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publications

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Current or former members of the Roth Lab are highlighted.


2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 pre-2002

2014

  • 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 Epub ahead of print (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 [EPub ahead of print] (2014). PDF

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

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


    2013

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

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

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

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


    2012

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

  • A Bicknell, C Cenik, FP Roth & M Moore. Introns in UTRs: Why we should stop ignoring them. BioEssays [Epub ahead of print, Oct 26] (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


    2011

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

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

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

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

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

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

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

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

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

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


    2010

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

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

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

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

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

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

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

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

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


    2009

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

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

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

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

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

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

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

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

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

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


  • 2008

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

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

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

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

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

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

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

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

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

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

  • 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). Full Text

  • 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). Full Text

  • 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). Full Text

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

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

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


  • 2007

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

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

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

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

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

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

  • 2006

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

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

  • 2005

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

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

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

  • J-F Rual, K Venkatesan, T Hao, T Hirozane-Kishikawa, A Dricot, N Li, GF Berriz, FD Gibbons, M Dreze, N Ayivi-Guedehoussou, N Klitgörd, 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 Sönnichsen, CJ Echeverri, FP Roth, M Vidal & F Piano. Predictive models of molecular machines involved in C. elegans early embryogenesis. Nature 436(7052):861-865 (2005). PDF Supplement

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

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

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

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

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

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

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


  • 2004

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

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

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

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

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

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

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

  • 2003

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

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

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

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

  • 2002

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

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

  • pre-2002

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

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


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