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Current or former members of the Roth Lab are highlighted.


2008 2007 2006 2005 2004 2003 2002 pre-2002

2008

  • 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. Large-scale coding isoform discovery using 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

  • 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

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

  • 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

  • JV White, FP Roth, C Sander, JW Lillie, MG Kauffman, & BM Bryant. Classifying tissue samples based on mRNA expression levels. Millennium Pharmaceuticals Internal Report. (1999).

  • FP Roth, JV White, CH van Huffel, B Li, BM Bryant, KS O'Connor, JW Lillie, A Shyjan, MG Kauffman & C Sander. ExMarkS: A new algorithm for finding marker genes and its application to paclitaxel drug sensitivity. Millennium Pharmaceuticals Internal Report (1999).

  • 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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    Harvard Medical School Department of Biological Chemistry and Molecular Pharmacology