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The paper develops a pangenome graph for Pyrus species to explore functional variation and identifies transcription factor-associated selective sweeps in arid-adapted species.

The paper shows that transposable elements (TEs) influence 3D genome structure by interacting with pericentromeric heterochromatin (PCH), affecting gene expression and evolution in Drosophila.

The paper predicts protein-protein interactions in Drosophila using AlphaFold2-multimer, highlighting the role of intrinsically disordered regions and providing an interactive interface for exploration.

This study shows that NOVA-1 regulates circRNA expression, alternative splicing, and aging in C. elegans by modulating splicing events and circRNA production.

This study presents a gap-free, phased genome assembly of tobacco, revealing subgenomic diversification of centromeres after allopolyploidization.

This paper improves genomic evaluation in Tanzanian smallholder dairy cattle by incorporating spatial modelling to better separate genetic and environmental effects.

The paper links karyotype evolution to meiotic recombination by analyzing holocentric genomes and crossover patterns in Rhynchospora species.

The paper develops and characterizes semi-immortalized Schwann cell lines from NF1-associated cutaneous neurofibromas to aid in studying and developing therapies for NF1.

The paper investigates the evolutionary dynamics of miRNA regulatory systems in Oryza AA-genome species, revealing TE-mediated co-option as a mechanism for generating new regulatory circuits.

This study optimizes single-cell long-read sequencing protocols for improved isoform detection in pancreatic islets, showing better transcript identification and longer reads through library preparation and transcript depletion strategies.

The paper validates a single reaction amplicon sequencing approach for generating high-quality WNV genomes and characterizes transmission dynamics during a 2023 outbreak in Nebraska.

Splice Ninja predicts tissue-specific splicing events using splicing factor expression, achieving accurate results on unseen tissues.

The paper identifies core regulators of cell surface PrPC expression through CRISPR screens in neuronal cells, revealing shared and unique regulators in different cell states.

The paper identifies CpG sites and pathways associated with gestational age and epigenetic age acceleration, and links perinatal exposures to these epigenetic changes.

The paper identifies novel m6A readers that regulate human embryonic stem cell differentiation through comprehensive profiling of m6A readouts across multiple cell lines.

MELODY quantifies total mediation effects in logistic regression for high-dimensional mediators and binary outcomes, outperforming traditional methods in non-rare disease scenarios.

This study examines how HCMV and SARS-CoV-2 affect the human tRNA pool and finds HCMV alters tRNA expression and modifications, while SARS-CoV-2 does not, with implications for viral codon usage and host-virus interactions.

This paper introduces WaveTAD, a wavelet-based method for analyzing 3D genome structures, showing improved accuracy and revealing new biological insights across species and conditions.

The paper shows that functional synergy between transcription factors explains why most TF binding does not affect gene expression, and highlights the need for more expressive regulatory network models.

The paper identifies highly conserved fragments in 3'UTRs across mammals using computational methods and a transformer model, finding they are A/T-rich and enriched in neuronal tissues with roles in neurodevelopment and RNA processing.