Publications by authors named "Jason A Greenbaum"

39Publications

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.

Cell 2020 06 20;181(7):1489-1501.e15. Epub 2020 May 20.

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901PMC
June 2020

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression.

Cell 2018 11 15;175(6):1701-1715.e16. Epub 2018 Nov 15.

La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.10.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289654PMC
November 2018

Response to Comment on "Development of Asthma in Inner-City Children: Possible Roles of MAIT Cells and Variation in the Home Environment".

J Immunol 2018 05;200(10):3317-3318

Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;

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http://dx.doi.org/10.4049/jimmunol.1800397DOI Listing
May 2018

Improved methods for predicting peptide binding affinity to MHC class II molecules.

Immunology 2018 07 6;154(3):394-406. Epub 2018 Feb 6.

Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.1111/imm.12889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002223PMC
July 2018

An automated benchmarking platform for MHC class II binding prediction methods.

Bioinformatics 2018 05;34(9):1522-1528

Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650, San Martín, Buenos Aires, Argentina.

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http://dx.doi.org/10.1093/bioinformatics/btx820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5925780PMC
May 2018

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing.

Hum Immunol 2015 Dec 28;76(12):917-22. Epub 2015 May 28.

Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.humimm.2015.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662932PMC
December 2015

Automated benchmarking of peptide-MHC class I binding predictions.

Bioinformatics 2015 Jul 25;31(13):2174-81. Epub 2015 Feb 25.

Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.

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http://dx.doi.org/10.1093/bioinformatics/btv123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481849PMC
July 2015

Immunological consequences of intragenus conservation of Mycobacterium tuberculosis T-cell epitopes.

Proc Natl Acad Sci U S A 2015 Jan 29;112(2):E147-55. Epub 2014 Dec 29.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and.

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http://dx.doi.org/10.1073/pnas.1416537112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299226PMC
January 2015

The immune epitope database (IEDB) 3.0.

Nucleic Acids Res 2015 Jan 9;43(Database issue):D405-12. Epub 2014 Oct 9.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, 9420 Athena Circle, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gku938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384014PMC
January 2015

Properties of MHC class I presented peptides that enhance immunogenicity.

PLoS Comput Biol 2013 Oct 24;9(10):e1003266. Epub 2013 Oct 24.

Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1003266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808449PMC
October 2013

Query enhancement through the practical application of ontology: the IEDB and OBI.

J Biomed Semantics 2013 Apr 15;4 Suppl 1:S6. Epub 2013 Apr 15.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1186/2041-1480-4-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633001PMC
April 2013

TiArA: a virtual appliance for the analysis of Tiling Array data.

PLoS One 2010 Apr 1;5(4):e9993. Epub 2010 Apr 1.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009993PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848623PMC
April 2010

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.

Proc Natl Acad Sci U S A 2009 Dec 16;106(48):20365-70. Epub 2009 Nov 16.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.0911580106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777968PMC
December 2009

The immune epitope database 2.0.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D854-62. Epub 2009 Nov 11.

La Jolla Institute for Allergy and Immunology, Center For Infectious Disease, Allergy and Asthma Research, 9420 Athena Circle, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkp1004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808938PMC
January 2010

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Construction of a genome-scale structural map at single-nucleotide resolution.

Genome Res 2007 Jun;17(6):947-53

Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1101/gr.6073107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891353PMC
June 2007

Detection of DNA structural motifs in functional genomic elements.

Genome Res 2007 Jun;17(6):940-6

Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5602807
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http://dx.doi.org/10.1101/gr.5602807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891352PMC
June 2007

Mapping nucleic acid structure by hydroxyl radical cleavage.

Curr Opin Chem Biol 2005 Apr;9(2):127-34

Department of Chemistry, Boston University, Boston MA 02215, USA.

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http://dx.doi.org/10.1016/j.cbpa.2005.02.009DOI Listing
April 2005