Jonathan Livny
Jonathan Livny
Associate Director, Broad Institute of MIT and Harvard
Verified email at
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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
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
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
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
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
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), 1-11, 2012
Identification of small RNAs in diverse bacterial species
J Livny, MK Waldor
Current opinion in microbiology 10 (2), 96-101, 2007
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
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
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
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
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
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
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
Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system
J Livny, DI Friedman
Molecular microbiology 51 (6), 1691-1704, 2004
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
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
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
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
Legionella pneumophila 6S RNA optimizes intracellular multiplication
SP Faucher, G Friedlander, J Livny, H Margalit, HA Shuman
Proceedings of the National Academy of Sciences 107 (16), 7533-7538, 2010
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