Clusters of Orthologous Groups (COG) Analysis Ontology

Names
More detailed information about this field from each metasource.

Clusters of Orthologous Groups (COG) Analysis Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

metasource: Biontology / Bioportal
version: 1.4 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CAO

CAO
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

metasource: Biontology / Bioportal
version: 1.4 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CAO

Other names: CAO

CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test. It is used for the ontology based application for statistical analysis on COG db.

Webpage:

http://sourceforge.net/projects/cao/

Publications:

Publications
More detailed information about this field from each metasource.

A genomic perspective on protein families
PMID: 9381173
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

http://www.hegroup.org/docs/OntoCOG_ICBO-2011_Proceeding.pdf
metasource: Biontology / Bioportal
version: 1.4 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CAO

A genomic perspective on protein families PubMed citations: 1542.

1542 articles citing: A genomic perspective on protein families

Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. PMID:35889115
Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish. PMID:35817827
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants' stool samples in Argentina. PMID:35804311
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. PMID:35733954
Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria. PMID:35704763
Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes. PMID:35638784
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. PMID:35610035
Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior. PMID:35563985
Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition. PMID:35435751
Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins. PMID:35377869
Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. PMID:35343764
Biomarkers of connective tissue disease-associated interstitial lung disease in bronchoalveolar lavage fluid: A label-free mass spectrometry-based relative quantification study. PMID:35334492
Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. PMID:35328479
Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome. PMID:35310842
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. PMID:35285712
Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency. PMID:35217614
The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome. PMID:35208722
Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. PMID:35154027
Genome Sequence of Dermacoccus Strain Tok2021, a Soil Actinobacterium Isolated from a Pinus radiata Forest. PMID:35112892
Differential word expression analyses highlight plague dynamics during the second pandemic. PMID:35070338
Identification of the Talaromyces cellulolyticus Gene Encoding an Extracellular Enzyme with β-galactosidase Activity and Testing it as a Reporter for Gene Expression Assays. PMID:35059977
Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. PMID:35048381
Pathogen resistance in Sphagneticola trilobata (Singapore daisy): molecular associations and differentially expressed genes in response to disease from a widespread fungus. PMID:35031940
Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. PMID:35028595
Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates. PMID:34982234
Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture. PMID:34946025
Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis. PMID:34893690
Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). PMID:34862931
In Silico Survey and Characterization of Babesia microti Functional and Non-Functional Proteases. PMID:34832610
Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. PMID:34817803
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Nutrition, Inflammation, and the Gut Microbiota among Outpatients with Active Tuberculosis Disease in India. PMID:34662867
Identifying the presence of bacteria on digital images by using asymmetric distribution with k-means clustering algorithm. PMID:34658529
Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. PMID:34603269
Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.). PMID:34579481
Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1. PMID:34566929
Coupling of spliceosome complexity to intron diversity. PMID:34555349
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. PMID:34525942
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi. PMID:34468307
Functional Genomic Insights into Probiotic Bacillus siamensis Strain B28 from Traditional Korean Fermented Kimchi. PMID:34441683
Proteomic analysis of microtubule inner proteins (MIPs) in Rib72 null Tetrahymena cells reveals functional MIPs. PMID:34406789
RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis). PMID:34388962
Transcriptome-wide identification and expression profiling of the ERF gene family suggest roles as transcriptional activators and repressors of fruit ripening in durian. PMID:34375337
The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System. PMID:34361895
Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52. PMID:34349810
Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. PMID:34319226
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. PMID:34315882
Metabolome and transcriptome profiling provide insights into green apple peel reveals light- and UV-B-responsive pathway in anthocyanins accumulation. PMID:34303342
Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort. PMID:34278055
Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes. PMID:34253028
DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors. PMID:34163149
Decreased Abundance of Akkermansia muciniphila Leads to the Impairment of Insulin Secretion and Glucose Homeostasis in Lean Type 2 Diabetes. PMID:34085773
Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus). PMID:34070532
The holobiont transcriptome of teneral tsetse fly species of varying vector competence. PMID:34058984
Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils. PMID:34012103
Complete chloroplast genome sequencing of Job's tears (Coix L.): genome structure, comparative analysis, and phylogenetic relationships. PMID:33948493
Nocardioides luti sp. nov., belonging to the family Nocardioidaceae isolated from kaolinite, exhibiting the biosynthesis potential of alkylresorcinol. PMID:33864547
Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity. PMID:33828147
Functional Annotation Genome Unravels Potential Probiotic Bacillus velezensis Strain KMU01 from Traditional Korean Fermented Kimchi. PMID:33803098
The first complete mitochondrial genome of eggplant (Solanum melongena). PMID:33763537
Non-essential ribosomal proteins in bacteria and archaea identified using COGs. PMID:33753464
Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome. PMID:33749576
De novo transcriptome assembly of transgenic tobacco (Nicotiana tabacum NC89) with early senescence characteristic. PMID:33707866
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
De Novo Transcriptome Assembly of Two Microsorum Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids. PMID:33669861
Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids. PMID:33659675
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PMID:33630960
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. PMID:33606106
Tumor-infiltrating dendritic cell states are conserved across solid human cancers. PMID:33601412
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. PMID:33558686
B. adolescentis ameliorates chronic colitis by regulating Treg/Th2 response and gut microbiota remodeling. PMID:33557671
Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304
Evolutionary Trajectory of the Replication Mode of Bacterial Replicons. PMID:33500342
The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae). PMID:33473525
PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PMID:33392435
Geochemical transition zone powering microbial growth in subsurface sediments. PMID:33288718
Zygosaccharomyces rouxii, an Aromatic Yeast Isolated From Chili Sauce, Is Able to Biosynthesize 2-Phenylethanol via the Shikimate or Ehrlich Pathways. PMID:33250885
Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees. PMID:33238067
The Order of Trait Emergence in the Evolution of Cyanobacterial Multicellularity. PMID:33231627
The expanding world of plant J-domain proteins. PMID:33223602
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics. PMID:33194371
Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data. PMID:33187991
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. PMID:33159067
Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland. PMID:33147874
From sequence to information. PMID:33131436
Characteristic and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Medicinal Plants of Schisandraceae. PMID:33123569
Origins and Molecular Evolution of the NusG Paralog RfaH. PMID:33109766
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2. PMID:33099302
Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea. PMID:33077635
The Genome of Staphylococcus epidermidis O47. PMID:32983045
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. PMID:32886787
Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants. PMID:32867090
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. PMID:32814973
Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses. PMID:32799801
Unexpected Cell Wall Alteration-Mediated Bactericidal Activity of the Antifungal Caspofungin against Vancomycin-Resistant Enterococcus faecium. PMID:32778553
Comparative Genomics Discloses the Uniqueness and the Biosynthetic Potential of the Marine Cyanobacterium Hyella patelloides. PMID:32774329
Producing polished prokaryotic pangenomes with the Panaroo pipeline. PMID:32698896
The genetic factors of bilaterian evolution. PMID:32672535
Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System. PMID:32670235
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. PMID:32657391
Mutual antagonism between Hippo signaling and cyclin E drives intracellular pattern formation. PMID:32642758
Anaerobic metabolism of Foraminifera thriving below the seafloor. PMID:32641728
GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae. PMID:32628669
Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.). PMID:32581321
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.). PMID:32576920
The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster. PMID:32571874
Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments. PMID:32561713
Putative circumsporozoite protein (CSP) of Plasmodium vivax is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway. PMID:32550551
Metformin Suppresses Development of the Echinococcus multilocularis Larval Stage by Targeting the TOR Pathway. PMID:32540980
Single-nucleotide polymorphisms in a vancomycin-resistant Staphylococcus aureus strain based on whole-genome sequencing. PMID:32535788
The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages. PMID:32528454
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
Global Distribution and Evolution of Mycobacterium bovis Lineages. PMID:32477295
Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). PMID:32466556
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. PMID:32427841
An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles. PMID:32397800
A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution. PMID:32316034
From pairs of most similar sequences to phylogenetic best matches. PMID:32308731
Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440. PMID:32256468
Characterization and functional analysis of SIAH1 during skin and hair follicle development in the angora rabbit (Oryctolagus cuniculus). PMID:32252830
Cell-type diversity and regionalized gene expression in the planarian intestine. PMID:32240093
Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection. PMID:32211067
Unraveling CAF-1 family in Plasmodium falciparum: comparative genome-wide identification and phylogenetic analysis among eukaryotes, expression profiling and protein-protein interaction studies. PMID:32206492
Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria. PMID:32182360
Genome analysis of Lactobacillus plantarum subsp. plantarum KCCP11226 reveals a well-conserved C30 carotenoid biosynthetic pathway. PMID:32181112
Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. PMID:32152358
Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes. PMID:32142116
Genome sequencing of Aspergillus glaucus 'CCHA' provides insights into salt-stress adaptation. PMID:32140304
Predictable modulation of cancer treatment outcomes by the gut microbiota. PMID:32138779
Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli. PMID:32108145
Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond. PMID:32106513
Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis. PMID:32104261
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. PMID:32093654
Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov. PMID:32075304
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PMID:32069277
Primary orthologs from local sequence context. PMID:32028880
Identification and characterization of novel filament-forming proteins in cyanobacteria. PMID:32024928
Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica. PMID:32010113
Best match graphs and reconciliation of gene trees with species trees. PMID:32002659
Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand. PMID:32001558
Effects of Bacillus velezensis FKM10 for Promoting the Growth of Malus hupehensis Rehd. and Inhibiting Fusarium verticillioides. PMID:31998247
Complete genome sequence of Bifidobacterium adolescentis P2P3, a human gut bacterium possessing strong resistant starch-degrading activity. PMID:31988825
The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales. PMID:31976174
Identification of putative Type-I sex pheromone biosynthesis-related genes expressed in the female pheromone gland of Streltzoviella insularis. PMID:31945099
Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. PMID:31941452
The Role of Treponema denticola Motility in Synergistic Biofilm Formation With Porphyromonas gingivalis. PMID:31921707
The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. PMID:31898479
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). PMID:31888476
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
PA0335, a Gene Encoding Histidinol Phosphate Phosphatase, Mediates Histidine Auxotrophy in Pseudomonas aeruginosa. PMID:31862725
Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus. PMID:31827189
Co-option of wing-patterning genes underlies the evolution of the treehopper helmet. PMID:31819237
Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. PMID:31798674
Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto. PMID:31798006
Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum). PMID:31730445
Complete Genome Sequence of Cellulomonas sp. Strain Y8, a High-GC-Content Plasmid-Free Heavy Metal-Resistant Bacterium Isolated from Farmland Soil. PMID:31727705
DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. PMID:31691822
Reciprocal best match graphs. PMID:31691135
A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features. PMID:31652625
Helicobacter pylori Stress-Response: Definition of the HrcA Regulon. PMID:31614448
Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus. PMID:31589296
Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway. PMID:31573151
Molecular function limits divergent protein evolution on planetary timescales. PMID:31532392
Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method. PMID:31527871
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Genome-wide analysis of the Dof gene family in durian reveals fruit ripening-associated and cultivar-dependent Dof transcription factors. PMID:31431665
Highly variable mRNA half-life time within marine bacterial taxa and functional genes. PMID:31298776
Bacillus Phage vB_BtS_B83 Previously Designated as a Plasmid May Represent a New Siphoviridae Genus. PMID:31284652
Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. PMID:31283204
On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics. PMID:31281302
Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses. PMID:31253827
Advances and Applications in the Quest for Orthologs. PMID:31241141
Stenotrophomonas maltophilia Encodes a VirB/VirD4 Type IV Secretion System That Modulates Apoptosis in Human Cells and Promotes Competition against Heterologous Bacteria, Including Pseudomonas aeruginosa. PMID:31235638
Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102. PMID:31177378
Adaptive Responses of Shewanella decolorationis to Toxic Organic Extracellular Electron Acceptor Azo Dyes in Anaerobic Respiration. PMID:31175185
The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. PMID:31173069
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. PMID:31127390
Mucosa-Associated Microbiota in Ileoanal Pouches May Contribute to Clinical Symptoms, Particularly Stool Frequency, Independent of Endoscopic Disease Activity. PMID:31117112
Alternative characterizations of Fitch's xenology relation. PMID:31111195
Birth-and-Death Evolution of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Diversification of Cuticular Hydrocarbon Synthesis in Drosophila. PMID:31076758
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop (Humulus Lupulus L.). PMID:31060295
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences. PMID:31045217
Best match graphs. PMID:30968198
Assessing reproducibility of matrix factorization methods in independent transcriptomes. PMID:30938767
Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. PMID:30911328
Gene Identification and Characterization of Correlations for DEPs_DEGs Same Trend Responding to Salinity Adaptation in Scylla paramamosain. PMID:30881981
Relative Mutation Rates in Nucleomorph-Bearing Algae. PMID:30859201
MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. PMID:30832740
Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. PMID:30814998
Identification and prevalence of in vivo-induced genes in enterohaemorrhagic Escherichia coli. PMID:30806162
Gene expression analysis of bud burst process in European hazelnut (Corylus avellana L.) using RNA-Seq. PMID:30804627
Evolution of the Highly Repetitive PEVK Region of Titin Across Mammals. PMID:30804022
Evolution of resilience in protein interactomes across the tree of life. PMID:30765515
Porcine Gastric Mucin Triggers Toxin Production of Enteropathogenic Bacillus cereus. PMID:30745328
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species. PMID:30704153
Genome Sequence of Morganella morganii DG56-16, Isolated from Shinisaurus crocodilurus. PMID:30701233
Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing. PMID:30699994
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. PMID:30689829
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). PMID:30660046
Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. PMID:30643200
Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. PMID:30622520
Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach. PMID:30607324
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
Sugarcane apoplast fluid modulates the global transcriptional profile of the diazotrophic bacteria Paraburkholderia tropica strain Ppe8. PMID:30550601
Identifying Differential Gene Expression in Wing Polymorphism of Adult Males of the Largest Water Strider: De novo Transcriptome Assembly for Gigantometra gigas (Hemiptera: Gerridae). PMID:30535417
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. PMID:30534351
Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome. PMID:30532085
Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains. PMID:30519380
Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress. PMID:30514299
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock. PMID:30459453
Automated selection of homologs to track the evolutionary history of proteins. PMID:30453878
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. PMID:30411473
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics. PMID:30400819
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. PMID:30380109
OrthoInspector 3.0: open portal for comparative genomics. PMID:30380106
cuRnet: an R package for graph traversing on GPU. PMID:30367572
Metabolic Determinants of Enzyme Evolution in a Genome-Scale Bacterial Metabolic Network. PMID:30351420
Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli FORC_035 Reveals the Essential Role of Iron Acquisition for Survival in Canola Sprouts and Water Dropwort. PMID:30349522
Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. PMID:30344889
First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. PMID:30338024
Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women. PMID:30337914
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. PMID:30262776
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123. PMID:30250634
Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. PMID:30239695
De novo Transcriptome Characterization of Rhodomyrtus tomentosa Leaves and Identification of Genes Involved in α/β-Pinene and β-Caryophyllene Biosynthesis. PMID:30197651
Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations. PMID:30177918
Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species. PMID:30170550
Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens. PMID:30158907
The Helicobacter pylori Heat-Shock Repressor HspR: Definition of Its Direct Regulon and Characterization of the Cooperative DNA-Binding Mechanism on Its Own Promoter. PMID:30154784
The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial. PMID:30145102
The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37. PMID:30125334
Biomarker panels for characterizing microbial community biofilm formation as composite molecular process. PMID:30092027
Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens. PMID:29992239
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Cotton Late Embryogenesis Abundant (LEA2) Genes Promote Root Growth and Confer Drought Stress Tolerance in Transgenic Arabidopsis thaliana. PMID:29934376
Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes. PMID:29899658
Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1. PMID:29892948
Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05. PMID:29892946
Parallels between experimental and natural evolution of legume symbionts. PMID:29891837
Dataset of the first transcriptome assembly of the tree crop "yerba mate" (Ilex paraguariensis) and systematic characterization of protein coding genes. PMID:29876460
Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops. PMID:29872448
Distinctive characters of Nostoc genomes in cyanolichens. PMID:29866043
Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish. PMID:29866041
Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. PMID:29784811
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes. PMID:29773659
The aquatic animals' transcriptome resource for comparative functional analysis. PMID:29764375
Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume). PMID:29740511
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. PMID:29724166
ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. PMID:29678129
Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis. PMID:29674561
Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis. PMID:29657968
Redefining the ancestral origins of the interleukin-1 superfamily. PMID:29559685
FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects. PMID:29533703
Characterization of the Adaptive Amoxicillin Resistance of Lactobacillus casei Zhang by Proteomic Analysis. PMID:29515561
Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. PMID:29467397
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. PMID:29435649
Transcriptomic and Functional Analyses Reveal That PpGLK1 Regulates Chloroplast Development in Peach (Prunus persica). PMID:29434612
Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model. PMID:29316921
HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. PMID:29315405
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. PMID:29202864
Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China. PMID:29201149
Anthelminthic activity of glibenclamide on secondary cystic echinococcosis in mice. PMID:29190739
COGcollator: a web server for analysis of distant relationships between homologous protein families. PMID:29187234
Genes Integral to the Reproductive Function of Male Reproductive Tissues Drive Heterogeneity in Evolutionary Rates in Japanese Quail. PMID:29158338
Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant. PMID:29152037
Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere. PMID:29146860
The role of public goods in planetary evolution. PMID:29133456
Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. PMID:29133402
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation. PMID:29133277
Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program. PMID:29107333
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. PMID:29106644
Pyomelanin produced by Vibrio cholerae confers resistance to predation by Acanthamoeba castellanii. PMID:29095994
The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. PMID:29088115
SMORE: Synteny Modulator of Repetitive Elements. PMID:29088079
Complete Genome Sequence of Bacillus paralicheniformis 14DA11, Exhibiting Resistance to Clindamycin and Erythromycin. PMID:29074671
Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal. PMID:29026656
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota. PMID:29017607
Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. PMID:28984846
Microbial genome analysis: the COG approach. PMID:28968633
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PMID:28924494
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. PMID:28881964
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift. PMID:28871246
Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome. PMID:28863779
Biologically feasible gene trees, reconciliation maps and informative triples. PMID:28861118
Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06. PMID:28860235
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. PMID:28827376
Bortezomib initiates endoplasmic reticulum stress, elicits autophagy and death in Echinococcus granulosus larval stage. PMID:28817601
Molecular signatures of longevity: Insights from cross-species comparative studies. PMID:28800931
Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles. PMID:28744269
DNA Methylation Influences Chlorogenic Acid Biosynthesis in Lonicera japonica by Mediating LjbZIP8 to Regulate Phenylalanine Ammonia-Lyase 2 Expression. PMID:28740500
Transcriptome Analyses Shed New Insights into Primary Metabolism and Regulation of Blumeria graminis f. sp. tritici during Conidiation. PMID:28713408
Genomic insights into the virulence and salt tolerance of Staphylococcus equorum. PMID:28710456
Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection. PMID:28693412
Bacteriophage evolution differs by host, lifestyle and genome. PMID:28692019
SparkBLAST: scalable BLAST processing using in-memory operations. PMID:28655296
Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk. PMID:28626583
Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens. PMID:28549175
Genome Sequence of Acinetobacter lactucae OTEC-02, Isolated from Hydrocarbon-Contaminated Soil. PMID:28546491
A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M. PMID:28535754
The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats. PMID:28526749
Structural conservation of the PIN domain active site across all domains of life. PMID:28508407
Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. PMID:28504699
Draft Genome Sequence of Mycobacterium boenickei CIP 107829. PMID:28473389
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. PMID:28460117
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1. PMID:28443080
Transcriptome analysis on the exoskeleton formation in early developmetal stages and reconstruction scenario in growth-moulting in Litopenaeus vannamei. PMID:28439089
Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol. PMID:28428289
An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony. PMID:28414739
Increased taxon sampling reveals thousands of hidden orthologs in flatworms. PMID:28400424
Draft Genome Sequence of Mycobacterium colombiense. PMID:28385843
Evolution of substrate specificity in a retained enzyme driven by gene loss. PMID:28362260
Recombination produces coherent bacterial species clusters in both core and accessory genomes. PMID:28348822
Enzyme IIANtr Regulates Salmonella Invasion Via 1,2-Propanediol And Propionate Catabolism. PMID:28333132
Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. PMID:28274202
Complete Genome Sequence of Staphylococcus succinus 14BME20 Isolated from a Traditional Korean Fermented Soybean Food. PMID:28254985
Winding paths to simplicity: genome evolution in facultative insect symbionts. PMID:28204477
The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat. PMID:28187716
Metformin exhibits preventive and therapeutic efficacy against experimental cystic echinococcosis. PMID:28182659
Characterization of Leaf Transcriptome in Banksia hookeriana. PMID:28161492
Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. PMID:28154822
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. PMID:28154557
Single-Molecule Sequencing of the Drosophila serrata Genome. PMID:28143951
Profile of Eugene V. Koonin. PMID:28115717
Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites. PMID:28112213
Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts. PMID:28082971
Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages. PMID:28082607
Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China. PMID:28082485
Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato. PMID:28078051
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes. PMID:28070515
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. PMID:28053163
Evolutionary conservation and in vitro reconstitution of microsporidian iron-sulfur cluster biosynthesis. PMID:28051091
GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences. PMID:28004786
A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans. PMID:27958277
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data. PMID:27922098
Identification, Heterologous Expression, and Functional Characterization of Bacillus subtilis YutF, a HAD Superfamily 5'-Nucleotidase with Broad Substrate Specificity. PMID:27907199
Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. PMID:27874830
Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. PMID:27852927
Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools. PMID:27814683
Primer on the Gene Ontology. PMID:27812933
Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO. PMID:27795235
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. PMID:27789703
Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. PMID:27769168
Geographic Impact on Genomic Divergence as Revealed by Comparison of Nine Citromicrobial Genomes. PMID:27736788
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
Theory of prokaryotic genome evolution. PMID:27702904
Divergence of cuticular hydrocarbons in two sympatric grasshopper species and the evolution of fatty acid synthases and elongases across insects. PMID:27677406
De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production. PMID:27669744
Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. PMID:27648812
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
High Transferability of Homoeolog-Specific Markers between Bread Wheat and Newly Synthesized Hexaploid Wheat Lines. PMID:27611704
Evolution of the Exon-Intron Structure in Ciliate Genomes. PMID:27603699
Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities. PMID:27602183
De novo Sequencing and Transcriptome Analysis of Pinellia ternata Identify the Candidate Genes Involved in the Biosynthesis of Benzoic Acid and Ephedrine. PMID:27579029
First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77. PMID:27570579
Gene-Family Extension Measures and Correlations. PMID:27527218
Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424. PMID:27516522
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects. PMID:27515968
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. PMID:27515907
COMAN: a web server for comprehensive metatranscriptomics analysis. PMID:27515514
Proteomic analysis of an engineered isolate of Lactobacillus plantarum with enhanced raffinose metabolic capacity. PMID:27510766
Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. PMID:27508073
The Molecular Chaperone DnaK Is a Source of Mutational Robustness. PMID:27497316
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering. PMID:27482905
The Genome of Undifilum oxytropis Provides Insights into Swainsonine Biosynthesis and Locoism. PMID:27477109
Role of Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase in Oleaginous Streptomyces sp. Strain G25. PMID:27474711
De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae. PMID:27428371
iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis. PMID:27415428
Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7. PMID:27363525
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PMID:27359102
Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. PMID:27329939
Draft Genome Sequences of Vancomycin-Intermediate Staphylococcus aureus Strains in South Korea. PMID:27313284
Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory. PMID:27307274
Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events. PMID:27303025
Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones. PMID:27289094
The Prehistory of Antibiotic Resistance. PMID:27252395
Genome sequence of Candida versatilis and comparative analysis with other yeast. PMID:27234221
Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T. PMID:27231376
Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T. PMID:27231371
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. PMID:27199545
DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes. PMID:27189986
Evaluating techniques for metagenome annotation using simulated sequence data. PMID:27162180
In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. PMID:27150914
One step beyond a ribosome: The ancient anaerobic core. PMID:27150504
Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. PMID:27135799
How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator. PMID:27129205
The Entner-Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants. PMID:27114545
CDROM: Classification of Duplicate gene RetentiOn Mechanisms. PMID:27080514
Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior. PMID:27073591
Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms. PMID:27065987
Homoeologs: What Are They and How Do We Infer Them? PMID:27021699
Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa. PMID:27014324
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. PMID:26973616
Transcriptional Profile during Deoxycholate-Induced Sporulation in a Clostridium perfringens Isolate Causing Foodborne Illness. PMID:26969700
Inferring Orthologs: Open Questions and Perspectives. PMID:26966373
Genome Sequence of a Unique t2247-ST692-III Livestock-Associated Methicillin-Resistant Staphylococcus aureus Strain from Chicken Carcass. PMID:26950323
Transcriptome-Wide Identification and Expression Profiling of the DOF Transcription Factor Gene Family in Chrysanthemum morifolium. PMID:26941763
A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica. PMID:26931371
Using intron position conservation for homology-based gene prediction. PMID:26893356
Identification of Novel Zoonotic Activity of Bartonella spp., France. PMID:26885624
Global Protein Oxidation Profiling Suggests Efficient Mitochondrial Proteome Homeostasis During Aging. PMID:26884511
Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. PMID:26884164
Whole genome sequencing of "Faecalibaculum rodentium" ALO17, isolated from C57BL/6J laboratory mouse feces. PMID:26877770
Origin and Evolution of Rickettsial Plasmids. PMID:26866478
Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna. PMID:26865909
Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex. PMID:26844549
Global biogeography of Prochlorococcus genome diversity in the surface ocean. PMID:26836261
Unique pioneer microbial communities exposed to volcanic sulfur dioxide. PMID:26791101
Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus. PMID:26779215
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. PMID:26774999
Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline. PMID:26756338
Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PMID:26751217
Abundant Intergenic TAACTGA Direct Repeats and Putative Alternate RNA Polymerase β' Subunits in Marine Beggiatoaceae Genomes: Possible Regulatory Roles and Origins. PMID:26733950
Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins During in vitro Culture Attenuation. PMID:26711524
Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle. PMID:26690083
Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach. PMID:26677339
Evolvability of an Optimal Recombination Rate. PMID:26660159
Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut. PMID:26649181
Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e. PMID:26649149
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs. PMID:26644001
Transcriptomic Response to Nitric Oxide Treatment in Larix olgensis Henry. PMID:26633380
Intein Clustering Suggests Functional Importance in Different Domains of Life. PMID:26609079
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation. PMID:26601103
Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099. PMID:26586900
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1. PMID:26566420
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. PMID:26554846
Transcriptome Analysis of Blunt Snout Bream (Megalobrama amblycephala) Reveals Putative Differential Expression Genes Related to Growth and Hypoxia. PMID:26554582
Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2. PMID:26545740
Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors. PMID:26545400
Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing. PMID:26543847
Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T. PMID:26543131
Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098. PMID:26543113
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
Transcriptional Profile of Bacillus subtilis sigF-Mutant during Vegetative Growth. PMID:26506528
Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. PMID:26482678
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes. PMID:26473921
Understanding the direction of evolution in Burkholderia glumae through comparative genomics. PMID:26454852
Genome-wide analysis of the IQD gene family in maize. PMID:26453258
WaspAtlas: a Nasonia vitripennis gene database and analysis platform. PMID:26452372
mmnet: An R Package for Metagenomics Systems Biology Analysis. PMID:26421278
Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033. PMID:26391348
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. PMID:26388849
Analysis of the Agrotis segetum pheromone gland transcriptome in the light of sex pheromone biosynthesis. PMID:26385554
Motility defects in Campylobacter jejuni defined gene deletion mutants caused by second-site mutations. PMID:26385289
Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia. PMID:26380645
Escherichia coli ASKA Clone Library Harboring tRNA-Specific Adenosine Deaminase (tadA) Reveals Resistance towards Xanthorrhizol. PMID:26370953
Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens. PMID:26367458
Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. PMID:26358624
The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme. PMID:26349049
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. PMID:26346536
Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab. PMID:26330095
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. PMID:26328666
Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3. PMID:26301592
Endosymbiotic origin and differential loss of eukaryotic genes. PMID:26287458
Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity. PMID:26279684
MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. PMID:26272906
Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T. PMID:26251499
Gene Expression Analysis of Four Radiation-resistant Bacteria. PMID:26244019
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum. PMID:26221421
Data for iTRAQ-based quantitative proteomics analysis of Brassica napus leaves in response to chlorophyll deficiency. PMID:26217696
Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491. PMID:26205866
Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344. PMID:26205865
Dynamic Response of Pseudomonas putida S12 to Sudden Addition of Toluene and the Potential Role of the Solvent Tolerance Gene trgI. PMID:26181384
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase. PMID:26175150
Discovery of bacterial fatty acid synthase type II inhibitors using a novel cellular bioluminescent reporter assay. PMID:26169404
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. PMID:26160651
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes. PMID:26159227
Transcriptome analysis of the biofilm formed by methicillin-susceptible Staphylococcus aureus. PMID:26149474
Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths. PMID:26146586
The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. PMID:26122045
Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors. PMID:26114113
Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. PMID:26099797
Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. PMID:26084810
Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. PMID:26057562
Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin. PMID:26052319
De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PMID:26047102
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype. PMID:26044427
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage. PMID:26044426
Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. PMID:25978838
Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection. PMID:25978460
Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies. PMID:25975821
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
Global Gene Expression of Kosteletzkya virginica Seedlings Responding to Salt Stress. PMID:25901608
Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes. PMID:25894918
Mongolian Almond (Prunus mongolica Maxim): The Morpho-Physiological, Biochemical and Transcriptomic Response to Drought Stress. PMID:25893685
Role of AcsR in expression of the acetyl-CoA synthetase gene in Vibrio vulnificus. PMID:25887971
Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci. PMID:25887812
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
PathwayBooster: a tool to support the curation of metabolic pathways. PMID:25887214
An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture. PMID:25880663
Function discovery and structural characterization of a methylphosphonate esterase. PMID:25873441
Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces. PMID:25861391
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
The transcriptional response of microbial communities in thawing Alaskan permafrost soils. PMID:25852660
Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers. PMID:25765814
Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation. PMID:25765460
Unexpected ancient paralogs and an evolutionary model for the COPII coat complex. PMID:25747251
Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes. PMID:25733873
An event-driven approach for studying gene block evolution in bacteria. PMID:25717195
The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. PMID:25714721
De novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-seq. PMID:25713814
No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. PMID:25710183
Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. PMID:25685259
Genome analysis of Flaviramulus ichthyoenteri Th78(T) in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine. PMID:25652846
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. PMID:25652835
Effects of the diet on the microbiota of the red palm weevil (Coleoptera: Dryophthoridae). PMID:25635833
Habitat visualization and genomic analysis of "Candidatus Pantoea carbekii," the primary symbiont of the brown marmorated stink bug. PMID:25587021
The multifaceted roles of metabolic enzymes in the Paracoccidioides species complex. PMID:25566229
Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. PMID:25566214
Insights into the origin and evolution of the plant hormone signaling machinery. PMID:25560880
Transcriptome-wide analysis of SAMe superfamily to novelty phosphoethanolamine N-methyltransferase copy in Lonicera japonica. PMID:25551601
Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure. PMID:25540358
Global transcriptome analysis of Mesorhizobium alhagi CCNWXJ12-2 under salt stress. PMID:25539655
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PMID:25503521
Modularized evolution in archaeal methanogens phylogenetic forest. PMID:25502908
Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. PMID:25487147
Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. PMID:25476580
Analysis of a draft genome sequence of Kitasatospora cheerisanensis KCTC 2395 producing bafilomycin antibiotics. PMID:25471184
Faster sequence homology searches by clustering subsequences. PMID:25432166
Evolutionary origin of a streamlined marine bacterioplankton lineage. PMID:25431989
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
Evolution of the insect desaturase gene family with an emphasis on social Hymenoptera. PMID:25425561
MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. PMID:25421434
Comparative transcriptomic analysis of the response to cold acclimation in Eucalyptus dunnii. PMID:25412179
Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440. PMID:25401072
Molecular toolbox for genetic manipulation of the stalked budding bacterium Hyphomonas neptunium. PMID:25398860
MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. PMID:25392421
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis. PMID:25344242
The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. PMID:25342549
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
The same or not the same: lineage-specific gene expansions and homology relationships in multigene families in nematodes. PMID:25323991
Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample. PMID:25323728
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
Origins of major archaeal clades correspond to gene acquisitions from bacteria. PMID:25317564
Optimizing high performance computing workflow for protein functional annotation. PMID:25313296
A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird. PMID:25279728
Curation, integration and visualization of bacterial virulence factors in PATRIC. PMID:25273106
Differential genome evolution between companion symbionts in an insect-bacterial symbiosis. PMID:25271287
Discovery of a small molecule that inhibits bacterial ribosome biogenesis. PMID:25233066
Binning metagenomic contigs by coverage and composition. PMID:25218180
ESTs analysis of putative genes engaged in Polyporus umbellatus sclerotial development. PMID:25210845
Changes of the human gut microbiome induced by a fermented milk product. PMID:25209713
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Comparative transcriptomic characterization of the early development in Pacific white shrimp Litopenaeus vannamei. PMID:25197823
Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov. PMID:25197492
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice. PMID:25197470
Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium. PMID:25197464
Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil. PMID:25197431
Genetic mechanisms underlying the pathogenicity of cold-stressed Salmonella enterica serovar typhimurium in cultured intestinal epithelial cells. PMID:25192993
Microbiome analysis - from technical advances to biological relevance. PMID:25184041
Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. PMID:25168460
The temporal transcriptomic response of Pinus massoniana seedlings to phosphorus deficiency. PMID:25165828
HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. PMID:25159222
An Integrated Genomic and Immunoinformatic Approach to H. pylori Vaccine Design. PMID:25152768
De novo transcriptome of the desert beetle Microdera punctipennis (Coleoptera: Tenebrionidae) using Illumina RNA-seq technology. PMID:25142502
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. PMID:25141959
Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. PMID:25126794
Variation in the fitness effects of mutations with population density and size in Escherichia coli. PMID:25121498
Clonality and Resistome analysis of KPC-producing Klebsiella pneumoniae strain isolated in Korea using whole genome sequencing. PMID:25105122
Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. PMID:25104113
Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus. PMID:25101061
Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi. PMID:25098249
Screening of a Leptospira biflexa mutant library to identify genes involved in ethidium bromide tolerance. PMID:25063661
The cell envelope proteome of Aggregatibacter actinomycetemcomitans. PMID:25055881
Elevated temperature alters proteomic responses of individual organisms within a biofilm community. PMID:25050524
Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin. PMID:25028574
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
Draft Genome Sequence of Mycobacterium neoaurum Strain DSM 44074T. PMID:25013147
Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers. PMID:24956277
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. PMID:24952641
Comparative genomics of Riemerella anatipestifer reveals genetic diversity. PMID:24935762
Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. PMID:24923884
Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution. PMID:24886397
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Prediction and redesign of protein-protein interactions. PMID:24878423
Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955. PMID:24874688
Draft Genome Sequence of Mycobacterium triplex DSM 44626. PMID:24874681
Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. PMID:24853639
Phylogenomic reconstruction of archaeal fatty acid metabolism. PMID:24818264
Draft Genome Sequence of Mycobacterium vulneris DSM 45247T. PMID:24812218
Draft Genome Sequence of Mycobacterium mageritense DSM 44476T. PMID:24786954
Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297. PMID:24744338
Draft Genome Sequence of Mycobacterium austroafricanum DSM 44191. PMID:24744336
Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829. PMID:24723727
Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. PMID:24708309
Protein-protein interaction detection: methods and analysis. PMID:24693427
Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage. PMID:24671745
Complete genome sequence of 285P, a novel T7-like polyvalent E. coli bacteriophage. PMID:24668157
Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea. PMID:24667707
The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli. PMID:24659771
A novel regio‑specific cyclosporin hydroxylase gene revealed through the genome mining of Pseudonocardia autotrophica. PMID:24659179
Genes associated with agronomic traits in non-heading Chinese cabbage identified by expression profiling. PMID:24655567
Gene expression profiling in winged and wingless cotton aphids, Aphis gossypii (Hemiptera: Aphididae). PMID:24644424
Genomic evidence reveals the extreme diversity and wide distribution of the arsenic-related genes in Burkholderiales. PMID:24632831
Genome sequence of type strain of Staphylococcus aureus subsp. aureus. PMID:24628867
Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1. PMID:24625872
Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. PMID:24607996
Porphyromonas gingivalis and Treponema denticola exhibit metabolic symbioses. PMID:24603978
Extracellular DNA metabolism in Haloferax volcanii. PMID:24600440
Investigating the interplay between nucleoid-associated proteins, DNA curvature, and CRISPR elements using comparative genomics. PMID:24595272
RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic). PMID:24586398
Computational prediction of the human-microbial oral interactome. PMID:24576332
Quantitative synteny scoring improves homology inference and partitioning of gene families. PMID:24564516
Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival. PMID:24563689
Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. PMID:24534435
Draft Genome Sequence of the Toxic Bloom-Forming Cyanobacterium Aphanizomenon flos-aquae NIES-81. PMID:24526634
Predicting the function of 4-coumarate:CoA ligase (LJ4CL1) in Lonicera japonica. PMID:24518682
Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol. PMID:24507483
Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure. PMID:24503989
Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil. PMID:24501646
Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium. PMID:24501638
Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols. PMID:24482523
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Nutrient limitation governs Staphylococcus aureus metabolism and niche adaptation in the human nose. PMID:24453967
Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. PMID:24451207
Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f. PMID:24438474
Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages. PMID:24433236
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. PMID:24398320
MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data. PMID:24391870
High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides. PMID:24371201
Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life. PMID:24354654
Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina). PMID:24317973
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries. PMID:24291226
Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure. PMID:24283940
Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. PMID:24281050
Discovery of genes related to witches broom disease in Paulownia tomentosa × Paulownia fortunei by a De Novo assembled transcriptome. PMID:24278262
A pluralistic account of homology: adapting the models to the data. PMID:24273322
Evolution of MHC class I in the order Crocodylia. PMID:24253731
Sequencing and de novo assembly of the Asian clam (Corbicula fluminea) transcriptome using the Illumina GAIIx method. PMID:24244519
Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms. PMID:24225886
EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. PMID:24214991
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634. PMID:24201192
Single-cell genomics shedding light on marine Thaumarchaeota diversification. PMID:24196320
Genome analysis of Pseudoalteromonas flavipulchra JG1 reveals various survival advantages in marine environment. PMID:24131871
Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased Paralichthys olivaceus. PMID:24092782
Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells. PMID:24092779
Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an Invasive Isolate That Caused Necrotizing Myositis. PMID:24092777
Prokaryotic phylogenies inferred from whole-genome sequence and annotation data. PMID:24073404
Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. PMID:24053607
In vivo substrate diversity and preference of small heat shock protein IbpB as revealed by using a genetically incorporated photo-cross-linker. PMID:24045939
Sorghum bmr6 mutant analysis demonstrates that a shared MYB1 transcription factor binding site in the promoter links the expression of genes in related pathways. PMID:24045932
Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica. PMID:24039725
Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. PMID:24028713
Novel determinants of intestinal colonization of Salmonella enterica serotype typhimurium identified in bovine enteric infection. PMID:24019407
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. PMID:23995932
Arabinoxylan oligosaccharide hydrolysis by family 43 and 51 glycosidases from Lactobacillus brevis DSM 20054. PMID:23995921
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. PMID:23977285
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. PMID:23975157
Probing bacterial metabolism during infection using high-resolution transcriptomics. PMID:23974023
Structure-guided discovery of new deaminase enzymes. PMID:23968233
Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. PMID:23961314
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea. PMID:23892291
Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. PMID:23873917
Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing. PMID:23872555
Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. PMID:23871937
Evolution of divergent life history strategies in marine alphaproteobacteria. PMID:23839216
Stability along with extreme variability in core genome evolution. PMID:23821522
Detailed analysis of putative genes encoding small proteins in legume genomes. PMID:23802007
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. PMID:23768067
Probing the boundaries of orthology: the unanticipated rapid evolution of Drosophila centrosomin. PMID:23749319
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
In-depth tanscriptomic analysis on giant freshwater prawns. PMID:23734171
Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species. PMID:23723974
Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. PMID:23711669
Precipitation of iron on the surface of Leptospira interrogans is associated with mutation of the stress response metalloprotease HtpX. PMID:23709510
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PMID:23675487
Computational meta'omics for microbial community studies. PMID:23670539
Commonalities and differences among symbiosis islands of three Mesorhizobium loti strains. PMID:23666538
Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. PMID:23657364
Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach. PMID:23645199
Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb. PMID:23638167
Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PMID:23626855
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. PMID:23625995
Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. PMID:23557328
Functional and evolutionary implications of gene orthology. PMID:23552219
Multiple roles of RNase Y in Streptococcus pyogenes mRNA processing and degradation. PMID:23543715
The complete genome and phenome of a community-acquired Acinetobacter baumannii. PMID:23527001
The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4. PMID:23516524
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. PMID:23511466
Comparative analysis of protein-protein interactions in the defense response of rice and wheat. PMID:23496930
Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil. PMID:23450133
A global approach to analysis and interpretation of metabolic data for plant natural product discovery. PMID:23447050
Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PMID:23437175
Why does a protein's evolutionary rate vary over time? PMID:23436005
Ancient complexity, opisthokont plasticity, and discovery of the 11th subfamily of Arf GAP proteins. PMID:23433073
Draft Genome Sequence of a Humic Substance-Degrading Paenibacillus sp. Isolated from the Subarctic Grasslands at Low Temperature. PMID:23409270
The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases. PMID:23405110
Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain. PMID:23384176
Identification of a cyclosporine-specific P450 hydroxylase gene through targeted cytochrome P450 complement (CYPome) disruption in Sebekia benihana. PMID:23354713
Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways. PMID:23349851
Autosomal similarity revealed by eukaryotic genomic comparison. PMID:23345874
Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. PMID:23345457
Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes. PMID:23324532
Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. PMID:23324436
Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources. PMID:23324387
Self consistency grouping: a stringent clustering method. PMID:23320864
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Ecology of marine Bacteroidetes: a comparative genomics approach. PMID:23303374
A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks. PMID:23303373
Methods of combinatorial optimization to reveal factors affecting gene length. PMID:23300345
Localization of Wolbachia-like gene transcripts and peptides in adult Onchocerca flexuosa worms indicates tissue specific expression. PMID:23281896
Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum. PMID:23259483
Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. PMID:23256477
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. PMID:23241446
The purine-utilizing bacterium Clostridium acidurici 9a: a genome-guided metabolic reconsideration. PMID:23240052
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. PMID:23222723
A nuclear single-nucleotide polymorphism (SNP) potentially useful for the separation of Rhodnius prolixus from members of the Rhodnius robustus cryptic species complex (Hemiptera: Reduviidae). PMID:23219914
MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. PMID:23216677
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PMID:23209392
Genome sequence of Afipia birgiae, a rare bacterium associated with Amoebae. PMID:23209256
Draft genome sequencing of Bacillus sp. strain M2-6, isolated from the roots of Korean ginseng, Panax ginseng C. A. Meyer, after high-hydrostatic-pressure processing. PMID:23209247
Draft genome sequence of the bean-nodulating Sinorhizobium fredii strain GR64. PMID:23209231
LUCApedia: a database for the study of ancient life. PMID:23193296
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. PMID:23184964
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. PMID:23172288
The protein interaction network of a taxis signal transduction system in a halophilic archaeon. PMID:23171228
A new protein superfamily: TPPP-like proteins. PMID:23166627
Complete genome sequence of the bacteriophage YMC01/01/P52 PAE BP, which causes lysis of verona integron-encoded metallo-β-lactamase-producing, carbapenem-resistant Pseudomonas aeruginosa. PMID:23166271
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Draft Genome sequence of Escherichia coli AI27, a porcine isolate belonging to phylogenetic group B1. PMID:23144394
Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes. PMID:23133637
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
Estimating the rate of irreversibility in protein evolution. PMID:23132897
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. PMID:23114024
Phylogeny vs genome reshuffling: horizontal gene transfer. PMID:23100716
Functional genomics as a tool in virus research. PMID:23100713
Microbial genomics: rhetoric or reality? PMID:23100710
Complete genome sequence of the podoviral bacteriophage YMC/09/02/B1251 ABA BP, which causes the lysis of an OXA-23-producing carbapenem-resistant Acinetobacter baumannii isolate from a septic patient. PMID:23087105
Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonica and their substitutes. PMID:23085319
