MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

doi:10.1186/s13059-015-0844-5

PMID: 26653891DOI: 10.1186/s13059-015-0844-5Dec 15, 2015

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Genome Biology

Greg FinakR Gottardo

Abstract

Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features. We argue that the cellular detection rate, the fraction of genes expressed in a cell, should be adjusted for as a source of nuisance variation. Our model provides gene set enrichment analysis tailored to single-cell data. It provides insights into how networks of co-expressed genes evolve across an experimental treatment. MAST is available at https://github.com/RGLab/MAST .

References

Combining independent p values: extensions of the Stouffer and binomial methods

Feb 24, 2001·Psychological Methods·R B Darlington, A F Hayes

Stochastic gene expression in a single cell

Aug 17, 2002·Science·Michael ElowitzPeter S Swain

Bioconductor: open software development for computational biology and bioinformatics

Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth

Stochastic gene expression: from single molecules to the proteome

Feb 24, 2007·Current Opinion in Genetics & Development·Benjamin B Kaufmann, Alexander van Oudenaarden

Profound enhancement of the IL-12/IL-18 pathway of IFN-gamma secretion in human CD8+ memory T cell subsets via IL-15

Apr 4, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Ronald B Smeltz

Imaging individual mRNA molecules using multiple singly labeled probes

Sep 23, 2008·Nature Methods·Arjun RajSanjay Tyagi

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Feb 5, 2009·BMC Bioinformatics·Eran EdenZohar Yakhini

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Nov 17, 2009·Bioinformatics·Mark D RobinsonGordon K Smyth

Differential expression analysis for sequence count data

Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

Nov 6, 2010·Nucleic Acids Research·Judith A BlakeMouse Genome Database Group

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Aug 6, 2011·BMC Bioinformatics·Bo Li, Colin N Dewey

Camera: a competitive gene set test accounting for inter-gene correlation

May 29, 2012·Nucleic Acids Research·Di Wu, Gordon K Smyth

Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells

Oct 30, 2012·Cell·Samuel MargueratJürg Bähler

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

Dec 26, 2012·Bioinformatics·Andrew N McDavidR Gottardo

Bystander-activated memory CD8 T cells control early pathogen load in an innate-like, NKG2D-dependent manner

Mar 26, 2013·Cell Reports·Talyn ChuMartin Prlic

Egr2 induced during DC development acts as an intrinsic negative regulator of DC immunogenicity

May 30, 2013·European Journal of Immunology·Mohammad Alam MiahYong-Soo Bae

Accounting for technical noise in single-cell RNA-seq experiments

Sep 24, 2013·Nature Methods·Philip BrenneckeMarcus G Heisler

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing

Dec 5, 2013·Genome Research·Georgi K MarinovBarbara J Wold

Genetic determinants and cellular constraints in noisy gene expression

Dec 7, 2013·Science·Alvaro Sanchez, Ido Golding

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

Dec 18, 2013·Nature Immunology·Shuzhao LiBali Pulendran

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth

Distinct requirements for activation of NKT and NK cells during viral infection

Mar 19, 2014·The Journal of Immunology : Official Journal of the American Association of Immunologists·Aaron J TyznikChris A Benedict

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

Mar 25, 2014·Nature Biotechnology·Cole TrapnellJohn L Rinn

Emergence of reproducible spatiotemporal activity during motor learning

May 9, 2014·Nature·Andrew J PetersTakaki Komiyama

Bayesian approach to single-cell differential expression analysis

May 20, 2014·Nature Methods·Peter KharchenkoDavid T Scadden

Normalization of RNA-seq data using factor analysis of control genes or samples

Aug 26, 2014·Nature Biotechnology·Davide RissoSandrine Dudoit

svaseq: removing batch effects and other unwanted noise from sequencing data

Oct 9, 2014·Nucleic Acids Research·Jeffrey T Leek

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Jan 20, 2015·Nature Biotechnology·Florian BuettnerOliver Stegle

Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms

Apr 14, 2015·Molecular Cell·Olivia Padovan-MerharArjun Raj

Citations

Design and computational analysis of single-cell RNA-sequencing experiments

Apr 8, 2016·Genome Biology·Rhonda Bacher, Christina Kendziorski

Beta-Poisson model for single-cell RNA-seq data analyses

May 7, 2016·Bioinformatics·Trung Nghia VuYudi Pawitan

Distinct activation thresholds of human conventional and innate-like memory T cells

Jun 23, 2016·JCI Insight·Chloe K SlichterMartin Prlic

SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation

Jun 10, 2016·BMC Bioinformatics·Hirotaka Matsumoto, Hisanori Kiryu

Diffusion pseudotime robustly reconstructs lineage branching

Aug 30, 2016·Nature Methods·Laleh HaghverdiFabian J Theis

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

Oct 7, 2016·Frontiers in Genetics·Olivier B PoirionLana Garmire

Exploring viral infection using single-cell sequencing

Nov 7, 2016·Virus Research·Sylvie RatoAngela Ciuffi

Revealing the vectors of cellular identity with single-cell genomics

Nov 9, 2016·Nature Biotechnology·Allon WagnerNir Yosef

Batch effects and the effective design of single-cell gene expression studies

Jan 4, 2017·Scientific Reports·Po-Yuan TungYoav Gilad

Single-cell mRNA quantification and differential analysis with Census

Jan 24, 2017·Nature Methods·Xiaojie QiuCole Trapnell

Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling

Jul 22, 2016·PLoS Computational Biology·Manikandan NarayananJohn S Tsang

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

May 2, 2017·Nature Biotechnology·Abbas H RizviRaul Rabadan

ROTS: An R package for reproducibility-optimized statistical testing

May 26, 2017·PLoS Computational Biology·Tomi SuomiLaura L Elo

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

Mar 30, 2017·Genome Biology·Peijie LinJoshua W K Ho

Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells

Jun 28, 2017·PLoS Pathogens·Diane L BoltonMario Roederer

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

May 26, 2017·Bioinformatics·Vincent GardeuxBart Deplancke

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

Jul 4, 2017·PloS One·Chengchen ZhaoYong Zhang

Identifying cell populations with scRNASeq

Jul 18, 2017·Molecular Aspects of Medicine·Tallulah S Andrews, Martin Hemberg

Bias, robustness and scalability in single-cell differential expression analysis

Feb 27, 2018·Nature Methods·Charlotte Soneson, Mark D Robinson

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

Mar 24, 2017·Biostatistics·Aaron T L Lun, John C Marioni

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

Dec 6, 2017·Genes·Yuan CaoZhongming Zhao

powsimR: power analysis for bulk and single cell RNA-seq experiments

Oct 17, 2017·Bioinformatics·Beate ViethInes Hellmann

Missing data and technical variability in single-cell RNA-sequencing experiments

Nov 10, 2017·Biostatistics·Stephanie C HicksRafael A Irizarry

A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data

Nov 16, 2017·Nucleic Acids Research·Martin BarronJun Li

Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data

Oct 17, 2017·Nucleic Acids Research·Cheng JiaNancy R Zhang

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

Nov 9, 2017·Genome Biology·Florian BuettnerOliver Stegle

Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes

Jun 2, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Karen CerosalettiPeter S Linsley

Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations

Jun 4, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Maxmillian MpinaMartin Prlic

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics

Nov 29, 2017·Scientific Reports·Nadia BoufaiedAxel A Thomson

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis

Jan 21, 2018·Science Immunology·Veena S PatilPandurangan Vijayanand

A single-cell survey of the small intestinal epithelium

Nov 17, 2017·Nature·Adam L HaberAviv Regev

Two-phase differential expression analysis for single cell RNA-seq

Apr 25, 2018·Bioinformatics·Zhijin WuHao Wu

Loss of mTORC1 signaling alters pancreatic α cell mass and impairs glucagon secretion

Nov 7, 2017·The Journal of Clinical Investigation·Nadejda BozadjievaErnesto Bernal-Mizrachi

bigSCale: an analytical framework for big-scale single-cell data

May 5, 2018·Genome Research·Giovanni IaconoHolger Heyn

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

Apr 28, 2018·Science·Daniel E WagnerAllon M Klein

Dissection of progenitor compartments resolves developmental trajectories in B-lymphopoiesis

Jun 15, 2018·The Journal of Experimental Medicine·Christina T JensenMikael Sigvardsson

Understanding development and stem cells using single cell-based analyses of gene expression

Jan 5, 2017·Development·Pavithra KumarPatrick Cahan

iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data

Jul 10, 2018·Bioinformatics·Mitulkumar V Patel

The Human Cell Atlas: Technical approaches and challenges

Nov 2, 2017·Briefings in Functional Genomics·Chung-Chau HonMichael J T Stubbington

Application of single-cell sequencing in human cancer

Nov 7, 2017·Briefings in Functional Genomics·Mattias Rantalainen

Quantitative single-cell transcriptomics

Mar 27, 2018·Briefings in Functional Genomics·Christoph ZiegenhainWolfgang Enard

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

Aug 11, 2018·PLoS Computational Biology·Luyi TianMatthew E Ritchie

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

Nov 14, 2017·ELife·Julien RacleDavid Gfeller

Computational approaches for high-throughput single-cell data analysis

Jul 31, 2018·The FEBS Journal·Helena Todorov, Yvan Saeys

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

Sep 5, 2018·PLoS Computational Biology·Davide RissoElizabeth Purdom

T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis

Jun 2, 2018·Arthritis & Rheumatology·Daniel R LuWilliam H Robinson

Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution

Apr 28, 2018·Circulation Research·Robert C WirkaThomas Quertermous

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

Oct 30, 2018·Nature Biotechnology·Qian ZhuGuo-Cheng Yuan

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Nov 3, 2018·Science·Jeffrey R MoffittXiaowei Zhuang

Helios is a key transcriptional regulator of outer hair cell maturation

Nov 23, 2018·Nature·Lauren ChessumRonna Hertzano

Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

Nov 14, 2018·Nature Medicine·Ana Mendanha FalcãoGonçalo Castelo-Branco

Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes

Oct 12, 2018·Journal of Virology·Daniel P DepledgeAngus C Wilson

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes

Nov 10, 2018·ELife·Diego BalboaTimo Otonkoski

ACDtool: a web-server for the generic analysis of large data sets of counts

Jul 19, 2018·Bioinformatics·Jean-Michel Claverie, Thi Ngan Ta

Optimal Gene Filtering for Single-Cell data (OGFSC)-a gene filtering algorithm for single-cell RNA-seq data

Dec 12, 2018·Bioinformatics·Jie HaoZe-Guang Han

A general and flexible method for signal extraction from single-cell RNA-seq data

Jan 20, 2018·Nature Communications·Davide RissoJean-Philippe Vert

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Jan 31, 2018·Genome Biology·Enrique Martin-GayoXu G Yu

SCANPY: large-scale single-cell gene expression data analysis

Feb 8, 2018·Genome Biology·F Alexander WolfFabian J Theis

ClusterMap: Compare multiple Single Cell RNA-Seq datasets across different experimental conditions

Jan 17, 2019·Bioinformatics·Xin GaoHua Li

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Feb 27, 2018·Genome Biology·Koen Van den BergeLieven Clement

Altered human oligodendrocyte heterogeneity in multiple sclerosis

Feb 13, 2019·Nature·Sarah JäkelGonçalo Castelo-Branco

Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints.

Dec 29, 2018·Blood·Noemi AndorHanlee P Ji

An accurate and robust imputation method scImpute for single-cell RNA-seq data

Mar 10, 2018·Nature Communications·Wei Vivian Li, Jingyi Jessica Li

An interpretable framework for clustering single-cell RNA-Seq datasets

Mar 11, 2018·BMC Bioinformatics·Jesse M ZhangDavid N Tse

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

Mar 21, 2019·PLoS Genetics·Kathryn J GrivePaula E Cohen

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

Sep 28, 2016·Scientific Reports·Martin Barron, Jun Li

GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection

May 12, 2018·Genome Biology·Daphne Tsoucas, Guo-Cheng Yuan

Machine learning and statistical methods for clustering single-cell RNA-sequencing data

Jun 28, 2019·Briefings in Bioinformatics·Raphael PetegrossoRui Kuang

Single-cell technologies in reproductive immunology

Jun 18, 2019·American Journal of Reproductive Immunology : AJRI·Jessica VazquezAleksandar K Stanic

DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data

Jun 15, 2019·Bioinformatics·Chengzhong YeAgus Salim

Neuronal vulnerability and multilineage diversity in multiple sclerosis

Jul 19, 2019·Nature·Lucas SchirmerDavid H Rowitch

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets

Jun 22, 2018·Molecular Systems Biology·Ricard ArgelaguetOliver Stegle

Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures

Sep 13, 2018·EMBO Reports·Carole SousaAlessandro Michelucci

Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy

Sep 4, 2019·Nature Communications·Sung Pil HongLuca Magnani

Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome

Sep 4, 2019·Nature Communications·Chao YangSubramaniam Malarkannan

A divergent population of autoantigen-responsive CD4+ T cells in infants prior to β cell autoimmunity

Feb 24, 2017·Science Translational Medicine·Anne-Kristin HeningerEzio Bonifacio

ascend: R package for analysis of single-cell RNA-seq data

Sep 11, 2019·GigaScience·Anne SenabouthJoseph Powell

Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease

Aug 14, 2019·Annals of the Rheumatic Diseases·Eleanor ValenziRobert Lafyatis

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

Feb 27, 2018·Briefings in Bioinformatics·Shun H YipJunwen Wang

scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data

Sep 11, 2019·Genome Biology·Ruoxin Li, Gerald Quon

Dissecting the human immune system with single cell RNA sequencing technology

Dec 6, 2019·Journal of Leukocyte Biology·Gang XuZheng Zhang

Detection of differentially expressed genes in discrete single-cell RNA sequencing data using a hurdle model with correlated random effects

Apr 23, 2019·Biometrics·Michael SekulaSusmita Datta

ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them

Jan 17, 2020·Database : the Journal of Biological Databases and Curation·Erik CzipaEndre Barta

Evaluating genetic causes of azoospermia: What can we learn from a complex cellular structure and single-cell transcriptomics of the human testis?

Jan 18, 2020·Human Genetics·Samuele SoraggiKristian Almstrup

Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospective

Dec 4, 2019·Current Eye Research·Darin ZertiMajlinda Lako

The human tissue-resident CCR5+ T cell compartment maintains protective and functional properties during inflammation

Dec 6, 2019·Science Translational Medicine·Amanda S Woodward DavisMartin Prlic

Semblance: An empirical similarity kernel on probability spaces

Dec 17, 2019·Science Advances·Divyansh Agarwal, Nancy R Zhang

CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq.

Feb 11, 2020·Journal of Translational Medicine·Logan A WalkerPearlly Yan

Anatomical and single-cell transcriptional profiling of the murine habenular complex

Feb 12, 2020·ELife·Michael L WallaceBernardo L Sabatini

netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis

Jan 30, 2020·Genome Research·Rebecca ElyanowBenjamin J Raphael

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

Feb 22, 2020·ELife·Anastasia A MinervinaAleksandra M Walczak

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer's disease

Jan 15, 2020·Nature Medicine·Yingyue ZhouMarco Colonna

MAFG-driven astrocytes promote CNS inflammation

Feb 14, 2020·Nature·Michael A WheelerFrancisco J Quintana

Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes

Apr 7, 2020·PLoS Biology·Noriki FujimotoLothar C Dieterich

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response

Apr 7, 2020·PLoS Pathogens·Dylan H de VriesMonique G P van der Wijst

Prediction of condition-specific regulatory genes using machine learning

Apr 25, 2020·Nucleic Acids Research·Qi SongSong Li

Dynamic changes in the regulatory T-cell heterogeneity and function by murine IL-2 mutein

Apr 10, 2020·Life Science Alliance·Daniel R LuHyewon Phee

BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization

May 12, 2020·Nucleic Acids Research·Federico TavernaPeter Carmeliet

ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data

Feb 14, 2020·Bioinformatics·Wenfei ZhangEthan Y Xu

Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection

Jan 16, 2020·MBio·Chang WangElodie Ghedin

Challenges and emerging directions in single-cell analysis

May 10, 2017·Genome Biology·Guo-Cheng YuanItay Tirosh

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

Jul 3, 2016·Genome Biology·Lan JiangGuo-Cheng Yuan

Generation of mesenchyme free intestinal organoids from human induced pluripotent stem cells

Jan 12, 2020·Nature Communications·Aditya MithalGustavo Mostoslavsky

Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth

Dec 4, 2019·Nature Communications·Jennifer E CowanAvinash Bhandoola

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

Jun 7, 2019·Nature·Silvia VelascoPaola Arlotta

PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing

Apr 30, 2020·Bioinformatics·Hyundoo Jeong, Zhandong Liu

Identification of amygdala-expressed genes associated with autism spectrum disorder

May 29, 2020·Molecular Autism·Maria Jesus HerreroJoshua G Corbin

Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium

Jul 4, 2019·Nature Communications·Raphael BrandtMarkus Morkel

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection.

Jul 3, 2020·PLoS Pathogens·Jiayi SunChristopher B Brooke

Single cell RNA sequencing identifies an early monocyte gene signature in acute respiratory distress syndrome

Jun 20, 2020·JCI Insight·Yale JiangPrabir Ray

Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome

Jul 1, 2020·The Journal of Experimental Medicine·Antony B HolmesKatia Basso

Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories

Aug 1, 2020·The Journal of Experimental Medicine·Kirby D JohnsonEmery H Bresnick

Stromal cell diversity associated with immune evasion in human triple-negative breast cancer

Aug 14, 2020·The EMBO Journal·Sunny Z WuAlexander Swarbrick

Identification and characterization of cellular heterogeneity within the developing renal interstitium

Jun 27, 2020·Development·Alicia R EnglandThomas Carroll

scDoc: correcting drop-out events in single-cell RNA-seq data.

May 5, 2020·Bioinformatics·Di RanLingling An

Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data

Sep 10, 2020·BMC Genomics·Siamak Zamani DadanehXiaoning Qian

Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease

Aug 18, 2020·Human Molecular Genetics·Samuel MorabitoVivek Swarup

Integrated Skin Transcriptomics and Serum Multiplex Assays Reveal Novel Mechanisms of Wound Healing in Diabetic Foot Ulcers

Aug 9, 2020·Diabetes·Georgios TheocharidisAristidis Veves

Single-cell transcriptomic profiling of the aging mouse brain.

