Richard Bonneau

Richard Bonneau

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Richard Bonneau

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Political psycholinguistics: A comprehensive analysis of the language habits of liberal and conservative social media users.

J Pers Soc Psychol 2020 Apr 9;118(4):805-834. Epub 2020 Jan 9.

Center for Genomics and Systems Biology, New York University.

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http://dx.doi.org/10.1037/pspp0000275DOI Listing
April 2020

Classification of the Molecular Defects Associated with Pathogenic Variants of the Creatine Transporter.

Biochemistry 2020 Mar 30. Epub 2020 Mar 30.

Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.

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http://dx.doi.org/10.1021/acs.biochem.9b00956DOI Listing
March 2020

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling.

Nat Commun 2020 Feb 6;11(1):747. Epub 2020 Feb 6.

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.

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http://dx.doi.org/10.1038/s41467-020-14497-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004981PMC
February 2020

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV.

Cell Rep 2020 Jan;30(3):914-931.e9

Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France; The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.12.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039998PMC
January 2020

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.

Structure 2019 11 12;27(11):1721-1734.e5. Epub 2019 Sep 12.

Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.08.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834914PMC
November 2019

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.

Cell Host Microbe 2019 11;26(5):680-690.e5

Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2019.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039456PMC
November 2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

Thermoresponsive Protein-Engineered Coiled-Coil Hydrogel for Sustained Small Molecule Release.

Biomacromolecules 2019 Sep 19;20(9):3340-3351. Epub 2019 Aug 19.

Department of Chemical and Biomolecular Engineering , New York University Tandon School of Engineering , Brooklyn , New York 11201 , United States.

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http://dx.doi.org/10.1021/acs.biomac.9b00107DOI Listing
September 2019

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells.

Immunity 2019 07 2;51(1):185-197.e6. Epub 2019 Jul 2.

Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1016/j.immuni.2019.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863506PMC
July 2019

Towards region-specific propagation of protein functions.

Bioinformatics 2019 May;35(10):1737-1744

Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513163PMC
May 2019

Generative Models for Quantification of DNA Modifications.

Methods Mol Biol 2018 ;1807:37-50

Department of Computer Science, Aalto University School of Science, Aalto, Finland.

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http://dx.doi.org/10.1007/978-1-4939-8561-6_4DOI Listing
March 2019

Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont.

Nature 2019 02;566(7744):E7

Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York, 10016, USA.

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http://www.nature.com/articles/s41586-019-0922-z
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http://dx.doi.org/10.1038/s41586-019-0922-zDOI Listing
February 2019

Multi-study inference of regulatory networks for more accurate models of gene regulation.

PLoS Comput Biol 2019 01 24;15(1):e1006591. Epub 2019 Jan 24.

New York University, New York, NY 10003, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1006591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363223PMC
January 2019

Computational-guided determination of the functional role of 447-52D long CDRH3.

Protein Eng Des Sel 2018 12;31(12):479-487

Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York NY, USA.

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http://dx.doi.org/10.1093/protein/gzz007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890530PMC
December 2018

deepNF: deep network fusion for protein function prediction.

Bioinformatics 2018 11;34(22):3873-3881

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.

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https://academic.oup.com/bioinformatics/article/34/22/3873/5
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http://dx.doi.org/10.1093/bioinformatics/bty440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223364PMC
November 2018

An adaptive geometric search algorithm for macromolecular scaffold selection.

Protein Eng Des Sel 2018 09;31(9):345-354

Computer ScienceDepartment, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.

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https://academic.oup.com/peds/advance-article/doi/10.1093/pr
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http://dx.doi.org/10.1093/protein/gzy028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373690PMC
September 2018

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures.

Biochemistry 2018 04 11;57(13):1939-1944. Epub 2017 Dec 11.

Center for Computational Biology, Flatiron Institute , Simons Foundation , 162 Fifth Avenue , New York , New York 10010 , United States.

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http://pubs.acs.org/doi/10.1021/acs.biochem.7b00995
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http://dx.doi.org/10.1021/acs.biochem.7b00995DOI Listing
April 2018

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.

Cell Rep 2018 Apr;23(2):376-388

Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Biology Department, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY 10003, USA; Center for Data Science, New York University, New York, NY 10003, USA; Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987223PMC
April 2018

Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.

Sci Rep 2018 03 13;8(1):4446. Epub 2018 Mar 13.

Medical School, University of Exeter, Exeter, EX1 2 LU, UK.

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http://dx.doi.org/10.1038/s41598-018-22476-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849751PMC
March 2018

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions.

Methods Mol Biol 2017 ;1561:291-307

Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.

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http://dx.doi.org/10.1007/978-1-4939-6798-8_17DOI Listing
February 2018

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.

Bioinformatics 2018 02;34(3):372-380

Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860357PMC
February 2018

c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont.

Nature 2018 02 7;554(7692):373-377. Epub 2018 Feb 7.

Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.

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http://dx.doi.org/10.1038/nature25500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814346PMC
February 2018

Why are there hotspot mutations in the TP53 gene in human cancers?

Cell Death Differ 2018 01 3;25(1):154-160. Epub 2017 Nov 3.

Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.

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http://dx.doi.org/10.1038/cdd.2017.180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729536PMC
January 2018

Fungi stabilize connectivity in the lung and skin microbial ecosystems.

Microbiome 2018 01 15;6(1):12. Epub 2018 Jan 15.

Center for Genomics and Systems Biology, New York University, New York, 10003, NY, USA.

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http://dx.doi.org/10.1186/s40168-017-0393-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769346PMC
January 2018

Detecting Bots on Russian Political Twitter.

Big Data 2017 12;5(4):310-324

1 Department of Politics, New York University , New York, New York.

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http://dx.doi.org/10.1089/big.2017.0038DOI Listing
December 2017

Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers.

Structure 2017 11 12;25(11):1771-1780.e3. Epub 2017 Oct 12.

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY 10009, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09692126173029
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http://dx.doi.org/10.1016/j.str.2017.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845441PMC
November 2017

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.

PLoS Comput Biol 2017 Oct 12;13(10):e1005625. Epub 2017 Oct 12.

Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638211PMC
October 2017

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2.

Cell Rep 2017 Oct;21(5):1267-1280

Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247173142
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http://dx.doi.org/10.1016/j.celrep.2017.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687844PMC
October 2017

Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes.

Biomacromolecules 2017 Sep 4;18(9):2688-2698. Epub 2017 Aug 4.

Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States.

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http://dx.doi.org/10.1021/acs.biomac.7b00203DOI Listing
September 2017

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells.

Inflamm Bowel Dis 2017 09;23(9):1544-1554

*Department of Microbiology, New York University School of Medicine, New York, New York; †Department of Medicine, Division of Gastroenterology, New York University School of Medicine, New York, New York; ‡Department of Veterans Affairs, New York Harbor Healthcare System, New York, New York; §Department of Pathology, New York University School of Medicine, New York, New York; ‖Department of Medicine, Division of Gastroenterology, Mount Sinai School of Medicine, New York, New York; ¶Immunology Institute, Mount Sinai School of Medicine, New York, New York; **Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York; and ††Simons Center for Data Analysis, Simons Foundation, New York, New York.

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http://dx.doi.org/10.1097/MIB.0000000000001208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613756PMC
September 2017

Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function.

Mol Biosyst 2017 Sep;13(10):2092-2106

Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, New York 11201, USA.

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http://dx.doi.org/10.1039/c7mb00196gDOI Listing
September 2017

Biophysically Motivated Regulatory Network Inference: Progress and Prospects.

Hum Hered 2016 12;81(2):62-77. Epub 2017 Jan 12.

Center for Computational Biology, Simons Foundation, New York, N.Y., USA.

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http://dx.doi.org/10.1159/000446614DOI Listing
June 2017

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

Nat Immunol 2017 04 6;18(4):412-421. Epub 2017 Feb 6.

Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ni.3683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5901650PMC
April 2017

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.

BMC Bioinformatics 2017 Feb 20;18(1):115. Epub 2017 Feb 20.

Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA.

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http://dx.doi.org/10.1186/s12859-017-1541-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319049PMC
February 2017

Fused Regression for Multi-source Gene Regulatory Network Inference.

PLoS Comput Biol 2016 12 6;12(12):e1005157. Epub 2016 Dec 6.

New York University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140053PMC
December 2016

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Nucleic Acids Res 2016 Oct 20;44(18):8714-8725. Epub 2016 Jul 20.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA Program of Applied Mathematics, Yale university, New Haven, CT, USA

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http://dx.doi.org/10.1093/nar/gkw568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062970PMC
October 2016

PPII Helical Peptidomimetics Templated by Cation-π Interactions.

Chembiochem 2016 10 19;17(19):1824-1828. Epub 2016 Aug 19.

Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.

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http://dx.doi.org/10.1002/cbic.201600248DOI Listing
October 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Side-Chain Conformational Preferences Govern Protein-Protein Interactions.

J Am Chem Soc 2016 08 9;138(33):10386-9. Epub 2016 Aug 9.

Center for Computational Biology, Simons Foundation , New York, New York 10010, United States.

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http://dx.doi.org/10.1021/jacs.6b04892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005188PMC
August 2016

Breaking TADs: insights into hierarchical genome organization.

Epigenomics 2015 ;7(4):523-6

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.2217/epi.15.25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624204PMC
June 2016

The Critical Periphery in the Growth of Social Protests.

PLoS One 2015 30;10(11):e0143611. Epub 2015 Nov 30.

Annenberg School for Communication, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143611PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664236PMC
June 2016

Robust classification of protein variation using structural modelling and large-scale data integration.

Nucleic Acids Res 2016 Apr 28;44(6):2501-13. Epub 2016 Feb 28.

Department of Biology, New York University, New York, NY 10003, USA New York University Center for Genomics and Systems Biology, New York, NY 10003, USA Computer Science Department, New York University, New York, NY 10003, USA Simons Center for Data Analysis, Simons Foundation, New York, NY 10010, USA Simons Foundation, New York, NY 10010, USA

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http://dx.doi.org/10.1093/nar/gkw120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824117PMC
April 2016

Helminth infection promotes colonization resistance via type 2 immunity.

Science 2016 Apr 14;352(6285):608-12. Epub 2016 Apr 14.

Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA. Departments of Microbiology and Medicine, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1126/science.aaf3229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905769PMC
April 2016

Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination.

J Exp Med 2016 Mar 22;213(3):303-12. Epub 2016 Feb 22.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France

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http://dx.doi.org/10.1084/jem.20141967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813673PMC
March 2016

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

PLoS Comput Biol 2016 Mar 3;12(3):e1004780. Epub 2016 Mar 3.

Department of Pathology, New York University School of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777514PMC
March 2016

A Miniature Protein Stabilized by a Cation-π Interaction Network.

J Am Chem Soc 2016 Feb 26;138(5):1543-50. Epub 2016 Jan 26.

Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States.

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http://pubs.acs.org/doi/10.1021/jacs.5b10285
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http://dx.doi.org/10.1021/jacs.5b10285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867217PMC
February 2016

Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability.

Proteins 2016 Jan 26;84(1):60-72. Epub 2015 Nov 26.

Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York.

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http://dx.doi.org/10.1002/prot.24955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715774PMC
January 2016

Tweeting From Left to Right: Is Online Political Communication More Than an Echo Chamber?

Psychol Sci 2015 Oct 21;26(10):1531-42. Epub 2015 Aug 21.

Center for Genomics and Systems Biology, New York University.

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http://dx.doi.org/10.1177/0956797615594620DOI Listing
October 2015

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses.

Cell 2015 Oct 24;163(2):381-93. Epub 2015 Sep 24.

Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.08.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621768PMC
October 2015

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms.

J Exp Med 2015 Oct 5;212(11):1833-50. Epub 2015 Oct 5.

