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2020 | 2016 | 2012 | 2008 | 2004
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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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)
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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).
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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)
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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).
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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).
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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).
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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).
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J Weile† & FP Roth†.
Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas.
Human Genetics 137(9):665–678 (2018).
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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).
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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).
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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).
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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)
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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)
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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FP Roth† & J Wakeley†.
Taking exception to human eugenics.
Genetics
206(2):821-823 (2016).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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
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
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
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
Related news:
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
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
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
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
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
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
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
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
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
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
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
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).
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