Published in PLoS One on March 20, 2012
A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol Cell Proteomics (2013) 0.85
Latent Tuberculosis: Models, Computational Efforts and the Pathogen's Regulatory Mechanisms during Dormancy. Front Bioeng Biotechnol (2013) 0.85
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics (2015) 0.79
Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling. Gut Pathog (2013) 0.77
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature (1998) 60.62
Lethality and centrality in protein networks. Nature (2001) 29.64
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol (2003) 16.82
The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A (1999) 16.35
Tuberculosis: commentary on a reemergent killer. Science (1992) 14.51
Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol (1969) 13.14
A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science (2004) 13.04
Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. J Exp Med (2003) 10.67
Maps of random walks on complex networks reveal community structure. Proc Natl Acad Sci U S A (2008) 10.42
Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol (2002) 9.97
Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci (1998) 9.94
Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci U S A (2003) 9.15
Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol (2002) 8.90
Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med (2003) 7.99
Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha -crystallin. Proc Natl Acad Sci U S A (2001) 7.65
EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res (2008) 7.05
Modular organization of cellular networks. Proc Natl Acad Sci U S A (2003) 6.24
Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol Microbiol (2003) 5.68
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology (2002) 5.17
Role of the major antigen of Mycobacterium tuberculosis in cell wall biogenesis. Science (1997) 4.96
Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc Natl Acad Sci U S A (2005) 4.43
Tuberculosis - metabolism and respiration in the absence of growth. Nat Rev Microbiol (2005) 4.38
Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin Microbiol Rev (2003) 4.14
Getting the noise out of gene arrays. Science (2004) 3.91
Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) (2004) 3.70
Tuberculosis: a problem with persistence. Nat Rev Microbiol (2003) 3.17
Boolean network model predicts cell cycle sequence of fission yeast. PLoS One (2008) 3.05
Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol Microbiol (2002) 2.91
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol (2004) 2.83
Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect Immun (2003) 2.79
Two sensor kinases contribute to the hypoxic response of Mycobacterium tuberculosis. J Biol Chem (2004) 2.71
Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. Proc Natl Acad Sci U S A (2007) 2.55
Dormancy phenotype displayed by extracellular Mycobacterium tuberculosis within artificial granulomas in mice. J Exp Med (2004) 2.46
The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro. Mol Microbiol (2008) 2.44
Gene expression profile of Mycobacterium tuberculosis in a non-replicating state. Tuberculosis (Edinb) (2004) 2.33
A logical model provides insights into T cell receptor signaling. PLoS Comput Biol (2007) 2.25
Mycobacterial persistence: adaptation to a changing environment. Trends Microbiol (2001) 2.13
Boolean network simulations for life scientists. Source Code Biol Med (2008) 2.05
Bacterial growth and cell division: a mycobacterial perspective. Microbiol Mol Biol Rev (2008) 2.01
Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics (2005) 1.94
Multidrug and extensively drug-resistant TB (M/XDR-TB): problems and solutions. Indian J Tuberc (2010) 1.92
GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems (2006) 1.85
Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol Biol Cell (2004) 1.73
Letting sleeping dos lie: does dormancy play a role in tuberculosis? Annu Rev Microbiol (2010) 1.66
The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. Tuberculosis (Edinb) (2004) 1.58
Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein. J Bacteriol (2005) 1.57
whmD is an essential mycobacterial gene required for proper septation and cell division. Proc Natl Acad Sci U S A (2000) 1.57
The rpf gene of Micrococcus luteus encodes an essential secreted growth factor. Mol Microbiol (2002) 1.56
The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol Syst Biol (2008) 1.56
Escherichia coli mutants lacking NADH dehydrogenase I have a competitive disadvantage in stationary phase. J Bacteriol (1993) 1.55
Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PLoS Comput Biol (2005) 1.55
Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics (2003) 1.41
Deletion of the Mycobacterium tuberculosis alpha-crystallin-like hspX gene causes increased bacterial growth in vivo. Infect Immun (2006) 1.38
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res (2003) 1.31
Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Res (2007) 1.23
Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J Biol Chem (2007) 1.17
Serine threonine protein kinases of mycobacterial genus: phylogeny to function. Physiol Genomics (2006) 1.12
The whcE gene of Corynebacterium glutamicum is important for survival following heat and oxidative stress. Biochem Biophys Res Commun (2005) 1.08
Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis. BMC Genomics (2009) 1.06
The crystal and solution structure of a putative transcriptional antiterminator from Mycobacterium tuberculosis. Structure (2004) 0.97
Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages. Mol Biosyst (2009) 0.92
Immunological diversity within a family of cutinase-like proteins of Mycobacterium tuberculosis. Vaccine (2008) 0.91
Mapping conformational transitions in cyclic AMP receptor protein: crystal structure and normal-mode analysis of Mycobacterium tuberculosis apo-cAMP receptor protein. Biophys J (2010) 0.87
A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system. PLoS One (2010) 0.83
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics (2009) 2.13
Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes. PLoS One (2008) 1.73
Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics (2007) 1.50
Metagenome of the gut of a malnourished child. Gut Pathog (2011) 1.39
The PPE18 of Mycobacterium tuberculosis interacts with TLR2 and activates IL-10 induction in macrophage. J Immunol (2009) 1.32
The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr Drug Targets Infect Disord (2002) 1.28
SPHINX--an algorithm for taxonomic binning of metagenomic sequences. Bioinformatics (2010) 1.25
Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Res (2007) 1.23
The unusual chaperonins of Mycobacterium tuberculosis. Tuberculosis (Edinb) (2005) 1.13
Functional studies of multiple thioredoxins from Mycobacterium tuberculosis. J Bacteriol (2008) 1.12
Conformational flexibility of Mycobacterium tuberculosis thioredoxin reductase: crystal structure and normal-mode analysis. Acta Crystallogr D Biol Crystallogr (2005) 1.09
Crystal structure of the 65-kilodalton heat shock protein, chaperonin 60.2, of Mycobacterium tuberculosis. J Bacteriol (2004) 1.07
Mycobacterium tuberculosis GroEL homologues unusually exist as lower oligomers and retain the ability to suppress aggregation of substrate proteins. J Mol Biol (2004) 1.06
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences. BMC Bioinformatics (2010) 1.06
PAR-3D: a server to predict protein active site residues. Nucleic Acids Res (2007) 1.05
Chimeric Vitreoscilla hemoglobin (VHb) carrying a flavoreductase domain relieves nitrosative stress in Escherichia coli: new insight into the functional role of VHb. Appl Environ Microbiol (2002) 1.01
Facilitated oligomerization of mycobacterial GroEL: evidence for phosphorylation-mediated oligomerization. J Bacteriol (2009) 1.01
Multiple gene duplication and rapid evolution in the groEL gene: functional implications. J Mol Evol (2006) 1.00
A novel nucleoid-associated protein of Mycobacterium tuberculosis is a sequence homolog of GroEL. Nucleic Acids Res (2009) 0.99
Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein. J Mol Biol (2008) 0.96
Involvement of a nine-residue loop of streptokinase in the generation of macromolecular substrate specificity by the activator complex through interaction with substrate kringle domains. J Biol Chem (2002) 0.96
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences. BMC Genomics (2011) 0.95
HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences. BMC Bioinformatics (2011) 0.94
INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms. J Biosci (2010) 0.92
Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages. Mol Biosyst (2009) 0.92
Dynamic changes in protein functional linkage networks revealed by integration with gene expression data. PLoS Comput Biol (2008) 0.91
Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols. Acta Crystallogr D Biol Crystallogr (2005) 0.90
TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences. Gene (2012) 0.89
Mapping conformational transitions in cyclic AMP receptor protein: crystal structure and normal-mode analysis of Mycobacterium tuberculosis apo-cAMP receptor protein. Biophys J (2010) 0.87
Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins (2008) 0.87
Expression, purification, crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis thioredoxin reductase. Acta Crystallogr D Biol Crystallogr (2004) 0.86
Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system. PLoS One (2011) 0.86
Site-directed mutagenesis reveals a novel catalytic mechanism of Mycobacterium tuberculosis alkylhydroperoxidase C. Biochem J (2002) 0.85
Human recombinant resistin protein displays a tendency to aggregate by forming intermolecular disulfide linkages. Biochemistry (2003) 0.85
DELIMINATE--a fast and efficient method for loss-less compression of genomic sequences: sequence analysis. Bioinformatics (2012) 0.85
Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets. J Biosci (2011) 0.84
Function of the 90-loop (Thr90-Glu100) region of staphylokinase in plasminogen activation probed through site-directed mutagenesis and loop deletion. Biochem J (2002) 0.82
The crystal structure of Mycobacterium tuberculosis NrdH at 0.87 Å suggests a possible mode of its activity. Biochemistry (2013) 0.81
Structure of Mycobacterium tuberculosis chaperonin-10 at 3.5 A resolution. Acta Crystallogr D Biol Crystallogr (2002) 0.81
Mathematical modeling of regulation of type III secretion system in Salmonella enterica serovar Typhimurium by SirA. In Silico Biol (2009) 0.80
Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis CRP/FNR family transcription regulator. Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 0.80
The 2.15 A crystal structure of Mycobacterium tuberculosis chorismate mutase reveals an unexpected gene duplication and suggests a role in host-pathogen interactions. Biochemistry (2006) 0.80
Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes. Genomics (2013) 0.79
C16S - a Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences. Genomics (2012) 0.79
Mycobacterium tuberculosis heat shock protein 60 modulates immune response to PPD by manipulating the surface expression of TLR2 on macrophages. Cell Microbiol (2008) 0.78
FQC: A novel approach for efficient compression, archival, and dissemination of fastq datasets. J Bioinform Comput Biol (2015) 0.78
Modelling of the regulation of the hilA promoter of type three secretion system of Salmonella enterica serovar Typhimurium. Syst Synth Biol (2007) 0.77
i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets. BMC Genomics (2011) 0.77
Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis chorismate mutase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.77
Structural biology of Mycobacterium tuberculosis proteins: the Indian efforts. Tuberculosis (Edinb) (2011) 0.77
Multiple chaperonins in bacteria--novel functions and non-canonical behaviors. Cell Stress Chaperones (2015) 0.77
Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets. J Biomol Struct Dyn (2012) 0.75
Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network. Genome Res (2011) 0.75
BIND - an algorithm for loss-less compression of nucleotide sequence data. J Biosci (2012) 0.75
Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly. J Bioinform Comput Biol (2015) 0.75
In silico dissection of Type VII Secretion System components across bacteria: New directions towards functional characterization. J Biosci (2016) 0.75
FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information. J Biosci (2015) 0.75
Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework. J Biosci (2016) 0.75
Identification of conserved residue patterns in small beta-barrel proteins. Protein Eng (2002) 0.75
Cation-mediated interplay of loops in chaperonin-10. J Biomol Struct Dyn (2006) 0.75