Integrated multi-omics approaches to improve classification of chronic kidney disease

S Eddy, LH Mariani, M Kretzler - Nature Reviews Nephrology, 2020‏ - nature.com
Chronic kidney diseases (CKDs) are currently classified according to their clinical features,
associated comorbidities and pattern of injury on biopsy. Even within a given classification …

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 …

Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data

D He, M Zakeri, H Sarkar, C Soneson, A Srivastava… - Nature …, 2022‏ - nature.com
The rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing
(scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few …

SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression

R Rodríguez-Quiroz… - Communications …, 2022‏ - nature.com
Abstract Transposable Elements (TEs) contribute to the repetitive fraction in almost every
eukaryotic genome known to date, and their transcriptional activation can influence the …

Simulation, power evaluation and sample size recommendation for single-cell RNA-seq

K Su, Z Wu, H Wu - Bioinformatics, 2020‏ - academic.oup.com
Motivation Determining the sample size for adequate power to detect statistical significance
is a crucial step at the design stage for high-throughput experiments. Even though a number …

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

A Srivastava, L Malik, H Sarkar, R Patro - Bioinformatics, 2020‏ - academic.oup.com
Motivation Droplet-based single-cell RNA-seq (dscRNA-seq) data are being generated at an
unprecedented pace, and the accurate estimation of gene-level abundances for each cell is …

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments

G Ebrahimi, B Orabi, M Robinson, C Chauve… - Iscience, 2022‏ - cell.com
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the
cell type level. However, because of its use of short-reads, it is severely limited at detecting …

TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator

F Karaoğlanoğlu, B Orabi, R Flannigan… - …, 2024‏ - academic.oup.com
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective
technology for probing various RNA features. Numerous tools have been developed to …

scReadSim: a single-cell RNA-seq and ATAC-seq read simulator

G Yan, D Song, JJ Li - Nature Communications, 2023‏ - nature.com
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-
Accessible Chromatin using sequencing (scATAC-seq) computational tools demands …

SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level

L Sun, G Wang, Z Zhang - Briefings in Bioinformatics, 2023‏ - academic.oup.com
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) has been a powerful
technology for transcriptome analysis. However, the systematic validation of diverse …