Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development

doi:10.1016/j.cell.2014.04.005

PMID: 24766814DOI: 10.1016/j.cell.2014.04.005Apr 29, 2014

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development

Cell

Sean C BendallDana Pe'er

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Abstract

Tissue regeneration is an orchestrated progression of cells from an immature state to a mature one, conventionally represented as distinctive cell subsets. A continuum of transitional cell states exists between these discrete stages. We combine the depth of single-cell mass cytometry and an algorithm developed to leverage this continuum by aligning single cells of a given lineage onto a unified trajectory that accurately predicts the developmental path de novo. Applied to human B cell lymphopoiesis, the algorithm (termed Wanderlust) constructed trajectories spanning from hematopoietic stem cells through to naive B cells. This trajectory revealed nascent fractions of B cell progenitors and aligned them with developmentally cued regulatory signaling including IL-7/STAT5 and cellular events such as immunoglobulin rearrangement, highlighting checkpoints across which regulatory signals are rewired paralleling changes in cellular state. This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer.

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Nov 2, 2017·Current Protocols in Immunology·Thomas Myles AshhurstNicholas Jonathan Cole King

TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis

Nov 11, 2019·Life Science Alliance·Reema BaskarSean C Bendall

Dissecting the human immune system with single cell RNA sequencing technology

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

Mind the Map: Technology Shapes the Myeloid Cell Space

Oct 23, 2019·Frontiers in Immunology·Patrick Günther, Joachim L Schultze

HiPPO and PANDA: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data

Dec 20, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Stefano PirròClaude Chelala

Autoreactive B cells in SLE, villains or innocent bystanders?

Oct 22, 2019·Immunological Reviews·Jennie A HamiltonJohn D Mountz

Visualizing structure and transitions in high-dimensional biological data

Dec 5, 2019·Nature Biotechnology·Kevin R MoonSmita Krishnaswamy

FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets.

Jan 15, 2020·Nature Protocols·Melissa E KoEli R Zunder

Discrete roles and bifurcation of PTEN signaling and mTORC1-mediated anabolic metabolism underlie IL-7-driven B lymphopoiesis

Feb 6, 2018·Science Advances·Hu ZengHongbo Chi

Learning Pathway Dynamics from Single-Cell Proteomic Data: A Comparative Study

Feb 27, 2020·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Kleio-Maria VerrouGeorgios Papoutsoglou

Inferring TF activation order in time series scRNA-Seq studies

Feb 19, 2020·PLoS Computational Biology·Chieh LinZiv Bar-Joseph

Application and utility of mass cytometry in vaccine development

Nov 3, 2017·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Patrick M ReevesMark C Poznansky

CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.

Feb 14, 2020·Nature Protocols·Wenjun KongSamantha A Morris

Uncovering axes of variation among single-cell cancer specimens.

Jan 15, 2020·Nature Methods·William S ChenSmita Krishnaswamy

Molecular natural history of breast cancer: Leveraging transcriptomics to predict breast cancer progression and aggressiveness

Mar 25, 2020·Cancer Medicine·Daniel J CookJens Nielsen

Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation

Dec 21, 2019·Bioinformatics·Luke A D HutchisonIsaac S Kohane

Profiling Cell Signaling Networks at Single-cell Resolution.

Mar 6, 2020·Molecular & Cellular Proteomics : MCP·Xiao-Kang Lun, Bernd Bodenmiller

Learning time-varying information flow from single-cell epithelial to mesenchymal transition data

Oct 30, 2018·PloS One·Smita KrishnaswamyBernd Bodenmiller

Intratumoral heterogeneity and clonal evolution in blood malignancies and solid tumors

Nov 8, 2017·Oncotarget·Ignacio VarelaAlejandra Sanjuan-Pla

Challenges and emerging directions in single-cell analysis

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

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution

Dec 8, 2019·Nature Communications·Loukia G KaracostaSylvia K Plevritis

Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data.

Apr 7, 2020·Current Protocols in Cytometry·Caroline E RoeJonathan M Irish

Advancing Stem Cell Research through Multimodal Single-Cell Analysis

Jan 15, 2020·Cold Spring Harbor Perspectives in Biology·Iwo Kucinski, Berthold Göttgens

Single-cell transcriptomics allows novel insights into aging and circadian processes.

Jul 8, 2020·Briefings in Functional Genomics·Sara S Fonseca CostaJürgen A Ripperger

TinGa: fast and flexible trajectory inference with Growing Neural Gas.

Jul 14, 2020·Bioinformatics·Helena TodorovYvan Saeys

A novel single-cell based method for breast cancer prognosis

Aug 25, 2020·PLoS Computational Biology·Xiaomei LiThuc Duy Le

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches

Aug 25, 2020·Briefings in Bioinformatics·Dohoon LeeSun Kim

Single-cell RNA sequencing in Drosophila: Technologies and applications

Sep 18, 2020·Wiley Interdisciplinary Reviews. Developmental Biology·Hongjie Li

Identification of Vaccine-Altered Circulating B Cell Phenotypes Using Mass Cytometry and a Two-Step Clustering Analysis

May 18, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·David PejoskiAnne-Sophie Beignon

The prospects of single-cell analysis in autoimmunity

Sep 2, 2020·Scandinavian Journal of Immunology·André SulenBergithe E Oftedal

Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis

Apr 4, 2017·Current Protocols in Molecular Biology·Nalin LeelatianJonathan M Irish

Human B-cell and progenitor stages as determined by probability state modeling of multidimensional cytometry data

Apr 9, 2015·Cytometry. Part B, Clinical Cytometry·C Bruce BagwellFrederic I Preffer

Cutting Edge: Redox Signaling Hypersensitivity Distinguishes Human Germinal Center B Cells

Jul 11, 2015·The Journal of Immunology : Official Journal of the American Association of Immunologists·Hannah G PolikowskyJonathan M Irish

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

Jul 30, 2016·Science·Naomi HabibAviv Regev

Cell size assays for mass cytometry

Oct 22, 2016·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Alan D SternMarc R Birtwistle

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

Jan 16, 2017·Bioinformatics·Davis J McCarthyQuin F Wills

Single-cell RNA-sequencing of the brain

Jun 10, 2017·Clinical and Translational Medicine·Raquel Cuevas-Diaz DuranJia Qian Wu

Reconstructing blood stem cell regulatory network models from single-cell molecular profiles

Jun 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·Fiona K HameyBerthold Göttgens

A Beginner's Guide to Analyzing and Visualizing Mass Cytometry Data

Dec 20, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Abigail K KimballEric T Clambey

Development of a Click-Chemistry Reagent Compatible with Mass Cytometry

Apr 29, 2018·Scientific Reports·Jessica ShakleeJop H van Berlo

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

Apr 3, 2018·Nature Biotechnology·Andrew ButlerRahul Satija

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

Nov 18, 2018·Nature Protocols·Atefeh LafziHolger Heyn

Semisoft clustering of single-cell data

Dec 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Lingxue ZhuKathryn Roeder

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

Jun 30, 2019·Development·Urs MayrPrisca Liberali

Proteomic tools and new insights for the study of B-cell precursor acute lymphoblastic leukemia

Sep 14, 2019·Hematology·Alí F Citalan-MadridMargarita L Martinez-Fierro

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Oct 22, 2019·European Journal of Immunology·Andrea CossarizzaArturo Zychlinsky

Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology

Jul 30, 2019·Frontiers in Immunology·Subarna PalitChristina E Zielinski

Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data

Jan 1, 2020·Scientific Reports·Bettina MiethDaniel Ziemek

Single-cell biology: beyond the sum of its parts

Jan 8, 2020·Nature Methods·Alexander F Schier

Single-Cell Approaches to Profile the Response to Immune Checkpoint Inhibitors

Apr 9, 2020·Frontiers in Immunology·Lara GibelliniAndrea Cossarizza

Identification of the immune checkpoint signature of multiple myeloma using mass cytometry-based single-cell analysis

May 2, 2020·Clinical & Translational Immunology·Jinheng WangJinbao Liu

scIGANs: single-cell RNA-seq imputation using generative adversarial networks

Jun 27, 2020·Nucleic Acids Research·Yungang XuXiaobo Zhou

Progressive B Cell Loss in Revertant X-SCID

Jul 19, 2020·Journal of Clinical Immunology·Connie H LinManish J Butte

Automated mapping of phenotype space with single-cell data

May 18, 2016·Nature Methods·Nikolay SamusikGarry P Nolan

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

May 25, 2016·Genome Biology·Joshua D WelchJan F Prins

Biologically Relevant Heterogeneity: Metrics and Practical Insights

Feb 24, 2017·SLAS Discovery·Albert GoughD Lansing Taylor

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

Dec 21, 2016·Scientific Data·Pang Wei KohKyle M Loh

Adaptive NKG2C+ CD57+ Natural Killer Cell and Tim-3 Expression During Viral Infections

May 8, 2018·Frontiers in Immunology·Hassen KaredAnis Larbi

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

Apr 3, 2018·Nature Biotechnology·Laleh HaghverdiJohn C Marioni

Immune Cell Dynamics Unfolded by Single-Cell Technologies

Jul 13, 2018·Frontiers in Immunology·Daniel J KunzKylie R James

Single-cell transcriptional profiling: a window into embryonic cell-type specification

Apr 19, 2018·Nature Reviews. Molecular Cell Biology·Blanca Pijuan-SalaBerthold Göttgens

A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis

Jul 19, 2018·Scientific Reports·Felix J HartmannSean C Bendall

scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3' mRNA profiling

Nov 22, 2018·Nucleic Acids Research·Burak DuraRong Fan

Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics

Oct 5, 2018·BMC Systems Biology·Daniel CookRajanikanth Vadigepalli

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

Jun 20, 2018·BMC Genomics·Kelly StreetSandrine Dudoit

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series

Nov 14, 2018·Bioinformatics·Christopher A PenfoldM Azim Surani

Single-cell genomics to guide human stem cell and tissue engineering

Sep 2, 2018·Nature Methods·J Gray CampBarbara Treutlein

Cell-specific network constructed by single-cell RNA sequencing data

Mar 14, 2019·Nucleic Acids Research·Hao DaiLuonan Chen

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

Mar 30, 2019·Nucleic Acids Research·Shuxiong WangQing Nie

A comparison of single-cell trajectory inference methods

Apr 3, 2019·Nature Biotechnology·Wouter SaelensYvan Saeys

Transcriptional Regulation in the Immune System: One Cell at a Time

Jul 2, 2019·Frontiers in Immunology·Ananda L Roy

Quantifying the Dynamics of Hematopoiesis by In Vivo IdU Pulse-Chase, Mass Cytometry, and Mathematical Modeling

Jun 1, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Amir ErezGrégoire Altan-Bonnet

Revolutionizing immunology with single-cell RNA sequencing

Feb 24, 2019·Cellular & Molecular Immunology·Haide ChenGuoji Guo

Cell lineage inference from SNP and scRNA-Seq data

Mar 2, 2019·Nucleic Acids Research·Jun DingZiv Bar-Joseph

Single-cell analysis of bone marrow-derived CD34+ cells from children with sickle cell disease and thalassemia.

Nov 8, 2019·Blood·Peng HuaJames O J Davies

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

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

Spatial and temporal tools for building a human cell atlas

Aug 30, 2019·Molecular Biology of the Cell·Jonah CoolAnanda L Roy

Epigenomics of Pancreatic Cancer: A Critical Role for Epigenome-Wide Studies

Nov 28, 2019·Epigenomes·Rahul R SinghRick J Jansen

From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies

Apr 5, 2020·Vaccines·Simone LucchesiAnnalisa Ciabattini

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Mar 7, 2020·Science·Nico BattichAlexander van Oudenaarden

Latent periodic process inference from single-cell RNA-seq data

Mar 20, 2020·Nature Communications·Shaoheng LiangKen Chen

Poincaré maps for analyzing complex hierarchies in single-cell data

Jun 13, 2020·Nature Communications·Anna KlimovskaiaMaximilian Nickel

Studying hematopoiesis using single-cell technologies

Jan 23, 2017·Journal of Hematology & Oncology·Fang YeGuoji Guo

Reconstructing cell cycle and disease progression using deep learning

Sep 8, 2017·Nature Communications·Philipp EulenbergF Alexander Wolf

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

Jun 21, 2017·Nature Communications·Zehua LiuTing Chen

SLICE: determining cell differentiation and lineage based on single cell entropy

Dec 22, 2016·Nucleic Acids Research·Minzhe GuoYan Xu

Neural stem cell heterogeneity through time and space in the ventricular-subventricular zone

