Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs

(2020) Marco Jost et al.   NATURE BIOTECHNOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

New 2-Ethylthio-4-methylaminoquinazoline derivatives inhibiting two subunits of cytochrome bc1 in Mycobacterium tuberculosis

(2020) Andréanne Lupien et al.   PLoS Pathogens

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

(2020) Daniel J Wilson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Redefining fundamental concepts of transcription initiation in bacteria

(2020) Citlalli Mejía-Almonte et al.   NATURE REVIEWS GENETICS

Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis

(2020) John S. Hawkins et al.   Cell Systems

A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth

(2020) Andrew D Mathis et al.   NUCLEIC ACIDS RESEARCH

Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism

(2020) Stefano Donati et al.   Cell Systems

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

Large-scale chemical–genetics yields new M. tuberculosis inhibitor classes

(2019) Eachan O. Johnson et al.   NATURE

Identification of new components of the RipC-FtsEX cell separation pathway of Corynebacterineae

(2019) Hoong Chuin Lim et al.   PLoS Genetics

Tuberculosis drug discovery in the CRISPR era

(2019) Jeremy Rock   PLoS Pathogens

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage

(2019) Rebecca R. Stanway et al.   CELL

Genome-wide Phenotypic Profiling Identifies and Categorizes Genes Required for Mycobacterial Low Iron Fitness

(2019) Marte S. Dragset et al.   Scientific Reports

Antimalarial activity of single-dose DSM265, a novel plasmodium dihydroorotate dehydrogenase inhibitor, in patients with uncomplicated Plasmodium falciparum or Plasmodium vivax malaria infection: a proof-of-concept, open-label, phase 2a study

(2018) Alejandro Llanos-Cuentas et al.   LANCET INFECTIOUS DISEASES

Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

(2018) Antoine Vigouroux et al.   Molecular Systems Biology

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

(2018) Lun Cui et al.   Nature Communications

TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities

(2018) Allison F. Carey et al.   PLoS Pathogens

Targeting the Proteostasis Network for Mycobacterial Drug Discovery

(2018) Tania J. Lupoli et al.   ACS Infectious Diseases

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

(2018) François Rousset et al.   PLoS Genetics

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

(2017) Evan A. Boyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis

(2017) Michael A. DeJesus et al.   mBio

Crosstalk between transcription and metabolism: how much enzyme is enough for a cell?

(2017) Stefano Donati et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

(2017) Byoung-Mo Koo et al.   Cell Systems

Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform

(2017) Jeremy M. Rock et al.   Nature Microbiology

Imidazo[1,2-a]Pyridine-3-Carboxamides Are Active Antimicrobial Agents against Mycobacterium avium InfectionIn Vivo

(2016) Garrett C. Moraski et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

(2016) Leeat Keren et al.   CELL

Investigating essential gene function inMycobacterium tuberculosisusing an efficient CRISPR interference system

(2016) Atul K. Singh et al.   NUCLEIC ACIDS RESEARCH

Validation of CoaBC as a Bactericidal Target in the Coenzyme A Pathway of Mycobacterium tuberculosis

(2016) Joanna C. Evans et al.   ACS Infectious Diseases

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis

(2015) Olga T. Schubert et al.   Cell Host & Microbe

Gene silencing by CRISPR interference in mycobacteria

(2015) Eira Choudhary et al.   Nature Communications

Structure, Activity, and Inhibition of the Carboxyltransferase β-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis

(2014) Manchi C. M. Reddy et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A Novel Inhibitor of Gyrase B Is a Potent Drug Candidate for Treatment of Tuberculosis and Nontuberculosis Mycobacterial Infections

(2014) Christopher P. Locher et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Respiratory Flexibility in Response to Inhibition of CytochromecOxidase in Mycobacterium tuberculosis

(2014) Kriti Arora et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Metabolic and Bactericidal Effects of Targeted Suppression of NadD and NadE Enzymes in Mycobacteria

(2014) I. A. Rodionova et al.   mBio

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Discovery of Q203, a potent clinical candidate for the treatment of tuberculosis

(2013) Kevin Pethe et al.   NATURE MEDICINE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

Depletion of antibiotic targets has widely varying effects on growth

(2011) J.-R. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism

(2011) Jennifer E. Griffin et al.   PLoS Pathogens

SnapShot: The Replisome

(2010) Nina Y. Yao et al.   CELL

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

The spectrum of latent tuberculosis: rethinking the biology and intervention strategies

(2009) Clifton E. Barry et al.   NATURE REVIEWS MICROBIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Biosynthesis and Recycling of Nicotinamide Cofactors inMycobacterium tuberculosis

(2008) Helena I. M. Boshoff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY