309 papers
Genomics is the study of an organism's complete set of DNA, offering a deep dive into the biological instructions that shape life. This field explores how genetic information influences traits, health, and evolution, moving beyond single genes to understand the complex interplay within entire genomes. From uncovering the roots of disease to mapping biodiversity, genomics provides the foundational data for many modern medical breakthroughs.
At Gist.Science, we process every new preprint in this category as it appears on bioRxiv, ensuring you stay ahead of the curve. Each paper is accompanied by both a clear, plain-language overview and a detailed technical summary, making cutting-edge research accessible to everyone regardless of their background. Below are the latest papers in genomics, freshly summarized and ready for you to explore.
EDTA v2 is an enhanced, scalable tool that enables automated transposable element annotation in animal genomes by integrating LINE/SINE detection, rewriting TIR-Learner for deployability, and significantly accelerating structural detectors.
The authors developed Saturation-seq, a high-throughput single-cell platform combining saturation genome editing with RNA-seq to comprehensively quantify the functional effects of NFE2L2 variants by linking endogenous genomic edits to transcriptional impacts, achieving high accuracy in distinguishing pathogenic from benign mutations and enabling clinical interpretation of tumor and germline data.
This study demonstrates that cohesin residence time acts as a critical molecular gate determining whether histone hyperacetylation triggers higher-order 3D genome reorganization, with rapid cohesin turnover sensitizing the genome to epigenomic changes while stabilized cohesin complexes render it refractory to such remodeling.
This study utilizes whole-genome resequencing to identify a large, adaptive genomic island on chromosome 18 containing an *lrrc9-like* homeolog that distinguishes specific upper Fraser River sockeye salmon run-timing groups, reinforcing the critical role of homeologous regions in driving local adaptation and run timing diversity.
The authors introduce GIFT, a scalable single-cell assay that simultaneously profiles whole transcriptomes and targeted somatic mutations in fixed tissues, enabling the resolution of clonal heterogeneity and genotype-to-phenotype relationships in myeloproliferative neoplasms.
This study presents the first chromosome-scale genome assemblies and comprehensive structural characterization of two historically significant Tunisian durum wheat landraces, Chili and Mahmoudi, utilizing PacBio HiFi and Hi-C data to generate high-quality, reproducible genomic resources that surpass existing references and are accessible via public platforms.
By integrating multi-species transcription factor binding maps with chromatin accessibility and gene expression data, this study reveals that the specific genomic position and chromatin context of transcription factor binding sites establish a "positional grammar" that partitions gene regulation into distinct developmental, stress-responsive, and repressive functions in plants.
This study demonstrates that nitrogen use efficiency in pigs is driven by coordinated, tissue-specific transcriptomic adaptations in the liver and skeletal muscle, where high-efficiency animals exhibit reduced amino acid catabolism and inflammation alongside enhanced pathways for protein synthesis, lipid processing, and lean growth.
This study utilizes bulk RNA sequencing in a porcine model to reveal that while both viable and post-treatment neurocysticercosis involve immune activation, they exhibit distinct transcriptional signatures, with viable infection suppressing blood-brain barrier (BBB) remodeling and post-treatment disruption driving inflammatory signaling and active neurovascular remodeling.
The paper introduces simSOMA, a modular simulator that links plant growth topologies with explicit cell-lineage dynamics to model and interpret complex somatic variant allele-frequency (VAF) spectra across diverse developmental scenarios and sampling methods.