238 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.
StrataBionn is a novel supervised neural network framework that outperforms traditional methods in classifying microbial communities into community state types across diverse anatomical sites by effectively capturing complex, non-linear taxonomic signatures to provide more robust and accurate microbiome stratification.
The paper introduces GrAdaBeam, a hybrid optimization algorithm that combines gradient-derived attention maps with adaptive beam search to outperform existing methods across 17 diverse nucleic acid design tasks in the new NucleoBench benchmark, demonstrating superior generalization and biological signal recovery.
This study characterizes over 100 autosomal loci called Inactivation/Stability Centers (I/SCs) that exhibit stochastic, mitotically stable, allele-specific epigenetic regulation of gene expression and replication timing, creating cellular mosaicism that impacts numerous dosage-sensitive genes associated with human diseases.
An analysis of 12 soil viromics datasets reveals that temperate bacteriophages consistently exhibit significantly higher microdiversity than virulent ones, suggesting that lysogeny promotes or preserves genetic variation within phage populations.
This study utilizes population genomics of *Schistosoma japonicum* in post-re-emergence Sichuan, China, to reveal that the disease's resurgence was driven by a genetically diverse parasite population sustained in non-human reservoirs and transmitted through a network of highly focal, locally connected villages.
This study utilizes whole-genome sequencing of 94 *Sporothrix* isolates to reveal distinct evolutionary strategies between *S. brasiliensis* and *S. schenckii*, highlighting how recent population expansion, specific copy number variations, and polygenic adaptations have driven the emergence and antifungal resistance of the epidemic *S. brasiliensis* in South America.
This study presents a near-complete, chromosome-level, haplotype-resolved genome assembly of common buckwheat (Fagopyrum esculentum) using a trio-binning approach, providing a high-quality genomic resource to overcome challenges posed by the species' high heterozygosity and accelerate future breeding and research efforts.
This study demonstrates that Oxford Nanopore whole-genome sequencing is a viable and often superior alternative to Illumina for large-scale genomic characterization of *Staphylococcus aureus*, offering improved detection of clinically relevant genes and variants despite minor lineage-specific error variations.
The study introduces SnakeHichipTF, a scalable framework integrating HiChIP analysis and AI-based footprinting to decode how distinct transcription factor programs govern region-specific enhancer-promoter wiring in the human brain, linking these regulatory architectures to psychiatric and metabolic traits as well as human evolutionary adaptations.
This study utilizes whole-genome resequencing of 94 farmer-maintained cacao trees across Costa Rica to reveal a complex genetic landscape containing both Criollo-derived lineages and unique local diversity, highlighting the critical role of smallholder farming systems as reservoirs for the crop's conservation and future breeding.