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The paper introduces a TF-independent method to identify cis-regulatory islands in plant genes, showing they reveal regulatory patterns not captured by motif-centric approaches.

The paper annotates conserved protein domains in human endogenous retroviruses using HMMER and InterProScan, revealing full-length retrovirus-like domains in multiple HERV families.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

This study characterizes insect-specific viruses in Aedes aegypti from Kwale County, Kenya, identifying complete and partial genomes of several ISVs.

The paper identifies and characterizes HSP70 family members in the Cuban painted snail Polymita picta to assess their role in thermoresistance and adaptation to climate change.

The paper experimentally measures CTCF-binding affinity across 276,765 human DNA sequences and develops a deep learning model to predict and interpret binding strength based on sequence features.

The paper introduces a deep learning framework for estimating epidemiological parameters from viral sequences, achieving high accuracy and speed compared to traditional methods.

This study presents a T2T genome and graph-based pan-genome of longan, identifying structural variants and QTLs associated with maturity period and providing resources for genetic improvement.

This study presents a chromosome-level genome assembly for Iberolacerta aurelioi and uses whole-genome sequencing to investigate phylogenomic relationships and adaptive traits in the genus Iberolacerta.

This paper introduces XAI-ecDNA, a framework for detecting extrachromosomal DNA using synthetic FISH and genomic data, achieving high performance and interpretability.

The paper identifies Epromoters as cis-regulatory elements that regulate clusters of stress-response genes by recruiting key transcription factors, showing their role across different stress models.

This paper presents a chromosome-scale genome assembly for Oxalis stricta, revealing its allotetraploid nature and synteny with related species.

The paper shows that end-repair in double-stranded DNA libraries reduces CpG methylation estimates and tissue origin accuracy, while trimming read termini mitigates this bias but reduces coverage.

The paper uses genomic analysis to trace the introduction routes of pathogenic B. gladioli strains into Bangladesh and identifies virulence gene changes associated with host transitions.

The paper describes eight new cyanobacterial species and one new genus from Hawaiian steam vents using genome-based classification and phylogenomic analysis.

This study identifies genomic strategies and trait trade-offs in pyrophilous fungi that enable survival and nutrient cycling post-fire, revealing gene duplication, horizontal gene transfer, and sexual recombination as key evolutionary mechanisms.

Dosa covalently bars proteins for high-throughput biochemical analysis by linking variants to RNA barcodes via a methyltransferase, enabling assessment of protein function through direct biochemical assays.

This study identifies and classifies 57 WRKY genes in Lagenaria siceraria, revealing their structural organization, evolutionary expansion, and tissue-specific expression patterns.

The paper examines prenatal environmental factors affecting CYP19A1 promoter methylation in cord blood using WQS regression, finding associations with bisphenols, sunlight, mould, phthalates, folate, and air pollution.