J
James J. Collins
Researcher at Massachusetts Institute of Technology
Publications - 700
Citations - 105255
James J. Collins is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Synthetic biology & Population. The author has an hindex of 151, co-authored 669 publications receiving 89476 citations. Previous affiliations of James J. Collins include Baylor College of Medicine & University at Albany, SUNY.
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Journal ArticleDOI
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,Manolis Kellis,James J. Collins,Gustavo Stolovitzky +9 more
TL;DR: In this paper, the authors performed a comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data.
Journal ArticleDOI
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6
Jonathan S. Gootenberg,Omar O. Abudayyeh,Max J. Kellner,Julia Joung,James J. Collins,Feng Zhang +5 more
TL;DR: ShERLOCK as discussed by the authors is a platform that combines isothermal preamplification with Cas13 to detect single molecules of RNA or DNA, which can detect Dengue or Zika virus single-stranded RNA and mutations in patient liquid biopsy samples via lateral flow.
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.
Journal ArticleDOI
Synthetic biology: applications come of age.
TL;DR: The de novo engineering of genetic circuits, biological modules and synthetic pathways is beginning to address these crucial problems and is being used in related practical applications.
Journal ArticleDOI
Inferring genetic networks and identifying compound mode of action via expression profiling
TL;DR: Systematic transcriptional perturbations are used to construct a first-order model of regulatory interactions in a nine-gene subnetwork of the SOS pathway in Escherichia coli that provides a framework for elucidating the functional properties of genetic networks and identifying molecular targets of pharmacological compounds.