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.
This study introduces STEAM, an evolutionary transfer learning framework that leverages single-cell chromatin accessibility data from mouse development and synteny-supervised training across 241 mammalian genomes to overcome data limitations and enable accurate, genome-wide inference of enhancer landscapes across diverse cell types and species.
This study introduces Nascent CUT&Tag to reveal that transcription factors like GAGA factor and Pleiohomeotic exhibit distinct, motif-dependent recovery kinetics on newly synthesized DNA following replication, with early GAF binding requiring BAF-mediated chromatin remodeling to support cell cycle progression.
This study analyzes deep whole-genome sequencing data from 440 endometrial tumors to reveal how endogenous mutational mechanisms, retrotransposition activity, and host metabolic factors like BMI distinctively shape the genomic architecture and evolutionary trajectories of molecular subtypes, offering a mutagenesis-centric framework for improved risk stratification and therapeutic strategies.
This paper introduces the personalized variant effect predictor (pVEP) framework, which demonstrates that an individual's genetic background significantly alters AI-predicted clinical variant effects, revealing that many variants are pathogenic in some genetic contexts but benign in others.
This study presents a pseudo-phased, chromosome-level genome assembly of the coffee leaf rust pathogen *Hemileia vastatrix* (isolate Hv178a), revealing a unique isolate-specific trisomy of chromosome 17 that likely underlies its increased virulence.
This study presents the first high-quality nuclear genome assembly of *Chaetoceros muelleri*, derived from resurrected Baltic Sea sediments, which reveals extensive gene duplication, transposable element-driven plasticity, and lineage-specific innovations that underpin the diatom's evolutionary adaptability and ecological success.
This study demonstrates that integrating the DNA language model GROVER with chromatin and regulatory features reveals that while cell-type specific information is crucial, much of the genome stability landscape governing double-strand break sensitivity is inherently encoded within the DNA sequence itself.
This study integrates ATAC-STARR-seq, CRISPR screens, and high-resolution chromatin mapping to demonstrate that enhancer hubs, organized through CTCF-independent interactions and driven by key elements like Batf, govern the 3D chromatin topology essential for establishing and maintaining Th17 cell identity.
By reconstructing an ancestral placental mammal karyotype and recombination map, this study reveals that while autosomal recombination landscapes are not conserved across species like the X chromosome, ancestral regions with low recombination rates are under stronger purifying selection and enriched for cellular functions, whereas high-recombination regions are less constrained and associated with regulatory and immune systems.
The paper introduces NanoPlasmiQC, a cost-effective, automated workflow utilizing Oxford Nanopore long-read sequencing to sequence and analyze full plasmids within a single day, offering a superior alternative to traditional Sanger sequencing.