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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <title>Roth Laboratory - Publications</title> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link href="rothlab.css" rel="stylesheet" type="text/css"> </head> <body><center><table cellpadding="0" cellspacing="0" border="0"><tr><td><img src="images/subheader.gif" width="760" height="52"></td> </tr><tr><td><a href="index.html"><img src="images/subbut1_home.gif" alt=" home " width="77" height="21" border="0"></a><a href="research.html"><img src="images/subbut2_research.gif" alt=" research " width="96" height="21" border="0"></a><a href="people.html"><img src="images/subbut3_people.gif" alt=" people " width="77" height="21" border="0"></a><a href="resources.html"><img src="images/subbut4_resources.gif" alt=" resources " width="97" height="21" border="0"></a><a href="publications.html"><img src="images/subbut5_publications_on.gif" alt=" publications " width="115" height="21" border="0"></a><a href="software.html"><img src="images/subbut6_software.gif" alt=" software " width="97" height="21" border="0"></a><a href="directions.html"><img src="images/subbut7_directions.gif" alt=" directions " width="102" height="21" border="0"></a><a href="contact.html"><img src="images/subbut8_contact.gif" alt=" contact " width="99" height="21" border="0"></a></td> </tr><TR><TD colspan=2 bgcolor="#FFFFFF"> <table><tr><td><img src="images/1x1.gif" width="60" height="400"></td><td valign=top align=left width="640"><img src="images/1x1.gif" width="640" height="10"> <img src="images/subhead_publications.gif" alt="publications" width="196" height="35">  Our publications can also be found via <a href= https://pmlegacy.ncbi.nlm.nih.gov/?term=%28%28roth+fp%5BAuthor%5DOR+roth+fp%5BIR%5D%29+AND+%281998%5BPDAT%5D+%3A+3000%5BPDAT%5D%29%29+NOT+speech%5BAFFL%5D+NOT+child%5BAFFL%5D+NOT+%22J+Speech+Lang+Hear+Res%22%5BJournal%5D&sort=date&size=200 >PubMed</a> or <a href="http://scholar.google.ca/citations?hl=en&user=a2FJg9wAAAAJ">Google Scholar</a>. Copyrighted text is provided here only to permit <a href="http://www.copyright.gov/title17/92chap1.html#107">fair use</a>. Current or former members of the Roth Lab are highlighted. <a href="#2020">2020</a> | <a href="#2016">2016</a> | <a href="#2012">2012</a> | <a href="#2008">2008</a> | <a href="#2004">2004</a> <h4><a name="2023">2023</a></h4> <li> 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&dagger;, M Garton&dagger;, FP Roth&dagger;. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. American Journal of Human Genetics 110(10):1769-1786 (2023). <a href="publications/vanLoggerenberg_AJHG_2023.html" target="_blank">Full Text</a> <li> 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&dagger;. Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries. bioRxiv https://doi.org/10.1101/2023.02.22.529427 (2023). <a href="publications/Weile_bioRxiv_2023.html" target="_blank">Full Text</a> <li> 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&dagger;. Pervasive mislocalization of pathogenic coding variants underlying human disorders. bioRxiv https://doi: 10.1101/2023.09.05.556368 (2023). <a href="publications/Lacoste_bioRxiv_2023.html" target="_blank">Full Text</a> <li> DM Fowler&dagger;, DJ Adams, AL Gloyn, WC Hahn, DS Marks, LA Muffley, JT Neal, FP Roth, AF Rubin, LM Starita, ME Hurles&dagger;. An Atlas of Variant Effects to understand the genome at nucleotide resolution. Genome Biology 24(1):147 (2023). <a href="publications/Fowler_GenomeBiology_2023.html" target="_blank">Full Text</a> <li> 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&dagger;. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Molecular Cell 83(15):2792-2809.e9 (2023). <a href="publications/Zhao_MolCell_2023.html" target="_blank">Full Text</a> <li> M Claussnitzer*, VN Parikh*, AH Wagner*, JA Arbesfeld, CJ Bult, HV Firth, LA Muffley, ANN Ba, K Riehle, FP Roth, D Tabet, B Bolognesi&dagger;, AM Glazer&dagger;, AF Rubin&dagger;. Minimum information and guidelines for reporting a multiplexed assay of variant effect. ArXiv arXiv:2306.15113v1 (2023). <a href="publications/Claussnitzer_arXiv_2023.html" target="_blank">Full Text</a> <li> S Gersing, TK Schulze, M Cagiada, A Stein, FP Roth, K Lindorff-Larsen&dagger;, R Hartmann-Petersen&dagger;. Characterizing glucokinase variant mechanisms using a multiplexed abundance assay. bioRxiv https://doi.org/10.1101/2023.05.24.542036 (2023). <a href="publications/Gersing_bioRxiv_2023.html" target="_blank">Full Text</a> <li> 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&dagger;, K Lindorff-Larsen&dagger;, R Hartmann-Petersen&dagger;. A comprehensive map of human glucokinase variant activity. Genome Biology 24(1):97 (2023). <a href="publications/Gersing_GenomeBiology_2023.html" target="_blank">Full Text</a> <li> 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&dagger;, M Vidal&dagger;, N Perrimon&dagger;, SE Mohr&dagger;. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nature Communications 14(1):2162 (2023). <a href="publications/Tang_NatureCommunications_2023.html" target="_blank">Full Text</a> <li> B Weller&dagger;, 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&dagger;, P Falter-Braun&dagger;. 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). <a href="publications/Weller_G3_2023.html" target="_blank">Full Text</a> <li> I Hoskins, S Sun, A Cote, FP Roth, C Cenik&dagger;. satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect. Genome Biology 24(1):82 (2023). <a href="publications/Hoskins_GenomeBiology_2023.html" target="_blank">Full Text</a> <li> B Floyd*, J Weile*, P Kannankeril, A Glazer, C Reuter, C MacRae, E Ashley, D Roden, FP Roth, V Parikh&dagger;. Proactive variant effect mapping aids diagnosis in pediatric cardiac arrest. Circulation:Genomic and Precision Medicine 16(1):e003792 (2023). <a href="publications/Floyd_CircGenPrecMed_2023.html" target="_blank">Full Text</a> <li> 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&dagger;, M Vidal&dagger;, MA Calderwood&dagger;, FP Roth&dagger;, P Falter-Braun&dagger;. A proteome-scale map of the SARS-CoV-2—human contactome. Nature Biotechnology 41(1):140-149 (2023). <a href="publications/Kim_NatBiotech_2023.html" target="_blank">Full Text</a> <h4><a name="2022">2022</a></h4> <li> 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&dagger;. 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). <a href="publications/Zhao_bioRxiv_2022.html" target="_blank">Full Text</a> <li> RA Silverstein, S Sun, M Verby, J Weile, Y Wu, M Gebbia, I Fotiadou, J Kitaygorodsky, FP Roth&dagger;. 