A reconstructed protein interactome from LECA reveals ancient systems linked to modern genetic diseases, including novel associations for bone density and birth defects.
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Cell Genomics
Elsevier BV · Genomics & Bioinformatics · ISSN 2666-979X
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Response eQTLs identified under environmental exposures share key properties with disease-associated loci, highlighting their role in context-dependent gene regulation.
Conserved and human-specific cis-regulatory elements in the brain show distinct roles in neuropsychiatric and neurodegenerative disease risk, with 9 mammalian species analyzed.
MOSHPIT enables fully reproducible, scalable metagenome analysis within the QIIME 2 framework, integrating validated tools and provenance tracking for diverse ecosystems.
Complete genomes and intraspecific variation analysis reveal 1,596 rapidly evolved human regions linked to brain and heart development.
Pre-diagnosis plasma cell-free DNA methylation signatures predict prostate and breast cancer risk up to eight years before clinical detection, with hazard ratios of 3.55 and 2.3 respectively.
Conservation of transcriptional signatures enables robust identification of homologous bone marrow cell types across four mouse species, outperforming larger gene lists.
Paternal age-related mutations and selection primarily shape de novo mutation risk for developmental disorders, with early mosaicism contributing to a smaller, high-risk subset.
29.6 million genetic variants were identified in a human pangenome reference graph, revealing extensive diversity beyond the GRCh38 reference.
Pouria Salehi Nowbandegani's work on pangenome graph variants advances genomic cataloging, focusing on defining and classifying genetic diversity across populations.
Base editing has achieved significant clinical progress, with promising applications in treating over half of pathogenic genetic variants, including sickle cell disease and hypercholesterolemia.
Cell-type fine-mapping reveals 79 independent cellular mechanisms explaining 39% of trait heritability across 63 GWASs.
Single-cell transcriptomics reveals cell-type-specific immune responses to stress hormones, identifying signatures linked to stress-related diseases in humans.
Over half of public RNA-seq samples originate from US institutions, with 90% from high-income countries, yet only 3% include population descriptors, revealing significant bias.
scXpand accurately detects T cell clonal expansion across multiple cancers using only single-cell RNA sequencing data, achieving high robustness without paired TCR sequencing.
PlantCAD2, a plant-specific DNA language model with 676 million parameters, outperforms larger models in 10 of 12 tasks across flowering plants.
PlantCAD2, a DNA foundation model, accurately interprets genomes across over 2,000 flowering plant species, advancing plant genomics research.
Chronic stress hormones alter immune cell signaling, revealing new insights into inflammation and disease mechanisms through single-cell RNA sequencing.
Polygenic risk scores combined with plasma proteomics reveal 90 cancer-associated proteins and 19 trans-regulated networks across 21 cancers.
Optimized CRISPRi-Cas9 library Katsano achieves high efficiency by integrating updated scoring and off-target analysis, enhancing gene repression precision.
Cooperative interactions enable low-affinity transcription-factor motifs to significantly influence chromatin accessibility and regulatory potential across the genome.
Cell-type-specific damage scores accurately map disease progression in kidney and liver diseases across multiple single-cell and spatial transcriptomics platforms.
A comprehensive single-cell and spatial atlas across 10 vertebrate species reveals that gene repurposing and new gene emergence drove gastrointestinal cellular evolution over 500 million years, with key innovations like tuft cells and immune structures.
Single-cell 3D genome imaging reveals that super-enhancer hubs are rare, nonspecific, and not essential for transcriptional bursting in mouse embryonic stem cells.
Verkko-Fillet enables the production of a complete giraffe genome from telomere to telomere, increasing assembly quality from Q61.5 to Q73.6.
Complete telomere-to-telomere genomes of a horse and donkey reveal unusual centromere evolution and plasticity in equids, with notable differences in satellite DNA and protein binding.
Multiple high-quality human genome assemblies from the Telomere-to-Telomere (T2T) Consortium are being published, advancing the completeness of the human reference genome.
Divergent regulation of 9p21 cell cycle genes is driven by chromatin topology and distal elements, with p15 INK4B dominating across tissues and cell types.
Repeated dosing with engineered virus-like particles enhances prime editing efficiency beyond previous limits.
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