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

Comparative analysis of common alignment tools for single-cell RNA sequencing

(2022) Ralf Schulze Brüning et al.   GigaScience

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

(2021) Charlotte Soneson et al.   PLoS Computational Biology

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets

(2021) Inbal Shainer et al.   BMC GENOMICS

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads

(2020) Stefan Niebler et al.   BMC BIOINFORMATICS

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

A Notch-mediated, temporal asymmetry in BMP pathway activation promotes photoreceptor subtype diversification

(2019) Elise Cau et al.   PLOS BIOLOGY

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

(2019) Hirak Sarkar et al.   BIOINFORMATICS

Agouti-Related Protein 2 Is a New Player in the Teleost Stress Response System

(2019) Inbal Shainer et al.   CURRENT BIOLOGY

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Nonparametric expression analysis using inferential replicate counts

(2019) Anqi Zhu et al.   NUCLEIC ACIDS RESEARCH

A space and time-efficient index for the compacted colored de Bruijn graph

(2018) Fatemeh Almodaresi et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A novel transgenic zebrafish line for red opsin expression in outer segments of photoreceptor cells

(2018) Cátia Crespo et al.   DEVELOPMENTAL DYNAMICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Regulation of Placental Development and Its Impact on Fetal Growth—New Insights From Mouse Models

(2018) Laura Woods et al.   Frontiers in Endocrinology

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Color opponency with a single kind of bistable opsin in the zebrafish pineal organ

(2018) Seiji Wada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

(2016) Avi Srivastava et al.   BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS