368 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 reveals that HPV-human hybrid extrachromosomal DNAs in cervical cancer exhibit distinct, allele-specific epigenetic landscapes with higher densities of active regulatory elements compared to human-only ecDNAs, highlighting how HPV integration shapes the regulatory architecture of these cancer-driving circular structures.
This paper introduces a "multipulse" BrdU labelling strategy combined with the ForkML machine-learning algorithm to achieve high-resolution, single-molecule replication profiling of the entire human genome at kilobase resolution.
By analyzing LTR retrotransposon sequences across 249 drosophilid genomes, this study reveals complex interspecies evolutionary patterns of Gypsy-family elements, highlighting how the loss or inactivation of the Envelope protein and the stability of sORF2 drive shifts in tissue-specific expression and co-evolution with host transcriptional control mechanisms.
This study utilizes deep mutational scanning to comprehensively map the sequence determinants of human programmed stop codon readthrough, revealing that while a core CUAG motif and immediate flanking nucleotides are conserved, readthrough efficiency is governed by gene-specific, context-dependent architectures involving extensive upstream and downstream interactions that define distinct local fitness peaks for each target gene.
This paper presents the gene model for the Density regulated protein (DENR) ortholog in *Drosophila grimshawi*, which was annotated using the Genomics Education Partnership protocol to support evolutionary studies of the Insulin/insulin-like growth factor signaling pathway across the *Drosophila* genus.
This study benchmarks 16S rRNA, FastANI, Mash, and FastAAI across 30,495 prokaryotic type-strain genomes to demonstrate that while each method has distinct strengths and limitations across taxonomic ranks, they function best as complementary tools within a rank-aware framework rather than as standalone solutions.
This study introduces a multimodal computational framework that analyzes hundreds of thousands of transcriptome samples to reveal a pervasive, biologically unjustified male bias across numerous disease areas, highlighting critical gaps in female-specific biomedical research.
By analyzing 198 eukaryotic genomes, this study reveals that the "G4 paradox" is maintained through compartment-dependent selection regimes where codon adaptation suppresses G-quadruplexes in coding sequences while direct structural selection preserves them in regulatory regions like introns and promoters.
This study presents a near-complete, high-quality genome assembly of the contact lens-associated keratitis isolate *Fusarium oxysporum* MRL8996, resolved into 16 chromosomes via a hybrid Nanopore and Hi-C approach, providing a critical resource for investigating the structural variations and evolutionary mechanisms underlying its pathogenicity.
This study demonstrates that a machine learning classifier analyzing 4-mer end motif profiles of cell-free DNA from routine first-trimester NIPT samples can accurately predict spontaneous preterm birth with high sensitivity and specificity, offering a non-invasive method to identify at-risk pregnancies without additional testing.