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View article: Single-cell spatial transcriptomics unravels the cellular landscape of abdominal aortic aneurysm
Single-cell spatial transcriptomics unravels the cellular landscape of abdominal aortic aneurysm Open
Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease with no effective pharmacological interventions. While single-cell transcriptomics has advanced our understanding of AAA, it lacks spatial context. Here, we employed Se…
View article: Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution
Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution Open
Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200–300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), …
View article: Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics
Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics Open
Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints fa…
View article: High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation
High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation Open
Skeletal muscle is essential for both movement and metabolic processes, characterized by a complex and ordered structure. Despite its importance, a detailed spatial map of gene expression within muscle tissue has been challenging to achiev…
View article: Germline CpG methylation signatures in the human population inferred from genetic polymorphism
Germline CpG methylation signatures in the human population inferred from genetic polymorphism Open
This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism".
View article: Germline CpG methylation signatures in the human population inferred from genetic polymorphism
Germline CpG methylation signatures in the human population inferred from genetic polymorphism Open
This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism".
View article: <i>FICTURE:</i>Scalable segmentation-free analysis of submicron resolution spatial transcriptomics
<i>FICTURE:</i>Scalable segmentation-free analysis of submicron resolution spatial transcriptomics Open
Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide gene expression analysis at submicron resolution over large areas. Analysis of high-resolution ST data relies heavily on image-based cell segmentation or …
View article: Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response
Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response Open
Multiplexed single-cell sequencing (mux-seq) using single-nucleotide polymorphisms (SNPs) has emerged as an efficient approach to perform expression quantitative trait loci (eQTL) studies that map interactions between genetic variants and …
View article: Inferring CpG methylation signatures accumulated along human history from genetic variation catalogs
Inferring CpG methylation signatures accumulated along human history from genetic variation catalogs Open
Understanding the DNA methylation patterns in the human genome is a key step to decipher gene regulatory mechanisms and model mutation rate heterogeneity in the human genome. While methylation rates can be measured e.g. with bisulfite sequ…
View article: Statistical Models for Large Scale Genomic Data
Statistical Models for Large Scale Genomic Data Open
Sequencing technologies transformed how scientists examine biological systems at both macroscopic and microscopic level. For example, population-scale genome sequencing has cataloged millions of common and rare genetic variants in humans a…
View article: Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19 Open
Type I interferon autoantibodies in patients with COVID-19 are associated with poor interferon responses and increased LAIR1 abundance in leukocytes.
View article: Seq-Scope protocol in MiSeq system for profiling hepatic and colonic spatial transcriptome.
Seq-Scope protocol in MiSeq system for profiling hepatic and colonic spatial transcriptome. Open
http://deepblue.lib.umich.edu/bitstream/2027.42/168395/5/Seq-Scope Protocol M1.0.0 version.pdf
View article: Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19 Open
Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocyt…
View article: Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms Open
Genotype imputation is an indispensable step in human genetic studies. Large reference panels with deeply sequenced genomes now allow interrogating variants with minor allele frequency < 1% without sequencing. Although it is critical to…
View article: Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms Open
Genotype imputation is an indispensable step in human genetic studies. Large reference panels with deeply sequenced genomes now allow interrogating variants with minor allele frequency < 1% without sequencing. While it is critical to consi…