Works matching DE "SHOTGUN sequencing"
Results: 1661
Comprehensive analysis of antimicrobial resistance dynamics among broiler and duck intensive production systems.
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- Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-89432-z
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Tracheal Aspirate Metagenomics Reveals Association of Antibiotic Resistance with Nonpulmonary Sepsis Mortality.
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- American Journal of Respiratory Cell & Molecular Biology, 2025, v. 72, n. 2, p. 219, doi. 10.1165/rcmb.2024-0192LE
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Impact of commercial gut health interventions on caecal metagenome and broiler performance.
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- Microbiome, 2025, v. 13, n. 1, p. 1, doi. 10.1186/s40168-024-02012-7
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Boosting natural history research via metagenomic clean-up of crowdsourced feces.
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- PLoS Biology, 2019, v. 17, n. 11, p. 1, doi. 10.1371/journal.pbio.3000517
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Better detection of Torque teno virus in children with leukemia by metagenomic sequencing than by quantitative PCR.
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- Journal of Medical Virology, 2022, v. 94, n. 2, p. 634, doi. 10.1002/jmv.27409
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A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents.
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- Molecular Medicine, 2021, v. 27, n. 1, p. 1, doi. 10.1186/s10020-021-00371-7
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First insight into the whole genome shotgun sequence of the endangered noble pen shell Pinna nobilis: a giant bivalve undergoing a mass mortality event.
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- Journal of Molluscan Studies, 2021, v. 87, n. 1, p. 1, doi. 10.1093/mollus/eyaa041
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The complete mitochondrial genomes of three species of Macridiscus Dall, 1902 (Bivalvia: Veneroidea: Veneridae) and their phylogenetic implications.
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- Journal of Molluscan Studies, 2019, v. 85, n. 2, p. 271, doi. 10.1093/mollus/eyz009
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ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.
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- Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae661
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Floria: fast and accurate strain haplotyping in metagenomes.
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- Bioinformatics, 2024, v. 40, p. i30, doi. 10.1093/bioinformatics/btae252
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ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.
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- Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae086
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Phables: from fragmented assemblies to high-quality bacteriophage genomes.
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- Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad586
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Coverage-preserving sparsification of overlap graphs for long-read assembly.
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- Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad124
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HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.
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- Bioinformatics, 2022, v. 38, n. 24, p. 5360, doi. 10.1093/bioinformatics/btac708
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expam—high-resolution analysis of metagenomes using distance trees.
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- Bioinformatics, 2022, v. 38, n. 20, p. 4814, doi. 10.1093/bioinformatics/btac591
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Metagenomic binning with assembly graph embeddings.
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- Bioinformatics, 2022, v. 38, n. 19, p. 4481, doi. 10.1093/bioinformatics/btac557
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SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data.
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- Bioinformatics, 2022, v. 38, n. 15, p. 3830, doi. 10.1093/bioinformatics/btac389
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HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs.
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- Bioinformatics, 2022, v. 38, n. 11, p. 2973, doi. 10.1093/bioinformatics/btac295
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HolistIC: leveraging Hi–C and whole genome shotgun sequencing for double minute chromosome discovery.
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- Bioinformatics, 2022, v. 38, n. 5, p. 1208, doi. 10.1093/bioinformatics/btab816
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ORT: a workflow linking genome-scale metabolic models with reactive transport codes.
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- Bioinformatics, 2022, v. 38, n. 3, p. 778, doi. 10.1093/bioinformatics/btab753
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BLight: efficient exact associative structure for k-mers.
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- Bioinformatics, 2021, v. 37, n. 18, p. 2858, doi. 10.1093/bioinformatics/btab217
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CoCoNet: an efficient deep learning tool for viral metagenome binning.
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- Bioinformatics, 2021, v. 37, n. 18, p. 2803, doi. 10.1093/bioinformatics/btab213
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OGRE: Overlap Graph-based metagenomic Read clustEring.
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- Bioinformatics, 2021, v. 37, n. 7, p. 905, doi. 10.1093/bioinformatics/btaa760
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mixtureS: a novel tool for bacterial strain genome reconstruction from reads.
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- Bioinformatics, 2021, v. 37, n. 4, p. 575, doi. 10.1093/bioinformatics/btaa728
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PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data.
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- Bioinformatics, 2020, v. 36, n. 22/23, p. 5499, doi. 10.1093/bioinformatics/btaa1056
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MetaviralSPAdes: assembly of viruses from metagenomic data.
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- Bioinformatics, 2020, v. 36, n. 14, p. 4126, doi. 10.1093/bioinformatics/btaa490
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Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics.
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- Bioinformatics, 2020, v. 36, n. 12, p. 3781, doi. 10.1093/bioinformatics/btaa206
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Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level.
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- Bioinformatics, 2020, v. 36, n. 7, p. 2308, doi. 10.1093/bioinformatics/btz910
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Struo: a pipeline for building custom databases for common metagenome profilers.
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- Bioinformatics, 2020, v. 36, n. 7, p. 2314, doi. 10.1093/bioinformatics/btz899
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PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics.
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- Bioinformatics, 2020, v. 36, n. 6, p. 1718, doi. 10.1093/bioinformatics/btz799
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- Article
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
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- Bioinformatics, 2020, v. 36, n. 4, p. 1289, doi. 10.1093/bioinformatics/btz722
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MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies.
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- Bioinformatics, 2020, v. 36, n. 2, p. 356, doi. 10.1093/bioinformatics/btz577
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SVIM: structural variant identification using mapped long reads.
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- Bioinformatics, 2019, v. 35, n. 17, p. 2907, doi. 10.1093/bioinformatics/btz041
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GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets.
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- Bioinformatics, 2019, v. 35, n. 13, p. 2318, doi. 10.1093/bioinformatics/bty963
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MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).
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- Bioinformatics, 2019, v. 35, n. 12, p. 2150, doi. 10.1093/bioinformatics/bty905
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MetaCache: context-aware classification of metagenomic reads using minhashing.
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- Bioinformatics, 2017, v. 33, n. 23, p. 3740, doi. 10.1093/bioinformatics/btx520
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PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive.
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- Bioinformatics, 2017, v. 33, n. 15, p. 2389, doi. 10.1093/bioinformatics/btx184
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MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
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- Bioinformatics, 2017, v. 33, n. 11, p. 1730, doi. 10.1093/bioinformatics/btx036
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Large-scale 16S gene assembly using metagenomics shotgun sequences.
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- Bioinformatics, 2017, v. 33, n. 10, p. 1447, doi. 10.1093/bioinformatics/btx018
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PALADIN: protein alignment for functional profiling whole metagenome shotgun data.
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- Bioinformatics, 2017, v. 33, n. 10, p. 1473, doi. 10.1093/bioinformatics/btx021
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KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
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- Bioinformatics, 2017, v. 33, n. 4, p. 574, doi. 10.1093/bioinformatics/btw663
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- Article
Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics.
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- Bioinformatics, 2017, v. 33, n. 4, p. 508, doi. 10.1093/bioinformatics/btw619
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Gene-set association tests for next-generation sequencing data.
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- Bioinformatics, 2016, v. 32, n. 17, p. i611, doi. 10.1093/bioinformatics/btw429
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- Article
CoLoRMap: Correcting Long Reads by Mapping short reads.
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- Bioinformatics, 2016, v. 32, n. 17, p. i545, doi. 10.1093/bioinformatics/btw463
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- Article
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
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- Bioinformatics, 2016, v. 32, n. 3, p. 354, doi. 10.1093/bioinformatics/btv584
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- Article
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
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- Bioinformatics, 2014, v. 30, n. 21, p. 3136, doi. 10.1093/bioinformatics/btu397
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Exploration and retrieval of whole-metagenome sequencing samples.
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- Bioinformatics, 2014, v. 30, n. 17, p. 2471, doi. 10.1093/bioinformatics/btu340
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- Article
Epigenetics: new insights into postoperative adhesion development.
- Published in:
- Minerva Obstetrics & Gynecology, 2024, v. 76, n. 3, p. 231, doi. 10.23736/S2724-606X.22.05158-2
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- Article
Long-Term Outdoor Cultivation of Nannochloropsis in California, Hawaii, and New Mexico.
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- Data (2306-5729), 2024, v. 9, n. 11, p. 126, doi. 10.3390/data9110126
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- Article
Proteomic Shift in Mouse Embryonic Fibroblasts Pfa1 during Erastin, ML210, and BSO-Induced Ferroptosis.
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- Data (2306-5729), 2023, v. 8, n. 7, p. 119, doi. 10.3390/data8070119
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- Article