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). <a href="publications/Silverstein_bioRxiv_2022.html" target="_blank">Full Text</a> <li> D Kuang, R Li, Y Wu, J Weile, RA Hegele, FP Roth&dagger;. 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). <a href="publications/Kuang_bioRxiv_2022.html" target="_blank">Full Text</a> <li> D Tabet, V Parikh, P Mali, FP Roth&dagger;, M Claussnitzer&dagger;. Scalable functional assays for the interpretation of human genetic variation. Annual Review of Genetics (2022). <a href="publications/Tabet_ARGenetics_2022_preview.pdf" target="_blank">PDF</a> <li> D Choi, N Khan, L Montermini, N Tawil, B Meehan, D-K Kim, FP Roth, M Divangahi, J Rak&dagger;. Quantitative proteomics and biological activity of extracellular vesicles engineered to express SARS-CoV-2 spike protein. Journal of Extracelluar Biology 2022;1:e58 (2022). <a href="publications/Choi_JExtracellularBio_2022.html" target="_blank">Full Text</a> <li> 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&dagger;, MA Calderwood&dagger;,JC Twizere&dagger;, M Vidal&dagger;. Binary interactome models of inner- versus outer-complexome organization. bioRxiv (doi:10.1101/2021.03.16.435663) (2022). <a href="publications/Lambourne_bioRxiv_2022.html" target="_blank">Full Text</a> <h4><a name="2021">2021</a></h4> <li> Y Wu, R Li, S Sun, J Weile, FP Roth&dagger;. Improved pathogenicity prediction for rare human missense variants. American Journal of Human Genetics 108(10):1891-1906 (2021). <a href="publications/Wu_AJHG_2021.html" target="_blank">Full Text</a> <li> 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&dagger;. Shifting landscapes of human MTHFR missense-variant effects. American Journal of Human Genetics 108(7):1283-1300 (2021). <a href="publications/Weile_AJHG_2021.html" target="_blank">Full Text</a> <li> A Savinov&dagger;, FP Roth&dagger;. Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads. Cell Systems 12(7):691-693 (2021). <a href="publications/Savinov_CellSystems_2021.html" target="_blank">Full Text</a> <li> D Kuang, J Weile, N Kishore, AF Rubin, S Fields, DM Fowler, FP Roth&dagger;. MaveRegistry: a collaboration platform for multiplexed assays of variant effect. Bioinformatics (2021). <a href="publications/Kuang_Bioinformatics_2021.html" target="_blank">Full Text</a> <h4><a name="2020">2020</a></h4> <li> D Kuang, R Truty, J Weile, B Johnson, K Nykamp, C Araya, RL Nussbaum, FP Roth&dagger;. Prioritizing genes for systematic variant effect mapping. Bioinformatics 36(22-23):5448-5455 (2020). <a href="publications/Kuang_Bioinformatics_2020b.html" target="_blank">Full Text</a> <li> 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&dagger;. A genetic interaction screen in yeast identifies genes relevant to human PAK1 function in glioma. Journal of Biological Chemistry 295(50):16906-16919 (2020). <a href="publications/Kim_JBiolChem_2020.html" target="_blank">Full Text</a> <li> 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&dagger; & C Boone&dagger;. Systematic analysis of bypass suppression of essential genes. Molecular Systems Biology 16(9):e9828 (2020). <a href="publications/vanLeeuwen_MolSysBio_2020.html" target="_blank">Full Text</a> <li> 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). <a href="publications/SamavarchiTehrani_BioRxiv_2020_v1.html" target="_blank">Full Text</a> <li> JR St-Germain, A Astori, P Samavarchi-Tehrani, H Abdouni, V Macwan, D-K Kim, JJ Knapp, FP Roth, A-C Gingras&dagger;, B Raught&dagger;. A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research. bioRxiv (2020). <a href="publications/StGermain_BioRxiv_2020_v1.html" target="_blank">Full Text</a> <li> 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&dagger;, C Demeret&dagger;, Y Jacob&dagger;, E Coyaud&dagger;. 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). <a href="publications/Laurent_BioRxiv_2020_v1.html" target="_blank">Full Text</a> <li> 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&dagger;, FP Roth&dagger;. A flexible genome-scale resource of SARS-CoV-2 coding sequence clones. G3: Genes|Genomes|Genetics 10(9):3399-3402 (2020). <a href="publications/Kim_G3_2020.html" target="_blank">Full Text</a> <li> D Kuang, J Weile, R Li, TW Ouellette, JA Barber, FP Roth&dagger;. MaveQuest: a web resource for planning experimental tests of human variant effects. Bioinformatics 36(12):3938-3940 (2020). <a href="publications/Kuang_Bioinformatics_2020.html" target="_blank">Full Text</a> <li> MA Chiasson, NJ Rollins, JJ Stephany, KA Sitko, KA Matreyek, M Verby, S Sun, FP Roth, D DeSloover, D Marks, AE Rettie, DM Fowler&dagger; Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020;9:e58026 (2020). <a href="publications/Chiasson_eLife_2020.html" target="_blank">Full Text</a> <li> 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&dagger;, M Vidal&dagger;, FP Roth&dagger;, MA Calderwood&dagger;. A reference map of the human protein interactome. Nature 580(7803):402-408 (2020). <a href="publications/Luck_Nature_2020.html" target="_blank">Full Text</a> <li> AO Helbig&dagger;, M Kofler, G Gish, K Lorenzen, M Tucholska, C Zhang, FP Roth, T Pawson, K Colwill & E Petsalaki&dagger;. Decoding the functional Fes kinase signaling network topology in a lymphocyte model. bioRxiv 125088 (2020). <a href="publications/Helbig_BioRxiv_2020_v3.html" target="_blank">Full Text</a> <li> 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&dagger;, O Rocks&dagger;. Systems-analysis of RhoGEF/RhoGAP regulatory proteins reveals spatially organized Rac1 signaling from integrin adhesions. Nature Cell Biology 22(4):498-511 (2020). <a href="publications/Muller_NatureCellBio_2020.pdf" target="_blank">PDF</a> <li> S Sun&dagger;, J Weile&dagger;, M Verby, Y Wu, Y Wang, AG Cote, I Fotiadou, J Kitaygorodsky, M Vidal, J Rine, P Jesina, V Kozich&dagger;, FP Roth&dagger;. A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Genome Medicine 12(1):13 (2020). <a href="publications/Sun_GenomeMedicine_2020.html" target="_blank">Full Text</a> <li>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&dagger; & FP Roth&dagger;. Highly combinatorial genetic interaction analysis reveals a multi-drug transporter influence network.. Cell Systems 9: 1–14 (2020) <a href="publications/Celaj_CellSystems_2020.html" target="_blank">Full Text</a> <h4><a name="2019">2019</a></h4> <li> D Esposito*, J Weile*, J Shendure, LM Starita, AT Papenfuss, FP Roth&dagger;, DM Fowler&dagger; & AF Rubin&dagger;. MaveDB: An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biology 20(1):223 (2019). <a href="publications/Esposito_GenomeBiology_2019.html" target="_blank">Full Text</a> <li> F Yang, D-K Kim, H Nakagawa, S Hayashi, S Imoto, L Stein, FP Roth&dagger;. Quantifying immune-based counterselection of somatic mutations.. PLoS Genetics 15(7): e1008227 (2019) <a href="publications/Yang_PLOSGenetics_2019.html" target="_blank">Full Text</a> <li>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&dagger;. Assessing predictions on fitness effects of missense variants in calmodulin. Human Mutation 40(9):1463-1473 (2019). <a href="publications/Zhang_HumanMutation_2019.pdf" target="_blank">PDF</a> <li> Y Wu, J Weile, AG Cote, S Sun, J Knapp, M Verby, FP Roth&dagger;. A web application and service for imputing and visualizing missense variant effect maps. Bioinformatics 35(17):3191-3193 (2019). <a href="publications/Wu_Bioinformatics_2019.html" target="_blank">Full Text</a> <li> A Sokolov, S Ashenden, N Sahin, R Lewis, N Erdem, E Ozaltan, A Bender, FP Roth, M Cokol&dagger;. Characterizing ABC-transporter substrate-likeness using a clean-slate genetic background. Frontiers in Pharmacology 10:448 (2019). <a href="publications/Sokolov_FrontiersPharmacology_2019.pdf" target="_blank">PDF</a> <li> 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&dagger;, SW Scherer&dagger;. CNTN5-/+ or EHMT2-/+ human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks. eLife 12(8):pii;e40092 (2019). <a href="publications/Deneault_eLife_2019.html" target="_blank">Full Text</a> <h4><a name="2018">2018</a></h4> <li> J Weile&dagger; & FP Roth&dagger;. Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Human Genetics 137(9):665–678 (2018). <a href="publications/Weile_HumanGenetics_2018.html" target="_blank">Full Text</a> <li> ZB Weinstein, N Kuru, S Kiriakov, AC Palmer, AS Khalil, PA Clemons, MH Zaman, FP Roth, M Cokol&dagger;. Modeling the impact of drug interactions on therapeutic selectivity. Nature Communications 9(1):3452 (2018). <a href="publications/Weinstein_NatureComm_2018.html" target="_blank">Full Text</a> <li> D Choi, L Montermini, D-K Kim, B Meehan, FP Roth, J Rak&dagger;. The impact of oncogenic EGFRvIII on the proteome of extracellular vesicles released from glioblastoma cells. Molecular and Cellular Proteomics. 17(10):1948-1964 (2018). <a href="publications/Choi_MolCellProteomics_2018.html" target="_blank">Full Text</a> <li> 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&dagger;. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Molecular Systems Biology 14(5):e7985 (2018). <a href="publications/Diaz-Mejia_MolSysBiol_2018.html" target="_blank">Full Text</a> <h4><a name="2017">2017</a></h4> <li> 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&dagger;. A framework for exhaustively mapping functional missense variants. Molecular Systems Biology 13:157 (2017) <a href="publications/Weile_MolSysBiol_2017.html" target="_blank">Full Text</a> <li> I Vigentini&dagger;, 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) <a href="publications/Vigentini_FoodMicrobio_2017.html" target="_blank">Full Text</a> <li> LM Starita&dagger;, N Ahituv, MJ Dunham, JO Kitzman, FP Roth, G Seelig, J Shendure, DM Fowler&dagger;. Variant interpretation: functional assays to the rescue. American Journal of Human Genetics 101(3):315-325 (2017). <a href="publications/Starita_AJHG_2017.html" target="_blank">Full Text</a> <li> J Zhang, LN Kinch, Q Cong, J Weile, S Sun, AG Cote, FP Roth, NV Grishin&dagger;. Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. Human Mutation 38(9):1051-1063 (2017). <a href="publications/Zhang_HumanMutation_2017.pdf" target="_blank">PDF</a> <li> M Jo, AY Chung, N Yachie, M Seo, H Jeon, Y Nam, Y Seo, E Kim, Q Zhong, M Vidal, HC Park&dagger;, FP Roth&dagger;, K Suk&dagger;. 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). <a href="publications/Jo_GenomeResearch_2017.html" target="_blank">Full Text</a> <li> A Celaj*, U Schlecht*, JD Smith, W Xu, S Suresh, M Miranda, AM Aparicio, M Proctor, RW Davis, FP Roth&dagger;, RP St Onge&dagger;. Quantitative analysis of protein interaction network dynamics in yeast. Molecular Systems Biology 13(7):934 (2017). <a href="publications/Celaj_MSB_2017.html" target="_blank">Full Text</a> <li> F Yang, S Sun, G Tan, M Costanzo, DE Hill, M Vidal, BJ Andrews, C Boone, FP Roth&dagger;. Identifying pathogenicity of human variants via paralog-based yeast complementation. PLOS Genetics 13(5):e1006779 (2017). <a href="publications/Yang_PLOSGenetics_2017.html" target="_blank">Full Text</a> <li> MJ Betts, O Wichmann, M Utz, T Andre, E Petsalaki, P Minguez, L Parca, FP Roth, AC Gavin, P Bork, RB Russell&dagger;. Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Computational Biology 13(3):e1005462 (2017). <a href="publications/Betts_PLOSCompBio_2017.html" target="_blank">Full Text</a> <li> C Cenik, HN Chua, G Singh, A Akef, MP Snyder, AF Palazzo, MJ Moore&dagger; & FP Roth&dagger;. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA 23(3):270-283 (2017). <a href="publications/Cenik_RNA_2017.html" target="_blank">Full Text</a> <h4><a name="2016">2016</a></h4> <li> 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&dagger;, BJ Andrews&dagger;, FP Roth&dagger; & C Boone&dagger;. Exploring genetic suppression interactions on a global scale. Science 354(6312):599,aag0839-1-11 (2016). <a href="publications/vanLeeuwen_Science_2016.pdf" target="_blank">PDF</a> <li> FP Roth&dagger; & J Wakeley&dagger;. Taking exception to human eugenics. Genetics 206(2):821-823 (2016). <a href="publications/Roth_Wakeley_Genetics_2016.html" target="_blank">Full Text</a> <li> 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&dagger;. Dual action antifungal small molecule modulates multidrug efflux and TOR signaling. Nature Chemical Biology 12(10):867-875 (2016). <a href="publications/Shekhar-Guturja_NatureChemBiol_2016.html" target="_blank">Full Text</a> <li> Q Zhong*&dagger;, 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&dagger; & M Vidal&dagger;. An inter-species protein-protein interaction network across vast evolutionary distance. Molecular Systems Biology 12(4):865 (2016). <a href="publications/Zhong_MolSystBiol_2016.html" target="_blank">Full Text</a> <li> N Yachie*&dagger;, 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&dagger;. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Molecular Systems Biology 12(4):863 (2016). <a href="publications/Yachie_Petsalaki_MolSystBiol_2016.html" target="_blank">Full Text</a> <li> 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&dagger;. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Research 26(5):670-80 (2016). <a href="publications/Sun_GenomeRes_2016.html" target="_blank">Full Text</a> <li> 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&dagger;, Y Xia&dagger; & M Vidal&dagger;. Widespread expansion of protein interaction capabilities by alternative splicing. Cell 164(4):805-817 (2016). <a href="publications/Yang_Cell_2016.pdf" target="_blank">PDF</a> <li>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&dagger;. A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human. Cell 164(1-2):310-323 (2016). <a href="publications/Vo_Cell_2016.pdf" target="_blank">PDF</a> <h4><a name="2015">2015</a></h4> <li>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&dagger; High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163(6):1515-1526 (2015). <a href="publications/Hart_Cell_2015.pdf" target="_blank">PDF</a> <li>E Petsalaki&dagger;, AO Helbig, A Gopal, A Pasculescu, FP Roth&dagger; & T Pawson Correlation-based identification of kinase-associated networks from global phospho-proteomics datasets. Nucleic Acids Research 43(W1): W276-W282 (2015). <a href="publications/Petsalaki_NAR_2015.html" target="_blank">Full Text</a> <li>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&dagger; & M Vidal&dagger; Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161(3):647-660 (2015). <a href="publications/Sahni_Cell_2015.pdf" target="_blank">PDF</a> <li>F Yang, E Petsalaki E, T Rolland, DE Hill, M Vidal & Roth FP&dagger;. Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Computational Biology 11(3):e1004147 (2015). <a href="publications/Yang_PLoSCompBio_2015.html" target="_blank">Full Text</a> <li> TR Pak, M Rodriguez & FP Roth&dagger;. Why clinical trials are terminated. bioRxiv DOI 10.1101/021543 (2015). <a href="publications/Pak_bioRxiv_2015.html" target="_blank">Full Text</a> <li>M Tasan*, G Musso*, T Hao, M Vidal, CA MacRae & FP Roth&dagger;. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nature Methods 12(2):154-159 (2015). <a href="publications/Tasan_NatureMethods_2015.pdf" target="_blank">PDF</a> <h4><a name="2014">2014</a></h4> <li>RC Deo&dagger;, 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&dagger;. Prioritizing causal disease genes using unbiased genomic features. Genome Biology 15:3274 (2014). <a href="publications/Deo_GenomeBiology_2014.pdf" target="_blank">PDF</a> <li>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&dagger;. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159(7): 1511-1523 (2014). <a href="publications/Irimia_Cell_2014.pdf" target="_blank">PDF</a> <li>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&dagger; & M Vidal&dagger;. A proteome-scale map of the human interactome network. Cell 159(5):1212-1226 (2014). <a href="publications/Rolland_Cell_2014.pdf" target="_blank">PDF</a> <li> K Yilancioglu, ZB Weinstein, C Meydan, A Akhmetov, I Toprak, A Durmaz, I Iossifov, H Kazan, FP Roth & M Cokol&dagger; Target-independent prediction of drug synergies using only drug lipophilicity. Journal of Chemical Information and Modeling 54(8): 2286-2293 (2014). <a href="publications/Yilancioglu_JChemInfModel_2014.pdf" target="_blank">PDF</a> <li> M Cokol&dagger;, 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&dagger;. Large-scale identification and analysis of suppressive drug interactions. Chemistry & Biology 21:541-551 (2014). <a href="publications/Cokol_Chem_and_Biol_2014.pdf" target="_blank">PDF</a> <li> VM Labunskyy, Y Suzuki, TJ Hanly, A Murao, FP Roth&dagger; & VN Gladyshev&dagger;. The Insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast. G3: Genes|Genomes|Genetics 4(7):1183-1191 (2014). <a href="publications/Labunskyy_G3_2014.pdf" target="_blank">PDF</a> <li> 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&dagger;, M Vidal&dagger;, LM Iakoucheva&dagger;. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nature Communications 5:3650 (2014). <a href="publications/Corominas_Nat_Commun_2014.pdf" target="_blank">PDF</a> <li> 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&dagger;, and CA MacRae&dagger;. Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development 141:224-235 (2014). <a href="publications/Musso_Development_2014.pdf" target="_blank">PDF</a> <h4><a name="2013">2013</a></h4> <li> SR Sunyaev&dagger; & Roth FP&dagger;. Systems biology and the analysis of genetic variation. Current Opinion in Genetics & Development 23(6):599-601 (2013). <a href="publications/SunyaevRoth_COGEDE_2013.pdf" target="_blank">PDF</a> <li> 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&dagger;. Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Science Signaling 6(276):ra38 (2013). <a href="publications/Das_ScienceSignaling_2013.pdf" target="_blank">PDF</a> <li> TR Pak & FP Roth&dagger;. ChromoZoom: a flexible, fluid, web-based genome browser. Bioinformatics 29(3):384-6 (2013). <a href="publications/Pak_Bioinformatics_2013.html" target="_blank">Full Text</a> <li> K Mahadevan, H Zhang, A Akef, XA Cui, S Gueroussov, C Cenik, FP Roth & AF Palazzo&dagger;. RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins. PLOS Biology 11(4):e1001545 (2013). <a href="publications/Mahadevan_PLOSBio_2013.html" target="_blank">Full Text</a> <h4><a name="2012">2012</a></h4> <li> 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). <a href="publications/Suzuki_JoVE_2012.html" target="_blank">Full Text</a> <li> A Bicknell, C Cenik, FP Roth & M Moore&dagger;. Introns in UTRs: Why we should stop ignoring them. BioEssays 34(12):1025-1034 (2012). <a href="publications/Bicknell_BioEssays_2012.pdf" target="_blank">PDF</a> <li> 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&dagger;, K Munger&dagger;, JA Marto&dagger;, J Quackenbush&dagger;, FP Roth&dagger;, JA DeCaprio&dagger; & M Vidal&dagger;. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 487(7408):491-495 (2012). <a href="publications/CEGS_Nature_2012.pdf" target="_blank">PDF</a> <a href = "supplements/CEGS_Nature_2012/">Supplementary Materials</a> Related news: Research Watch: Tumor Virus-Induced Host Network Perturbations Identify Cancer Genes. Cancer Discovery <a href = "publications/CancerDiscovery_2012_pub.html" target="_blank">Full Text</a> Research Highlights: Identifying driver mutations with the help of viruses. Nature Reviews Clinical Oncology <a href = "publications/NatRevClinOncology_2012_pub.html" target="_blank">Full Text</a> <li> 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&dagger; & AL Barabasi&dagger;. Viral perturbations of host networks reflect disease etiology. PLoS Computational Biology 8(6):e1002531 (2012). <a href="publications/Gulbahce_PLoSCompBio_2012.html" target="_blank">Full Text</a> <li> E Cheng, JA Vaisica, J Ou, A Baryshnikova, Y Lu, FP Roth, GW Brown&dagger;. Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae. Genetics 192(1):147-160 (2012). <a href="publications/Cheng_Genetics_2012.html" target="_blank">Full Text</a> <li> M Tasan, HJ Drabkin, JE Beaver, HN Chua, J Dunham, W Tian, JA Blake & FP Roth&dagger;. A resource of quantitative functional annotation for Homo sapiens genes. G3: Genes, Genomes, Genetics 2(2):223-233 (2012). <a href="publications/Tasan_G3_2012.html" target="_blank">Full Text</a> <li> A Derti & FP Roth&dagger;. 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). <a href="publications/Derti_BioEssays_2012.pdf" target="_blank">PDF</a> <li> 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). <a href="publications/Stegle_PSB_2012.pdf" target="_blank">PDF</a> <h4><a name="2011">2011</a></h4> <li> 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&dagger;. Systematic exploration of synergistic drug pairs. Molecular Systems Biology 7(544):1-9 (2011). <a href="publications/Cokol_MSB_2011.pdf" target="_blank">PDF</a> <li> 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). <a href="publications/ArabIntxnMapCnsrtm_Science_2011.pdf" target="_blank">PDF</a> <li> 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&dagger;, J Beynon&dagger;, P Braun&dagger;, JL Dangl&dagger;. Independently evolved virulence effectors converge onto cellular hubs in a plant immune system network. Science 333(6042):596-601 (2011). <a href="publications/Mukhtar_Science_2011.pdf" target="_blank">PDF</a> <li> HN Chua & FP Roth&dagger;. Discovering the targets of drugs via computational systems biology. Journal of Biological Chemistry 286(27):23653-23658 (2011). <a href="publications/Chua_JBC_2011.html" target="_blank">Full Text</a> <li> 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&dagger;. Next-generation sequencing to generate interactome datasets. Nature Methods 8(6):478-80 (2011). <a href="publications/Yu_NatMethods_2011.pdf" target="_blank">PDF</a> <li> C Cenik, HN Chua, H Zhang, S Tarnawsky, A Akef, A Derti, M Tasan, MJ Moore, AF Palazzo&dagger; & FP Roth&dagger; Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS Genetics 7(4):e1001366 (2011). <a href="publications/Cenik_PLoSGenetics_2011.html" target="_blank">Full Text</a> <li> K Suk, J Choi, Y Suzuki, SB Ozturk, JC Mellor, KH Wong, JL MacKay, RI Gregory & FP Roth&dagger; Reconstitution of human RNA interference in budding yeast. Nucleic Acids Research 39(7):e43 (2011). <a href="publications/Suk_NAR_2011.html" target="_blank">Full Text</a> Research Highlight: Lab Times 4:46 (2011). <a href="publications/Zahringer_LabTimes_2011.pdf" target="_blank">PDF</a> <li> 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&dagger;. Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nature Methods 8(2):159-64 (2011). <a href="publications/Suzuki_NatMethods_2011.pdf" target="_blank">PDF</a> <li> CF Sephton, C Cenik, A Kucukural, EB Dammer, B Cenik, Y Han, CM Dewey, FP Roth, J Herz, J Peng, MJ Moore & Yu G&dagger; Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. Journal of Biological Chemistry 286(2):1204-15. (2011) <a href="publications/Sephton_JBiolChem_2011.html" target="_blank">Full Text</a> <h4><a name="2010">2010</a></h4> <li> 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&dagger;. Metabolic signatures of exercise in human plasma. Science Translational Medicine 2(33):33ra37 (2010). <a href="publications/Lewis_ScienceTransMed_2010.pdf" target="_blank">PDF</a> <li> JE Beaver, M Tasan, F Gibbons, W Tian, TR Hughes & FP Roth&dagger;. FuncBase: A resource for quantitative gene function annotation. Bioinformatics 26(14):1806-7 (2010). <a href="publications/Beaver_Bioinformatics_2010.html" target="_blank">Full Text</a> <a href = "software.html" target="_blank">Software</a> <li> A Derti, C Cenik, P Kraft & FP Roth&dagger; Absence of evidence for MHC-dependent mate selection within HapMap populations. PLoS Genetics 6(4):e1000925 (2010). <a href="publications/Derti_PLoSGenetics_2010.html" target="_blank">Full Text</a> <li> C Cenik, A Derti, JC Mellor, GF Berriz & FP Roth&dagger;. Genome-wide functional analysis of human 5' untranslated region introns. Genome Biology 11(3):R29 (2010). <a href="publications/Cenik_GenomeBiology_2010.pdf" target="_blank">PDF</a> <li> E Kugelberg&dagger;, 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). <a href="publications/Kugelberg_Genetics_2010.html" target="_blank">Full Text</a> <li> H Yan, K Venkatesan, JE Beaver, N Klitgord, MA Yildirim, T Hao, DE Hill, ME Cusick, N Perrimon, FP Roth&dagger; & M Vidal&dagger; A genome-wide gene function prediction resource for Drosophila melanogaster. PLoS One 5(8):e12139 (2010). <a href="publications/Yan_PLoSONE_2010.html" target="_blank">Full Text</a> <li> RC Deo, L Hunter, GD Lewis, G Pare, RS Vasan, D Chasman, TJ Wang, RE Gerszten & FP Roth&dagger;. Interpreting metabolomic profiles using unbiased pathway models. PLoS Computational Biology 6(2):e1000692 (2010). <a href="publications/Deo_PLoSCompBio_2010.html" target="_blank">Full Text</a> <li> I Jurak, MF Kramer, JC Mellor, AL van Lint, FP Roth, DM Knipe & DM Coen&dagger;. Numerous conserved and divergent microRNAs expressed by Herpes Simplex Viruses 1 and 2. Journal of Virology 84(9):4659-72 (2010). <a href="publications/Jurak_JVirol_2010.pdf" target="_blank">PDF</a> <li> 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&dagger;, BJ Andrews&dagger; & C Boone&dagger;. The genetic landscape of a cell. Science 327:425-431 (2010). <a href="publications/Costanzo_Science_2010.pdf" target="_blank">PDF</a> <h4><a name="2009">2009</a></h4> <li> GF Berriz, JE Beaver, C Cenik, M Tasan & FP Roth&dagger;. Next generation software for functional trend analysis. Bioinformatics 25(22):3043-3044 (2009). <a href="publications/Berriz_Bioinformatics_2009.html" target="_blank">Full Text</a> <a href = "software.html" target="_blank">Software</a> <li> 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&dagger;. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Research 19(12):2334-42 (2009). <a href="publications/Salehi_GenResearch_2009.pdf" target="_blank">PDF</a> <li> RC Deo&dagger; & FP Roth. Pathways of the heart. Circulation: Cardiovascular Genetics 2(4):303-305 (2009). <a href="publications/Deo_Circulation_Cardio_Genetics_2009.pdf" target="_blank">PDF</a> <li> AM Smith, LE Heisler, J Mellor, F Kaper, MJ Thompson, M Chee, FP Roth, G Giaever&dagger; & C Nislow&dagger;. Quantitative phenotyping via deep barcode sequencing. Genome Research 19(10):1836-42 (2009) <a href="publications/Smith_GenRes_2009.pdf" target="_blank">PDF</a> </li> <li> FP Roth, HD Lipshitz & BJ Andrews. Q&A: Epistasis. Journal of Biology 8:35 (2009). <a href="publications/Roth_JBiol_2009.pdf" target="_blank">PDF</a> , <a href="http://jbiol.com/content/8/4/35" target="_blank">Full Text</a> </li> <li> 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&dagger;, JL Wrana&dagger;, FP Roth&dagger; & M Vidal&dagger;. An experimentally derived confidence score for binary protein-protein interactions. Nature Methods 6(1):91-97 (2009). <a href="publications/Braun_NatMethods_2009.pdf" target="_blank">PDF</a> 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). <a href="http://pubs.acs.org/action/showStoryContent?doi=10.1021%2Fon.2009.02.11.258968" target="_blank">Full text</a> </li> <li> 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&dagger;, EE Wanker&dagger;, AL Barabasi&dagger; & M Vidal&dagger;. An empirical framework for binary interactome mapping. Nature Methods 6(1):83-90 (2009). <a href="publications/Venkatesan_NatMethods_2009.pdf" target="_blank">PDF</a> </li> <li> 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&dagger;, J Tavernier&dagger;, FP Roth&dagger; & M Vidal&dagger;. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods 6(1):47-54 (2009). <a href="publications/Simonis_NatMethods_2009.pdf" target="_blank">PDF</a> </li> <li> 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&dagger;. Literature-curated protein interaction datasets. Nature Methods (Perspective) 6(1):39-46 (2009). <a href="publications/Cusick_NatMethods_2009.pdf" target="_blank">PDF</a> </li> <h4><a name="2008">2008</a></h4> <li> NJ Martinez, MC Ow, MI Barrasa, M Hammell, R Sequerra, L Doucette-Stamm, FP Roth, VR Ambros & AJ Walhout&dagger;. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes & Development 22(18):2535-2549 (2008). <a href="publications/Martinez_GeneDev_2008.pdf" target="_blank">PDF</a> Research Highlight: Nature Reviews Genetics 9:813 (2008). <a href="http://www.nature.com/nrg/journal/v9/n11/full/nrg2472.html" target="_blank">Full Text</a> </li> <li> J Klekota & FP Roth&dagger;. Chemical substructures that enrich for biological activity. Bioinformatics 24(21):2518-2525 (2008). <a href="publications/Klekota_Bioinformatics_2008.html" target="_blank">Full Text</a> </li> <li> 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&dagger;. Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. J Clin Invest 118(10):3503-3512 (2008). <a href="publications/Lewis_JClinInvest_2008.html" target="_blank">Full Text</a> News article: How to spot a heart attack soon after it occurs. ScienceDaily Sep 5 (2008). <a href="http://www.sciencedaily.com/releases/2008/09/080902221733.htm" target="_blank">Full text</a> News article: S Stiles. Groundwork laid for assays that point to MI within minutes of infarct onset. theHeart.Org Sep 19 (2008). <a href="http://www.theheart.org/article/906149.do" target="_blank">Full text</a> </li> <li> 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&dagger;. High-quality binary protein interaction map of the yeast interactome network. Science 322(5898):104-10 (2008). <a href="publications/Yu_Science_2008.pdf" target="_blank">PDF</a> </li> <li> GF Berriz & FP Roth&dagger;. The Synergizer service for translating gene, protein, and other biological identifiers. Bioinformatics 24(19):2272-3 (2008). <a href="publications/Berriz_Bioinformatics_2008.html" target="_blank">Full Text</a> </li> <li> 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&dagger;. A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134(3):534-545 (2008). <a href="publications/Boxem_Cell_2008.pdf" target="_blank">PDF</a> </li> <li> TR Hughes & FP Roth. A race through the maze of genomic evidence. Genome Biology 9 Suppl 1:S1 (2008). <a href="publications/Hughes_GenomeBiology_2008.pdf" target="_blank">PDF</a> </li> <li> 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&dagger; & FP Roth&dagger;. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology 9 Suppl 1:S2 (2008). <a href="publications/PenaCastillo_GenomeBiology_2008.pdf" target="_blank">PDF</a> </li> <li> W Tian, LV Zhang, M Tasan, FD Gibbons, OD King, J Park, Z Wunderlich, JM Cherry & FP Roth&dagger;. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology 9 Suppl 1:S7 (2008). <a href="publications/Tian_GenomeBiology_2008.pdf" target="_blank">PDF</a> </li> <li> M Tasan, W Tian, DP Hill, FD Gibbons, JA Blake & FP Roth&dagger;. An en masse phenotype and function prediction system for M. musculus. Genome Biology 9 Suppl 1:S8 (2008). <a href="publications/Tasan_GenomeBiology_2008.pdf" target="_blank">PDF</a> </li> <li> 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&dagger; & M Vidal&dagger;. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature Methods 5(7):597-600 (2008). <a href="publications/Salehi_NatMethods_2008.pdf" target="_blank">PDF</a> <a href = "supplements/Salehi_NatMethods_2008/Salehi_NatMethods_2008_Suppl.pdf">Supplement</a> </li> <li> R Mani, RP St.Onge., JL Hartman IV, G Giaever & FP Roth&dagger;. Defining genetic interaction. Proceedings of the National Academy of Sciences 105(9):3461-3466 (2008). <a href="publications/Mani_PNAS_2008.pdf" target="_blank">PDF</a> <a href = "http://www.pnas.org/cgi/content/full/0712255105/DC1" target="_top">Supplement</a> Research Highlight: Nature Reviews Genetics 9:253 (2008). <a href="http://npg.nature.com/nrg/journal/v9/n4/pdf/nrg2355.pdf" target="_blank">PDF</a> </li> <h4><a name="2007">2007</a></h4> <li> S Komili, NG Farny, FP Roth&dagger; & PA Silver&dagger;. Functional specificity among ribosomal proteins regulates gene expression. Cell 131:557-571 (2007). <a href="publications/Komili_Cell_2007.pdf" target="_blank">PDF</a> <a href = "supplements/Komili_Cell_2007/Komili_Cell_2007_Supplement.zip" target="_top">Supplement</a> Preview article: K McIntosh & J Warner. Yeast Ribosomes: Variety Is the Spice of Life Cell 131(3):450-451 (2007). <a href="publications/McIntosh_Warner_Cell_2007.html" target="_blank">Full text</a> News article: M Leslie. Unique tasks for ribosomal paralogues. Journal of Cell Biology 179(5):808 (2007). <a href="publications/Leslie_JCB_2007.html" target="_blank">Full text</a> News article: C Humphries. Ribosomes: More Special than You Think. Focus Nov 9 (2007). <a href="publications/Humphries_Focus_2007.html" target="_blank">Full text</a> Research Highlight: Nature Reviews Genetics 8:909 (2007). <a href="http://npg.nature.com/nrg/journal/v8/n12/pdf/nrg2286.pdf" target="_blank">PDF</a> </li> <li> FP Roth & B Andrews. Systems biology: A shared goal with diverse views. ASBMB Today September (2007). <a href="publications/RothAndrews_ASBMBToday_2007.pdf" target="_blank">PDF</a> </li> <li> N Bertin, N Simonis, D Dupuy, ME Cusick, J-DJ Han, HB Fraser&dagger;, FP Roth&dagger; & M Vidal&dagger;. Confirmation of organized modularity in the yeast interactome. PLoS Biology 5(6) e153 (2007). <a href="publications/Bertin_PLoS_Biology_2007.html" target="_blank">Full text</a> </li> <li> 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&dagger;, D Baillie&dagger; & M Vidal&dagger;. Genome-scale analysis of in vivo spatiotemporal promoter activity in C. elegans. Nature Biotechnology 25(6):663-668 (2007). <a href="publications/Dupuy_NatBiotech_2007.pdf" target="_blank">PDF</a> <a href = "supplements/Dupuy_NatBiotech_2007/Dupuy_NatGenetics_Supplement.zip" target="_top">Supplement</a> </li> <li> S Komili & FP Roth&dagger;. Genetic interaction screens advance in reverse. Genes & Development (Perspective) 21(2):137-42 (2007). <a href="publications/Komili_GenesDev_2007.pdf" target="_blank">PDF</a> </li> <li> RP St Onge, R Mani, J Oh, M Proctor, E Fung, RW Davis, C Nislow, FP Roth&dagger; & G Giaever&dagger;. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nature Genetics 39(2):199-206 (2007). <a href="publications/StOnge_NatGenetics_2007.pdf" target="_blank">PDF</a> <a href = "supplements/StOnge_NatGenetics_2007/StOnge_NatGenetics_Supplement.zip" target="_top">Supplement</a> </li> <li>H Huang, LV Zhang, FP Roth & JS Bader&dagger;. Probabilistic paths in protein interaction networks. Proceedings of the RECOMB Conferences on Systems Biology and Computational Proteomics (2007). <a href="publications/Huang_RECOMB_2007.pdf" target="_blank">PDF</a> </li> <h4><a name="2006">2006</a></h4> <li>A Derti, FP Roth, GM Church & C-T Wu&dagger;. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nature Genetics 38(10):1216-1220 (2006). <a href="publications/Derti_NatGenetics_2006.pdf" target="_blank">PDF</a> <a href = "supplements/Derti_NatGenetics_2006/Derti_NatGenetics_Supplement.zip" target="_top">Supplement</a> </li> <li>Y Suzuki & FP Roth&dagger;. Systematic genetics swims forward elegantly. Molecular Systems Biology (News and Views) 2:48 (2006). <a href="publications/Suzuki_MSB_2006_pub.html" target="_blank">Full Text</a> </li> <li>J Klekota&dagger;, E Brauner, FP Roth&dagger; & 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). <a href = "publications/Klekota_JChemInfModel_2006.pdf" target="_blank">PDF</a> <li>J Klekota&dagger;, FP Roth & SL Schreiber. Query Chem: a Google-powered web search combining text and chemical structures. Bioinformatics 22(13):1670-1673 (2006). <a href="publications/Klekota_Bioinformatics_2006A.html" target="_blank">Full Text</a> <a href = "software.html" target="_blank">Software</a> </li> <h4><a name="2005">2005</a></h4> <li> MS Sabatine, E Liu, DA Morrow, E Heller, M Askenazi, R McCarroll, R Weigand, GF Berriz, FP Roth & RE Gerszten&dagger;. Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation 112(25):3868-3875 (2005). <a href = "publications/Sabatine_Circulation_2005.pdf" target="_blank">PDF</a> <li> FD Gibbons, M Proft, K Struhl & FP Roth&dagger;. Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biology 6(11):R96 (2005). <a href = "publications/Gibbons_GenomeBiology_2005.pdf" target="_blank">PDF</a> <a href = "software.html" target="_blank">Software</a> <li> SL Wong & FP Roth&dagger;. Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae. Genetics 171(2):829-833 (2005). <a href = "publications/Wong_Genetics_2005.pdf" target="_blank">PDF</a> <a href = "supplements/Wong_Genetics_2005/" target="_blank">Supplement</a> <li> 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&dagger;, FP Roth&dagger; & M Vidal&dagger;. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-1178 (2005). <a href = "publications/Rual_Nature_2005.pdf" target="_blank">PDF</a> <a href = "supplements/Rual_Nature_2005/" target="_blank">Supplement</a> <li> 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&dagger;, M Vidal&dagger; & F Piano&dagger;. Predictive models of molecular machines involved in C. elegans early embryogenesis. Nature 436(7052):861-865 (2005). <a href = "publications/Gunsalus_Nature_2005.pdf" target="_blank">PDF</a> <a href = "supplements/Gunsalus_Nature_2005/" target="_top">Supplement</a> Related news piece: E Kritikou Molecular networks - The power of prediction. Nature Reviews Molecular Cell Biology 6(10):752-753 (2005). <a href = "publications/Kritikou_NatRevMCB_2005_pub.html" target="_blank">Full Text</a> <li> M Proft, FD Gibbons, Copeland M, Roth FP & K Struhl&dagger;. 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). <a href = "publications/Proft_EukCell_2005.pdf" target="_blank">PDF</a> <li> SL Wong, LV Zhang, & FP Roth&dagger;. Discovering functional relationships: biochemistry versus genetics. Trends in Genetics 21(8): 424-427 (2005). <a href = "publications/Wong_TIG_2005.pdf" target="_blank">PDF</a> <a href = "supplements/Wong_TIG_2005/" target="_blank">Supplement</a> <li> LV Zhang, OD King, SL Wong, DS Goldberg, AHY Tong, G Lesage, B Andrews, H Bussey, C Boone & FP Roth&dagger;. Motifs, themes and thematic maps of an integrated S. cerevisiae interaction network. Journal of Biology 4:6 (2005). <a href = "publications/Zhang_JBiol_2005_pub.html" target="_blank">Full Text</a> Related news piece: JB Weitzman. A road map of yeast interactions. Journal of Biology 4:4 (2005). <a href = "publications/Weitzman_JBiol_2005_pub.html" target="_blank">Full Text</a> Related news piece: Research highlights. Nature 435:717 (2005). <a href = "publications/Nature_highlights_2005.pdf" target="_blank">PDF</a> Related minireview: MJ Herrgard & BO Palsson. Untangling the web of functional and physical interactions in yeast. Journal of Biology 4:5 (2005). <a href = "publications/Herrgard_JBiol_2005_pub.html" target="_blank">PDF</a></li> <h4><a name="2004">2004</a></h4> <li> SL Wong, LV Zhang, AHY Tong, Z Li, DS Goldberg, OD King, G Lesage, M Vidal, B Andrews, H Bussey, C Boone & FP Roth&dagger;. Combining biological networks to predict genetic interactions. Proceedings of the National Academy of Sciences 101(44): 15682-15687 (2004). <a href = "publications/Wong_PNAS_2004.pdf" target="_blank">PDF</a> <a href = "supplements/Wong_PNAS_2004/" target="_blank">Supplement</a> <li> S Asthana,OD King,FD Gibbons & FP Roth&dagger;. Predicting protein complex membership using probabilistic network reliability. Genome Research 14(6):1170-1175 (2004). <a href = "publications/Asthana_GenomeRes_2004.pdf" target="_blank">PDF</a> <a href = "software.html" target="_blank">Software</a> <li> J-DJ Han, N Bertin, T Hao, DS Goldberg, GF Berriz, LV Zhang, D Dupuy, AJM Walhout, ME Cusick, FP Roth & M Vidal&dagger;. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430(6995):88-93 (2004). <a href = "publications/Han_Nature_2004.pdf" target="_blank">PDF</a> <li> YH Grad, FP Roth, MS Halfon & GM Church&dagger;. 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). <a href = "publications/Grad_Bioinformatics_2004.pdf" target="_blank">PDF</a> <li>FD Gibbons, JE Elias, SP Gygi & FP Roth&dagger;. 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). <a href ="publications/Gibbons_JASMS_2004.pdf" target="_blank">PDF</a> <a href = "software.html" target="_blank">Software</a> <li> LV Zhang, SL Wong, OD King & FP Roth&dagger;. Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5:38 (2004). <a href = "publications/Zhang_BMCBioinformatics_2004.pdf" target="_blank">PDF</a> <li>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&dagger;, H Bussey&dagger; & C Boone&dagger;. Global mapping of the yeast genetic interaction network. Science 303: 808-813 (2004). <a href ="publications/Tong_Science_2004.pdf" target="_blank">PDF</a> <a href = "supplements/Tong_Science_2004/Tong_Science_2004_supplement.pdf" target="_blank">Supplement</a> </li> <li>JE Elias, FD Gibbons, OD King, FP Roth*&dagger; & SP Gygi*. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology, 22(2):214-9 (2004). <a href ="publications/Elias_NatBiotech_2004.pdf" target="_blank">PDF</a></li> <li>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&dagger;. A map of the interactome network of the metazoan C. elegans. Science, 303: 540-543 (2004). <a href ="publications/Li_Science_2004.pdf" target="_blank">PDF</a> </li> <h4><a name="2003">2003</a></h4> <li>GF Berriz, OD King, B Bryant, C Sander & FP Roth&dagger;. Characterizing gene sets with FuncAssociate. Bioinformatics 19(18):2502-2504 (2003). <a href="publications/Berriz_Bioinformatics_2003B.html" target="_blank">Full Text</a> <a href = "software.html" target="_blank">Software</a> <li>JR Roth&dagger;, E Kofoid, FP Roth, OG Berg, J Seger & DI Andersson. Adaptive mutation requires no mutagenesis&#8212only growth under selection: a response. Genetics 165(4): 2319-2321 (2003). <a href ="publications/Roth_Genetics_2003b.pdf" target="_blank">PDF</a></li> <li>OD King&dagger; & FP Roth. A non-parametric model for transcription factor binding sites. Nucleic Acids Research 31(19):e116 (2003). <a href="publications/King_NucleicAcidsResearch_2003.html" target="_blank">Full Text</a></li> <li>OD King&dagger;. Bounds for DNA codes with constant GC-content. Electronic Journal of Combinatorics 10(1):R33 (2003). <a href="publications/King_EJCombinatorics_2003.pdf" target="_blank">PDF</a></li> <li>MF Kramer, WJ Cook, FP Roth, J Zhu, H Holman, DM Knipe & DM Coen&dagger;. Latent Herpes Simplex Virus infection of sensory neurons alters neuronal gene expression. Journal of Virology 77(17):9533-9541 (2003).</li> <a href="publications/Kramer_JVirology_2003.pdf" target="_blank">PDF</a></li> <li>OD King, JC Lee, AM Dudley, DM Janse, GM Church & FP Roth&dagger;. Predicting phenotype from patterns of annotation. Bioinformatics (ISMB Proceedings Issue) 19 Suppl 1:I183-I189 (2003). <a href ="publications/King_Bioinformatics_2003.pdf" target="_blank">PDF</a></li> <li>JR Roth&dagger;, 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). <a href ="publications/Roth_Genetics_2003a.pdf" target="_blank">PDF</a></li> <li>GF Berriz, JV White, OD King & FP Roth&dagger;. GoFish finds genes with combinations of Gene Ontology attributes, Bioinformatics 19(6):788-789 (2003). <a href="publications/Berriz_Bioinformatics_2003A.html" target="_blank">Full Text</a> <a href = "software.html" target="_blank">Software</a> <li>OD King, RE Foulger, SS Dwight, JV White & FP Roth. Predicting gene function from patterns of annotation. Genome Research 13(5):896-904 (2003). <a href ="publications/King_GenRes_2003.pdf" target="_blank">PDF</a> </li> <li>DS Goldberg & FP Roth&dagger;. Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences 100(8): 4372-4376 (2003). <a href ="publications/Goldberg_PNAS_2003.pdf" target="_blank">PDF</a></li> <h4><a name="2002">2002</a></h4> <li>FD Gibbons & FP Roth. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Research 12(10): 1574-1581 (2002). <a href="publications/Gibbons_GenomeRes_2002.pdf" target="_blank">PDF</a> <a href = "software.html" target="_blank">Software</a> <li>M Damelin, I Simon, TI Moy, B Wilson, S Komili , P Tempst, FP Roth, RA Young, BR Cairns & PA Silver&dagger;. 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). <a href="publications/Damelin_MolCell_2002.pdf" target="_blank">PDF</a></li> <h4><a name="pre-2002">pre-2002</a></h4> <li>FP Roth, Bringing out the best features of expression data. Genome Research(Insight/Outlook). 11(11):1801-1802 (2001). <a href="publications/Roth_GenomeRes_2001.pdf" target="_blank">PDF</a></li> <li>FP Roth, JD Hughes, PW Estep & GM Church&dagger;. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology, 16: 939-945 (1998). <a href="publications/Roth_NatBiotech_1998.pdf" target="_blank">PDF</a></li> <a href = "http://atlas.med.harvard.edu/" target="_blank">Software</a> <li>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). <a href="publications/Roth_HarvardPhDThesis_1998.pdf" target="_blank">PDF</a></li> </ul>  </td> </tr></table> <center> <a href="index.html">home</a>   |   <a href="research.html">research</a>   |   <a href="people.html">people</a>   |   <a href="resources.html">resources</a>   |   <a href="publications.html">publications</a>   |   <a href="software.html">software</a>   |   <a href="directions.html">directions</a>   |   <a href="contact.html">contact</a> </center></TD> </TR><tr><td> <img src="images/homefooter.gif" width="760" height="81" border="0" usemap="#Map2"></td> </tr></table></center> <map name="Map2"> <area shape="rect" coords="199,7,617,22" href="http://tdccbr.med.utoronto.ca" alt="Donnelly Centre for Cellular & Biomolecular Research, University of Toronto"> <area shape="rect" coords="200,23,512,37" href="http://www.lunenfeld.ca" alt="Samuel Lunenfeld Research Institute, Mt. 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