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Items: 1 to 50 of 52

1.

Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation.

Kannaiah S, Livny J, Amster-Choder O.

Mol Cell. 2019 Aug 31. pii: S1097-2765(19)30629-X. doi: 10.1016/j.molcel.2019.08.013. [Epub ahead of print]

PMID:
31540875
2.

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.

Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, Livny J, Vlamakis H, Clish C, Bullock K, Deik A, Scott J, Pierce KA, Xavier RJ, Alm EJ.

Nat Med. 2019 Sep;25(9):1442-1452. doi: 10.1038/s41591-019-0559-3. Epub 2019 Sep 2.

PMID:
31477907
3.

Mucosal infection rewires TNFɑ signaling dynamics to skew susceptibility to recurrence.

Yu L, O'Brien VP, Livny J, Dorsey D, Bandyopadhyay N, Colonna M, Caparon MG, Roberson ED, Hultgren SJ, Hannan TJ.

Elife. 2019 Aug 20;8. pii: e46677. doi: 10.7554/eLife.46677.

4.

Chemical disarming of isoniazid resistance in Mycobacterium tuberculosis.

Flentie K, Harrison GA, Tükenmez H, Livny J, Good JAD, Sarkar S, Zhu DX, Kinsella RL, Weiss LA, Solomon SD, Schene ME, Hansen MR, Cairns AG, Kulén M, Wixe T, Lindgren AEG, Chorell E, Bengtsson C, Krishnan KS, Hultgren SJ, Larsson C, Almqvist F, Stallings CL.

Proc Natl Acad Sci U S A. 2019 May 21;116(21):10510-10517. doi: 10.1073/pnas.1818009116. Epub 2019 May 6.

PMID:
31061116
5.

Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.

Bhattacharyya RP, Walker M, Boykin R, Son SS, Liu J, Hachey AC, Ma P, Wu L, Choi K, Cummins KC, Benson M, Skerry J, Ryu H, Wong SY, Goldberg MB, Han J, Pierce VM, Cosimi LA, Shoresh N, Livny J, Beechem J, Hung DT.

Sci Rep. 2019 Mar 14;9(1):4516. doi: 10.1038/s41598-019-40792-3.

6.

Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027.

Daou N, Wang Y, Levdikov VM, Nandakumar M, Livny J, Bouillaut L, Blagova E, Zhang K, Belitsky BR, Rhee K, Wilkinson AJ, Sun X, Sonenshein AL.

PLoS One. 2019 Jan 30;14(1):e0206896. doi: 10.1371/journal.pone.0206896. eCollection 2019.

7.

Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response.

Gerrick ER, Barbier T, Chase MR, Xu R, François J, Lin VH, Szucs MJ, Rock JM, Ahmad R, Tjaden B, Livny J, Fortune SM.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6464-6469. doi: 10.1073/pnas.1718003115. Epub 2018 Jun 5.

8.

A putative Vibrio cholerae two-component system controls a conserved periplasmic protein in response to the antimicrobial peptide polymyxin B.

Matson JS, Livny J, DiRita VJ.

PLoS One. 2017 Oct 11;12(10):e0186199. doi: 10.1371/journal.pone.0186199. eCollection 2017.

9.

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine.

Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R.

Science. 2017 Sep 15;357(6356):1156-1160. doi: 10.1126/science.aah5043.

10.

The Capacity of Mycobacterium tuberculosis To Survive Iron Starvation Might Enable It To Persist in Iron-Deprived Microenvironments of Human Granulomas.

Kurthkoti K, Amin H, Marakalala MJ, Ghanny S, Subbian S, Sakatos A, Livny J, Fortune SM, Berney M, Rodriguez GM.

MBio. 2017 Aug 15;8(4). pii: e01092-17. doi: 10.1128/mBio.01092-17.

11.

Nucleic acid detection with CRISPR-Cas13a/C2c2.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F.

Science. 2017 Apr 28;356(6336):438-442. doi: 10.1126/science.aam9321. Epub 2017 Apr 13.

12.

Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death.

Botella L, Vaubourgeix J, Livny J, Schnappinger D.

Nat Commun. 2017 Mar 28;8:14731. doi: 10.1038/ncomms14731.

13.

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections.

Schreiber HL 4th, Conover MS, Chou WC, Hibbing ME, Manson AL, Dodson KW, Hannan TJ, Roberts PL, Stapleton AE, Hooton TM, Livny J, Earl AM, Hultgren SJ.

Sci Transl Med. 2017 Mar 22;9(382). pii: eaaf1283. doi: 10.1126/scitranslmed.aaf1283.

14.

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT.

Elife. 2017 Feb 21;6. pii: e20420. doi: 10.7554/eLife.20420.

15.

One size doesn't fit all: unraveling the diversity of factors and interactions that drive E. coli urovirulence.

Schreiber HL 4th, Spaulding CN, Dodson KW, Livny J, Hultgren SJ.

Ann Transl Med. 2017 Jan;5(2):28. doi: 10.21037/atm.2016.12.73. No abstract available.

16.

A mucosal imprint left by prior Escherichia coli bladder infection sensitizes to recurrent disease.

O'Brien VP, Hannan TJ, Yu L, Livny J, Roberson ED, Schwartz DJ, Souza S, Mendelsohn CL, Colonna M, Lewis AL, Hultgren SJ.

Nat Microbiol. 2016 Oct 31;2:16196. doi: 10.1038/nmicrobiol.2016.196.

17.

RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs.

Arnold WK, Savage CR, Brissette CA, Seshu J, Livny J, Stevenson B.

PLoS One. 2016 Oct 5;11(10):e0164165. doi: 10.1371/journal.pone.0164165. eCollection 2016.

18.

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.

Avraham R, Haseley N, Fan A, Bloom-Ackermann Z, Livny J, Hung DT.

Nat Protoc. 2016 Aug;11(8):1477-91. doi: 10.1038/nprot.2016.090. Epub 2016 Jul 21.

PMID:
27442864
19.

A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus.

Waters NR, Samuels DJ, Behera RK, Livny J, Rhee KY, Sadykov MR, Brinsmade SR.

Mol Microbiol. 2016 Aug;101(3):495-514. doi: 10.1111/mmi.13404. Epub 2016 Jun 10.

20.

Simultaneous generation of many RNA-seq libraries in a single reaction.

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J.

Nat Methods. 2015 Apr;12(4):323-5. doi: 10.1038/nmeth.3313. Epub 2015 Mar 2.

21.

Pilicide ec240 disrupts virulence circuits in uropathogenic Escherichia coli.

Greene SE, Pinkner JS, Chorell E, Dodson KW, Shaffer CL, Conover MS, Livny J, Hadjifrangiskou M, Almqvist F, Hultgren SJ.

MBio. 2014 Oct 28;5(6):e02038. doi: 10.1128/mBio.02038-14.

22.

Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection.

Livny J, Zhou X, Mandlik A, Hubbard T, Davis BM, Waldor MK.

Nucleic Acids Res. 2014 Oct 29;42(19):12212-23. doi: 10.1093/nar/gku891. Epub 2014 Sep 27.

23.

Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

Brinsmade SR, Alexander EL, Livny J, Stettner AI, Segrè D, Rhee KY, Sonenshein AL.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8227-32. doi: 10.1073/pnas.1321308111. Epub 2014 May 19.

24.

TargetRNA2: identifying targets of small regulatory RNAs in bacteria.

Kery MB, Feldman M, Livny J, Tjaden B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W124-9. doi: 10.1093/nar/gku317. Epub 2014 Apr 21.

25.

High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization.

Johnson JG, Livny J, Dirita VJ.

J Bacteriol. 2014 Jun;196(11):1958-67. doi: 10.1128/JB.01395-13. Epub 2014 Mar 14.

26.

Identification of novel sRNAs in mycobacterial species.

Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM.

PLoS One. 2013 Nov 14;8(11):e79411. doi: 10.1371/journal.pone.0079411. eCollection 2013.

27.

The complete Campylobacter jejuni transcriptome during colonization of a natural host determined by RNAseq.

Taveirne ME, Theriot CM, Livny J, DiRita VJ.

