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Chad Nusbaum
Researcher at Massachusetts Institute of Technology
Publications - 70
Citations - 69227
Chad Nusbaum is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 48, co-authored 69 publications receiving 62980 citations. Previous affiliations of Chad Nusbaum include Barts Health NHS Trust & Uniformed Services University of the Health Sciences.
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Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z. Levin,Moran Yassour,Moran Yassour,Xian Adiconis,Chad Nusbaum,Dawn Thompson,Nir Friedman,Andreas Gnirke,Aviv Regev +8 more
TL;DR: A comprehensive computational pipeline is developed to compare library quality metrics from any RNA-seq method and identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing.
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A Catalog of Reference Genomes from the Human Microbiome
Karen E. Nelson,George M. Weinstock,Sarah K. Highlander,Kim C. Worley,Heather Huot Creasy,Jennifer R. Wortman,Douglas B. Rusch,Makedonka Mitreva,Erica Sodergren,Asif T. Chinwalla,Michael Feldgarden,Dirk Gevers,Brian J. Haas,Ramana Madupu,Doyle V. Ward,Bruce W. Birren,Richard A. Gibbs,Barbara A. Methé,Joseph F. Petrosino,Robert L. Strausberg,Granger G. Sutton,Owen White,Richard K. Wilson,Scott Durkin,Michelle G. Giglio,Sharvari Gujja,Clint Howarth,Chinnappa D. Kodira,Nikos C. Kyrpides,Teena Mehta,Donna M. Muzny,Matthew D. Pearson,Kymberlie H. Pepin,Amrita Pati,Xiang Qin,Chandri N. Yandava,Qiandong Zeng,Lan Zhang,Aaron M. Berlin,Lei Chen,Theresa A. Hepburn,Justin Johnson,Jamison McCorrison,Jason R. Miller,Patrick Minx,Chad Nusbaum,Carsten Russ,Sean M. Sykes,Chad Tomlinson,Sarah Young,Wesley C. Warren,Jonathan H. Badger,Jonathan Crabtree,Victor Markowitz,Joshua Orvis,Andrew Cree,Steve Ferriera,Lucinda Fulton,Robert S. Fulton,Marcus Gillis,Lisa Hemphill,Vandita Joshi,Christie Kovar,Manolito Torralba,Kris A. Wetterstrand,Amr Abouellleil,Aye Wollam,Christian J. Buhay,Yan Ding,Shannon Dugan,Michael Fitzgerald,Mike Holder,Jessica B. Hostetler,Sandra W. Clifton,Emma Allen-Vercoe,Ashlee M. Earl,Candace N. Farmer,Konstantinos Liolios,Michael G. Surette,Qiang Xu,Craig Pohl,Katarzyna Wilczek-Boney,Dianhui Zhu +82 more
TL;DR: Results from an initial reference genome sequencing of 178 microbial genomes allow for ~40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used, suggesting that the authors are still far from saturating microbial species genetic data sets.
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Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry.
Fan Zhang,Kevin Wei,Kamil Slowikowski,Chamith Y. Fonseka,Deepak A. Rao,Stephen Kelly,Susan M. Goodman,Susan M. Goodman,Darren Tabechian,Laura B. Hughes,Karen Salomon-Escoto,Gerald F. Watts,A. Helena Jonsson,Javier Rangel-Moreno,Nida Meednu,Cristina Rozo,William Apruzzese,Thomas Eisenhaure,David J. Lieb,David L. Boyle,Arthur M. Mandelin,Brendan F. Boyce,Edward F. DiCarlo,Ellen M. Gravallese,Peter K. Gregersen,Larry W. Moreland,Gary S. Firestein,Nir Hacohen,Chad Nusbaum,James A. Lederer,Harris Perlman,Costantino Pitzalis,Andrew Filer,V. Michael Holers,Vivian P. Bykerk,Vivian P. Bykerk,Laura T. Donlin,Laura T. Donlin,Jennifer H. Anolik,Michael B. Brenner,Soumya Raychaudhuri +40 more
TL;DR: Several single-cell -omics approaches are used to define the cellular processes and pathways in the human RA joint and attributed IL6 expression to THY1+HLA-DRAhi fibroblasts and IL1B production to pro-inflammatory monocytes, potentially key mediators of RA pathogenesis.
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The Genome of M. Acetivorans Reveals Extensive Metabolic and Physiological Diversity
James E. Galagan,Chad Nusbaum,Alice Roy,Matthew G. Endrizzi,Matthew G. Endrizzi,Matthew G. Endrizzi,Pendexter Macdonald,Pendexter Macdonald,Pendexter Macdonald,William Fitzhugh,Sarah E. Calvo,Reinhard Engels,Serge Smirnov,Deven Atnoor,Adam Brown,Nicole R. Allen,Nicole R. Allen,Nicole R. Allen,Jerome Naylor,Nicole Stange-Thomann,Kurt DeArellano,Robin Johnson,Lauren Linton,Paul A. McEwan,Kevin McKernan,Jessica A. Talamas,Andrea Tirrell,Andrea Tirrell,Wenjuan Ye,Wenjuan Ye,Andrew Zimmer,Robert D. Barber,Isaac K. O. Cann,David E. Graham,David A. Grahame,Adam M. Guss,Reiner Hedderich,Cheryl Ingram-Smith,Cheryl Ingram-Smith,Cheryl Ingram-Smith,H. Craig Kuettner,Joseph A. Krzycki,Joseph A. Krzycki,John A. Leigh,Weixi Li,Jinfeng Liu,Biswarup Mukhopadhyay,John N. Reeve,Kerry S. Smith,Timothy A. Springer,Timothy A. Springer,Timothy A. Springer,Lowell Umayam,Owen White,Robert H. White,Everly Conway de Macario,Everly Conway de Macario,James G. Ferry,Ken F. Jarrell,Ken F. Jarrell,Hua Jing,Hua Jing,Hua Jing,Alberto J.L. Macario,Ian T. Paulsen,Ian T. Paulsen,Ian T. Paulsen,Matthew A. Pritchett,Kevin R. Sowers,Ronald V. Swanson,Steven H. Zinder,Steven H. Zinder,Eric S. Lander,Eric S. Lander,Eric S. Lander,William W. Metcalf,Bruce W. Birren +76 more
TL;DR: The complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A, is reported, which indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth.
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High-resolution mapping of copy-number alterations with massively parallel sequencing
Derek Y. Chiang,Gad Getz,David B. Jaffe,Michael J. T. O’Kelly,Xiaojun Zhao,Scott L. Carter,Carsten Russ,Chad Nusbaum,Matthew Meyerson,Matthew Meyerson,Eric S. Lander +10 more
TL;DR: A collection of ∼14 million aligned sequence reads from human cell lines has comparable power to detect events as the current generation of DNA microarrays and has over twofold better precision for localizing breakpoints (typically, to within ∼1 kilobase).