Sep 26, 2019·Nature Neuroscience·Methodios XimerakisLee L Rubin

Cisplatin-induced peripheral neuropathy is associated with neuronal senescence-like response.

Jul 1, 2020·Neuro-oncology·Aina CallsJordi Bruna

Functional interpretation of single cell similarity maps

Sep 28, 2019·Nature Communications·David DeTomasoNir Yosef

TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data.

Sep 30, 2020·Genetic Epidemiology·Eric Van BurenYun Li

m6A RNA methylation impacts fate choices during skin morphogenesis

Aug 28, 2020·ELife·Linghe XiElaine Fuchs

Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses

May 11, 2019·The Journal of Experimental Medicine·Mélanie DurandElodie Segura

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

Jun 23, 2019·The Journal of Experimental Medicine·James ClarkePandurangan Vijayanand

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

Jan 16, 2017·Bioinformatics·Davis McCarthyQuin F Wills

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

Oct 27, 2016·Genome Biology·Keegan KorthauerChristina Kendziorski

Computational approaches for interpreting scRNA-seq data

May 20, 2017·FEBS Letters·Raghd RostomGozde Kar

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer

Aug 11, 2017·Nature Communications·Ruli GaoNicholas E Navin

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

Oct 17, 2017·Genome Research·Aaron T L LunJohn C Marioni

Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations

May 12, 2018·Diagnostics·Francesc Castro-GinerNicola Aceto

Human MAIT cells exit peripheral tissues and recirculate via lymph in steady state conditions

Apr 6, 2018·JCI Insight·Valentin VoilletMartin Prlic

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

Jun 20, 2018·BMC Bioinformatics·Shuonan Chen, Jessica C Mar

Experimental Considerations for Single-Cell RNA Sequencing Approaches

Sep 21, 2018·Frontiers in Cell and Developmental Biology·Quy H NguyenKai Kessenbrock

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type

Aug 14, 2018·Nucleic Acids Research·Junil KimKyoung Jae Won

Lineage dynamics of murine pancreatic development at single-cell resolution

Sep 27, 2018·Nature Communications·Lauren E ByrnesJulie B Sneddon

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

Nov 18, 2018·Nature Protocols·Atefeh LafziHolger Heyn

SREBP1 drives Keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ERα breast cancer

May 11, 2019·Nature Communications·Ylenia PeroneLuca Magnani

Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia

May 12, 2019·Blood Advances·Jesus Izaguirre-CarbonellNan Zhu

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development

Jul 28, 2019·Disease Models & Mechanisms·Claire NashAxel A Thomson

Mono- and multi-nucleated ventricular cardiomyocytes constitute a transcriptionally homogenous cell population

Aug 11, 2019·Basic Research in Cardiology·Michail YekelchykThomas Braun

Molecular and anatomical organization of the dorsal raphe nucleus

Aug 15, 2019·ELife·Kee Wui HuangBernardo L Sabatini

Characterizing Human Cell Types and Tissue Origin Using the Benford Law

Sep 1, 2019·Cells·Sne Morag, Mali Salmon-Divon

A statistical simulator scDesign for rational scRNA-seq experimental design

Sep 13, 2019·Bioinformatics·Wei Vivian Li, Jingyi Jessica Li

Clustering-independent analysis of genomic data using spectral simplicial theory

Nov 23, 2019·PLoS Computational Biology·Kiya W GovekPablo G Camara

Droplet scRNA-seq is not zero-inflated

Jan 16, 2020·Nature Biotechnology·Valentine Svensson

Exploring and analysing single cell multi-omics data with VDJView

Feb 20, 2020·BMC Medical Genomics·Jerome SamirFabio Luciani

Single-Cell RNA Sequencing of the Cardiovascular System: New Looks for Old Diseases

Jan 11, 2020·Frontiers in Cardiovascular Medicine·Farhan ChaudhryPhillip D Levy

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing

Feb 5, 2020·Frontiers in Genetics·Tian MouTrung Nghia Vu

Interstitial microRNA miR-214 attenuates inflammation and polycystic kidney disease progression

Mar 18, 2020·JCI Insight·Ronak LakhiaVishal Patel

Single-cell RNA sequencing identifies senescent cerebromicrovascular endothelial cells in the aged mouse brain

Apr 3, 2020·GeroScience·Tamas KissZoltan Ungvari

Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses

Apr 9, 2020·Frontiers in Cellular Neuroscience·Kee Wui Huang, Bernardo L Sabatini

Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes

Jan 22, 2020·Nature Microbiology·Ya-Ting WangHerbert W Virgin

Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells

Mar 17, 2020·Frontiers in Immunology·Amaia Martinez-UsatorrePedro Romero

Data-based RNA-seq simulations by binomial thinning

May 26, 2020·BMC Bioinformatics·David Gerard

Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies.

Mar 30, 2020·Nature Communications·Ying MaXiang Zhou

Cell Atlas of The Human Fovea and Peripheral Retina.

Jun 20, 2020·Scientific Reports·Wenjun YanJoshua R Sanes

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.

Jul 6, 2020·Communications Biology·Åsa Wallén-MackenzieÅsa K Björklund

Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature

May 15, 2020·ELife·Chao YangSubramaniam Malarkannan

Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Jun 3, 2020·Nature Methods·Daniel SchraivogelLars M Steinmetz

T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers.

May 13, 2020·Nature Medicine·Prabhu S ArunachalamBali Pulendran

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19

Jul 12, 2020·Science Immunology·Jeong Seok LeeEui-Cheol Shin

Metabolic plasticity of HIV-specific CD8+ T cells is associated with enhanced antiviral potential and natural control of HIV-1 infection

Jul 23, 2020·Nature Metabolism·Mathieu AnginAsier Sáez-Cirión

Distinct subnetworks of the thalamic reticular nucleus.

Jul 24, 2020·Nature·Yinqing LiGuoping Feng

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data

Aug 5, 2020·Genome Biology·Matteo CalgaroNicola Vitulo

Cell type prioritization in single-cell data.