PLoS One. 2013 Aug 21;8(8):e73586. doi: 10.1371/journal.pone.0073586. eCollection 2013.

28.

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data.

Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK.

Nucleic Acids Res. 2013 Oct;41(19):9033-48. doi: 10.1093/nar/gkt654. Epub 2013 Jul 30.

29.

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J.

BMC Genomics. 2012 Dec 27;13:734. doi: 10.1186/1471-2164-13-734.

30.

Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs.

Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE.

Genes Dev. 2012 Jul 1;26(13):1498-507. doi: 10.1101/gad.192732.112.

31.

Bioinformatic discovery of bacterial regulatory RNAs using SIPHT.

Livny J.

Methods Mol Biol. 2012;905:3-14. doi: 10.1007/978-1-61779-949-5_1.

PMID:
22735994
32.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

33.

RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.

Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK.

Cell Host Microbe. 2011 Aug 18;10(2):165-74. doi: 10.1016/j.chom.2011.07.007.

34.

NanoRNAs prime transcription initiation in vivo.

Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE.

Mol Cell. 2011 Jun 24;42(6):817-25. doi: 10.1016/j.molcel.2011.06.005.

35.

Identification of small RNAs in Francisella tularensis.

Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL.

BMC Genomics. 2010 Nov 10;11:625. doi: 10.1186/1471-2164-11-625.

36.

Legionella pneumophila 6S RNA optimizes intracellular multiplication.

Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7533-8. doi: 10.1073/pnas.0911764107. Epub 2010 Apr 5.

37.

Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis.

DiChiara JM, Contreras-Martinez LM, Livny J, Smith D, McDonough KA, Belfort M.

Nucleic Acids Res. 2010 Jul;38(12):4067-78. doi: 10.1093/nar/gkq101. Epub 2010 Feb 24.

38.

Mining regulatory 5'UTRs from cDNA deep sequencing datasets.

Livny J, Waldor MK.

Nucleic Acids Res. 2010 Mar;38(5):1504-14. doi: 10.1093/nar/gkp1121. Epub 2009 Dec 7.

39.

Pivotal role of the Francisella tularensis heat-shock sigma factor RpoH.

Grall N, Livny J, Waldor M, Barel M, Charbit A, Meibom KL.

Microbiology. 2009 Aug;155(Pt 8):2560-72. doi: 10.1099/mic.0.029058-0. Epub 2009 May 14.

40.

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.

Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A.

Nucleic Acids Res. 2009 Apr;37(6):e46. doi: 10.1093/nar/gkp080. Epub 2009 Feb 17.

41.

Identification and isolation of lysogens with induced prophage.

Livny J, Larock CN, Friedman DI.

Methods Mol Biol. 2009;501:253-65. doi: 10.1007/978-1-60327-164-6_22.

PMID:
19066826
42.

Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011.

Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G.

BMC Genomics. 2008 Sep 16;9:416. doi: 10.1186/1471-2164-9-416.

43.

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.

Livny J, Teonadi H, Livny M, Waldor MK.

PLoS One. 2008 Sep 12;3(9):e3197. doi: 10.1371/journal.pone.0003197. Erratum in: PLoS ONE. 2008;3(11). doi: 10.1371/annotation/a03e1870-1dd7-4c16-8c46-2268eeb2a50a.

45.

Distribution of centromere-like parS sites in bacteria: insights from comparative genomics.

Livny J, Yamaichi Y, Waldor MK.

J Bacteriol. 2007 Dec;189(23):8693-703. Epub 2007 Sep 28.

46.

Identification of small RNAs in diverse bacterial species.

Livny J, Waldor MK.

Curr Opin Microbiol. 2007 Apr;10(2):96-101. Epub 2007 Mar 23. Review.

PMID:
17383222
47.

Global gene expression and phenotypic analysis of a Vibrio cholerae rpoH deletion mutant.

Slamti L, Livny J, Waldor MK.

J Bacteriol. 2007 Jan;189(2):351-62. Epub 2006 Nov 3.

49.

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes.

Livny J, Fogel MA, Davis BM, Waldor MK.

Nucleic Acids Res. 2005 Jul 26;33(13):4096-105. Print 2005.

50.

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