Single-cell genomics to understand disease pathogenesis

Immunology in the Era of Single-Cell Technologies

(2020) Mirjana Efremova et al.   Annual Review of Immunology

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging

(2020) Shuai Ma et al.   CELL

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease

(2020) David Gate et al.   NATURE

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs

(2020) Marco Jost et al.   NATURE BIOTECHNOLOGY

Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function

(2020) Li Wang et al.   NATURE CELL BIOLOGY

Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report

(2020) Doyoung Kim et al.   NATURE MEDICINE

Single-cell genomic approaches for developing the next generation of immunotherapies

(2020) Ido Yofe et al.   NATURE MEDICINE

An immune-cell signature of bacterial sepsis

(2020) Miguel Reyes et al.   NATURE MEDICINE

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Tissue clearing and its applications in neuroscience

(2020) Hiroki R. Ueda et al.   NATURE REVIEWS NEUROSCIENCE

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants

(2020) Margaret K. R. Donovan et al.   Nature Communications

Advancing Cancer Research and Medicine with Single-Cell Genomics

(2020) Bora Lim et al.   CANCER CELL

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

(2020) Sarah Bowling et al.   CELL

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Dissecting cellular crosstalk by sequencing physically interacting cells

(2020) Amir Giladi et al.   NATURE BIOTECHNOLOGY

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Simultaneous quantification of protein–DNA interactions and transcriptomes in single cells with scDam&T-seq

(2020) Corina M. Markodimitraki et al.   Nature Protocols

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Dimensionality reduction by UMAP to visualize physical and genetic interactions

(2020) Michael W. Dorrity et al.   Nature Communications

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

(2020) David Y. Oh et al.   CELL

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

(2020) Christian M. Schürch et al.   CELL

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

High-throughput single-molecule RNA imaging analysis reveals heterogeneous responses of cardiomyocytes to hemodynamic overload

(2019) Masahiro Satoh et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

(2019) Longqi Liu et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Cell composition analysis of bulk genomics using single-cell data

(2019) Amit Frishberg et al.   NATURE METHODS

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging

(2019) Weizhe Li et al.   Nature Protocols

Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice

(2019) Weike Pei et al.   Nature Protocols

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Exploring single cells in space and time during tissue development, homeostasis and regeneration

(2019) Urs Mayr et al.   DEVELOPMENT

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

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

(2019) Jonathan S. Packer et al.   SCIENCE

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Unravelling cellular relationships during development and regeneration using genetic lineage tracing

(2019) Chloé S. Baron et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload–Driven Heart Failure Reveals Extent of Immune Activation

(2019) Elisa Martini et al.   CIRCULATION

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

(2018) Aleksandra Wroblewska et al.   CELL

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure

(2018) Seitaro Nomura et al.   Nature Communications

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo

(2017) Kelvin See et al.   Nature Communications

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene 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

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

(2016) Iain C Macaulay et al.   Nature Protocols

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

(2016) P. L. Stahl et al.   SCIENCE

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

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

(2013) Simone Picelli et al.   NATURE METHODS

RNAscope

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS