Frederick P. Roth, B.A. Ph.D.

Associate Professor, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School

Member, Center for Cancer Systems Biology, Dana-Farber Cancer Institute

Contact Info

Frederick Roth
Harvard Medical School
250 Longwood Avenue
Boston, MA, 02115
Mailstop: BCMP / SGM322
Phone: 617-432-3551
Fax: 617-432-3557
fritz_roth@hms.harvard.edu

Assistant

Not Available.

DF/HCC Program Affiliation

Research Abstract

Publications

• St Onge RP, Mani R, Oh J, Proctor M, Fung E, Davis RW, Nislow C, Roth FP, Giaever G.Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.Nat Genet 2007 Feb;39(2):199-206.
  17206143
• Wong SL, Roth FP.Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae.Genetics 2005 Oct;171(2):829-33.
  15998714
• Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP.Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.J Biol 2005;4(2):6.
  15982408
• Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth FP.Combining biological networks to predict genetic interactions.Proc Natl Acad Sci U S A 2004 Nov 2;101(44):15682-7.
  15496468
• Gerszten RE, Accurso FJ, Bernard GR, Caprioli RM, Klee EW, Klee GG, Kullo IJ, Laguna TA, Roth FP, Sabatine M, Srinivas P, Wang TJ, Ware LB.Challenges in Translating Plasma Proteomics from Bench to Bedside: Update from the NHLBI Clinical Proteomics Program
  18456800
• Mani R, St Onge RP, Hartman JL 4th, Giaever G, Roth FP.Defining genetic interaction.Proc Natl Acad Sci U S A 2008 Mar 4;105(9):3461-6.
  18305163
• Komili S, Farny NG, Roth FP, Silver PA.Functional specificity among ribosomal proteins regulates gene expression.Cell 2007 Nov 2;131(3):557-71.
  17981122
• Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, Vidal M.Confirmation of organized modularity in the yeast interactome.PLoS Biol 2007 Jun;5(6):e153.
  17564493
• Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Ba
  17486083
• Komili S, Roth FP.Genetic interaction screens advance in reverse.Genes Dev 2007 Jan 15;21(2):137-42.
  17234880
• Derti A, Roth FP, Church GM, Wu CT.Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.Nat Genet 2006 Oct;38(10):1216-20.
  16998490
• Suzuki Y, Roth FP.Systematic genetics swims forward elegantly.Mol Syst Biol 2006;2:48.
  16969340
• Klekota J, Brauner E, Roth FP, Schreiber SL.Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects.J Chem Inf Model 2006 Jul-Aug;46(4):1549-62.
  16859287
• Klekota J, Roth FP, Schreiber SL.Query Chem: a Google-powered web search combining text and chemical structures.Bioinformatics 2006 Jul 1;22(13):1670-3.
  16672261
• Sabatine MS, Liu E, Morrow DA, Heller E, McCarroll R, Wiegand R, Berriz GF, Roth FP, Gerszten RE.Metabolomic identification of novel biomarkers of myocardial ischemia.Circulation 2005 Dec 20;112(25):3868-75.
  16344383
• Gibbons FD, Proft M, Struhl K, Roth FP.Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.Genome Biol 2005;6(11):R96.
  16277751
• Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton
  16189514
• Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sönnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F.Predictive models of molecular machines involved in Caenorhabditis elegans e
  16094371
• Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K.Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae.Eukaryot Cell 2005 Aug;4(8):1343-52.
  16087739
• Wong SL, Zhang LV, Roth FP.Discovering functional relationships: biochemistry versus genetics.Trends Genet 2005 Aug;21(8):424-7.
  15982781
• Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M.Evidence for dynamically organized modularity in the yeast protein-protein interaction network.Nature 2004 Jul 1;430(6995):88-93.
  15190252
• Grad YH, Roth FP, Halfon MS, Church GM.Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.Bioinformatics 2004 Nov 1;20(16):2738-50.
  15145800
• Gibbons FD, Elias JE, Gygi SP, Roth FP.SILVER helps assign peptides to tandem mass spectra using intensity-based scoring.J Am Soc Mass Spectrom 2004 Jun;15(6):910-2.
  15144981
• Asthana S, King OD, Gibbons FD, Roth FP.Predicting protein complex membership using probabilistic network reliability.Genome Res 2004 Jun;14(6):1170-5.
  15140827
• Zhang LV, Wong SL, King OD, Roth FP.Predicting co-complexed protein pairs using genomic and proteomic data integration.BMC Bioinformatics 2004 Apr 16;5:38.
  15090078
• Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Rya
  14764870
• Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP.Intensity-based protein identification by machine learning from a library of tandem mass spectra.Nat Biotechnol 2004 Feb;22(2):214-9.
  14730315
• Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Ga
  14704431
• Berriz GF, King OD, Bryant B, Sander C, Roth FP.Characterizing gene sets with FuncAssociate.Bioinformatics 2003 Dec 12;19(18):2502-4.
  14668247
• King OD, Roth FP.A non-parametric model for transcription factor binding sites.Nucleic Acids Res 2003 Oct 1;31(19):e116.
  14500844
• Kramer MF, Cook WJ, Roth FP, Zhu J, Holman H, Knipe DM, Coen DM.Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression.J Virol 2003 Sep;77(17):9533-41.
  12915567
• King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP.Predicting phenotype from patterns of annotation.Bioinformatics 2003;19 Suppl 1:i183-9.
  12855456
• Roth JR, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI.Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation.Genetics 2003 Apr;163(4):1483-96.
  12702691
• King OD, Foulger RE, Dwight SS, White JV, Roth FP.Predicting gene function from patterns of annotation.Genome Res 2003 May;13(5):896-904.
  12695322
• Berriz GF, White JV, King OD, Roth FP.GoFish finds genes with combinations of Gene Ontology attributes.Bioinformatics 2003 Apr 12;19(6):788-9.
  12691998
• Goldberg DS, Roth FP.Assessing experimentally derived interactions in a small world.Proc Natl Acad Sci U S A 2003 Apr 15;100(8):4372-6.
  12676999
• Gibbons FD, Roth FP.Judging the quality of gene expression-based clustering methods using gene annotation.Genome Res 2002 Oct;12(10):1574-81.
  12368250
• Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA.The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress.Mol Cell 2002 Mar;9(3):563-73.
  11931764
• Roth FP.Bringing out the best features of expression data.Genome Res 2001 Nov;11(11):1801-2.
  11691842
• Roth FP, Hughes JD, Estep PW, Church GM.Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.Nat Biotechnol 1998 Oct;16(10):939-45.
  9788350