Apr 4, 2017·Frontiers in Biology·Gabrielle Rushing, Rebecca A Ihrie

Single-cell RNA sequencing for the study of development, physiology and disease

May 24, 2018·Nature Reviews. Nephrology·Andrew S Potter

Single-Cell Transcriptome Analysis of Neural Stem Cells

Apr 1, 2017·Current Pharmacology Reports·Ying LiLi Cai

HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape

Sep 9, 2017·Bioinformatics·Jing Guo, Jie Zheng

Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology

Nov 30, 2018·Frontiers in Immunology·Fatima Valdes-MoraDavid Gallego-Ortega

Molecular Regulation of Differentiation in Early B-Lymphocyte Development

Jul 4, 2018·International Journal of Molecular Sciences·Mikael Sigvardsson

Emerging approaches and technologies in transplantation: the potential game changers

Feb 15, 2019·Cellular & Molecular Immunology·Anil DangiXunrong Luo

Microbial life cycles link global modularity in regulation to mosaic evolution.

Jul 24, 2019·Nature Ecology & Evolution·Jordi van GestelAndreas Wagner

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Mar 21, 2019·Genome Biology·F Alexander WolfFabian J Theis

Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart

Dec 14, 2018·Frontiers in Cardiovascular Medicine·Andrea MassaiaMichela Noseda

Recording development with single cell dynamic lineage tracing

Jun 30, 2019·Development·Aaron McKenna, James A Gagnon

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

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

Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells

Mar 14, 2019·Nature Communications·Samuel C KimmeySean C Bendall

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

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

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

Oct 13, 2019·Genome Biology·Yael BaranAmos Tanay

Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps

Dec 14, 2019·Advanced Science·Yusen YeShihua Zhang

Immune monitoring using mass cytometry and related high-dimensional imaging approaches.

Jan 2, 2020·Nature Reviews. Rheumatology·Felix J Hartmann, Sean C Bendall

Cancer systems immunology.

Jul 14, 2020·ELife·Nathan E Reticker-Flynn, Edgar G Engleman

APEC: an accesson-based method for single-cell chromatin accessibility analysis

May 14, 2020·Genome Biology·Bin LiKun Qu

Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis

Jun 3, 2020·Nature Reviews. Gastroenterology & Hepatology·Prakash RamachandranNeil C Henderson

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

May 13, 2020·Nature Communications·Yapeng SuJames R Heath

Deciphering Cell Fate Decision by Integrated Single-Cell Sequencing Analysis

Aug 12, 2020·Annual Review of Biomedical Data Science· Sagar, Dominic Grün

Regulatory myeloid cells: an underexplored continent in B-cell lymphomas

Jul 10, 2017·Cancer Immunology, Immunotherapy : CII·Mikael RousselThierry Fest

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

May 6, 2017·Science·Peter SeeFlorent Ginhoux

Wishbone identifies bifurcating developmental trajectories from single-cell data

May 3, 2016·Nature Biotechnology·Manu SettyDana Pe'er

Single-Cell Transcriptome Analysis of Developing and Regenerating Spiral Ganglion Neurons

Aug 1, 2017·Current Pharmacology Reports·Kelvin Y Kwan

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

May 26, 2017·BMC Bioinformatics·Zhuo WangYadong Wang

Computational approaches for interpreting scRNA-seq data

May 20, 2017·FEBS Letters·Raghd RostomGozde Kar

Adaptation trajectories during adhesion and spreading affect future cell states

Sep 28, 2017·Scientific Reports·Stéphanie M C BruekersWilhelm T S Huck

High-resolution myogenic lineage mapping by single-cell mass cytometry

Apr 18, 2017·Nature Cell Biology·Ermelinda PorpigliaHelen M Blau

Single-Cell Transcriptional Analysis

Mar 17, 2017·Annual Review of Analytical Chemistry·Angela R WuYanyi Huang

SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles

Oct 3, 2017·Bioinformatics·Nan Papili GaoRudiyanto Gunawan

Integral membrane proteins: bottom-up, top-down and structural proteomics

Jul 25, 2017·Expert Review of Proteomics·Upendra K KarJulian P Whitelegge

Single-cell RNA sequencing technologies and bioinformatics pipelines.

Aug 10, 2018·Experimental & Molecular Medicine·Byungjin HwangDuhee Bang

Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells

May 24, 2019·Nature Communications·Kim-Long TruongBirgit Sawitzki

GrandPrix: scaling up the Bayesian GPLVM for single-cell data

Dec 19, 2018·Bioinformatics·Sumon AhmedAlexis Boukouvalas

Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation

Aug 11, 2018·Frontiers in Immunology·Lauren SternEmily Blyth

Mass cytometry-based single-cell analysis of human stem cell reprogramming uncovers differential regulation of specific pluripotency markers

Oct 2, 2019·The Journal of Biological Chemistry·Ilkyun ImJanghwan Kim

Minimizing Batch Effects in Mass Cytometry Data

Nov 5, 2019·Frontiers in Immunology·Ronald P SchuylerElena W Y Hsieh

Decomposition of a set of distributions in extended exponential family form for distinguishing multiple oligo-dimensional marker expression profiles of single-cell populations and visualizing their dynamics

Apr 11, 2020·PloS One·Daigo Okada, Ryo Yamada

Applications of single cell RNA sequencing to research of stem cells

Nov 7, 2019·World Journal of Stem Cells·Xiao Zhang, Lei Liu

scGen predicts single-cell perturbation responses

Aug 1, 2019·Nature Methods·Mohammad LotfollahiFabian J Theis

Isotopically Encoded Nanotags for Multiplexed Ion Beam Imaging.

Jul 15, 2020·Advanced Materials Technologies·Stefan HarmsenSanjiv S Gambhir

Predicting cell lineages using autoencoders and optimal transport

Apr 29, 2020·PLoS Computational Biology·Karren Dai YangCaroline Uhler

Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis.

May 9, 2020·Communications Biology·Maeve O'HuallachainGarry P Nolan

Breathing fresh air into respiratory research with single-cell RNA sequencing

Jul 6, 2020·European Respiratory Review : an Official Journal of the European Respiratory Society·Michael J AlexanderPaul A Reyfman

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

Oct 17, 2017·Genome Research·Jiaxu WangLawrence W Stanton

Single-cell mass cytometry and machine learning predict relapse in childhood leukemia

Sep 29, 2018·Molecular & Cellular Oncology·Jolanda Sarno, Kara L Davis

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system

Mar 17, 2018·Briefings in Functional Genomics·Peter Vegh, Muzlifah Haniffa

Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute?

May 8, 2019·Journal of Leukocyte Biology·Jayajit Das, Lewis L Lanier

Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities

Feb 29, 2020·Scientific Reports·Karsten KuritzFrank Allgöwer

Lineage tracing meets single-cell omics: opportunities and challenges

Apr 3, 2020·Nature Reviews. Genetics·Daniel E Wagner, Allon M Klein

Algorithmic Tools for Mining High-Dimensional Cytometry Data

Jul 19, 2015·The Journal of Immunology : Official Journal of the American Association of Immunologists·Cariad Chester, Holden T Maecker

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics

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

Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification.

Apr 5, 2020·Genes·Maryam Zand, Jianhua Ruan

Single-cell transcriptomics uncover distinct innate and adaptive cell subsets during tissue homeostasis and regeneration.

Oct 19, 2020·Journal of Leukocyte Biology·Kevin Y YangKathy O Lui

Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis

Oct 20, 2020·Briefings in Bioinformatics·Tian LanJinyan Li

Developmental scRNAseq Trajectories in Gene- and Cell-State Space-The Flatworm Example

Oct 22, 2020·Genes·Maria SchmidtHans Binder

Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

Nov 1, 2020·Nature Communications·Igor MandricEran Halperin

Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Disease 2019

Oct 31, 2020·ERJ Open Research·Darcy E WagnerAmy L Ryan

Review of Single-Cell RNA Sequencing in the Heart

Nov 12, 2020·International Journal of Molecular Sciences·Shintaro Yamada, Seitaro Nomura

A pseudo-temporal causality approach to identifying miRNA-mRNA interactions during biological processes

Oct 19, 2020·Bioinformatics·Andres M Cifuentes-BernalThuc Duy Le

Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients.

Nov 27, 2020·Journal of the American Society of Nephrology : JASN·Christian HinzeKai M Schmidt-Ott

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

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

Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia

Nov 29, 2020·Cell·Jun WangYuxia Zhang

Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data.

Jan 7, 2021·Cell Reports·Tianshi LuTao Wang

Computational Stem Cell Biology: Open Questions and Guiding Principles

Jan 9, 2021·Cell Stem Cell·Patrick CahanChristine A Wells

Integration of single-cell multi-omics for gene regulatory network inference

Aug 11, 2020·Computational and Structural Biotechnology Journal·Xinlin HuJing Qin

Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry

Apr 24, 2020·Computational and Structural Biotechnology Journal·Paulina RybakowskaConcepción Marañón

The bone marrow hematopoietic niche and its adaptation to infection

Jun 20, 2020·Seminars in Cell & Developmental Biology·Ana Cordeiro GomesMaria Salomé Gomes

Immune cell profiles associated with measured exposure to phthalates in the Norwegian EuroMix biomonitoring study - A mass cytometry approach in toxicology

Jan 6, 2021·Environment International·Unni C NygaardHubert Dirven

The Whole Body as the System in Systems Immunology

Sep 14, 2020·IScience·Maya M L Poon, Donna L Farber

Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity

Nov 19, 2020·IScience·Nora Vivanco GonzalezSean C Bendall

Elucidating the cellular dynamics of the brain with single-cell RNA sequencing.

Jan 28, 2021·RNA Biology·Aida Cardona-AlberichChristopher R Sibley

DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence.

Jan 23, 2021·Briefings in Bioinformatics·Qianqian Song, Jing Su

Regulatory Dynamics of Cell Differentiation Revealed by True Time Series From Multinucleate Single Cells.

Jan 26, 2021·Frontiers in Genetics·Anna PretschnerWolfgang Marwan

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.

Feb 2, 2021·Nucleic Acids Research·Ruben Chazarra-GilMartin Hemberg

Nanoscopic subcellular imaging enabled by ion beam tomography.

Feb 6, 2021·Nature Communications·Ahmet F CoskunGarry P Nolan

Progress and applications of mass cytometry in sketching immune landscapes

Nov 3, 2020·Clinical and Translational Medicine·Ting ZhangXianting Ding

Multidimensional Proteomic Approach of Endothelial Progenitors Demonstrate Expression of KDR Restricted to CD19 Cells

Nov 19, 2020·Stem Cell Reviews and Reports·Coralie L GuerinDavid M Smadja

Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets

Jan 10, 2020·Bio Systems·Viktoria RätzelWolfgang Marwan

Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells.

Nov 14, 2020·Nature Medicine·Isabel SchulienChristoph Neumann-Haefelin

Profiling Cell Signaling Networks at Single-cell Resolution

Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Xiao-Kang Lun, Bernd Bodenmiller

Toward Therapeutic Targeting of Bone Marrow Leukemic Niche Protective Signals in B-Cell Acute Lymphoblastic Leukemia.

Jan 26, 2021·Frontiers in Oncology·Marjorie C DelahayeStéphane J C Mancini

Characterizing Highly Cited Papers in Mass Cytometry through H-Classics.

Feb 6, 2021·Biology·Daniel E Di Zeo-SánchezM Isabel Lucena

The transcriptome dynamics of single cells during the cell cycle.

Nov 19, 2020·Molecular Systems Biology·Daniel SchwabeNikolaus Rajewsky

Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells.

Feb 10, 2021·Cell Metabolism·Nont KosaisaweJohn G Albeck

Current trends in flow cytometry automated data analysis software.

Feb 20, 2021·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Melissa CheungJon Petzing

Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity.

Sep 24, 2020·Cell Reports·Rebecca LeylekJuliana Idoyaga

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STAT5b Transcription Factor

Pro-B Lymphocytes

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