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Molecular Biology

D-Index
47
Citations
10254
World Ranking
2732
National Ranking
1322

Overview

Jonathan Livny is affiliated with the Broad Institute in the United States. Their research spans multiple fields, primarily within Medicine and Biochemistry, Genetics, and Molecular Biology. The work focuses on several subfields, including Infectious Diseases, Molecular Biology, Pharmacology, Ecology, and Biomedical Engineering.

The scientist has contributed to topics such as SARS-CoV-2 and COVID-19 research, SARS-CoV-2 detection and testing, bacteriophages and microbial interactions, gut microbiota and health, genomics and phylogenetic studies, COVID-19 clinical research studies, and antibiotic resistance in bacteria.

Notable recent papers include:

  • Best practices on the differential expression analysis of multi-species RNA-seq, 2021, Genome Biology
  • Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome, 2023, Nature Microbiology
  • SARS-CoV-2 antibody persistence in COVID-19 convalescent plasma donors: Dependency on assay format and applicability to serosurveillance, 2021, Transfusion
  • Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics, 2021, eLife
  • Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays, 2022, PNAS Nexus

Jonathan Livny frequently publishes in venues such as bioRxiv (Cold Spring Harbor Laboratory), Open Forum Infectious Diseases, Genome Biology, Nature Microbiology, and Transfusion.

Their work involves collaboration with several co-authors, including Deborah T. Hung, Peijun Ma, Marek Orzechowski, Ashlee M. Earl, and Roby P. Bhattacharyya.

Best Publications

  • Nucleic acid detection with CRISPR-Cas13a/C2c2

    Jonathan S. Gootenberg;Omar O. Abudayyeh;Jeong Wook Lee;Patrick Essletzbichler

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

    M. Poyet;M. Poyet;M. Groussin;M. Groussin;S. M. Gibbons;J. Avila-Pacheco

  • Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli

    Patrick L. Wagner;Jonathan Livny;Melody N. Neely;David W. K. Acheson

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

    Alexander A Shishkin;Georgia Giannoukos;Alper Kucukural;Dawn Ciulla

  • Distribution of Centromere-Like parS Sites in Bacteria: Insights from Comparative Genomics

    Jonathan Livny;Yoshiharu Yamaichi;Matthew K. Waldor

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

    Georgia Giannoukos;Dawn M Ciulla;Katherine Huang;Brian J Haas

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

    Brian J Haas;Melissa Chin;Chad Nusbaum;Bruce W Birren

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

    Jonathan Livny;Hidayat Teonadi;Miron Livny;Matthew K. Waldor

  • Identification of small RNAs in diverse bacterial species.

    Jonathan Livny;Matthew K Waldor

  • RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression

    Anjali Mandlik;Jonathan Livny;Jonathan Livny;Jonathan Livny;William P. Robins;Jennifer M. Ritchie;Jennifer M. Ritchie

  • Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2

    Jonathan Livny;Anja Brencic;Stephen Lory;Matthew K. Waldor

  • TargetRNA2: identifying targets of small regulatory RNAs in bacteria

    Mary Beth Kery;Monica Feldman;Jonathan Livny;Brian Tjaden

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

    Jane M. Liu;Jonathan Livny;Michael S. Lawrence;Marc D. Kimball

  • Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system

    Jonathan Livny;David I. Friedman

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

    Jeanne M. DiChiara;Lydia M. Contreras-Martinez;Jonathan Livny;Dorie Smith

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

    Henry L. Schreiber;Henry L. Schreiber;Matt S. Conover;Wen Chi Chou;Michael E. Hibbing

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

    Michael C. Chao;Justin R. Pritchard;Yanjia J. Zhang;Eric J. Rubin

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

    Jonathan Livny;Michael A. Fogel;Brigid M. Davis;Matthew K. Waldor

  • NanoRNAs prime transcription initiation in vivo

    Seth R. Goldman;Josh S. Sharp;Irina O. Vvedenskaya;Jonathan Livny;Jonathan Livny

  • Mining regulatory 5′UTRs from cDNA deep sequencing datasets

    Jonathan Livny;Matthew K. Waldor

Frequent Co-Authors

Deborah T. Hung
Deborah T. Hung Harvard University
Matthew K. Waldor
Matthew K. Waldor Harvard Medical School
Scott J. Hultgren
Scott J. Hultgren Washington University in St. Louis
Ashlee M. Earl
Ashlee M. Earl Broad Institute
Alain Charbit
Alain Charbit Université Paris Cité
Marco Colonna
Marco Colonna Washington University in St. Louis
Aviv Regev
Aviv Regev Genentech
David I. Friedman
David I. Friedman University of Michigan–Ann Arbor
Andreas Gnirke
Andreas Gnirke Broad Institute
Pardis C. Sabeti
Pardis C. Sabeti Harvard University

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