgord, MA Yildirim, T Hao, DE Hill, ME Cusick, N Perrimon, FP Roth† & M Vidal† A genome-wide gene function prediction resource for Drosophila melanogaster. PLoS One 5(8):e12139 (2010). Full Text

  • RC Deo, L Hunter, GD Lewis, G Pare, RS Vasan, D Chasman, TJ Wang, RE Gerszten & FP Roth†. Interpreting metabolomic profiles using unbiased pathway models. PLoS Computational Biology 6(2):e1000692 (2010). Full Text

  • I Jurak, MF Kramer, JC Mellor, AL van Lint, FP Roth, DM Knipe & DM Coen†. Numerous conserved and divergent microRNAs expressed by Herpes Simplex Viruses 1 and 2. Journal of Virology 84(9):4659-72 (2010). PDF

  • M Costanzo, A Baryshnikova, J Bellay, Y Kim, ED Spear, CS Sevier, H Ding, JLY Koh, K Toufighi, S Mostafavi, J Prinz, RP St. Onge, B VanderSluis, T Makhnevych, FJ Vizeacoumar, S Alizadeh, S Bahr, RL Brost, Y Chen, M Cokol, R Deshpande, Z Li, Z-Y Lin, W Liang, M Marback, J Paw, B-J San Luis, E Shuteriqi, AHY Tong, N van Dyk, IM Wallace, JA Whitney, MT Weirauch, G Zhong, H Zhu, WA Houry, M Brudno, S Ragibizadeh, B Papp, C Pal, FP Roth, G Giaever, C Nislow, OG Troyanskaya, H Bussey, GD Bader, A-C Gingras, QD Morris, PM Kim, CA Kaiser, CL Myers†, BJ Andrews† & C Boone†. The genetic landscape of a cell. Science 327:425-431 (2010). PDF


    2009

  • GF Berriz, JE Beaver, C Cenik, M Tasan & FP Roth†. Next generation software for functional trend analysis. Bioinformatics 25(22):3043-3044 (2009). Full Text Software

  • K Salehi-Ashtiani, C Lin, T Hao, Y Shen, D Szeto, X Yang, L Ghamsari, H Lee, C Fan, RR Murray, S Milstein, N Svrzikapa, ME Cusick, FP Roth, DE Hill & Marc Vidal†. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Research 19(12):2334-42 (2009). PDF

  • RC Deo† & FP Roth. Pathways of the heart. Circulation: Cardiovascular Genetics 2(4):303-305 (2009). PDF

  • AM Smith, LE Heisler, J Mellor, F Kaper, MJ Thompson, M Chee, FP Roth, G Giaever† & C Nislow†. Quantitative phenotyping via deep barcode sequencing. Genome Research 19(10):1836-42 (2009) PDF

  • FP Roth, HD Lipshitz & BJ Andrews. Q&A: Epistasis. Journal of Biology 8:35 (2009). PDF , Full Text

  • P Braun, M Tasan, M Dreze, M Barrios-Rodiles, I Lemmens, H Yu, JM Sahalie, RR Murray, L Roncari, AS de Smet, K Venkatesan, JF Rual, J Vandenhaute, ME Cusick, T Pawson, DE Hill, J Tavernier†, JL Wrana†, FP Roth† & M Vidal†. An experimentally derived confidence score for binary protein-protein interactions. Nature Methods 6(1):91-97 (2009). PDF

    News article: K. Cottingham. Confidence score for interactions: Researchers report a new way to determine whether a binary PPI is a true positive. Journal of Proteome Research Feb 17 (2009). Full text

  • K Venkatesan, JF Rual, A Vazquez, U Stelzl, I Lemmens, T Hirozane-Kishikawa, T Hao, M Zenkner, X Xin, KI Goh, MA Yildirim, N Simonis, K Heinzmann, F Gebreab, JM Sahalie, S Cevik, C Simon, AS de Smet, E Dann, A Smolyar, A Vinayagam, H Yu, D Szeto, H Borick, A Dricot, N Klitgord, RR Murray, C Lin, M Lalowski, J Timm, K Rau, C Boone, P Braun, ME Cusick, FP Roth, DE Hill, J Tavernier†, EE Wanker†, AL Barabasi† & M Vidal†. An empirical framework for binary interactome mapping. Nature Methods 6(1):83-90 (2009). PDF

  • N Simonis, J-F Rual, A-R Carvunis, M Tasan, I Lemmens, T Hirozane-Kishikawa, T Hao, JM Sahalie, K Venkatesan, F Gebreab, S Cevik, N Klitgord, C Fan, P Braun, N Li, N Ayivi-Guedehoussou, E Dann, N Bertin, D Szeto, A Dricot, M Yildirim, C Lin, A-S de Smet, H-L Kao, C Simon, A Smolyar, J S Ahn, M Tewari, M Boxem, S Milstein, H Yu, M Dreze, J Vandenhaute, KC Gunsalus, ME Cusick, DE Hill†, J Tavernier†, FP Roth† & M Vidal†. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods 6(1):47-54 (2009). PDF

  • ME Cusick, H Yu, A Smolyar, K Venkatesan, A-R Carvunis, N Simonis, J-F Rual, H Borick, P Braun, M Dreze, J Vandenhaute, M Galli, J Yazaki, DE Hill, JR Ecker, FP Roth & Marc Vidal†. Literature-curated protein interaction datasets. Nature Methods (Perspective) 6(1):39-46 (2009). PDF


  • 2008

  • NJ Martinez, MC Ow, MI Barrasa, M Hammell, R Sequerra, L Doucette-Stamm, FP Roth, VR Ambros & AJ Walhout†. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes & Development 22(18):2535-2549 (2008). PDF

    Research Highlight: Nature Reviews Genetics 9:813 (2008). Full Text

  • J Klekota & FP Roth†. Chemical substructures that enrich for biological activity. Bioinformatics 24(21):2518-2525 (2008). Full Text

  • GD Lewis, R Wei, E Liu, E Yang, X Shi, M Martinovic, L Farrell, A Asnani, M Cyrille, A Ramanathan, O Shaham, GF Berriz, PA Lowry, IF Palacios, M Tasan, FP Roth, J Min, C Baumgartner, H Keshishian, T Addona, VK Mootha, A Rosenzweig, SA Carr, MA Fifer, MS Sabatine & RE Gerszten†. Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. J Clin Invest 118(10):3503-3512 (2008). Full Text

    News article: How to spot a heart attack soon after it occurs. ScienceDaily Sep 5 (2008). Full text

    News article: S Stiles. Groundwork laid for assays that point to MI within minutes of infarct onset. theHeart.Org Sep 19 (2008). Full text

  • H Yu*, P Braun*, MA Yildirim*, I Lemmens, K Venkatesan, J Sahalie, T Hirozane-Kishikawa, F Gebreab, N Li, N Simonis, T Hao, JF Rual, A Dricot, A Vazquez, RR Murray, C Simon, L Tardivo, S Tam, N Svrzikapa, C Fan, AS de Smet, A Motyl, ME Hudson, J Park, X Xin, ME Cusick, T Moore, C Boone, M Snyder, FP Roth, AL Barabasi, J Tavernier, DE Hill & M Vidal†. High-quality binary protein interaction map of the yeast interactome network. Science 322(5898):104-10 (2008). PDF

  • GF Berriz & FP Roth†. The Synergizer service for translating gene, protein, and other biological identifiers. Bioinformatics 24(19):2272-3 (2008). Full Text

  • M Boxem, Z Maliga, N Klitgord, N Li, I Lemmens, M Mana, L de Lichtervelde, J Mul, D van de Peut, M Devos, N Simonis, MA Yildirim, M Cokol, H-L Kao, H Wang, A-S de Smet, A-L Schlaitz, T Hao, S Milstein, C Fan, M Tipsword, K Drew, M Galli, K Rhrissorrakrai, D Drechsel, D Koller, FP Roth, LM Iakoucheva, K Dunker, R Bonneau, KC Gunsalus, DE Hill, F Piano, J Tavernier, S van den Heuvel, AA Hyman & M Vidal†. A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134(3):534-545 (2008). PDF

  • TR Hughes & FP Roth. A race through the maze of genomic evidence. Genome Biology 9 Suppl 1:S1 (2008). PDF