Jul 22, 2020·Nature Biotechnology·Michael A SkinniderGrégoire Courtine

High-Resolution Transcriptomic Profiling of the Heart During Chronic Stress Reveals Cellular Drivers of Cardiac Fibrosis and Hypertrophy

Aug 17, 2020·Circulation·Micheal A McLellanAlexander R Pinto

Genetic mapping of etiologic brain cell types for obesity

Sep 22, 2020·ELife·Pascal N TimshelTune H Pers

Single Cell RNA-seq Data Analysis Reveals the Potential Risk of SARS-CoV-2 Infection Among Different Respiratory System Conditions

Sep 26, 2020·Frontiers in Genetics·Qiang ZhangLi Xiao

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

Mar 21, 2017·Nature Genetics·Huipeng LiShyam Prabhakar

SCnorm: robust normalization of single-cell RNA-seq data

Apr 19, 2017·Nature Methods·Rhonda BacherChristina Kendziorski

Normalizing single-cell RNA sequencing data: challenges and opportunities

May 16, 2017·Nature Methods·Catalina A VallejosJohn C Marioni

Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint

Jun 18, 2017·Frontiers in Genetics·Sören Müller, Aaron Diaz

Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes

Oct 21, 2017·Scientific Reports·Mengjie Chen, Xiang Zhou

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

Jun 8, 2017·Frontiers in Genetics·Alessandra Dal MolinBarbara Di Camillo

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics

Feb 20, 2018·Frontiers in Neuroscience·Hyobin Jeong, Vijay K Tiwari

Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis

Mar 10, 2018·Frontiers in Medicine·Francesc Castro-GinerNicola Aceto

Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data

Jun 24, 2018·Nature Communications·Kieran R Campbell, Christopher Yau

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm

Apr 18, 2018·Nature Communications·Hongxu DingAndrea Califano

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.

Jul 10, 2018·Gates Open Research·Greg FinakR Gottardo

SAVER: gene expression recovery for single-cell RNA sequencing

Jun 27, 2018·Nature Methods·Mo HuangNancy R Zhang

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

Aug 3, 2018·Nature·Daniel T MontoroJayaraj Rajagopal

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Jan 20, 2019·BMC Bioinformatics·Tianyu WangSheida Nabavi

Deterministic column subset selection for single-cell RNA-Seq

Jan 27, 2019·PloS One·Shannon R McCurdyLior Pachter

Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8+ T cell responses

Jun 28, 2019·Science Translational Medicine·Anthony E ZamoraPaul G Thomas

Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma

May 24, 2019·Cell Communication and Signaling : CCS·Dongsheng YuanTieliu Shi

Single Cell Profiling Reveals PTEN Overexpression in Influenza-Specific B cells in Aging HIV-infected individuals on Anti-retroviral Therapy

Feb 23, 2019·Scientific Reports·Lesley R de ArmasSavita Pahwa

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data

Jul 19, 2019·Genome Biology·Rebekka WegmannCaroline Gubser Keller

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

Apr 27, 2019·Frontiers in Genetics·Geng ChenTieliu Shi

Siah2 control of T-regulatory cells limits anti-tumor immunity

Jan 9, 2020·Nature Communications·Marzia ScortegagnaZe'ev A Ronai

Single-cell analysis reveals T cell infiltration in old neurogenic niches.

Jul 5, 2019·Nature·Ben W DulkenAnne Brunet

Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers

May 23, 2020·Nature Communications·John P SfakianosDavid J Mulholland

A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation

Jun 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yukiteru NakayamaIchiro Manabe

Chronic Immune Activation in Systemic Lupus Erythematosus and the Autoimmune PTPN22 Trp620 Risk Allele Drive the Expansion of FOXP3+ Regulatory T Cells and PD-1 Expression

Nov 30, 2019·Frontiers in Immunology·Ricardo C FerreiraJohn A Todd

Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm

May 5, 2020·Frontiers in Genetics·Liang ChenMinghua Deng

Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis

May 26, 2020·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Sofia B WingeKristian Almstrup

Prdm8 regulates pMN progenitor specification for motor neuron and oligodendrocyte fates by modulating Shh signaling response

Jul 19, 2020·Development·Kayt ScottBruce Appel

CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells.

Jul 16, 2020·Communications Biology·Rebeca Arroyo HorneroJoanna Hester

Aggregating transcript-level analyses for single-cell differential gene expression.

Jun 3, 2020·Nature Methods·Etienne BechtR Gottardo

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

Aug 5, 2020·Nature Medicine·Daniele CorridoniAlison Simmons

Uncovering the key dimensions of high-throughput biomolecular data using deep learning

Apr 2, 2020·Nucleic Acids Research·Shixiong ZhangKa-Chun Wong

A systematic evaluation of single-cell RNA-sequencing imputation methods

Aug 29, 2020·Genome Biology·Wenpin HouStephanie C Hicks

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Apr 17, 2016·Genome Biology·Catalina A VallejosJohn C Marioni

DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

May 26, 2017·BMC Bioinformatics·Zhuo WangYadong Wang

BCseq: accurate single cell RNA-seq quantification with bias correction

May 3, 2018·Nucleic Acids Research·Liang Chen, Sika Zheng

Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

May 5, 2018·Science·Maria Antonietta ToschesGilles Laurent

Gene expression distribution deconvolution in single-cell RNA sequencing

Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Jingshu WangNancy R Zhang

UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Jun 2, 2018·Genome Biology·Wenan ChenXiang Chen

Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway

Jul 4, 2018·Nature Communications·Tsing-Lee Tang-HuauElodie Segura

A practical guide to methods controlling false discoveries in computational biology

Jun 6, 2019·Genome Biology·Keegan KorthauerStephanie C Hicks

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

Nov 20, 2018·Nature Communications·Guangshuai JiaThomas Braun

Deep generative modeling for single-cell transcriptomics

Dec 7, 2018·Nature Methods·Romain LopezNir Yosef

A test metric for assessing single-cell RNA-seq batch correction

Dec 23, 2018·Nature Methods·Maren BüttnerFabian J Theis

scClustViz - Single-cell RNAseq cluster assessment and visualization

Apr 25, 2019·F1000Research·Brendan T Innes, Gary D Bader

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data

Oct 5, 2019·Bioinformatics·Wenhao TangVahid Shahrezaei

LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data

Aug 3, 2019·Nucleic Acids Research·Changlin WanChi Zhang

Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation

Feb 6, 2019·Nature Microbiology·Malika SaintSamuel Marguerat

The bone marrow microenvironment at single-cell resolution.

Apr 12, 2019·Nature·Anastasia N TikhonovaIannis Aifantis

Orchestrating single-cell analysis with Bioconductor

Dec 4, 2019·Nature Methods·Robert A AmezquitaStephanie C Hicks

Regenerative lineages and immune-mediated pruning in lung cancer metastasis.

Feb 12, 2020·Nature Medicine·Ashley M LaughneyJoan Massagué

Robust production of uniform human cerebral organoids from pluripotent stem cells

Apr 19, 2020·Life Science Alliance·Adam A SivitilliLiliana Attisano

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.

May 14, 2020·Nature Medicine·Mingfeng LiaoZheng Zhang

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

Sep 13, 2019·Bioinformatics·Hirak SarkarRob Patro

M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data

Dec 22, 2019·BMC Bioinformatics·Yu ZhangChi Zhang

A comparison of automatic cell identification methods for single-cell RNA sequencing data

Sep 11, 2019·Genome Biology·Tamim AbdelaalAhmed Mahfouz

Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma

Jun 14, 2020·Science Immunology·Grégory SeumoisPandurangan Vijayanand

Combinatorial prediction of marker panels from single-cell transcriptomic data

Oct 28, 2019·Molecular Systems Biology·Conor DelaneyMeromit Singer

Eleven grand challenges in single-cell data science

Feb 9, 2020·Genome Biology·David LähnemannAlexander Schönhuth

Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells

Sep 12, 2020·Cancers·Michal MarczykVignesh Gunasekharan

Selective LXR agonist DMHCA corrects retinal and bone marrow dysfunction in type 2 diabetes

Jul 10, 2020·JCI Insight·Cristiano P VieiraMaria B Grant

Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy

Jun 24, 2020·Proceedings of the National Academy of Sciences of the United States of America·Jason I GriffithsAndrea H Bild

An era of single-cell genomics consortia

Sep 16, 2020·Experimental & Molecular Medicine·Yoshinari AndoJay W Shin

Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq.

Apr 22, 2020·Oncoimmunology·Santiago J CarmonaDavid Gfeller

Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii

Jun 11, 2020·MBio·Suchita RastogiJohn C Boothroyd

Molecular design of hypothalamus development

Jun 6, 2020·Nature·Roman A RomanovTibor Harkany

Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer

Aug 1, 2020·Nature Communications·Aitziber BuquéLorenzo Galluzzi

Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue.

Jul 23, 2020·Nature Metabolism·Emily L GoldbergVishwa Deep Dixit

Splatter: simulation of single-cell RNA sequencing data

Sep 14, 2017·Genome Biology·Luke ZappiaAlicia Oshlack

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

Apr 3, 2018·Nature Biotechnology·Andrew ButlerRahul Satija

Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction

Dec 13, 2018·Nature Immunology·Sarah A DickSlava Epelman

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

Jan 22, 2019·Nature Methods·Vasilis NtranosLior Pachter

T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant

Jun 27, 2019·Nature Medicine·A G ChapuisP D Greenberg

Colonic epithelial cell diversity in health and inflammatory bowel disease

Mar 1, 2019·Nature·Kaushal ParikhAlison Simmons

VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies

Nov 14, 2018·Genome Biology·Mengjie Chen, Xiang Zhou

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

Jun 21, 2019·Molecular Systems Biology·Malte D Luecken, Fabian J Theis

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities

Nov 19, 2019·Frontiers in Microbiology·Qin MaSenthil Subramanian

Characterization of cell fate probabilities in single-cell data with Palantir

Mar 23, 2019·Nature Biotechnology·Manu SettyDana Pe'er

RESCUE: imputing dropout events in single-cell RNA-sequencing data

Jul 14, 2019·BMC Bioinformatics·Sam TracyRuben Dries

DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing

Jul 25, 2019·Scientific Reports·Christian T WohnhaasPatrick Baum

Single-Cell RNA-seq: Introduction to Bioinformatics Analysis

Jun 27, 2019·Current Protocols in Molecular Biology·Fei Ji, Ruslan I Sadreyev

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data

Aug 16, 2019·Genome Biology·Nelson Johansen, Gerald Quon

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

Jan 12, 2020·Nature Communications·Alyssa SheihCameron J Turtle

A systematic evaluation of single cell RNA-seq analysis pipelines

Oct 13, 2019·Nature Communications·Beate ViethInes Hellmann

Macrophage-tumor cell interaction promotes ATRT progression and chemoresistance

Dec 19, 2019·Acta Neuropathologica·Viktoria MelcherKornelius Kerl

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse.

Jul 17, 2020·Nature·Tabula Muris Consortium

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data.

Jul 1, 2020·BMC Genomics·Antony Kaspi, Mark Ziemann

Engineered immunogen binding to alum adjuvant enhances humoral immunity.

Feb 19, 2020·Nature Medicine·Tyson J MoyerDarrell J Irvine

Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

May 18, 2020·Scientific Reports·Maxime CaronGuillaume Bourque

M1hot tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer.

Jul 24, 2020·Journal for Immunotherapy of Cancer·Eva M Garrido-MartinTilman Sanchez-Elsner

Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human

May 1, 2020·Cell Discovery·Juanjuan ZhaoZheng Zhang

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

Jul 10, 2020·Genome Biology·Ralph PatrickKitty K Lo

Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq.

Jul 14, 2020·Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·R ZhongH Zhong

Transcriptomic and clonal characterization of T cells in the human central nervous system

Sep 20, 2020·Science Immunology·Jenna L PappalardoDavid A Hafler

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

Mar 27, 2019·Nature·Chee-Huat Linus EngLong Cai

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

Sep 26, 2018·Nature Communications·K G PaulsonA G Chapuis

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

May 18, 2019·Science·Dmitry VelmeshevArnold R Kriegstein

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Apr 10, 2019·Nature Methods·Carmen Bravo González-BlasStein Aerts

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing.

