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

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

(2019) Vasilis Ntranos et al.   NATURE METHODS

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

(2019) D. Merino et al.   Nature Communications

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

(2019) Lin Guo et al.   MOLECULAR CELL

Microglial Function Is Distinct in Different Anatomical Locations during Retinal Homeostasis and Degeneration

(2019) Emily G. O’Koren et al.   IMMUNITY

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

(2019) Julien Delile et al.   DEVELOPMENT

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

(2019) Brian S. Clark et al.   NEURON

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

(2018) Luyi Tian et al.   PLoS Computational Biology

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Age-sensitive bibliographic coupling reflecting the history of science: The case of the Species Problem

(2013) Sándor Soós   SCIENTOMETRICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS