Maintenance and functional regulation of immune memory to COVID-19 vaccines in tissues

J Davis-Porada, AB George, N Lam, DP Caron, JI Gray… - Immunity, 2024 - cell.com
Memory T and B cells in tissues are essential for protective immunity. Here, we performed a
comprehensive analysis of the tissue distribution, phenotype, durability, and transcriptional …

The impact of package selection and versioning on single-cell RNA-seq analysis

JM Rich, L Moses, PH Einarsson, K Jackson… - …, 2024 - pmc.ncbi.nlm.nih.gov
Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting
raw read data into cell-gene count matrices through sequence alignment, followed by …

Biophysically interpretable inference of cell types from multimodal sequencing data

T Chari, G Gorin, L Pachter - Nature Computational Science, 2024 - nature.com
Multimodal, single-cell genomics technologies enable simultaneous measurement of
multiple facets of DNA and RNA processing in the cell. This creates opportunities for …

Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers

K Eldjárn Hjörleifsson, DK Sullivan, NP Swarna… - BioRxiv, 2022 - biorxiv.org
In single-cell and single-nucleus RNA sequencing, the coexistence of nascent
(unprocessed) and mature (processed) mRNA poses challenges in accurate read map** …

Characterization of prostate macrophage heterogeneity, foam cell markers, and CXCL17 upregulation in a mouse model of steroid hormone imbalance

SV Silver, KJ Tucker, RE Vickman, NA Lanman… - Scientific Reports, 2024 - nature.com
Benign prostatic hyperplasia (BPH) is a prevalent age-related condition often characterized
by debilitating urinary symptoms. Its etiology is believed to stem from hormonal imbalance …

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq

DK Sullivan, KE Hjörleifsson, NP Swarna… - Nucleic Acids …, 2025 - academic.oup.com
In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent
(unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in …

Long-read sequencing transcriptome quantification with lr-kallisto

RK Loving, DK Sullivan, AS Booeshagi, F Reese… - …, 2025 - pmc.ncbi.nlm.nih.gov
RNA abundance quantification has become routine and affordable thanks to high-
throughput “short-read” technologies that provide accurate molecule counts at the gene …

[PDF][PDF] Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers

KE Hjörleifsson, DK Sullivan, NP Swarna, G Holley… - bioRxiv, 2024 - biorxiv.org
In single-cell and single-nucleus RNA sequencing, the coexistence of nascent
(unprocessed) and mature (processed) mRNA poses challenges in accurate read map** …

Algorithms for a Commons Cell Atlas

AS Booeshaghi, Á Galvez-Merchán, L Pachter - bioRxiv, 2024 - biorxiv.org
Cell atlas projects curate representative datasets, cell types, and marker genes for tissues
across an organism. Despite their ubiquity, atlas projects rely on duplicated and manual …

A human commons cell atlas reveals cell type specificity for OAS1 isoforms

Á Galvez-Merchán, AS Booeshaghi, L Pachter - bioRxiv, 2024 - biorxiv.org
We describe an open source Human Commons Cell Atlas comprising 2.9 million cells
across 27 tissues that can be easily updated and that is structured to facilitate custom …