Jan 16, 2020·Genome Biology·Zilu ZhouNancy R Zhang

Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity

Jul 30, 2019·Frontiers in Genetics·Tao Zeng, Hao Dai

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Jan 21, 2020·Genome Biology·Koki TsuyuzakiItoshi Nikaido

Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis.

Jul 1, 2020·Nature Medicine·Stefano AliverniniMariola Kurowska-Stolarska

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

Dec 25, 2019·Genome Biology·F William TownesRafael A Irizarry

DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning

Jul 12, 2020·Genome Biology·Yao HeZhi Xie

Human fetal microglia acquire homeostatic immune-sensing properties early in development

Aug 1, 2020·Science·L KrachtB J L Eggen

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Aug 10, 2020·Genome Biology·Chenfei WangX Shirley Liu

Identification of differentially expressed genes in lung adenocarcinoma cells using single-cell RNA sequencing not detected using traditional RNA sequencing and microarray

Apr 25, 2020·Laboratory Investigation; a Journal of Technical Methods and Pathology·Zhencong ChenLijie Tan

Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control

Aug 26, 2020·Bioinformatics·Daniel Osorio, James J Cai

Limited proliferation capacity of aortic intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression

Sep 9, 2020·Nature Immunology·Jesse W WilliamsGwendalyn J Randolph

High-resolution label-free 3D mapping of extracellular pH of single living cells

Dec 8, 2019·Nature Communications·Yanjun ZhangYuri Korchev

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

Jan 30, 2020·BMC Genomics·Xiaohong LiEric C Rouchka

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Dec 25, 2019·Genome Biology·Christoph Hafemeister, Rahul Satija

Loss of the transcription factor MAFB limits β-cell derivation from human PSCs

Jun 4, 2020·Nature Communications·Ronan RussellMatthias Hebrok

Mesenchymal stem cells alleviate LPS-induced acute lung injury by inhibiting the proinflammatory function of Ly6C+ CD8+ T cells

Oct 8, 2020·Cell Death & Disease·Jiaqi ZhuHongcui Cao

SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation

Oct 9, 2020·NAR Genomics and Bioinformatics·Zhirui HuJun S Liu

Gli1+ mesenchymal stromal cells form a pathological niche to promote airway progenitor metaplasia in the fibrotic lung

Oct 14, 2020·Nature Cell Biology·Monica CassandrasTien Peng

Staphylococcus epidermidis Boosts Innate Immune Response by Activation of Gamma Delta T Cells and Induction of Perforin-2 in Human Skin

Oct 13, 2020·Frontiers in Immunology·Irena PastarNatasa Strbo

Single-Cell Transcriptomics of Engineered Cardiac Tissues From Patient-Specific Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveals Abnormal Developmental Trajectory and Intrinsic Contractile Defects in Hypoplastic Right Heart Syndrome.

Oct 17, 2020·Journal of the American Heart Association·Yin-Yu LamYiu-Fai Cheung

Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19

Oct 22, 2020·Scientific Reports·Anna A ValyaevaEugene V Sheval

A rank-based marker selection method for high throughput scRNA-seq data

Oct 25, 2020·BMC Bioinformatics·Alexander H S Vargo, Anna C Gilbert

RUNX1 marks a luminal castration resistant lineage established at the onset of prostate development

Oct 8, 2020·ELife·Renaud MevelGeorges Lacaud

Comprehensive mapping of the human cytokine gene regulatory network.

Nov 13, 2020·Nucleic Acids Research·Clarissa S SantosoJuan I Fuxman Bass

A Transcriptome-Based Drug Discovery Paradigm for Neurodevelopmental Disorders.

Nov 8, 2020·Annals of Neurology·Ryan S DhindsaDavid B Goldstein

Emergence of non-canonical parvalbumin-containing interneurons in hippocampus of a murine model of Type I lissencephaly

Nov 6, 2020·ELife·Tyler G EkinsChris J McBain

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

Nov 21, 2020·PLoS Biology·Alexandros SountoulidisChristos Samakovlis

Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency.

Sep 1, 2020·Nature·Jiasheng ZhangEric J Huang

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

Nov 28, 2020·Science·Xin JinPaola Arlotta

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

Dec 2, 2020·Nature Communications·Helena L CrowellMark D Robinson

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.

Dec 9, 2020·Nature Protocols·Tallulah S AndrewsMartin Hemberg

Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm

Nov 15, 2020·Science Advances·Philip A MuddAli H Ellebedy

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data

Dec 11, 2020·GigaScience·Lukas M SimonZhongming Zhao

Experimental and computational technologies to dissect the kidney at the single-cell level

Dec 18, 2020·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Christoph KuppeRafael Kramann

FLASH Irradiation Spares Lung Progenitor Cells and Limits the Incidence of Radio-induced Senescence

Dec 5, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Charles FouilladeVincent Favaudon

Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

Oct 23, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Imran G HousePaul A Beavis

Constitutive activation of cellular immunity underlies the evolution of resistance to infection in Drosophila

Dec 29, 2020·ELife·Alexandre B LeitãoFrancis M Jiggins

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Jan 7, 2021·Cell·David Fawkner-CorbettAlison Simmons

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis.

Jan 5, 2021·PeerJ·Daniel Dimitrov, Quan Gu

Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria.

Dec 10, 2020·Cell·Rui YangJean-Laurent Casanova

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

Jan 10, 2021·Cell Research·Luca MazzuranaJenny Mjösberg

Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes

Jan 8, 2021·Neuron·Ethan J ArmandEran A Mukamel

Single-cell RNA sequencing in vision research: Insights into human retinal health and disease

Jan 1, 2021·Progress in Retinal and Eye Research·Andrew P VoigtRobert F Mullins

Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients.

Dec 29, 2020·Cell Reports·Changfu YaoPeter Chen

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

Aug 22, 2020·Cell·Ashley MaynardTrever G Bivona

Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells

Oct 26, 2020·Cell Stem Cell·Finn J HawkinsDarrell N Kotton

Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells

Jan 7, 2021·Cell Reports·Daniel G BunisTrevor D Burt

A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing

Apr 24, 2020·Computational and Structural Biotechnology Journal·Wenan ChenXiang Chen

Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging.

