EggNOG-mapper
For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.
Description
More detailed information about this field from each metasource.
For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:05.829198
Webpage:
http://beta-eggnogdb.embl.de/#/app/emapperWebpage
More detailed information about this field from each metasource.
http://beta-eggnogdb.embl.de/#/app/emapper
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:05.829198
Licence:
Name: GPL-3.0Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
PMID: 28460117
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
PMID: 34597405
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PMID: 28053165
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
Publications
More detailed information about this field from each metasource.
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
PMID: 28460117
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
PMID: 34597405
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PMID: 28053165
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:05.829198
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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
PubMed citations: 804.
804 articles citing: Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. PMID:36050782
Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. PMID:36042324
Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity. PMID:36042194
Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments. PMID:36033848
Genomic and physiological analysis of C50 carotenoid-producing novel Halorubrum ruber sp. nov. PMID:36029458
Isolation and Characterization of a Newly Discovered Phage, V-YDF132, for Lysing Vibrio harveyi. PMID:36016424
In Situ Genomics and Transcriptomics of SAR202 Subclusters Revealed Subtle Distinct Activities in Deep-Sea Water. PMID:36014047
Expression Profiles of Microsatellites in Fruit Tissues of Akebia trifoliata and Development of Efficient EST-SSR Markers. PMID:36011362
Transcriptomic and Behavioral Studies of Small Yellow Croaker (Larimichthyspolyactis) in Response to Noise Exposure. PMID:36009652
Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains. PMID:36008774
Integrated transcriptomic and transgenic analyses reveal potential mechanisms of poplar resistance to Alternaria alternata infection. PMID:36008749
A Long-Read Genome Assembly of a Native Mite in China Pyemotes zhonghuajia Yu, Zhang & He (Prostigmata: Pyemotidae) Reveals Gene Expansion in Toxin-Related Gene Families. PMID:36006233
Divergent genomic trajectories predate the origin of animals and fungi. PMID:36002568
A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa. PMID:36000319
A pan-Zea genome map for enhancing maize improvement. PMID:35999561
Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes. PMID:35976223
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate. PMID:35970961
Comparative chloroplast genome and transcriptome analysis on the ancient genus Isoetes from China. PMID:35968088
Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. PMID:35965344
Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. PMID:35950761
Short-Term Test for Toxicogenomic Analysis of Ecotoxic Modes of Action in Lemna minor. PMID:35926083
Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing. PMID:35918353
Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota. PMID:35913596
(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota. PMID:35913193
De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae. PMID:35909967
Genome-wide identification and expression pattern analysis of lipoxygenase gene family in turnip (Brassica rapa L. subsp. rapa). PMID:35898937
Complete Genomes of Theileria orientalis Chitose and Buffeli Genotypes Reveal within Species Translocations and Differences in ABC Transporter Content. PMID:35890045
Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila. PMID:35889069
Hyphomonas sediminis sp. nov., isolated from marine sediment. PMID:35876987
A Candidate Gene Cluster for the Bioactive Natural Product Gyrophoric Acid in Lichen-Forming Fungi. PMID:35867425
Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber. PMID:35858888
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. PMID:35858453
A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation. PMID:35852419
Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens. PMID:35847106
On the Compatibility of Fish Meal Replacements in Aquafeeds for Rainbow Trout. A Combined Metabolomic, Proteomic and Histological Study. PMID:35846007
A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. PMID:35835784
Isolation and Genome Sequence of a Novel Phosphate-Solubilizing Rhizobacterium Bacillus altitudinis GQYP101 and Its Effects on Rhizosphere Microbial Community Structure and Functional Traits of Corn Seedling. PMID:35834051
Genomic analysis uncovers laccase-coding genes and biosynthetic gene clusters encoding antimicrobial compounds in laccase-producing Acinetobacter baumannii. PMID:35831359
Fictibacillus marinisediminis sp. nov., a nitrate-reducing bacterium isolated from marine sediment in Hupo Basin, Republic of Korea. PMID:35829821
Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex. PMID:35822822
Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. PMID:35809049
Differences between the global transcriptomes of Salmonella enterica serovars Dublin and Cerro infecting bovine epithelial cells. PMID:35804292
The evolutionary origin of host association in the Rickettsiales. PMID:35798888
CT295 Is Chlamydia trachomatis' Phosphoglucomutase and a Type 3 Secretion Substrate. PMID:35795184
Genome-wide comparison deciphers lifestyle adaptation and glass biodeterioration property of Curvularia eragrostidis C52. PMID:35794131
Genomic and phenotypic comparison of Prevotella intermedia strains possessing different virulence in vivo. PMID:35791444
Proteomic response of Turicibacter bilis MMM721 to chicken bile and its bile acids. PMID:35780123
A chromosome-level genome assembly of Neotoxoptera formosana (Takahashi, 1921) (Hemiptera: Aphididae). PMID:35775933
Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. PMID:35766381
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. PMID:35764601
A genome and gene catalog of glacier microbiomes. PMID:35760913
An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth. PMID:35744704
A Comprehensive Study of the WRKY Transcription Factor Family in Strawberry. PMID:35736736
Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. PMID:35736002
Biosynthetic potential of the global ocean microbiome. PMID:35732736
Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China. PMID:35727019
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. PMID:35725628
Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. PMID:35725368
Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes. PMID:35715496
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Transcriptome analysis provides new insights into the tolerance and aerobic reduction of Shewanella decolorationis Ni1-3 to bromate. PMID:35708750
Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool. PMID:35705621
Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. PMID:35701646
Draft Genome Sequences of Five Cystobasidium ongulense Strains Isolated from Areas near Syowa Station, East Antarctica. PMID:35695498
A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants. PMID:35688828
Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. PMID:35678932
Closed, Circular Genome Sequence of Aureococcus anophagefferens Virus, a Lytic Virus of a Brown Tide-Forming Alga. PMID:35678577
Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms. PMID:35676296
The Gut Microbiota Composition of Cnaphalocrocis medinalis and Their Predicted Contribution to Larval Nutrition. PMID:35668757
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Transcriptomic analysis provides insights into molecular mechanisms of thermal physiology. PMID:35659182
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca. PMID:35646071
Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. PMID:35640266
Genomic and Physiological Characterization of Metabacillus flavus sp. nov., a Novel Carotenoid-Producing Bacilli Isolated from Korean Marine Mud. PMID:35630423
Whole-Genome Sequencing Reveals Lignin-Degrading Capacity of a Ligninolytic Bacterium (Bacillus cereus) from Buffalo (Bubalus bubalis) Rumen. PMID:35627226
Taxonomic and Bioactivity Characterizations of Mameliella alba Strain LZ-28 Isolated from Highly Toxic Marine Dinoflagellate Alexandrium catenella LZT09. PMID:35621971
Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae. PMID:35605195
Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. PMID:35602010
Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.). PMID:35596045
A Chromosome-Level Genome of the Camphor Tree and the Underlying Genetic and Climatic Factors for Its Top-Geoherbalism. PMID:35592577
Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes. PMID:35588244
Fuel source shift or cost reduction: Context-dependent adaptation strategies in closely related Neodon fuscus and Lasiopodomys brandtii against hypoxia. PMID:35585802
Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology. PMID:35573199
Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species. PMID:35562911
Patients with Primary and Secondary Bile Duct Stones Harbor Distinct Biliary Microbial Composition and Metabolic Potential. PMID:35548466
Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations. PMID:35547121
Evaluating metagenomic assembly approaches for biome-specific gene catalogues. PMID:35524337
Response of the Anaerobic Methanotrophic Archaeon Candidatus "Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment. PMID:35509320
Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas. PMID:35505882
Walnut N-Acetylserotonin Methyltransferase Gene Family Genome-Wide Identification and Diverse Functions Characterization During Flower Bud Development. PMID:35498672
Retracted Article: Investigation of yellow horn (Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study. PMID:35496033
Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. PMID:35495730
ARVCF catenin controls force production during vertebrate convergent extension. PMID:35476939
Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats. PMID:35467389
Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. PMID:35465165
Characterisation of Bacteriophage vB_SmaM_Ps15 Infective to Stenotrophomonas maltophilia Clinical Ocular Isolates. PMID:35458438
Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features. PMID:35447921
Honeybee gut Lactobacillus modulates host learning and memory behaviors via regulating tryptophan metabolism. PMID:35440638
Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex. PMID:35438177
Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. PMID:35435701
Temporal Dynamic Transcriptome Landscape Reveals Regulatory Network During the Early Differentiation of Female Strobilus Buds in Ginkgo biloba. PMID:35432408
Genomic Evidence for the Recycling of Complex Organic Carbon by Novel Thermoplasmatota Clades in Deep-Sea Sediments. PMID:35430893
Comparative Genomics of Seasonal Senescence in Forest Trees. PMID:35409113
Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. PMID:35406987
Multiple Hybridization Events Punctuate the Evolutionary Trajectory of Malassezia furfur. PMID:35404119
Short Linear Motifs (SLiMs) in "Core" RxLR Effectors of Phytophthora parasitica var. nicotianae: a Case of PpRxLR1 Effector. PMID:35404090
Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. PMID:35401599
Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats. PMID:35392807
Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli. PMID:35388735
Extensive epigenetic modification with large-scale chromosomal and plasmid recombination characterise the Legionella longbeachae serogroup 1 genome. PMID:35388097
Genome Sequence of Streptomyces sp. Strain GQFP Isolated from Soil Near the Roots of Pharmaceutical Plant Elaeagnus pungens. PMID:35377185
Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function. PMID:35372117
Unifying the known and unknown microbial coding sequence space. PMID:35356891
Bacteriocin Producing Streptococcus agalactiae Strains Isolated from Bovine Mastitis in Brazil. PMID:35336163
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences. PMID:35330728
Genomic and Experimental Analysis of the Insecticidal Factors Secreted by the Entomopathogenic Fungus Beauveria pseudobassiana RGM 2184. PMID:35330256
Proteomic Analysis Reveals Enzymes for β-D-Glucan Formation and Degradation in Levilactobacillus brevis TMW 1.2112. PMID:35328813
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome. PMID:35324915
Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function. PMID:35320603
The virota and its transkingdom interactions in the healthy infant gut. PMID:35320047
A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians. PMID:35311560
Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn's Disease. PMID:35308389
Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. PMID:35306876
Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. PMID:35300488
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. PMID:35298369
A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). PMID:35294470
An artificial host system enables the obligate parasite Cuscuta campestris to grow and reproduce in vitro. PMID:35294033
Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction. PMID:35293790
Bulinus truncatus transcriptome - a resource to enable molecular studies of snail and schistosome biology. PMID:35284899
Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. PMID:35283890
The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. PMID:35273345
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae. PMID:35272717
A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. PMID:35269627
Distinct Roles of Honeybee Gut Bacteria on Host Metabolism and Neurological Processes. PMID:35266810
The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species. PMID:35255946
Phosphonate production by marine microbes: Exploring new sources and potential function. PMID:35254902
Virome and Blood Meal-Associated Host Responses in Ixodes persulcatus Naturally Fed on Patients. PMID:35250897
Considerations for constructing a protein sequence database for metaproteomics. PMID:35242286
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. PMID:35241796
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. PMID:35241788
Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. PMID:35230132
Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption. PMID:35229641
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing. PMID:35228861
Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis. PMID:35225671
Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. PMID:35222299
Catabolic protein degradation in marine sediments confined to distinct archaea. PMID:35220398
The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide. PMID:35217776
Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. PMID:35196120
Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PMID:35190783
Heat-Killed Lacticaseibacillus paracasei GMNL-653 Exerts Antiosteoporotic Effects by Restoring the Gut Microbiota Dysbiosis in Ovariectomized Mice. PMID:35187034
Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide. PMID:35178038
Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. PMID:35177826
Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. PMID:35177000
Genome-Annotated Bacterial Collection of the Barley Rhizosphere Microbiota. PMID:35175125
A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae). PMID:35171284
Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate. PMID:35171033
Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PMID:35167626
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. PMID:35166655
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon. PMID:35145489
The microbiome of the buffalo digestive tract. PMID:35145088
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida. PMID:35135479
Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics. PMID:35130123
Genome-wide evolutionary response of European oaks during the Anthropocene. PMID:35127134
Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas). PMID:35126426
Interactions between strains govern the eco-evolutionary dynamics of microbial communities. PMID:35119363
Genomic and Functional Dissections of Dickeya zeae Shed Light on the Role of Type III Secretion System and Cell Wall-Degrading Enzymes to Host Range and Virulence. PMID:35107329
Gradients in gene essentiality reshape antibacterial research. PMID:35104846
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. PMID:35089086
Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum. PMID:35084297
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng. PMID:35069616
Genomic Features and Construction of Streamlined Genome Chassis of Nisin Z Producer Lactococcus lactis N8. PMID:35056496
Resolving the structure of phage-bacteria interactions in the context of natural diversity. PMID:35042853
Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae. PMID:35042848
Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication. PMID:35037017
Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PMID:35036136
Respiratory tract infections and gut microbiome modifications: A systematic review. PMID:35025938
Complete genome sequence data of tropical thermophilic bacterium Parageobacillus caldoxylosilyticus ER4B. PMID:35024395
Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station. PMID:35019675
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption. PMID:35012704
Complete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing. PMID:34996906
Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. PMID:34988389
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. PMID:34983386
Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail. PMID:34980289
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. PMID:34972821
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Genetic diversity of Leptospira isolates in Lao PDR and genome analysis of an outbreak strain. PMID:34962921
Halomonas populi sp. nov. isolated from Populus euphratica. PMID:34961889
Alterations in the Transcriptome of Rye Plants following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis. PMID:34961191
Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader. PMID:34956332
First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene. PMID:34956133
The Genome of the "Sea Vomit" Didemnum vexillum. PMID:34947908
Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. PMID:34937940
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections. PMID:34928200
Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont. PMID:34925404
Towards the biogeography of prokaryotic genes. PMID:34912116
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. PMID:34911965
Chromosomal Fusions Facilitate Adaptation to Divergent Environments in Threespine Stickleback. PMID:34908155
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. PMID:34893913
The Second Chromosome Promotes the Adaptation of the Genus Flammeovirga to Complex Environments. PMID:34878294
Genome insights of Enterococcus raffinosus CX012922, isolated from the feces of a Crohn's disease patient. PMID:34876224
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. PMID:34873295
Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains. PMID:34867904
Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota. PMID:34862421
Emergence and global spread of Listeria monocytogenes main clinical clonal complex. PMID:34851675
Genetic Characterization of Salmonella Infantis with Multiple Drug Resistance Profiles Isolated from a Poultry-Farm in Chile. PMID:34835497
A Deep Learning Approach with Data Augmentation to Predict Novel Spider Neurotoxic Peptides. PMID:34830173
Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants. PMID:34826099
Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. PMID:34822492
De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PMID:34820176
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen. PMID:34819644
A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking. PMID:34797875
High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain. PMID:34797858
Complete genome sequence of Lactobacillus amylovorus 1394N20, a potential probiotic strain, isolated from a Hanwoo calf. PMID:34796359
Whole Genome Sequencing Analysis of Bacillus thuringiensis GR007 Reveals Multiple Pesticidal Protein Genes. PMID:34795652
Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii. PMID:34789157
Vaccine Design by Reverse Vaccinology and Machine Learning. PMID:34784028
The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. PMID:34768799
An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. PMID:34763597
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand. PMID:34733249
Underwater CAM photosynthesis elucidated by Isoetes genome. PMID:34732722
Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator. PMID:34725408
Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola. PMID:34724179
Genomic Characterisation of Campylobacter jejuni Isolates Recovered During Commercial Broiler Production. PMID:34721320
The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra). PMID:34712757
Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid. PMID:34711172
Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales. PMID:34711170
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. PMID:34700384
Influence of formic acid treatment on the proteome of the ectoparasite Varroa destructor. PMID:34699527
Genome Evolution of Filamentous Cyanobacterium Nostoc Species: From Facultative Symbiosis to Free Living. PMID:34683336
The Response of Airborne Mycobiome to Dust Storms in the Eastern Mediterranean. PMID:34682226
Molecular Cytogenetic Analysis of the Introgression between Agropyron cristatum P Genome and Wheat Genome. PMID:34681868
Depside and Depsidone Synthesis in Lichenized Fungi Comes into Focus through a Genome-Wide Comparison of the Olivetoric Acid and Physodic Acid Chemotypes of Pseudevernia furfuracea. PMID:34680078
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem. PMID:34668130
Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. PMID:34665012
Genome analysis of alginate synthesizing Pseudomonas aeruginosa strain SW1 isolated from degraded seaweeds. PMID:34661815
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. PMID:34654884
Expanding the Burkholderia pseudomallei Complex with the Addition of Two Novel Species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. PMID:34644162
Na+-Coupled Respiration and Reshaping of Extracellular Polysaccharide Layer Counteract Monensin-Induced Cation Permeability in Prevotella bryantii B14. PMID:34638543
Transcriptomic Profiling Reveals Shared Signalling Networks Between Flower Development and Herbivory-Induced Responses in Tomato. PMID:34630470
Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms. PMID:34605764
Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment. PMID:34604935
Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing. PMID:34601502
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. PMID:34593997
Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. PMID:34593802
Chromosome-Level Genome Assembly and Annotation of the Fiber Flax (Linum usitatissimum) Genome. PMID:34589116
The genomic basis of army ant chemosensory adaptations. PMID:34582590
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing. PMID:34581030
OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. PMID:34580179
Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes. PMID:34578230
Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. PMID:34576801
Global Transcriptome Profile of the Oleaginous Yeast Saitozyma podzolica DSM 27192 Cultivated in Glucose and Xylose. PMID:34575796
Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology. PMID:34575738
The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3. PMID:34568919
Different evolutionary trends form the twilight zone of the bacterial pan-genome. PMID:34559043
The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids. PMID:34556718
The Acinetobacter baumannii disinfectant resistance protein, AmvA, is a spermidine and spermine efflux pump. PMID:34552198
The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. PMID:34549894
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. PMID:34546073
The molecular interplay of the establishment of an infection - gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus. PMID:34544390
Insights Into Walnut Lipid Metabolism From Metabolome and Transcriptome Analysis. PMID:34539744
Draft genome sequencing and functional annotation and characterization of biofilm-producing bacterium Bacillus novalis PD1 isolated from rhizospheric soil. PMID:34537868
Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi. PMID:34528823
Disease-induced changes in plant microbiome assembly and functional adaptation. PMID:34526096
Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae). PMID:34508228
Chromosome-Level Genome Sequence of Aspergillus puulaauensis MK2, a Fungus Isolated from a Dead Hard Tick. PMID:34498921
Genome Structural Variation Landscape and Its Selection Signatures in the Fast-growing Strains of the Pacific Oyster, Crassostrea gigas. PMID:34498173
Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species. PMID:34490050
Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey. PMID:34489902
Pseudomonas palmensis sp. nov., a Novel Bacterium Isolated From Nicotiana glauca Microbiome: Draft Genome Analysis and Biological Potential for Agriculture. PMID:34489881
Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. PMID:34484146
A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration. PMID:34476377
Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. PMID:34475528
Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model. PMID:34470652
Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer. PMID:34465850
The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions. PMID:34454597
Aryl Hydrocarbon Receptor Deficiency in Intestinal Epithelial Cells Aggravates Alcohol-Related Liver Disease. PMID:34454169
Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species. PMID:34448059
Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing. PMID:34447652
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. PMID:34446072
Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. PMID:34440014
Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens. PMID:34437838
Genetic response to nitrogen starvation in the aggressive Eucalyptus foliar pathogen Teratosphaeria destructans. PMID:34432124
Identification of Candidate Genes Regulating the Seed Coat Color Trait in Sesame (Sesamum indicum L.) Using an Integrated Approach of QTL Mapping and Transcriptome Analysis. PMID:34422002
Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development. PMID:34418952
Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence. PMID:34413844
Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes. PMID:34411120
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. PMID:34408268
Adaptive Laboratory Evolution as a Means To Generate Lactococcus lactis Strains with Improved Thermotolerance and Ability To Autolyze. PMID:34406823
De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families. PMID:34376711
Transcriptional response of mushrooms to artificial sun exposure. PMID:34367595
Clostridium cellulovorans Proteomic Responses to Butanol Stress. PMID:34367082
Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis. PMID:34361922
Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens. PMID:34361691
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution. PMID:34343278
The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae. PMID:34343248
The Dynamic Transition of Persistence toward the Viable but Nonculturable State during Stationary Phase Is Driven by Protein Aggregation. PMID:34340538
Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus. PMID:34335500
The abaI/abaR Quorum Sensing System Effects on Pathogenicity in Acinetobacter baumannii. PMID:34322102
Public good exploitation in natural bacterioplankton communities. PMID:34321201
Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation. PMID:34315471
Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae. PMID:34313008
The balance of crystalline and amorphous regions in the fibroin structure underpins the tensile strength of bagworm silk. PMID:34311769
Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community. PMID:34308332
Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing. PMID:34307461
Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs. PMID:34305992
Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. PMID:34298887
Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles. PMID:34294881
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients. PMID:34292148
Chromosome-Level Genome Sequence of the Black Koji Fungus Aspergillus luchuensis RIB2601. PMID:34292062
The Interspecific Fungal Hybrid Verticillium longisporum Displays Subgenome-Specific Gene Expression. PMID:34281400
Dynamics in Bacterial Community Affected by Mesoscale Eddies in the Northern Slope of the South China Sea. PMID:34272992
Towards omics-based predictions of planktonic functional composition from environmental data. PMID:34272373
Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. PMID:34272286
At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. PMID:34268133
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Discerning the role of a functional arsenic-resistance cassette in the evolution and adaptation of a rice pathogen. PMID:34254933
Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum. PMID:34254817
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PMID:34252082
Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov., two novel moderately halotolerant bacteria isolated from the coastal algae. PMID:34251527
Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars' Variation in Grain Zn Concentration. PMID:34248914
Diploidy within a Haploid Genus of Entomopathogenic Fungi. PMID:34247231
Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment. PMID:34235213
Achromobacter spp. genetic adaptation in cystic fibrosis. PMID:34232117
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance. PMID:34222039
A genome wide transcriptional study of Populus alba x P. tremula var. glandulosa in response to nitrogen deficiency stress. PMID:34220043
Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. PMID:34216519
Genome sequences and in silico effector mining of Corynespora cassiicola CC_29 and Corynespora olivacea CBS 114450. PMID:34213598
Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. PMID:34211188
Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov. PMID:34209778
Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D. PMID:34205451
Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. PMID:34201869
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. PMID:34197621
Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia). PMID:34189321
Pangenomics reveals alternative environmental lifestyles among chlamydiae. PMID:34188040
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov. PMID:34184980
Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. PMID:34184916
A Significantly High Abundance of "Candidatus Liberibacter asiaticus" in Citrus Fruit Pith: in planta Transcriptome and Anatomical Analyses. PMID:34177866
Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp. PMID:34177856
Development of a Multiplex PCR Assay for Genotyping the Fish Pathogen Piscirickettsia salmonis Through Comparative Genomics. PMID:34177855
Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia. PMID:34177840
Flavobacterium difficile sp. nov., isolated from a freshwater waterfall. PMID:34136928
Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. PMID:34135337
The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology. PMID:34115121
Selective DNA and Protein Isolation From Marine Macrophyte Surfaces. PMID:34108951
Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor. PMID:34108360
Screening of potential vaccine candidates against pathogenic Brucella spp. using compositive reverse vaccinology. PMID:34078437
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. PMID:34072576
Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches. PMID:34051845
Diversity and prevalence of ANTAR RNAs across actinobacteria. PMID:34051745
High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534. PMID:34042486
Draft Genome Sequences of Five Fungal Strains Isolated from Kefir. PMID:34042484
One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE). PMID:34042466
Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900 Insertions Reveals Strain Type-Specific Modalities. PMID:34040595
The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. PMID:34040089
Characterization of the public transit air microbiome and resistome reveals geographical specificity. PMID:34039416
Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum. PMID:34038483
Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis). PMID:34025698
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. PMID:34022814
Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. PMID:34022804
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
Genome-wide insights into population structure and host specificity of Campylobacter jejuni. PMID:33990625
Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model. PMID:33986113
Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages. PMID:33981291
Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses. PMID:33975962
Diversity and distribution of viruses inhabiting the deepest ocean on Earth. PMID:33972725
Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. PMID:33971924
The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid. PMID:33970547
Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. PMID:33970538
Host Trait Prediction from High-Resolution Microbial Features. PMID:33961225
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. PMID:33961220
Comparative Analysis of Core and Accessory Genes in Coexpression Network. PMID:33961216
Ecologically coherent population structure of uncultivated bacterioplankton. PMID:33953362
A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. PMID:33945788
Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. PMID:33941887
Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider. PMID:33936141
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. PMID:33927381
Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate. PMID:33924830
Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. PMID:33920164
Functional genome-centric view of the CO-driven anaerobic microbiome. PMID:33911204
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. PMID:33911077
Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex. PMID:33910529
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. PMID:33880605
Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. PMID:33865444
Halobellus ruber sp. nov., a deep red-pigmented extremely halophilic archaeon isolated from a Korean solar saltern. PMID:33864546
Functional genome-centric view of the CO-driven anaerobic microbiome. PMID:33911204
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. PMID:33911077
Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex. PMID:33910529
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. PMID:33880605
Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. PMID:33865444
Halobellus ruber sp. nov., a deep red-pigmented extremely halophilic archaeon isolated from a Korean solar saltern. PMID:33864546
Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus. PMID:33863703
Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil. PMID:33854845
Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14. PMID:33854112
Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts. PMID:33850039
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). PMID:33848236
Actirhodobacter atriluteus gen. nov., sp. nov., isolated from the surface water of the Yellow Sea. PMID:33847861
Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay. PMID:33827913
Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. PMID:33815342
Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. PMID:33794184
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. PMID:33787851
Environmental Plasticity of the RNA Content of Staphylococcus aureus Extracellular Vesicles. PMID:33776967
Transcribed germline-limited coding sequences in Oxytricha trifallax. PMID:33772542
The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis. PMID:33768699
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics. PMID:33752740
A novel class of sulfur-containing aminolipids widespread in marine roseobacters. PMID:33750904
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. PMID:33741058
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. PMID:33739402
Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. PMID:33732433
Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity. PMID:33720991
Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. PMID:33693712
Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes. PMID:33693605
Genetic characterisation of a subset of Campylobacter jejuni isolates from clinical and poultry sources in Ireland. PMID:33690659
A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions. PMID:33672193
Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant. PMID:33668977
Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults. PMID:33668840
De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress. PMID:33660094
Establishment of a Cuscuta campestris-mediated enrichment system for genomic and transcriptomic analyses of 'Candidatus Liberibacter asiaticus'. PMID:33655703
Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. PMID:33648559
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. PMID:33632122
Strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome. PMID:33622400
Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. PMID:33622394
Genome sequencing, annotation and exploration of the SO2-tolerant non-conventional yeast Saccharomycodes ludwigii. PMID:33622260
Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis. PMID:33608555
Massive expansion of human gut bacteriophage diversity. PMID:33606979
De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope. PMID:33604669
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus. PMID:33602135
Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. PMID:33598705
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome. PMID:33597514
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce. PMID:33594001
The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria. PMID:33584563
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). PMID:33570560
A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. PMID:33568477
Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. PMID:33564053
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. PMID:33563787
Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort. PMID:33563781
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PMID:33561126
Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection. PMID:33557100
An antimicrobial Staphylococcus sciuri with broad temperature and salt spectrum isolated from the surface of the African social spider, Stegodyphus dumicola. PMID:33543432
Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century. PMID:33541841
Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome. PMID:33540903
Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants. PMID:33537009
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source. PMID:33514061
Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion. PMID:33512490
Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella. PMID:33512418
Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I. PMID:33510760
Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. PMID:33509087
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny. PMID:33477842
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. PMID:33452484
Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly. PMID:33452024
Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. PMID:33441560
Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival. PMID:33439894
Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana. PMID:33439411
Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. PMID:33436514
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. PMID:33430106
The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium. PMID:33407900
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. PMID:33401391
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. PMID:33398099
Macrel: antimicrobial peptide screening in genomes and metagenomes. PMID:33384902
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
DeepNOG: Fast and accurate protein orthologous group assignment. PMID:33367584
Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor. PMID:33361320
Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. PMID:33361201
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. PMID:33361111
Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum. PMID:33347470
Comparative genomic analysis of the principal Cryptosporidium species that infect humans. PMID:33344091
Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA129 to Cow's Milk Versus Soymilk Environments Modulates Its Stress Tolerance and Proteome. PMID:33335514
Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation. PMID:33329454
Discovery of Euryhaline Phycoerythrobilin-Containing Synechococcus and Its Mechanisms for Adaptation to Estuarine Environments. PMID:33323414
Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria. PMID:33322390
Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. PMID:33320415
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. PMID:33319778
Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes. PMID:33316049
Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. PMID:33312167
Environmental conditions modulate the protein content and immunomodulatory activity of extracellular vesicles produced by the probiotic Propionibacterium freudenreichii. PMID:33310709
Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. PMID:33294194
Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. PMID:33287185
Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. PMID:33271881
Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. PMID:33257523
Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria. PMID:33250920
Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PMID:33240652
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. PMID:33193240
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA. PMID:33175843
Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. PMID:33172994
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid. PMID:33172400
Survey of metaproteomics software tools for functional microbiome analysis. PMID:33170893
Transposon Insertion Sequencing in a Clinical Isolate of Legionella pneumophila Identifies Essential Genes and Determinants of Natural Transformation. PMID:33168636
Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae). PMID:33168070
Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria. PMID:33157023
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. PMID:33154426
Subgroup level differences of physiological activities in marine Lokiarchaeota. PMID:33149207
Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants. PMID:33137950
Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. PMID:33127909
Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus. PMID:33117433
Timing the origin of eukaryotic cellular complexity with ancient duplications. PMID:33106602
Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung. PMID:33101250
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. PMID:33087062
Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines. PMID:33082320
Short-Chain Fatty Acids Modulate Metabolic Pathways and Membrane Lipids in Prevotella bryantii B14. PMID:33081314
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. PMID:33077930
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. PMID:33072050
A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses. PMID:33064149
Life-history strategies of soil microbial communities in an arid ecosystem. PMID:33051582
HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts. PMID:33050146
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta. PMID:33028976
Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential. PMID:33022985
RskA Is a Dual Function Activator-Inhibitor That Controls SigK Activity Across Distinct Bacterial Genera. PMID:33013790
ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. PMID:32974096
Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata. PMID:32968134
Transcriptome Profiling of Potato (Solanum tuberosum L.) Responses to Root-Knot Nematode (Meloidogyne javanica) Infestation during A Compatible Interaction. PMID:32967109
Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. PMID:32938803
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. PMID:32923644
Mapping of the Denitrification Pathway in Burkholderia thailandensis by Genome-Wide Mutant Profiling. PMID:32900830
Genome sequence of segmented filamentous bacteria present in the human intestine. PMID:32887924
Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance. PMID:32864208
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. PMID:32859984
Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PMID:32853201
RIGD: A Database for Intronless Genes in the Rosaceae. PMID:32849839
Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution. PMID:32849820
Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings. PMID:32845829
Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. PMID:32842972
Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation. PMID:32825765
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet. PMID:32806628
Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium. PMID:32801182
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. PMID:32797185
Identification of Genes Required for Resistance to Peptidomimetic Antibiotics by Transposon Sequencing. PMID:32793157
Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis. PMID:32790833
Complete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces. PMID:32782425
Complementary Dynamics of Banana Root Colonization by the Plant Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at Spatial and Temporal Scales. PMID:32778917
Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea. PMID:32770005
Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. PMID:32764694
Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. PMID:32762019
Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano. PMID:32760381
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. PMID:32753501
Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway. PMID:32733422
Genome sequencing and functional characterization of a Dictyopanus pusillus fungal enzymatic extract offers a promising alternative for lignocellulose pretreatment of oil palm residues. PMID:32730337
Mining sequences with similarity to XTH genes in the Solanum tuberosum L. transcriptome: introductory step for identifying homologous XTH genes. PMID:32727267
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. PMID:32698001
A unified catalog of 204,938 reference genomes from the human gut microbiome. PMID:32690973
Completed Genomic Sequence of Bacillus thuringiensis HER1410 Reveals a Cry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage. PMID:32690586
Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction. PMID:32673387
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897. PMID:32670245
Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus. PMID:32670207
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. PMID:32665274
A non-canonical RNAi pathway controls virulence and genome stability in Mucorales. PMID:32658892
Novel xylanase producing Bacillus strain X2: molecular phylogenetic analysis and its application for production of xylooligosaccharides. PMID:32656061
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. PMID:32651390
Mycoavidus sp. Strain B2-EB: Comparative Genomics Reveals Minimal Genomic Features Required by a Cultivable Burkholderiaceae-Related Endofungal Bacterium. PMID:32651207
An expanded cell wall damage signaling network is comprised of the transcription factors Rlm1 and Sko1 in Candida albicans. PMID:32639995
Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. PMID:32631866
Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". PMID:32625179
The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. PMID:32620776
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. PMID:32616809
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. PMID:32605604
Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis. PMID:32596333
The First Draft Genome Assembly of Snow Sheep (Ovis nivicola). PMID:32592471
Diverse and unique viruses discovered in the surface water of the East China Sea. PMID:32590932
Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds. PMID:32582129
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. PMID:32571209
Lineage dynamics of the endosymbiotic cell type in the soft coral Xenia. PMID:32555454
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments. PMID:32552798
Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. PMID:32552739
Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. PMID:32551936
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis. PMID:32538778
Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species. PMID:32531278
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. PMID:32513234
Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. PMID:32499817
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. PMID:32482164
In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms. PMID:32456002
Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics. PMID:32455615
Impact of C-terminal amino acid composition on protein expression in bacteria. PMID:32449593
Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. PMID:32443820
Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes. PMID:32424209
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi. PMID:32421770
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. PMID:32416061
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. PMID:32414048
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. PMID:32411107
Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. PMID:32398647
Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. PMID:32443820
Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes. PMID:32424209
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi. PMID:32421770
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. PMID:32416061
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. PMID:32414048
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. PMID:32411107
Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. PMID:32398647
Carbon monoxide-dependent transcriptional changes in a thermophilic, carbon monoxide-utilizing, hydrogen-evolving bacterium Calderihabitans maritimus KKC1 revealed by transcriptomic analysis. PMID:32388815
Complete Genome Sequence of an Efficient Rhizobium leguminosarum bv. viciae Strain, A1. PMID:32381612
A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion. PMID:32380653
Phages Actively Challenge Niche Communities in Antarctic Soils. PMID:32371471
Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae. PMID:32365808
Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. PMID:32359152
Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. PMID:32349676
Genomic characterization of Lactobacillus fermentum DSM 20052. PMID:32349666
Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. PMID:32349406
Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment. PMID:32342339
Integrative functional genomics decodes herpes simplex virus 1. PMID:32341360
Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. PMID:32341166
Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map. PMID:32321933
A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli. PMID:32291345
Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017. PMID:32269101
Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses. PMID:32246084
Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma japonicum. PMID:32244675
Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. PMID:32238227
Bifidobacterium breve UCC2003 Exopolysaccharide Modulates the Early Life Microbiota by Acting as a Potential Dietary Substrate. PMID:32235410
Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. PMID:32232367
OXA-48 Carbapenemase in Klebsiella pneumoniae Sequence Type 307 in Ecuador. PMID:32204571
Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. PMID:32201928
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China. PMID:32188734
Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets. PMID:32188014
Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems. PMID:32184251
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. PMID:32170201
Phenotypic and Transcriptomic Analysis of Two Pinellia ternata Varieties T2 line and T2Plus line. PMID:32165650
Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms. PMID:32071394
Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius. PMID:32071159
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii. PMID:32066773
Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor. PMID:32051205
The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities. PMID:32047059
Comparative transcriptome profiling of selected osmotic regulatory proteins in the gill during seawater acclimation of chum salmon (Oncorhynchus keta) fry. PMID:32029805
The Cannabis Proteome Draft Map Project. PMID:32024021
Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly. PMID:32019832
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. PMID:32019604
Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus. PMID:31998266
Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. PMID:31992632
Gene gain and loss across the metazoan tree of life. PMID:31988444
Giant virus diversity and host interactions through global metagenomics. PMID:31968354
Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. PMID:31964893
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. PMID:31959969
Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. PMID:31956321
The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico. PMID:31934497
The CtrA Regulon of Rhodobacter sphaeroides Favors Adaptation to a Particular Lifestyle. PMID:31932315
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. PMID:31919110
Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing. PMID:31917800
Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria. PMID:31911493
Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa NIES-102. PMID:31892993
Production of tetra-methylpyrazine using engineered Corynebacterium glutamicum. PMID:31890587
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. PMID:31861401
The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. PMID:31861318
A transposable element insertion is associated with an alternative life history strategy. PMID:31848330
Shigella sonnei infection of zebrafish reveals that O-antigen mediates neutrophil tolerance and dysentery incidence. PMID:31830135
The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data. PMID:31827121
Phagocytosis-like cell engulfment by a planctomycete bacterium. PMID:31827088
Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain. PMID:31810255
A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species. PMID:31807698
Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in Hydra. PMID:31799436
Genome-Wide Identification of Myxobacterial Predation Genes and Demonstration of Formaldehyde Secretion as a Potentially Predation-Resistant Trait of Pseudomonas aeruginosa. PMID:31798566
Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility. PMID:31798553
Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome. PMID:31797948
Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh. PMID:31796006
Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits. PMID:31772223
Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens. PMID:31768192
Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium. PMID:31767854
A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet. PMID:31757113
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. PMID:31752666
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? PMID:31749784
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea. PMID:31744906
Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. PMID:31740752
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. PMID:31730850
Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. PMID:31717820
Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha. PMID:31702774
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. PMID:31693149
Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri. PMID:31690847
Lignin degradation potential and draft genome sequence of Trametes trogii S0301. PMID:31687044
cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America. PMID:31685464
Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica. PMID:31681251
Draft Genome Sequences of Two Bacterial Strains, Muricauda sp. 72 and NH166, Isolated from the South China Sea and West Pacific Ocean. PMID:31672745
Ancestral reconstruction of protein interaction networks. PMID:31658251
Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. PMID:31649284
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. PMID:31647412
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. PMID:31647096
A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. PMID:31636702
Adaptive Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment. PMID:31632374
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress. PMID:31623206
A high-quality cucumber genome assembly enhances computational comparative genomics. PMID:31620884
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. PMID:31607556
Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean. PMID:31601926
Functional annotation and identification of MADS-box transcription factors related to tuber dormancy in Helianthus tuberosus L. PMID:31588402
The Draft Genome of a Hydrogen-producing Cyanobacterium, Arthrospira platensis NIES-46. PMID:31588248
Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway. PMID:31573151
Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages. PMID:31572441
Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes. PMID:31571125
Regulation of the Larval Transcriptome of Diatraea saccharalis (Lepidoptera: Crambidae) by Maternal and Other Factors of the Parasitoid Cotesia flavipes (Hymenoptera: Braconidae). PMID:31555143
Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids. PMID:31553300
Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. PMID:31547186
Evolutionary and functional patterns of shared gene neighbourhood in fungi. PMID:31527797
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. PMID:31521200
Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes. PMID:31516688
Study protocol: characterising the clinical, epidemiological and aetiological aspects of leptospirosis in Sri Lanka: a hospital based clinico-epidemiological study. PMID:31511281
Mucilaginibacter limnophilus sp. nov., isolated from a lake. PMID:31463791
Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. PMID:31437442
Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom. PMID:31428077
Complete Genome Sequence of Weissella hellenica 0916-4-2 and Its Comparative Genomic Analysis. PMID:31396169
Whole-genome sequence data and analysis of Lactobacillus delbrueckii subsp. lactis ACA-DC 178 isolated from Greek Kasseri cheese. PMID:31388525
Complete Sequence of Succinamopine Ti-Plasmid pTiEU6 Reveals Its Evolutionary Relatedness with Nopaline-Type Ti-Plasmids. PMID:31386108
Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. PMID:31384012
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. PMID:31375138
Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group. PMID:31368886
Coherence of Microcystis species revealed through population genomics. PMID:31363173
Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). PMID:31357931
A Novel Two-Component System, Encoded by the sco5282/sco5283 Genes, Affects Streptomyces coelicolor Morphology in Liquid Culture. PMID:31354667
Whole-Genome Sequencing and Annotation of Clostridium tyrobutyricum Strain Cirm BIA 2237, Isolated from Silage. PMID:31346011
Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. PMID:31337658
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. PMID:31296857
SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes. PMID:31257417
Advances and Applications in the Quest for Orthologs. PMID:31241141
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. PMID:31235587
Hypervirulent Listeria monocytogenes clones' adaption to mammalian gut accounts for their association with dairy products. PMID:31171794
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. PMID:31159881
Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production. PMID:31143170
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PMID:31120895
Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. PMID:31086829
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
Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. PMID:31036911
Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection. PMID:31015329
Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations. PMID:31000506
Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. PMID:30918404
Whole Genome Analysis of Lactobacillus plantarum Strains Isolated From Kimchi and Determination of Probiotic Properties to Treat Mucosal Infections by Candida albicans and Gardnerella vaginalis. PMID:30894844
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium "Thiodictyon syntrophicum". PMID:30891015
Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. PMID:30877285
Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection. PMID:30832578
First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina. PMID:30800585
Exploring K2G30 Genome: A High Bacterial Cellulose Producing Strain in Glucose and Mannitol Based Media. PMID:30761107
Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno. PMID:30760771
Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus. PMID:30715337
Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256. PMID:30704413
Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. PMID:30702898
Whole-Genome Sequencing of Legionella jordanis Strains NML 060502 and NML 130005, Recovered from a Lower Respiratory Tract Infection and Water, Respectively. PMID:30701246
Genomic diversity landscape of the honey bee gut microbiota. PMID:30683856
Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2'-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat. PMID:30683741
Genomic and metagenomic insights into the microbial community of a thermal spring. PMID:30674352
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID:30661755
Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. PMID:30626928
Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges. PMID:30625112
Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets. PMID:30619233
Innate immunity in the simplest animals - placozoans. PMID:30611207
Physiochemical and protein datasets related to citrus juice sac cells-derived nanovesicles and microvesicles. PMID:30591944
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. PMID:30585382
Carbapenemases on the move: it's good to be on ICEs. PMID:30574213
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. PMID:30559407
Whole-Genome Sequences of Propionibacterium australiense NML (LCDC) 98A072T and NML (LCDC) 98A078, Associated with Granulomatous Bovine Lesions. PMID:30533813
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Transcriptome-based mining and expression profiling of Pythium responsive transcription factors in Zingiber sp. PMID:30415383
The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci. PMID:30404935
Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. PMID:30320230
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
In silico characterization of the global Geobacillus and Parageobacillus secretome. PMID:30285747
Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium. PMID:30239727
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. PMID:30223879
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. PMID:30192979
Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. PMID:30187987
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. PMID:29988535
Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes. PMID:29982456
The draft genome sequence of cork oak. PMID:29786699
Cotesia congregata Bracovirus Circles Encoding PTP and Ankyrin Genes Integrate into the DNA of Parasitized Manduca sexta Hemocytes. PMID:29769342
PANNZER2: a rapid functional annotation web server. PMID:29741643
A Capsular Polysaccharide-Specific Antibody Alters Streptococcus pneumoniae Gene Expression during Nasopharyngeal Colonization of Mice. PMID:29735523
High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. PMID:29725499
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
Embryophyte stress signaling evolved in the algal progenitors of land plants. PMID:29581286
Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria. PMID:29553064
High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T. PMID:29483968
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. PMID:29463659
Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. PMID:29445130
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PMID:29423345
Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. PMID:29420719
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. PMID:29410487
Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. PMID:29403020
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. PMID:29385081
De novo assembly and characterization of the Hucho taimen transcriptome. PMID:29375797
Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium tetraurelia. PMID:29348333
Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors. PMID:29312194
FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells. PMID:29253234
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights. PMID:29044436
Succinate Transport Is Not Essential for Symbiotic Nitrogen Fixation by Sinorhizobium meliloti or Rhizobium leguminosarum. PMID:28916561
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. PMID:28837129
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. PMID:28053165 -
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
PubMed citations: 102.
