Dana-Farber Cancer Institute (DFCI)  | Dept of Cancer Biology (DFCI)  | Harvard Medical School (HMS)  | Dept of Genetics (HMS)     
2008 Publications 
 
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Hartley_etal_NatMeth
Hartley JL, Salehi-Ashtiani K, Hill DE.
Proteome expression moves in vitro: resources and tools for harnessing the human proteome.
Nat Methods 2008; 5:1001-2.
Hartley_etal_NatMeth
Nishikawa T, Gulbahce N, Motter AE.
Spontaneous reaction silencing in metabolic optimization.
PLoS Comput Biol 2008; 4: e1000236.
J_lim-nature
de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, Andre P, Rabourdin-Combe C, Lotteau V.
Hepatitis C virus infection protein network.
Mol Syst Biol 2008; 4:230.
 
J_lim-nature
Klekota J, Roth FP.
Chemical substructures that enrich for biological activity.
Bioinformatics 2008; 24:2518-25.
 
J_lim-nature
Yu H, Braun P, Yildirim MA, Lemmons I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual J-F, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási A-L, Tavernier J, Hill DE, Vidal M.
High quality binary protein interaction map of the yeast interactome network.
Science 2008; 322:104-10.
 
 
J_lim-nature
Berriz GF, Roth FP.
The Synergizer service for translating gene, protein and other biological identifiers.
Bioinformatics 2008; 24:2272-3.
 
Boxem_Cell_08
Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M.
A protein domain-based interactome network for C. elegans early embryogenesis.
Cell 2008; 134:534-45.
 
 
Boxem_Cell_08
Lehmann S, Jackson AD, Lautrup BE.
A quantitative analysis of indicators of scientific performance.
Scientometrics 2008; 76:369-90.
  
Boxem_Cell_08
Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP.
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.
Genome Biol 2008; 9:S7.
  
Boxem_Cell_08
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
Genome Biol 2008; 9:S2.
  
Boxem_Cell_08
Hughes TR, Roth FP.
A race through the maze of genomic evidence.
Genome Biol 2008; 9:S1.
  
mol_bio
Li S, Liu C, Li N, Hao T, Han T, Hill DE, Vidal M, Lin JD.
Genome-wide coactivation analysis of PGC-1α identifies BAF60a as a regulator of hepatic lipid metabolism.
Cell Metab 2008; 8:105-17.
mol_bio
Komatsu H, Chao MY, Larkins-Ford J, Corkins ME, Somers GA, Tucey T, Dionne HM. White JQ, Wani K, Boxem M, Hart AC.
OSM-11 facilitates LIN-12 Notch signaling during Caenorhabditis elegans vulval development.
PLoS Biol 2008: 6:1730-45.
  
J_lim-nature
Li QR, Carvunis AR, Yu H, Han JDJ, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.
Revisiting the Saccharomyces cerevisiae predicted ORFeome.
Genome Res 2008; 18:1294-303. 
Braun_PNAS08_cover
 
Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabasi AL.
The implications of human metabolic network topology for disease comorbidity.
Proc Natl Acad Sci USA 2008; 105:9880-5.
 
Braun_PNAS08_cover
 
Braun P, Rietman E, Vidal M.
Networking metabolites and diseases.
Proc Natl Acad Sci USA 2008; 105:9849-50.
 
 
mol_bio
Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK.
A mitochondrial protein compendium elucidates complex I disease biology.
Cell 2008; 134:112-23.
 
Salehi_NatMeth_08
Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D, Tusneem N, Smith DR, Cusick ME, Hill DE, Roth FP, Vidal M.
Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.
Nat Methods 2008; 5:597-600.
 
 
Djebali_NatMeth_08
Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigo R.
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
Nat Methods 2008; 5:629-35.
 
  
Djebali_NatMeth_08
Lehmann S, Schwartz M, Hansen LK.
Biclique communities.
Phys Rev E 2008; 78:016108.
Djebali_NatMeth_08
Gonzalez MC, Hidalgo CA, Barabasi AL.
Understanding individual human mobility patterns.
Nature 2008; 453:779-82.
Lim J, Crespo-Barreto J, Jafar-Nejad P, Bowman AB, Richman R, Hill DE, Orr HT, Zoghbi HY.
Opposing effects of polyglutamine expansion on native protein complexes contribute to SCA1.
Nature 2008; 452:713-19.
 
  
Yildirim_MSB_08
Yildirim MA, Vidal M.
Systems engineering to systems biology.
Mol Syst Biol 2008; 4:185.
Yildirim_MSB_08
Mani R, St Onge RP, Hartman JL 4th, Giaever G, Roth FP.
Defining genetic interaction.
Proc Natl Acad Sci USA 2008; 105:3461-66.
Yildirim_MSB_08
Motter AE, Gulbahce N, Almaas E, Barabasi AL.
Predicting synthetic rescues in metabolic networks.
Mol Syst Biol 2008; 4:168.
 
 
 

 

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