database / resource

The paper quantifies T6SS prevalence in Gram-negative bacteria using genome analysis and finds it is present in 41% of well-sampled genera.

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

TIGRdisco identifies TIGR arrays and Tas proteins from nucleotide sequences, recovering most array units and uncovering unannotated loci across datasets.

The paper highlights the lack of standardized genomic metadata in plant and metazoan genome assemblies and proposes making ploidy, cultivar, and subgenome structure mandatory metadata fields.

This paper presents a chromosome-level genome assembly for the wolverine, providing a more complete and sex chromosome-inclusive reference for conservation studies.

The paper presents GAIA, a global atlas of immune alleles, showing that underrepresented groups have more diverse alleles needed for vaccine design than Northwest European groups.

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

This paper presents the genome of Braarudosphaera bigelowii, revealing genomic and metabolic adaptations associated with its symbiotic nitrogen-fixing organelle.

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

The paper introduces the SAR11 Genome Atlas, a resource integrating SAR11 genomes and functional data to support ecological and genomic analysis of oceanic bacteria.

This study identifies genomic adaptations in an endangered California plant to coastal fog, revealing candidate genes and potential impacts of wind farms on gene flow.

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

The paper identifies subterminal heterochromatin in tetrapods using k-mer distributions, revealing ancient subgenome-specific repeats in Xenopus laevis.

The yEvo Mutation Browser helps students and researchers visualize and interpret genome sequencing data from experimental evolution studies of yeast.

This paper describes two novel Corynebacterium species isolated from human nasal passages and skin, along with characteristics of two strains of a recently named species.

The paper uses a genomic language model to cluster and annotate noncoding sequences in prokaryotic genomes, identifying structured RNAs and their potential functions.

The paper presents a chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana using PacBio and Hi-C data.

CnidoSite provides a centralized multi-omics database for cnidarians, integrating genomic, transcriptomic, proteomic, and phenotypic data to study thermal tolerance and environmental adaptation.

Carbon-A annotates protein-coding genes across eukaryotic genomes using a large encoder model, achieving high accuracy and enabling the creation of a comprehensive annotation database.

The paper characterizes mitochondrial genomes from leafhoppers and a parasitoid fly in the Eastern Canadian Arctic, expanding molecular resources for studying insect biodiversity and ecological changes.

The paper argues that low diversity in pathogen proteins does not necessarily indicate evolutionary constraint and introduces a tool to explore diversity and divergence in Plasmodium falciparum proteins.

Bolero predicts cell-state-specific gene regulation from DNA across species by integrating cell-state embeddings and biological variables.

This paper introduces an Oxford Nanopore sequencing framework for hantavirus genome assembly and variant analysis, revealing defective viral genomes as a new feature of hantavirus populations.

PigGPA improves genomic breeding analysis by combining domain knowledge with verifiable tool execution, achieving consistent results across tasks.

OFC-SV is a web portal that interprets structural variants in genomic data from African and Asian cohorts with non-syndromic orofacial clefts, identifying 41 novel SV genes and their regulatory impacts.

The paper presents high-quality reference genomes for three sympatric Cyprinodon pupfish species to study speciation mechanisms and genomic architecture.

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

The paper compares chromosome-scale genomes of two B. caapi ethnovarieties to identify genomic features associated with ethnovariety differentiation.