  • L Pena-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, M Leone, A Pagnani, WK Kim, C Krumpelman, W Tian, G Obozinski, Y Qi, S Mostafavi, GN Lin, GF Berriz, FD Gibbons, G Lanckriet, J Qiu, C Grant, Z Barutcuoglu, DP Hill, D Warde-Farley, C Grouios, D Ray, JA Blake, M Deng, M Jordan, WS Noble, Q Morris, J Klein-Seetharaman, Z Bar-Joseph, T Chen, F Sun, OG Troyanskaya, EM Marcotte, D Xu, TR Hughes† & FP Roth†. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology 9 Suppl 1:S2 (2008). PDF

  • W Tian, LV Zhang, M Tasan, FD Gibbons, OD King, J Park, Z Wunderlich, JM Cherry & FP Roth†. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology 9 Suppl 1:S7 (2008). PDF

  • M Tasan, W Tian, DP Hill, FD Gibbons, JA Blake & FP Roth†. An en masse phenotype and function prediction system for M. musculus. Genome Biology 9 Suppl 1:S8 (2008). PDF

  • K Salehi-Ashtiani, X Yang, A Derti, W Tian, T Hao, C Lin, K Makowski, L Shen, RR Murray, D Szeto, N Tusneem, DR Smith, ME Cusick, DE Hill, FP Roth† & M Vidal†. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature Methods 5(7):597-600 (2008). PDF Supplement

  • R Mani, RP St.Onge., JL Hartman IV, G Giaever & FP Roth†. Defining genetic interaction. Proceedings of the National Academy of Sciences 105(9):3461-3466 (2008). PDF Supplement

    Research Highlight: Nature Reviews Genetics 9:253 (2008). PDF


  • 2007

  • S Komili, NG Farny, FP Roth† & PA Silver†. Functional specificity among ribosomal proteins regulates gene expression. Cell 131:557-571 (2007). PDF Supplement

    Preview article: K McIntosh & J Warner. Yeast Ribosomes: Variety Is the Spice of Life Cell 131(3):450-451 (2007). Full text

    News article: M Leslie. Unique tasks for ribosomal paralogues. Journal of Cell Biology 179(5):808 (2007). Full text

    News article: C Humphries. Ribosomes: More Special than You Think. Focus Nov 9 (2007). Full text

    Research Highlight: Nature Reviews Genetics 8:909 (2007). PDF

  • FP Roth & B Andrews. Systems biology: A shared goal with diverse views. ASBMB Today September (2007). PDF
  • N Bertin, N Simonis, D Dupuy, ME Cusick, J-DJ Han, HB Fraser†, FP Roth† & M Vidal†. Confirmation of organized modularity in the yeast interactome. PLoS Biology 5(6) e153 (2007). Full text
  • D Dupuy, N Bertin, CA Hidalgo R, K Venkatesan, D Tu, D Lee, J Rosenberg, N Svrzikapa, A Blanc, A Carnec, A-R Carvunis, R Pulak, J Shingles, J Reece-Hoyes, R Hunt-Newbury, R Viveiros, WA Mohler, M Tasan, FP Roth, C Le Peuch, IA Hope, R Johnsen, DG Moerman, A-L Barabasi†, D Baillie† & M Vidal†. Genome-scale analysis of in vivo spatiotemporal promoter activity in C. elegans. Nature Biotechnology 25(6):663-668 (2007). PDF Supplement
  • S Komili & FP Roth†. Genetic interaction screens advance in reverse. Genes & Development (Perspective) 21(2):137-42 (2007). PDF
  • RP St Onge, R Mani, J Oh, M Proctor, E Fung, RW Davis, C Nislow, FP Roth† & G Giaever†. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nature Genetics 39(2):199-206 (2007). PDF Supplement
  • H Huang, LV Zhang, FP Roth & JS Bader†. Probabilistic paths in protein interaction networks. Proceedings of the RECOMB Conferences on Systems Biology and Computational Proteomics (2007). PDF

  • 2006

  • A Derti, FP Roth, GM Church & C-T Wu†. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nature Genetics 38(10):1216-1220 (2006). PDF Supplement
  • Y Suzuki & FP Roth†. Systematic genetics swims forward elegantly. Molecular Systems Biology (News and Views) 2:48 (2006). Full Text
  • J Klekota†, E Brauner, FP Roth† & SL Schreiber. Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects. J. Chem. Inf. Model. 46: 1549-1562 (2006). PDF

  • J Klekota†, FP Roth & SL Schreiber. Query Chem: a Google-powered web search combining text and chemical structures. Bioinformatics 22(13):1670-1673 (2006). Full Text Software

  • 2005

  • MS Sabatine, E Liu, DA Morrow, E Heller, M Askenazi, R McCarroll, R Weigand, GF Berriz, FP Roth & RE Gerszten†. Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation 112(25):3868-3875 (2005). PDF

  • FD Gibbons, M Proft, K Struhl & FP Roth†. Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biology 6(11):R96 (2005). PDF Software

  • SL Wong & FP Roth†. Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae. Genetics 171(2):829-833 (2005). PDF Supplement

  • J-F Rual, K Venkatesan, T Hao, T Hirozane-Kishikawa, A Dricot, N Li, GF Berriz, FD Gibbons, M Dreze, N Ayivi-Guedehoussou, N Klitgord, C Simon, M Boxem, S Milstein, J Rosenberg, DS Goldberg, LV Zhang, SL Wong, G Franklin, S Li, JS Albala, J Lim, C Fraughton, E Llamosas, S Cevik, C Bex, P Lamesch, RS Sikorski, J Vandenhaute, HY Zoghbi, A Smolyar, S Bosak, R Sequerra, L Doucette-Stamm, ME Cusick, DE Hill†, FP Roth† & M Vidal†. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-1178 (2005). PDF Supplement

  • KC Gunsalus*, H Ge*, AJ Schetter*, DS Goldberg*, J-DJ Han, T Hao, N Bertin, N Li, J Huang, L-S Chuang, R Mani, GF Berriz, AA Hyman, B Sonnichsen, CJ Echeverri, FP Roth†, M Vidal† & F Piano†. Predictive models of molecular machines involved in C. elegans early embryogenesis. Nature 436(7052):861-865 (2005). PDF Supplement

    Related news piece: E Kritikou Molecular networks - The power of prediction. Nature Reviews Molecular Cell Biology 6(10):752-753 (2005). Full Text

  • M Proft, FD Gibbons, Copeland M, Roth FP & K Struhl†. Genome-wide identification of Sko1 target promoters reveals a regulatory network operated upon osmotic stress in Saccharomyces cerevisiae. Eukaryotic Cell 4(8):1343-1352 (2005). PDF

  • SL Wong, LV Zhang, & FP Roth†. Discovering functional relationships: biochemistry versus genetics. Trends in Genetics 21(8): 424-427 (2005). PDF Supplement

  • LV Zhang, OD King, SL Wong, DS Goldberg, AHY Tong, G Lesage, B Andrews, H Bussey, C Boone & FP Roth†. Motifs, themes and thematic maps of an integrated S. cerevisiae interaction network. Journal of Biology 4:6 (2005). Full Text

    Related news piece: JB Weitzman. A road map of yeast interactions. Journal of Biology 4:4 (2005). Full Text

    Related news piece: Research highlights. Nature 435:717 (2005). PDF

    Related minireview: MJ Herrgard & BO Palsson. Untangling the web of functional and physical interactions in yeast. Journal of Biology 4:5 (2005). PDF


  • 2004

  • SL Wong, LV Zhang, AHY Tong, Z Li, DS Goldberg, OD King, G Lesage, M Vidal, B Andrews, H Bussey, C Boone & FP Roth†. Combining biological networks to predict genetic interactions. Proceedings of the National Academy of Sciences 101(44): 15682-15687 (2004). PDF Supplement

  • S Asthana,OD King,FD Gibbons & FP Roth†. Predicting protein complex membership using probabilistic network reliability. Genome Research 14(6):1170-1175 (2004). PDF Software

  • J-DJ Han, N Bertin, T Hao, DS Goldberg, GF Berriz, LV Zhang, D Dupuy, AJM Walhout, ME Cusick, FP Roth & M Vidal†. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430(6995):88-93 (2004). PDF

  • YH Grad, FP Roth, MS Halfon & GM Church†. Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura. Bioinformatics 20(16):2738-2750 (2004). PDF

  • FD Gibbons, JE Elias, SP Gygi & FP Roth†. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Journal of the American Society for Mass Spectrometry 15(6):910-912 (2004). PDF Software

  • LV Zhang, SL Wong, OD King & FP Roth†. Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5:38 (2004). PDF

