N
Nicolas Simonis
Researcher at Université libre de Bruxelles
Publications - 32
Citations - 6404
Nicolas Simonis is an academic researcher from Université libre de Bruxelles. The author has contributed to research in topics: Interactome & Gene. The author has an hindex of 24, co-authored 32 publications receiving 5907 citations. Previous affiliations of Nicolas Simonis include Free University of Brussels & University of Liège.
Papers
More filters
Journal ArticleDOI
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Haiyuan Yu,Pascal Braun,Muhammed A. Yildirim,Irma Lemmens,Kavitha Venkatesan,Julie M. Sahalie,Tomoko Hirozane-Kishikawa,Fana Gebreab,Nan Li,Nicolas Simonis,Tong Hao,Jean François Rual,Amélie Dricot,Alexei Vazquez,Ryan R. Murray,Christophe Simon,Leah Tardivo,Stanley Tam,Nenad Svrzikapa,Changyu Fan,Anne-Sophie De Smet,Adriana Motyl,Michael E. Hudson,Juyong Park,Juyong Park,Xiaofeng Xin,Michael E. Cusick,Troy Moore,Charles Boone,Michael Snyder,Frederick P. Roth,Albert-László Barabási,Albert-László Barabási,Jan Tavernier,David E. Hill,Marc Vidal +35 more
TL;DR: A comparative quality assessment of current yeast interactome data sets is carried out, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information.
Journal ArticleDOI
Assessing computational tools for the discovery of transcription factor binding sites.
Martin Tompa,Nan Li,Timothy L. Bailey,George M. Church,Bart De Moor,Eleazar Eskin,Alexander V. Favorov,Martin C. Frith,Yutao Fu,W. James Kent,Vsevolod J. Makeev,Andrei A. Mironov,William Stafford Noble,Giulio Pavesi,Graziano Pesole,Mireille Régnier,Nicolas Simonis,Saurabh Sinha,Gert Thijs,Jacques van Helden,Mathias Vandenbogaert,Zhiping Weng,Christopher T. Workman,Chun Ye,Zhou Zhu +24 more
TL;DR: The purpose of the current assessment is to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.
Journal ArticleDOI
An empirical framework for binary interactome mapping
Kavitha Venkatesan,Kavitha Venkatesan,Jean François Rual,Alexei Vazquez,Alexei Vazquez,Ulrich Stelzl,Irma Lemmens,Tomoko Hirozane-Kishikawa,Tong Hao,Martina Zenkner,Xiaofeng Xin,Kwang-Il Goh,Kwang-Il Goh,Kwang-Il Goh,Muhammed A. Yildirim,Nicolas Simonis,Kathrin Heinzmann,Fana Gebreab,Julie M. Sahalie,Sebiha Cevik,Sebiha Cevik,Christophe Simon,Anne Sophie de Smet,Elizabeth Dann,Alex Smolyar,Arunachalam Vinayagam,Haiyuan Yu,David Szeto,Heather Borick,Heather Borick,Amélie Dricot,Niels Klitgord,Niels Klitgord,Ryan R. Murray,Chenwei Lin,Maciej Lalowski,Jan Timm,Kirstin Rau,Charles Boone,Pascal Braun,Michael E. Cusick,Frederick P. Roth,David E. Hill,Jan Tavernier,Erich E. Wanker,Albert-László Barabási,Albert-László Barabási,Marc Vidal +47 more
TL;DR: The results indicate that high-throughput yeast two-hybrid interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome.
Journal ArticleDOI
Proto-genes and de novo gene birth
Anne-Ruxandra Carvunis,Thomas Rolland,Ilan Wapinski,Michael A. Calderwood,Muhammed A. Yildirim,Nicolas Simonis,Nicolas Simonis,Benoit Charloteaux,Benoit Charloteaux,César A. Hidalgo,Justin Barbette,Balaji Santhanam,Gloria A. Brar,Jonathan S. Weissman,Aviv Regev,Aviv Regev,Nicolas Thierry-Mieg,Michael E. Cusick,Marc Vidal +18 more
TL;DR: In this article, the authors formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences.
Journal ArticleDOI
Edgetic perturbation models of human inherited disorders.
Quan Zhong,Nicolas Simonis,Qian -Ru Li,Benoit Charloteaux,Benoit Charloteaux,Fabien Heuze,Fabien Heuze,Niels Klitgord,Stanley Tam,Haiyuan Yu,Kavitha Venkatesan,Danny Mou,Venus Swearingen,Muhammed A. Yildirim,Han Yan,Amélie Dricot,David Szeto,Chenwei Lin,Tong Hao,Changyu Fan,Stuart Milstein,Denis Dupuy,Robert Brasseur,David E. Hill,Michael E. Cusick,Marc Vidal +25 more
TL;DR: This work investigates how perturbations of interactome networks may differ between complete loss of gene products (‘node removal’) and interaction‐specific or edge‐specific alterations (“edgetic”) alterations.