BLAST+: architecture and applications

Basic local alignment search tool

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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

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Initial sequencing and comparative analysis of the mouse genome

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A Greedy Algorithm for Aligning DNA Sequences

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NCBI BLAST: a better web interface

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Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

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Database indexing for production MegaBLAST searches

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[33] Analysis of compositionally biased regions in sequence databases

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A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

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Protein sequence similarity searches using patterns as seeds

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WindowMasker: window-based masker for sequenced genomes

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IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

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Improved sensitivity of nucleic acid database searches using application-specific scoring matrices

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A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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OrthoFinder: phylogenetic orthology inference for comparative genomics

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Accelerated Profile HMM Searches

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Kraken: ultrafast metagenomic sequence classification using exact alignments

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

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A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

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Spatially resolved, highly multiplexed RNA profiling in single cells

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Phylogenomics resolves the timing and pattern of insect evolution

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BUSCO applications from quality assessments to gene prediction and phylogenomics

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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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BLAST: a more efficient report with usability improvements

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Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

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MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

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Mapping human microbiome drug metabolism by gut bacteria and their genes

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Ensembl 2015

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Proteome-wide covalent ligand discovery in native biological systems

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Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

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SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses

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Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing

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Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

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MetaQUAST: evaluation of metagenome assemblies

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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

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Isolation of an archaeon at the prokaryote–eukaryote interface

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Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

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Subsistence strategies in traditional societies distinguish gut microbiomes

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Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era

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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

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Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019

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Identification of Novel Mobilized Colistin Resistance Gene <i>mcr-9</i> in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate

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Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome

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Chapter 12: Human Microbiome Analysis

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Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

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Cell type transcriptome atlas for the planarian <i>Schmidtea mediterranea</i>

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ECOD: an evolutionary classification of protein domains

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The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

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Community characteristics of the gut microbiomes of competitive cyclists

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The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity

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Benchmarking <scp>AlphaFold</scp> for protein complex modeling reveals accuracy determinants

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CRISPR/cas9 genome editing in wheat

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Clustering predicted structures at the scale of the known protein universe

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Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy

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Human germinal centres engage memory and naive B cells after influenza vaccination

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Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

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Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

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Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

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A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1

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High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

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Diagnostic potential and interactive dynamics of the colorectal cancer virome

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The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

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High-throughput microbial culturomics using automation and machine learning

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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

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Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

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A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

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Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

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Comparing and evaluating metagenome assembly tools from a microbiologist's perspective - not only size matters!

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Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

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A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

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Deeply conserved synteny and the evolution of metazoan chromosomes

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Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition

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Changes in the intestinal bacterial community during the growth of white shrimp, <i>Litopenaeus vannamei</i>

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MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

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Twenty-Five Years of Structural Parvovirology

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The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

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