Published in 2012

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  1. Franzosa EA, Garamszegi S, Xia Y. Toward a three-dimensional view of protein networks between species. Front Microbiol 2012; 3:428. PDF
  2. 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. PDF
  3. 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. PDF
  4. 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. PDF 
  5. 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. PDF
  6. Liu YY, Csoka E, Zhou HJ, Posfai M. Core percolation on complex networks. Phys Rev Lett 2012; 109:205703. PDF
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  8. Liu YY, Slotine JJ, Barabási AL. Control centrality and hierarchical structure in complex networks. PLoS ONE 2012; 7:e44459. PDF
  9. 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. PDF
  10. 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. PDF 
  11. Research Watch, Cancer Discovery
  12. Research Highlight, Nat Rev Cancer
  13. Research Highlight, Nat Rev Clin Oncol
  14. Research Highlight, Nat Methods 
  15. 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. PDF 
  16. 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. PDF
  17. Research Highlight, Nat Rev Genet
  18. BioBabel blog
  19. Beast Bard Bot blog
  20. EuroEpinomics blog
  21. All Alone, New Scientist 2013
  22. Editorial, Cell Commun Signal 2012
  23. Evolutionary Origin of Orphan Genes, eLS 2013
  24. The Continuing Evolution of Genes, NY Times 2014
  25. 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. PDF 
  26. Slotine JJ, Liu YY. Complex Networks: The missing link. Nat Physics 2012; 8:512-3. PDF
  27. 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. PDF 
  28. 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. PDF 
  29. 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. PDF
  30. 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. PDF 
  31. Karsai M, Kaski K, Barabasi AL, Kertesz J. Universal features of correlated bursty behaviour. Sci Rep 2012; 2:397. PDF 
  32. 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. PDF 
  33. Palchykov V, Kaski K, Kertész J, Barabási AL, Dunbar RI. Sex differences in intimate relationships. Sci Rep 2012; 2:370. PDF 
  34. Simini F, González MC, Maritan A, Barabási AL. A universal model for mobility and migration patterns. Nature 2012; 484:96-100. PDF
  35. Carvunis AR, Dreze M. Virulence effectors target key proteins of interactome networks of host plant cells. Méd Sci (Paris) 2012; 28:237-9. PDF
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  37. 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. PDF 
  38. 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. PDF
  39. Pu CL, Zhou SY, Wang K, Zhang YF, Pei WJ. Efficient and robust routing on scale-free networks. Physica A 2012; 391:866-71. PDF 
  40. Barabási AL. The network takeover. Nat Phys 2012; 7:14-6. PDF
  41. 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. PDF