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Mini-Review

Large-scale genomic analysis of the domestic dog informs biological discovery

  • First Published July 2, 2024
Research

Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles

  • First Published July 2, 2024
Resource

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

  • First Published July 1, 2024
Method

CodonBERT large language model for mRNA vaccines

  • First Published July 1, 2024
Resource

Wolffia australiana" > Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

  • First Published July 1, 2024
Method

Delineating yeast cleavage and polyadenylation signals using deep learning

  • First Published June 24, 2024
Method

Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution

  • First Published June 21, 2024
Method

Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters

  • First Published June 17, 2024
Method

Size-based expectation maximization for characterizing nucleosome positions and subtypes

  • First Published June 17, 2024
Method

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

  • First Published June 12, 2024
Method

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

  • First Published June 12, 2024
Method

Identifying genes within pathways in unannotated genomes with PaGeSearch

  • First Published June 10, 2024
Method

fibertools" > DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

  • First Published June 7, 2024
Mini-Review

Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

  • First Published June 7, 2024
Method

Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation

  • First Published June 5, 2024
Research

Cardiocondyla obscurior" > Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior

  • First Published June 5, 2024
Method

Full-resolution HLA and KIR gene annotations for human genome assemblies

  • First Published June 5, 2024
Research

Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy

  • First Published May 22, 2024
Research

Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

  • First Published May 22, 2024
Research

Drosophila melanogaster ovary" > Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

  • First Published May 15, 2024
Resource

A harmonized public resource of deeply sequenced diverse human genomes

  • First Published May 15, 2024
Research

N6-adenine methylation in a unicellular eukaryote" > Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote

  • First Published May 14, 2024
Perspective

Ribosome decision graphs for the representation of eukaryotic RNA translation complexity

  • First Published May 7, 2024
Method

A new framework for exploratory network mediator analysis in omics data

  • First Published May 7, 2024
Research

Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions

  • First Published May 6, 2024
Research

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

  • First Published May 6, 2024
Research

Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription

  • First Published May 6, 2024
Review

Navigating the landscape of epitranscriptomics and host immunity

  • First Published May 3, 2024
Research

Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice

  • First Published May 3, 2024
Method

Simulation of nanopore sequencing signal data with tunable parameters

  • First Published May 1, 2024
Corrigendum

Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data

  • First Published April 25, 2024
Method

cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements

  • First Published April 17, 2024
Method

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

  • First Published April 16, 2024
Review

A systematic review on the biochemical threshold of mitochondrial genetic variants

  • First Published April 16, 2024
Research

Oikopleura dioica cryptic species" > Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species

  • First Published April 15, 2024
Research

Systematic identification and characterization of exon–intron circRNAs

  • First Published April 12, 2024
Research

Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

  • First Published April 11, 2024
Research

Drosophila knock-in tauopathy model" > Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model

  • First Published April 10, 2024
Method

Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples

  • First Published April 8, 2024
Method

Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches

  • First Published April 5, 2024
Method

Robust chromatin state annotation

  • First Published March 21, 2024
Resource

Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals" > The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

  • First Published March 20, 2024
Research

Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation

  • First Published March 20, 2024
Research

Inference of selective forces on house mouse genomes during secondary contact in East Asia

  • First Published March 20, 2024
Review

The structure, function, and evolution of plant centromeres

  • First Published March 14, 2024
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