Siri of the Cell: What Biology Could Learn from the iPhone

מאת Carvunis, Anne-Ruxandra, Ideker, Trey
יצא לאור 2014

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

מאת Ernst, Peter B., Carvunis, Anne-Ruxandra
הוצא לאור ב Nat Immunol (2018)

De novo gene birth

מאת Van Oss, Stephen Branden, Carvunis, Anne-Ruxandra
הוצא לאור ב PLoS Genet (2019)

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

מאת Vakirlis, Nikolaos, Carvunis, Anne-Ruxandra, McLysaght, Aoife
הוצא לאור ב eLife (2020)

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

מאת Parikh, Saurin Bipin, Castilho Coelho, Nelson, Carvunis, Anne-Ruxandra
הוצא לאור ב G3 (Bethesda) (2021)

Integrative approaches for finding modular structure in biological networks

מאת Mitra, Koyel, Carvunis, Anne-Ruxandra, Ramesh, Sanath Kumar, Ideker, Trey
יצא לאור 2013

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

מאת Keeling, Diane Marie, Garza, Patricia, Nartey, Charisse Michelle, Carvunis, Anne-Ruxandra
הוצא לאור ב eLife (2019)

The Recalcitrance and Resilience of Scientific Function

מאת Keeling, Diane Marie, Garza, Patricia, Nartey, Charisse Michelle, Carvunis, Anne-Ruxandra
הוצא לאור ב Poroi (2020)

Evidence for a common evolutionary rate in metazoan transcriptional networks

מאת Carvunis, Anne-Ruxandra, Wang, Tina, Skola, Dylan, Yu, Alice, Chen, Jonathan, Kreisberg, Jason F, Ideker, Trey
הוצא לאור ב eLife (2015)

Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model

מאת Feinbaum, Rhonda L., Urbach, Jonathan M., Liberati, Nicole T., Djonovic, Slavica, Adonizio, Allison, Carvunis, Anne-Ruxandra, Ausubel, Frederick M.
יצא לאור 2012

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

מאת Domazet-Lošo, Tomislav, Carvunis, Anne-Ruxandra, Albà, M. Mar, Šestak, Martin Sebastijan, Bakarić, Robert, Neme, Rafik, Tautz, Diethard
הוצא לאור ב Mol Biol Evol (2017)

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

מאת Wang, Tina, Ma, Jianzhu, Hogan, Andrew N., Fong, Samson, Licon, Katherine, Tsui, Brian, Kreisberg, Jason F., Adams, Peter D., Carvunis, Anne-Ruxandra, Bannasch, Danika L., Ostrander, Elaine A., Ideker, Trey
הוצא לאור ב Cell Syst (2020)

A UV–Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring

מאת Srivas, Rohith, Costelloe, Thomas, Carvunis, Anne-Ruxandra, Sarkar, Sovan, Malta, Erik, Sun, Su Ming, Pool, Marijke, Licon, Katherine, van Welsem, Tibor, van Leeuwen, Fred, McHugh, Peter J., van Attikum, Haico, Ideker, Trey
יצא לאור 2013

Literature-curated protein interaction datasets

מאת Cusick, Michael E, Yu, Haiyuan, Smolyar, Alex, Venkatesan, Kavitha, Carvunis, Anne-Ruxandra, Simonis, Nicolas, Rual, Jean-François, Borick, Heather, Braun, Pascal, Dreze, Matija, Galli, Mary, Yazaki, Junshi, Hill, David E, Ecker, Joseph R, Roth, Frederick P, Vidal, Marc
יצא לאור 2009

Revisiting the Saccharomyces cerevisiae predicted ORFeome

מאת Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, Tam, Stanley, Hao, Tong, Klitgord, Niels J., Dupuy, Denis, Mou, Danny, Wapinski, Ilan, Regev, Aviv, Hill, David E., Cusick, Michael E., Vidal, Marc
יצא לאור 2008

Proto-genes and de novo gene birth

מאת Carvunis, Anne-Ruxandra, Rolland, Thomas, Wapinski, Ilan, Calderwood, Michael A., Yildirim, Muhammed A., Simonis, Nicolas, Charloteaux, Benoit, Hidalgo, César A., Barbette, Justin, Santhanam, Balaji, Brar, Gloria A., Weissman, Jonathan S., Regev, Aviv, Thierry-Mieg, Nicolas, Cusick, Michael E., Vidal, Marc
יצא לאור 2012

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

מאת Vakirlis, Nikolaos, Acar, Omer, Hsu, Brian, Castilho Coelho, Nelson, Van Oss, S. Branden, Wacholder, Aaron, Medetgul-Ernar, Kate, Bowman, Ray W., Hines, Cameron P., Iannotta, John, Parikh, Saurin Bipin, McLysaght, Aoife, Camacho, Carlos J., O’Donnell, Allyson F., Ideker, Trey, Carvunis, Anne-Ruxandra
הוצא לאור ב Nat Commun (2020)

Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

מאת Vakirlis, Nikolaos, Acar, Omer, Hsu, Brian, Coelho, Nelson Castilho, Van Oss, S. Branden, Wacholder, Aaron, Medetgul-Ernar, Kate, Bowman, Ray W., Hines, Cameron P., Iannotta, John, Parikh, Saurin Bipin, McLysaght, Aoife, Camacho, Carlos J., O’Donnell, Allyson F., Ideker, Trey, Carvunis, Anne-Ruxandra
הוצא לאור ב Nat Commun (2021)

Mapping transcription factor interactome networks using HaloTag protein arrays

מאת Yazaki, Junshi, Galli, Mary, Kim, Alice Y., Nito, Kazumasa, Aleman, Fernando, Chang, Katherine N., Carvunis, Anne-Ruxandra, Quan, Rosa, Nguyen, Hien, Song, Liang, Alvarez, José M., Huang, Shao-shan Carol, Chen, Huaming, Ramachandran, Niroshan, Altmann, Stefan, Gutiérrez, Rodrigo A., Hill, David E., Schroeder, Julian I., Chory, Joanne, LaBaer, Joshua, Vidal, Marc, Braun, Pascal, Ecker, Joseph R.
הוצא לאור ב Proc Natl Acad Sci U S A (2016)

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

מאת Mukhtar, M. Shahid, Carvunis, Anne-Ruxandra, Dreze, Matija, Epple, Petra, Steinbrenner, Jens, Moore, Jonathan, Tasan, Murat, Galli, Mary, Hao, Tong, Nishimura, Marc T., Pevzner, Samuel J., Donovan, Susan E., Ghamsari, Lila, Santhanam, Balaji, Romero, Viviana, Poulin, Matthew M., Gebreab, Fana, Gutierrez, Bryan J., Tam, Stanley, Monachello, Dario, Boxem, Mike, Harbort, Christopher J., McDonald, Nathan, Gai, Lantian, Chen, Huaming, He, Yijian, Vandenhaute, Jean, Roth, Frederick P., Hill, David E., Ecker, Joseph R., Vidal, Marc, Beynon, Jim, Braun, Pascal, Dangl, Jeffery L.
יצא לאור 2011