Applications of single-cell RNA sequencing in drug discovery and development

Single‐Cell Immune Mapping of Melanoma Sentinel Lymph Nodes Reveals an Actionable Immunotolerant Microenvironment

(2022) Kavitha Yaddanapudi et al.   CLINICAL CANCER RESEARCH

A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk

(2022) Andrew C. Yang et al.   NATURE

Twin study reveals non-heritable immune perturbations in multiple sclerosis

(2022) Florian Ingelfinger et al.   NATURE

Clonally Expanded B Cells in Multiple Sclerosis Bind EBV EBNA1 and GlialCAM

(2022) Tobias V. Lanz et al.   NATURE

Massively parallel phenotyping of coding variants in cancer with Perturb-seq

(2022) Oana Ursu et al.   NATURE BIOTECHNOLOGY

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

CellRank for directed single-cell fate mapping

(2022) Marius Lange et al.   NATURE METHODS

Temporal modelling using single-cell transcriptomics

(2022) Jun Ding et al.   NATURE REVIEWS GENETICS

Protection against SARS-CoV-2 after Covid-19 Vaccination and Previous Infection

(2022) Victoria Hall et al.   NEW ENGLAND JOURNAL OF MEDICINE

Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with multiple sclerosis

(2022) Kjetil Bjornevik et al.   SCIENCE

MAPK4 promotes triple negative breast cancer growth and reduces tumor sensitivity to PI3K blockade

(2022) Wei Wang et al.   Nature Communications

Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

(2022) Hanbing Song et al.   Nature Communications

Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target

(2022) Nourhan Abdelfattah et al.   Nature Communications

Single-cell chromatin accessibility landscape in kidney identifies additional cell-of-origin in heterogenous papillary renal cell carcinoma

(2022) Qi Wang et al.   Nature Communications

Learning from natural variation across the proteomes of single cells

(2022) Nikolai Slavov   PLOS BIOLOGY

Analysis and Visualization of Spatial Transcriptomic Data

(2022) Boxiang Liu et al.   Frontiers in Genetics

Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer

(2022) Kaiyang Zhang et al.   Science Advances

Single-cell RNA sequencing uncovers the individual alteration of intestinal mucosal immunocytes in Dusp6 knockout mice

(2022) Cherng-Shyang Chang et al.   iScience

Recent advances in single-cell sequencing technologies

(2022) Lu Wen et al.   Precision Clinical Medicine

Biomarkers of response to PD-1 pathway blockade

(2022) Hanxiao Li et al.   BRITISH JOURNAL OF CANCER

Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy

(2022) Jiannong Li et al.   CLINICAL CANCER RESEARCH

Standing Watch: Immune Activation and Failure in Melanoma Sentinel Lymph Nodes

(2022) Amanda W. Lund   CLINICAL CANCER RESEARCH

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control

(2022) Hannah P. Gideon et al.   IMMUNITY

Somatic genomic changes in single Alzheimer’s disease neurons

(2022) Michael B. Miller et al.   NATURE

Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

(2022) Aparna Nathan et al.   NATURE

Cell transcriptomic atlas of the non-human primate Macaca fascicularis

(2022) Lei Han et al.   NATURE

A genome-scale screen for synthetic drivers of T cell proliferation

(2022) Mateusz Legut et al.   NATURE

Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

(2022) Tushar Kamath et al.   NATURE NEUROSCIENCE

Parkinson’s disease in the single-cell era

(2022) Ernest Arenas   NATURE NEUROSCIENCE

Clinical relevance of tumour-associated macrophages

(2022) Mikael J. Pittet et al.   Nature Reviews Clinical Oncology

Cross-tissue immune cell analysis reveals tissue-specific features in humans

(2022) C. Domínguez Conde et al.   SCIENCE

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

(2022) et al.   SCIENCE

Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617

(2022) Lei Peng et al.   Nature Communications

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

(2022) Benjamin E. Mead et al.   Nature Biomedical Engineering

Classification of human chronic inflammatory skin disease based on single-cell immune profiling

