{"id":231,"date":"2018-01-16T15:06:27","date_gmt":"2018-01-16T20:06:27","guid":{"rendered":"https:\/\/carvunislab.csb.pitt.edu\/?page_id=231"},"modified":"2026-01-23T05:28:02","modified_gmt":"2026-01-23T10:28:02","slug":"publications","status":"publish","type":"page","link":"https:\/\/carvunislab.csb.pitt.edu\/?page_id=231","title":{"rendered":"Publications"},"content":{"rendered":"\n
\n\n

\"\"Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics<\/a><\/h2>\n

Aaron Wacholder<\/strong>,<\/strong>\u00a0<\/span><\/span>Eric W Deutsch,\u00a0<\/span><\/span>Leron W Kok,\u00a0<\/span><\/span>Jip T van Dinter,\u00a0<\/span><\/span>Jiwon Lee<\/strong>,\u00a0<\/span><\/span>James C Wright,\u00a0<\/span><\/span>Sebastien Leblanc,\u00a0<\/span><\/span>Ayodya H Jayatissa,\u00a0<\/span><\/span>Kevin Jiang,\u00a0<\/span><\/span>Ihor Arefiev,\u00a0<\/span><\/span>Kevin Cao,\u00a0<\/span><\/span>Francis Bourassa,\u00a0<\/span><\/span>Felix-Antoine Trifiro,\u00a0<\/span><\/span>Michal Bassani-Sternberg,\u00a0<\/span><\/span>Pavel V Baranov,\u00a0<\/span><\/span>Annelies Bogaert,\u00a0<\/span><\/span>Sonia Chothani,\u00a0<\/span><\/span>Ivo Fierro-Monti,\u00a0<\/span><\/span>Daria Fijalkowska,\u00a0<\/span><\/span>Kris Gevaert,\u00a0<\/span><\/span>Norbert Hubner,\u00a0<\/span><\/span>Jonathan M Mudge,\u00a0<\/span><\/span>Jorge Ruiz-Orera,\u00a0<\/span><\/span>Jana Schulz,\u00a0<\/span><\/span>Juan Antonio Vizcaino,\u00a0<\/span><\/span>John R Prensner,\u00a0<\/span><\/span>Marie A Brunet,\u00a0<\/span><\/span>Thomas F Martinez,\u00a0<\/span><\/span>Sarah A Slavoff,\u00a0<\/span><\/span>Xavier Roucou,\u00a0<\/span><\/span>Jyoti S Choudhary,\u00a0<\/span><\/span>Sebastiaan van Heesch,\u00a0<\/span><\/span>Robert L Moritz,\u00a0<\/span><\/span>Anne-Ruxandra Carvunis<\/span><\/strong><\/p>\n

Nature Communications (2026)<\/p>\n

\n

\u00a0<\/h2>\n

\"\"Emergence and tandem repeat-mediated elongation of a translated de novo<\/i> open reading frame in human oncogenic RNA gene VPS9D1-AS1 (MYU)<\/a><\/h2>\n

Lin Chou<\/strong>, Shu-Ting Cho, Jiwon Lee<\/strong>, David Laub, Douglas Meyer, Hannah Carter, Anne-Ruxandra Carvunis<\/strong><\/p>\n

Genome Biology and Evolution (2026)<\/p>\n

\n

\"\"Translon: a single term for translated regions<\/a><\/h2>\n

Micha\u0142 I. \u015awirski, Jack A. S. Tierney, M. Mar Alb\u00e0, Dmitry E. Andreev, Julie L. Aspden, John F. Atkins, Michal Bassani-Sternberg, Marla J. Berry, Stefano Biffo, Kathleen Boris-Lawrie, Mark Borodovsky, Ian Brierley, Matthew Brook, Marie A. Brunet, Janusz M. Bujnicki, Neva Caliskan, Lorenzo Calviello, Anne-Ruxandra Carvunis<\/strong>, Jamie H. D. Cate, Can Cenik, Kung Yao Chang, Yiwen Chen, Sonia Chothani, Jyoti S. Choudhary, Patricia L. Clark, Jim Clauwaert, Lynn Cooley, Erik Dassi, Kellie Dean, Jean-Jacques Diaz, Christoph Dieterich, Rivka Dikstein, Jonathan D. Dinman, Sergey E. Dmitriev, Olga A. Dontsova, Christine M. Dunham, Sandeep M. Eswarappa, Philip J. Farabaugh, Pouya Faridi, Ivo Fierro-Monti, Andrew E. Firth, David Gatfield, F\u00e1tima Gebauer, Mikhail S. Gelfand, Nicola K. Gray, Rachel Green, Chris H. Hill, Ya-Ming Hou, Norbert H\u00fcbner, Zoya Ignatova, Pavel Ivanov, Shintaro Iwasaki, Rory Johnson, Ahmad Jomaa, Marko Jovanovic, Irwin Jungreis, Manolis Kellis, Jeffrey S. Kieft, Alex V. Kochetov, Eugene V. Koonin, Andrei A. Korostelev, Joanna Kufel, Ivan V. Kulakovskiy, Leo Kurian, Denis L. J. Lafontaine, Ola Larsson, Gary Loughran, Julius Luke\u0161, Marco Mariotti, Elena S. Martens-Uzunova, Thomas F. Martinez, Akinobu Matsumoto, Joel McManus, Jan Medenbach, Sergey V. Melnikov, Gerben Menschaert, Catharina Merchante, Martin Mikl, W. Allen Miller, Oliver M\u00fchlemann, Olivier Namy, Danny D. Nedialkova, Jozef Nosek, Sandra Orchard, Petar Ozreti\u0107, Mihaela Pertea, Dmitri D. Pervouchine, Lu\u00edsa Rom\u00e3o, David Ron, Xavier Roucou, Maria P. Rubtsova, Jorge Ruiz-Orera, Alan Saghatelian, Steven L. Salzberg, Lucia A. Seale, Cathal Seoighe, Petr V. Sergiev, Premal Shah, Nikolay Shirokikh, Sarah A. Slavoff, Nahum Sonenberg, Timothy J. Stasevich, Roman J. Szczesny, Tiina Tamm, Marek Tch\u00f3rzewski, Ivan Topisirovic, Michel L. Tremblay, Tamir Tuller, Igor Ulitsky, Leo\u0161 Shivaya Val\u00e1\u0161ek, Petra Van Damme, Gabriella Viero, Juan Antonio Vizcaino, Christine Vogel, Edward W. J. Wallace, Jonathan S. Weissman, Eric Westhof, Nicola Whiffin, Daniel N. Wilson, Zhi Xie, Jonathan W. Yewdell, Martina M. Yordanova, Chien-Hung Yu, Vyacheslav Yurchenko, Bojan Zagrovic, TRANSLACORE, Eivind Valen & Pavel V. Baranov<\/p>\n

Nature Methods (2025)<\/p>\n

\n

\u00a0<\/h2>\n

\"\"An expanded reference catalog of translated open reading frames for biomedical research<\/a><\/h2>\n

Sonia Chothani, Jorge Ruiz-Orera, Jack A. S. Tierney, Jim Clauwaert, Eric W Deutsch, M. Mar Alba, Julie L. Aspden, Pavel V. Baranov, Ariel Alejandro Bazzini, Elspeth A. Bruford, Marie A. Brunet, Tristan Cardon, Anne-Ruxandra Carvunis<\/strong>, Claudio Casola, Jyoti Sharma Choudhary, Kellie Dean, Pouya Faridi, Ivo Fierro-Monti, Isabelle Fournier, Adam Frankish, Mark Gerstein, Norbert Hubner, Yunzhe Jiang, Manolis Kellis, Leron W. Kok, Thomas F Martinez, Gerben Menschaert, Pengyu Ni, Sandra Orchard, Xavier Roucou, Joel Rozowsky, Michel Salzet, Mauro Siragusa, Sarah Slavoff, Michal I Swirski, Nicola Ternette, Eivind Valen, Juan Antonio Vizcaino, Aaron Wacholder<\/strong>, Wei Wu, Zhi Xie, Yucheng T. Yang, Robert L. Moritz, Jonathan Mudge, Sebastiaan van Heesch, John R Prensner, Owen JL Rackham<\/p>\n

bioRxiv (2025)<\/p>\n

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\u00a0<\/h2>\n

\"\"What is the current bottleneck in mapping molecular interaction networks?<\/a><\/h2>\n

Michael A.\u00a0Skinnider<\/span><\/span> , Katja Luck<\/span><\/span>,\u00a0M. Shahid Mukhtar<\/span><\/span>,\u00a0Martin Garrido-Rodriguez,<\/span><\/span><\/span>\u00a0Julio Saez-Rodriguez,<\/span><\/span><\/span>\u00a0Jolanda van Leeuwen,<\/span><\/span><\/span>\u00a0Pedro Beltrao,<\/span><\/span><\/span>\u00a0Anne-Ruxandra Carvunis,<\/span><\/span><\/strong><\/span>\u00a0Mikko Taipale,<\/span><\/span><\/span>\u00a0Andrew Emili,<\/span><\/span>\u00a0Martha L. Bulyk,<\/span><\/span>\u00a0Nevan J. Krogan<\/span><\/span><\/p>\n

Cell Systems (2025)<\/p>\n

\n\n

\"\"Constructive neutral evolution of homodimer to heterodimer transition<\/a><\/h2>\n

Chou L<\/strong>, Houghton CJ<\/strong>, Wacholder A<\/strong>,Carvunis AR<\/strong>.<\/p>\n

Trends in Biochemical Sciences (2024)<\/p>\n

<\/h2>\n
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\"\"High-quality peptide evidence for annotating non-canonical open reading frames as human proteins<\/a><\/h2>\n

Eric W Deutsch,\u00a0<\/span><\/span>Leron W Kok,\u00a0<\/span><\/span>Jonathan M Mudge,\u00a0<\/span><\/span>Jorge Ruiz-Orera,\u00a0<\/span><\/span>Ivo Fierro-Monti,\u00a0<\/span><\/span>Zhi Sun,\u00a0<\/span><\/span>Jennifer G Abelin,\u00a0<\/span><\/span>M Mar Alba,\u00a0<\/span><\/span>Julie L Aspden,\u00a0<\/span><\/span>Ariel A Bazzini,\u00a0<\/span><\/span>Elspeth A Bruford,<\/span>\u00a0<\/span><\/span>Marie A Brunet,\u00a0<\/span><\/span>Lorenzo Calviello,\u00a0<\/span><\/span>Steven A Carr,\u00a0<\/span><\/span>Anne-Ruxandra Carvunis<\/strong>,\u00a0<\/span><\/span>Sonia Chothani,\u00a0<\/span><\/span>Jim Clauwaert,\u00a0<\/span><\/span>Kellie Dean,\u00a0<\/span><\/span>Pouya Faridi,\u00a0<\/span><\/span>Adam Frankish,<\/span>\u00a0<\/span><\/span>Norbert Hubner,\u00a0<\/span><\/span>Nicholas T Ingolia,\u00a0<\/span><\/span>Michele Magrane,\u00a0<\/span><\/span>Maria Jesus Martin,\u00a0<\/span><\/span>Thomas F Martinez,<\/span>\u00a0<\/span><\/span>Gerben Menschaert,\u00a0<\/span><\/span>Uwe Ohler,\u00a0<\/span><\/span>Sandra Orchard,\u00a0<\/span><\/span>Owen Rackham,\u00a0<\/span><\/span>Xavier Roucou,\u00a0<\/span><\/span>Sarah A Slavoff,\u00a0<\/span><\/span>Eivind Valen,\u00a0<\/span><\/span>Aaron Wacholder<\/strong>,\u00a0<\/span><\/span>Jonathan S Weissman,\u00a0<\/span><\/span>Wei Wu,\u00a0<\/span><\/span>Zhi Xie,\u00a0<\/span><\/span>Jyoti Choudhary,\u00a0<\/span><\/span>Michal Bassani-Sternberg,\u00a0<\/span><\/span>Juan Antonio Vizca\u00edno,\u00a0<\/span><\/span>Nicola Ternette,\u00a0<\/span><\/span>Robert L Moritz,\u00a0<\/span><\/span>John R Prensner,\u00a0<\/span><\/span>Sebastiaan van Heesch<\/span><\/p>\n

bioRxiv (2024)<\/p>\n

<\/h2>\n
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\"\"Cellular processing of beneficial de novo emerging proteins<\/a><\/h2>\n

Houghton CJ<\/strong>, Castilho Coelho N<\/strong>, Chiang A, Hedayati S, Parikh SB<\/strong>,\u00a0Ozbaki-Yagan N, Wacholder A<\/strong>, Iannotta J<\/strong>, Berger A<\/strong>, Carvunis AR<\/strong>, O’Donnell AF.<\/p>\n

bioRxiv (2024)<\/p>\n

<\/h2>\n
\n

\"\"Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence<\/a><\/h2>\n

Vakirlis N, Acar O<\/strong>, Cherupally V<\/strong>,\u00a0Carvunis AR<\/strong>.<\/p>\n

Genome Biology and Evolution (2024)<\/p>\n

<\/h2>\n
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\"\"Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome<\/a><\/h2>\n

Rich A<\/strong>, Acar O<\/strong>,\u00a0Carvunis AR<\/strong>.<\/p>\n

Genome Biology (2024)<\/p>\n

<\/h2>\n
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\"\"Integrative detection of genome-wide translation using iRibo<\/a><\/h2>\n

Turcan A<\/strong>, Lee J<\/strong>, Wacholder A<\/strong>,\u00a0Carvunis AR<\/strong>.<\/p>\n

STAR Protocols (2024)<\/p>\n

<\/h2>\n

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\"\"Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry<\/a><\/h2>\n

Wacholder A<\/strong> & Carvunis AR<\/strong>.<\/p>\n

PLOS Biology\u00a0(2023)<\/p>\n

<\/h2>\n
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\"\"<\/a>Unannotated Open Reading Frame in Saccharomyces cerevisiae Encodes Protein Localizing to the Endoplasmic Reticulum<\/a><\/h2>\n

Chang S*<\/strong>, Joyson M*<\/strong>, Kelly A*<\/strong>, Tang L*<\/strong>, Iannotta J<\/strong>, Rich A<\/strong>, Castilho Coelho N<\/strong>, Carvunis AR<\/strong>.<\/p>\n

microPublication Biology (2023)<\/p>\n

<\/h2>\n

\u00a0<\/h2>\n

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\"\"<\/a>A vast evolutionarily transient translatome contributes to phenotype and fitness<\/a><\/h2>\n

Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR<\/strong><\/p>\n

Cell Systems<\/em> (2023). Link<\/a> to the perspective written by Zachary Ardern and Md Hassan uz-Zaman in Cell Systems. <\/em>This work is also recommended in H1 connect<\/a>.<\/p>\n<\/div>\n

<\/h2>\n
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\"\"De novo gene increases brain size<\/a><\/h2>\n

Rich A<\/strong>, Carvunis AR<\/strong>.<\/p>\n

Nature Ecology & Evolution<\/em> (2023)<\/p>\n<\/div>\n

<\/h2>\n
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\"\"On the illusion of auxotrophy: met15\u0394<\/em> yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w<\/a><\/h2>\n

Van Oss SB<\/strong>, Parikh SB<\/strong>, Castilho\u00a0<\/strong>Coelho N<\/strong>, Wacholder A<\/strong>, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM<\/strong>, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR<\/strong>.<\/p>\n

Journal of Biological Chemistry<\/em> (2022)
Link to spotlight<\/a> in ASBMB Today.<\/p>\n<\/div>\n

<\/h2>\n
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\"\"
Origins, evolution, and physiological implications of de novo<\/em> genes in yeast<\/a><\/h2>\n

Parikh SB<\/strong>, Houghton C<\/strong>, Van Oss SB<\/strong>, Wacholder A<\/strong>,\u00a0Carvunis AR<\/strong><\/p>\n

Yeast<\/em>\u00a0(2022)<\/p>\n<\/div>\n

<\/h2>\n
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\"\"<\/a>Standardized annotation of translated open reading frames
<\/a><\/h2>\n

