# terms

term_key: term:55ff67026d9bc294dbb55270
claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:48c9e04c1cce8e98a5fd
term_type: celltype
sub_span: lower quality CECs entering senescence and EMT
provenance: explicit
ontology_term: CL:0000132
normalized_label:
lower quality corneal endothelial cell entering senescence and endothelial-to-mesenchymal transition


# paper_metadata

paper_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad
manuscript_path: data/biorxiv/meca/001efeeb-7491-1014-a82f-ef19de5990ad/manuscript.md
metadata_source: corpus-paper-index
title:
Integrative Multi-Omic Profiling of the Human Phosphatome Identifies DUSP15 as a Tumour-Selective Regulator of Immune-Metabolic Reprogramming in Chromophobe Renal Cell Carcinoma

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/001efeeb-7491-1014-a82f-ef19de5990ad/manuscript.md


paper_key: biorxiv:00f35402-6c29-1014-b443-c03ca585b6ab
title: Label-free imaging flow cytometry: analysis and sorting of enzymatically dissociated tissues
manuscript_path: data/biorxiv/meca/00f35402-6c29-1014-b443-c03ca585b6ab/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/00f35402-6c29-1014-b443-c03ca585b6ab/manuscript.md


paper_key: biorxiv:0136dd0f-6c39-1014-a9ca-cd3ee66443fe
manuscript_path: data/biorxiv/meca/0136dd0f-6c39-1014-a9ca-cd3ee66443fe/manuscript.md
metadata_source: corpus-paper-index
title:
CRISPR/Cas-9 mediated knock-in by homology dependent repair in the West Nile Virus vector Culex quinquefasciatus Say

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0136dd0f-6c39-1014-a9ca-cd3ee66443fe/manuscript.md


paper_key: biorxiv:013a7c23-7117-1014-9b42-823175dea768
manuscript_path: data/biorxiv/meca/013a7c23-7117-1014-9b42-823175dea768/manuscript.md
metadata_source: corpus-paper-index
title:
A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/013a7c23-7117-1014-9b42-823175dea768/manuscript.md


paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
manuscript_path: data/biorxiv/meca/01e5e65d-751c-1014-a8e3-b5f1d7a951ab/manuscript.md
metadata_source: corpus-paper-index
title:
singIST: an integrative method for comparative single-cell transcriptomics between disease models and humans

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/01e5e65d-751c-1014-a8e3-b5f1d7a951ab/manuscript.md


paper_key: biorxiv:02107348-6c12-1014-a284-d4a1f7037327
manuscript_path: data/biorxiv/meca/02107348-6c12-1014-a284-d4a1f7037327/manuscript.md
metadata_source: corpus-paper-index
title:
Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/02107348-6c12-1014-a284-d4a1f7037327/manuscript.md


paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
manuscript_path: data/biorxiv/meca/03092aac-75a4-1014-b9cc-d44d468fbd97/manuscript.md
metadata_source: corpus-paper-index
title:
Deciphering Tumor Microenvironment Dynamics in Tumorigenesis and Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma using Single-cell RNA Sequencing

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/03092aac-75a4-1014-b9cc-d44d468fbd97/manuscript.md


paper_key: biorxiv:03a1691c-70ce-1014-bf1a-b6bd63c41968
title: A single-cell immune atlas of primary and secondary lymphoid organs in pigs
manuscript_path: data/biorxiv/meca/03a1691c-70ce-1014-bf1a-b6bd63c41968/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/03a1691c-70ce-1014-bf1a-b6bd63c41968/manuscript.md


paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
manuscript_path: data/biorxiv/meca/03bcb34d-755c-1014-ade5-9b7bdb3d9312/manuscript.md
metadata_source: corpus-paper-index
title:
Optical tissue clearing and 3D imaging of intact primate testicular tissue: a novel technology development

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/03bcb34d-755c-1014-ade5-9b7bdb3d9312/manuscript.md


paper_key: biorxiv:0517eca3-71a7-1014-8287-ebb9aa6433a6
manuscript_path: data/biorxiv/meca/0517eca3-71a7-1014-8287-ebb9aa6433a6/manuscript.md
metadata_source: corpus-paper-index
title:
Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0517eca3-71a7-1014-8287-ebb9aa6433a6/manuscript.md


paper_key: biorxiv:06056998-6fcf-1014-a978-d2cf5726c0ad
manuscript_path: data/biorxiv/meca/06056998-6fcf-1014-a978-d2cf5726c0ad/manuscript.md
metadata_source: corpus-paper-index
title:
Molecular Mechanisms of Chinese Medicine in Regulating Colorectal Cancer Immune Microenvironment: Insights from Single-Cell Transcriptomics and Network Pharmacology

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/06056998-6fcf-1014-a978-d2cf5726c0ad/manuscript.md


paper_key: biorxiv:066e7933-6c23-1014-9764-c2e8306362fb
title: Evaluating Cell Identity from Transcription Profiles
manuscript_path: data/biorxiv/meca/066e7933-6c23-1014-9764-c2e8306362fb/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/066e7933-6c23-1014-9764-c2e8306362fb/manuscript.md


paper_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92
title: Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties
manuscript_path: data/biorxiv/meca/0900c414-6db3-1014-86e7-ea4583587c92/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0900c414-6db3-1014-86e7-ea4583587c92/manuscript.md


paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
manuscript_path: data/biorxiv/meca/09d40fbc-6c3d-1014-b39f-eee50a07ad3b/manuscript.md
metadata_source: corpus-paper-index
title:
Integrative omics analysis reveals gene regulatory mechanisms distinguishing organoid-derived hepatocytes from primary human hepatocytes

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/09d40fbc-6c3d-1014-b39f-eee50a07ad3b/manuscript.md


paper_key: biorxiv:0a537c3c-6dba-1014-a3da-a09fc644eb0b
title: Time-resolved immune dynamics in rheumatoid arthritis under methotrexate therapy
manuscript_path: data/biorxiv/meca/0a537c3c-6dba-1014-a3da-a09fc644eb0b/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0a537c3c-6dba-1014-a3da-a09fc644eb0b/manuscript.md


paper_key: biorxiv:0a6d6372-6dad-1014-aa2c-84eb1d405c37
manuscript_path: data/biorxiv/meca/0a6d6372-6dad-1014-aa2c-84eb1d405c37/manuscript.md
metadata_source: corpus-paper-index
title:
Uncovering strain- and age-dependent differences in innate immune response to SARS-CoV-2 infection in nasal epithelia using 10X single-cell sequencing

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0a6d6372-6dad-1014-aa2c-84eb1d405c37/manuscript.md


paper_key: biorxiv:0b080d95-70b5-1014-9f85-f75794076023
manuscript_path: data/biorxiv/meca/0b080d95-70b5-1014-9f85-f75794076023/manuscript.md
metadata_source: corpus-paper-index
title:
Identification of critical cell-types using genetic modules: A case study of neurodevelopmental disorders

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0b080d95-70b5-1014-9f85-f75794076023/manuscript.md


paper_key: biorxiv:0b572d92-6c10-1014-9fee-b7ba4db4740b
title: On the prediction of protein abundance from RNA
manuscript_path: data/biorxiv/meca/0b572d92-6c10-1014-9fee-b7ba4db4740b/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0b572d92-6c10-1014-9fee-b7ba4db4740b/manuscript.md


paper_key: biorxiv:0bcdadb5-70f3-1014-974d-abbf00aa9865
manuscript_path: data/biorxiv/meca/0bcdadb5-70f3-1014-974d-abbf00aa9865/manuscript.md
metadata_source: corpus-paper-index
title:
Mouse-Geneformer: A Deep Learning Model for Mouse Single-Cell Transcriptome and Its Cross-Species Utility

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0bcdadb5-70f3-1014-974d-abbf00aa9865/manuscript.md


paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
manuscript_path: data/biorxiv/meca/0bd28b37-6e2e-1014-871e-a496f0a6bacd/manuscript.md
metadata_source: corpus-paper-index
title:
Mesenchymal-epithelial transition in lymph node metastases of oral squamous cell carcinoma is accompanied by ZEB1 expression

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0bd28b37-6e2e-1014-871e-a496f0a6bacd/manuscript.md


paper_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954
manuscript_path: data/biorxiv/meca/0c36d8d8-6cad-1014-ad28-fa021d92b954/manuscript.md
metadata_source: corpus-paper-index
title:
Transcriptomic Hallmarks of Mortality Reveal Universal and Specific Mechanisms of Aging, Chronic Disease, and Rejuvenation

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0c36d8d8-6cad-1014-ad28-fa021d92b954/manuscript.md


paper_key: biorxiv:0c424138-6e62-1014-af20-f8123674b4d1
title: A dataset of differentiable biologically-derived single neuron models
manuscript_path: data/biorxiv/meca/0c424138-6e62-1014-af20-f8123674b4d1/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0c424138-6e62-1014-af20-f8123674b4d1/manuscript.md


paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
title: Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma
manuscript_path: data/biorxiv/meca/0c5b4463-70b4-1014-b7ae-f953f2710002/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0c5b4463-70b4-1014-b7ae-f953f2710002/manuscript.md


paper_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44
manuscript_path: data/biorxiv/meca/0c7fdd53-755f-1014-abd5-c154158d9e44/manuscript.md
metadata_source: corpus-paper-index
title:
Engineering fluorescent reporters in human pluripotent cells and strategies for live imaging human neurogenesis

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0c7fdd53-755f-1014-abd5-c154158d9e44/manuscript.md


paper_key: biorxiv:0d005ebb-6c05-1014-a888-cf4cdb861f63
manuscript_path: data/biorxiv/meca/0d005ebb-6c05-1014-a888-cf4cdb861f63/manuscript.md
metadata_source: corpus-paper-index
title:
In situ single-cell analysis of canonical breast cancer biomarkers: phenotypic heterogeneity and implications on response to HER2 targeting agents

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0d005ebb-6c05-1014-a888-cf4cdb861f63/manuscript.md


paper_key: biorxiv:0d0fe934-6c52-1014-9f5d-fbe8eb84282e
manuscript_path: data/biorxiv/meca/0d0fe934-6c52-1014-9f5d-fbe8eb84282e/manuscript.md
metadata_source: corpus-paper-index
title:
Publication, Funding, and Experimental Data in Support of Human Reference Atlas Construction and Usage

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0d0fe934-6c52-1014-9f5d-fbe8eb84282e/manuscript.md


paper_key: biorxiv:0e0023bc-6fb8-1014-8fdc-a5e7354ecc53
manuscript_path: data/biorxiv/meca/0e0023bc-6fb8-1014-8fdc-a5e7354ecc53/manuscript.md
metadata_source: corpus-paper-index
title:
Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0e0023bc-6fb8-1014-8fdc-a5e7354ecc53/manuscript.md


paper_key: biorxiv:0e1885b4-6c0f-1014-862f-a7f02207dcc6
title: A convex optimization approach for identification of human tissue-specific interactomes
manuscript_path: data/biorxiv/meca/0e1885b4-6c0f-1014-862f-a7f02207dcc6/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0e1885b4-6c0f-1014-862f-a7f02207dcc6/manuscript.md


paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
title: Detailed Survey of an in-vitro Intestinal Epithelium Model by Single-Cell Transcriptomics
manuscript_path: data/biorxiv/meca/0e94bf21-6c7c-1014-b6a7-bcc9b09c8181/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0e94bf21-6c7c-1014-b6a7-bcc9b09c8181/manuscript.md


paper_key: biorxiv:0ea346cb-7048-1014-a5d3-d23c8828e500
title: Continuous DNA Methylation Deconvolution-Based Surrogate for B-Cell Differentiation State in CLL
manuscript_path: data/biorxiv/meca/0ea346cb-7048-1014-a5d3-d23c8828e500/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/0ea346cb-7048-1014-a5d3-d23c8828e500/manuscript.md


paper_key: biorxiv:10734c8a-6c0a-1014-92cc-d1ee9ab862fc
manuscript_path: data/biorxiv/meca/10734c8a-6c0a-1014-92cc-d1ee9ab862fc/manuscript.md
metadata_source: corpus-paper-index
title:
Longitudinal differential abundance analysis of microbial marker-gene surveys using smoothing splines

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/10734c8a-6c0a-1014-92cc-d1ee9ab862fc/manuscript.md


paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
manuscript_path: data/biorxiv/meca/10f6f17d-749e-1014-bdcf-fe1d1407f022/manuscript.md
metadata_source: corpus-paper-index
title:
Single-cell proteomics of pancreatic islet cells reveals type 1 diabetes and donor-specific features

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/10f6f17d-749e-1014-bdcf-fe1d1407f022/manuscript.md


paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
title: Donor monocyte-derived macrophages promote human acute graft versus host disease
manuscript_path: data/biorxiv/meca/11b72b7e-6c1b-1014-84e4-aaf6df161d14/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/11b72b7e-6c1b-1014-84e4-aaf6df161d14/manuscript.md


paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
title: Multiscale networks in multiple sclerosis
manuscript_path: data/biorxiv/meca/1219c420-6c6a-1014-afb9-e13c88e111ed/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/1219c420-6c6a-1014-afb9-e13c88e111ed/manuscript.md


paper_key: biorxiv:13c39b66-72f2-1014-9c8c-e313c291b504
manuscript_path: data/biorxiv/meca/13c39b66-72f2-1014-9c8c-e313c291b504/manuscript.md
metadata_source: corpus-paper-index
title:
Development of immortalized Callithrix jacchus kidney cell lines supporting infection with a panel of viruses

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/13c39b66-72f2-1014-9c8c-e313c291b504/manuscript.md


paper_key: biorxiv:15193886-7949-1014-85b7-a7b77d3859e6
manuscript_path: data/biorxiv/meca/15193886-7949-1014-85b7-a7b77d3859e6/manuscript.md
metadata_source: corpus-paper-index
title:
The Dual Molecular Identity of Vestibular Kinocilia: Bridging Structural and Functional Traits of Primary and Motile Cilia

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/15193886-7949-1014-85b7-a7b77d3859e6/manuscript.md


paper_key: biorxiv:15360e56-7361-1014-9683-c96cb33ab32f
title: M. tuberculosis invades and disrupts the blood brain barrier directly to initiate meningitis
manuscript_path: data/biorxiv/meca/15360e56-7361-1014-9683-c96cb33ab32f/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/15360e56-7361-1014-9683-c96cb33ab32f/manuscript.md


paper_key: biorxiv:15502cad-6fa3-1014-af49-efb26407f09f
manuscript_path: data/biorxiv/meca/15502cad-6fa3-1014-af49-efb26407f09f/manuscript.md
metadata_source: corpus-paper-index
title:
ImmCellTyper: an integrated computational pipeline for systematic mining of Mass Cytometry data to assist deep immune profiling

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/15502cad-6fa3-1014-af49-efb26407f09f/manuscript.md


paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
manuscript_path: data/biorxiv/meca/166eb232-7528-1014-af8e-ff8db1c08d2e/manuscript.md
metadata_source: corpus-paper-index
title:
An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/166eb232-7528-1014-af8e-ff8db1c08d2e/manuscript.md


paper_key: biorxiv:1733c102-6e42-1014-9550-8e3adf788fb0
title: Cell Type-Agnostic Transcriptomic Signatures Enable Uniform Comparisons of Neurodevelopment
manuscript_path: data/biorxiv/meca/1733c102-6e42-1014-9550-8e3adf788fb0/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/1733c102-6e42-1014-9550-8e3adf788fb0/manuscript.md


paper_key: biorxiv:17b22fef-6c42-1014-9172-81e1e1e715e2
manuscript_path: data/biorxiv/meca/17b22fef-6c42-1014-9172-81e1e1e715e2/manuscript.md
metadata_source: corpus-paper-index
title:
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/17b22fef-6c42-1014-9172-81e1e1e715e2/manuscript.md


paper_key: biorxiv:17b98f90-75a4-1014-8c7c-92eb33e9a97c
title: Sample-level modeling of single-cell data at scale with tinydenseR
manuscript_path: data/biorxiv/meca/17b98f90-75a4-1014-8c7c-92eb33e9a97c/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/17b98f90-75a4-1014-8c7c-92eb33e9a97c/manuscript.md


paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
title: Cross-species consensus atlas of the primate basal ganglia
manuscript_path: data/biorxiv/meca/1819420a-7028-1014-9d82-b8532c727b67/manuscript.md
metadata_source: corpus-paper-index
source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/1819420a-7028-1014-9d82-b8532c727b67/manuscript.md


paper_key: biorxiv:18602a3d-6dc0-1014-810c-a2e4e5ffbc67
title: Nucleoredoxin regulates WNT signaling during pituitary stem cell differentiation
manuscript_path: data/biorxiv/meca/18602a3d-6dc0-1014-810c-a2e4e5ffbc67/manuscript.md
metadata_source: corpus-paper-index
source_url:
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paper_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496
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Single cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

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Microbial Similarity Between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures

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title:
Single-cell RNA sequencing of peripheral blood defines two immunological subtypes of Sjögren’s disease

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Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

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An ultrasound-guided biopsy technique for obtaining supraclavicular brown fat biopsies and preadipocytes

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Population-scale sequencing resolves correlates and determinants of latent Epstein-Barr Virus infection

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Crowdsourcing Temporal Transcriptomic Coronavirus Host Infection Data: resources, guide, and novel insights

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Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease

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Toward a privacy-preserving predictive foundation model of single-cell transcriptomics with federated learning and tabular modeling

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Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding

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A rule-based multiscale model of hepatic stellate cell plasticity: critical role of the inactivation loop in fibrosis progression

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Tissue-specific immune transcriptional signatures in the bordering tissues of the mouse brain and retina

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Ly6Chi monocytes are metabolically reprogrammed in the blood during inflammatory stimulation allowing for macrophage lineage commitment

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Aquaporins enriched in endothelial vacuole membrane regulate the diameters of microvasculature in hyperglycemia

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cytoGPNet: Enhancing Clinical Outcome Prediction Accuracy Using Longitudinal Cytometry Data in Small Cohort Studies

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Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes

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Loss of mutually protective effects between osteoclasts and chondrocytes in damaged joints drives osteoclast-mediated cartilage degradation via matrix metalloproteinases

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Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells

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OPTIMAL: An OPTimised Imaging Mass cytometry AnaLysis framework for Segmentation and Data Exploration

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ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia

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Celda: A Bayesian model to perform bi-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data

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Critical role for the TGF-β1/mTORC1 signalling axis in defining the transcriptional identity of CTHRC1+ pathologic fibroblasts

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NKG7 is a stable marker of cytotoxicity across immune contexts and within the tumor microenvironment

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On the discovery of subpopulation-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data

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title:
In vivo single-cell high-dimensional mass cytometry analysis to track the interaction between Klebsiella pneumoniae and myeloid cells

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Feature extraction approach in single-cell gene expression profiling for cell-type marker identification

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title: Microglial Heterogeneity in a Mouse Model of Alzheimer’s Disease: A Mass Cytometry Analysis
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Trimodal Single-Cell Gene Regulatory Networks Reveal Principles of Stemness Loss and Cell Fate Acquisition in Human Hematopoiesis

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Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunisation in the pig lung

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spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization

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signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data

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Fluorochrome-dependent specific changes in spectral profiles using different compensation beads or human cells in full spectrum cytometry

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Progressive change in expression of killer-like receptorsr and GPR56 expression defines the cytokine production potential of human CD4+ T memory cells

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Exploring the interaction between immune cells in the testicular microenvironment of azoospermia combining RNA-seq and scRNA-seq

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Direct imaging of anthrax intoxication in animals reveals shared and individual functions of CMG-2 and TEM-8 in cellular toxin entry

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Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as the primary mechanism of vaccine-induced protection against HIV-1

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Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of metformin treatment type 2 diabetes mellitus

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Cell-type specific open chromatin profiling in human postmortem brain infers functional roles for non-coding schizophrenia loci

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SenePy: Unveiling the Cell-Type Specific Landscape of Cellular Senescence through Single-Cell Analysis in Living Organisms

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Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

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Single cell kinetic modeling of redox-based drug metabolism in head and neck squamous cell carcinoma

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Hippocampal single-cell RNA Atlas of chronic methamphetamine abuse-induced cognitive decline in mice

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scCaT: an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing

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Data-driven Identification of Total RNA Expression Genes (TREGs) for Estimation of RNA Abundance in Heterogeneous Cell Types

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Machine learning based classification of cells into chronological stages using single-cell transcriptomics

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title: Clinical Phenotype Prediction From Single-cell RNA-seq Data using Attention-Based Neural Networks
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Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing

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Stabilized marker gene identification and functional annotation from single-cell transcriptomic data

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Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells

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title: Interleukin Enhancer Binding Factor 2 (Ilf2) and Kidney Epithelial Stress Resilience
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title: Exploring the Role of PEDOT Electrodes in Electrostimulation of Vascular Endothelial Cells
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paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
title: A Tonic Signaling Code Predicts CAR-T Cell Efficacy in Diffuse Midline Glioma
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paper_key: biorxiv:42949288-7420-1014-8a1b-88a214a26e1c
title: Cell Type Differentiation Using Network Clustering Algorithms
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paper_key: biorxiv:42e08e95-6e50-1014-bd52-d41de57c8c2e
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title:
Dual inhibition of the nonsense mediated mRNA decay enhances tumour immunogenicity, drives immunoediting, and potentiates checkpoint blockade

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paper_key: biorxiv:43f76ba1-77d9-1014-bca2-dc4d32e94b3c
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title:
Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

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paper_key: biorxiv:445fc79c-6e85-1014-986a-a54df23fa10e
title: EVA: a Foundation Model Advancing Translational Drug Development in Immuno-Inflammation
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paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
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title:
Single-Cell Transcriptome Analyses Reveal the Cell Diversity and Developmental Features of Human Gastric and Metaplastic Mucosa

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paper_key: biorxiv:452092ed-6c90-1014-931b-aac044d9bc27
title: DenVar: Density-based Variation analysis of multiplex imaging data
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paper_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072
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title:
Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities

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paper_key: biorxiv:4655c4fb-747d-1014-95d4-eaa8a37d0e20
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title:
Study on Liver Sinusoidal Endothelial Cell Fenestrations Based on Cellular Omics-Structure Integration Technology and Its Application in Metabolic Diseases

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paper_key: biorxiv:466eace1-7692-1014-9cbc-8d16e477b905
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title:
Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures

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paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
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title:
Direct pathway bias and altered striatal neurogenesis in human iPSC models of 16p11.2 CNVs: Evidence from single-cell and functional analyses

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paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
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title:
Human pluripotent stem cell model of multiple epiphyseal dysplasia with MATN3 mutation identifies altered Matrix organisation and upregulation of the cholesterol biosynthesis pathway

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paper_key: biorxiv:482887d4-6ccc-1014-a120-c4ead15165f2
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title:
MicroGenomer: A Foundation Model for Transferable Microbial Genome Representations Enabling Multi-scale Genomic Understanding and Ecophysiological Trait Prediction

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paper_key: biorxiv:4880cd32-73be-1014-b2dd-99af72fbcbb2
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title:
Discovery and performance of DNA methylation panels for cancer detection and classification in blood

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paper_key: biorxiv:4a32479b-73fb-1014-85c7-f90d12f74d62
title: Evaluating genetic-ancestry inference from single-cell transcriptomic datasets
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paper_key: biorxiv:4aeb17c2-7217-1014-8df0-d02b097fce2e
title: easybio: an R Package for Single-Cell Annotation with CellMarker2.0
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paper_key: biorxiv:4b0647b9-6cd3-1014-b6d7-d846ab9fdea8
title: Integrated spatiotemporal transcriptomic resolution of embryonic palate osteogenesis
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paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
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title:
CyTOF-Lec: Single-cell Glycomics Analysis Reveals Glycan Features Defining Cells Differentially Susceptible to HIV

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paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
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title:
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

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paper_key: biorxiv:4c82a0b3-6cf7-1014-ac6a-f32ea14bb405
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title:
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

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paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
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title:
Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression

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paper_key: biorxiv:4d82e271-6c19-1014-9dbc-85c7d06c8caf
title: The Landscape of Receptor-Mediated Precision Cancer Combination Therapy: A Single-Cell Perspective
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paper_key: biorxiv:4e41d3ce-6c81-1014-ba6e-96a60e199c7c
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title:
An end-to-end framework for Cell DIVE multiplexed imaging and spatial immune microenvironment analysis

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paper_key: biorxiv:4e78a243-6e42-1014-b592-f5f048c69237
title: Analysis of cell-associated DENV RNA by oligo(dT) primed 5’ capture scRNAseq
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paper_key: biorxiv:4ee4af78-6da4-1014-bf4b-c4cc5adf9713
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title:
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

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paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
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title:
CoPhaser: generic modeling of biological cycles in scRNA-seq with context-dependent periodic manifolds

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paper_key: biorxiv:50c888ca-6c09-1014-89ca-dc13eaf87e62
title: Tumor cell phenotype and heterogeneity differences in IDH1 mutant vs wild-type gliomas
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paper_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7
title: Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types
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paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
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title:
A Variational Inference Approach to Single-Cell Gene Regulatory Network Inference using Probabilistic Matrix Factorization

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paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
title: Placental immune factors change during the first half of healthy pregnancy
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paper_key: biorxiv:5279fb06-6d7b-1014-b9ec-f76e38a7b616
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title:
scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons of Pirt-EGFPf mice in neuropathic pain condition

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paper_key: biorxiv:527d19aa-6dc2-1014-be48-c462f9c5cf67
title: A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma
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paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
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title:
Boolean Implication Analysis Improves Prediction Accuracy of In Silico Gene Reporting of Retinal Cell Types

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Spatial Transcriptomics Expression Prediction from Histopathology Based on Cross-Modal Mask Reconstruction and Contrastive Learning

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paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
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title:
High-resolution integrative analysis allows characterization and spatial annotation of normal and cancer-associated colon fibroblasts

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paper_key: biorxiv:541f1ba5-6d24-1014-bb2d-873ea98e8a4c
title: Ariadne: Barcoded Linked-Read Deconvolution Using de Bruijn Graphs
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paper_key: biorxiv:5490dcbd-7693-1014-852a-a6c3ae543801
title: Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage
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paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
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Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma

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paper_key: biorxiv:5535de0f-73de-1014-aebb-d96e791a8ccc
title: Domain shifts in infant brain diffusion MRI: Quantification and mitigation for fODF estimation
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paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
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Macrophage-like vascular smooth muscle cells dominate early atherosclerosis and are inhibited by targeting iron regulation

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paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
title: Single-cell analysis of signalling and transcriptional responses to type I interferons
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paper_key: biorxiv:56fbd5bc-6ca3-1014-8aad-94dc9b3d5255
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FlashDeconv enables atlas-scale, multi-resolution spatial deconvolution via structure-preserving sketching

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paper_key: biorxiv:57950bf0-6d23-1014-84a0-cf7390c18414
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title:
Single Nucleus Multiome Analysis Reveals Early Inflammatory Response to High-Fat Diet in Mouse Pancreatic Islets

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paper_key: biorxiv:57ac822b-6c7d-1014-a047-d6c2f45edeb7
title: CAPTAIN: A multimodal foundation model pretrained on co-assayed single-cell RNA and protein
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Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture

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High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

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Phenotypic dissection of epithelial lineages and therapeutic manipulation of differentiation programs in human Adenoid Cystic Carcinomas (ACCs)

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Differential correlation across subpopulations of single cells in subtypes of acute myeloid leukemia

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Single cell transcriptome of CD8+ T cells in multiple cancers reveals comprehensive exhaustion associated mechanisms

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Single-cell transcriptome analysis of CD34+ stem cell-derived myeloid cells identifies a CFU-GEMM-like population permissive to human cytomegalovirus infection

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Cell-Projection Pumping of Fibroblast Contents into Osteosarcoma SAOS-2 Cells Correlates with Increased SAOS-2 Proliferation and Migration, and also with Altered Morphology

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Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex

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High-throughput RNA and Single-cell RNA Sequencing to Identify Sepsis associated Molecular Mechanisms and the Blood Immune Cell Landscape

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From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

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Decoding the porcine developing spatial processing system and production of human entorhinal stellate cell-like cells by a direct programming approach

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A neural network-based framework to understand the Type 2 Diabetes (T2D)-related alteration of the human gut microbiome

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A comprehensive atlas of testicular interstitium reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitors

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Estimation of genomic prediction accuracy from reference populations with varying degrees of relationship

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SEC-seq: Association of molecular signatures with antibody secretion in thousands of single human plasma cells

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High-dimensional mass cytometry reveals stemness state heterogeneity in pancreatic ductal adenocarcinoma

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Endocrine disruption of early uterine differentiation causes adenocarcinoma mediated by Wnt/β-catenin- and PI3K/AKT signaling

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Comprehensive characterization of tumor microenvironment in colorectal cancer via histopathology-molecular analysis

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Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

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Transcriptional Profiling of Patient Isolates Identifies a Novel TOR Regulatory Pathway in Cryptococcal Virulence

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Analysis of cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription

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Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events

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Imaging mass cytometry reveals early β-cell dysfunction and changes in immune signatures during type 1 diabetes progression in human pancreata

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Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis

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title:
Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson’s disease tissue

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title:
Single-cell RNA-sequencing data analysis reveals a highly correlated triphasic transcriptional response to SARS-CoV-2 infection

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paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
title: Generation of an in vitro 3D multicellular culture model of ovarian high-grade serous carcinoma
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paper_key: biorxiv:714a78b1-71fa-1014-9d67-b3c1b8ab525d
title: Notebook-based alignment of human and agentic reasoning in single-cell biology
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title:
Acidovorax temperans polarizes T17 cells and skews neutrophil maturation to promote lung adenocarcinoma development

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paper_key: biorxiv:72d8cdf5-6fa5-1014-b805-ea9c7c557043
title: CausalCell: applying causal discovery to single-cell analyses
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paper_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964
title: Flexible and robust cell type annotation for highly multiplexed tissue images
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paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
title: Wounding triggers invasive progression in human basal cell carcinoma
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paper_key: biorxiv:74029b8c-6ce2-1014-895d-efaff54ffb70
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title:
Trypanosoma brucei cattle infections contain cryptic transmission-adapted bloodstream forms at low parasitaemia

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paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
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title:
Identification of a sub-population of synovial mesenchymal stem cells with enhanced treatment efficacy in a rat model of Osteoarthritis

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paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
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title:
Enhanced Annotation of CD45RA to Distinguish T cell Subsets in Single Cell RNA-seq via Machine Learning

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paper_key: biorxiv:759eb02e-7162-1014-8aed-a152593f2c53
title: Bringing PanglaoDB to 5-star Linked Open Data using Wikidata
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paper_key: biorxiv:76570cd7-6d2b-1014-8bce-a856d86cda31
title: Detecting SARS-CoV-2 variants with SNP genotyping
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paper_key: biorxiv:770577ab-6c15-1014-a8da-bd5994514db6
title: Comparing transcriptional dynamics of the epithelial-mesenchymal transition
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paper_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702
title: Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals
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paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
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title:
Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

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paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
title: A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
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paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
title: Transcriptomic analysis of the human habenula in schizophrenia
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paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
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title:
The centrosomal protein 83 (CEP83) regulates human pluripotent stem cell differentiation towards the kidney lineage

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paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
title: Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs
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paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
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title:
Analysis of single-cell RNA-sequencing data to identify quiescent and proliferating neural cell populations in Glioblastoma

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paper_key: biorxiv:7b112e1c-7312-1014-8132-b667bffdb7c9
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title:
Rethinking the Estrogen Receptor Beta Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing Meta-analysis

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paper_key: biorxiv:7b12a61e-6fce-1014-85ee-aa7b9d657ce6
title: Sensei: How many samples to tell evolution in single-cell studies?
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paper_key: biorxiv:7c2da8c6-7024-1014-8c11-de157ff3a710
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title:
Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration

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paper_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82
title: S3R: Modeling spatially varying associations with Spatially Smooth Sparse Regression
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paper_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1
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title:
Mouse-to-human modeling of microglia single-nuclei transcriptomics identifies immune signaling pathways and potential therapeutic candidates associated with Alzheimer’s disease

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paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
title: A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures
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paper_key: biorxiv:7d4ba889-7057-1014-89ac-e20dcbc1c90f
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title:
Effects of diffusion MRI spatial resolution on human brain short-range association fiber reconstruction and structural connectivity estimation

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paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
title: A single-cell transposable element atlas of human cell identity
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HiIDDD: A high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells

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title:
TERT expression is associated with metastasis from thin primaries, exhausted CD4+ T cells in melanoma and with DNA repair across cancer entities

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title:
Integrated bioinformatics and wet-lab analysis revealed prominent inflammatory genes of Extracellular Matrix as prognostic biomarkers in patients with advance IBD requiring early surgery

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title:
Single-Cell RNA and ATAC Sequencing Reveal Cellular Heterogeneity and Chromatin Accessibility Dynamics in Young Chinese Breast Cancer Patients across Pre- and Post-Neoadjuvant Therapy

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title:
Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

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title:
Topography-dependent gene expression and function of common cell archetypes in large and small porcine airways

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paper_key: biorxiv:83bdb6b6-6c6e-1014-9f71-e3b544524924
title: Leveraging gene correlations in single cell transcriptomic data
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paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
title: Transcriptomic perspective on acromegaly- related PIT-1/SF-1 positive pituitary tumors
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paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
title: Take ACTION to characterize the functional identity of single cells
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paper_key: biorxiv:84ed12c4-6e9b-1014-9992-a35711e43c7c
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title:
Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

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paper_key: biorxiv:84f938de-6f01-1014-a936-f09782a0030f
title: LincRNA sequences are biased to counteract their translation
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Stochastic Single Cell Behaviour Leads to Robust Horizontal Cell Layer Formation in the Vertebrate Retina

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Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes

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paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
title: Integrative Single-cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Haematopoiesis
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title:
Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures

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paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
title: Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells
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Identification of five characteristic ferroptosis-related genes as novel biomarkers for ischemic stroke using bioinformatic and machine learning strategies

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Bronchoalveolar Lavage Single-Cell Transcriptomics Identifies Immune Cells Driving COVID-19 Severity in Patients

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Redefining Nephrotic Syndrome in Molecular Terms: Outcome-associated molecular clusters and patient stratification with noninvasive surrogate biomarkers

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Systemic Lupus Erythematosus Serum Stimulation of Human Intestinal Organoids Induces Changes in Goblet Cell Differentiation and Mitochondrial Fitness

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ACVR1R206H increases osteogenic/ECM gene expression and impairs myofiber formation in human skeletal muscle stem cells

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Drug combination prioritization for cancer treatment using single-cell RNA-seq based transfer learning

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Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

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High-throughput single-cell phenotypic profiling and backtracing exposes and predicts clinically relevant subpopulations in isogenic Staphylococcus aureus communities

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ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders

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Terminal type-specific cannabinoid CB1 receptor alterations in patients with schizophrenia: a pilot study

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Systematic temporal analysis of transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as an early hallmark of severe COVID-19

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Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

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Deciphering sources of PET signals in the tumor microenvironment of glioblastoma at cellular resolution

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Unveiling the influence of tumor and immune signatures on immune checkpoint therapy in advanced lung cancer

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A spinal cord injury time and severity consensus transcriptomic reference suite in rat reveals translationally-relevant biomarker genes

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Improved detection of pre-symptomatic, non-central nervous system TDP-43 pathology in amyotrophic lateral sclerosis using RNA aptamer

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SERPINB3 induces the basal-like/squamous subtype and enhances disease progression in pancreatic cancer

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Simultaneous Label-free Imaging of Nucleolar Dynamics and Subcellular Metabolic Shifts Across Tissue Contexts

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APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19

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Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection

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Characterization of the human fetal rete region by single cell transcriptional analysis of gonads and mesonephros/epididymis

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Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

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Deep multiplexed 50-marker imaging of circulating tumor cells expands actionable biomarker profiling for precision oncology

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Cardiac Specific Overexpression of Adenylyl Cyclase 8 Reprograms the Mouse Sinoatrial Node Transcriptome

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A new hypothesis for type 1 diabetes risk: The at-risk allele at rs3842753 associates with increased beta cell INS mRNA in a meta-analysis of single cell RNA sequencing data

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Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

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Identification and Validation of N-Acetylputrescine in Combination With Non-Canonical Clinical Features As a Parkinson’s Disease Biomarker Panel

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Heterogeneity of normal human breast stem and progenitor cells as revealed by transcriptional profiling

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A Method for Rapid Flow-cytometric Isolation of Endothelial Nuclei and RNA from Archived Frozen Brain Tissue

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High-risk neuropsychiatric copy number variants are associated with convergent transcriptomic changes in human brain cells

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Mapping early patterning events in human neural development using an in-vitro microfluidic stem cell model

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Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes

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Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome

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Cryobanking of human distal lung epithelial cells for preservation of their phenotypic and functional characteristics

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Multi-Omics Single-Cell Analysis Reveals Key Regulators of HIV-1 Persistence and Aberrant Host Immune Responses in Early Infection

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Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA clusters in cancer

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High-throughput differentiation of human blood vessel organoids reveals overlapping and distinct functions of the cerebral cavernous malformation proteins

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PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses

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A multi-gene predictive model for the radiation sensitivity of nasopharyngeal carcinoma based on machine learning

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Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host

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Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

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Intraductal Papillary Mucinous Neoplasm Cellular Plasticity linked with Repeat Element Dysregulation

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Resting natural killer cells promote the progress of colon cancer liver metastasis by elevating tumor-derived sSCF

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Single cell RNA sequencing reveals limited effects of Lrrk2 genotype in a mouse model of acute CNS inflammation

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

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Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

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Conservation and divergence of myelin proteome and oligodendrocyte transcriptome profiles between humans and mice

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scWGBS-GPT: A Foundation Model for Capturing Long-Range CpG Dependencies in Single-Cell Whole-Genome Bisulfite Sequencing to Enhance Epigenetic Analysis

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Modeling gene x environment interactions in PTSD using glucocorticoid-induced transcriptomics in human neurons

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Primary infection by E. multilocularis induces distinct patterns of crosstalk between hepatic regulatory T and natural killer T cells in mice

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Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis

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Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules

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Multi-omics analysis reveals key immunogenic signatures induced by oncolytic Zika virus infection of paediatric brain tumour cells

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An optimal transport-based low-dimensional visualization framework for high-parameter flow cytometry

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Depicting pathogenesis of osteomyelitis by single cell RNA-sequencing and an involvement of Morrbid in the autoinflammatory disease

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paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
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A cancer stem cell population underlies a multi-lineage phenotype and drug resistance in prostate cancer

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Selective whole genome amplification as a tool to enrich specimens with low Treponema pallidum genomic DNA copies for whole genome sequencing

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paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
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Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

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Single-cell transcriptomics and machine learning reveal RNF144B and C5AR1 as immune-related biomarkers and therapeutic targets in myocardial infarction

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Quantifying immune cell telomere content at single-cell resolution in context of PD-1 checkpoint immunotherapy

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Distinct oncogenes drive distinct genome and epigenome alterations in human mammary epithelial cells

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title:
Single-cell Transcriptomic Profiling of Pancreatic Ductal Adenocarcinoma: Epithelial Reprogramming and Systemic Immune Exhaustion

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Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty

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Single-cell Sequencing Highlights Heterogeneity and Malignant Progression in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma

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Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala

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Single-cell characterization and machine learning-based classification reveal the transcriptional identity and antigen-experienced features of peripheral CD4⁺CD8⁺ double-positive T cells

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CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

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Immunological Differences in Atopic Dermatitis Across Age Groups: Insights from Single-Cell Multi-Omics

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Harnessing fusion of genome-edited human stem cells to rapidly screen for novel protein functions in vivo

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eSPred: Explainable scRNA-seq Prediction via Customized Foundation Models and Pathway-Aware Fine-tuning

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Brain-Metastatic Melanoma Models Uncover Immune and Molecular Correlates of Response to Immunotherapy

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Combining Bulk and Single-Cell RNA Sequencing Data to Identify RNA methylation and Autophagy-Related Signatures in Patients with Chronic Obstructive Pulmonary Disease

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Cyclic pentapeptide cRGDfK enhances the inhibitory effect of sunitinib on TGF-β1-induced epithelial-to-mesenchymal transition in human non-small cell lung cancer cells

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Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates

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A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

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STHELAR, a multi-tissue dataset linking spatial transcriptomics and histology for cell type annotation

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The ACE2 expression of maternal-fetal interface and fetal organs indicates potential risk of vertical transmission of SARS-COV-2

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Spatial and Single-Cell Dissection of Fibroblast Subpopulation Reprogramming Driving Stromal Collapse in Breast Cancer Lymph Node Metastasis

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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

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Time series scRNAseq analysis in mouse and human informs optimization of rapid astrocyte differentiation protocols

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Predicting targeted- and immunotherapeutic response outcomes in melanoma with single-cell Raman Spectroscopy and AI

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Recovery of high quality metagenome–assembled genomes from full–scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling

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A Single-Cell RNA-Seq Analysis Unravels the Heterogeniety of Primary Cultured Human Corneal Endothelial Cells

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Single-cell alternative polyadenylation analysis reveals mechanistic insights of COVID-19-associated neurological and psychiatric effects

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Characterization of DNA methylation in PBMCs and donor-matched iPSCs shows methylation is reset during stem cell reprogramming

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Robust and accurate method for measuring tumor volume using optical 3D scanning for nonclinical in vivo efficacy study

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Moiety Modeling Framework for Deriving Moiety Abundances from Mass Spectrometry Measured Isotopologues

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mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

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Single cell profiling reveals functional heterogeneity and serial killing in human peripheral and ex vivo-generated CD34+ progenitor derived Natural Killer cells

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A TCF4/BRD4-dependent regulatory network confers cross-resistance to targeted and immune checkpoint therapy in melanoma

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scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker

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Single-Cell RNA Sequencing Reveals Regulatory Mechanism for Trophoblast Cell-Fate Divergence in Human Peri-Implantation Embryo

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Microglia and macrophages alterations in the CNS during acute SIV infection: a single-cell analysis in rhesus macaques

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Single Cell Analysis of Treatment–Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies

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Glioblastoma-instructed microglia transit to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts

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Spatial and Single-Cell Transcriptomics Decipher the Crosstalk Environment of DEFB1+ Cancer Cells and IFI30+ Macrophages in Intrahepatic Cholangiocarcinoma

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Contrasting autoimmune and treatment effects reveals baseline set points of immune toxicity following checkpoint inhibitor treatment

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Identification of neurodevelopmental organization of the cell populations of juvenile Huntington’s disease using dorso-ventral HD organoids and HD mouse embryos

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p57Kip2 regulates embryonic haematopoietic stem cell numbers by controlling the size of the sympathoadrenal progenitor pool

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Characterizing intra- and inter-tumor heterogeneity in Ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics

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Metastatic tumor cells in bone marrow differ from paired neuroblastoma tumor and contain subsets with therapy-resistant characteristics

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Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem

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Shortening of 3’ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism

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Tumour genotype shapes blood biomarker expression for use in pancreatic cancer detection and diagnosis

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The evolution of genomic, transcriptomic, and single-cell protein markers of metastatic upper tract urothelial carcinoma

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Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer

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paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
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title:
Identifying Distinct Molecular Response of CAR-T cells to Solid Tumors by Synthetic Single-Cell Transcriptomic Analyses

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paper_key: biorxiv:e215da8f-6c0d-1014-8e2a-995cd6c28f85
title: Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
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paper_key: biorxiv:e23331bf-7510-1014-82e6-fe697c7128c1
title: Predicting gene expression from cell morphology in human induced pluripotent stem cells
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paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
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title:
Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer

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paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
title: A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer
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paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
title: γδ T cells modulate anti-tumor immunity in small cell lung cancer
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paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
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title:
Therapeutic Eradication of Cancer-associated Fibroblasts Inhibits in vivo progression of Pancreatic Cancer

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paper_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d
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title:
Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

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paper_key: biorxiv:e3d65daf-6f06-1014-87c8-89d311736362
title: Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito
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paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
title: CXCR6⁺ CD127⁻ Tr1 Cells Balance Immunity and Persistence in Plasmodium falciparum Infection
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paper_key: biorxiv:e47bbd06-71db-1014-8573-807590af5b25
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title:
Protein catabolites as blood-based biomarkers of aging physiology: Findings from the Dog Aging Project

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paper_key: biorxiv:e568b53a-6d0f-1014-b567-f89875467104
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title:
scRNAseq of healthy and irradiated mouse parotid glands highlights crosstalk between immune and secretory cells during chronic injury

source_url:
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paper_key: biorxiv:e5f6bdd5-6c3e-1014-9f6b-b86c26c0af34
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title:
ldentify potential feature genes and immune cell infiltration of HIRI based on branched-chain amino acid-related genes by machine learning and experimental validation

source_url:
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paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
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metadata_source: corpus-paper-index
title:
PLAE web app enables powerful searching and multiple visualizations across one million unified single-cell ocular transcriptomes

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paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
manuscript_path: data/biorxiv/meca/e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8/manuscript.md
metadata_source: corpus-paper-index
title:
Tissue microenvironment dictates the state of human induced pluripotent stem cell-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues

source_url:
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paper_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6
title: Decontamination of ambient RNA in single-cell RNA-seq with DecontX
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metadata_source: corpus-paper-index
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paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
manuscript_path: data/biorxiv/meca/e70d54a8-74bd-1014-b600-d60c5a656b30/manuscript.md
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title:
Tracing the stemness and malignant transition in a heritable colorectal cancer Lynch Syndrome by single-cell RNA-seq analysis

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/e70d54a8-74bd-1014-b600-d60c5a656b30/manuscript.md


paper_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da
title: Deep Learning Based Models for Preimplantation Mouse and Human Development
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metadata_source: corpus-paper-index
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paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
manuscript_path: data/biorxiv/meca/e78eaa01-6c93-1014-839e-bb3dc2108ab1/manuscript.md
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title:
Experimental study of modified human tendon stem cells to promote graft ligamentation and tendon-bone healing after anterior cruciate ligament reconstruction

source_url:
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paper_key: biorxiv:e82ec9db-7c73-1014-9391-b678aa473b23
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title:
Cortical-layer EEG-fMRI at 7T: experimental setup and analysis pipeline to elucidate generating mechanisms of alpha oscillations

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/e82ec9db-7c73-1014-9391-b678aa473b23/manuscript.md


paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
manuscript_path: data/biorxiv/meca/e8350987-7003-1014-ae7a-192d8e5e2a06/manuscript.md
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title:
Metabolic Maturation Unveils Left Ventricular Identity in WNT ON/OFF Human Pluripotent Stem Cell-Derived Cardiomyocytes

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/e8350987-7003-1014-ae7a-192d8e5e2a06/manuscript.md


paper_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae
title: Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization
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metadata_source: corpus-paper-index
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paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
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metadata_source: corpus-paper-index
title:
SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms

source_url:
https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/e91c125a-709d-1014-bc43-9d192767cd15/manuscript.md


paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
title: Resistance to Naïve and Formative Pluripotency Conversion in RSeT Human Embryonic Stem Cells
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metadata_source: corpus-paper-index
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paper_key: biorxiv:ea25adb3-7984-1014-a325-f254254cbb54
title: Cell-Type Specific Single-Cell Signatures Reveal Nephrotoxic Drug Affects
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metadata_source: corpus-paper-index
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paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
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title:
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data

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paper_key: biorxiv:eacc5519-6e13-1014-beef-f0ad14ca58dd
title: Rat Deconvolution as Knowledge Miner for Immune Cell Trafficking from Toxicogenomics Databases
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paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
manuscript_path: data/biorxiv/meca/ebaf49e5-7438-1014-8951-c3e925f71d14/manuscript.md
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title:
scMILD: Single-cell Multiple Instance Learning for Sample Classification and Associated Subpopulation Discovery

