Publications

A vast evolutionarily transient translatome contributes to phenotype and fitness

Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR Cell Systems (2023). Link to the perspective written by Zachary Ardern and Md Hassan uz-Zaman in Cell Systems. This work is also recommended in H1 connect.

De novo gene increases brain size

Rich A, Carvunis AR. Nature Ecology & Evolution (2023)

On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w

Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. Journal of Biological Chemistry (2022) Link to spotlight in ASBMB Today.

Origins, evolution, and physiological implications of de novo genes in yeast

Parikh SB, Houghton C, Van Oss SB, Wacholder A, Carvunis AR Yeast (2022)

Standardized annotation of translated open reading frames

Mudge JM, … Carvunis AR, van Heesch S Nature Biotechnology (2022)

RNF219 regulates CCR4-NOT function in mRNA translation and deadenylation

Guénolé A, Velilla F, Chartier A, Rich A, Carvunis AR, Sardet C, Simonelig M, Sobhian B. Scientific Reports (2022)

Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow

Acar O, Zhang S, Bahar I, Carvunis AR. Plos Computational Biology (2022)

Evolutionary characterization of the short protein SPAAR

Lee J, Wacholder A, Carvunis AR. Genes (2021)

Li Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects

Parikh SB, Castilho Coelho N, Carvunis AR. G3 (2021)

New genes from borrowed parts

Wacholder AC, Carvunis AR. Science (2021)

Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.

Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Kreisberg JF, Adams PD, Carvunis AR, Bannasch DL, Ostrander EA, Ideker T. Cell Systems (2020).

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.

Vakirlis N, Carvunis AR*, McLysaght A*. *=corresponding authors eLIFE (2020). Link to spotlight in eLIFE.

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De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.

Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman II RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF*, Ideker T*, Carvunis AR*. *=corresponding authors Nature Communications (2020). Recommended on F1000.

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The Recalcitrance and Resilience of Scientific Function.

Keeling DM, Garza P, Nartey CM, Carvunis AR. Poroi (2020).

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

Keeling DM, Garza P, Nartey CM*, Carvunis AR*. *=corresponding authors eLife (2019). Recommended on F1000.

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De novo gene birth.

Van Oss SB, Carvunis AR. PLOS Genetics (2019). Wikipedia.

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

Ernst P, Carvunis AR. Nature Immunology (2018).

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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. MBE (2017).

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Mapping transcription factor interactome networks using HaloTag protein arrays.

Yazakia 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).

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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). Recommended on F1000.

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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).

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Integrative approaches for finding modular structure in biological networks.

Mitra K*, Carvunis AR*, Ramesh SK, Ideker T. *=co-first authors. Nature Reviews Genetics (2013).

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).

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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). Recommended on F1000.

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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).

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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).

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Interactome networks.

Carvunis AR, Roth FP, Calderwood MA, Cusick ME, Superti-Furga G, Vidal M Handbook of Systems Biology (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).

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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)

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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).

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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).

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).

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).

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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).

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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).