Photo of Marc Vidal,  PhD

Marc Vidal, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 632-5114
Fax: (617) 632-5739


Marc_Vidal@dfci.harvard.edu

Marc Vidal, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Professor, Genetics, Harvard Medical School
  • Professor, Cancer Biology, Dana-Farber Cancer Institute

DF/HCC PROGRAM AFFILIATION

Research Abstract

Biological processes are carried out by complex networks of interconnected components, since most gene products in the cell mediate their function together with other gene products. Within such cellular networks physical protein-protein interactions are crucial. The research addresses the following questions: How are protein interactions organized at the scale of the whole cell? Are there global principles that organize such complex networks of interactions? What are the global topological features of networks? And how are such organizational principles disrupted in human disease?

To determine how proteins function in complex cellular networks, we engage in "interactome" modeling, the mapping and systematic characterization of protein-protein interactions at proteome scale. Initially we focused on the multicellular model organism Caenorhabditis elegans, and more recently we have expanded our efforts to the model yeast Saccharomyces cerevisiae, the model plant Arabidopsis thaliana, the model insect Drosophila melanogaster and human, as well as to interactions between viral proteins and host proteins.

The biological information learned in the course of interactome modeling expands understanding of the biology of human cancer.

Publications

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  • Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 2016; 351:1450-4. PubMed
  • Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res 2016. PubMed
  • Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell 2016; 164:805-17. PubMed
  • Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol 2016; 12:863. PubMed
  • Guney E, Menche J, Vidal M, Barábasi AL. Network-based in silico drug efficacy screening. Nat Commun 2016; 7:10331. PubMed
  • Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M. An inter-species protein-protein interaction network across vast evolutionary distance. Mol Syst Biol 2016; 12:865. PubMed
  • Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, Culhane AC, Barry WT, Schumacher SE, Beroukhim R, Szallasi Z, Vidal M, Hill DE, Silver DP. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. 2015. PubMed
  • Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJ, Lindquist S, Vidal M. Widespread macromolecular interaction perturbations in human genetic disorders. Cell 2015; 161:647-60. PubMed
  • Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJ. Human gene-centered transcription factor networks for enhancers and disease variants. Cell 2015; 161:661-73. PubMed
  • Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP. Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Comput. Biol. 2015; 11:e1004147. PubMed
  • Taşan M, Musso G, Hao T, Vidal M, MacRae CA, Roth FP. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nat Methods 2015; 12:154-9. PubMed
  • Vidal M, Fields S. The yeast two-hybrid assay: still finding connections after 25 years. Nat Methods 2015; 11:1203-6. PubMed
  • Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM. Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature 2014. PubMed
  • Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. A proteome-scale map of the human interactome network. Cell 2014; 159:1212-26. PubMed
  • Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev 2014; 28:1957-75. PubMed
  • Wang W, Zhong Q, Teng L, Bhatnagar N, Sharma B, Zhang X, Luther W, Haynes LP, Burgoyne RD, Vidal M, Volchenboum S, Hill DE, George RE. Mutations that disrupt PHOXB interaction with the neuronal calcium sensor HPCAL1 impede cellular differentiation in neuroblastoma. Oncogene 2014; 33:3316-24. PubMed
  • Dittmer TA, Sahni N, Kubben N, Hill DE, Vidal M, Burgess RC, Roukos V, Misteli T. Systematic identification of pathological lamin A interactors. Mol Biol Cell 2014; 25:1493-510. PubMed
  • Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat Commun 2014; 5:3650. PubMed
  • Sahni N, Yi S, Zhong Q, Jailkhani N, Charloteaux B, Cusick ME, Vidal M. Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev 2013; 23:649-57. PubMed
  • Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods 2013; 10:1239-45. PubMed
  • Mehra A, Zahra A, Thompson V, Sirisaengtaksin N, Wells A, Porto M, Köster S, Penberthy K, Kubota Y, Dricot A, Rogan D, Vidal M, Hill DE, Bean AJ, Philips JA. Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking. PLoS Pathog. 2013; 9:e1003734. PubMed
  • Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD. SH3 interactome conserves general function over specific form. Mol Syst Biol 2013; 9:652. PubMed
  • Baas D, Caussanel-Boude S, Guiraud A, Calhabeu F, Delaune E, Pilot F, Chopin E, Machuca-Gayet I, Vernay A, Bertrand S, Rual JF, Jurdic P, Hill DE, Vidal M, Schaeffer L, Goillot E. CKIP-1 regulates mammalian and zebrafish myoblast fusion. J Cell Sci 2012; 125:3790-800. PubMed
  • Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 2012; 487:491-5. PubMed
  • Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M. Proto-genes and de novo gene birth. Nature 2012; 487:370-4. PubMed
  • Lambert B, Vandeputte J, Remacle S, Bergiers I, Simonis N, Twizere JC, Vidal M, Rezsohazy R. Protein interactions of the transcription factor Hoxa1. BMC Dev Biol 2012; 12:29. PubMed
  • Fine DA, Rozenblatt-Rosen O, Padi M, Korkhin A, James RL, Adelmant G, Yoon R, Guo L, Berrios C, Zhang Y, Calderwood MA, Velmurgan S, Cheng J, Marto JA, Hill DE, Cusick ME, Vidal M, Florens L, Washburn MP, Litovchick L, DeCaprio JA. Identification of FAM111A as an SV40 host range restriction and adenovirus helper factor. PLoS Pathog. 2012; 8:e1002949. PubMed
  • Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, Decaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL. Viral perturbations of host networks reflect disease etiology. PLoS Comput. Biol. 2012; 8:e1002531. PubMed
  • Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S, . The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clin. Proteomics 2012; 9:6. PubMed
  • Vidal M, Cusick ME, Barabási AL. Interactome networks and human disease. Cell 2011; 144:986-98. PubMed
  • Suzuki Y, St Onge RP, Mani R, King OD, Heilbut A, Labunskyy VM, Chen W, Pham L, Zhang LV, Tong AH, Nislow C, Giaever G, Gladyshev VN, Vidal M, Schow P, Lehár J, Roth FP. Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nat Methods 2011; 8:159-64. PubMed
  • Johannessen CM, Boehm JS, Kim SY, Thomas SR, Wardwell L, Johnson LA, Emery CM, Stransky N, Cogdill AP, Barretina J, Caponigro G, Hieronymus H, Murray RR, Salehi-Ashtiani K, Hill DE, Vidal M, Zhao JJ, Yang X, Alkan O, Kim S, Harris JL, Wilson CJ, Myer VE, Finan PM, Root DE, Roberts TM, Golub T, Flaherty KT, Dummer R, Weber BL, Sellers WR, Schlegel R, Wargo JA, Hahn WC, Garraway LA. COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature 2010; 468:968-72. PubMed
  • Brehme M, Vidal M. A global protein-lipid interactome map. Mol Syst Biol 2010; 6:443. PubMed
  • Heard E, Tishkoff S, Todd JA, Vidal M, Wagner GP, Wang J, Weigel D, Young R. Ten years of genetics and genomics: what have we achieved and where are we heading? Nat Rev Genet 2010; 11:723-33. PubMed
  • Giordano-Santini R, Milstein S, Svrzikapa N, Tu D, Johnsen R, Baillie D, Vidal M, Dupuy D. An antibiotic selection marker for nematode transgenesis. Nat Methods 2010; 7:721-3. PubMed
  • Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK. The landscape of C. elegans 3'UTRs. Science 2010; 329:432-5. PubMed
  • Pilot-Storck F, Chopin E, Rual JF, Baudot A, Dobrokhotov P, Robinson-Rechavi M, Brun C, Cusick ME, Hill DE, Schaeffer L, Vidal M, Goillot E. Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol Cell Proteomics 2010; 9:1578-93. PubMed
  • Nielsen J, Vidal M. Systems biology of microorganisms. Curr Opin Microbiol 2010; 13:335-6. PubMed
  • Gómez-Baldó L, Schmidt S, Maxwell CA, Bonifaci N, Gabaldón T, Vidalain PO, Senapedis W, Kletke A, Rosing M, Barnekow A, Rottapel R, Capellá G, Vidal M, Astrinidis A, Piekorz RP, Pujana MA. TACC3-TSC2 maintains nuclear envelope structure and controls cell division. Cell Cycle 2010. PubMed
  • Yadav VK, Balaji S, Suresh PS, Liu XS, Lu X, Li Z, Guo XE, Mann JJ, Balapure AK, Gershon MD, Medhamurthy R, Vidal M, Karsenty G, Ducy P. Pharmacological inhibition of gut-derived serotonin synthesis is a potential bone anabolic treatment for osteoporosis. Nat Med 2010; 16:308-12. PubMed
  • Wang J, Robida-Stubbs S, Tullet JM, Rual JF, Vidal M, Blackwell TK. RNAi screening implicates a SKN-1-dependent transcriptional response in stress resistance and longevity deriving from translation inhibition. PLoS Genet. 2010. PubMed
  • Yan H, Venkatesan K, Beaver JE, Klitgord N, Yildirim MA, Hao T, Hill DE, Cusick ME, Perrimon N, Roth FP, Vidal M. A genome-wide gene function prediction resource for Drosophila melanogaster. PLoS ONE 2010; 5:e12139. PubMed
  • Dreze M, Monachello D, Lurin C, Cusick ME, Hill DE, Vidal M, Braun P. High-quality binary interactome mapping. Methods Enzymol 2010; 470:281-315. PubMed
  • Vidal M. A unifying view of 21st century systems biology. FEBS Lett 2009; 583:3891-4. PubMed
  • Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, Vidal M. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Res 2009; 19:2334-42. PubMed
  • Dreze M, Charloteaux B, Milstein S, Vidalain PO, Yildirim MA, Zhong Q, Svrzikapa N, Romero V, Laloux G, Brasseur R, Vandenhaute J, Boxem M, Cusick ME, Hill DE, Vidal M. 'Edgetic' perturbation of a C. elegans BCL2 ortholog. Nat Methods 2009; 6:843-9. PubMed
  • Joubert PE, Meiffren G, Grégoire IP, Pontini G, Richetta C, Flacher M, Azocar O, Vidalain PO, Vidal M, Lotteau V, Codogno P, Rabourdin-Combe C, Faure M. Autophagy induction by the pathogen receptor CD46. Cell Host Microbe 2009; 6:354-66. PubMed
  • Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009; 7:e1000218. PubMed
  • Markson G, Kiel C, Hyde R, Brown S, Charalabous P, Bremm A, Semple J, Woodsmith J, Duley S, Salehi-Ashtiani K, Vidal M, Komander D, Serrano L, Lehner P, Sanderson CM. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res 2009; 19:1905-11. PubMed
  • De Nicolo A, Parisini E, Zhong Q, Dalla Palma M, Stoeckert KA, Domchek SM, Nathanson KL, Caligo MA, Vidal M, Cusick ME, Garber JE. Multimodal assessment of protein functional deficiency supports pathogenicity of BRCA1 p.V1688del. Cancer Res 2009; 69:7030-7. PubMed
  • Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods 2009; 6:589-92. PubMed
  • Xin X,Rual JF,Hirozane-Kishikawa T,Hill DE,Vidal M,Boone C,Thierry-Mieg N. Shifted Transversal Design smart-pooling for high coverage interactome mapping. Genome Res 2009; 19:1262-9. PubMed
  • van der Voet M,Berends CW,Perreault A,Nguyen-Ngoc T,Gonczy P,Vidal M,Boxem M,van den Heuvel S. NuMA-related LIN-5, ASPM-1, calmodulin and dynein promote meiotic spindle rotation independently of cortical LIN-5/GPR/Galpha. Nat Cell Biol 2009; 11:269-77. PubMed
  • Aebersold R,Auffray C,Baney E,Barillot E,Brazma A,Brett C,Brunak S,Butte A,Califano A,Celis J,Cufer T,Ferrell J,Galas D,Gallahan D,Gatenby R,Goldbeter A,Hace N,Henney A,Hood L,Iyengar R,Jackson V,Kallioniemi O,Klingmuller U,Kolar P,Kolch W,Kyriakopoulou C,Laplace F,Lehrach H,Marcus F,Matrisian L,Nolan G,Pelkmans L,Potti A,Sander C,Seljak M,Singer D,Sorger P,Stunnenberg H,Superti-Furga G,Uhlen M,Vidal M,Weinstein J,Wigle D,Williams M,Wolkenhauer O,Zhivotovsky B,Zinovyev A,Zupan B. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol 2009; 3:9-17. PubMed
  • Lievens S,Vanderroost N,Van der Heyden J,Gesellchen V,Vidal M,Tavernier J. Array MAPPIT: high-throughput interactome analysis in mammalian cells. J Proteome Res 2009; 8:877-86. PubMed
  • Braun P,Tasan M,Dreze M,Barrios-Rodiles M,Lemmens I,Yu H,Sahalie JM,Murray RR,Roncari L,de Smet AS,Venkatesan K,Rual JF,Vandenhaute J,Cusick ME,Pawson T,Hill DE,Tavernier J,Wrana JL,Roth FP,Vidal M. An experimentally derived confidence score for binary protein-protein interactions. Nat Methods 2008; 6:91-7. PubMed
  • Simonis N,Rual JF,Carvunis AR,Tasan M,Lemmens I,Hirozane-Kishikawa T,Hao T,Sahalie JM,Venkatesan K,Gebreab F,Cevik S,Klitgord N,Fan C,Braun P,Li N,Ayivi-Guedehoussou N,Dann E,Bertin N,Szeto D,Dricot A,Yildirim MA,Lin C,de Smet AS,Kao HL,Simon C,Smolyar A,Ahn JS,Tewari M,Boxem M,Milstein S,Yu H,Dreze M,Vandenhaute J,Gunsalus KC,Cusick ME,Hill DE,Tavernier J,Roth FP,Vidal M. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods 2009; 6:47-54. PubMed
  • Venkatesan K,Rual JF,Vazquez A,Stelzl U,Lemmens I,Hirozane-Kishikawa T,Hao T,Zenkner M,Xin X,Goh KI,Yildirim MA,Simonis N,Heinzmann K,Gebreab F,Sahalie JM,Cevik S,Simon C,de Smet AS,Dann E,Smolyar A,Vinayagam A,Yu H,Szeto D,Borick H,Dricot A,Klitgord N,Murray RR,Lin C,Lalowski M,Timm J,Rau K,Boone C,Braun P,Cusick ME,Roth FP,Hill DE,Tavernier J,Wanker EE,Barabasi AL,Vidal M. An empirical framework for binary interactome mapping. Nat Methods 2008; 6:83-90. PubMed
  • Cusick ME,Yu H,Smolyar A,Venkatesan K,Carvunis AR,Simonis N,Rual JF,Borick H,Braun P,Dreze M,Vandenhaute J,Galli M,Yazaki J,Hill DE,Ecker JR,Roth FP,Vidal M. Literature-curated protein interaction datasets. Nat Methods 2009; 6:39-46. PubMed
  • Chatr-aryamontri A,Ceol A,Peluso D,Nardozza A,Panni S,Sacco F,Tinti M,Smolyar A,Castagnoli L,Vidal M,Cusick ME,Cesareni G. VirusMINT: a viral protein interaction database. Nucleic Acids Res 2008; 37:D669-73. PubMed
  • Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M. Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009; 5:321. PubMed
  • Yu H,Braun P,Yildirim MA,Lemmens I,Venkatesan K,Sahalie J,Hirozane-Kishikawa T,Gebreab F,Li N,Simonis N,Hao T,Rual JF,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,Barabasi AL,Tavernier J,Hill DE,Vidal M. High-quality binary protein interaction map of the yeast interactome network. Science 2008; 322:104-10. PubMed
  • 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. PubMed
  • Li S,Liu C,Li N,Hao T,Han T,Hill DE,Vidal M,Lin JD. Genome-wide coactivation analysis of PGC-1alpha identifies BAF60a as a regulator of hepatic lipid metabolism. Cell Metab 2008; 8:105-17. PubMed
  • Li QR,Carvunis AR,Yu H,Han JD,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. PubMed
  • Braun P,Rietman E,Vidal M. Networking metabolites and diseases. Proc Natl Acad Sci U S A 2008; 105:9849-50. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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. PubMed
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  • Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S, Richardson AL, Greulich H, Stewart CJ, Mulvey LA, Shen RR, Ambrogio L, Hirozane-Kishikawa T, Hill DE, Vidal M, Meyerson M, Grenier JK, Hinkle G, Root DE, Roberts TM, Lander ES, Polyak K, Hahn WC. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 2007; 129:1065-79. PubMed
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