Integrated analysis of multimodal single-cell data

TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells

(2020) Elena Vendrame et al.   AIDS

MAIT Cells in Health and Disease

(2020) Nicholas M. Provine et al.   Annual Review of Immunology

Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

(2020) Yuri Kotliarov et al.   NATURE MEDICINE

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

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

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

MAIT Cell Activation and Functions

(2020) Timothy S. C. Hinks et al.   Frontiers in Immunology

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

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

(2019) Samuel G. Rodriques et al.   SCIENCE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Revolutionizing immunology with single-cell RNA sequencing

(2019) Haide Chen et al.   Cellular & Molecular Immunology

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

(2019) Federico Gaiti et al.   NATURE

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

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

Select sequencing of clonally expanded CD8+ T cells reveals limits to clonal expansion

(2019) Huang Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The Functional Requirement for CD69 in Establishment of Resident Memory CD8+ T Cells Varies with Tissue Location

(2019) Daniel A. Walsh et al.   JOURNAL OF IMMUNOLOGY

Location, location, location: Tissue resident memory T cells in mice and humans

(2019) Peter A. Szabo et al.   Science Immunology

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

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

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Immunology Driven by Large-Scale Single-Cell Sequencing

(2019) Tomás Gomes et al.   TRENDS IN IMMUNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Production of IL-17 by MAIT Cells Is Increased in Multiple Sclerosis and Is Associated with IL-7 Receptor Expression

(2018) Anne Willing et al.   JOURNAL OF IMMUNOLOGY

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

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

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

Tissue-Resident Memory CD8+ T Cells: From Phenotype to Function

(2018) David J. Topham et al.   Frontiers in Immunology

Immune Modulation by Human Secreted RNases at the Extracellular Space

(2018) Lu Lu et al.   Frontiers in Immunology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Safety and tolerability of HIV-1 multiantigen pDNA vaccine given with IL-12 plasmid DNA via electroporation, boosted with a recombinant vesicular stomatitis virus HIV Gag vaccine in healthy volunteers in a randomized, controlled clinical trial

(2018) Marnie L. Elizaga et al.   PLoS One

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Natural Killer Cells: Development, Maturation, and Clinical Utilization

(2018) Alex M. Abel et al.   Frontiers in Immunology

The Emerging Role of CD8+ Tissue Resident Memory T (TRM) Cells in Antitumor Immunity: A Unique Functional Contribution of the CD103 Integrin

(2018) Stéphanie Corgnac et al.   Frontiers in Immunology

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

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

(2017) Sebastian Pott   eLife

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Functional Mutations Form at CTCF-Cohesin Binding Sites in Melanoma Due to Uneven Nucleotide Excision Repair across the Motif

(2016) Rebecca C. Poulos et al.   Cell Reports

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Memory CD8+ T cells colocalize with IL-7+ stromal cells in bone marrow and rest in terms of proliferation and transcription

(2015) Özen Sercan Alp et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Cytomegalovirus Infection Drives Adaptive Epigenetic Diversification of NK Cells with Altered Signaling and Effector Function

(2015) Heinrich Schlums et al.   IMMUNITY

Epigenetic Modification and Antibody-Dependent Expansion of Memory-like NK Cells in Human Cytomegalovirus-Infected Individuals

(2015) Jaewon Lee et al.   IMMUNITY

Barcoding of Live Human Peripheral Blood Mononuclear Cells for Multiplexed Mass Cytometry

(2015) Henrik E. Mei et al.   JOURNAL OF IMMUNOLOGY

Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data

(2015) Kirsten E. Diggins et al.   METHODS

Cytomegalovirus Infection and Memory T Cell Inflation

(2015) Jihye Kim et al.   Immune Network

Optimization of a whole blood phenotyping assay for enumeration of peripheral blood leukocyte populations in multicenter clinical trials

(2014) Tiffany Hensley-McBain et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Specific MAIT cell behaviour among innate-like T lymphocytes in critically ill patients with severe infections

(2013) David Grimaldi et al.   INTENSIVE CARE MEDICINE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity

(2012) D. E. Zak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Supervised principal component analysis: Visualization, classification and regression on subspaces and submanifolds

(2010) Elnaz Barshan et al.   PATTERN RECOGNITION

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY