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Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49587-1
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Genomic insights into an endophytic Streptomyces sp. VITGV156 for antimicrobial compounds.
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- Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1407289
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Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49060-z
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Cell-free biosynthesis and engineering of ribosomally synthesized lanthipeptides.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48726-y
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- Article
Exploring Alashan Ground Squirrel (Spermophilus alashanicus) Diversity: Metagenomic and Transcriptomic Datasets from the Helan Mountains.
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- Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03183-6
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Investigating the degradation potential of microbial consortia for perfluorooctane sulfonate through a functional "top-down" screening approach.
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- PLoS ONE, 2024, v. 19, n. 5, p. 1, doi. 10.1371/journal.pone.0303904
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Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities.
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- Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03332-x
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Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae206
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AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae229
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Transcriptional regulators of secondary metabolite biosynthesis in Streptomyces.
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- World Journal of Microbiology & Biotechnology, 2024, v. 40, n. 5, p. 1, doi. 10.1007/s11274-024-03968-2
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Many purported pseudogenes in bacterial genomes are bona fide genes.
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- BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10137-0
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Mechanism of improving anaerobic fermentation performance of kitchen waste pretreated by ionizing irradiation—part 1: rice.
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- Environmental Science & Pollution Research, 2024, v. 31, n. 17, p. 25287, doi. 10.1007/s11356-024-32731-1
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Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.
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- Microorganisms, 2024, v. 12, n. 4, p. 791, doi. 10.3390/microorganisms12040791
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An in-depth evaluation of metagenomic classifiers for soil microbiomes.
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- Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00561-w
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- Article
Photocobilins integrate B<sub>12</sub> and bilin photochemistry for enzyme control.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46995-1
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- Article
Antimicrobial Peptide Screening from Microbial Genomes in Sludge Based on Deep Learning.
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- Applied Sciences (2076-3417), 2024, v. 14, n. 5, p. 1936, doi. 10.3390/app14051936
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Mining Biosynthetic Gene Clusters of Pseudomonas vancouverensis Utilizing Whole Genome Sequencing.
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- Microorganisms, 2024, v. 12, n. 3, p. 548, doi. 10.3390/microorganisms12030548
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Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.
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- Molecular Biology & Evolution, 2024, v. 41, n. 3, p. 1, doi. 10.1093/molbev/msae017
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Pro-SMP finder–A systematic approach for discovering small membrane proteins in prokaryotes.
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- PLoS ONE, 2024, v. 19, n. 2, p. 1, doi. 10.1371/journal.pone.0299169
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Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.
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- Urolithiasis, 2024, v. 52, n. 1, p. 1, doi. 10.1007/s00240-024-01534-x
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Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery.
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- Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1343029
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A genomic view of environmental and life history controls on microbial nitrogen acquisition strategies.
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- Environmental Microbiology Reports, 2024, v. 16, n. 1, p. 1, doi. 10.1111/1758-2229.13220
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NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.
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- Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad499
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Human Metagenome Analysis with COVID-19 Infectious Disease.
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- Current Trends in Biotechnology & Pharmacy, 2024, v. 18, n. 1, p. 1616, doi. 10.5530/ctbp.2024.1.10
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Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.
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- Microbial Biotechnology, 2024, v. 17, n. 1, p. 1, doi. 10.1111/1751-7915.14396
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Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies.
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- Microbial Biotechnology, 2024, v. 17, n. 1, p. 1, doi. 10.1111/1751-7915.14364
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Statistical prediction of microbial metabolic traits from genomes.
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- PLoS Computational Biology, 2023, v. 19, n. 12, p. 1, doi. 10.1371/journal.pcbi.1011705
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Genomic analysis of endophytic Bacillus altitudinis strain VUMS1 from Kappaphycus alvarezii and its inhibitory effect against Vibrio parahaemolyticus.
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- Malaysian Journal of Microbiology, 2023, v. 19, n. 6, p. 577, doi. 10.21161/mjm.230001
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Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43216-z
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- Article
Pediococcus Acidilactici Demonstrates Probiotic Properties and Inhibits the Growth of Enterotoxigenic Escherichia Coli.
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- Journal of Animal Science, 2023, v. 101, p. 393, doi. 10.1093/jas/skad281.466
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- Article
ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool.
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- Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad381
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- Article
Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes.
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- Microorganisms, 2023, v. 11, n. 11, p. 2819, doi. 10.3390/microorganisms11112819
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Building Phylogenetic Trees From Genome Sequences With kSNP4.
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- Molecular Biology & Evolution, 2023, v. 40, n. 11, p. 1, doi. 10.1093/molbev/msad235
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- Article
A bioinformatic workflow for in silico secretome prediction with the lignocellulose degrading ascomycete fungus Parascedosporium putredinis NO1.
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- Molecular Microbiology, 2023, v. 120, n. 5, p. 754, doi. 10.1111/mmi.15144
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Circular and L50-like leaderless enterocins share a common ABC-transporter immunity gene.
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- BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09750-2
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Adversarial and variational autoencoders improve metagenomic binning.
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- Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05452-3
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Single-cell analysis and spatial resolution of the gut microbiome.
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- Frontiers in Cellular & Infection Microbiology, 2023, p. 1, doi. 10.3389/fcimb.2023.1271092
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The microbial biodiversity at the archeological site of Tel Megiddo (Israel).
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- Frontiers in Microbiology, 2023, p. 01, doi. 10.3389/fmicb.2023.1253371
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Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes.
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- Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1147007
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- Article
Based on the Co-Evolution of lncRNAs-Microbiota and Metabolites in Rumen Epithelium to Analyze the Adaptation Characteristics of Tibetan Sheep to Nutrient Stress in the Cold Season.
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- Fermentation (Basel), 2023, v. 9, n. 10, p. 892, doi. 10.3390/fermentation9100892
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A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.
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- Microorganisms, 2023, v. 11, n. 10, p. 2560, doi. 10.3390/microorganisms11102560
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Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41174-0
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- Article
iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences.
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- Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad508
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Microbial genome (Illumina MiSeq) sequencing of drinking water treatment residuals to evaluate compatibility with environmental applications.
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- Environmental Monitoring & Assessment, 2023, v. 195, n. 9, p. 1, doi. 10.1007/s10661-023-11511-3
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- Article
Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.
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- Molecular Biology & Evolution, 2023, v. 40, n. 9, p. 1, doi. 10.1093/molbev/msad189
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- Article
Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41099-8
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- Article
Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.
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- PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011391
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Metagenome sequencing and 103 microbial genomes from ballast water and sediments.
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- Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02447-x
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- Article
Effects of Florfenicol on nirS -Type Denitrification Community Structure of Sediments in an Aquatic Microcosm Model.
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- Antibiotics (2079-6382), 2023, v. 12, n. 8, p. 1254, doi. 10.3390/antibiotics12081254
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- Article
The intratumor microbiome is associated with microsatellite instability.
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- JNCI: Journal of the National Cancer Institute, 2023, v. 115, n. 8, p. 989, doi. 10.1093/jnci/djad083
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- Article