Dana-Farber Cancer Institute (DFCI)  | Dept of Cancer Biology (DFCI)  | Harvard Medical School (HMS)  | Dept of Genetics (HMS)     

2016 Publications 

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  Kitsak M, Sharma A, Menche J, Guney E, Ghiassian SD, Loscalzo J, Barabási AL.
Tissue Specificity of Human DiseaseModule
Sci Rep. 2016 Oct 17;6:35241. doi: 10.1038/srep35241
 
  Vidal M
Playing Hide-and-Seek with Yeast.
Cell. 2016 Aug 25;166(5):1069-73. doi: 10.1016/j.cell.2016.08.018
 
  Chaiboonchoa A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, Salehi-Ashtiani K.
Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.
Mol Biosyst.  2016 Jul 19;12(8):2394-407. doi: 10.1039/c6mb00237d
 
  Junshi Yazaki, Mary Galli, Alice Y. Kim, Kazumasa Nito, Fernando Aleman, Katherine N. Chang, Anne-Ruxandra Carvunis, Rosa Quan, Hien Nguyen, Liang Song, José M. Alvarez, Shao-shan Carol Huang, Huaming Chen, Niroshan Ramachandran, Stefan Altmann, Rodrigo A. Gutiérrez, David E. Hill, Julian I. Schroeder, Joanne Chory, Joshua LaBaer, Marc Vidal, Pascal Braun, and Joseph R. Ecker.
Mapping transcription factor interactome networks using HaloTag protein arrays.
PNAS.  2016 Jul 19;113(29):E4238-47. doi:10.1073/pnas.1603229113
 
  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 June 6. doi: 1038/nsmb.3243
 
  Deville P, Song C, Eagle N, Blondel VD, Barabási AL, Wang D.
Scaling identity connects human mobility and social interactions.
Proc Natl Acad Sci U S A. 2016 June 6. pii: 201525443
 
  Vidal M
How much of the human protein interactome remains to be mapped?
Sci Signal. 2016 May 10;9(427):eg7
 
  Vinayagam A, Gibson TE, Lee HJ, Yilmazel B, Roesel C, Hu Y, Kwon Y, Sharma A, Liu YY, Perrimon N, Barabási AL.
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.
Proc Natl Acad Sci U S A. 2016 May 3;113(18):4976-81
 
  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 April 22; 12(4):863
 
  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 April 22; 12(4):865
 
  Barrera LA, Vendenko 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 Si, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML
Survey of variation in human transcription factors reveals prevalent DNA binding changes.
Science. 2016 Mar 25; 351(6280):1450-4
 
  Tsokanos FF, Albert MA, Demetriades C, Spirohn K, Boutros M, Teleman AA.
eIF4A inactivates TORC1 in response to amino acid starvation.
EMBO J.2016 Mar 17. pii: e201593118
 
  Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld C, 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 Mar 14. pii: gr.192526.115
 
  ORFeome Collaboration.
The ORFeome Collaboration: a genome-scale human ORF-clone resource.
Nat Methods. 2016 Feb 25;13(3):191-2
  Gao J, Barzel B, Barabási AL
Universal resilience patterns in complex networks.
Nature. 2016 Feb 18;530:307-12
  Chiu CN, Rihel J, Lee DA, Singh C, Mosser EA, Chen S, Sapin V, Pham U, Engle J, Niles BJ, Montz CJ, Chakravarthy S, Zimmerman S, Salehi-Ashtiani K, Vidal M, Schier AF, Prober DA.
A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States.
Neuron. 2016 Feb 17;89(4):842-56
 
  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 Feb 11;164(4):805-17
 
  Li X, Chatterjee N, Spirohn K, Boutros M, Bohmann D.
Cdk12 Is A Gene-Selective RNA Polymerase II Kinase That Regulates a Subset of the Transcriptome, Including Nrf2 Target Genes.
Sci Rep. 2016 Feb 1;6:21455
  Guney E, Menche J, Vidal M, Barábasi AL.
Network-based in silico drug efficacy screening.
Nat Commun. 2016 Feb 1;7:10331
  Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H.
A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
Cell. 2016 Jan 14;164(1-2):310-23
 
  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.
Cancer Discov. 2016 Jan;6(1):45-58
 
 

 

 

 

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