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

Photo of Marc Vidal, PhD

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


Marc_Vidal@dfci.harvard.edu

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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 from Harvard Catalyst Profiles

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  • Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Sci Adv 2021. PubMed
  • Cheng F, Zhao J, Wang Y, Lu W, Liu Z, Zhou Y, Martin WR, Wang R, Huang J, Hao T, Yue H, Ma J, Hou Y, Castrillon JA, Fang J, Lathia JD, Keri RA, Lightstone FC, Antman EM, Rabadan R, Hill DE, Eng C, Vidal M, Loscalzo J. Comprehensive characterization of protein-protein interactions perturbed by disease mutations. Nat Genet 2021. PubMed
  • Kim JH, Seo Y, Jo M, Jeon H, Kim YS, Kim EJ, Seo D, Lee WH, Kim SR, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways. J Biol Chem 2020; 295:16906-16919. PubMed
  • Kim JH, Seo Y, Jo M, Jeon H, Kim YS, Kim EJ, Seo D, Lee WH, Kim SR, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways. J Biol Chem 2020; 295:16906-16919. PubMed
  • Ng AHM, Khoshakhlagh P, Rojo Arias JE, Pasquini G, Wang K, Swiersy A, Shipman SL, Appleton E, Kiaee K, Kohman RE, Vernet A, Dysart M, Leeper K, Saylor W, Huang JY, Graveline A, Taipale J, Hill DE, Vidal M, Melero-Martin JM, Busskamp V, Church GM. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 2020. PubMed
  • Sheynkman GM, Tuttle KS, Laval F, Tseng E, Underwood JG, Yu L, Dong D, Smith ML, Sebra R, Willems L, Hao T, Calderwood MA, Hill DE, Vidal M. ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. Nat Commun 2020; 11:2326. PubMed
  • Kim JH, Seo Y, Jo M, Jeon H, Lee WH, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Yeast-Based Genetic Interaction Analysis of Human Kinome. Cells 2020. PubMed
  • Yadav A, Vidal M, Luck K. Precision medicine - networks to the rescue. Curr. Opin. Biotechnol. 2020; 63:177-189. PubMed
  • Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. A reference map of the human binary protein interactome. Nature 2020; 580:402-408. PubMed
  • Choi SG, Olivet J, Cassonnet P, Vidalain PO, Luck K, Lambourne L, Spirohn K, Lemmens I, Dos Santos M, Demeret C, Jones L, Rangarajan S, Bian W, Coutant EP, Janin YL, van der Werf S, Trepte P, Wanker EE, De Las Rivas J, Tavernier J, Twizere JC, Hao T, Hill DE, Vidal M, Calderwood MA, Jacob Y. Maximizing binary interactome mapping with a minimal number of assays. Nat Commun 2019; 10:3907. PubMed
  • Cheng F, Lu W, Liu C, Fang J, Hou Y, Handy DE, Wang R, Zhao Y, Yang Y, Huang J, Hill DE, Vidal M, Eng C, Loscalzo J. A genome-wide positioning systems network algorithm for in silico drug repurposing. Nat Commun 2019; 10:3476. PubMed
  • Lee EJ, Kim N, Park JW, Kang KH, Kim WI, Sim NS, Jeong CS, Blackshaw S, Vidal M, Huh SO, Kim D, Lee JH, Kim JW. Global Analysis of Intercellular Homeodomain Protein Transfer. Cell Rep 2019; 28:712-722.e3. PubMed
  • Alonso-López D, Campos-Laborie FJ, Gutiérrez MA, Lambourne L, Calderwood MA, Vidal M, De Las Rivas J. APID database: redefining protein-protein interaction experimental evidences and binary interactomes. Database (Oxford) 2019. PubMed
  • Kovács IA, Luck K, Spirohn K, Wang Y, Pollis C, Schlabach S, Bian W, Kim DK, Kishore N, Hao T, Calderwood MA, Vidal M, Barabási AL. Network-based prediction of protein interactions. Nat Commun 2019; 10:1240. PubMed
  • Martínez-Noël G, Luck K, Kühnle S, Desbuleux A, Szajner P, Galligan JT, Rodriguez D, Zheng L, Boyland K, Leclere F, Zhong Q, Hill DE, Vidal M, Howley PM. Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. J Mol Biol 2018; 430:1024-1050. PubMed
  • Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. How many human proteoforms are there? Nat Chem Biol 2018; 14:206-214. PubMed
  • Choi SG, Richardson A, Lambourne L, Hill DE, Vidal M. Protein Interactomics by Two-Hybrid Methods. Methods Mol Biol 2018; 1794:1-14. PubMed
  • Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP. A framework for exhaustively mapping functional missense variants. Mol Syst Biol 2017; 13:957. PubMed
  • Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W. Challenges and recommendations for epigenomics in precision health. Nat Biotechnol 2017; 35:1128-1132. PubMed
  • Ghadie MA, Lambourne L, Vidal M, Xia Y. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PLoS Comput. Biol. 2017; 13:e1005717. PubMed
  • Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, Roth FP. Identifying pathogenicity of human variants via paralog-based yeast complementation. PLoS Genet. 2017; 13:e1006779. PubMed
  • Luck K, Sheynkman GM, Zhang I, Vidal M. Proteome-Scale Human Interactomics. Trends Biochem Sci 2017. PubMed
  • Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D'Andrea AD, Whitesell L, Lindquist S. HSP90 Shapes the Consequences of Human Genetic Variation. Cell 2017; 168:856-866.e12. PubMed
  • Lievens S, Van der Heyden J, Masschaele D, De Ceuninck L, Petta I, Gupta S, De Puysseleyr V, Vauthier V, Lemmens I, De Clercq DJ, Defever D, Vanderroost N, De Smet AS, Eyckerman S, Van Calenbergh S, Martens L, De Bosscher K, Libert C, Hill DE, Vidal M, Tavernier J. Proteome-scale Binary Interactomics in Human Cells. Mol Cell Proteomics 2016; 15:3624-3639. PubMed
  • Rambout X, Detiffe C, Bruyr J, Mariavelle E, Cherkaoui M, Brohée S, Demoitié P, Lebrun M, Soin R, Lesage B, Guedri K, Beullens M, Bollen M, Farazi TA, Kettmann R, Struman I, Hill DE, Vidal M, Kruys V, Simonis N, Twizere JC, Dequiedt F. The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression. Nat Struct Mol Biol 2016; 23:663-72. PubMed
  • Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SC, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR. Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A 2016. PubMed
  • 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
  • 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
  • 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
  • Vidal M. How much of the human protein interactome remains to be mapped? Sci Signal 2016; 9:eg7. PubMed
  • Guney E, Menche J, Vidal M, Barábasi AL. Network-based in silico drug efficacy screening. Nat Commun 2016; 7:10331. 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 2014; 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 2009; 6:83-90. 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
  • 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 2009; 37:D669-73. 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 2009; 6:91-7. 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 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
  • 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
  • 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, Barabási AL, Baillie D, Vidal M. 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
  • 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
  • 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
  • Lim J, Hao T, Shaw C, Patel AJ, Szabó G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabási AL, Vidal M, Zoghbi HY. 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
  • Carvunis AR, Gomez E, Thierry-Mieg N, Trilling L, Vidal M. [Systems biology: from yesterday's concepts to tomorrow's discoveries] Med Sci (Paris) ; 25:578-84. PubMed
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DF/HCC members that share similar concepts* with Marc Vidal, PhD but have yet to coauthor a publication with this researcher.

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