Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis ARCell 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.
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.
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).
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.
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).
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).
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).
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).
Integrative detection of genome-wide translation using iRibo
Ancestral Sequence Reconstruction as a tool to detect and study de novo gene emergence
Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry
Unannotated Open Reading Frame in Saccharomyces cerevisiae Encodes Protein Localizing to the Endoplasmic Reticulum
Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the noncanonical translatome
A vast evolutionarily transient translatome contributes to phenotype and fitness
De novo gene increases brain size
On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w
Origins, evolution, and physiological implications of de novo genes in yeast
Standardized annotation of translated open reading frames
RNF219 regulates CCR4-NOT function in mRNA translation and deadenylation
Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow
Evolutionary characterization of the short protein SPAAR
Li Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects
New genes from borrowed parts
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.
The Recalcitrance and Resilience of Scientific Function.
The meanings of ‘function’ in biology and the problematic case of de novo gene emergence.
De novo gene birth.
Of mice, men and immunity: a case for evolutionary systems biology.
No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution.
Mapping transcription factor interactome networks using HaloTag protein arrays.
Evidence for a common evolutionary rate in metazoan transcriptional networks.
A proteome-scale map of the human interactome network.
Siri of the Cell – what biology could learn from the iPhone.
A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. 
Integrative approaches for finding modular structure in biological networks.
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).
Proto-genes and de novo gene birth.
Interpreting cancer genomes using systematic host perturbations by tumour virus proteins.
Genome-Wide Identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model.
Interactome networks.
Independently Evolved Virulence Effectors Converge onto Cellular Hubs in a Plant Immune System Network.
Evidence for Network Evolution in an Arabidopsis Interactome Map.
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.
Biologie systémique: des concepts d’hier aux découvertes de demain (Systems biology: from yesterday’s concepts to tomorrow’s discoveries).
Literature-curated protein interaction datasets.
Revisiting the Saccharomyces cerevisiae predicted ORFeome.
Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans..
Dynamics of three-state excitable units on Poisson versus power-law random networks.