102 articles citing: eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu). PMID:36051764
A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID:36050292
Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments. PMID:36033848
Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato. PMID:36014977
Transcriptomic Differences between Free-Living and Parasitic Chilodonella uncinata (Alveolata, Ciliophora). PMID:36014062
Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. PMID:36011267
Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics, and QTLs. PMID:36011264
Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. PMID:36006456
The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids. PMID:36002843
Phenotypic screen and transcriptomics approach complement each other in functional genomics of defensive stink gland physiology. PMID:35987630
mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation. PMID:35979445
High-quality reference genome sequences of two Cannaceae species provide insights into the evolution of Cannaceae. PMID:35968134
Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. PMID:35966843
Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing. PMID:35955752
Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus. PMID:35953903
Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. PMID:35950761
Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes. PMID:35938717
Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning. PMID:35938008
The chromosome-scale genome sequence of Triadica sebifera provides insight into fatty acids and anthocyanin biosynthesis. PMID:35927438
Short-Term Test for Toxicogenomic Analysis of Ecotoxic Modes of Action in Lemna minor. PMID:35926083
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics. PMID:35910650
Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure. PMID:35899254
Transcriptome Analysis Reveals Key Gene Expression Changes in Blue Catfish Sperm in Response to Cryopreservation. PMID:35886966
The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta). PMID:35883316
A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. PMID:35835784
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus. PMID:35835775
Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain. PMID:35812926
The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes. PMID:35801108
Isolation of a novel Lactiplantibacillus plantarum strain resistant to nitrite stress and its transcriptome analysis. PMID:35781626
An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. PMID:35773279
Strain Variation in Clostridioides difficile Cytotoxicity Associated with Genomic Variation at Both Pathogenic and Nonpathogenic Loci. PMID:35766503
Genomic characterization of Streptococcus parasuis, a close relative of Streptococcus suis and also a potential opportunistic zoonotic pathogen. PMID:35752768
Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. PMID:35751614
Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss. PMID:35746669
Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes. PMID:35744652
Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance. PMID:35731940
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. PMID:35727987
Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces. PMID:35697683
Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L. PMID:35682645
Short- and long-read metagenomics expand individualized structural variations in gut microbiomes. PMID:35676264
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. PMID:35639770
Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. PMID:35627219
Double-Stranded RNA Viruses Are Released From Trichomonas vaginalis Inside Small Extracellular Vesicles and Modulate the Exosomal Cargo. PMID:35602021
Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source. PMID:35586859
Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library. PMID:35580146
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. PMID:35580059
A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth. PMID:35548270
Metatranscriptomic Assessment of the Microbial Community Associated With the Flavescence dorée Phytoplasma Insect Vector Scaphoideus titanus. PMID:35516423
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets. PMID:35495109
Organizing the Global Diversity of Microviruses. PMID:35491833
Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains. PMID:35475644
PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database. PMID:35462956
Draft genome sequence of 'Candidatus Phytoplasma australasia', strain SS02 associated with sesame phyllody disease. PMID:35462955
Safety Assessment of Lactiplantibacillus plantarum TWK10 Based on Whole-Genome Sequencing, Phenotypic, and Oral Toxicity Analysis. PMID:35456834
Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. PMID:35456753
Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species. PMID:35446150
Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments. PMID:35438770
THOR's Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community. PMID:35435700
KEMET - A python tool for KEGG Module evaluation and microbial genome annotation expansion. PMID:35422973
The first de novo genome assembly and sex marker identification of Pluang Chomphu fish (Tor tambra) from Southern Thailand. PMID:35422970
Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent. PMID:35418954
The Ovarian Transcriptome at the Early Stage of Testis Removal-Induced Male-To-Female Sex Change in the Protandrous Black Porgy Acanthopagrus schlegelii. PMID:35401660
Corrigendum: Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. PMID:35401476
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. PMID:35395709
Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand. PMID:35371566
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. PMID:35357493
Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication. PMID:35356113
SHOOT: phylogenetic gene search and ortholog inference. PMID:35346327
Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey. PMID:35345581
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria. PMID:35343799
Proteomic Analysis Reveals Enzymes for β-D-Glucan Formation and Degradation in Levilactobacillus brevis TMW 1.2112. PMID:35328813
Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. PMID:35311563
Proteomic Responses of Dark-Adapted Euglena gracilis and Bleached Mutant Against Light Stimuli. PMID:35309998
The genomic basis of the Streptococcus thermophilus health-promoting properties. PMID:35291951
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. PMID:35285712
Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles. PMID:35279211
Conserved exchange of paralog proteins during neuronal differentiation. PMID:35273078
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PMID:35255079
Exploratory Growth in Streptomyces venezuelae Involves a Unique Transcriptional Program, Enhanced Oxidative Stress Response, and Profound Acceleration in Response to Glycerol. PMID:35254103
Microbial Consortiums of Putative Degraders of Low-Density Polyethylene-Associated Compounds in the Ocean. PMID:35229650
Transcriptome Analysis of Halotolerant Staphylococcus saprophyticus Isolated from Korean Fermented Shrimp. PMID:35206000
Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. PMID:35196120
Oceanobacter mangrovi Sp. Nov., a Novel Poly-β-hydroxybutyrate Accumulating Bacterium Isolated from Mangrove Sediment. PMID:35150341
Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection. PMID:35145925
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. PMID:35069469
Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup. PMID:34997867
A R2R3-MYB Transcription Factor Gene, BpMYB123, Regulates BpLEA14 to Improve Drought Tolerance in Betula platyphylla. PMID:34956289
Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina. PMID:34946942
DNA Methylation Patterns Differ between Free-Living Rhizobium leguminosarum RCAM1026 and Bacteroids Formed in Symbiosis with Pea (Pisum sativum L.). PMID:34946059
Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella). PMID:34943167
Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer. PMID:34908127
An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana. PMID:34834996
Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of Littorina fabalis and L. obtusata. PMID:34827080
Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme. PMID:34791213
Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen. PMID:34709726
Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. PMID:34707580
Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance. PMID:34691008
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae). PMID:34623414
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022 -
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PubMed citations: 37.
37 articles citing: proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. PMID:35075131
Prokaryotic Genome Annotation. PMID:34718997
Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model. PMID:34659185
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Dispersal strategies shape persistence and evolution of human gut bacteria. PMID:34111423
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PMID:33868800
Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy. PMID:33859339
Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota. PMID:33808469
Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data. PMID:33763122
The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis. PMID:33681304
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Rewiring the specificity of extracytoplasmic function sigma factors. PMID:33318184
Prevalence of phase variable epigenetic invertons among host-associated bacteria. PMID:33119758
Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. PMID:33072721
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. PMID:32047279
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines. PMID:32025702
Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly. PMID:32019832
Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. PMID:32019803
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
CAMITAX: Taxon labels for microbial genomes. PMID:31909794
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. PMID:31647096
Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre. PMID:31632377
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity. PMID:31501539
Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. PMID:30949677
Microbial abundance, activity and population genomic profiling with mOTUs2. PMID:30833550
Co-culture and biogeography of Prochlorococcus and SAR11. PMID:30742057
Antibiotics-induced monodominance of a novel gut bacterial order. PMID:30658995
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. PMID:30630933
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. PMID:29771380
Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment. PMID:29235508
MVP: a microbe-phage interaction database. PMID:29177508
metaSNV: A tool for metagenomic strain level analysis. PMID:28753663
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