Jonathan M. Mudge,\u00a0Jorge Ruiz-Orera,\u00a0John R. Prensner,\u00a0Marie A. Brunet,\u00a0Ferriol Calvet,\u00a0Irwin Jungreis,\u00a0Jose Manuel Gonzalez,\u00a0Michele Magrane,\u00a0Thomas F. Martinez,\u00a0Jana Felicitas Schulz,\u00a0Yucheng T. Yang,\u00a0M. Mar Alb\u00e0,\u00a0Julie L. Aspden,\u00a0Pavel V. Baranov,\u00a0Ariel A. Bazzini,\u00a0Elspeth Bruford,\u00a0Maria Jesus Martin,\u00a0Lorenzo Calviello,\u00a0Anne-Ruxandra Carvunis,\u00a0<\/strong>Jin Chen,\u00a0Juan Pablo Couso,\u00a0Eric W. Deutsch,\u00a0Paul Flicek,\u00a0Adam Frankish,\u00a0Mark Gerstein,\u00a0Norbert Hubner,\u00a0Nicholas T. Ingolia,\u00a0Manolis Kellis,\u00a0Gerben Menschaert,\u00a0Robert L. Moritz,\u00a0Uwe Ohler,\u00a0Xavier Roucou,\u00a0Alan Saghatelian, Jonathan S. Weissman, & Sebastiaan van Heesch\u00a0<\/p>\n

Nature Biotechnology<\/em>\u00a0(2022)<\/p>\n<\/div>\n

<\/h2>\n
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\"\"RNF219 regulates CCR4-NOT function in mRNA translation and deadenylation<\/a><\/h2>\n

Gu\u00e9nol\u00e9 A, Velilla F, Chartier A, Rich A<\/strong>, Carvunis AR<\/strong>, Sardet C, Simonelig M, Sobhian B.<\/p>\n

Scientific Reports<\/em>\u00a0(2022)<\/p>\n<\/div>\n

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\"\"<\/a>Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow<\/a><\/h2>\n

Acar O<\/strong>, Zhang S, Bahar I, Carvunis AR<\/strong>.<\/p>\n

Plos Computational Biology<\/em>\u00a0(2022)<\/p>\n<\/div>\n

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\"\"Evolutionary characterization of the short protein SPAAR<\/a><\/h2>\n

Lee J<\/strong>, Wacholder A<\/strong>, Carvunis AR<\/strong>.<\/p>\n

Genes<\/em> (2021)<\/p>\n<\/div>\n

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\"\"Li Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects<\/a><\/h2>\n

Parikh SB<\/strong>, Castilho Coelho N<\/strong>, Carvunis AR<\/strong>.<\/p>\n

G3<\/em> (2021)<\/p>\n<\/div>\n

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\"\"New genes from borrowed parts<\/a><\/h2>\n

Wacholder AC<\/strong>, Carvunis AR<\/strong>.<\/p>\n

Science<\/em> (2021)<\/p>\n<\/div>\n

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\"\"Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.<\/a><\/h2>\n

Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Kreisberg JF, Adams PD, Carvunis AR<\/strong>, Bannasch DL, Ostrander EA, Ideker T.<\/p>\n

Cell Systems<\/em> (2020).<\/p>\n<\/div>\n

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\"\"Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.<\/a><\/h2>\n

Vakirlis N, Carvunis AR<\/strong>*, McLysaght A*. *=corresponding authors<\/p>\n

eLIFE<\/em>\u00a0(2020).
Link to spotlight<\/a> in eLIFE.<\/p>\n

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\"\"De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.<\/a><\/h2>\n

Vakirlis N, Acar O<\/strong>, Hsu B, Castilho Coelho N<\/strong>, Van Oss SB<\/strong>, Wacholder A<\/strong>, Medetgul-Ernar K, Bowman II RW, Hines CP, Iannotta J<\/strong>, Parikh SB<\/strong>, McLysaght A, Camacho CJ, O\u2019Donnell AF*, Ideker T*, Carvunis AR<\/strong>*. *=corresponding authors<\/p>\n

Nature Communications<\/em>\u00a0(2020).
Recommended on F1000<\/a>.<\/p>\n

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\"\"The Recalcitrance and Resilience of Scientific Function.<\/a><\/h2>\n

Keeling DM, Garza P, Nartey CM, Carvunis AR<\/strong>.<\/p>\n

Poroi<\/em>\u00a0(2020).<\/p>\n<\/div>\n

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\"\"The meanings of ‘function’ in biology and the problematic case of de novo<\/em> gene emergence.<\/a><\/h2>\n

Keeling DM, Garza P, Nartey CM*, Carvunis AR<\/strong>*. *=corresponding authors<\/p>\n

eLife<\/em>\u00a0(2019).
Recommended on F1000<\/a>.<\/p>\n

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\"\"De novo<\/em> gene birth.<\/a><\/h2>\n

Van Oss SB<\/strong>, Carvunis AR<\/strong>.<\/p>\n

PLOS Genetics<\/em> (2019). Wikipedia<\/a>.<\/p>\n<\/div>\n

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\"\"Of mice, men and immunity: a case for evolutionary systems biology.<\/a><\/h2>\n

Ernst P, Carvunis AR<\/strong>.<\/p>\n

Nature Immunology<\/em> (2018).<\/p>\n<\/div>\n

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\"\"No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution.<\/a><\/h2>\n

Domazet-Lo\u0161o T*, Carvunis AR*,#,<\/strong> Alb\u00e0 MM, \u0160estak MS, Bakari\u0107 R, Neme R, Tautz D#. *=co-first authors. #=co-corresponding authors.<\/p>\n

MBE<\/em> (2017).<\/p>\n<\/div>\n

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Mapping transcription factor interactome networks using HaloTag protein arrays.<\/a><\/h2>\n

Yazakia J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR<\/strong>, Quan R, Nguyen H, Song L, Alvarez JM, Huang SC, Chen H, Ramachandran N, Altmann S, Guti\u00e9rrez RA, Hill DE, Schroederd JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR<\/p>\n

PNAS<\/em> (2016).<\/p>\n

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\"\"Evidence for a common evolutionary rate in metazoan transcriptional networks.<\/a><\/h2>\n

Carvunis AR*<\/strong>, Wang T*, Skola D*, Yu A, Chen J, Kreisberg J, Ideker T. *=co-first authors.<\/p>\n

Elife <\/em>(2015).<\/p>\n<\/div>\n

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\"\"A proteome-scale map of the human interactome network.<\/a><\/h2>\n

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<\/strong>, 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 \u00a0ME, \u00a0Xia \u00a0Y, \u00a0Barab\u00e1si \u00a0AL, Iakoucheva\u00a0 LM, \u00a0Aloy \u00a0P, \u00a0De \u00a0Las \u00a0Rivas\u00a0 J, \u00a0Tavernier\u00a0 J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.\u00a0*=co-first authors.<\/p>\n

Cell <\/em>(2014). Recommended on F1000<\/a>.<\/p>\n

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\"\"Siri of the Cell \u2013 what biology could learn from the iPhone.<\/a><\/h2>\n

Carvunis AR<\/strong>, Ideker T<\/p>\n

Cell <\/em>(2014).<\/p>\n<\/div>\n

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\"\"A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. <\/a><\/h2>\n

Srivas R*, Costelloe T*, Carvunis AR<\/strong>, 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.<\/p>\n

Cell Reports (2013).<\/em><\/p>\n

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\"\"Integrative approaches for finding modular structure in biological networks.<\/a><\/h2>\n

Mitra K*, Carvunis AR*<\/strong>, Ramesh SK, Ideker T. *=co-first authors.<\/p>\n

Nature Reviews Genetics (2013).<\/em><\/p>\n<\/div>\n

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\"\"Les facteurs de virulence ciblent des prot\u00e9ines cl\u00e9s de l\u2019interactome de l\u2019h\u00f4te (Virulence effectors target key proteins of interactome networks of host plant cells).<\/a><\/h2>\n

Carvunis AR<\/strong>, Dreze M<\/p>\n

M\u00e9decine\/Sciences (2012).<\/em><\/p>\n<\/div>\n

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\"\"Proto-genes and de novo <\/em>gene birth.<\/a><\/h2>\n

Carvunis AR<\/strong>, 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<\/p>\n

Nature (2012).<\/em>
Recommended on F1000<\/a>.<\/p>\n<\/div>\n

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\n

\"\"Interpreting cancer genomes using systematic host perturbations by tumour virus proteins.<\/a><\/h2>\n

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<\/strong>, Roecklein-Canfield J, Johannsen E, Barab\u00e1si AL, Beroukhim R, Kieff E, Cusick ME, Hao T, Hill DE, M\u00fcnger K, Marto JA, Quackenbush J, Roth FR, DeCaprio JA, Vidal M. *=co-first authors.<\/p>\n

Nature (2012).<\/em><\/p>\n

<\/h2>\n
<\/div>\n
\n

\"\"Genome-Wide Identification of Pseudomonas aeruginosa<\/em> virulence-related genes using a Caenorhabditis elegans<\/em> infection model.<\/a><\/h2>\n

Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR<\/strong>, Ausubel FM<\/p>\n

PLoS Pathogens (2012).<\/em><\/p>\n<\/div>\n

<\/div>\n
\n

\"\"Interactome networks.<\/a><\/h2>\n

Carvunis AR<\/strong>, Roth FP, Calderwood MA, Cusick ME, Superti-Furga G, Vidal M<\/p>\n

Handbook of Systems Biology (2012).<\/em><\/p>\n<\/div>\n

<\/h2>\n
\n
\n

\"\"Independently Evolved Virulence Effectors Converge onto Cellular Hubs in a Plant Immune System Network.<\/a><\/h2>\n

Mukhtar MS*, Carvunis AR*<\/strong>, 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.<\/p>\n

Science (2011).<\/em><\/p>\n

<\/h2>\n
<\/div>\n
\n

\"\"Evidence for Network Evolution in an Arabidopsis<\/em> Interactome Map.<\/a><\/h2>\n

Arabidopsis Interactome Mapping Consortium (Dreze M*, Carvunis AR*<\/strong>, Charloteaux B*, Galli M*, Pevzner S*, Tasan M. *=co-first authors.)<\/p>\n

Science (2011)<\/em><\/p>\n<\/div>\n

<\/div>\n
\n

\"\"Empirically controlled mapping of the Caenorhabditis elegans<\/em> protein-protein interactome network.<\/a><\/h2>\n

Simonis N*, Rual JF*, Carvunis AR*<\/strong>, 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.<\/p>\n

Nature Methods (2009).<\/em><\/p>\n

<\/h2>\n
<\/div>\n
\n

\"\"Biologie syst\u00e9mique: des concepts d\u2019hier aux d\u00e9couvertes de demain (Systems biology: from yesterday’s concepts to tomorrow’s discoveries).<\/a><\/h2>\n

Carvunis AR<\/strong>, G\u00f3mez E, Thierry-Mieg N, Trilling L, Vidal M<\/p>\n

M\u00e9decine\/Sciences (2009).<\/em><\/p>\n<\/div>\n

<\/h2>\n
\n
\n

\"\"Literature-curated protein interaction datasets.<\/a><\/h2>\n

Cusick ME*, Yu H*, Smolyar A, Venkatesan K, Carvunis AR<\/strong>, 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.<\/p>\n

Nature Methods (2009).<\/em><\/p>\n<\/div>\n

<\/h2>\n
\n
\n

\"\"Revisiting the Saccharomyces cerevisiae<\/em> predicted ORFeome.<\/a><\/h2>\n

Li QR*, Carvunis AR<\/strong>*, 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.<\/p>\n

Genome Research (2008).<\/em><\/p>\n

<\/h2>\n
<\/div>\n
\n

\"\"Genome-scale analysis of in vivo<\/em> spatiotemporal promoter activity in Caenorhabditis elegans.<\/em>.<\/a><\/h2>\n

Dupuy D*, Bertin N*, Hidalgo CA*, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR<\/strong>, 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, Barab\u00e1si AL, Baillie D, Vidal M. *=co-first authors.<\/p>\n

Nature Biotechnology (2007).<\/em><\/p>\n

<\/h2>\n
<\/div>\n
\n

\"\"Dynamics of three-state excitable units on Poi<\/a>sson versus power-law random networks.<\/a><\/h2>\n

Carvunis AR<\/strong>, Latapy M, Lesne A, Magnien C, Pezard L<\/p>\n

Physica \u00a0A (2006).<\/em><\/p>\n<\/div>\n

<\/p>\n

<\/figure>\n

<\/p>\n

<\/p>\n

<\/p>\n

<\/p>\n

<\/p>","protected":false},"excerpt":{"rendered":"Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics Aaron Wacholder,\u00a0Eric W Deutsch,\u00a0Leron W Kok,\u00a0Jip T van Dinter,\u00a0Jiwon \n [...]<\/a>","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"layouts\/fullwidth.php","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-231","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/pages\/231","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=231"}],"version-history":[{"count":261,"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/pages\/231\/revisions"}],"predecessor-version":[{"id":2496,"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=\/wp\/v2\/pages\/231\/revisions\/2496"}],"wp:attachment":[{"href":"https:\/\/carvunislab.csb.pitt.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=231"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}