Publications

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution.

Domazet-Lošo T*, Carvunis AR*,#, Albà MM, Šestak MS, Bakarić R, Neme R, Tautz D# *=co-first authors, #= co-corresponding authors

Molecular Biology and Evolution (2017)

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 SC, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroederd JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR

PNAS (2016)

Evidence for a common evolutionary rate in metazoan transcriptional networks.

Carvunis AR*, Wang T*, Skola D*, Yu A, Chen J, Kreisberg J, Ideker T *=co-first authors.

eLife (2015)

A proteome-scale map of the Human interactome network.

Rolland T*, Tasan M*, Charloteaux B*, Pevzner SJ*, Zhong Q*, Sahni N*, Yi S*, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian S, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Hardy MF, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, 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 J, 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 *=co-first authors.
Cell (2014)

Siri of the Cell – what biology could learn from the iPhone.

Carvunis AR, Ideker T

Cell (2014)

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 *=co-first authors.

Cell Reports (2013)

Integrative approaches for finding modular structure in biological networks.

Mitra K*, Carvunis AR*, Ramesh SK, Ideker T *=co-first authors.

Nature Reviews Genetics (2013)

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)

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

Rozenblatt-Rosen O*, Deo RC*, Megha Padi*, Adelmant G*, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares T, Pevzner S, Abderazzaq F, Byrdsong D, Chen A, Cheng J, Correll M, Duarte M, Fan C, Ficarro SB, Franchi R, Garg B, Gulbahce N, Holthaus A, 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, Carvunis AR, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hao T, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FR, DeCaprio JA, Vidal M *=co-first authors.

Nature (2012)

Interactome networks

Carvunis AR, Roth FP, Calderwood MA, Cusick ME, Superti-Furga G, Vidal M

Handbook of Systems Biology (2012)

Les facteurs de virulence ciblent des protéines clés de l’interactome de l’hôte (Virulence effectors target key proteins of interactome networks of host plant cells).

Carvunis AR, Dreze M

Médecine/Sciences (2012)

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 Pathogens (2012)

Independently Evolved Virulence Effectors Converge onto Cellular Hubs in a Plant Immune System Network.

Mukhtar MS*, Carvunis AR*, Dreze M*, Epple P*, Steinbrener J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Balaji S, Romero V, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Harbort C, McDonald N, Gai L, Chen H, EU Effectoromics Consortium, Roth FP Ecker JR, Vidal M, Beynon J, Braun P, Dangl J *=co-first authors.

Science (2011)

Evidence for Network Evolution in an Arabidopsis Interactome Map.

Arabidopsis Interactome Mapping Consortium, Dreze M*, Carvunis AR*, Charloteaux B*, Galli M*, Pevzner S*, Tasan M  *=co-first authors.

Science (2011)

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 *=co-first authors.

Nature Methods (2009)

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 *=co-first authors.

Nature Methods (2009)

Biologie systémique: des concepts d’hier aux découvertes de demain (Systems biology: from yesterday’s concepts to tomorrow’s discoveries)

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

Médecine/Sciences (2009)

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 *=co-first authors.

Genome Research (2008)

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 *=co-first authors.

Nature Biotechnology (2007)

Dynamics of three-state excitable units on Poisson versus power-law random networks.

Carvunis AR, Latapy M, Lesne A, Magnien C, Pezard L

Physica A (2006).