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reComBat-seq: Regularized negative binomial regression for batch-effect correction in underdetermined transcriptomics datasets
Motivation: Batch effect correction is essential for the integration of large-scale transcriptomics datasets such as single-cell RNA-seq or multi-study bulk RNA-seq datasets for reducing technical noise that may mask biological signal. Existing correction methods, either do not produce count data output which is crucial for state-of-the-art downstream analyses such as differential expression analysis or fail to converge in underdetermined study designs. Results: We present reComBat-seq, a...
Seq-DeepIPC: Sequential Sensing for End-to-End Control in Legged Robot Navigation
arXiv:2510.23057v2 Announce Type: replace Abstract: We present Seq-DeepIPC, a sequential end-to-end perception-to-control model for legged robot navigation in real-world environments. Seq-DeepIPC advances intelligent sensing for autonomous legged navigation by tightly integrating multi-modal perception (RGB-D + GNSS) with temporal fusion and control. The model jointly predicts semantic segmentation and depth estimation, giving richer spatial features for planning and control.
Scalable in vivo cardiac functional genomics with compressed AAV-Perturb-seq reveals a common mitochondrial response to perturbation
Efficient identification of new targets to treat human disease requires a scalable way to link genotype to phenotype directly in the target organ. Pooled CRISPR screening with single-cell RNA sequencing as a readout (Perturb-seq) has emerged as a method for functional genomics but is typically applied in vitro and is limited in scale. Here, we combine in vivo Perturb-seq via adeno-associated virus (AAV)-mediated delivery with a statistical framework allowing for signal deconvolution after...
Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle
Traditional short-read RNA-seq lacks the resolution to fully capture full-length isoforms and complex alternative splicing, leaving a "missing regulation" gap in existing molecular atlases. Here, we present a population-scale, multi-omics dissection of bovine complex traits using matched deep whole-genome sequencing (30), long-read (ONT) and short-read RNA-seq, as well as metabolome data from 432 dairy cows across four distinct lactation stages. We expanded the bovine transcript atlas with...
D&D-seq maps DNA-protein interactions in single cells with multi-omics compatibility
D&D-seq maps DNA-protein interactions in single cells with multi-omics compatibility Sadie Harley Scientific Editor Robert Egan Associate Editor A new technology allows scientists to map, in single cells, the DNA binding sites of transcription factors and other regulatory proteins that control gene activity, according to a study led by investigators at Weill Cornell Medicine and the New York Genome Center. With key advantages over methods currently in use, the technology is expected to be a...
Ultra-low biomass sequencing workflow (LBV-Seq) enables de novo metagenomic reconstruction of DNA and RNA viral genomes
Genome-resolved virome analysis remains inaccessible for many samples, including those with clinical relevance, because viral nucleic acid recovered after enrichment is often too scarce to support de novo genome assembly. As a result, many analyses are limited to sparse read-level detection, which cannot recover divergent viruses, resolve strains, or interpret gene-level variation. Here, we developed Low Biomass Viral Sequencing (LBV-Seq), a workflow that couples low-input viral sample...
rsx: A high-performance streaming toolkit for RAD-seq sex determination
Announce Type: cross Abstract: Restriction site-associated DNA sequencing (RAD-seq) is widely used to discover sex-linked markers in non-model organisms, but large studies produce marker tables with millions of RAD tags. RADSex provides the reference workflow for building marker-by-individual depth tables and testing sex-biased marker distributions, but its depth, merge, and related table-building commands grow memory-hungry, and its standard output reports frequentist calls with no...
Auditable recovery of single-cell RNA-seq zeros with SPARE
In Single-cell RNA-seq, observed zeroes are the mix between biological absence and technical limitations. However, current evaluation metrics fail to distinguish between these two states, focusing on reconstruction accuracy rather than the biological validity of edits. We introduce SPARE, a partition-aware framework that audits the imputation process by cataloging observed zeros as edited, unchanged, or marker-vetoed prior to sequence reconstruction.
Longitudinal RNA Seq analyses reveal the prominent role of Vagococcus in broiler meat spoilage microbiome
Background Raw broiler meat products are highly perishable, and microbial activity is the main factor limiting their shelf lives. The spoilage microbiomes of broiler meat products have been studied mainly using traditional culturing methods and 16S rRNA gene amplicon sequencing, neither of which can show the activity of whole microbiome. Previous metatranscriptomic research of broiler spoilage has also remained limited to specific spoilage organisms rather than entire microbiomes.
Integrating gene regulatory priors into Transformer attention with scTransformer for interpretable scRNA-seq analysis
Announce Type: cross Abstract: Motivation: Transformer-based models are increasingly applied to large-scale single-cell transcriptomics, showing strong performance through self-supervised learning on millions of cells. However, most existing approaches treat genes as independent features, and largely ignore prior biological knowledge, which limits interpretability and robustness. In this paper, we explore whether explicitly incorporating gene regulatory information can improve both model...