kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq

DK Sullivan, KH Min, KE Hjörleifsson, L Luebbert… - Nature …, 2024‏ - nature.com
The term 'RNA-seq'refers to a collection of assays based on sequencing experiments that
involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto …

Navigating bottlenecks and trade-offs in genomic data analysis

B Berger, YW Yu - Nature Reviews Genetics, 2023‏ - nature.com
Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

A Gayoso, P Weiler, M Lotfollahi, D Klein, J Hong… - Nature …, 2024‏ - nature.com
RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in
snapshot single-cell data; however, current approaches for estimating RNA velocity lack …

Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references

AH Pool, H Poldsam, S Chen, M Thomson, Y Oka - Nature methods, 2023‏ - nature.com
Single-cell RNA-sequencing (scRNA-seq) is an indispensable tool for characterizing cellular
diversity and generating hypotheses throughout biology. Droplet-based scRNA-seq datasets …

Fulgor: a fast and compact k-mer index for large-scale matching and color queries

J Fan, J Khan, NP Singh, GE Pibiri, R Patro - Algorithms for Molecular …, 2024‏ - Springer
The problem of sequence identification or matching—determining the subset of reference
sequences from a given collection that are likely to contain a short, queried nucleotide …

Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2025‏ - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

Y You, L Tian, S Su, X Dong, JS Jabbari, PF Hickey… - Genome biology, 2021‏ - Springer
Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated
analysis methods have rapidly developed in recent years. This includes preprocessing …

Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis

JA Morris, JS Sun, NE Sanjana - Trends in Genetics, 2024‏ - cell.com
Programmable genome-engineering technologies, such as CRISPR (clustered regularly
interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens …

[HTML][HTML] Recent advances in T-cell receptor repertoire analysis: bridging the gap with multimodal single-cell RNA sequencing

S Valkiers, N de Vrij, S Gielis, S Verbandt, B Ogunjimi… - ImmunoInformatics, 2022‏ - Elsevier
T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating
cytokines or regulation of tolerance, collectively resulting in an effective control of immune …

IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps

X **e, P Wang, M **, Y Wang, L Qi, C Wu… - Nature …, 2024‏ - nature.com
Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases,
including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated …