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.
This paper introduces a practical framework for validating somatic mutation burden assays without a ground truth, which is implemented in the SomaticCODEC tool to demonstrate strong linearity and high precision in quantifying SNV burden in primary human samples.
By integrating near-complete diploid genome assemblies with long-read sequencing from 212 individuals, this study constructs a comprehensive atlas revealing that unique, heritable telomere variant repeat (TVR) codes at chromosome ends influence chromatin organization and facilitate rare telomerase-independent telomere extension mechanisms in the human germline.
The paper introduces GENERator-v2, a family of autoregressive genomic foundation models that achieve scalable, single-nucleotide resolution over 98k base pair contexts by reconciling efficient k-mer tokenization with precise supervision through Factorized Nucleotide Supervision and gene-centric Genome Compression Pretraining.
This study reveals that histone H3K27 methylation patterns are faithfully maintained in cycling cells through a sequential, stepwise methylation process following DNA replication, a mechanism that is particularly crucial for preserving the plasticity of developmentally silenced genes during early S-phase.
This study defines the cell type-specific regulatory logic of astrocyte inflammatory responses by mapping genome-wide transcription initiation to reveal how lineage-restricted and inflammatory transcription factors cooperate on distinct enhancer landscapes to drive stimulus-dependent gene expression, linking these mechanisms to human neurological disease susceptibility.
This study identifies and validates a novel sense-to-sense codon reassignment in a specific clade of uncultivated Acidimicrobiales bacteria, where the ACA codon, typically encoding threonine, has been repurposed to encode aspartate.
This paper proposes a data-driven biophysical framework demonstrating that a specific gene ensemble acts as a genomic Maxwell's demon and self-organized criticality controller, orchestrating cancer cell fate commitment by coupling entropy-information flux with mechanical work to drive critical transitions and establish time-gated rules for intervention.
This study systematically analyzes over 100,000 GWAS to demonstrate that while protein-altering variant support strongly predicts therapeutic success, combining this evidence with intermediate levels of gene pleiotropy (affecting 2–5 traits) optimizes drug discovery by balancing efficacy with organism-level safety, thereby identifying a high-probability profile already validated by numerous approved therapies.
This study establishes that human endogenous retroviruses (HERVs) serve as pervasive, family-specific building blocks of RNA regulatory architecture by embedding distinct RNA-binding protein motifs, contributing to thousands of long non-coding RNAs, and forming unique antisense configurations that influence post-transcriptional gene regulation and immune responses.
MethylBench provides a comprehensive cross-platform benchmark of six DNA methylation profiling technologies using GIAB and human samples, demonstrating that while sequencing-based methods offer superior genome-wide coverage and long-read platforms enable phasing, all methods consistently identify robust epigenetic hotspots in promoters and introns when coverage and annotation redundancies are properly addressed.