Comparative genomics of Serratia spp.: two paths towards endosymbiotic life. PMID:23077583
Epistasis as the primary factor in molecular evolution. PMID:23064225
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
GenoSets: visual analytic methods for comparative genomics. PMID:23056299
A fish-specific member of the TPPP protein family? PMID:23053195
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. PMID:23046950
Genome sequence of Legionella tunisiensis strain LegM(T), a new Legionella species isolated from hypersaline lake water. PMID:23045493
Genomic comparison of Kingella kingae strains. PMID:23045489
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. PMID:23043000
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Draft genome sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T. PMID:23012294
Draft genome sequence of Weissella koreensis KCTC 3621T. PMID:23012287
Genome sequence of Reyranella massiliensis, a bacterium associated with amoebae. PMID:23012280
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. PMID:23001650
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58. PMID:22984411
Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production. PMID:22967216
Solitary restriction endonucleases in prokaryotic genomes. PMID:22965118
Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457
ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs. PMID:22958836
Identification and analysis of the putative pentose sugar efflux transporters in Escherichia coli. PMID:22952739
A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1. PMID:22950023
Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii. PMID:22938175
Draft genome sequence of Escherichia coli W26, an enteric strain isolated from cow feces. PMID:22933771
Insights from the genome sequence of a Salmonella enterica serovar Typhi strain associated with a sporadic case of typhoid fever in Malaysia. PMID:22933756
Promoter propagation in prokaryotes. PMID:22933716
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. PMID:22920415
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. PMID:22915837
Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. PMID:22908010
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. PMID:22853326
A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin. PMID:22850507
Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. PMID:22848105
Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PMID:22844541
Draft genome sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1, isolated from the gills of a Korean rockfish, Sebastes schlegeli Hilgendorf, after high hydrostatic pressure processing. PMID:22843581
Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions. PMID:22843344
Patterns and architecture of genomic islands in marine bacteria. PMID:22839777
Complete genome sequence of Bacillus anthracis H9401, an isolate from a Korean patient with anthrax. PMID:22815438
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Global transcriptional analysis of stress-response strategies in Acidithiobacillus ferrooxidans ATCC 23270 exposed to organic extractant--Lix984n. PMID:22805826
GFam: a platform for automatic annotation of gene families. PMID:22790981
De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. PMID:22776250
Predicted protein subcellular localization in dominant surface ocean bacterioplankton. PMID:22773648
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Genome sequence of Escherichia coli J53, a reference strain for genetic studies. PMID:22740669
Engineering ecosystems and synthetic ecologies. PMID:22722235
Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. PMID:22717884
Draft genome sequence of Enterococcus faecium strain LCT-EF90. PMID:22689242
The multiplicity of divergence mechanisms in a single evolving population. PMID:22682524
Expressed sequence tags in cultivated peanut (Arachis hypogaea): discovery of genes in seed development and response to Ralstonia solanacearum challenge. PMID:22648474
Genome and transcriptome analysis of the food-yeast Candida utilis. PMID:22629373
Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen. PMID:22628513
The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. PMID:22618875
Comparative proteomic analysis of Aedes aegypti larval midgut after intoxication with Cry11Aa toxin from Bacillus thuringiensis. PMID:22615881
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. PMID:22607188
The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PMID:22590603
Genome sequence of the probiotic bacterium Sporolactobacillus vineae SL153T. PMID:22582374
A genome-wide study of recombination rate variation in Bartonella henselae. PMID:22577862
GHOSTM: a GPU-accelerated homology search tool for metagenomics. PMID:22574135
Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice. PMID:22566494
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. PMID:22563243
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PMID:22558305
Genome sequence of the anaerobic bacterium Clostridium arbusti SL206(T). PMID:22535938
Genome sequence of Myroides injenensis M09-0166(T), isolated from clinical specimens. PMID:22535932
Transcriptional portrait of Actinobacillus pleuropneumoniae during acute disease--potential strategies for survival and persistence in the host. PMID:22530048
Genome sequence of Peptoniphilus rhinitidis 1-13T, an anaerobic coccus strain isolated from clinical specimens. PMID:22493209
Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PMID:22479625
Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes. PMID:22447597
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. PMID:22443545
Phylogeny of the staphylococcal major autolysin and its use in genus and species typing. PMID:22427631
Lateral gene transfer as a support for the tree of life. PMID:22416123
Differential assembly of polypeptides of the light-harvesting 2 complex encoded by distinct operons during acclimation of Rhodobacter sphaeroides to low light intensity. PMID:22396151
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. PMID:22385976
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. PMID:22377718
Protease-associated cellular networks in malaria parasite Plasmodium falciparum. PMID:22369208
Genome scanning for conditionally essential genes in Salmonella enterica Serotype Typhimurium. PMID:22367088
Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes. PMID:22363520
Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. PMID:22362734
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. PMID:22355196
Complete genome sequence of Pseudomonas aeruginosa lytic bacteriophage PA1O which resembles temperate bacteriophage D3112. PMID:22354942
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. PMID:22333191
Toward community standards in the quest for orthologs. PMID:22332236
Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress. PMID:22321773
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. PMID:22300633
Deciphering the magainin resistance process of Escherichia coli strains in light of the cytosolic proteome. PMID:22290970
Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PMID:22279554
Environmental factors affecting the expression of pilAB as well as the proteome and transcriptome of the grass endophyte Azoarcus sp. strain BH72. PMID:22276194
The core and unique proteins of haloarchaea. PMID:22272718
Insights into the gene expression profile of uncultivable hemotrophic Mycoplasma suis during acute infection, obtained using proteome analysis. PMID:22267506
Rates of evolution in stress-related genes are associated with habitat preference in two Cardamine lineages. PMID:22257588
Global analysis of small molecule binding to related protein targets. PMID:22253582
Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically. PMID:22249883
Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. PMID:22230142
A vector space model approach to identify genetically related diseases. PMID:22227640
Inhibition of specific gene expressions by protein-mediated mRNA interference. PMID:22215082
Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. PMID:22210896
Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. PMID:22201529
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
Molecular cloning and characterization of a matrix metalloproteinase, from Caenorhabditis elegans: employed to identify homologous protein from Angiostrongylus cantonensis. PMID:22167371
Identifying single copy orthologs in Metazoa. PMID:22144877
Cube-DB: detection of functional divergence in human protein families. PMID:22139934
Algorithm for large-scale clustering across multiple genomes. PMID:22125394
Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. PMID:22123759
CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization. PMID:22114666
Candidate targets of balancing selection in the genome of Staphylococcus aureus. PMID:22114360
Phytozome: a comparative platform for green plant genomics. PMID:22110026
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
YhiQ is RsmJ, the methyltransferase responsible for methylation of G1516 in 16S rRNA of E. coli. PMID:22079366
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. PMID:22070167
Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638. PMID:22057919
Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation. PMID:22053731
Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm. PMID:22038960
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PMID:22003381
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Genome-scale analysis of Mycoplasma agalactiae loci involved in interaction with host cells. PMID:21966487
Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. PMID:21965651
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes. PMID:21965536
Genomic basis of endosymbiont-conferred protection against an insect parasitoid. PMID:21948522
Ehrlichia chaffeensis transcriptome in mammalian and arthropod hosts reveals differential gene expression and post transcriptional regulation. PMID:21915290
Genome sequence of Lactobacillus versmoldensis KCTC 3814. PMID:21914893
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes. PMID:21910823
The response of Lactococcus lactis to membrane protein production. PMID:21904605
Differential assembly of polypeptides of the light-harvesting 2 complex encoded by distinct operons during acclimation of Rhodobacter sphaeroides to low light intensity. PMID:21863386
Transcriptome analysis of potato leaves expressing the trehalose-6-phosphate synthase 1 gene of yeast. PMID:21858131
Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective. PMID:21856648
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria. PMID:21840974
Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer. PMID:21816042
Synergistic use of plant-prokaryote comparative genomics for functional annotations. PMID:21810204
Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling. PMID:21801415
Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. PMID:21788470
Complete genome and proteome of Acholeplasma laidlawii. PMID:21784942
Transcriptome analysis of probiotic Lactobacillus casei Zhang during fermentation in soymilk. PMID:21779970
Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase. PMID:21763692
Detection of fused genes in eukaryotic genomes using gene deFuser: analysis of the Tetrahymena thermophila genome. PMID:21745395
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. PMID:21742897
Genome sequence of Lactobacillus johnsonii PF01, isolated from piglet feces. PMID:21742886
Genome sequence of Lactobacillus cypricasei KCTC 13900. PMID:21742864
Spinning gland transcriptomics from two main clades of spiders (order: Araneae)--insights on their molecular, anatomical and behavioral evolution. PMID:21738742
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. PMID:21725006
Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. PMID:21718514
Metagenomic biomarker discovery and explanation. PMID:21702898
Testing the ortholog conjecture with comparative functional genomic data from mammals. PMID:21695233
Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. PMID:21693016
Computational methods for Gene Orthology inference. PMID:21690100
Genome sequence of Acinetobacter sp. strain P8-3-8, isolated from Fistularia commersonii in Vietnam. PMID:21685286
Draft genome sequence of Methylophaga aminisulfidivorans MP T. PMID:21685284
Genome sequence of the 17β-estradiol-utilizing bacterium Sphingomonas strain KC8. PMID:21685282
Draft genome sequence of Kocuria rhizophila P7-4. PMID:21685281
Genome sequence of Lactococcus garvieae 8831, isolated from rainbow trout lactococcosis outbreaks in Spain. PMID:21685280
Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. PMID:21685158
Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. PMID:21667246
An alternative approach to multiple genome comparison. PMID:21646341
Global gene expression profile for swarming Bacillus cereus bacteria. PMID:21642396
Rapid evolution of coral proteins responsible for interaction with the environment. PMID:21633702
Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential. PMID:21631945
Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia. PMID:21622739
Comparative genomics of the dormancy regulons in mycobacteria. PMID:21602344
Genome sequence of Escherichia coli AA86, isolated from cow feces. PMID:21602332
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. PMID:21595937
Evolutionary plasticity determination by orthologous groups distribution. PMID:21586164
The giant Cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of Life. PMID:21559486
Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. PMID:21541312
Evaluating ortholog prediction algorithms in a yeast model clade. PMID:21533202
Tandem BRCT Domains: DNA's Praetorian Guard. PMID:21533002
Complete genome sequence and immunoproteomic analyses of the bacterial fish pathogen Streptococcus parauberis. PMID:21531805
The anaerobe-specific orange protein complex of Desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ54 and a cognate transcriptional regulator. PMID:21531797
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. PMID:21515685
Statistically validated networks in bipartite complex systems. PMID:21483858
Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD. PMID:21441509
Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601. PMID:21423275
Draft genome sequence of Caloramator australicus strain RC3T, a thermoanaerobe from the Great Artesian Basin of Australia. PMID:21421756
Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium. PMID:21418628
Loss of genetic redundancy in reductive genome evolution. PMID:21379323
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts. PMID:21317336
Genome sequence of Citromicrobium strain JLT1363, isolated from the South China Sea. PMID:21317332
Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments. PMID:21305044
Gene gain and loss events in Rickettsia and Orientia species. PMID:21303508
Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. PMID:21292630
Modeling and comparing the organization of circular genomes. PMID:21278186
Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona and the larvacean Oikopleura. PMID:21251251
The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1. PMID:21192830
Genome sequence of Leuconostoc inhae KCTC 3774, isolated from Kimchi. PMID:21183671
Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. PMID:21167037
mll ortholog containing functional domains of human MLL is expressed throughout the zebrafish lifespan and in haematopoietic tissues. PMID:21155757
Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses. PMID:21151962
Dichotomy in the NRT gene families of dicots and grass species. PMID:21151904
COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. PMID:21149270
Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential. PMID:21143895
Genome Sequence of Leuconostoc gelidum KCTC 3527, Isolated from Kimchi. PMID:21131494
An integrative study of a meromictic lake ecosystem in Antarctica. PMID:21124488
RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis. PMID:21102555
Distinct time-resolved roles for two catabolite-sensing pathways during Streptococcus pyogenes infection. PMID:21098101
Genome Sequence of Weissella cibaria KACC 11862. PMID:21097615
Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. PMID:21097610
Bovipain-2, the falcipain-2 ortholog, is expressed in intraerythrocytic stages of the tick-transmitted hemoparasite Babesia bovis. PMID:21092313
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. PMID:21092245
Assembling networks of microbial genomes using linear programming. PMID:21092133
Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. PMID:21087491
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. PMID:21062453
Evolution of xyloglucan-related genes in green plants. PMID:21054875
Purification, crystallization and preliminary X-ray crystallographic analysis of 23S RNA m(2)G2445 methyltransferase RlmL from Escherichia coli. PMID:21045301
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. PMID:21045053
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti. PMID:20955556
Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera. PMID:20942950
Uncovering the human methyltransferasome. PMID:20930037
The tree and net components of prokaryote evolution. PMID:20889655
Predicting phenotypic traits of prokaryotes from protein domain frequencies. PMID:20868492
Classification of protein kinases on the basis of both kinase and non-kinase regions. PMID:20856812
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? PMID:20844558
Evolution of diverse cell division and vesicle formation systems in Archaea. PMID:20818414
Members of the YjgF/YER057c/UK114 family of proteins inhibit phosphoribosylamine synthesis in vitro. PMID:20817725
Gut microbial gene expression in mother-fed and formula-fed piglets. PMID:20805981
Transcriptional response of Leptospira interrogans to iron limitation and characterization of a PerR homolog. PMID:20805337
A genome-wide gene function prediction resource for Drosophila melanogaster. PMID:20711346
BiDiBlast: comparative genomics pipeline for the PC. PMID:20691399
Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. PMID:20678208
Replication-biased genome organisation in the crenarchaeon Sulfolobus. PMID:20667100
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. PMID:20664636
Chaperonin-dependent accelerated substitution rates in prokaryotes. PMID:20660111
Genome networks root the tree of life between prokaryotic domains. PMID:20624742
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. PMID:20624725
Gene encoding gamma-carbonic anhydrase is cotranscribed with argC and induced in response to stationary phase and high CO2 in Azospirillum brasilense Sp7. PMID:20598158
Increased mutation frequency in redox-impaired Escherichia coli due to RelA- and RpoS-mediated repression of DNA repair. PMID:20581184
Analysis of the differential expression of the genes related to Brassica napus seed development. PMID:20571911
The phosphatomes of the multicellular myxobacteria Myxococcus xanthus and Sorangium cellulosum in comparison with other prokaryotic genomes. PMID:20567509
Proteomic analysis of the fish pathogen Flavobacterium columnare. PMID:20525376
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. PMID:20500869
Sequence space and the ongoing expansion of the protein universe. PMID:20485343
TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions. PMID:20471400
The annotation of full zinc proteomes. PMID:20443034
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. PMID:20418398
Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155. PMID:20412585
Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. PMID:20411118
Detecting genomic islands using bioinformatics approaches. PMID:20395967
Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities. PMID:20368341
Evolution of Conus peptide toxins: analysis of Conus californicus Reeve, 1844. PMID:20363338
Getting started in gene orthology and functional analysis. PMID:20361041
Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback. PMID:20348253
An expression analysis of 57 transcription factors derived from ESTs of developing seeds in Maize (Zea mays). PMID:20336461
Construction and analysis of protein-protein interaction networks. PMID:20334628
Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. PMID:20333224
Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. PMID:20333181
Identification of Bacillus cereus genes specifically expressed during growth at low temperatures. PMID:20190083
Reconstructing genome trees of prokaryotes using overlapping genes. PMID:20181237
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. PMID:20139989
Universal distribution of protein evolution rates as a consequence of protein folding physics. PMID:20133769
Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages. PMID:20122178
Relationship between operon preference and functional properties of persistent genes in bacterial genomes. PMID:20109203
Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PMID:20090843
Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes. PMID:20078895
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. PMID:20042074
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. PMID:20017929
Francisella tularensis T-cell antigen identification using humanized HLA-DR4 transgenic mice. PMID:20016043
The impact of long-distance horizontal gene transfer on prokaryotic genome size. PMID:20007373
Comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature. PMID:19997626
Coexistence of two different photosynthetic operons in Citromicrobium bathyomarinum JL354 as revealed by whole-genome sequencing. PMID:19966001
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. PMID:19965768
3D genome tuner: compare multiple circular genomes in a 3D context. PMID:19944387
In silico analysis of the potential infection mechanisms of Magnaporthe grisea from horizontal gene transfer hypothesis. PMID:19944380
An evaluation of minimal cellular functions to sustain a bacterial cell. PMID:19943949
C. elegans sym-1 is a downstream target of the hunchback-like-1 developmental timing transcription factor. PMID:19923914
Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa. PMID:19907650
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se. PMID:19887375
Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PMID:19865481
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. PMID:19860884
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp. PMID:19852815
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. PMID:19846609
A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. PMID:19801558
Translation termination in pyrrolysine-utilizing archaea. PMID:19796638
Exploration of uncharted regions of the protein universe. PMID:19787035
2-DE analysis indicates that Acinetobacter baumannii displays a robust and versatile metabolism. PMID:19785748
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. PMID:19783819
Comparative genomics of ethanolamine utilization. PMID:19783625
Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. PMID:19767433
Identification and characterization of metagenomic fragments from tidal flat sediment. PMID:19763413
The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. PMID:19734336
The phylogenetic forest and the quest for the elusive tree of life. PMID:19687142
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. PMID:19656385
The transcriptional response of Pasteurella multocida to three classes of antibiotics. PMID:19607655
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. PMID:19594957
Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. PMID:19570746
Comparative transcriptomics in the Triticeae. PMID:19558723
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. PMID:19543979
Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. PMID:19521530
Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification. PMID:19503786
Genome flexibility in Neisseria meningitidis. PMID:19477564
Evolutionary constraints on structural similarity in orthologs and paralogs. PMID:19472362
A complex-centric view of protein network evolution. PMID:19465379
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Modelling prokaryote gene content. PMID:19455209
Positional homology in bacterial genomes. PMID:19455203
Improving protein structure similarity searches using domain boundaries based on conserved sequence information. PMID:19454035
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PMID:19402753
Detection of biochemical pathways by probabilistic matching of phyletic vectors. PMID:19390636
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. PMID:19356244
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. PMID:19351897
Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PMID:19343224
Complete genome sequence of Burkholderia glumae BGR1. PMID:19329631
From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex. PMID:19304752
Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus. PMID:19291314
Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species. PMID:19284579
Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. PMID:19278556
Phylogenetic diversity of stress signalling pathways in fungi. PMID:19232129
MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium. PMID:19228437
Methods for comparative metagenomics. PMID:19208111
Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PMID:19194535
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271
Algorithm of OMA for large-scale orthology inference. PMID:19055798
A bioinformatician's guide to metagenomics. PMID:19052320
RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. PMID:19043046
Complete genome sequence of Rhodobacter sphaeroides KD131. PMID:19028901
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. PMID:19025650
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. PMID:19015141
Extension of the COG and arCOG databases by amino acid and nucleotide sequences. PMID:19014535
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. PMID:19014525
Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. PMID:19000750
Syntenator: multiple gene order alignments with a gene-specific scoring function. PMID:18990215
Large-scale assignment of orthology: back to phylogenetics? PMID:18983710
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. PMID:18978059
Turkey fecal microbial community structure and functional gene diversity revealed by 16S rRNA gene and metagenomic sequences. PMID:18974945
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PMID:18974821
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. PMID:18974178
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. PMID:18948295
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Evolution of genome architecture. PMID:18929678
Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. PMID:18927222
Long simple sequence repeats in host-adapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes. PMID:18925380
Unique genes in plants: specificities and conserved features throughout evolution. PMID:18847470
Probing metagenomics by rapid cluster analysis of very large datasets. PMID:18846219
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. PMID:18845571
MetaSim: a sequencing simulator for genomics and metagenomics. PMID:18841204
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. PMID:18840284
The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. PMID:18813928
Predictive analysis of transmissible quinolone resistance indicates Stenotrophomonas maltophilia as a potential source of a novel family of Qnr determinants. PMID:18793450
Identification of pseudouridine methyltransferase in Escherichia coli. PMID:18755836
Global alignment of multiple protein interaction networks with application to functional orthology detection. PMID:18725631
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562. PMID:18700039
The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PMID:18698409
Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer. PMID:18677521
Conserved upstream open reading frames in higher plants. PMID:18667093
Differences in evolutionary pressure acting within highly conserved ortholog groups. PMID:18637201
Flavin-dependent thymidylate synthase X limits chromosomal DNA replication. PMID:18621705
Evolutionary history of a specialized p450 propane monooxygenase. PMID:18619466
Circular reasoning rather than cyclic expression. PMID:18598377
A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PMID:18596979
Genetic classification of severe early childhood caries by use of subtracted DNA fragments from Streptococcus mutans. PMID:18596144
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. PMID:18586738
Group 2 sigma factor SigB of Corynebacterium glutamicum positively regulates glucose metabolism under conditions of oxygen deprivation. PMID:18567683
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins. PMID:18564434
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. PMID:18562662
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. PMID:18559112
On the origin of new genes in Drosophila. PMID:18550802
Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima. PMID:18540059
A korarchaeal genome reveals insights into the evolution of the Archaea. PMID:18535141
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. PMID:18523433
The structure of an archaeal homodimeric ligase which has RNA circularization activity. PMID:18511537
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. PMID:18511460
Modularity of stress response evolution. PMID:18495925
Uncovering rate variation of lateral gene transfer during bacterial genome evolution. PMID:18492275
The LptA protein of Escherichia coli is a periplasmic lipid A-binding protein involved in the lipopolysaccharide export pathway. PMID:18480051
Microbial genotype-phenotype mapping by class association rule mining. PMID:18467347
The deep archaeal roots of eukaryotes. PMID:18463089
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes. PMID:18456706
Assembly of viral metagenomes from yellowstone hot springs. PMID:18441115
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. PMID:18426584
The emergence and fate of horizontally acquired genes in Escherichia coli. PMID:18404206
Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation. PMID:18400081
Large-scale analysis of gene clustering in bacteria. PMID:18390694
Analysis of the Actinobacillus pleuropneumoniae ArcA regulon identifies fumarate reductase as a determinant of virulence. PMID:18378638
Estimating the extent of horizontal gene transfer in metagenomic sequences. PMID:18366724
Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB. PMID:18359806
Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. PMID:18346278
Evolution of exceptionally large genes in prokaryotes. PMID:18322635
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. PMID:18317809
Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions. PMID:18310429
A gene pattern mining algorithm using interchangeable gene sets for prokaryotes. PMID:18302784
Genome evolution in cyanobacteria: the stable core and the variable shell. PMID:18268351
Comparing patterns of natural selection across species using selective signatures. PMID:18266472
Protein databases on the internet. PMID:18265344
Comparison of envelope-related genes in unicellular and filamentous cyanobacteria. PMID:18253473
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PMID:18248097
Coevolution of gene families in prokaryotes. PMID:18230804
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. PMID:18218977
Superhelical destabilization in regulatory regions of stress response genes. PMID:18208321
An automated protein annotation filter for integrating web-based annotation tools. PMID:18188426
Persistence drives gene clustering in bacterial genomes. PMID:18179692
A Botrytis cinerea emopamil binding domain protein, required for full virulence, belongs to a eukaryotic superfamily which has expanded in euascomycetes. PMID:18156289
AlterORF: a database of alternate open reading frames. PMID:18096612
Computational prediction of protein-protein interactions. PMID:18095187
AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips. PMID:18065560
Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek. PMID:18063717
Evolutionary history of bacteriophages with double-stranded DNA genomes. PMID:18062816
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. PMID:18047665
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. PMID:18042280
Quantification of ortholog losses in insects and vertebrates. PMID:18021399
Modeling protein network evolution under genome duplication and domain shuffling. PMID:17999763
Gene family evolution across 12 Drosophila genomes. PMID:17997610
Molecular basis for evolving modularity in the yeast protein interaction network. PMID:17997598
Role of hypermutability in the evolution of the genus Oenococcus. PMID:17993526
Genome-scale analysis of positionally relocated genes. PMID:17989252
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. PMID:17984228
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
Host pathogen protein interactions predicted by comparative modeling. PMID:17965183
eggNOG: automated construction and annotation of orthologous groups of genes. PMID:17942413
On the detection of functionally coherent groups of protein domains with an extension to protein annotation. PMID:17937820
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
IMG/M: a data management and analysis system for metagenomes. PMID:17932063
Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. PMID:17921277
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PMID:17912365
Abundance and functional diversity of riboswitches in microbial communities. PMID:17908319
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PMID:17895995
Lon protease promotes survival of Escherichia coli during anaerobic glucose starvation. PMID:17891379
Uncovering the mutation-fixation correlation in short lineages. PMID:17883872
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes. PMID:17877818
The anatomy of microbial cell state transitions in response to oxygen. PMID:17785531
Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: a novel superfamily with a two-layer sandwich architecture. PMID:17766377
Extensive parallelism in protein evolution. PMID:17705846
Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli. PMID:17693496
Identification of genes encoding tRNA modification enzymes by comparative genomics. PMID:17673083
The essential tacF gene is responsible for the choline-dependent growth phenotype of Streptococcus pneumoniae. PMID:17660291
Identification of gene targets against dormant phase Mycobacterium tuberculosis infections. PMID:17655757
Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae. PMID:17605819
Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:17601789
The entire organization of transcription units on the Bacillus subtilis genome. PMID:17598888
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. PMID:17586819
Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization. PMID:17584922
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. PMID:17578578
The human phylome. PMID:17567924
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. PMID:17551511
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. PMID:17550610
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. PMID:17545284
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. PMID:17535793
A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases. PMID:17526915
Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12. PMID:17526711
KAAS: an automatic genome annotation and pathway reconstruction server. PMID:17526522
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. PMID:17521444
COMPASS server for remote homology inference. PMID:17517780
Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PMID:17511520
Low concentrations of bile salts induce stress responses and reduce motility in Bacillus cereus ATCC 14579 [corrected]. PMID:17496091
BLASTO: a tool for searching orthologous groups. PMID:17483516
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. PMID:17483455
The early response to acid shock in Lactobacillus reuteri involves the ClpL chaperone and a putative cell wall-altering esterase. PMID:17449683
Characterization of a novel bile-inducible operon encoding a two-component regulatory system in Lactobacillus acidophilus. PMID:17449631
Assessing performance of orthology detection strategies applied to eukaryotic genomes. PMID:17440619
Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis. PMID:17426379
BranchClust: a phylogenetic algorithm for selecting gene families. PMID:17425803
Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies. PMID:17370070
Hierarchical classification of functionally equivalent genes in prokaryotes. PMID:17353185
Orthology prediction at scalable resolution by phylogenetic tree analysis. PMID:17346331
Finding the needles in the metagenome haystack. PMID:17345132
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. PMID:17344419
Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus. PMID:17329823
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). PMID:17313674
Identification of Lactobacillus sakei genes induced during meat fermentation and their role in survival and growth. PMID:17308175
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. PMID:17286872
Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. PMID:17277072
Genome-wide identification and characterization of putative cytochrome P450 genes in the model legume Medicago truncatula. PMID:17273868
Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes. PMID:17269728
FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar Typhimurium (ATCC 14028s). PMID:17220229
GenomeBlast: a web tool for small genome comparison. PMID:17217510
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). PMID:17202165
Evolutionary conservation of domain-domain interactions. PMID:17184549
The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2. PMID:17158670
Operon prediction in Pyrococcus furiosus. PMID:17148478
Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine. PMID:17145952
PATRIC: the VBI PathoSystems Resource Integration Center. PMID:17142235
Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems. PMID:17140285
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. PMID:17135200
Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. PMID:17122336
Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers. PMID:17121677
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PMID:17112314
In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans. PMID:17109759
Arabidopsis-rice-wheat gene orthologues for Na+ transport and transcript analysis in wheat-L. elongatum aneuploids under salt stress. PMID:17103227
Patterns of sequence conservation in presynaptic neural genes. PMID:17096848
Xanthusbase: adapting wikipedia principles to a model organism database. PMID:17090585
Evolutionary genomics of lactic acid bacteria. PMID:17085562
A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. PMID:17085509
Global analysis of mRNA stability in the archaeon Sulfolobus. PMID:17067383
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. PMID:17065606
Bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 beta-galactosidases are arabinogalactan type I oligomer hydrolases. PMID:17056685
Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. PMID:17054778
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PMID:17054397
Integration of curated databases to identify genotype-phenotype associations. PMID:17038185
Comparative genomics of the lactic acid bacteria. PMID:17030793
Protein superfamily evolution and the last universal common ancestor (LUCA). PMID:17021929
The Seventh International Conference on the Genetics of Streptococci, Lactococci, and Enterococci. PMID:17012391
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PMID:17009864
Bacterial postgenomics: the promise and peril of systems biology. PMID:16997947
Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires. PMID:16995943
Effects of temperature on gene expression patterns in Leptospira interrogans serovar Lai as assessed by whole-genome microarrays. PMID:16988264
Genes involved in intrinsic antibiotic resistance of Acinetobacter baylyi. PMID:16940057
Data mining for proteins characteristic of clades. PMID:16936320
Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. PMID:16936055
The cyanobacterial genome core and the origin of photosynthesis. PMID:16924101
Graemlin: general and robust alignment of multiple large interaction networks. PMID:16899655
Cross genome comparisons of serine proteases in Arabidopsis and rice. PMID:16895613
Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families. PMID:16895434
Transport of multidrug resistance substrates by the Streptococcus agalactiae hemolysin transporter. PMID:16885467
Identification of biofilm proteins in non-typeable Haemophilus Influenzae. PMID:16854240
Protein-protein interactions more conserved within species than across species. PMID:16854211
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. PMID:16845020
Bacterial regulatory networks are extremely flexible in evolution. PMID:16840530
Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits. PMID:16835308
Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. PMID:16828186
PHOG: a database of supergenomes built from proteome complements. PMID:16792803
Identification of novel virulence determinants in Mycobacterium paratuberculosis by screening a library of insertional mutants. PMID:16790754
Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PMID:16789831
Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PMID:16789826
Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis. PMID:16789813
Analysis of circular genome rearrangement by fusions, fissions and block-interchanges. PMID:16768797
The Escherichia coli proteome: past, present, and future prospects. PMID:16760308
Similarity searches in genome-wide numerical data sets. PMID:16734895
Variation among species in proteomic sulphur content is related to environmental conditions. PMID:16720405
Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract. PMID:16714589
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. PMID:16709240
Detecting uber-operons in prokaryotic genomes. PMID:16682449
Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. PMID:16651665
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. PMID:16641319
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. PMID:16614445
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. PMID:16606443
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. PMID:16547041
The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity. PMID:16522649
Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. PMID:16513756
The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. PMID:16505379
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. PMID:16478540
A phylogenetic and structural analysis of truncated hemoglobins. PMID:16474979
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. PMID:16473855
Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. PMID:16472398
Active-site residues in the type IV prepilin peptidase homologue PibD from the archaeon Sulfolobus solfataricus. PMID:16452426
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. PMID:16436801
Genome-wide acceleration of protein evolution in flies (Diptera). PMID:16436210
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. PMID:16434444
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. PMID:16423288
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. PMID:16417636
The UCSC Archaeal Genome Browser. PMID:16381898
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. PMID:16381887
The integrated microbial genomes (IMG) system. PMID:16381883
Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. PMID:16377746
Mapping of orthologous genes in the context of biological pathways: An application of integer programming. PMID:16373500
The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine. PMID:16369018
A comparative categorization of protein function encoded in bacterial or archeal genomic islands. PMID:16341468
Computational identification of strain-, species- and genus-specific proteins. PMID:16305751
Evidence of a large novel gene pool associated with prokaryotic genomic islands. PMID:16299586
Correlation between sequence conservation and the genomic context after gene duplication. PMID:16257980
The last common ancestor: what's in a name? PMID:16254691
A collection of amino acid replacement matrices derived from clusters of orthologs. PMID:16245010
The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis. PMID:16207374
Inducible gene expression in Lactobacillus reuteri LTH5531 during type II sourdough fermentation. PMID:16204499
Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus. PMID:16204490
Phylogenetic detection of conserved gene clusters in microbial genomes. PMID:16202130
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks. PMID:16202129
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. PMID:16199763
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". PMID:16172379
Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. PMID:16169924
Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution. PMID:16150155
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. PMID:16147987
GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. PMID:16131397
Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. PMID:16113260
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PMID:16110343
Bioinformatics for whole-genome shotgun sequencing of microbial communities. PMID:16110337
Characterization of an unusual cold-active beta-glucosidase belonging to family 3 of the glycoside hydrolases from the psychrophilic isolate Paenibacillus sp. strain C7. PMID:16085807
Predicting specificity-determining residues in two large eukaryotic transcription factor families. PMID:16085755
Estimating the tempo and mode of gene family evolution from comparative genomic data. PMID:16077014
Protein content of minimal and ancestral ribosome. PMID:16043494
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. PMID:16026603
The MicrobesOnline Web site for comparative genomics. PMID:15998914
Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis. PMID:15995210
Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold. PMID:15987908
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. PMID:15980564
BASys: a web server for automated bacterial genome annotation. PMID:15980511
The net of life: reconstructing the microbial phylogenetic network. PMID:15965028
The maize root transcriptome by serial analysis of gene expression. PMID:15965024
AutoFACT: an automatic functional annotation and classification tool. PMID:15960857
Protein length in eukaryotic and prokaryotic proteomes. PMID:15951512
A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. PMID:15942028
Novel carotenoid oxidase involved in biosynthesis of 4,4'-diapolycopene dialdehyde. PMID:15933032
SplitTester: software to identify domains responsible for functional divergence in protein family. PMID:15929795
Genes coding for tryptophan-rich proteins are transcribed throughout the asexual cycle of Plasmodium falciparum. PMID:15924221
Prediction of functional modules based on comparative genome analysis and Gene Ontology application. PMID:15901854
Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. PMID:15888677
Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes. PMID:15876568
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. PMID:15867197
