BLAST+: architecture and applications

Basic local alignment search tool

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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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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Database indexing for production MegaBLAST searches

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

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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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Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

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Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil

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Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

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gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota

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The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families

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Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

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Introducing difference recurrence relations for faster semi-global alignment of long sequences

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Staphylococcus aureus viewed from the perspective of 40,000+ genomes

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Non‐random association patterns in a plant–mycorrhizal fungal network reveal host–symbiont specificity

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mlDEEPre: Multi-Functional Enzyme Function Prediction With Hierarchical Multi-Label Deep Learning

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Interspecific hybridization facilitates niche adaptation in beer yeast

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Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes

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Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids

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Genome and transcriptome mechanisms driving cephalopod evolution

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A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases

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Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

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Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

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Lactobacilli Have a Niche in the Human Nose

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Improved genome assembly and pan‐genome provide key insights into eggplant domestication and breeding

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Gut microbiota reinforce host antioxidant capacity via the generation of reactive sulfur species

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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases

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VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

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Maternal High Fiber Diet during Pregnancy and Lactation Influences Regulatory T Cell Differentiation in Offspring in Mice

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Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

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Heritability of the Symbiodinium community in vertically- and horizontally-transmitting broadcast spawning corals

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Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield

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Venus flytrap carnivorous lifestyle builds on herbivore defense strategiesPreprint

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Identification of candidate long non-coding RNAs in response to myocardial infarction

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Integration Frequency and Intermolecular Recombination of rAAV Vectors in Non-human Primate Skeletal Muscle and Liver

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Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer

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DNA methylation footprints during soybean domestication and improvement

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De novo design of a non-local β-sheet protein with high stability and accuracy

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Genome-wide association analysis of stalk biomass and anatomical traits in maize

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Horizontal transfer and evolution of transposable elements in vertebrates

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Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)

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Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

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The Caulobacter crescentus phage phiCbK: genomics of a canonical phage

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Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

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Structural and regulatory diversity shape HLA-C protein expression levels

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Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

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The Predominant Oral Microbiota Is Acquired Early in an Organized Pattern

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Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS

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BTN3A3 evasion promotes the zoonotic potential of influenza A viruses

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The complete sequence and comparative analysis of ape sex chromosomes

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Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

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Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

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The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

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Identification of Novel Zoonotic Activity of Bartonella spp., France

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Comparative genomics provides a timeframe for Wolbachia evolution and exposes a recent biotin synthesis operon transfer

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Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

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A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew

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One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

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Insecticide resistance by a host-symbiont reciprocal detoxification

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FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

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Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes

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TriTrypDB: An integrated functional genomics resource for kinetoplastida

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The Vitis vinifera C‐repeat binding protein 4 (VvCBF4) transcriptional factor enhances freezing tolerance in wine grape

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Expanding our view of genomic diversity in C andidatus A ccumulibacter clades

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Reference genome of wild goat (Capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

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Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

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Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species

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Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks

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The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities

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Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish ( Seriola lalandi )

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PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

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A global survey of arsenic-related genes in soil microbiomes

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Mangrove lagoons of the Great Barrier Reef support coral populations persisting under extreme environmental conditions

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A high-quality, chromosome-level genome assembly of the Black Soldier Fly ( Hermetia illucens L.)

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Completion of the gut microbial epi-bile acid pathway

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Chloranthus genome provides insights into the early diversification of angiosperms

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The Ubiquitous Human Skin Commensal Staphylococcus hominis Protects against Opportunistic Pathogens

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The power of next-generation sequencing as illustrated by the neuropeptidome of the crayfish Procambarus clarkii

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Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates

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Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

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Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains

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PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes

Li, F., Zhang, M., Li, Y., Liu, Y., Cui, Q., & Wang, N. (2016) · PPAR Research · doi:10.1155/2016/6042162 · Cited by 115

Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles ( C erambycidae)

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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

Winter, D. J., Ganley, A. R. D., Young, C. A., Liachko, I., Schardl, C. L., Dupont, P., Berry, D., Ram, A., Scott, B., & Cox, M. P. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007467 · Cited by 115

Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual

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TCR3d: The T cell receptor structural repertoire database

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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

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CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments

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Soil health is associated with higher primary productivity across Europe

Romero, F., Labouyrie, M., Orgiazzi, A., Ballabio, C., Panagos, P., Jones, A., Tedersoo, L., Bahram, M., Guerra, C. A., Eisenhauer, N., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02511-8 · Cited by 115

The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments

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Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

Moyers, B. A., & Zhang, J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu286 · Cited by 114

A giant virus infecting green algae encodes key fermentation genes

Schvarcz, C. R., & Steward, G. F. (2018) · Virology · doi:10.1016/j.virol.2018.03.010 · Cited by 114

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

Linz, A. M., Crary, B. C., Shade, A. L., Owens, S. M., Gilbert, J. A., Knight, R. D., & McMahon, K. D. (2017) · mSphere · doi:10.1128/msphere.00169-17 · Cited by 114

Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization

Garcia, A. K., McShea, H. S., Kolaczkowski, B., & Kaçar, B. (2020) · Geobiology · doi:10.1111/gbi.12381 · Cited by 116

Trace Metal Substitution in Marine Phytoplankton

Morel, F. M. M., Lam, P. J., & Saito, M. A. (2020) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev-earth-053018-060108 · Cited by 116

Donkey genomes provide new insights into domestication and selection for coat color

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SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability

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Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida

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LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations

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Origin and evolution of the bread wheat D genome

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Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes

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Simultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly

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Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish

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TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice

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Comprehensive classification of the PIN domain-like superfamily

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Plant host habitat and root exudates shape fungal diversity

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BLAST: improvements for better sequence analysis

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NCBI BLAST: a better web interface

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High speed BLASTN: an accelerated MegaBLAST search tool

Chen, Y., Ye, W., Zhang, Y., & Xu, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv784 · Cited by 768

BLAST++: a tool for BLASTing queries in batches

Wang, H., Ong, T.-H., Ooi, B. C., & Tan, K. (2003) · Asia-Pacific Bioinformatics Conference · Cited by 9

Improved BLAST searches using longer words for protein seeding

Shiryev, S. A., Papadopoulos, J. S., Schäffer, A. A., & Agarwala, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm479 · Cited by 113