Howard Hughes Medical Institute, Department of Pathology, and Center for Health Informatics and Bioinformatics, School of Medicine and Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10016 Howard Hughes Medical Institute, Department of Pathology, and Center for Health Informatics and Bioinformatics, School of Medicine and Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10016

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http://dx.doi.org/10.1084/jem.20151323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612095PMC
October 2015

Interpreting 4C-Seq data: how far can we go?

Epigenomics 2014 ;6(5):455-7

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.2217/epi.14.47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406053PMC
July 2015

Sparse and compositionally robust inference of microbial ecological networks.

PLoS Comput Biol 2015 May 7;11(5):e1004226. Epub 2015 May 7.

Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America; Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America; Simons Center for Data Analysis, Simons Foundation, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423992PMC
May 2015

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Bioinformatics 2015 Feb 22;31(4):501-8. Epub 2014 Aug 22.

Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325539PMC
February 2015

Engineered coiled-coil protein microfibers.

Biomacromolecules 2014 Oct 2;15(10):3503-10. Epub 2014 Oct 2.

Department of Chemical and Biomolecular Engineering, NYU Polytechnic School of Engineering , Brooklyn, New York 11201, United States.

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http://dx.doi.org/10.1021/bm5004948DOI Listing
October 2014

Conformational preferences of peptide-peptoid hybrid oligomers.

Biopolymers 2014 Sep;102(5):369-78

Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box, 129188, Abu Dhabi, United Arab Emirates.

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http://dx.doi.org/10.1002/bip.22516DOI Listing
September 2014

ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells.

Blood 2014 Aug 1;124(7):1070-80. Epub 2014 Jul 1.

Abramson Cancer Center and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA;

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http://dx.doi.org/10.1182/blood-2013-10-535245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133482PMC
August 2014

Improved stability and half-life of fluorinated phosphotriesterase using Rosetta.

Chembiochem 2014 Aug 25;15(12):1761-4. Epub 2014 Jul 25.

Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, 6 Metrotech, Brooklyn, NY 11201 (USA).

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http://dx.doi.org/10.1002/cbic.201402062DOI Listing
August 2014

Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine.

Chem Commun (Camb) 2014 Jul;50(52):6909-12

Department of Chemistry, New York University, New York, 10003, USA.

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http://dx.doi.org/10.1039/c4cc01928hDOI Listing
July 2014

CX₃CR1⁺ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22.

J Exp Med 2014 Jul 14;211(8):1571-83. Epub 2014 Jul 14.

The Kimmel Center for Biology and Medicine of the Skirball Institute and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016The Kimmel Center for Biology and Medicine of the Skirball Institute and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016

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http://dx.doi.org/10.1084/jem.20140678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113938PMC
July 2014

A rotamer library to enable modeling and design of peptoid foldamers.

J Am Chem Soc 2014 Jun 9;136(24):8772-82. Epub 2014 Jun 9.

Center for Genomics and Systems Biology, Department of Biology, ‡Department of Chemistry, and §Courant Institute of Mathematical Sciences, Computer Science Department, New York University , New York, New York 10003, United States.

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http://dx.doi.org/10.1021/ja503776zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227732PMC
June 2014

Negative example selection for protein function prediction: the NoGO database.

PLoS Comput Biol 2014 Jun 12;10(6):e1003644. Epub 2014 Jun 12.

Department of Computer Science, New York University, New York, New York, United States of America; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055410PMC
June 2014

Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions.

J Am Chem Soc 2014 Jun 23;136(22):7877-88. Epub 2014 May 23.

Department of Chemistry and ‡Departments of Biology and Computer Science, New York University , New York, New York 10003, United States.

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http://dx.doi.org/10.1021/ja502310rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353027PMC
June 2014

Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors.

Dev Cell 2014 May 1;29(3):263-76. Epub 2014 May 1.

Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045103PMC
May 2014

Helminth colonization is associated with increased diversity of the gut microbiota.

PLoS Negl Trop Dis 2014 May 22;8(5):e2880. Epub 2014 May 22.

Department of Microbiology, New York University School of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0002880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031128PMC
May 2014