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https://github.com/sbooeshaghi/llmarkers/blob/main/data/biorxiv/meca/ebaf49e5-7438-1014-8951-c3e925f71d14/manuscript.md


paper_key: biorxiv:ebcc1e89-6c96-1014-a9cf-f07473ed0888
title: MAVS mediates a protective immune response in the brain to Rift Valley fever virus
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metadata_source: corpus-paper-index
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paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
title: The level of HAND1 controls the specification of multipotent cardiac and extraembryonic progenitors
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metadata_source: corpus-paper-index
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paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
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title:
Gene-Expression Programs in Salivary Gland Adenoid Cystic Carcinoma Analyzed Using Single-Cell and Spatial Transcriptomics

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paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
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title:
SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

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paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
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title:
Comparative transcriptomic analysis defines shared and mammary-specific gene expression programs across glandular tissues

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paper_key: biorxiv:ef092899-708f-1014-8b28-e3068206525c
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title:
SCellBOW: AI-Driven Tumor Risk Stratification from Single-Cell Transcriptomics Using Phenotype Algebra

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paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
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title:
Extensive monolayer formation depends on a subpopulation of transplanted human iPSC-derived RPE cells

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paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
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title:
Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer’s disease neuropathology

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paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
title: Local Oxygen Tension Dictates Hematopoietic Cell Growth and Potency
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paper_key: biorxiv:f1ef177f-6c82-1014-b840-bab78d461cd0
title: Inhibition of Type I PRMTs Reforms Muscle Stem Cell Identity Enhancing their Therapeutic Capacity
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paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
title: Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
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paper_key: biorxiv:f3523bb0-7455-1014-87bd-f1300ddfbf6f
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title:
Unraveling tumor heterogeneity: Quantitative insights from scRNA-seq analysis in breast cancer subtypes

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paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
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Single-cell transcriptomics reveals immunosuppressive microenvironment and highlights stumor-promoting macrophage cells in Glioblastoma

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paper_key: biorxiv:f59b3cab-6d1a-1014-a9d4-9041ec881993
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Novel ‘housekeeping’ genes and an unusually heterogeneous distribution of transporter expression profiles in human tissues and cell lines, assessed using the Gini coefficient

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title:
Functional immune state classification of unlabeled live human monocytes using holotomography and machine learning

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paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
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Human and mouse transcriptome profiling identifies cross-species homology in pulmonary and lymph node mononuclear phagocytes

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Creating an atlas of the bone microenvironment during oral inflammatory-related bone disease using single-cell profiling

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Whole body cell map tracks tissue-specific immune cell accumulation and plasticity loss through ageing

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A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model

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Sequential chromogenic immunohistochemistry: spatial analysis of lymph nodes identifies contact interactions between plasmacytoid dendritic cells and plasmablasts

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The Human Dendritic Cell Atlas: An integrated transcriptional tool to study human dendritic cell biology

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Revised International Staging System (R-ISS) stage-dependent analysis uncovers oncogenes and potential immunotherapeutic targets in multiple myeloma

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Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics

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MPCD Index for Hepatocellular Carcinoma Patients Based on Mitochondrial Function and Cell Death Patterns

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Multi-omics reveal critical differentiation target for Parkinson’s Disease-vulnerable midbrain dopaminergic neurons

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paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
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Loss of the H4 lysine methyltransferase KMT5B drives tumorigenic phenotypes by depleting H3K27me3 at loci otherwise retained in H3K27M mutant DIPG cells

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Cross-disease modeling of peripheral blood identifies biomarkers of type 2 diabetes predictive of Alzheimer’s disease

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title:
Morphological Landscapes from High Content Imaging Identify Optimal Priming Strategies that Enhance MSC Immunosuppression

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paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
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A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan


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A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.


paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
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Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs.


paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
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A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease


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A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates


paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
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A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion


paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
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A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders.


paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
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A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics.


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A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells.


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A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.


paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
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A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells


paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
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A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast.


paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
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An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics.


paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
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An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies


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Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease


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Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease


paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
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B cell signatures and tertiary lymphoid structures contribute to outcome in head and neck squamous cell carcinoma


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Hematopoietic cell transplantation donor-derived memory-like NK cells functionally persist after transfer into patients with leukemia.


paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
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COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis.


paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
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Heterogeneity of the intestinal mononuclear phagocyte compartment in health and inflammatory bowel disease


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Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics


paper_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189
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Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids.


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Cellular and molecular landscapes of human tendons across the lifespan revealed by spatial and single-cell transcriptomics


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Cellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencing


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doi: 10.1101/2021.09.16.460628
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Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq


paper_key: hca:0096_10.1126_sciadv.abo2467_05989af98e
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Characterization of altered molecular mechanisms in Parkinson's disease through cell type-resolved multiomics analyses


paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
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Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis


paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
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Combinatorial transcription factor profiles predict mature and functional human islet α and β cells.


paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
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Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.


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Systematic Comparison of High-throughput Single-Cell and  Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation


paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
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Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues


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Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade


paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
doi: 10.1101/2022.02.09.479667
source_url: https://doi.org/10.1101/2022.02.09.479667
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title:
Single-cell analysis reveals a pathogenic cellular module associated with early allograft dysfunction after liver transplantation.


paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
doi: 10.1101/2021.04.28.441762
source_url: https://doi.org/10.1101/2021.04.28.441762
manuscript_path: data/hca/manuscripts/0113_10.1101_2021.04.28.441762_c83625bbe4/manuscript.md
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title:
Cross-tissue immune cell analysis reveals tissue-specific adaptations and clonal architecture in humans


paper_key: hca:0115_10.1038_s41587-023-01734-7_fb10bf071f
doi: 10.1038/s41587-023-01734-7
source_url: https://doi.org/10.1038/s41587-023-01734-7
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title:
Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins


paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
doi: 10.1038/s41467-022-34255-z
source_url: https://doi.org/10.1038/s41467-022-34255-z
manuscript_path: data/hca/manuscripts/0120_10.1038_s41467-022-34255-z_c90043e943/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis.


paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
doi: 10.1016/j.cell.2021.11.031
source_url: https://doi.org/10.1016/j.cell.2021.11.031
manuscript_path: data/hca/manuscripts/0127_10.1016_j.cell.2021.11.031_38bd899f1b/manuscript.md
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title:
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps


paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
doi: 10.1016/j.stem.2020.11.010
source_url: https://doi.org/10.1016/j.stem.2020.11.010
manuscript_path: data/hca/manuscripts/0129_10.1016_j.stem.2020.11.010_32cb10758c/manuscript.md
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title:
Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response


paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
doi: 10.1038/s41422-020-00455-9
source_url: https://doi.org/10.1038/s41422-020-00455-9
manuscript_path: data/hca/manuscripts/0130_10.1038_s41422-020-00455-9_6ab85d317a/manuscript.md
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title:
Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages


paper_key: hca:0131_10.1016_j.celrep.2018.08.056_3eef7708e9
doi: 10.1016/j.celrep.2018.08.056
source_url: https://doi.org/10.1016/j.celrep.2018.08.056
manuscript_path: data/hca/manuscripts/0131_10.1016_j.celrep.2018.08.056_3eef7708e9/manuscript.md
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title:
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing


paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
doi: 10.1038/s41467-020-16239-z
source_url: https://doi.org/10.1038/s41467-020-16239-z
manuscript_path: data/hca/manuscripts/0132_10.1038_s41467-020-16239-z_001d78a35b/manuscript.md
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title:
Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium.


paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
doi: 10.3389/fimmu.2021.636720
source_url: https://doi.org/10.3389/fimmu.2021.636720
manuscript_path: data/hca/manuscripts/0134_10.3389_fimmu.2021.636720_9a958ecc4e/manuscript.md
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title:
Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28


paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
doi: 10.1167/iovs.62.6.18
source_url: https://doi.org/10.1167/iovs.62.6.18
manuscript_path: data/hca/manuscripts/0136_10.1167_iovs.62.6.18_7e8926eaf2/manuscript.md
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title:
Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing-Opening Pathways to New Therapeutic Strategies?


paper_key: hca:0137_10.1084_jem.20221350_7ac74dedfd
doi: 10.1084/jem.20221350
source_url: https://doi.org/10.1084/jem.20221350
manuscript_path: data/hca/manuscripts/0137_10.1084_jem.20221350_7ac74dedfd/manuscript.md
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title:
Distinct fibroblast progenitor subpopulation expedites regenerative mucosal healing by immunomodulation.


paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
doi: 10.1016/j.immuni.2023.01.032
source_url: https://doi.org/10.1016/j.immuni.2023.01.032
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title:
Dysregulated lung stroma drives emphysema exacerbation by potentiating resident lymphocytes to suppress an epithelial stem cell reservoir


paper_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6
doi: 10.1016/j.ebiom.2025.106036
source_url: https://doi.org/10.1016/j.ebiom.2025.106036
manuscript_path: data/hca/manuscripts/0144_10.1016_j.ebiom.2025.106036_833fbd27b6/manuscript.md
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title:
Early lymph node T follicular helper cell signalling hub drives influenza vaccine response in an ancestrally diverse cohort


paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
doi: 10.1038/s41368-023-00238-z
source_url: https://doi.org/10.1038/s41368-023-00238-z
manuscript_path: data/hca/manuscripts/0149_10.1038_s41368-023-00238-z_c77e60a0ab/manuscript.md
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title:
Extracellular matrix remodelling in dental pulp tissue of carious human teeth through the prism of single-cell RNA sequencing


paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
doi: 10.15252/embr.201847483
source_url: https://doi.org/10.15252/embr.201847483
manuscript_path: data/hca/manuscripts/0152_10.15252_embr.201847483_d14f9b2105/manuscript.md
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title:
Reporter-based fate mapping in human kidney organoids confirms nephron lineage relationships and reveals synchronous nephron formation.


paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
doi: 10.1038/s41556-020-00607-4
source_url: https://doi.org/10.1038/s41556-020-00607-4
manuscript_path: data/hca/manuscripts/0153_10.1038_s41556-020-00607-4_a7b29ac44b/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation.


paper_key: hca:0156_10.1101_2020.12.21.423830_b1006f56a0
doi: 10.1101/2020.12.21.423830
source_url: https://doi.org/10.1101/2020.12.21.423830
manuscript_path: data/hca/manuscripts/0156_10.1101_2020.12.21.423830_b1006f56a0/manuscript.md
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title:
Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection


paper_key: hca:0158_10.2337_db21-0830_d021248f76
doi: 10.2337/db21-0830
source_url: https://doi.org/10.2337/db21-0830
manuscript_path: data/hca/manuscripts/0158_10.2337_db21-0830_d021248f76/manuscript.md
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title:
Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy


paper_key: hca:0159_10.1172_jci157279_71a5ff671c
doi: 10.1172/jci157279
source_url: https://doi.org/10.1172/jci157279
manuscript_path: data/hca/manuscripts/0159_10.1172_jci157279_71a5ff671c/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition


paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
doi: 10.1016/j.stem.2017.09.003
source_url: https://doi.org/10.1016/j.stem.2017.09.003
manuscript_path: data/hca/manuscripts/0160_10.1016_j.stem.2017.09.003_8fb14888a8/manuscript.md
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Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development


paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
doi: 10.1681/asn.2020030326
source_url: https://doi.org/10.1681/asn.2020030326
manuscript_path: data/hca/manuscripts/0161_10.1681_asn.2020030326_bf5d42b566/manuscript.md
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title:
Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant.


paper_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c
doi: 10.1016/j.kint.2021.11.031
source_url: https://doi.org/10.1016/j.kint.2021.11.031
manuscript_path: data/hca/manuscripts/0162_10.1016_j.kint.2021.11.031_93f85a569c/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Glomerular endothelial cell-podocyte stresses and crosstalk in structurally normal kidney transplants


paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
doi: 10.1126/sciimmunol.abb4432
source_url: https://doi.org/10.1126/sciimmunol.abb4432
manuscript_path: data/hca/manuscripts/0163_10.1126_sciimmunol.abb4432_91494cf647/manuscript.md
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title:
Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses.


paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
doi: 10.1111/cpr.13557
source_url: https://doi.org/10.1111/cpr.13557
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title:
High-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathy


paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
doi: 10.1038/s41588-024-02048-3
source_url: https://doi.org/10.1038/s41588-024-02048-3
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Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns


paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
doi: 10.1038/s41587-020-00796-1
source_url: https://doi.org/10.1038/s41587-020-00796-1
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Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19


paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
doi: 10.1016/j.ebiom.2021.103618
source_url: https://doi.org/10.1016/j.ebiom.2021.103618
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Synovial tissue from sites of joint pain in knee osteoarthritis patients exhibits a differential phenotype with distinct fibroblast subsets.


paper_key: hca:0183_10.1126_sciimmunol.abd1554_52a79b9d12
doi: 10.1126/sciimmunol.abd1554
source_url: https://doi.org/10.1126/sciimmunol.abd1554
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Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19.


paper_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45
doi: 10.1038/s41598-019-45842-4
source_url: https://doi.org/10.1038/s41598-019-45842-4
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An optimised tissue disaggregation and data processing pipeline for characterising fibroblast phenotypes using single-cell RNA sequencing.


paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
doi: 10.1126/sciimmunol.abh3768
source_url: https://doi.org/10.1126/sciimmunol.abh3768
manuscript_path: data/hca/manuscripts/0191_10.1126_sciimmunol.abh3768_bc0f7a7105/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci.


paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
doi: 10.1038/s41467-021-27619-4
source_url: https://doi.org/10.1038/s41467-021-27619-4
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Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing


paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
doi: 10.1242/dev.172361
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Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells.


paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
doi: 10.1038/s41467-019-13382-0
source_url: https://doi.org/10.1038/s41467-019-13382-0
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Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation


paper_key: hca:0202_10.1101_2021.03.09.21253155_14ff4e9eec
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High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection.


paper_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902
doi: 10.1038/s41598-021-95532-3
source_url: https://doi.org/10.1038/s41598-021-95532-3
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Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range


paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
doi: 10.1016/j.immuni.2020.11.017
source_url: https://doi.org/10.1016/j.immuni.2020.11.017
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Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.


paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
doi: 10.1038/nbt.2967
source_url: https://doi.org/10.1038/nbt.2967
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Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.


paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
doi: 10.1016/j.cels.2022.06.005
source_url: https://doi.org/10.1016/j.cels.2022.06.005
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Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution


paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
doi: 10.1016/j.ccell.2022.11.001
source_url: https://doi.org/10.1016/j.ccell.2022.11.001
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Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer.


paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
doi: 10.1186/s40478-023-01568-z
source_url: https://doi.org/10.1186/s40478-023-01568-z
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Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function


paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
doi: 10.1038/s42003-021-02562-8
source_url: https://doi.org/10.1038/s42003-021-02562-8
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Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma.


paper_key: hca:0221_10.7554_elife.69603_ab573a325d
doi: 10.7554/elife.69603
source_url: https://doi.org/10.7554/elife.69603
manuscript_path: data/hca/manuscripts/0221_10.7554_elife.69603_ab573a325d/manuscript.md
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title:
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids.


paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
doi: 10.1128/mbio.02583-20
source_url: https://doi.org/10.1128/mbio.02583-20
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title:
Molecular Signatures of Inflammatory Profile and B-Cell Function in Patients with Severe Fever with Thrombocytopenia Syndrome.


paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
doi: 10.1101/2023.08.08.551504
source_url: https://doi.org/10.1101/2023.08.08.551504
manuscript_path: data/hca/manuscripts/0231_10.1101_2023.08.08.551504_0d646c9546/manuscript.md
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Multi-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma


paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
doi: 10.1038/s41467-022-32972-z
source_url: https://doi.org/10.1038/s41467-022-32972-z
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title:
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression


paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
doi: 10.1016/j.isci.2024.111337
source_url: https://doi.org/10.1016/j.isci.2024.111337
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Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia


paper_key: hca:0238_10.1002_art.41813_55de40d8f6
doi: 10.1002/art.41813
source_url: https://doi.org/10.1002/art.41813
manuscript_path: data/hca/manuscripts/0238_10.1002_art.41813_55de40d8f6/manuscript.md
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title:
Expansion of Fcγ Receptor IIIa-Positive Macrophages, Ficolin 1-Positive Monocyte-Derived Dendritic Cells, and Plasmacytoid Dendritic Cells Associated With Severe Skin Disease in Systemic Sclerosis.


paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
doi: 10.1172/jci138519
source_url: https://doi.org/10.1172/jci138519
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title:
Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.


paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
doi: 10.1016/j.stem.2020.12.001
source_url: https://doi.org/10.1016/j.stem.2020.12.001
manuscript_path: data/hca/manuscripts/0248_10.1016_j.stem.2020.12.001_c5f98f4c3c/manuscript.md
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Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk.


paper_key: hca:0256_10.1038_nbt.2859_240ea4136e
doi: 10.1038/nbt.2859
source_url: https://doi.org/10.1038/nbt.2859
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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells


paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
doi: 10.1038/s41590-019-0425-y
source_url: https://doi.org/10.1038/s41590-019-0425-y
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title:
Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues.


paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
doi: 10.1038/s41467-020-20082-7
source_url: https://doi.org/10.1038/s41467-020-20082-7
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title:
Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds.


paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
doi: 10.1016/j.neuron.2021.05.003
source_url: https://doi.org/10.1016/j.neuron.2021.05.003
manuscript_path: data/hca/manuscripts/0266_10.1016_j.neuron.2021.05.003_0cca870e2c/manuscript.md
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title:
Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans.


paper_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0
doi: 10.1007/s00395-021-00897-1
source_url: https://doi.org/10.1007/s00395-021-00897-1
manuscript_path: data/hca/manuscripts/0268_10.1007_s00395-021-00897-1_9d51738bc0/manuscript.md
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title:
Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level.


paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
doi: 10.1016/j.cell.2020.04.035
source_url: https://doi.org/10.1016/j.cell.2020.04.035
manuscript_path: data/hca/manuscripts/0272_10.1016_j.cell.2020.04.035_15a2d05837/manuscript.md
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title:
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.


paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
doi: 10.1016/j.isci.2021.103592
source_url: https://doi.org/10.1016/j.isci.2021.103592
manuscript_path: data/hca/manuscripts/0274_10.1016_j.isci.2021.103592_3ec037cca1/manuscript.md
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title:
Salivary ZG16B expression loss follows exocrine gland dysfunction related to oral chronic graft-versus-host disease.


paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
doi: 10.1007/s10911-020-09466-z
source_url: https://doi.org/10.1007/s10911-020-09466-z
manuscript_path: data/hca/manuscripts/0278_10.1007_s10911-020-09466-z_d1b799dcf6/manuscript.md
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title:
Single Cell RNA Sequencing of Human Milk-Derived Cells Reveals Sub-Populations of Mammary Epithelial Cells with Molecular Signatures of Progenitor and Mature States: a Novel, Non-invasive Framework for Investigating Human Lactation Physiology.


paper_key: hca:0280_10.1681_asn.2017080890_022062f455
doi: 10.1681/asn.2017080890
source_url: https://doi.org/10.1681/asn.2017080890
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title:
Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney


paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
doi: 10.1016/j.devcel.2019.06.001
source_url: https://doi.org/10.1016/j.devcel.2019.06.001
manuscript_path: data/hca/manuscripts/0281_10.1016_j.devcel.2019.06.001_238d93bfef/manuscript.md
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title:
In VivoDevelopmental Trajectories of Human PodocyteInformIn VitroDifferentiation of Pluripotent Stem Cell-Derived Podocytes


paper_key: hca:0282_10.1016_j.stem.2020.06.006_67000edb63
doi: 10.1016/j.stem.2020.06.006
source_url: https://doi.org/10.1016/j.stem.2020.06.006
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title:
A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells


paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
doi: 10.1002/hep4.1854
source_url: https://doi.org/10.1002/hep4.1854
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title:
Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity


paper_key: hca:0285_10.26502_fccm.92920277_c5e967ab20
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title:
Single Nucleus RNA-sequencing Reveals Altered Intercellular Communication and Dendritic Cell Activation in Nonobstructive Hypertrophic Cardiomyopathy.


paper_key: hca:0287_10.1101_gr.228080.117_9206d994b7
doi: 10.1101/gr.228080.117
source_url: https://doi.org/10.1101/gr.228080.117
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title:
Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data


paper_key: hca:0290_10.1101_235499_566cff6e3c
doi: 10.1101/235499
source_url: https://doi.org/10.1101/235499
manuscript_path: data/hca/manuscripts/0290_10.1101_235499_566cff6e3c/manuscript.md
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title:
High throughput single cell RNA-seq of developing mouse kidney and human kidney
organoids reveals a roadmap for recreating the kidney


paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
doi: 10.1172/jci.insight.150861
source_url: https://doi.org/10.1172/jci.insight.150861
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title:
Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing.


paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
doi: 10.1038/s41467-021-25328-6
source_url: https://doi.org/10.1038/s41467-021-25328-6
manuscript_path: data/hca/manuscripts/0296_10.1038_s41467-021-25328-6_8814b43a21/manuscript.md
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Grafting of iPS cell-derived tenocytes promotes motor function recovery after Achilles tendon rupture.


paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
doi: 10.1038/s42003-021-02223-w
source_url: https://doi.org/10.1038/s42003-021-02223-w
manuscript_path: data/hca/manuscripts/0297_10.1038_s42003-021-02223-w_f1c781baae/manuscript.md
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title:
Single-cell RNA sequencing of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium


paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
doi: 10.1101/2021.07.28.453839
source_url: https://doi.org/10.1101/2021.07.28.453839
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title:
Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues


paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
doi: 10.1038/s41467-019-11266-x
source_url: https://doi.org/10.1038/s41467-019-11266-x
manuscript_path: data/hca/manuscripts/0299_10.1038_s41467-019-11266-x_d55119ff52/manuscript.md
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Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors


paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
doi: 10.1186/s13287-023-03256-0
source_url: https://doi.org/10.1186/s13287-023-03256-0
manuscript_path: data/hca/manuscripts/0300_10.1186_s13287-023-03256-0_d71fd1c1ed/manuscript.md
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title:
Single cell and lineage tracing studies reveal the impact of CD34+ cells on myocardial fibrosis during heart failure


paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
doi: 10.1016/j.isci.2022.104772
source_url: https://doi.org/10.1016/j.isci.2022.104772
manuscript_path: data/hca/manuscripts/0302_10.1016_j.isci.2022.104772_3e028c0be0/manuscript.md
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title:
Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations


paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
doi: 10.1126/sciimmunol.abg5539
source_url: https://doi.org/10.1126/sciimmunol.abg5539
manuscript_path: data/hca/manuscripts/0304_10.1126_sciimmunol.abg5539_d30f748444/manuscript.md
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Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells


paper_key: hca:0305_10.1158_0008-5472.can-19-2306_dd7931fca8
doi: 10.1158/0008-5472.can-19-2306
source_url: https://doi.org/10.1158/0008-5472.can-19-2306
manuscript_path: data/hca/manuscripts/0305_10.1158_0008-5472.can-19-2306_dd7931fca8/manuscript.md
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title:
Hypoxia Induces Transcriptional and Translational Downregulation of the Type I IFN Pathway in Multiple Cancer Cell Types.


paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
doi: 10.1038/s41467-021-22368-w
source_url: https://doi.org/10.1038/s41467-021-22368-w
manuscript_path: data/hca/manuscripts/0306_10.1038_s41467-021-22368-w_5524560e05/manuscript.md
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Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney


paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
doi: 10.1038/s41419-021-03724-6
source_url: https://doi.org/10.1038/s41419-021-03724-6
manuscript_path: data/hca/manuscripts/0307_10.1038_s41419-021-03724-6_32b837a8da/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single cell transcriptional zonation of human psoriasis skin identifies an alternative immunoregulatory axis conducted by skin resident cells.


