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

2012 Publications 

Where text is copyrighted it is provided here only to permit fair use

 

 Variome-Virome Franzosa EA, Garamszegi S, Xia Y.
Toward a three-dimensional view of protein networks between species.
Front Microbiol 2012; 3:428.
 
 Fragmentome Erratum
Erratum
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 2012; 151(7):1633.
 
 Variome-Virome Carvunis AR, Roth FP, Calderwood MA, Cusick ME, Superti-Furga G, Vidal M.
Interactome Networks.
in Handbook of Systems Biology 2012; Ch. 3, pp. 45-63.
 
 Variome-Virome 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.
 
 Variome-Virome Neveu G, Cassonnet P, Vidalain PO, Rolloy C, Mendoza J, Jones L, Tangy F, Muller M, Demeret C, Tafforeau L, Lotteau V, Rabourdin-Combe C, Travé G, Dricot A, Hill DE, Vidal M, Favre M, Jacob Y.
Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase.
Methods 2012; 58:349-59.
 
 Variome-Virome Liu YY, Csoka E, Zhou HJ, Posfai M.
Core percolation on complex networks.
Phys Rev Lett 2012; 109:205703.
 
 Variome-Virome 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.
 
 Variome-Virome Liu YY, Slotine JJ, Barabási AL.
Control centrality and hierarchical structure in complex networks.
PLoS ONE 2012; 7:e44459.
 
 Variome-Virome Blumm N, Ghoshal G, Forró Z, Schich M, Bianconi G, Bouchaud JP, Barabási AL.
Dynamics of ranking processes in complex systems.
Phys Rev Lett 2012; 109:128701.
 
 Variome-Virome 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.
 
 
 Gulbahce-etal_PLoSComputBiol_12 Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM.
Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model.
PLoS Pathog 2012; 8:e1002813.
 
 Gulbahce-etal_PLoSComputBiol_12 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.
 
Access the recommendation on F1000 Prime
 
 Gulbahce-etal_PLoSComputBiol_12 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, 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.
 
 Gulbahce-etal_PLoSComputBiol_12 Slotine JJ, Liu YY.
Complex Networks: The missing link.
Nat Physics 2012; 8:512-3.
 
 Gulbahce-etal_PLoSComputBiol_12 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; 125:3790-3800.
 
 Simonis-etal_Retrovirology_12 Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S, Apweiler R, Bader J, Barnes S, Bettauer R, Chan MM, Coon J, Dolinski K, Dowell BL, Edmonds CG, Gaudet S, Gerszten R, Kagan J, Mazurchuk R, McShane L, Moritz RL, Palmer-Toy D, Pandey A, Polanski M, Quackenbush J, Sheeley D, Skates S, Srivastava S, Wang W, Weng Z, White F.
The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare.
Clin Proteomics 2012; 9:6.
 
 Simonis-etal_Retrovirology_12 Chalancon G, Ravarani CN, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM.
Interplay between gene expression noise and regulatory network architecture.
Trends Genet 2012; 28:221-32.
 
 Simonis-etal_Retrovirology_12 Simonis N, Rual JF, Lemmens I, Boxus M, Hirozane-Kishikawa T, Gatot JS, Dricot A, Hao T, Vertommen D, Legros S, Daakour S, Klitgord N, Martin M, Willaert JF, Dequiedt F, Navratil V, Cusick ME, Burny A, Van Lint C, Hill DE, Tavernier J, Kettmann R, Vidal M, Twizere JC.
Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses.
Retrovirology 2012; 9:26.
 
 Simonis-etal_Retrovirology_12 Karsai M, Kaski K, Barabasi AL, Kertesz J.
Universal features of correlated bursty behaviour.
Sci Rep 2012; 2:397.
 
 Simonis-etal_Retrovirology_12 Gaudet S, Spencer SL, Chen WH, Sorger PK.
Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis.
PLoS Comput Biol 2012; 8:e1002482.
 
 Simonis-etal_Retrovirology_12 Palchykov V, Kaski K, Kertész J, Barabási AL, Dunbar RI
Sex differences in intimate relationships.
Sci Rep 2012; 2:370.
 
 Simonis-etal_Retrovirology_12 Simini F, González MC, Maritan A, Barabási AL.
A universal model for mobility and migration patterns
Nature 2012; 484:96-100.
 
 Carvunis & Dreze Nouvelles Carvunis AR, Dreze M.
Virulence effectors target key proteins of interactome networks of host plant cells.
Méd Sci (Paris) 2012; 28:237-9.
 
 Carvunis & Dreze Nouvelles Parikh VN, Jin RC, Rabello S, Gulbahce N, White K, Hale A, Cottrill KA, Shaik RS, Waxman AB, Zhang YY, Maron BA, Hartner JC, Fujiwara Y, Orkin SH, Haley KJ, Barabási AL, Loscalzo J, Chan SY
MicroRNA-21 integrates pathogenic signaling to control pulmonary hypertension: Results of a network bioinformatics approach.
Circulation 2012; 125:1520-32.
 
 Tasan-etal_G3_12 Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A; Berger MF, Zhou B, Bulyk ML, Michelson AM.
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.
Development 2012; 139: 1164-74.
 
 Tasan-etal_G3_12 Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP.
A resource of quantitative functional annotation for Homo sapiens genes.
Genes Genomes Genet 2012; 2:223-33.
 
 Tasan-etal_G3_12 Pu CL, Zhou SY, Wang K, Zhang YF, Pei WJ.
Efficient and robust routing on scale-free networks.
Physica A 2012; 391:866-71.
 
 Djebali_PLoS-ONE_12 Barabási AL.
The network takeover.
Nat Phys 2012; 7:14-6.
 
 Djebali_PLoS-ONE_12 Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.
Evidence for transcript networks composed of chimeric RNAs in human cells.
PLoS ONE 2012; 7:e28213.
 
 

 

 

 

2003 - © CCSB - Center for Cancer Systems Biology DFCI - Dana-Faber Cancer Institute Print version  Accessible Version