  • AHY Tong, G Lesage, GD Bader, H Ding, H Xu, X Xin, J Young, GF Berriz, RL Brost, M Chang, Y Chen, X Cheng, G Chua, H Friesen, DS Goldberg, J Haynes, C Humphries, G He, S Hussein, L Ke, N Krogan, Z Li, JN Levinson, H Lu, P Menard, C Munyana, AB Parsons, O Ryan, R Tonikian, T Roberts, A-M Sdicu, J Shapiro, B Sheikh, B Suter, SL Wong, LV Zhang, H Zhu, CG Burd, S Munro, C Sander, J Rine, J Greenblatt, M Peter, A Bretscher, G Bell, FP Roth, GW Brown, B Andrews†, H Bussey† & C Boone†. Global mapping of the yeast genetic interaction network. Science 303: 808-813 (2004). PDF Supplement
  • JE Elias, FD Gibbons, OD King, FP Roth*† & SP Gygi*. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology, 22(2):214-9 (2004). PDF
  • S Li, CM Armstrong, N Bertin, H Ge, S Milstein, M Boxem, P-O Vidalain, J-DJ Han, A Chesneau, T Hao, DS Goldberg, N Li, M Martinez, J-F Rual, P Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose, H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S van den Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill & M Vidal†. A map of the interactome network of the metazoan C. elegans. Science, 303: 540-543 (2004). PDF

  • 2003

  • GF Berriz, OD King, B Bryant, C Sander & FP Roth†. Characterizing gene sets with FuncAssociate. Bioinformatics 19(18):2502-2504 (2003). Full Text Software

  • JR Roth†, E Kofoid, FP Roth, OG Berg, J Seger & DI Andersson. Adaptive mutation requires no mutagenesis—only growth under selection: a response. Genetics 165(4): 2319-2321 (2003). PDF
  • OD King† & FP Roth. A non-parametric model for transcription factor binding sites. Nucleic Acids Research 31(19):e116 (2003). Full Text
  • OD King†. Bounds for DNA codes with constant GC-content. Electronic Journal of Combinatorics 10(1):R33 (2003). PDF
  • MF Kramer, WJ Cook, FP Roth, J Zhu, H Holman, DM Knipe & DM Coen†. Latent Herpes Simplex Virus infection of sensory neurons alters neuronal gene expression. Journal of Virology 77(17):9533-9541 (2003).
  • PDF

  • OD King, JC Lee, AM Dudley, DM Janse, GM Church & FP Roth†. Predicting phenotype from patterns of annotation. Bioinformatics (ISMB Proceedings Issue) 19 Suppl 1:I183-I189 (2003). PDF
  • JR Roth†, E Kofoid, FP Roth, OG Berg, J Seger & DI Andersson. Regulating general mutation rates: Examination of the Hypermutable State Model for Cairnsian adaptive mutation. Genetics 163(4):1483-1496 (2003). PDF
  • GF Berriz, JV White, OD King & FP Roth†. GoFish finds genes with combinations of Gene Ontology attributes, Bioinformatics 19(6):788-789 (2003). Full Text Software

  • OD King, RE Foulger, SS Dwight, JV White & FP Roth. Predicting gene function from patterns of annotation. Genome Research 13(5):896-904 (2003). PDF
  • DS Goldberg & FP Roth†. Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences 100(8): 4372-4376 (2003). PDF

  • 2002

  • FD Gibbons & FP Roth. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Research 12(10): 1574-1581 (2002). PDF Software

  • M Damelin, I Simon, TI Moy, B Wilson, S Komili , P Tempst, FP Roth, RA Young, BR Cairns & PA Silver†. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Molecular Cell 9: 563-573 (2002). PDF

  • pre-2002

  • FP Roth, Bringing out the best features of expression data. Genome Research(Insight/Outlook). 11(11):1801-1802 (2001). PDF
  • FP Roth, JD Hughes, PW Estep & GM Church†. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology, 16: 939-945 (1998). PDF
  • Software

  • FP Roth. Regulons revealed with gene expression data and studies on DNA sequencing via ion conductance. Doctoral Thesis Presented to the Harvard University Committee on Higher Degrees in Biophysics (1998). PDF


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    Donnelly Centre for Cellular & Biomolecular Research, University of Toronto Samuel Lunenfeld Research Institute, Mt. Sinai Hospital