transcriptomic atlas
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Related Articles from SNS
An Aspergillus lncRNA atlas reveals a novel modulator of aflatoxin biosynthesis
Long non-coding RNAs (lncRNAs) represent a significant fraction of the transcriptome and are vital regulators in eukaryotes, yet their functional landscape in fungi remains largely undefined. Here we present a transcriptomic atlas of 8,553 lncRNAs across four evolutionarily and biotechnologically diverse Aspergillus species. We observed marked diversity in the long non-coding repertoire between species, with only 39% shared between at least two species.
Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features
Cancer arises from extensive genetic and epigenetic alterations that reshape chromatin, transcriptional regulation, and malignant cell states. To systematically chart cancer-intrinsic regulatory programs, we constructed a pan-cancer single-cell transcriptomic and epigenomic atlas encompassing 60 human cell lines representing 16 tissue origins and 20 cancer types, comprising 240,957 single-nucleus RNA-seq and 223,347 single-nucleus ATAC-seq profiles. Integrative analyses revealed extensive...
STITCH: Spatial Transcriptomics Imputation via Flow Matching with Internal Learning
Spatial transcriptomics datasets frequently suffer from spatial gaps and missing regions due to sectioning artifacts, tissue damage, and the high cost of sequencing that limits tissue coverage. We present STITCH, a scalable and robust generative framework for multidimensional virtual spatial transcriptomics reconstruction. STITCH models intrinsic spatial-transcriptomic patterns directly from individual tissue samples, enabling reconstruction without requiring external reference atlases or...
A mitochondrial-immune axis drives the transcriptomic transition from brain aging to Alzheimer's disease
Aging is the primary risk factor for Alzheimer's disease (AD), yet the molecular transitions linking normal brain aging to neurodegeneration remain poorly defined. Here, we performed integrative bulk transcriptomic analyses across a multi-region mouse aging atlas, a human aging-to-AD cohort, and an independent human AD validation dataset. Aging is associated with a progressive, region-specific increase in transcriptional perturbation, with the entorhinal cortex and choroid plexus showing the...
Genomic-Adjusted Radiation Dose from Bulk RNA Sequencing for Personalized Radiotherapy
Radiotherapy is delivered to more than half of all patients with cancer yet is prescribed using uniform physical doses despite well-established interpatient variability in biological response. The genomic-adjusted radiation dose (GARD), derived from the radiosensitivity index (RSI), integrates tumor transcriptomics with radiation dose to estimate patient-specific treatment effect, and has been clinically validated as a predictor of radiotherapy benefit across diverse disease sites, including...
Cross-scale spatially-aware generative modeling of transcriptomic programs underlying neurodegenerative brain organization
arXiv:2606.05870v1 Announce Type: cross Abstract: Neurodegenerative disorders such as Alzheimer's disease exhibit highly organized patterns of regional brain vulnerability, yet the biological mechanisms underlying this spatial selectivity remain incompletely understood. Existing imaging-transcriptomic studies have largely relied on correlation-based analyses between gene expression and neuroimaging phenotypes, limiting their ability to model how molecular organization gives rise to...
Spatial Transcriptomics-Guided Alignment Enhances Molecular Profiling in Pathology Foundation Model
Announce Type: new Abstract: Comprehensive molecular profiling is essential for modern precision oncology but remains hindered by prohibitive costs, specimen exhaustion, and protracted turnaround times. While pathology foundation models (PFMs) have demonstrated potential for inferring molecular phenotypes from routine hematoxylin and eosin (H&E) whole-slide images (WSIs), current architectures primarily rely on vision-centric self-supervised learning or vision-language alignment, lacking...
Cellpin enables reference-based imputation and denoising of spatial transcriptomes
Spatially resolved transcriptomics enables gene expression profiling within tissue architecture, but targeted panels leave much of the transcriptome unmeasured and spatial artifacts such as RNA diffusion and segmentation errors introduce technical noise. These limitations necessitate computational imputation and denoising, yet existing methods typically incorporate spatial measurements during training, limiting scalability and risking the embedding of technology-specific artifacts into...
Mapping genetic risk mechanisms for immune-mediated diseases across human dendritic cell differentiation
Defining the cell types and mechanisms through which genetic variation operates is essential to understand the biological basis of disease. Although human dendritic cells (DCs) are crucial in regulating immunity, their rarity and limitations in available genomic data have hampered efforts to link inherited disease risk to specific DC subsets. Here, we present a single-cell multi-omic atlas of human DC differentiation from hematopoietic stem and progenitor cells (HSPCs) that includes...