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Items: 20

1.

The meanings of 'function' in biology and the problematic case of de novo gene emergence.

Keeling DM, Garza P, Nartey CM, Carvunis AR.

Elife. 2019 Nov 1;8. pii: e47014. doi: 10.7554/eLife.47014.

2.

De novo gene birth.

Van Oss SB, Carvunis AR.

PLoS Genet. 2019 May 23;15(5):e1008160. doi: 10.1371/journal.pgen.1008160. eCollection 2019 May. No abstract available.

3.

Of mice, men and immunity: a case for evolutionary systems biology.

Ernst PB, Carvunis AR.

Nat Immunol. 2018 May;19(5):421-425. doi: 10.1038/s41590-018-0084-4. No abstract available.

4.

No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.

Domazet-Lošo T, Carvunis AR, Albà MM, Šestak MS, Bakaric R, Neme R, Tautz D.

Mol Biol Evol. 2017 Apr 1;34(4):843-856. doi: 10.1093/molbev/msw284.

5.

Mapping transcription factor interactome networks using HaloTag protein arrays.

Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4238-47. doi: 10.1073/pnas.1603229113. Epub 2016 Jun 29.

6.

Evidence for a common evolutionary rate in metazoan transcriptional networks.

Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T.

Elife. 2015 Dec 18;4. pii: e11615. doi: 10.7554/eLife.11615.

7.

A proteome-scale map of the human interactome network.

Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

8.

Siri of the cell: what biology could learn from the iPhone.

Carvunis AR, Ideker T.

Cell. 2014 Apr 24;157(3):534-8. doi: 10.1016/j.cell.2014.03.009.

9.

A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.

Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T.

Cell Rep. 2013 Dec 26;5(6):1714-24. doi: 10.1016/j.celrep.2013.11.035. Epub 2013 Dec 19.

10.

Integrative approaches for finding modular structure in biological networks.

Mitra K, Carvunis AR, Ramesh SK, Ideker T.

Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552. Review.

11.

Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model.

Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM.

PLoS Pathog. 2012;8(7):e1002813. doi: 10.1371/journal.ppat.1002813. Epub 2012 Jul 26.

12.

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

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.

Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288.

13.

Proto-genes and de novo gene birth.

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.

Nature. 2012 Jul 19;487(7407):370-4. doi: 10.1038/nature11184.

14.

[Virulence effectors target key proteins of interactome networks of host plant cells].

Carvunis AR, Dreze M.

Med Sci (Paris). 2012 Mar;28(3):237-9. doi: 10.1051/medsci/2012283003. Epub 2012 Apr 6. French. No abstract available.

15.

Independently evolved virulence effectors converge onto hubs in a plant immune system network.

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.

Science. 2011 Jul 29;333(6042):596-601. doi: 10.1126/science.1203659.

16.

[Systems biology: from yesterday's concepts to tomorrow's discoveries].

Carvunis AR, Gomez E, Thierry-Mieg N, Trilling L, Vidal M.

Med Sci (Paris). 2009 Jun-Jul;25(6-7):578-84. doi: 10.1051/medsci/2009256-7578. French.

17.

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens 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.

Nat Methods. 2009 Jan;6(1):47-54.

18.

Literature-curated protein interaction datasets.

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.

Nat Methods. 2009 Jan;6(1):39-46. doi: 10.1038/nmeth.1284.

19.

Revisiting the Saccharomyces cerevisiae predicted ORFeome.

Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.

Genome Res. 2008 Aug;18(8):1294-303. doi: 10.1101/gr.076661.108. Epub 2008 May 23.

20.

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.

Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Barabási AL, Baillie D, Vidal M.

Nat Biotechnol. 2007 Jun;25(6):663-8. Epub 2007 May 7.

PMID:
17486083

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