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

2009 Publications 

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 Shapira
 
Shapira SD, Gat-Viks I, Shum BOV, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N.
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.
Cell 2009; 139:1255-67.
 
Vidal_FEBS_09

Vidal M. 
A unifying view of 21st century systems biology.
FEBS Letters 2009; 583:3891-94.

 
 Salehi-Ashtiani_GenomeResearch_09
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 delineation of C. elegans ORFeome.
Genome Res 2009; 19:2334-42.
 
 
MGC Tea,

The MGC Project Team (Center for Cancer Systems Biology contributors: Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E and Lin C). 
The completion of the Mammalian Gene Collection.
Genome Res 2009; 19:2324-33.

 

MGC Tea,

Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. 
Next generation software for functional trend analysis.
Bioinformatics 2009; 25: 3043-4.

 

zhong
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.
 
 
Dreze
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 BCL-2 ortholog.
Nat Methods 2009; 6:843-9.
 
Joubert
Tonikian R, Xin X, Toret C, 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 D, Kim P, Sidhu S, Boone C.
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
PLoS Biol 2009; 7:e1000218

 

Joubert
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.
 
 
Markson

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.

 

DeNicolo
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.

 

DeNicolo
Venancio TM, Balaji S, Aravind L
High-confidence mapping of chemical compounds and protein complexes reveals novel aspects of chemical stress response in yeast.
Mol Biosyst 2009; 6:175-81.

 

Manichuaikul
Manichaikul A, Ghamsari L, Hom EFY, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen YC, Arvind K., 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.
 
 
Manichuaikul
Adams JC, Keiser MJ, Basuino L, Chambers, HF, Lee DS, Wiest OG, Babbitt PC.
A mapping of drug space from the viewpoint of small molecule metabolism.
PLoS Comput Biol 2009; 5:e1000474.
 
 
publicationimages
Carvunis AR, Gomez E, Thierry-Mieg N, Trilling L, Vidal M.
Systems biology: from yesterday's concepts to tomorrow's discoveries.
Méd Sci (Paris) 2009; 25:578-584.
Xin_GenomeRes_09
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.
  
Xin_GenomeRes_09
Santini S, Crowet JM, Thomas A, Paquot, M, Vandenbol M, Thonart P, Wathelet JP, Blecker C, Lognay G, Brasseur R, Lins L, Charloteaux B.
Study of Thermomyces lanuginosa lipase in the presence of tributyrylglycerol and water.
Biophys J 2009; 12:4812-25.
  

 

aubersold

Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, David Galas, Daniel Gallahan, Robert Gatenby, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V,
Kallioniemi O, Klingmüller 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
Mol Oncol 2009; 3:9-17

 

publicationimages
Park J, Lee DS, Christakis NA, Barabási AL.
The impact of cellular networks on disease comorbidity.
Mol Syst Biol 2009; 2009;5:262.
 
publicationimages
van der Voet M, Berends CWH, Perreault A, Nguyen-Ngoc T, Gönczy 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/Gα.
Nat Cell Biol 2009; 11:269-77.
 
 
Lievens
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; 8:877-886.
 
 
J_lim-nature
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.
 
 
J_lim-nature
Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmons 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
 
 
Venkatesan_NatMeth_09
Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh K-I, 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, Barabási A-L, Vidal M.
An empirical framework for binary interactome mapping.
Nat Methods 2009; 6:83-90
 
 
J_lim-nature
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; 6:91-97.
 
 
J_lim-nature
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.
 
 

 

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