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Ribo-ITP identifies thousands of translons from low-input samples, revealing their regulatory roles and impact on cell growth.

This study identifies molecular mechanisms underlying the mutualistic relationship between anemone and anemonefish by analyzing transcriptional changes after association.

The paper reports a near telomere-to-telomere genome assembly of Micractinium conductrix, enabling genomic studies of endosymbiosis and biotechnological applications.

The paper introduces a standard for unambiguously representing, retrieving, and comparing reference genomes and transcriptomes, revealing inconsistencies across 60 human and 36 mouse references.

Sequential-GAM constructs the single-cell geometric 3D genome structure by estimating radial positions and hierarchical organization of chromosomes and genes.

This paper introduces speculative decoding to accelerate genomic and proteomic sequence generation using foundation models without compromising prediction quality.

The paper reports a small mitochondrial genome from a planktonic foraminiferan, showing gene loss and accelerated evolution compared to other rhizarian mitogenomes.

The paper uses CRISPRi Perturb-seq to identify 238 enhancer-gene regulatory associations in colorectal cancer and integrates chromatin data to understand their spatial organization.

The paper classifies TAD boundaries by chromatin accessibility in K562 cells and identifies ZNF316 as a novel architectural protein that contributes to boundary strength.

The paper identifies AP-1 transcription factors as regulators of a transitional state in lung alveolar type 2 cells during injury-repair, linking chromatin changes to both regeneration and tumorigenesis.

The paper presents a high-resolution map of RHO missense variants' trafficking and evaluates pharmacologic correction with YC-001, identifying pathogenic variants and therapeutic potential.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

The paper shows re-replication is a physiological mechanism in human stem cell differentiation, increasing gene copy numbers to meet protein demands during differentiation.

The paper analyzes the genomic diversity of C. tropicalis, finding geographic correlation and hyper-divergent regions linked to environmental adaptation.

The paper identifies hypermutable regions in the nuclear genome of Bigelowiella natans, showing extreme mutation rate variation and a distinctive mutational signature in virus-derived sequences.

CellCover identifies marker gene panels for cell types by solving a set-covering problem, outperforming differential expression methods in capturing cell-specific signals and developmental progression.

The paper introduces CABBAGE, a large-scale AMR genotype-phenotype database linking bacterial genomes to antibiotic susceptibility data and metadata, enabling analysis of resistance trends and predictive method benchmarks.

The paper analyzes somatic mutation profiles in normal human tissues to identify mutagenic mechanisms and their association with age, disease, and environmental exposures.

The paper identifies plant genes whose expression changes are associated with genetic variation in the nematode Meloidogyne hapla and shows these patterns are conserved across different host plants.

This paper introduces Gnomix, a high-resolution ancestry deconvolution method for next-generation genomic data, achieving higher accuracy and faster performance than existing methods.