CMR
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The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.
Description
More detailed information about this field from each metasource.
The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
Webpage:
http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgiWebpage
More detailed information about this field from each metasource.
http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
Publications:
Publications
More detailed information about this field from each metasource.
The Comprehensive Microbial Resource
PMID: 11125067
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
Publications
More detailed information about this field from each metasource.
The Comprehensive Microbial Resource
PMID: 11125067
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
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The Comprehensive Microbial Resource
PubMed citations: 190.
190 articles citing: The Comprehensive Microbial Resource
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Prediction of Horizontally and Widely Transferred Genes in Prokaryotes. PMID:30546254
Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens. PMID:30158907
Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred. PMID:29556740
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Differential Gene Expression in Response to Salinity and Temperature in a Haloarcula Strain from Great Salt Lake, Utah. PMID:29361787
A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. PMID:27899536
In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes. PMID:27793092
Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog. PMID:27683573
Resistance Mutations in gyrA and parC are Common in Escherichia Communities of both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments. PMID:26696975
Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India. PMID:26498929
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. PMID:25968644
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. PMID:25765281
Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. PMID:25421055
Genetic mechanisms underlying the pathogenicity of cold-stressed Salmonella enterica serovar typhimurium in cultured intestinal epithelial cells. PMID:25192993
Towards an informative mutant phenotype for every bacterial gene. PMID:25112473
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. PMID:24865553
PhoB activates Escherichia coli O157:H7 virulence factors in response to inorganic phosphate limitation. PMID:24710330
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. PMID:24607996
Haemophilus ducreyi Hfq contributes to virulence gene regulation as cells enter stationary phase. PMID:24520065
Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000. PMID:24516535
Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium. PMID:24015186
Measurements of mRNA degradation in Borrelia burgdorferi. PMID:23974029
Genetic determinants of swimming motility in the squid light-organ symbiont Vibrio fischeri. PMID:23907990
Whole-genome transcriptional analysis of Escherichia coli during heat inactivation processes related to industrial cooking. PMID:23770902
Prediction of molecular mimicry candidates in human pathogenic bacteria. PMID:23715053
Evidence for late resolution of the aux codon box in evolution. PMID:23696642
Indirect and suboptimal control of gene expression is widespread in bacteria. PMID:23591776
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites. PMID:23578135
Biochemistry and physiology of the β class carbonic anhydrase (Cpb) from Clostridium perfringens strain 13. PMID:23475974
Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa. PMID:23354714
Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans. PMID:23354702
Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium. PMID:23226353
TIGRFAMs and Genome Properties in 2013. PMID:23197656
Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. PMID:23148582
GenoSets: visual analytic methods for comparative genomics. PMID:23056299
Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PMID:22952675
Comparative transcriptomics of H. pylori strains AM5, SS1 and their hpyAVIBM deletion mutants: possible roles of cytosine methylation. PMID:22879937
Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness. PMID:22843519
Structural analysis of hypothetical proteins from Helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins. PMID:22837682
Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes. PMID:22223756
Listeria monocytogenes mutants with altered growth phenotypes at refrigeration temperature and high salt concentrations. PMID:22179239
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PMID:22125499
Untwisting of the DNA helix stimulates the endonuclease activity of Bacillus subtilis Nth at AP sites. PMID:21954439
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. PMID:21867535
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data. PMID:21840390
iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. PMID:21777427
Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. PMID:21746949
The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. PMID:21597881
Finding subtypes of transcription factor motif pairs with distinct regulatory roles. PMID:21486752
Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PMID:21437252
The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments. PMID:21255338
Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry. PMID:21189417
COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. PMID:21149270
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. PMID:20929876
Studies on a novel serine protease of a ΔhapAΔprtV Vibrio cholerae O1 strain and its role in hemorrhagic response in the rabbit ileal loop model. PMID:20927349
A systematic study of genome context methods: calibration, normalization and combination. PMID:20920312
Economy of operon formation: cotranscription minimizes shortfall in protein complexes. PMID:20877578
Identification and characterization of two families of F420 H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation. PMID:20807200
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. PMID:20627862
Correlations between bacterial ecology and mobile DNA. PMID:20577742
Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. PMID:20537180
Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation. PMID:20515462
Revisiting the assignment of Rv0241c to fatty acid synthase type II of Mycobacterium tuberculosis. PMID:20511508
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
The Scottish Structural Proteomics Facility: targets, methods and outputs. PMID:20419351
Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. PMID:20333228
DraGnET: software for storing, managing and analyzing annotated draft genome sequence data. PMID:20175920
Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. PMID:20167116
Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs. PMID:20141640
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. PMID:20102603
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. PMID:19955237
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. PMID:19906735
The evolution of RecD outside of the RecBCD complex. PMID:19841849
Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance. PMID:19798411
Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. PMID:19703284
A comparative genomics, network-based approach to understanding virulence in Vibrio cholerae. PMID:19666715
Cj0596 is a periplasmic peptidyl prolyl cis-trans isomerase involved in Campylobacter jejuni motility, invasion, and colonization. PMID:19664234
Modulation of gene expression in Actinobacillus pleuropneumoniae exposed to bronchoalveolar fluid. PMID:19578537
What we can learn about Escherichia coli through application of Gene Ontology. PMID:19576778
Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. PMID:19495914
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PMID:19277208
Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. PMID:19251847
Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). PMID:19241370
The Thermotoga maritima Trk potassium transporter--from frameshift to function. PMID:19168617
Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells. PMID:19139196
Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PMID:19132092
Reconstruction of biochemical networks in microorganisms. PMID:19116616
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family. PMID:19102758
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. PMID:19077236
A bioinformatician's guide to metagenomics. PMID:19052320
Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant. PMID:19038054
CoCoNUT: an efficient system for the comparison and analysis of genomes. PMID:19014477
Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily. PMID:19011751
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. PMID:18978025
The Helicobacter pylori HpyAXII restriction-modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components. PMID:18978016
Tn7 elements: engendering diversity from chromosomes to episomes. PMID:18951916
OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. PMID:18948290
Metabolic function of Corynebacterium glutamicum aminotransferases AlaT and AvtA and impact on L-valine production. PMID:18931286
Rare codons cluster. PMID:18923675
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. PMID:18842600
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. PMID:18840283
Dynamic localization of MreB in Vibrio parahaemolyticus and in the ectopic host bacterium Escherichia coli. PMID:18791022
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. PMID:18767192
Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence. PMID:18705888
Global gene expression as a function of the iron status of the bacterial cell: influence of differentially expressed genes in the virulence of the human pathogen Vibrio vulnificus. PMID:18573903
Onto-CC: a web server for identifying Gene Ontology conceptual clusters. PMID:18544607
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. PMID:18416670
PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes. PMID:18366802
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. PMID:18366731
Replacement of the arginine biosynthesis operon in Xanthomonadales by lateral gene transfer. PMID:18305979
A temperature-regulated Campylobacter jejuni gluconate dehydrogenase is involved in respiration-dependent energy conservation and chicken colonization. PMID:18284594
GenoList: an integrated environment for comparative analysis of microbial genomes. PMID:18032431
e-Fungi: a data resource for comparative analysis of fungal genomes. PMID:18028535
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. PMID:17965431
Metagenomic characterization of Chesapeake Bay virioplankton. PMID:17921274
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. PMID:17877794
Redox stress proteins are involved in adaptation response of the hyperthermoacidophilic archaeon Sulfolobus solfataricus to nickel challenge. PMID:17692131
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. PMID:17690205
The protein network of bacterial motility. PMID:17667950
A survey of orphan enzyme activities. PMID:17623104
The chlamydial invasin-like protein gene conundrum. PMID:17533147
Identification of two Mycobacterium smegmatis lipoproteins exported by a SecA2-dependent pathway. PMID:17496088
Genomic methylation: a tool for typing Helicobacter pylori isolates. PMID:17483255
YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica. PMID:17400740
Small RNA regulators and the bacterial response to stress. PMID:17381274
Transcriptional profiling of Actinobacillus pleuropneumoniae under iron-restricted conditions. PMID:17355629
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology. PMID:17323930
Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. PMID:17295908
Mechanisms of adaptation to nitrosative stress in Bacillus subtilis. PMID:17293416
Performance of the translational apparatus varies with the ecological strategies of bacteria. PMID:17277058
Genome re-annotation: a wiki solution? PMID:17274839
Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. PMID:17194796
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. PMID:17151080
Operon prediction in Pyrococcus furiosus. PMID:17148478
PATRIC: the VBI PathoSystems Resource Integration Center. PMID:17142235
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. PMID:17135193
Operon prediction for sequenced bacterial genomes without experimental information. PMID:17122389
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PMID:17112314
Identification of Helicobacter pylori genes that contribute to stomach colonization. PMID:17101654
MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization. PMID:17044936
Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima. PMID:16980482
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. PMID:16930487
BBP: Brucella genome annotation with literature mining and curation. PMID:16842628
A Vibrio cholerae protease needed for killing of Caenorhabditis elegans has a role in protection from natural predator grazing. PMID:16754867
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. PMID:16751553
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PMID:16710450
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
BioWarehouse: a bioinformatics database warehouse toolkit. PMID:16556315
Genetic and transcriptional analysis of the siderophore malleobactin biosynthesis and transport genes in the human pathogen Burkholderia pseudomallei K96243. PMID:16452439
The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. PMID:16391122
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. PMID:16381888
The Gene Set Builder: collation, curation, and distribution of sets of genes. PMID:16371163
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PMID:16292354
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. PMID:16246909
Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes. PMID:16237015
Successful selection of cross-protective vaccine candidates for Ornithobacterium rhinotracheale infection. PMID:16177359
Highways of gene sharing in prokaryotes. PMID:16176988
Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PMID:16176121
Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PMID:16118665
Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. PMID:16077009
The MicrobesOnline Web site for comparative genomics. PMID:15998914
Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium. PMID:15995201
BASys: a web server for automated bacterial genome annotation. PMID:15980511
Proteomics for biodefense applications: progress and opportunities. PMID:15892565
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. PMID:15752426
Specialized microbial databases for inductive exploration of microbial genome sequences. PMID:15698474
Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen. PMID:15618144
AMPDB: the Arabidopsis Mitochondrial Protein Database. PMID:15608271
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. PMID:15608211
BacMap: an interactive picture atlas of annotated bacterial genomes. PMID:15608206
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. PMID:15514110
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PMID:15383840
Comparative immunopeptidomics of humans and their pathogens. PMID:15326311
Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. PMID:15155910
Trends between gene content and genome size in prokaryotic species with larger genomes. PMID:14973198
Functional selection of vaccine candidate peptides from Staphylococcus aureus whole-genome expression libraries in vitro. PMID:12874343
PROBEmer: A web-based software tool for selecting optimal DNA oligos. PMID:12824409
Comparing bacterial genomes through conservation profiles. PMID:12695324
A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. PMID:12566398
MBGD: microbial genome database for comparative analysis. PMID:12519947
Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry. PMID:12444920
The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. PMID:12399492
The genome of M. acetivorans reveals extensive metabolic and physiological diversity. PMID:11932238
AraC-XylS database: a family of positive transcriptional regulators in bacteria. PMID:11752325
TIGRFAMs: a protein family resource for the functional identification of proteins. PMID:11125044
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Tags
More detailed information about this field from each metasource.
sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
whole genome sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.439109
Tags
More detailed information about this field from each metasource.
sequencing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
whole genome sequencing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.439109
sequencing genomics whole genome sequencing comparative genomics
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