(2022) Yale Liu et al.   Science Immunology

Single‐cell RNA sequencing technologies and applications: A brief overview

(2022) Dragomirka Jovic et al.   Clinical and Translational Medicine

The metastatic spread of breast cancer accelerates during sleep

(2022) Zoi Diamantopoulou et al.   NATURE

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

(2022) Winston R. Becker et al.   NATURE GENETICS

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

(2022) Ignasius Joanito et al.   NATURE GENETICS

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

(2022) Daniel Dimitrov et al.   Nature Communications

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

(2022) Martin Jinye Zhang et al.   NATURE GENETICS

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

(2022) Karthik A. Jagadeesh et al.   NATURE GENETICS

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™

(2021) Namit Kumar et al.   BMC GENOMICS

Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages

(2021) Els Wauters et al.   CELL RESEARCH

The Organoid Cell Atlas

(2021) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics

(2021) Ze Zhang et al.   NATURE METHODS

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

(2021) Kevin Litchfield et al.   CELL

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

(2021) Christoph H Mayr et al.   EMBO Molecular Medicine

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens

(2021) Efthymia Papalexi et al.   NATURE GENETICS

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

(2021) Chris J. Frangieh et al.   NATURE GENETICS

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

(2021) Yael C. Cohen et al.   NATURE MEDICINE

Single-Cell Proteomics

(2021) Luke F. Vistain et al.   TRENDS IN BIOCHEMICAL SCIENCES

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Dissection of intercellular communication using the transcriptome-based framework ICELLNET

(2021) Floriane Noël et al.   Nature Communications

Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer

(2021) Alexandre F. Aissa et al.   Nature Communications

Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data

(2021) Jiebiao Wang et al.   GENOME RESEARCH

A molecular single-cell lung atlas of lethal COVID-19

(2021) Johannes C. Melms et al.   NATURE

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

(2021) Toni M. Delorey et al.   NATURE

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

(2021) Akira Cortal et al.   NATURE BIOTECHNOLOGY

Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

(2021) Steven J. Wu et al.   NATURE BIOTECHNOLOGY

Single-cell multi-omics analysis of the immune response in COVID-19

(2021) Emily Stephenson et al.   NATURE MEDICINE

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

(2021) Ayse Bassez et al.   NATURE MEDICINE

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

(2021) Pablo Moreno et al.   NATURE METHODS

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

(2021) Li Song et al.   NATURE METHODS

Leveraging Single-Cell Sequencing for Chimeric Antigen Receptor T Cell Therapies

(2021) Rocío Castellanos-Rueda et al.   TRENDS IN BIOTECHNOLOGY

Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy

(2021) Gregory M Chen et al.   Cancer Discovery

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models

(2021) Martin Treppner et al.   Scientific Reports

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Likelihood-based deconvolution of bulk gene expression data using single-cell references

(2021) Dan D. Erdmann-Pham et al.   GENOME RESEARCH

A single-cell tumor immune atlas for precision oncology

(2021) Paula Nieto et al.   GENOME RESEARCH

T cells and monocyte-derived myeloid cells mediate immunotherapy-related hepatitis in a mouse model

(2021) Heather P. Llewellyn et al.   JOURNAL OF HEPATOLOGY

Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics

(2021) Tito Candelli et al.   LEUKEMIA

Cycling cancer persister cells arise from lineages with distinct programs

(2021) Yaara Oren et al.   NATURE

Clonal fitness inferred from time-series modelling of single-cell cancer genomes

(2021) Sohrab Salehi et al.   NATURE

Single-cell proteomics takes centre stage

(2021) Jeffrey M. Perkel   NATURE

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing

(2021) Michael VanInsberghe et al.   NATURE

Single-cell measurement of higher-order 3D genome organization with scSPRITE

(2021) Mary V. Arrastia et al.   NATURE BIOTECHNOLOGY

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19

(2021) Jihoon W. Lee et al.   NATURE BIOTECHNOLOGY

A single-cell and spatially resolved atlas of human breast cancers

(2021) Sunny Z. Wu et al.   NATURE GENETICS

The Emerging Role of the Innate Immune Response in Idiosyncratic Drug Reactions

(2021) Samantha Christine Sernoskie et al.   PHARMACOLOGICAL REVIEWS

Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response

(2021) Yuping Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition

(2021) Karol Nowicki-Osuch et al.   SCIENCE

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

(2021) Daniel Dar et al.   SCIENCE

Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis

(2021) Xiannian Zhang et al.   Nature Communications

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

(2021) Robrecht Cannoodt et al.   Nature Communications

Single-cell sequencing of immune cells from anticitrullinated peptide antibody positive and negative rheumatoid arthritis