Practical lessons from protein structure prediction. PMID:15805122
Systematic association of genes to phenotypes by genome and literature mining. PMID:15799710
Complex genomic rearrangements lead to novel primate gene function. PMID:15710750
Specialized microbial databases for inductive exploration of microbial genome sequences. PMID:15698474
Accelerated evolution associated with genome reduction in a free-living prokaryote. PMID:15693943
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PMID:15684069
Making connections between novel transcription factors and their DNA motifs. PMID:15653829
fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis. PMID:15630478
Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. PMID:15618402
GenDiS: Genomic Distribution of protein structural domain Superfamilies. PMID:15608190
Update on human genome completion and annotations: gene nomenclature. PMID:15601535
Computing prokaryotic gene ubiquity: rescuing the core from extinction. PMID:15574825
Periplasmic cleavage and modification of the 1-phosphate group of Helicobacter pylori lipid A. PMID:15489235
PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms. PMID:15488147
'Conserved hypothetical' proteins: prioritization of targets for experimental study. PMID:15479782
Crystal structure of Bacillus subtilis YdaF protein: a putative ribosomal N-acetyltransferase. PMID:15468321
Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. PMID:15461803
Automated prediction of protein function and detection of functional sites from structure. PMID:15456910
Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved. PMID:15448184
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. PMID:15375139
Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. PMID:15317790
The LuxR homolog ExpR, in combination with the Sin quorum sensing system, plays a central role in Sinorhizobium meliloti gene expression. PMID:15292148
Indel-based evolutionary distance and mouse-human divergence. PMID:15289479
Identification of 315 genes essential for early zebrafish development. PMID:15256591
cis-Regulatory and protein evolution in orthologous and duplicate genes. PMID:15256508
Prevalence of intron gain over intron loss in the evolution of paralogous gene families. PMID:15254274
Duplicated genes evolve slower than singletons despite the initial rate increase. PMID:15238160
National center for biotechnology information viral genomes project. PMID:15220402
Computational inference of scenarios for alpha-proteobacterial genome evolution. PMID:15210995
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. PMID:15173116
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. PMID:15170256
MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria. PMID:15166137
Prolinks: a database of protein functional linkages derived from coevolution. PMID:15128449
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. PMID:15128446
The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. PMID:15123580
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. PMID:15121896
Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. PMID:15096577
Segmentally variable genes: a new perspective on adaptation. PMID:15094797
Functional classification of proteins and protein variants. PMID:15087495
Identification of candidate disease genes by EST alignments, synteny, and expression and verification of Ensembl genes on rat chromosome 1q43-54. PMID:15060005
Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli. PMID:15004283
Quantifying modularity in the evolution of biomolecular systems. PMID:14993205
Comparative genomics and the gene complement of a minimal cell. PMID:14979660
Trends between gene content and genome size in prokaryotic species with larger genomes. PMID:14973198
Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions. PMID:14973045
Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. PMID:14973021
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. PMID:14759257
The Arabidopsis thaliana dihydroxyacetone phosphate reductase gene SUPPRESSSOR OF FATTY ACID DESATURASE DEFICIENCY1 is required for glycerolipid metabolism and for the activation of systemic acquired resistance. PMID:14729910
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. PMID:14724320
A cross-genomic approach for systematic mapping of phenotypic traits to genes. PMID:14707173
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. PMID:14681411
The compositional adjustment of amino acid substitution matrices. PMID:14663142
Comparative genome analysis of Vibrio vulnificus, a marine pathogen. PMID:14656965
Genetic analysis of the capsule locus of Haemophilus influenzae serotype f. PMID:14638817
Gene essentiality determines chromosome organisation in bacteria. PMID:14602916
PCAS--a precomputed proteome annotation database resource. PMID:14594458
Evolution of the yeast protein interaction network. PMID:14557537
Comprehensive analysis of orthologous protein domains using the HOPS database. PMID:14525933
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. PMID:14525925
Thermophile-specific proteins: the gene product of aq_1292 from Aquifex aeolicus is an NTPase. PMID:14503925
Complete genome sequence and analysis of Wolinella succinogenes. PMID:14500908
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. PMID:14500884
The COG database: an updated version includes eukaryotes. PMID:12969510
OrthoMCL: identification of ortholog groups for eukaryotic genomes. PMID:12952885
Comparative genomics of Archaea: how much have we learned in six years, and what's next? PMID:12914651
Protein families and TRIBES in genome sequence space. PMID:12888524
Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. PMID:12888511
Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. PMID:12877745
Gene content and organization of an 85-kb DNA segment from the genome of the phytopathogenic mollicute Spiroplasma kunkelii. PMID:12845528
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. PMID:12840036
Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease. PMID:12816550
Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity. PMID:12813086
The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus. PMID:12810954
Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. PMID:12805597
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. PMID:12799346
Physical map and genome sequencing survey of Mycoplasma haemofelis (Haemobartonella felis). PMID:12761157
Homologous npdGI genes in 2,4-dinitrophenol- and 4-nitrophenol-degrading Rhodococcus spp. PMID:12732545
Comparing bacterial genomes through conservation profiles. PMID:12695324
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. PMID:12682364
Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. PMID:12594930
Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level. PMID:12537549
Strategies and tools for whole-genome alignments. PMID:12529308
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. PMID:12529304
MBGD: microbial genome database for comparative analysis. PMID:12519947
Ensembl 2002: accommodating comparative genomics. PMID:12519943
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. PMID:12515583
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. PMID:12515582
Genomic scale analysis of Pasteurella multocida gene expression during growth within the natural chicken host. PMID:12438364
The society of genes: networks of functional links between genes from comparative genomics. PMID:12429063
Genomic functional annotation using co-evolution profiles of gene clusters. PMID:12429059
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. PMID:12364605
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. PMID:12270832
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. PMID:12235368
Membrane association and kinase-like motifs of the RamC protein of Streptomyces coelicolor. PMID:12169618
Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. PMID:12119367
Phylogenetic analysis of the human basic helix-loop-helix proteins. PMID:12093377
Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. PMID:12049666
Evolution of gene fusions: horizontal transfer versus independent events. PMID:12049665
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. PMID:12045149
Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. PMID:12032089
Connected gene neighborhoods in prokaryotic genomes. PMID:12000841
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. PMID:11930014
Comparative genomics using data mining tools. PMID:11927774
Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. PMID:11918828
Comparative genomics and evolution of proteins involved in RNA metabolism. PMID:11917006
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). PMID:11875039
Selection in the evolution of gene duplications. PMID:11864370
Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes. PMID:11847285
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. PMID:11847126
Functional genomics of pathogenic bacteria. PMID:11839188
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. PMID:11790256
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. PMID:11790254
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. PMID:11788711
Predictome: a database of putative functional links between proteins. PMID:11752322
Genome trees constructed using five different approaches suggest new major bacterial clades. PMID:11734060
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". PMID:11731503
Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. PMID:11438739
Massive sequence comparisons as a help in annotating genomic sequences. PMID:11435413
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. PMID:11433035
Identification of conserved C2H2 zinc-finger gene families in the Bilateria. PMID:11387037
Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea. PMID:11381026
Isolation of PDX2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria. PMID:11344146
The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. PMID:11337471
The celA gene, encoding a glycosyl hydrolase family 3 beta-glucosidase in Azospirillum irakense, is required for optimal growth on cellobiosides. PMID:11319128
Lineage-specific gene expansions in bacterial and archaeal genomes. PMID:11282971
A novel site of antibiotic action in the ribosome: interaction of evernimicin with the large ribosomal subunit. PMID:11259679
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. PMID:11238985
The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. PMID:11206077
Functional prediction: identification of protein orthologs and paralogs. PMID:11206056
Interkingdom gene fusions. PMID:11178267
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). PMID:11178258
Gene discovery through genomic sequencing of Brucella abortus. PMID:11159979
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. PMID:11157787
Genomewide function conservation and phylogeny in the Herpesviridae. PMID:11156614
The COG database: new developments in phylogenetic classification of proteins from complete genomes. PMID:11125040
Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining. PMID:11119305
Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. PMID:11076853
Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. PMID:11024184
Lineage-specific loss and divergence of functionally linked genes in eukaryotes. PMID:11016957
Comparative genomics of plant chromosomes. PMID:11006329
Comparative genomics and understanding of microbial biology. PMID:10998382
From complete genomes to measures of substitution rate variability within and between proteins. PMID:10899148
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. PMID:10854412
Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP. PMID:10841541
Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. PMID:10810093
Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2. PMID:10809443
In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants. PMID:10809006
Gene content phylogeny of herpesviruses. PMID:10805793
Analysis of a complete homeobox gene repertoire: implications for the evolution of diversity. PMID:10781048
Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. PMID:10737802
Characterization of a 12-kilodalton rhodanese encoded by glpE of Escherichia coli and its interaction with thioredoxin. PMID:10735872
Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily. PMID:10704478
Genetics of mosquito vector competence. PMID:10704476
Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. PMID:10678983
Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. PMID:10633087
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. PMID:10592199
XREFdb: cross-referencing the genetics and genes of mammals and model organisms. PMID:10592198
ProtoMap: automatic classification of protein sequences and hierarchy of protein families. PMID:10592179
The COG database: a tool for genome-scale analysis of protein functions and evolution. PMID:10592175
Automated diagnosis of data-model conflicts using metadata. PMID:10495098
Pathway alignment: application to the comparative analysis of glycolytic enzymes. PMID:10493919
A single gene (tts) located outside the cap locus directs the formation of Streptococcus pneumoniae type 37 capsular polysaccharide. Type 37 pneumococci are natural, genetically binary strains. PMID:10432287
Genomics, mutations and the Internet: the naming and use of parts. PMID:10407783
Feasibility in the inverse protein folding protocol. PMID:10338011
Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. PMID:10228173
The use of gene clusters to infer functional coupling. PMID:10077608
Genomics and antimicrobial drug discovery. PMID:10049248
Expanding yeast knowledge online. PMID:9885151
The Hsc66-Hsc20 chaperone system in Escherichia coli: chaperone activity and interactions with the DnaK-DnaJ-grpE system. PMID:9852006
Comparison of the complete protein sets of worm and yeast: orthology and divergence. PMID:9851918
Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. PMID:9843945
Molecular characterization of the complete 23F capsular polysaccharide locus of Streptococcus pneumoniae. PMID:9748469
Sequencing of cDNA clones from the genetic map of tomato (Lycopersicon esculentum). PMID:9724330
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. PMID:9722641
Detection and identification of previously unrecognized microbial pathogens. PMID:9716951
Self-identification of protein-coding regions in microbial genomes. PMID:9707594
Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. PMID:9689093
Measuring genome evolution. PMID:9600883
The organization and evolution of the spinach stress 70 molecular chaperone gene family. PMID:9548981
The underlying pathway structure of biochemical reaction networks. PMID:9539712
http://www.hegroup.org/docs/OntoCOG_ICBO-2011_Proceeding.pdf

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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

transcript
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: CAO; Clusters of Orthologous Groups (COG) Analysis Ontology; DOI: https://doi.org/10.25504/FAIRsharing.wp0134; Last edited: Aug. 8, 2019, 10:56 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

gene orthology protein transcript polypeptide region

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Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes

Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups

Database of Orthologous Groups

KusakiDB

SourceForge

Databases of Orthologous Promoters

Orthologous Group Ontology

ORTHOlogous MAmmalian Markers

Automatic molecular interaction predictions

COG-UK Viral Genome Sequences

Protein Clusters

Ontology of Glucose Metabolism Disorder

pVOGs

Drosophila developmental ontology

PhytoMine

Sequence Ontology

Fission Yeast Phenotype Ontology

SARS-CoV-2 viral sequencing data (COG-UK data) - Lineage/Variant Data - England

VOGDB

Minimal Information for Protein Functional Evaluation