R
Richard Bonneau
Researcher at New York University
Publications - 327
Citations - 27174
Richard Bonneau is an academic researcher from New York University. The author has contributed to research in topics: Gene regulatory network & Social media. The author has an hindex of 74, co-authored 302 publications receiving 20587 citations. Previous affiliations of Richard Bonneau include Howard Hughes Medical Institute & Courant Institute of Mathematical Sciences.
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Wisdom of crowds for robust gene network inference
Daniel Marbach,James C. Costello,Robert Küffner,Nicole M. Vega,Robert J. Prill,Diogo M. Camacho,Kyle R. Allison,Andrej Aderhold,Richard Bonneau,Yukun Chen,James J. Collins,Francesca Cordero,Martin Crane,Frank Dondelinger,Mathias Drton,Roberto Esposito,Rina Foygel,Alberto de la Fuente,Jan Gertheiss,Pierre Geurts,Alex Greenfield,Marco Grzegorczyk,Anne-Claire Haury,Benjamin Holmes,Torsten Hothorn,Dirk Husmeier,Vân Anh Huynh-Thu,Alexandre Irrthum,Manolis Kellis,Guy Karlebach,Sophie Lèbre,Vincenzo De Leo,Aviv Madar,Subramani Mani,Fantine Mordelet,Harry Ostrer,Zhengyu Ouyang,Ravi Pandya,Tobias Petri,Andrea Pinna,Christopher S. Poultney,Serena Rezny,Heather J. Ruskin,Yvan Saeys,Ron Shamir,Alina Sîrbu,Mingzhou Song,Nicola Soranzo,Alexander Statnikov,Gustavo Stolovitzky,Nicci Vega,Paola Vera-Licona,Jean-Philippe Vert,Alessia Visconti,Haizhou Wang,Louis Wehenkel,Lukas Windhager,Yang Zhang,Ralf Zimmer +58 more
TL;DR: A comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data defines the performance, data requirements and inherent biases of different inference approaches, and provides guidelines for algorithm application and development.
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The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts
Alexander G. Baltz,Mathias Munschauer,Björn Schwanhäusser,Alexandra Vasile,Yasuhiro Murakawa,Markus Schueler,Noah Youngs,Duncan Penfold-Brown,Kevin Drew,Miha Milek,Emanuel Wyler,Richard Bonneau,Matthias Selbach,Christoph Dieterich,Markus Landthaler +14 more
TL;DR: Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms.
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A Validated Regulatory Network for Th17 Cell Specification
Maria Ciofani,Aviv Madar,Aviv Madar,Carolina Galan,MacLean Sellars,Kieran Mace,Florencia Pauli,Ashish Agarwal,Wendy Huang,Christopher N. Parkurst,Michael Muratet,Kim M. Newberry,Sarah Meadows,Alex Greenfield,Yi Yang,Preti Jain,Francis K. Kirigin,Carmen Birchmeier,Erwin F. Wagner,Kenneth M. Murphy,Kenneth M. Murphy,Richard M. Myers,Richard Bonneau,Richard Bonneau,Dan R. Littman,Dan R. Littman +25 more
TL;DR: It is found that cooperatively bound BATF and IRF4 contribute to initial chromatin accessibility and, with STAT3, initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci.
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Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Zachary D. Kurtz,Christian L. Müller,Emily R. Miraldi,Dan R. Littman,Martin J. Blaser,Richard Bonneau +5 more
TL;DR: SParse InversE Covariance Estimation for Ecological Association Inference is presented, a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that outperforms state-of-the-art methods to recover edges and network properties on synthetic data under a variety of scenarios.
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Tweeting From Left to Right Is Online Political Communication More Than an Echo Chamber
TL;DR: It is concluded that previous work may have overestimated the degree of ideological segregation in social-media usage and liberals were more likely than conservatives to engage in cross-ideological dissemination.