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Structure-aware M. tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Fuzziness enables context dependence of protein interactions

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Protein structure prediction center in CASP8

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Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

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PROGRAM DESCRIPTION

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Host Evasion and Exploitation Schemes of Mycobacterium tuberculosis

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Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

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Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence

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Mutation in the Transcriptional Regulator PhoP Contributes to Avirulence of Mycobacterium tuberculosis H37Ra Strain

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De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic

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Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis

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Expression of Mycobacterium tuberculosis NLPC/p60 family protein Rv0024 induce biofilm formation and resistance against cell wall acting anti-tuberculosis drugs in Mycobacterium smegmatis

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Expression of Mycobacterium tuberculosis pe_pgrs33 is repressed during stationary phase and stress conditions, and its transcription is mediated by sigma factor A

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Rapid identification of veterinary-relevant Mycobacterium tuberculosis complex species using 16S rDNA, IS6110 and Regions of Difference-targeted dual-labelled hydrolysis probes

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Subversion of Retrograde Trafficking by Translocated Pathogen Effectors

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Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition

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Pyrazinamide Resistance Is Caused by Two Distinct Mechanisms: Prevention of Coenzyme A Depletion and Loss of Virulence Factor Synthesis

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The DinB Superfamily Includes Novel Mycothiol, Bacillithiol, and GlutathioneS-Transferases

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Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy

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Gene Ontology: tool for the unification of biology

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Pyrazinamide inhibits the eukaryotic-like fatty acid synthetase I (FASI) of Mycobacterium tuberculosis

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Substrate-bound structure of the E. coli multidrug resistance transporter MdfA

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The Mycobacterium tuberculosis regulatory network and hypoxia

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Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus

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In vivo gene silencing identifies the Mycobacterium tuberculosis proteasome as essential for the bacteria to persist in mice

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Targeting of host organelles by pathogenic bacteria: a sophisticated subversion strategy

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Within-host evolution of bacterial pathogens

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Pathogenesis of HIV-1 and Mycobacterium tuberculosis co-infection

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Membrane transport proteins: surprises in structural sameness

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Gene inversion potentiates bacterial evolvability and virulence

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PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase

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Anti-tubercular Activity of Pyrazinamide is Independent of trans-Translation and RpsA

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Mycobacterium tuberculosis Inhibits RAB7 Recruitment to Selectively Modulate Autophagy Flux in Macrophages

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Role of Cathepsins in Mycobacterium tuberculosis Survival in Human Macrophages

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Exosomes function in antigen presentation during an in vivo Mycobacterium tuberculosis infection

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Isotuberculosinol: the unusual case of an immunomodulatory diterpenoid from Mycobacterium tuberculosis

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

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Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c

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Structural basis for nuclear import of splicing factors by human Transportin 3

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In vivo transposition of mariner -based elements in enteric bacteria and mycobacteria

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Characterization and Inhibition of a Class II Diterpene Cyclase from Mycobacterium tuberculosis

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Crystal Structure and Computational Analyses Provide Insights into the Catalytic Mechanism of 2,4-Diacetylphloroglucinol Hydrolase PhlG from Pseudomonas fluorescens

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Characterization of a Carbon-Carbon Hydrolase from Mycobacterium tuberculosis Involved in Cholesterol Metabolism

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Proteolytic Activation of Human Cathepsin A

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Glutamine Binding Opens the Ammonia Channel and Activates Glucosamine-6P Synthase

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Crystal Structures and Site-directed Mutagenesis of a Mycothiol-dependent Enzyme Reveal a Novel Folding and Molecular Basis for Mycothiol-mediated Maleylpyruvate Isomerization

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BIOLOGICAL STUDIES OF THE TUBERCLE BACILLUS

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A Bayesian Sampler for Optimization of Protein Domain Hierarchies

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Simple topological properties predict functional misannotations in a metabolic network

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Relation between sequence and structure in membrane proteins

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Mode of action of pyrazinamide: disruption of Mycobacterium tuberculosis membrane transport and energetics by pyrazinoic acid

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‘Happy the man, who, studying nature's laws, Thro' known effects can trace the secret cause.’† Do we have enough pieces to solve the pyrazinamide puzzle?

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Non-Random Inversion Landscapes in Prokaryotic Genomes Are Shaped by Heterogeneous Selection Pressures

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UniProt: the Universal Protein knowledgebase

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Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes

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The HHpred interactive server for protein homology detection and structure prediction

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TM-align: a protein structure alignment algorithm based on the TM-score

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TB database: an integrated platform for tuberculosis research

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COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

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BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

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RefSeq microbial genomes database: new representation and annotation strategy

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Precision methylome characterization ofMycobacterium tuberculosiscomplex (MTBC) using PacBio single-molecule real-time (SMRT) technology

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OUP accepted manuscript

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KEGG: new perspectives on genomes, pathways, diseases and drugs

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CATH: an expanded resource to predict protein function through structure and sequence

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UniProt: the universal protein knowledgebase

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Expansion of the Gene Ontology knowledgebase and resources

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COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

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Type V secretion: mechanism(s) of autotransport through the bacterial outer membrane

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Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv

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PROCHECK: validation of protein-structure coordinates

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PROCHECK: a program to check the stereochemical quality of protein structures

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Multiple deletions in the polyketide synthase gene repertoire ofMycobacterium tuberculosisreveal functional overlap of cell envelope lipids in host-pathogen interactions

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aprABC : a Mycobacterium tuberculosis complex‐specific locus that modulates pH‐driven adaptation to the macrophage phagosome

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Efflux as a mechanism for drug resistance inMycobacterium tuberculosis: Table 1

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Phylogeny to function: PE / PPE protein evolution and impact on M ycobacterium tuberculosis pathogenicity

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The changes in mycolic acid structures caused by hadC mutation have a dramatic effect on the virulence of Mycobacterium tuberculosis

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A Fluoroquinolone Resistance Protein from Mycobacterium tuberculosis That Mimics DNA

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Pyrazinamide Inhibits Trans-Translation in Mycobacterium tuberculosis

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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

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Identification of Novel Mutations in LprG ( rv1411c ), rv0521 , rv3630 , rv0010c , ppsC , and cyp128 Associated with Pyrazinoic Acid/Pyrazinamide Resistance in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1128/aac.00529-10openalex-snapshot

Mutually Exclusive Genotypes for Pyrazinamide and 5-Chloropyrazinamide Resistance Reveal a Potential Resistance-Proofing Strategy

inferredcites →https://doi.org/10.1128/aac.00967-15openalex-snapshot

Uncoupling Environmental pH and Intrabacterial Acidification from Pyrazinamide Susceptibility in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1128/aac.02293-13openalex-snapshot

Energy Metabolism and Drug Efflux in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1128/aac.04028-14openalex-snapshot

Pantothenate and Pantetheine Antagonize the Antitubercular Activity of Pyrazinamide

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Transcriptional Profiling of Mycobacterium tuberculosis Exposed toIn VitroLysosomal Stress

inferredcites →https://doi.org/10.1128/iai.00207-11openalex-snapshot

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

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Identification of Autophagy-Inhibiting Factors of Mycobacterium tuberculosis by High-Throughput Loss-of-Function Screening

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Novel l -Cysteine-Dependent Maleylpyruvate Isomerase in the Gentisate Pathway of Paenibacillus sp. Strain NyZ101

inferredcites →https://doi.org/10.1128/jb.00166-10openalex-snapshot

Variation among Genome Sequences of H37Rv Strains of Mycobacterium tuberculosis from Multiple Laboratories

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A Genomic View of Sugar Transport inMycobacterium smegmatisandMycobacterium tuberculosis

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Mycobacterium tuberculosis Is Able To Accumulate and Utilize Cholesterol

inferredcites →https://doi.org/10.1128/jb.00935-15openalex-snapshot

Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks

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The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival

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Effects of Pyrazinamide on Fatty Acid Synthesis by Whole Mycobacterial Cells and Purified Fatty Acid Synthase I

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

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Intracellular Density of Wolbachia Is Mediated by Host Autophagy and the Bacterial Cytoplasmic Incompatibility Gene cifB in a Cell Type-Dependent Manner in Drosophila melanogaster

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Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis

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Identification of CTL Epitopes on Efflux Pumps of the ATP-Binding Cassette and the Major Facilitator Superfamily of Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1159/000454680openalex-snapshot

Natural Terpenes Influence the Activity of Antibiotics against Isolated Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1186/1471-2164-14-710openalex-snapshot

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression

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Evidence for symmetric chromosomal inversions around the replication origin in bacteria

inferredcites →https://doi.org/10.1186/s12864-015-2311-9openalex-snapshot

MycoBASE: expanding the functional annotation coverage of mycobacterial genomes

inferredcites →https://doi.org/10.1186/s12864-017-3687-5openalex-snapshot

SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.12688/wellcomeopenres.10036.2openalex-snapshot

Pathogenic mycobacteria achieve cellular persistence by inhibiting the Niemann-Pick Type C disease cellular pathway

inferredcites →https://doi.org/10.1371/journal.pcbi.1000605openalex-snapshot

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

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Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

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Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

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Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

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Simultaneous Analysis of Multiple Mycobacterium tuberculosis Knockdown Mutants In Vitro and In Vivo

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Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints

inferredcites →https://doi.org/10.1371/journal.pone.0034302openalex-snapshot

Annotation of the M. tuberculosis Hypothetical Orfeome: Adding Functional Information to More than Half of the Uncharacterized Proteins

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Creating an ignorance-base: Exploring known unknowns in the scientific literature

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Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates

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