(2021) Xunyao Wu et al.   Nature Communications

Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells

(2021) Sarah M. Hücker et al.   Nature Communications

Single-cell RNA sequencing of peripheral blood mononuclear cells from acute Kawasaki disease patients

(2021) Zhen Wang et al.   Nature Communications

Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma

(2021) Yun-Fan Sun et al.   Nature Communications

Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets

(2021) Ian A. Taukulis et al.   Frontiers in Molecular Neuroscience

Multiplexing Methods for Simultaneous Large‐Scale Transcriptomic Profiling of Samples at Single‐Cell Resolution

(2021) Junyun Cheng et al.   Advanced Science

Machine learning for perturbational single-cell omics

(2021) Yuge Ji et al.   Cell Systems

Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease

(2021) Pingping Wang et al.   Cell Discovery

Credentialing and Pharmacologically Targeting PTP4A3 Phosphatase as a Molecular Target for Ovarian Cancer

(2021) John S. Lazo et al.   Biomolecules

Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma

(2021) Alexander Bondoc et al.   Communications Biology

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

(2021) Yuanyuan Zhang et al.   CANCER CELL

Charting the tumor antigen maps drawn by single-cell genomics

(2021) Caleb A. Lareau et al.   CANCER CELL

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

(2021) Andrew M. Leader et al.   CANCER CELL

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma

(2021) Chloé B. Steen et al.   CANCER CELL

Expression of chimeric antigen receptor therapy targets detected by single-cell sequencing of normal cells may contribute to off-tumor toxicity

(2021) Ying Jing et al.   CANCER CELL

Complement activation induces excessive T cell cytotoxicity in severe COVID-19

(2021) Philipp Georg et al.   CELL

Atlas of clinically distinct cell states and ecosystems across human solid tumors

(2021) Bogdan A. Luca et al.   CELL

A single-cell atlas of chromatin accessibility in the human genome

(2021) Kai Zhang et al.   CELL

New frontiers in single-cell genomics

(2021) Nicholas E. Navin et al.   GENOME RESEARCH

Human neocortical expansion involves glutamatergic neuron diversification

(2021) Jim Berg et al.   NATURE

Hybrid immunity improves B cells and antibodies against SARS-CoV-2 variants

(2021) Emanuele Andreano et al.   NATURE

Single-cell immunology of SARS-CoV-2 infection

(2021) Yuan Tian et al.   NATURE BIOTECHNOLOGY

Multiscale and integrative single-cell Hi-C analysis with Higashi

(2021) Ruochi Zhang et al.   NATURE BIOTECHNOLOGY

A single-cell transcriptomic landscape of the lungs of patients with COVID-19

(2021) Si Wang et al.   NATURE CELL BIOLOGY

Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response

(2021) Kevin C. Johnson et al.   NATURE GENETICS

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

(2021) Ronan Chaligne et al.   NATURE GENETICS

High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells

(2021) Ke-Yue Ma et al.   NATURE IMMUNOLOGY

BNT162b2 vaccine induces divergent B cell responses to SARS-CoV-2 S1 and S2

(2021) R. Camille Brewer et al.   NATURE IMMUNOLOGY

Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19

(2021) Sarthak Sinha et al.   NATURE MEDICINE

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Single-cell metabolomics hits its stride

(2021) Caroline Seydel   NATURE METHODS

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

Multiple rereads of single proteins at single–amino acid resolution using nanopores

(2021) Henry Brinkerhoff et al.   SCIENCE

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy

(2021) Teresa G. Krieger et al.   Nature Communications

Single-cell transcriptomic analysis of the tumor ecosystems underlying initiation and progression of papillary thyroid carcinoma

(2021) Weilin Pu et al.   Nature Communications

Longitudinal single-cell analysis of a myeloma mouse model identifies subclonal molecular programs associated with progression

(2021) Danielle C. Croucher et al.   Nature Communications

Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

(2021) Zhijian Li et al.   Nature Communications

Dual checkpoint blockade of CD47 and PD-L1 using an affinity-tuned bispecific antibody maximizes antitumor immunity

(2021) Shih-Hsun Chen et al.   Journal for ImmunoTherapy of Cancer

Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

(2021) Davide Simone et al.   Communications Biology

Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018

(2020) Olivier J. Wouters et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

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

(2020) Ido Yofe 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

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

(2020) Jong-Eun Park et al.   SCIENCE

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

(2020) Orit Rozenblatt-Rosen et al.   CELL

How repertoire data is changing antibody science

(2020) Claire Marks et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Consensus molecular subtype (CMS) as a novel integral biomarker in colorectal cancer: A phase II trial of bintrafusp alfa in CMS4 metastatic CRC.

(2020) Amir Mehrvarz Sarshekeh et al.   JOURNAL OF CLINICAL ONCOLOGY

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

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

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

(2020) Patryk Jarnot et al.   NUCLEIC ACIDS RESEARCH

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

(2020) Anniina Färkkilä et al.   Nature Communications

Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

(2020) Yann Kieffer et al.   Cancer Discovery

SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing

(2020) Rujin Wang et al.   Cell Systems

From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases

(2020) Eddie Cano-Gamez et al.   Frontiers in Genetics

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

(2020) Yonatan Katzenelenbogen et al.   CELL

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

(2020) Junbin Qian et al.   CELL RESEARCH

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

(2020) Bo Li et al.   NATURE METHODS

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF MEDICINE

Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction

(2020) Fangda Song et al.   Nature Communications

Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies

(2020) Kevin R. Parker et al.   CELL

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

(2020) Sai Ma et al.   CELL

Single-cell sequencing techniques from individual to multiomics analyses

(2020) Yukie Kashima et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

High-Fidelity Drug Induced Liver Injury Screen Using Human PSC-derived Organoids

(2020) Tadahiro Shinozawa et al.   GASTROENTEROLOGY

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Characteristics of anti-CD19 CAR T cell infusion products associated with efficacy and toxicity in patients with large B cell lymphomas

(2020) Qing Deng et al.   NATURE MEDICINE

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

(2020) James M. McFarland et al.   Nature Communications

Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis

(2020) Frank Penkava et al.   Nature Communications

A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response

(2020) Donghai Xiong et al.   Nature Communications

Single cell transcriptomics comes of age

(2020) Sarah Aldridge et al.   Nature Communications

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

(2020) Nicola Thrupp et al.   Cell Reports

Single-Cell Transcriptomic Analysis Reveals BCMA CAR-T Cell Dynamics in a Patient with Refractory Primary Plasma Cell Leukemia

(2020) Xue Li et al.   MOLECULAR THERAPY

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

(2020) Xin Jin et al.   SCIENCE

CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies

(2020) Dongrui Wang et al.   Cancer Discovery

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning

(2020) Ozlem Muslu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

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

(2019) Xuran Wang et al.   Nature Communications

Molecular signatures of multiple myeloma progression through single cell RNA-Seq

(2019) Jin Sung Jang et al.   Blood Cancer Journal

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Cell lineage and communication network inference via optimization for single-cell transcriptomics

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Cell-level somatic mutation detection from single-cell RNA sequencing

(2019) Trung Nghia Vu et al.   BIOINFORMATICS

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

(2019) Fan Zhang et al.   NATURE IMMUNOLOGY

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways

(2019) Evan Der et al.   NATURE IMMUNOLOGY

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

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

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

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

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

Model-based understanding of single-cell CRISPR screening

(2019) Bin Duan et al.   Nature Communications

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

(2019) Danuta R. Gawel et al.   Genome Medicine

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

(2019) Jerome C. Martin et al.   CELL

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

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

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance

(2019) Lovelace J. Luquette et al.   Nature Communications

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak et al.   Nature Communications

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

(2019) Allegra A. Petti et al.   Nature Communications

Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy

(2019) Claudia X Dominguez et al.   Cancer Discovery

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data

(2019) Erica A.K. DePasquale et al.   Cell Reports

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

(2019) Ian Setliff et al.   CELL

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

(2019) Caroline S. Jansen et al.   NATURE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

(2018) Simone Rizzetto et al.   BIOINFORMATICS

Minimal/measurable residual disease in AML: a consensus document from the European LeukemiaNet MRD Working Party

(2018) Gerrit J. Schuurhuis et al.   BLOOD

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

(2018) Kelly Street et al.   BMC GENOMICS

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives

(2018) Alessandra Dal Molin et al.   BRIEFINGS IN BIOINFORMATICS

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation

(2018) Monika M. Gladka et al.   CIRCULATION

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

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