Computational Methods Archives

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

Zhu et al.,
bioRxiv,
2024

Congenital T cell activation impairs transitional to follicular B cell maturation in humans

Allard-Chamard et al.,
bioRxiv,
2024

Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis

Corleis et al.,
Science Translational Medicine,
2023

CD8+ lymphocytes are critical for early control of tuberculosis in macaques

Winchell et al.,
Journal of Experimental Medicine,
2023

Comparative analysis of cell–cell communication at single-cell resolution

Wilk et al.,
Nature Biotechnology,
2023

Compressed phenotypic screens for complex multicellular models and high-content assays

Mead et al.,
bioRxiv,
2023

NIAID Workshop on T Cell Technologies

Gondré-Lewis et al.,
Nature Immunology,
2023

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

Jaiswal et al.,
BMC Genomics,
2023

Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform

Gerdemann et al.,
Frontiers in Immunology,
2023

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Mead et al.,
Nature Biomedical Engineering,
2022

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Raghavan et al.,
Cell,
2021

Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity

Genshaft et al.,
bioRxiv,
2021

A Treatment-Naive Cellular Atlas of Pediatric Crohn's Disease Predicts Disease Severity and Therapeutic Response

Zheng et al.,
bioRxiv,
2021

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

Ziegler et al.,
Cell,
2021

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Delorey et al.,
Nature,
2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Muus et al.,
Nature Medicine,
2021

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Delorey et al.,
bioRxiv,
2021

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Berger et al.,
Nature Communications,
2020

The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer

Raghavan et al.,
bioRxiv,
2020

A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood

Sangesland et al.,
Cell Reports,
2020

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

Bassler et al.,
bioRxiv,
2020

Computational Methods for Single-Cell RNA Sequencing

Hie et al.,
Annual Reviews,
2020

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Muus et al.,
bioRxiv,
2020

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Rozenblatt-Rosen et al.,
Cell,
2020

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding et al.,
Nature Biotechnology,
2020

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

Kazer et al.,
Nature Medicine,
2020

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues

Ziegler et al.,
SSRN,
2020

Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes

Huang et al.,
bioRxiv,
2019

Voices in methods development

Anikeeva et al.,
Nature Methods,
2019

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Martin-Gayo et al.,
Genome Biology,
2018

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Finak et al.,
Genome Biology,
2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Macosko et al.,
Cell,
2015

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

Congenital T cell activation impairs transitional to follicular B cell maturation in humans

Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis

CD8+ lymphocytes are critical for early control of tuberculosis in macaques

Comparative analysis of cell–cell communication at single-cell resolution

Compressed phenotypic screens for complex multicellular models and high-content assays

NIAID Workshop on T Cell Technologies

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity

A Treatment-Naive Cellular Atlas of Pediatric Crohn's Disease Predicts Disease Severity and Therapeutic Response

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer

A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

Computational Methods for Single-Cell RNA Sequencing

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues

Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes

Voices in methods development

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

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