paper_key: hca:0308_10.1242_dev.199711_724ab19d33
doi: 10.1242/dev.199711
source_url: https://doi.org/10.1242/dev.199711
manuscript_path: data/hca/manuscripts/0308_10.1242_dev.199711_724ab19d33/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific features.


paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
doi: 10.1172/jci.insight.133267
source_url: https://doi.org/10.1172/jci.insight.133267
manuscript_path: data/hca/manuscripts/0310_10.1172_jci.insight.133267_ab6c49313c/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker


paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
doi: 10.1016/j.celrep.2022.110467
source_url: https://doi.org/10.1016/j.celrep.2022.110467
manuscript_path: data/hca/manuscripts/0313_10.1016_j.celrep.2022.110467_a2771a8ae7/manuscript.md
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title:
Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms.


paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
doi: 10.1016/j.cell.2017.09.004
source_url: https://doi.org/10.1016/j.cell.2017.09.004
manuscript_path: data/hca/manuscripts/0314_10.1016_j.cell.2017.09.004_62170aa227/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.


paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
doi: 10.1158/2159-8290.cd-21-0683
source_url: https://doi.org/10.1158/2159-8290.cd-21-0683
manuscript_path: data/hca/manuscripts/0315_10.1158_2159-8290.cd-21-0683_4c7216e47a/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer


paper_key: hca:0321_10.1002_stem.3302_bfd2270715
doi: 10.1002/stem.3302
source_url: https://doi.org/10.1002/stem.3302
manuscript_path: data/hca/manuscripts/0321_10.1002_stem.3302_bfd2270715/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Directed induction of alveolar type I cells derived from pluripotent stem cells via Wnt signaling inhibition.


paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
doi: 10.3389/fonc.2021.719564
source_url: https://doi.org/10.3389/fonc.2021.719564
manuscript_path: data/hca/manuscripts/0322_10.3389_fonc.2021.719564_a0cfb67753/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell RNA Sequencing in Multiple Pathologic Types of Renal Cell Carcinoma Revealed Novel Potential Tumor-Specific Markers.


paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
doi: 10.1016/j.celrep.2017.10.030
source_url: https://doi.org/10.1016/j.celrep.2017.10.030
manuscript_path: data/hca/manuscripts/0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma


paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
doi: 10.1164/rccm.201712-2410oc
source_url: https://doi.org/10.1164/rccm.201712-2410oc
manuscript_path: data/hca/manuscripts/0329_10.1164_rccm.201712-2410oc_fdd97d9097/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis.


paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
doi: 10.1016/j.celrep.2020.01.007
source_url: https://doi.org/10.1016/j.celrep.2020.01.007
manuscript_path: data/hca/manuscripts/0330_10.1016_j.celrep.2020.01.007_2459125119/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures.


paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
doi: 10.1681/asn.2018020125
source_url: https://doi.org/10.1681/asn.2018020125
manuscript_path: data/hca/manuscripts/0334_10.1681_asn.2018020125_804c4742d9/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response


paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
doi: 10.3389/fnmol.2020.00134
source_url: https://doi.org/10.3389/fnmol.2020.00134
manuscript_path: data/hca/manuscripts/0338_10.3389_fnmol.2020.00134_d9eafa03d0/manuscript.md
metadata_source: hca-manuscript-manifest
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Profiling Microglia From Alzheimer's Disease Donors and Non-demented Elderly in Acute Human Postmortem Cortical Tissue.


paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
doi: 10.1038/s41467-020-16164-1
source_url: https://doi.org/10.1038/s41467-020-16164-1
manuscript_path: data/hca/manuscripts/0340_10.1038_s41467-020-16164-1_15fae00c00/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma


paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
doi: 10.3389/fimmu.2021.645666
source_url: https://doi.org/10.3389/fimmu.2021.645666
manuscript_path: data/hca/manuscripts/0345_10.3389_fimmu.2021.645666_15198bd9bb/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer's Disease.


paper_key: hca:0346_10.34067_kid.0005522021_6c9059bd87
doi: 10.34067/kid.0005522021
source_url: https://doi.org/10.34067/kid.0005522021
manuscript_path: data/hca/manuscripts/0346_10.34067_kid.0005522021_6c9059bd87/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19-associated AKI


paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
doi: 10.1186/s12943-021-01419-2
source_url: https://doi.org/10.1186/s12943-021-01419-2
manuscript_path: data/hca/manuscripts/0347_10.1186_s12943-021-01419-2_236ba26890/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma


paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
doi: 10.1126/sciadv.aba1972
source_url: https://doi.org/10.1126/sciadv.aba1972
manuscript_path: data/hca/manuscripts/0348_10.1126_sciadv.aba1972_746bae0b3c/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis


paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
doi: 10.1038/s41467-023-36296-4
source_url: https://doi.org/10.1038/s41467-023-36296-4
manuscript_path: data/hca/manuscripts/0349_10.1038_s41467-023-36296-4_67ae3c1e19/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment


paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
doi: 10.1038/s41422-018-0103-x
source_url: https://doi.org/10.1038/s41422-018-0103-x
manuscript_path: data/hca/manuscripts/0351_10.1038_s41422-018-0103-x_169d6c1666/manuscript.md
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Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens.


paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
doi: 10.1016/j.neuron.2017.02.014
source_url: https://doi.org/10.1016/j.neuron.2017.02.014
manuscript_path: data/hca/manuscripts/0353_10.1016_j.neuron.2017.02.014_ebc3a9c467/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.


paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
doi: 10.3389/fcell.2020.00384
source_url: https://doi.org/10.3389/fcell.2020.00384
manuscript_path: data/hca/manuscripts/0356_10.3389_fcell.2020.00384_845548ef53/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell RNA-Seq Analysis Uncovers Distinct Functional Human NKT Cell Sub-Populations in Peripheral Blood.


paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
doi: 10.1126/sciadv.aba1983
source_url: https://doi.org/10.1126/sciadv.aba1983
manuscript_path: data/hca/manuscripts/0358_10.1126_sciadv.aba1983_17b603cdcb/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis


paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
doi: 10.1084/jem.20161135
source_url: https://doi.org/10.1084/jem.20161135
manuscript_path: data/hca/manuscripts/0360_10.1084_jem.20161135_0465d3ea50/manuscript.md
metadata_source: hca-manuscript-manifest
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Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs


paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
doi: 10.1038/s41591-019-0733-7
source_url: https://doi.org/10.1038/s41591-019-0733-7
manuscript_path: data/hca/manuscripts/0362_10.1038_s41591-019-0733-7_d499f1b21b/manuscript.md
metadata_source: hca-manuscript-manifest
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Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report


paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
doi: 10.1016/j.omtn.2021.03.017
source_url: https://doi.org/10.1016/j.omtn.2021.03.017
manuscript_path: data/hca/manuscripts/0363_10.1016_j.omtn.2021.03.017_8083e53d24/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics reveals the landscape of intra-tumoral heterogeneity and transcriptional activities of ECs in CC


paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
doi: 10.1161/circulationaha.120.046528
source_url: https://doi.org/10.1161/circulationaha.120.046528
manuscript_path: data/hca/manuscripts/0364_10.1161_circulationaha.120.046528_00aa2deb4c/manuscript.md
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title:
Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue.


paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
doi: 10.3389/fendo.2022.874915
source_url: https://doi.org/10.3389/fendo.2022.874915
manuscript_path: data/hca/manuscripts/0365_10.3389_fendo.2022.874915_81de77d539/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell RNA Sequencing of Human Corpus Cavernosum Reveals Cellular Heterogeneity Landscapes in Erectile Dysfunction


paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
doi: 10.1038/s41467-021-22164-6
source_url: https://doi.org/10.1038/s41467-021-22164-6
manuscript_path: data/hca/manuscripts/0366_10.1038_s41467-021-22164-6_097f05776f/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions.


paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
doi: 10.1073/pnas.2103240118
source_url: https://doi.org/10.1073/pnas.2103240118
manuscript_path: data/hca/manuscripts/0367_10.1073_pnas.2103240118_fda266512b/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response.


paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
doi: 10.1016/j.cell.2019.08.008
source_url: https://doi.org/10.1016/j.cell.2019.08.008
manuscript_path: data/hca/manuscripts/0368_10.1016_j.cell.2019.08.008_98c14c4ebe/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy


paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
doi: 10.1038/s41598-020-64929-x
source_url: https://doi.org/10.1038/s41598-020-64929-x
manuscript_path: data/hca/manuscripts/0369_10.1038_s41598-020-64929-x_0cb78e8038/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity


paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
doi: 10.1038/s41698-022-00251-1
source_url: https://doi.org/10.1038/s41698-022-00251-1
manuscript_path: data/hca/manuscripts/0370_10.1038_s41698-022-00251-1_1483c4b104/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity


paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
doi: 10.1016/j.ccell.2021.10.009
source_url: https://doi.org/10.1016/j.ccell.2021.10.009
manuscript_path: data/hca/manuscripts/0372_10.1016_j.ccell.2021.10.009_d6ab4790aa/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification.


paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
doi: 10.1136/annrheumdis-2018-214865
source_url: https://doi.org/10.1136/annrheumdis-2018-214865
manuscript_path: data/hca/manuscripts/0374_10.1136_annrheumdis-2018-214865_9f6cd4034f/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease


paper_key: hca:0377_10.7554_elife.64875_32e53ae733
doi: 10.7554/elife.64875
source_url: https://doi.org/10.7554/elife.64875
manuscript_path: data/hca/manuscripts/0377_10.7554_elife.64875_32e53ae733/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans.


paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
doi: 10.1101/2022.06.17.496207
source_url: https://doi.org/10.1101/2022.06.17.496207
manuscript_path: data/hca/manuscripts/0378_10.1101_2022.06.17.496207_92cb140ff3/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes


paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
doi: 10.1038/s41698-022-00300-9
source_url: https://doi.org/10.1038/s41698-022-00300-9
manuscript_path: data/hca/manuscripts/0379_10.1038_s41698-022-00300-9_7bb9a273c6/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment


paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
doi: 10.1038/s41593-020-00794-1
source_url: https://doi.org/10.1038/s41593-020-00794-1
manuscript_path: data/hca/manuscripts/0380_10.1038_s41593-020-00794-1_0ecbc1eb47/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia.


paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
doi: 10.1038/s41593-022-01061-1
source_url: https://doi.org/10.1038/s41593-022-01061-1
manuscript_path: data/hca/manuscripts/0387_10.1038_s41593-022-01061-1_5c1bbb5824/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease.


paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
doi: 10.1038/s41591-024-02807-z
source_url: https://doi.org/10.1038/s41591-024-02807-z
manuscript_path: data/hca/manuscripts/0389_10.1038_s41591-024-02807-z_9d82b71a18/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids


paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
doi: 10.1038/s42255-022-00531-x
source_url: https://doi.org/10.1038/s42255-022-00531-x
manuscript_path: data/hca/manuscripts/0393_10.1038_s42255-022-00531-x_b92878970e/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.


paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
doi: 10.1016/j.xgen.2022.100164
source_url: https://doi.org/10.1016/j.xgen.2022.100164
manuscript_path: data/hca/manuscripts/0395_10.1016_j.xgen.2022.100164_f07698cf8e/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.


paper_key: hca:0396_10.7554_elife.62522_10df7c4591
doi: 10.7554/elife.62522
source_url: https://doi.org/10.7554/elife.62522
manuscript_path: data/hca/manuscripts/0396_10.7554_elife.62522_10df7c4591/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes.


paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
doi: 10.1186/s13059-023-03111-8
source_url: https://doi.org/10.1186/s13059-023-03111-8
manuscript_path: data/hca/manuscripts/0397_10.1186_s13059-023-03111-8_05defe1911/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation


paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
doi: 10.3389/fimmu.2022.1034159
source_url: https://doi.org/10.3389/fimmu.2022.1034159
manuscript_path: data/hca/manuscripts/0398_10.3389_fimmu.2022.1034159_e51dfc8bb5/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals


paper_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e
doi: 10.1016/j.immuni.2019.08.008
source_url: https://doi.org/10.1016/j.immuni.2019.08.008
manuscript_path: data/hca/manuscripts/0399_10.1016_j.immuni.2019.08.008_d590b8282e/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease


paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
doi: 10.1038/s41467-022-35297-z
source_url: https://doi.org/10.1038/s41467-022-35297-z
manuscript_path: data/hca/manuscripts/0400_10.1038_s41467-022-35297-z_0eab5d0ba9/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity.


paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
doi: 10.21203/rs.3.rs-151881/v1
source_url: https://doi.org/10.21203/rs.3.rs-151881/v1
manuscript_path: data/hca/manuscripts/0401_10.21203_rs.3.rs-151881_v1_d8e8733600/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation


paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
doi: 10.1016/j.ccell.2021.03.007
source_url: https://doi.org/10.1016/j.ccell.2021.03.007
manuscript_path: data/hca/manuscripts/0405_10.1016_j.ccell.2021.03.007_50f32173d6/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.


paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
doi: 10.1093/brain/awab446
source_url: https://doi.org/10.1093/brain/awab446
manuscript_path: data/hca/manuscripts/0406_10.1093_brain_awab446_1c9ee67691/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state.


paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
doi: 10.1101/2021.04.05.438347
source_url: https://doi.org/10.1101/2021.04.05.438347
manuscript_path: data/hca/manuscripts/0408_10.1101_2021.04.05.438347_e17dfd8c36/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell sequencing unveils distinct immune microenvironment with CCR6-CCL20 crosstalk in human chronic pancreatitis


paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
doi: 10.1136/gutjnl-2021-324546
source_url: https://doi.org/10.1136/gutjnl-2021-324546
manuscript_path: data/hca/manuscripts/0409_10.1136_gutjnl-2021-324546_a227082482/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis


paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
doi: 10.3389/fcell.2021.820274
source_url: https://doi.org/10.3389/fcell.2021.820274
manuscript_path: data/hca/manuscripts/0410_10.3389_fcell.2021.820274_b0973e038f/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Sequencing Unveils the Heterogeneity of Nonimmune Cells in Chronic Apical Periodontitis.


paper_key: hca:0411_10.1016_j.immuni.2019.06.027_4a3b9ca5c7
doi: 10.1016/j.immuni.2019.06.027
source_url: https://doi.org/10.1016/j.immuni.2019.06.027
manuscript_path: data/hca/manuscripts/0411_10.1016_j.immuni.2019.06.027_4a3b9ca5c7/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils


paper_key: hca:0413_10.1016_j.celrep.2021.109524_894f3930a6
doi: 10.1016/j.celrep.2021.109524
source_url: https://doi.org/10.1016/j.celrep.2021.109524
manuscript_path: data/hca/manuscripts/0413_10.1016_j.celrep.2021.109524_894f3930a6/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development.


paper_key: hca:0415_10.1038_s41467-020-20358-y_582bbd075a
doi: 10.1038/s41467-020-20358-y
source_url: https://doi.org/10.1038/s41467-020-20358-y
manuscript_path: data/hca/manuscripts/0415_10.1038_s41467-020-20358-y_582bbd075a/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse.


paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
doi: 10.1101/gr.212720.116
source_url: https://doi.org/10.1101/gr.212720.116
manuscript_path: data/hca/manuscripts/0417_10.1101_gr.212720.116_ba8d2583ab/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes


paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
doi: 10.1038/s41588-021-00806-1
source_url: https://doi.org/10.1038/s41588-021-00806-1
manuscript_path: data/hca/manuscripts/0419_10.1038_s41588-021-00806-1_d66603cd99/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma.


paper_key: hca:0420_10.1111_cas.15979_052ebae233
doi: 10.1111/cas.15979
source_url: https://doi.org/10.1111/cas.15979
manuscript_path: data/hca/manuscripts/0420_10.1111_cas.15979_052ebae233/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs.


paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
doi: 10.1038/s41467-019-12780-8
source_url: https://doi.org/10.1038/s41467-019-12780-8
manuscript_path: data/hca/manuscripts/0423_10.1038_s41467-019-12780-8_0da964452a/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.


paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
doi: 10.1038/s41467-019-12464-3
source_url: https://doi.org/10.1038/s41467-019-12464-3
manuscript_path: data/hca/manuscripts/0426_10.1038_s41467-019-12464-3_0f8440336d/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease


paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
doi: 10.7150/ijbs.58886
source_url: https://doi.org/10.7150/ijbs.58886
manuscript_path: data/hca/manuscripts/0427_10.7150_ijbs.58886_44183be8e8/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics reveals heterogeneous progression and EGFR activation in pancreatic adenosquamous carcinoma.


paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
doi: 10.1073/pnas.1914143116
source_url: https://doi.org/10.1073/pnas.1914143116
manuscript_path: data/hca/manuscripts/0428_10.1073_pnas.1914143116_42027a0378/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration


paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
doi: 10.1172/jci.insight.156341
source_url: https://doi.org/10.1172/jci.insight.156341
manuscript_path: data/hca/manuscripts/0432_10.1172_jci.insight.156341_02dc39adcf/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney.


paper_key: hca:0435_10.1038_nm.4336_19432336d2
doi: 10.1038/nm.4336
source_url: https://doi.org/10.1038/nm.4336
manuscript_path: data/hca/manuscripts/0435_10.1038_nm.4336_19432336d2/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia


paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
doi: 10.1016/j.jtos.2020.12.004
source_url: https://doi.org/10.1016/j.jtos.2020.12.004
manuscript_path: data/hca/manuscripts/0436_10.1016_j.jtos.2020.12.004_24ddeb29a4/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea.


paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
doi: 10.1101/2021.01.22.21250336
source_url: https://doi.org/10.1101/2021.01.22.21250336
manuscript_path: data/hca/manuscripts/0437_10.1101_2021.01.22.21250336_e963bc0939/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single nuclei profiling identifies cell specific markers of skeletal muscle aging, sarcopenia and senescence


paper_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16
doi: 10.1016/j.celrep.2023.112086
source_url: https://doi.org/10.1016/j.celrep.2023.112086
manuscript_path: data/hca/manuscripts/0438_10.1016_j.celrep.2023.112086_4947038a16/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-nucleus RNA sequencing in ischemic cardiomyopathy reveals common transcriptional profile underlying end-stage heart failure.


paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
doi: 10.1186/s13073-023-01179-2
source_url: https://doi.org/10.1186/s13073-023-01179-2
manuscript_path: data/hca/manuscripts/0440_10.1186_s13073-023-01179-2_de903e74e7/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles.


paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
doi: 10.1038/s41593-020-0621-y
source_url: https://doi.org/10.1038/s41593-020-0621-y
manuscript_path: data/hca/manuscripts/0441_10.1038_s41593-020-0621-y_a3edefca60/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons.


paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
doi: 10.1038/s41591-024-03011-9
source_url: https://doi.org/10.1038/s41591-024-03011-9
manuscript_path: data/hca/manuscripts/0442_10.1038_s41591-024-03011-9_e42f5ec07c/manuscript.md
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Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry


paper_key: hca:0446_10.1186_s13073-021-00933-8_a1bc5f6475
doi: 10.1186/s13073-021-00933-8
source_url: https://doi.org/10.1186/s13073-021-00933-8
manuscript_path: data/hca/manuscripts/0446_10.1186_s13073-021-00933-8_a1bc5f6475/manuscript.md
metadata_source: hca-manuscript-manifest
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Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19.


paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
doi: 10.1101/2022.02.15.480622
source_url: https://doi.org/10.1101/2022.02.15.480622
manuscript_path: data/hca/manuscripts/0448_10.1101_2022.02.15.480622_6cb3eae5b8/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-nucleus transcriptomic analysis reveals divergence of glial cells in peripheral somatosensory system between human and mouse


paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
doi: 10.1084/jem.20202345
source_url: https://doi.org/10.1084/jem.20202345
manuscript_path: data/hca/manuscripts/0449_10.1084_jem.20202345_e99c99a876/manuscript.md
metadata_source: hca-manuscript-manifest
title:
Single-cell analysis of human skin identifies CD14+ type 3 dendritic cells co-producing IL1B and IL23A in psoriasis


paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
doi: 10.1016/j.jid.2018.01.016
source_url: https://doi.org/10.1016/j.jid.2018.01.016
manuscript_path: data/hca/manuscripts/0451_10.1016_j.jid.2018.01.016_d2589a157e/manuscript.md
metadata_source: hca-manuscript-manifest
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Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations


paper_key: hca:0461_10.1101_2022.10.24.513598_7706771889
doi: 10.1101/2022.10.24.513598
source_url: https://doi.org/10.1101/2022.10.24.513598
manuscript_path: data/hca/manuscripts/0461_10.1101_2022.10.24.513598_7706771889/manuscript.md
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Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression


paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
doi: 10.7554/elife.81525
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title:
Spatially resolved transcriptomics reveals pro-inflammatory fibroblast involved in lymphocyte recruitment through CXCL8 and CXCL10


paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
doi: 10.1038/s41467-019-11947-7
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title:
Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome.


paper_key: hca:0477_10.1172_jci157338_273d70a217
doi: 10.1172/jci157338
source_url: https://doi.org/10.1172/jci157338
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title:
The ZIP8/SIRT1 axis regulates alveolar progenitor cell renewal in aging and idiopathic pulmonary fibrosis


paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
doi: 10.1016/j.immuni.2023.01.002
source_url: https://doi.org/10.1016/j.immuni.2023.01.002
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title:
The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon


paper_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09
doi: 10.1101/2025.10.19.683341
source_url: https://doi.org/10.1101/2025.10.19.683341
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title:
The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomic


paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
doi: 10.1038/s41467-021-26495-2
source_url: https://doi.org/10.1038/s41467-021-26495-2
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title:
The serine proteases dipeptidyl-peptidase 4 and urokinase are key molecules in human and mouse scar formation.


paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
doi: 10.1038/s41591-021-01332-7
source_url: https://doi.org/10.1038/s41591-021-01332-7
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title:
Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition


paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
doi: 10.1038/s41467-021-27895-0
source_url: https://doi.org/10.1038/s41467-021-27895-0
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title:
Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk


paper_key: hca:0498_10.1038_s41598-017-11044-z_4cb11e808c
doi: 10.1038/s41598-017-11044-z
source_url: https://doi.org/10.1038/s41598-017-11044-z
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title:
Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing


paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
doi: 10.1016/j.xcrm.2024.101556
source_url: https://doi.org/10.1016/j.xcrm.2024.101556
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Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease.


paper_key: hca:0504_10.1101_2020.01.26.919753_a4a4e6fc9a
doi: 10.1101/2020.01.26.919753
source_url: https://doi.org/10.1101/2020.01.26.919753
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title:
Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes.


paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
doi: 10.1126/scitranslmed.abh2624
source_url: https://doi.org/10.1126/scitranslmed.abh2624
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Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19


paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
doi: 10.1038/s41591-022-01680-y
source_url: https://doi.org/10.1038/s41591-022-01680-y
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title:
Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity.


paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
doi: 10.1186/s13073-021-00941-8
source_url: https://doi.org/10.1186/s13073-021-00941-8
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title:
Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets.


paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
doi: 10.1016/j.gastha.2022.12.004
source_url: https://doi.org/10.1016/j.gastha.2022.12.004
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title:
Single Nucleus Sequencing of Human Colon Myenteric Plexus-Associated Visceral Smooth Muscle Cells, Platelet Derived Growth Factor Receptor Alpha Cells, and Interstitial Cells of Cajal


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doi: 10.1186/s13059-019-1906-x
source_url: https://doi.org/10.1186/s13059-019-1906-x
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title:
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation


