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<h4>Motivation</h4>Advances in single-cell sequencing have enabled multiomics profiling at unprecedented resolution; however, mass spectrometry-based single-cell proteomics (scMS) remains inherently destructive, precluding simultaneous transcriptomic capture. Unlike antibody-based methods such as CITE-seq, which permit paired profiling but …
Read PDF<h4>Motivation</h4>Intracellular signaling pathways regulate essential cellular functions and orchestrate complex biological processes, yet their dynamic activity remains challenging to quantify with precision. Advances in single-cell omics enable pathway activity inference at the transcriptional level; however, …
Read PDF<h4>Motivation</h4>Psoriasis is a chronic, immune-mediated disorder with an unmet need for effective treatments. To systematically prioritize therapeutic targets, we integrated proteome-wide Mendelian randomization (MR) with expression validation in blood/skin, genetic susceptibility analysis, differential gene expression …
Read PDF<h4>Motivation</h4>The advent of single-cell RNA sequencing (scRNA-seq) technology has allowed researchers to measure gene expression profiles at the single-cell level, providing valuable insights into cellular heterogeneity. However, due to the limitations of current sequencing platforms, …
Read PDF<h4>Motivation</h4>The assessment of aberrant transcription events in rare disease patients holds great promise for enhancing the prioritization of causative genes-a strategy already widely adopted in clinical settings to improve diagnostic accuracy. Nevertheless, the accurate identification …
Read PDF<h4>Summary</h4>The examination of high-risk cells and regions in tissue samples from spatially resolved transcriptomics platforms offers meaningful insights into specific disease processes. For existing methods, while cell types or clusters can be identified and associated …
Read PDF<h4>Motivation</h4>Single-cell sequencing technologies allow researchers to study cell-cell variation within a cell population. Variations between cells are driven by the underlying biological network, particularly gene regulatory networks (GRNs). GRNs rewire as cells evolve, and different …
Read PDF<h4>Summary</h4>Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularized by the Python scverse ecosystem. However, accessing these datasets from R, allowing users to take advantage of the strengths of …
Read PDF<h4>Summary</h4>Multimodal approaches are increasingly leveraged for integrating omics data with textual biological knowledge. Yet there is still no accessible, standardized framework that enables systematic comparison of omics representations with different text encoders within a unified …
Read PDF<h4>Motivation</h4>Spatial transcriptomics (ST) enables the measurement of gene expression while preserving the spatial context of tissues. However, the sparsity of ST data leads to poor usage of gene expression and spatial information, resulting in the …
Read PDF<h4>Summary</h4>Although RNA-sequencing has replaced microarrays for gene expression profiling over the past 15 years, its full potential for splicing analysis in clinical settings remains underexploited. Most available tools are tailored for large cohorts or known …
Read PDF<h4>Motivation</h4>Single-cell RNA sequencing (scRNA-seq) is now a core technology for resolving cellular heterogeneity in complex samples, and standard analysis workflows produce a wide range of outputs, each requiring tailored visualization. To support this, a wide …
Read PDF<h4>Motivation</h4>Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of the poly(A) tail was shown to directly impact mRNA stability and translation, broadening its regulatory scope. …
Read PDFRNA methylation, notably m6A modification, is a predominant epitranscriptomic alteration in mRNA, yet its evolutionary properties and the selective constraints acting on it across mammals remain poorly understood. Here, we generated a single-base-resolution m6A modification …
Read PDF<h4>Background</h4>Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer and is marked by pronounced intra-tumoural heterogeneity that complicates therapeutic response. Patient-derived organoids offer a physiologically relevant model to capture this …
Read PDF<h4>Motivation</h4>Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches struggle to accurately demultiplex raw nanopore signals, failing to capture …
Read PDFAdvancements in single-cell RNA sequencing (scRNA-seq) techniques have expanded the study of cellular heterogeneity and transcriptional dynamics. Early methods relied on manual cell isolation followed by barcode introduction, but subsequent approaches integrated automated cell isolation …
Read PDF<h4>Motivation</h4>Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order …
Read PDF<h4>Motivation</h4>High-quality genome annotations are essential for transcriptomic analyses investigating plant responses to environmental stress. While nanopore long-read direct RNA sequencing offers a powerful approach for improving genome annotations, studies benchmarking optimal tools for this process …
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