MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

(2019) Dongju Shin et al.   Science Advances

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

PHLDA1 Mediates Drug Resistance in Receptor Tyrosine Kinase-Driven Cancer

(2018) Abbie E. Fearon et al.   Cell Reports

Monocytes Differentiate to Immune Suppressive Precursors of Metastasis-Associated Macrophages in Mouse Models of Metastatic Breast Cancer

(2018) Takanori Kitamura et al.   Frontiers in Immunology

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery

(2018) Chaoyang Ye et al.   Nature Communications

Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence

(2017) Marieke Aarts et al.   GENES & DEVELOPMENT

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

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

(2017) Naomi Habib et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Monocytic and granulocytic myeloid derived suppressor cells differentially regulate spatiotemporal tumour plasticity during metastatic cascade

(2017) Maria Ouzounova et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

The regulation of pre-metastatic niche formation by neutrophils

(2017) Jadwiga Jablonska et al.   Oncotarget

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

(2017) Paul Savage et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Regulation of Tumor Metastasis by Myeloid-Derived Suppressor Cells

(2015) Thomas Condamine et al.   Annual Review of Medicine

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes

(2015) Sheida Nabavi et al.   BIOINFORMATICS

RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states

(2015) Kaiyu Jiang et al.   BMC Medical Genomics

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Pulmonary Alveolar Macrophages Contribute to the Premetastatic Niche by Suppressing Antitumor T Cell Responses in the Lungs

(2015) Sharad K. Sharma et al.   JOURNAL OF IMMUNOLOGY

Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

(2015) Devon A. Lawson et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Efficient Targeting of Fatty-Acid Modified Oligonucleotides to Live Cell Membranes through Stepwise Assembly

(2014) Robert J. Weber et al.   BIOMACROMOLECULES

Bone Marrow–Derived Gr1 + Cells Can Generate a Metastasis-Resistant Microenvironment Via Induced Secretion of Thrombospondin-1

(2013) Raúl Catena et al.   Cancer Discovery

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes

(2011) Yoko S DeRose et al.   NATURE MEDICINE

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Molecular Distinctions between Stasis and Telomere Attrition Senescence Barriers Shown by Long-term Culture of Normal Human Mammary Epithelial Cells

(2009) J. C. Garbe et al.   CANCER RESEARCH

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors

(2009) D Chitale et al.   ONCOGENE