Discover how analysis of #scRNA-seq data supports AAV gene therapy research. You will learn how it helps with everything from identifying target cells to predicting treatment response and resistance!

www.fiosgenomics.com/advancing-aav-gene-thera...

#bioinformatics

Discover how analysis of #scRNA-seq data supports AAV gene therapy research. You will learn how it helps with everything from identifying target cells to predicting treatment response and resistance!

www.fiosgenomics.com/advancing-aav-gene-thera...

#bioinformatics

Discover how analysis of #scRNA-seq data supports AAV gene therapy research. You will learn how it helps with everything from identifying target cells to predicting treatment response and resistance!

www.fiosgenomics.com/advancing-aav-gene-thera...

#bioinformatics

From now on all high profile paper title perhaps should shift from "#scRNAseq revealed this" to "#AI assisted analysis of #scRNA and #spatial #data revealed this.." lol

2/ 🔍 We investigated the proinflammatory response to TNF in primary human cells using #scRNA and #scATAC sequencing and fluorescence microscopy. We identified ~1,500 TNF-regulated genes (TRGs) that often clustered in the genome and exhibited induced co-expression.

CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap - Molecular Systems Biology Single-cell RNA sequencing allows defining cellular identities based on transcriptional similarity using unsupervised clustering. However, a single clustering resolution may not yield groups of cells ...

📣🚨📣 NEW PAPER ALERT!! Did you ever struggle to differentiate very similar populations in #scRNA? Struggle no more with CANTAO! Really enjoyable collaboration between our lab and the Khiabanian lab @rutgerscancer.bsky.social!!

link.springer.com/article/10.1...

Weekly reads 10/11/25 Context is everything: from immune barriers to mechanistic and spatial AI models

Weekly reads 10/11/25
Context is everything: from immune barriers to mechanistic and spatial AI models

open.substack.com/pub/behindth...

#Cancer #SpatialOmics #SystemsBiology #scRNA #AI

Dr Wenting Liu from #Fudan Univ. Representing #Chinese #Society for #Immunology ( #CSI ) & #Tumor Immunology & #Biological #Therapy ( #TIBT ) talks on Tu-specific PMNs / #scRNA HLA-DR+IGF1R+ TAN promote tu suppression #WIC2025 #SITC2025

Discover how analysis of #scRNA-seq data supports AAV gene therapy research. You will learn how it helps with everything from identifying target cells to predicting treatment response and resistance!

www.fiosgenomics.com/advancing-aav-gene-thera...

#bioinformatics

A comprehensive benchmarking for spatially resolved transcriptomics clustering methods across variable technologies, organs, and replicates Spatial clustering is a critical step in spatially resolved transcriptomics. Here, we conducted a comprehensive benchmarking analysis of 14 spatial clustering methods using ~600 datasets, including b...

🧬 Benchmarking 14 spatial clustering methods across ~600 #SpatialTranscriptomics datasets
🧫 10 technologies, 8 organs — consistent insights
⚙️ Clear guidance for method choice & preprocessing
🔗 doi.org/10.1002/imt2...
#Bioinformatics #SpatialOmics #scRNA

#scRNA analysis of human adenoids from @michaelshiloh.bsky.social @samuelalvarez.bsky.social and colleagues identify molecular features of airway microfold cells; online now: www.mucosalimmunology.org/article/S193...

TBCancer: A database for exploring characteristics and functions of tissue‐biased genes in cancer This study defined 10,921 tissue-biased genes across 54 normal tissues and 41 cancer types. Tumor-associated tissue-biased genes exhibit downregulation, mutations, and epigenetic modifications, corre...

TBCancer: A #database for exploring characteristics and functions of tissue‐biased genes in #cancer #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#scRNA #TME #immun

Novel insights into immunopathogenesis and crucial biomarkers between primary open‐angle glaucoma and systemic lupus erythematosus This study revealed a novel correlation between systemic lupus erythematosus (SLE) and primary open-angle glaucoma (POAG) through comprehensive bioinformatics analysis and experimentation, identifyin...

Novel insights into #immunopathogenesis and crucial #biomarkers between primary open‐angle #glaucoma and systemic lupus erythematosus onlinelibrary.wiley.com/doi/10.1002/...
#scRNA #SLE #PPI #MachineLearning

scRiskCell: A single‐cell framework for quantifying islet risk cells and their adaptive dynamics in type 2 diabetes scRiskCell is an interpretable intelligent computational framework that leverages nearly 500,000 islet cell expression profiles from 106 donors across different continuous disease states. By calculat...

scRiskCell: A single‐cell framework for quantifying #islet risk cells and their adaptive dynamics in type 2 diabetes onlinelibrary.wiley.com/doi/10.1002/...
#scRNA #T2D #Bioinformatics

Single‐cell sequencing reveals the role of IL‐33+ endothelial subsets in promoting early gastric cancer progression A single-cell atlas was established to reveal the molecular characteristics of early gastric cancer (EGC). In combination with organoids, animal models, and clinical samples, it was found that subpop...

Single‐cell sequencing reveals the role of IL‐33+ endothelial subsets in promoting early gastric #cancer progression onlinelibrary.wiley.com/doi/10.1002/...
#angiogenesis #EGC #CancerResearch #scRNA

A multi‐centered prospective birth cohort study in Western China The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a regi...

A multi‐centered prospective #birth #cohort study in Western China onlinelibrary.wiley.com/doi/10.1002/... #MultiOmics #genome #metabolome #metagenome #scRNA

Single‐cell landscape revealed immune characteristics associated with disease phases in brucellosis patients Single-cell RNA sequencing of 290,369 cells from 29 brucellosis patients and 6 healthy donors reveals distinct immune profiles across acute, subacute, and chronic phases of the disease. Acute patient...

Single‐cell landscape revealed #immune characteristics associated with disease phases in #brucellosis patients onlinelibrary.wiley.com/doi/10.1002/...
#scRNA

Efficacy and biomarker analysis of neoadjuvant disitamab vedotin (RC48‐ADC) combined immunotherapy in patients with muscle‐invasive bladder cancer: A multi‐center real‐world study In this study, 102 cisplatin-ineligible patients with muscle-invasive bladder cancer (MIBC) who received neoadjuvant RC48-ADC combined with immunotherapy were included. We evaluated the pathological ...

Efficacy and biomarker analysis of neoadjuvant disitamab vedotin (RC48‐ADC) combined #immunotherapy in patients with muscle‐invasive bladder cancer: A multi‐center real‐world study onlinelibrary.wiley.com/doi/10.1002/...
#Cancer #CancerResearch #ICI #MIBC #Bladder #scRNA

Guiding clustering and annotation in single-cell RNA sequencing using the average overlap metric Defining cell types using unsupervised clustering algorithms based on transcriptional similarity is a powerful application of single-cell RNA sequencing. A single clustering resolution may not yield c...

Did you ever struggle to differentiate very similar populations in #scRNA? Struggle no more with average overlap! we can now fully differentiate double-negative thymocytes, a long-standing issue! Congrats to Chris Thai for an amazing job! @rutgerscancer.bsky.social

www.biorxiv.org/content/10.1...

Singe cell RNA sequencing data processing using cloud-based serverless computing Singe cell RNA sequencing (scRNA-seq) has become a routine method for measuring cell activities. Processing large scRNA-seq datasets requires high-performance computing resources. The emergence of cloud computing allows us to leverage its on-demand capabilities without major investment in infrastructure. Serverless computing provides cost efficiency by allowing users to pay only for actual resource usage, eliminating the necessity for pre-allocated server capacities. Additionally, there is no requirement to set up servers in advance. We present a novel and generalizable methodology using serverless cloud computing to accelerate computationally intensive workflows. We create an on-demand supercomputer using rapidly deployable cloud serverless functions as automatically provisioned computation units. We tested our methodology of optimizing a scRNA-seq workflow by leveraging serverless functions on the cloud using two publicly available peripheral blood mononuclear cell (PBMC) datasets. In addition, we demonstrate our approach using data generated by the NIH MorPhiC program, where we process a 450 GB human scRNA-seq dataset across 86 cell lines designed to study the temporal impact of perturbations on pancreatic differentiation. We compared the total execution time of the scRNA-seq serverless workflow with the traditional workflow without using serverless functions, and demonstrate major speedup for large scRNA-seq datasets. ### Competing Interest Statement L.H.H. and K.Y.Y. have equity interest in Biodepot LLC. The terms of this arrangement have been reviewed and approved by the University of Washington in accordance with its policies governing outside work and financial conflicts of interest in research. National Institutes of Health, https://ror.org/01cwqze88, U24HG012674, UM1HG012654 Virginia and Prentice Bloedel Endowment at University of Washington, ,

Ok, this is pretty slick! Serverless processing of single-cell RNA seq using piscem -> alevin-fry by taking advantage of splitting the data & the ability to merge independent RAD files upstream of alevin-fry! #scrna #rnaseq www.biorxiv.org/content/10.1...

Single‐microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Although our understanding of the species and functional composition of the human gut micro....

Single‐microbe #RNA #sequencing uncovers unexplored specialized metabolic functions of keystone species in the human #gut onlinelibrary.wiley.com/doi/full/10.... #microbiome #microbiota #scRNA

Peripheral blood immune landscape and NXPE3 as a novel biomarker for hypertensive intracerebral hemorrhage risk prediction and targeted therapy We employed bulk RNA-seq and scRNA-seq techniques to analyze the immune dysregulation in patients with intracerebral hemorrhage (ICH). The study revealed that excessive inflammatory responses, neutro...

Peripheral blood #immune landscape and NXPE3 as a novel #biomarker for hypertensive intracerebral hemorrhage risk prediction and targeted therapy onlinelibrary.wiley.com/doi/full/10.... #hypertension #Bioinformatics #scRNA

scAtlasVAE: a deep learning framework for generating a human CD8+ T cell atlas - Nature Reviews Cancer In this Tools of the Trade article, Ziwei Xue describes the development and use of scAtlasVAE, a deep learning framework that integrates single-cell RNA-sequencing data from CD8+ T cells across studies.

#Tools of the Trade 🚨
Ziwei Xue describes the development and use of #scAtlasVAE, a deep learning framework integrating #scRNA-sequencing data from CD8+ T cells across studies.
📖 ⬇️

DYK we have a series of #BitesizeBioinformatics videos on our YouTube channel?
Today's webinar on #Rpackage #AnchorView is available now
youtu.be/cqpuJ8lFOjk
#Bioinformatics #NGS #scRNA #BigData #ComputationalBiology #ECRchat #PhDchat

In defense of their patents, 10x Genomics presented a series of meritless arguments, which included disputing the publication date of a peer reviewed article. The Patent Trial and Appeal Board (PTAB) of the United States Patent and Trademark Office (USPTO) stated Parse’s evidence provided “the figurative nail in the coffin” to reject 10x Genomics’ arguments. The Final Written Decisions further noted that the patent specifications were not even focused on single cell analysis, but rather described an unrelated method.

For those who are interested in how 10x Genomics uses "meritless" lawsuits to try to suppress competition in single cell sequencing #scRNA, Parse Biosciences has now successfully invalidated all the relevant patent claims in the ongoing litigation.
www.parsebiosciences.com/news/parse-b...

BUND 023 2-COURSE BUNDLE - Foundations for Practical Single Cell RNA-seq Analyses and Advanced Topics in Single Cell Analyses

I'm teaching single-cell data analysis in #Rstats this Spring 2025
@FAESatNIH_EDU
! 📊

Two-course series:
Updated Seurat v5 tutorials
+ multi-modal analysis
+ spatial transcriptomics content
Real datasets & self-directed projects

Register @ tinyurl.com/FAESscBioS2025
#bioinformatics #scRNA

Remember to register and get special give away kits and gifts tomorrow at Cure -flatrion district! #singlecell #spatial #spatialtranscriptomics #multiomics #scRNA #microenvironment #RNA #transcriptomics #10xGenomics

Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference GRNPT is a powerful tool for reconstructing gene regulatory networks (GRNs) from single-cell data. By combining gene embeddings from large language models with temporal information, GRNPT accurately ...

Combining an LLM trained on prior knowledge and a TCN module enables accurate GRN inference using a fraction of the data and generalizable across cells/TFs!

Great work by Guangzheng from the Won lab! Glad to have been part of the effort!
#scRNA #LLM

onlinelibrary.wiley.com/doi/10.1002/...

10x Genomics

Discover how @10xgenomics.bsky.social keeps innovating single cell analysis with GEM-X Flex and On Chip Multiplexing. 🧬 These new technologies offer you unparalleled flexibility and efficiency.

Join our webinar to learn more!

#10XGenomics #scRNA #Chromium

pages.10xgenomics.com/wbr-2024-10-...

Could this be a Rorschach test or is this possibly a sneak preview to our next preprint…? As a #biologist I love these although in the #scRNA field #UMAP plots are controversial. Any opinions?