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Jonathan Livny
Jonathan Livny
Associate Director, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard
Verified email at broadinstitute.org
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Cited by
Year
Nucleic acid detection with CRISPR-Cas13a/C2c2
JS Gootenberg, OO Abudayyeh, JW Lee, P Essletzbichler, AJ Dy, J Joung, ...
Science 356 (6336), 438-442, 2017
27032017
Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine
LT Geller, M Barzily-Rokni, T Danino, OH Jonas, N Shental, D Nejman, ...
Science 357 (6356), 1156-1160, 2017
12822017
Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli
PL Wagner, J Livny, MN Neely, DWK Acheson, DI Friedman, MK Waldor
Molecular microbiology 44 (4), 957-970, 2002
3052002
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
BJ Haas, M Chin, C Nusbaum, BW Birren, J Livny
BMC genomics 13, 1-11, 2012
2712012
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
J Livny, H Teonadi, M Livny, MK Waldor
PloS one 3 (9), e3197, 2008
2702008
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
G Giannoukos, DM Ciulla, K Huang, BJ Haas, J Izard, JZ Levin, J Livny, ...
Genome biology 13, 1-13, 2012
2672012
Simultaneous generation of many RNA-seq libraries in a single reaction
AA Shishkin, G Giannoukos, A Kucukural, D Ciulla, M Busby, C Surka, ...
Nature methods 12 (4), 323-325, 2015
2652015
Distribution of Centromere-Like parS Sites in Bacteria: Insights from Comparative Genomics
J Livny, Y Yamaichi, MK Waldor
Journal of bacteriology 189 (23), 8693-8703, 2007
2652007
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
M Poyet, M Groussin, SM Gibbons, J Avila-Pacheco, X Jiang, SM Kearney, ...
Nature medicine 25 (9), 1442-1452, 2019
2642019
RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression
A Mandlik, J Livny, WP Robins, JM Ritchie, JJ Mekalanos, MK Waldor
Cell host & microbe 10 (2), 165-174, 2011
2542011
Identification of small RNAs in diverse bacterial species
J Livny, MK Waldor
Current opinion in microbiology 10 (2), 96-101, 2007
2472007
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
J Livny, A Brencic, S Lory, MK Waldor
Nucleic acids research 34 (12), 3484-3493, 2006
2362006
TargetRNA2: identifying targets of small regulatory RNAs in bacteria
MB Kery, M Feldman, J Livny, B Tjaden
Nucleic acids research 42 (W1), W124-W129, 2014
2132014
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
JM Liu, J Livny, MS Lawrence, MD Kimball, MK Waldor, A Camilli
Nucleic acids research 37 (6), e46-e46, 2009
2102009
Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system
J Livny, DI Friedman
Molecular microbiology 51 (6), 1691-1704, 2004
1642004
Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis
JM DiChiara, LM Contreras-Martinez, J Livny, D Smith, KA McDonough, ...
Nucleic acids research 38 (12), 4067-4078, 2010
1482010
Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections
HL Schreiber IV, MS Conover, WC Chou, ME Hibbing, AL Manson, ...
Science translational medicine 9 (382), eaaf1283, 2017
1442017
sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
J Livny, MA Fogel, BM Davis, MK Waldor
Nucleic acids research 33 (13), 4096-4105, 2005
1352005
High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data
MC Chao, JR Pritchard, YJ Zhang, EJ Rubin, J Livny, BM Davis, ...
Nucleic acids research 41 (19), 9033-9048, 2013
1312013
NanoRNAs prime transcription initiation in vivo
SR Goldman, JS Sharp, IO Vvedenskaya, J Livny, SL Dove, BE Nickels
Molecular cell 42 (6), 817-825, 2011
1272011
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