Dec 4, 2020·Immunity·Denis A MogilenkoMaxim N Artyomov

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet

Aug 24, 2019·Cell·Chia-Wei ChengÖmer H Yilmaz

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

Jan 20, 2021·Nature Biotechnology·Ruli GaoNicholas E Navin

Ubiquitination of MHC Class II by March-I Regulates Dendritic Cell Fitness

Dec 16, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Hei Jung KimPaul A Roche

Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi.

Dec 30, 2020·Endocrinology·Melody Allensworth-JamesAngus M MacNicol

Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells.

Jan 20, 2021·Laboratory Investigation; a Journal of Technical Methods and Pathology·Bilian ZhuChaodong Wu

Whole-body senescent cell clearance alleviates age-related brain inflammation and cognitive impairment in mice.

Jan 21, 2021·Aging Cell·Mikolaj OgrodnikDiana Jurk

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling.

Jan 22, 2021·BMC Genomics·Tracy M YamawakiChi-Ming Li

Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques.

Dec 6, 2020·Cell·Timothy N HoangMirko Paiardini

Single-Cell RNA Sequencing Reveals Heterogeneity of Vascular Cells in Early Stage Murine Abdominal Aortic Aneurysm.

Jan 22, 2021·Arteriosclerosis, Thrombosis, and Vascular Biology·Huan YangBo Liu

A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines.

Jan 25, 2021·Genomics·Richa Nayak, Yasha Hasija

Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells.

Jan 23, 2021·Science Immunology·Anthony KusnadiChristian H Ottensmeier

A cell atlas of the chick retina based on single-cell transcriptomics.

Jan 5, 2021·ELife·Masahito YamagataJoshua R Sanes

Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma.

Jan 29, 2021·Frontiers in Genetics·Bo PangLin Pang

Transcriptional Diversity and Niche-Specific Distribution of Leukocyte Populations during Staphylococcus aureus Craniotomy-Associated Biofilm Infection.

Jan 10, 2021·The Journal of Immunology : Official Journal of the American Association of Immunologists·Amy L AldrichTammy Kielian

Increased APOE ε4 expression is associated with the difference in Alzheimer's disease risk from diverse ancestral backgrounds.

Feb 2, 2021·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Anthony J GriswoldJeffery M Vance

Binary Fate Choice between Closely Related Interneuronal Types Is Determined by a Fezf1-Dependent Postmitotic Transcriptional Switch

Dec 10, 2019·Neuron·Yi-Rong PengJoshua R Sanes

Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.

Nov 27, 2020·Cell Reports·Sherina MalkaniAfshin Beheshti

A new bioinformatics tool to recover missing gene expression in single-cell RNA sequencing data

Oct 1, 2020·Journal of Molecular Cell Biology·Jingyi Jessica Li

Simulation, power evaluation and sample size recommendation for single-cell RNA-seq.

Jul 3, 2020·Bioinformatics·Kenong SuHao Wu

Single-cell analysis identified lung progenitor cells in COVID-19 patients

Oct 24, 2020·Cell Proliferation·Zixian ZhaoWei Zuo

JOINT for large-scale single-cell RNA-sequencing analysis via soft-clustering and parallel computing

Jan 13, 2021·BMC Genomics·Tao Cui, Tingting Wang

Single-cell mapping of focused ultrasound-transfected brain.

Feb 3, 2021·Gene Therapy·A S MathewR J Price

IL36 is a critical upstream amplifier of neutrophilic lung inflammation in mice.

Feb 10, 2021·Communications Biology·Carolin K KossKarim C El Kasmi

Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation.

Feb 12, 2021·Science Advances·Juan Pablo LopezAlon Chen

A spinal organ of proprioception for integrated motor action feedback.

Feb 13, 2021·Neuron·Laurence D PictonAbdeljabbar El Manira

A molecular cell atlas of the human lung from single-cell RNA sequencing

Nov 20, 2020·Nature·Kyle J TravagliniMark A Krasnow

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

Dec 29, 2020·Nature Biotechnology·Saskia TrumpIrina Lehmann

A practical solution to pseudoreplication bias in single-cell studies.

Feb 4, 2021·Nature Communications·Kip D ZimmermanCarl D Langefeld

Exuberant fibroblast activity compromises lung function via ADAMTS4.

Oct 30, 2020·Nature·David F BoydPaul G Thomas

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy

Nov 17, 2020·Frontiers in Cell and Developmental Biology·Yanglan GanGuobing Zou

SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model

Jan 8, 2021·BMC Bioinformatics·Yan ZhengXuequn Shang

Gut-licensed IFNγ+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes.

Jan 8, 2021·Nature·Liliana M SanmarcoFrancisco J Quintana

Skin-resident innate lymphoid cells converge on a pathogenic effector state.

Feb 5, 2021·Nature·Piotr BieleckiRichard A Flavell

Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle.

Feb 7, 2021·Biochemical and Biophysical Research Communications·Ryuichi YamadaYoshiakira Kanai

Deep soft K-means clustering with self-training for single-cell RNA sequence data.

Feb 13, 2021·NAR Genomics and Bioinformatics·Liang ChenMinghua Deng

Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.

Feb 17, 2021·Nature Communications·Haohao WuFrançois Lallemend

Lung megakaryocytes display distinct transcriptional and phenotypic properties

Dec 23, 2020·Blood Advances·Anthony K YeungGeorge J Murphy

Normalizing single-cell RNA sequencing data with internal spike-in-like genes.

Feb 13, 2021·NAR Genomics and Bioinformatics·Li LinLiye Zhang

Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data.

Dec 19, 2020·Cell Systems·Nan Miles Xi, Jingyi Jessica Li

Optimal marker gene selection for cell type discrimination in single cell analyses.

Feb 21, 2021·Nature Communications·Bianca DumitrascuBarbara E Engelhardt

Identification of Novel Population-Specific Cell Subsets in Chinese Ulcerative Colitis Patients Using Single-Cell RNA Sequencing.

Feb 6, 2021·Cellular and Molecular Gastroenterology and Hepatology·Guang LiYang Li

Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.

Feb 21, 2021·Cell Stem Cell·Léo MachadoPhilippos Mourikis

Single-cell Clustering Based on Word Embedding and Nonparametric Methods

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