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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  • 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
  • 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
  • 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
  • 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
  • Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM. Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature 2014. 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy WM, Rual JF, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Sole X, Hernandez P, Lazaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD, Vidal M. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 2007; 39:1338-49. PubMed
  • Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119-26. PubMed
  • Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 2007; 25:894-8. PubMed
  • Simarro M, Mauger D, Rhee K, Pujana MA, Kedersha NL, Yamasaki S, Cusick ME, Vidal M, Garcia-Blanco MA, Anderson P. Fas-activated serine/threonine phosphoprotein (FAST) is a regulator of alternative splicing. Proc Natl Acad Sci U S A 2007; 104:11370-5. PubMed
  • 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
  • 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, Barab. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 2007; 25:663-8. PubMed
  • Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 2007; 104:7606-11. PubMed
  • Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007; 5:44. PubMed
  • Yu A, Rual JF, Tamai K, Harada Y, Vidal M, He X, Kirchhausen T. Association of Dishevelled with the clathrin AP-2 adaptor is required for Frizzled endocytosis and planar cell polarity signaling. Dev Cell 2007; 12:129-41. PubMed
  • Lim J, Hao T, Shaw C, Patel AJ, Szab. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 2006; 125:801-14. PubMed
  • Temple G, Lamesch P, Milstein S, Hill DE, Wagner L, Moore T, Vidal M. From genome to proteome: developing expression clone resources for the human genome. Hum Mol Genet 2006; 15 Suppl 1:R31-43. PubMed
  • Davison EM, Harrison MM, Walhout AJ, Vidal M, Horvitz HR. lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics 2005; 171:1017-31. PubMed
  • Gillette WK, Esposito D, Frank PH, Zhou M, Yu LR, Jozwik C, Zhang X, McGowan B, Jacobowitz DM, Pollard HB, Hao T, Hill DE, Vidal M, Conrads TP, Veenstra TD, Hartley JL. Pooled ORF expression technology (POET): using proteomics to screen pools of open reading frames for protein expression. Mol Cell Proteomics 2005; 4:1647-52. PubMed
  • 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 C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005; 437:1173-8. PubMed
  • Cusick ME, Klitgord N, Vidal M, Hill DE. Interactome: gateway into systems biology. Hum Mol Genet 2005; 14 Spec No. 2:R171-81. PubMed
  • Scholtens D, Vidal M, Gentleman R. Local modeling of global interactome networks. Bioinformatics 2005; 21:3548-57. PubMed
  • 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, S. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 2005; 436:861-5. PubMed
  • Sieburth D, Ch'ng Q, Dybbs M, Tavazoie M, Kennedy S, Wang D, Dupuy D, Rual JF, Hill DE, Vidal M, Ruvkun G, Kaplan JM. Systematic analysis of genes required for synapse structure and function. Nature 2005; 436:510-7. PubMed
  • Caruso ME, Jenna S, Beaulne S, Lee EH, Bergeron A, Chauve C, Roby P, Rual JF, Hill DE, Vidal M, Boss. Biochemical clustering of monomeric GTPases of the Ras superfamily. Mol Cell Proteomics 2005; 4:936-44. PubMed
  • Han JD, Dupuy D, Bertin N, Cusick ME, Vidal M. Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol 2005; 23:839-44. PubMed
  • Milstein S, Vidal M. Perturbing interactions. Nat Methods 2005; 2:412-4. PubMed
  • Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G. Functional genomic analysis of RNA interference in C. elegans. Science 2005; 308:1164-7. PubMed
  • Wei C, Lamesch P, Arumugam M, Rosenberg J, Hu P, Vidal M, Brent MR. Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Genome Res 2005; 15:577-82. PubMed
  • Fernandez AG, Gunsalus KC, Huang J, Chuang LS, Ying N, Liang HL, Tang C, Schetter AJ, Zegar C, Rual JF, Hill DE, Reinke V, Vidal M, Piano F. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res 2005; 15:250-9. PubMed
  • Fox RM, Von Stetina SE, Barlow SJ, Shaffer C, Olszewski KL, Moore JH, Dupuy D, Vidal M, Miller DM. A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics 2005; 6:42. PubMed
  • 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; 101:15682-7. PubMed
  • Rual JF, Ceron J, Koreth J, Hao T, Nicot AS, Hirozane-Kishikawa T, Vandenhaute J, Orkin SH, Hill DE, van den Heuvel S, Vidal M. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 2004; 14:2162-8. PubMed
  • Hope IA, Stevens J, Garner A, Hayes J, Cheo DL, Brasch MA, Vidal M. Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res 2004; 14:2070-5. PubMed
  • Lamesch P, Milstein S, Hao T, Rosenberg J, Li N, Sequerra R, Bosak S, Doucette-Stamm L, Vandenhaute J, Hill DE, Vidal M. C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res 2004; 14:2064-9. PubMed
  • Brasch MA, Hartley JL, Vidal M. ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res 2004; 14:2001-9. PubMed
  • Luan CH, Qiu S, Finley JB, Carson M, Gray RJ, Huang W, Johnson D, Tsao J, Reboul J, Vaglio P, Hill DE, Vidal M, Delucas LJ, Luo M. High-throughput expression of C. elegans proteins. Genome Res 2004; 14:2102-10. PubMed
  • Deplancke B, Dupuy D, Vidal M, Walhout AJ. A gateway-compatible yeast one-hybrid system. Genome Res 2004; 14:2093-101. PubMed
  • Dricot A, Rual JF, Lamesch P, Bertin N, Dupuy D, Hao T, Lambert C, Hallez R, Delroisse JM, Vandenhaute J, Lopez-Goni I, Moriyon I, Garcia-Lobo JM, Sangari FJ, Macmillan AP, Cutler SJ, Whatmore AM, Bozak S, Sequerra R, Doucette-Stamm L, Vidal M, Hill DE, Letesson JJ, De Bolle X. Generation of the Brucella melitensis ORFeome version 1.1. Genome Res 2004; 14:2201-6. PubMed
  • Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA, Hill DE, Walhout AJ, Vidal M. A first version of the Caenorhabditis elegans Promoterome. Genome Res 2004; 14:2169-75. PubMed
  • Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C, Vandenhaute J, Cusick ME, Albala JS, Hill DE, Vidal M. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 2004; 14:2128-35. PubMed
  • 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; 430:88-93. PubMed
  • Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 2004; 14:1107-18. PubMed
  • Vidalain PO, Boxem M, Ge H, Li S, Vidal M. Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 2004; 32:363-70. PubMed
  • Tewari M, Hu PJ, Ahn JS, Ayivi-Guedehoussou N, Vidalain PO, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD, Busiguina S, Rual JF, Ibarrola N, Chaklos ST, Bertin N, Vaglio P, Edgley ML, King KV, Albert PS, Vandenhaute J, Pandey A, Riddle DL, Ruvkun G, Vidal M. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 2004; 13:469-82. PubMed
  • 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, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. A map of the interactome network of the metazoan C. elegans. Science 2004; 303:540-3. PubMed
  • Carvunis AR, Gomez E, Thierry-Mieg N, Trilling L, Vidal M. [Systems biology: from yesterday's concepts to tomorrow's discoveries] Med Sci (Paris) 2009; 25:578-84. PubMed
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