Dissecting human disease with single-cell omics: application in model systems and in the clinic

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

(2018) Vikas Trivedi et al.   DEVELOPMENT

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models

(2018) Bahareh Ajami et al.   NATURE NEUROSCIENCE

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

(2018) Valentine Svensson et al.   Nature Protocols

Defining Cell Identity with Single-Cell Omics

(2018) Laura Mincarelli et al.   PROTEOMICS

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

(2018) Adam J Reid et al.   eLife

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

(2018) Yael Steuerman et al.   Cell Systems

Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research

(2017) Jianlin Liu et al.   International Journal of Biological Sciences

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

(2017) Alice Giustacchini et al.   NATURE MEDICINE

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

Aging and neurodegeneration are associated with increased mutations in single human neurons

(2017) Michael A. Lodato et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

(2017) Emmanouil I. Athanasiadis et al.   Nature Communications

Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics

(2017) Feng Guo et al.   Cell Reports

Dissecting the human microbiome with single-cell genomics

(2017) Andrew C. Tolonen et al.   Genome Medicine

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

(2016) Meital Gury-BenAri et al.   CELL

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

(2016) Kristin A. Knouse et al.   GENOME RESEARCH

High-dimensional single-cell analysis reveals the immune signature of narcolepsy

(2016) Felix J. Hartmann et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Single-Cell Detection of Secreted Aβ and sAPPα from Human IPSC-Derived Neurons and Astrocytes

(2016) Mei-Chen Liao et al.   JOURNAL OF NEUROSCIENCE

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes

(2016) Irma Virant-Klun et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell sequencing of the small-RNA transcriptome

(2016) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Integrated transcriptomic and proteomic analyses ofP. falciparumgametocytes: molecular insight into sex-specific processes and translational repression

(2016) Edwin Lasonder et al.   NUCLEIC ACIDS RESEARCH

Tools for Single-Cell Kinetic Analysis of Virus-Host Interactions

(2016) Jay W. Warrick et al.   PLoS One

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

(2016) Antoine-Emmanuel Saliba et al.   Nature Microbiology

Integrated analysis of the Plasmodium species transcriptome

(2016) Regina Hoo et al.   EBioMedicine

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

High-Throughput Single-Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles

(2015) Fulya Akpinar et al.   JOURNAL OF VIROLOGY

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors

(2015) A K Mitra et al.   LEUKEMIA

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

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

(2015) Devon A. Lawson et al.   NATURE

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance

(2015) D. T. Miyamoto et al.   SCIENCE

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

(2014) Thomas D Otto et al.   BMC BIOLOGY

Age-Dependent, Non-Cell-Autonomous Deposition of Amyloid from Synthesis of  -Amyloid by Cells Other Than Excitatory Neurons

(2014) K. Veeraraghavalu et al.   JOURNAL OF NEUROSCIENCE

Single-Cell Analysis Uncovers Extensive Biological Noise in Poliovirus Replication

(2014) M. B. Schulte et al.   JOURNAL OF VIROLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Epigenetics reloaded: the single-cell revolution

(2014) Poonam Bheda et al.   TRENDS IN CELL BIOLOGY

Tumor Evolution in Response to Chemotherapy: Phenotype versus Genotype

(2014) Nicholas E. Navin   Cell Reports

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS