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

2011 Publications 

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 Tasan-etal_G3_12 Gaudet S, Langlois MJ, Lue RA, Rivard N, Viel A.
The MEK2-binding tumor suppressor hDlg is recruited by E-cadherin to the midbody ring.
BMC Cell Biol 2011; 12:55.
 
 Tasan-etal_G3_12 Ahn YY, Ahnert SE, Bagrow JP, Barabási AL.
Flavor network and the principles of food pairing.
Sci Rep 2011; 1:196.
 
 Yu_NatMeth_11 Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw H, Zhu H, Dekker J, Walhout A.
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.
Nat Methods 2011; 8:1050-2.
 
 Yu_NatMeth_11 Aldridge BB, Gaudet S, Lauffenburger DA, Sorger PK.
Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis.
Mol Syst Biol 2011; 7:553.
 
 Yu_NatMeth_11
Anders L, Ke N, Hydbring P, Choi YJ, Widlund HR, Chick JM, Zhai H, Vidal M, Gygi SP, Braun P, Sicinski P.
A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells.
Cancer Cell 2011; 20:620-34.
 
 Yu_NatMeth_11
Maxwell CA, Benitez J, Gomez-Baldo L, Osorio A, Bonifaci N, et al, (Center for Cancer Systems Biology contributer: Marc Vidal).
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.
PLoS Biol 2011; 9:e1001199.
 
 Yu_NatMeth_11
Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP.
Systematic exploration of synergistic drug pairs.
Mol Syst Biol 2011; 7:544.
 
 Arabidopsis_Science_11
Loscalzo J, Barabasi AL.
Systems biology and the future of medicine.
Wiley Interdiscip Rev Syst Biol Med 2011; 3:619-27.
 Arabidopsis_Science_11
Schild-Prüfert K, Saito TT, Smolikov S, Gu Y, Hincapie M, Hill DE, Vidal M, McDonald K, Colaiácovo MP.
Organization of the synaptonemal complex during meiosis in Caenorhabditis elegans.
Genetics 2011; 189:411-21.
 
 
 Arabidopsis_Science_11
Charloteaux B, Zhong Q, Dreze M, Cusick ME, Hill DE, Vidal M.
Protein-protein interactions and networks: forward and reverse edgetics.
Methods Mol Biol 2011; 759:197-213.
 Arabidopsis_Science_11
Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA.
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.
Mol Syst Biol 2011; 7:518.
 
 Arabidopsis_Science_11
Yang X, Boehm JS, Yang X, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE.
A public genome-scale lentiviral expression library of human ORFs.
Nat Methods 2011; 8:659-61.
 
 Arabidopsis_Science_11
Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y; European Union Effectoromics Consortium, Vandenhaute J, Roth FP, Hill DE, Ecker JR, Vidal M, Beynon J, Braun P, Dangl JL.
Independently evolved virulence effectors converge onto hubs in a plant immune system network.
Science 2011; 333:596-601.
 
 
 Arabidopsis_Science_11
Arabidopsis Interactome Mapping Consortium. (Dreze M, Carvunis AR, Charloteaux B, Galli M, Pevzner SJ, Tasan M co-first authors; Braun P, Vidal M, Ecker JR, Hill DE co-corresponding authors)
Evidence for network evolution in an Arabidopsis interactome map.
Science 2011; 333:601-7.
 
 
 Arabidopsis_Science_11
Ghoshal G, Barabási AL.
Ranking stability and super-stable nodes in complex networks.
Nat Commun 2011; 2:394.
 Arabidopsis_Science_11
Chua HN, Roth FP.
Discovering the targets of drugs via computational systems biology.
J Biol Chem 2011; 286:23653-8.
 Yu_NatMeth_11
de Barsy M, Jamet A, Filopon D, Nicolas C, Laloux G, Rual JF, Muller A, Twizere JC, Nkengfac B, Vandenhaute J, Hill DE, Salcedo SP, Gorvel JP, Letesson JJ, De Bolle X.
Identification of a Brucella spp. secreted effector specifically interacting with human small GTPase Rab2.
Cell Microbiol 2011; 13:1044-58.
 
 Yu_NatMeth_11
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K.
Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii.
BMC Genomics 2011; 12 Suppl 1:S4.
 
 Yu_NatMeth_11
Sakai Y, Shaw CA, Dawson BC, Dugas DV, Al-Mohtaseb Z, Hill DE, Zoghbi HY.
Protein interactome reveals converging molecular pathways among autism disorders.
Sci Transl Med 2011; 3:86ra49.
 
 Yu_NatMeth_11
Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P, Vidal M.
Next-generation sequencing to generate interactome datasets.
Nat Methods 2011; 8:478-80.
 
 Yu_NatMeth_11
Liu YY, Slotine JJ, Barabási AL.
Controllability of complex networks.
Nature 2011; 473:167-73.
 

Suk_NucAcidRes_11

 

 

 

Suk K, Choi J, Suzuki Y, Ozturk SB, Mellor JC, Wong KH, Mackay JL, Gregory RI, Roth FP.
Reconstitution of human RNA interference in budding yeast.
Nucleic Acids Res 2011; 39:e43.
Ahn_PLoS-ComputBiol_2011
Sohn Y, Choi MK, Ahn YY, Lee J, Jeong J.
Topological cluster analysis reveals the systemic organization of the Caenorhabditis elegans connectome.
PLoS Comput Biol 2011; 7:e1001139.
 
Onnela_PLoS-ONE_2011
Onnela JP, Arbesman S, González MC, Barabási AL, Christakis NA.
Geographic constraints on social network groups.
PLoS ONE 2011; 6:e16939.
 
Kahle_HumMolGen_1_11
Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP.
Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes.
PLoS Genet 2011; 7:e1001366.
 
Kahle_HumMolGen_1_11
Bagrow JP, Wang D, Barabási AL.
Collective response of human populations to large-scale emergencies.
PLoS ONE 2011; 6:e17680.
 
Vidal_Cell_11
Vidal M, Cusick ME, Barabási AL.
Interactome networks and human disease.
Cell 2011; 144:986-98.
 
 
Vidal_Cell_11
Pu CL, Pei WJ.
Integrating local and global routing on scale-free networks.
Int J Mod Phys C 2011; 22: 297-304.

Ding_nature_11

 

 

 
Ding Z, Wu CJ, Chu GC, Xiao Y, Ho D, Zhang J, Perry SR, Labrot ES, Wu X, Lis R, Hoshida Y, Hiller D, Hu B, Jiang S, Zheng H, Stegh AH, Scott KL, Signoretti S, Bardeesy N, Wang YA, Hill DE, Golub TR, Stampfer MJ, Wong WH, Loda M, Mucci L, Chin L, DePinho RA.
SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression.
Nature 2011; 470:269-73.
  
Kahle_HumMolGen_1_11
Kahle JJ, Gulbahce N, Shaw CA, Lim J, Hill DE, Barabási AL, Zoghbi HY.
Comparison of an expanded ataxia interactome with patient medical records reveals a relationship between macular degeneration and ataxia.
Hum Mol Genet 2011; 20:510-27.
 
Suzuki_NatMeth_02_11
Suzuki Y, 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.
 
Barabasi_nature_01
Barabási AL, Gulbahce N, Loscalzo J.
Network medicine: a network-based approach to human disease.
Nat Rev Genet 2011; 12:56-68.
 
 

 

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