Literature DB >> 27320317

Computational flow cytometry: helping to make sense of high-dimensional immunology data.

Yvan Saeys1,2, Sofie Van Gassen1,3, Bart N Lambrecht1,2,4.   

Abstract

Recent advances in flow cytometry allow scientists to measure an increasing number of parameters per cell, generating huge and high-dimensional datasets. To analyse, visualize and interpret these data, newly available computational techniques should be adopted, evaluated and improved upon by the immunological community. Computational flow cytometry is emerging as an important new field at the intersection of immunology and computational biology; it allows new biological knowledge to be extracted from high-throughput single-cell data. This Review provides non-experts with a broad and practical overview of the many recent developments in computational flow cytometry.

Mesh:

Year:  2016        PMID: 27320317     DOI: 10.1038/nri.2016.56

Source DB:  PubMed          Journal:  Nat Rev Immunol        ISSN: 1474-1733            Impact factor:   53.106


  82 in total

1.  Subjectivity and flow cytometric variability.

Authors:  Gisela Pachón; Isabel Caragol; Jordi Petriz
Journal:  Nat Rev Immunol       Date:  2012-04-25       Impact factor: 53.106

2.  Publication of optimized multicolor immunofluorescence panels.

Authors:  Yolanda Mahnke; Pratip Chattopadhyay; Mario Roederer
Journal:  Cytometry A       Date:  2010-09       Impact factor: 4.355

3.  Rapid cell population identification in flow cytometry data.

Authors:  Nima Aghaeepour; Radina Nikolic; Holger H Hoos; Ryan R Brinkman
Journal:  Cytometry A       Date:  2011-01       Impact factor: 4.355

4.  Data File Standard for Flow Cytometry, version FCS 3.1.

Authors:  Josef Spidlen; Wayne Moore; David Parks; Michael Goldberg; Chris Bray; Pierre Bierre; Peter Gorombey; Bill Hyun; Mark Hubbard; Simon Lange; Ray Lefebvre; Robert Leif; David Novo; Leo Ostruszka; Adam Treister; James Wood; Robert F Murphy; Mario Roederer; Damir Sudar; Robert Zigon; Ryan R Brinkman
Journal:  Cytometry A       Date:  2010-01       Impact factor: 4.355

5.  flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

Authors:  Mehrnoush Malek; Mohammad Jafar Taghiyar; Lauren Chong; Greg Finak; Raphael Gottardo; Ryan R Brinkman
Journal:  Bioinformatics       Date:  2014-10-16       Impact factor: 6.937

6.  Automated flow cytometric analysis across large numbers of samples and cell types.

Authors:  Xiaoyi Chen; Milena Hasan; Valentina Libri; Alejandra Urrutia; Benoît Beitz; Vincent Rouilly; Darragh Duffy; Étienne Patin; Bernard Chalmond; Lars Rogge; Lluis Quintana-Murci; Matthew L Albert; Benno Schwikowski
Journal:  Clin Immunol       Date:  2015-01-07       Impact factor: 3.969

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

Authors:  Kirsten E Diggins; P Brent Ferrell; Jonathan M Irish
Journal:  Methods       Date:  2015-05-13       Impact factor: 3.608

8.  Standardized Multi-Color Flow Cytometry and Computational Biomarker Discovery.

Authors:  Stephan Schlickeiser; Mathias Streitz; Birgit Sawitzki
Journal:  Methods Mol Biol       Date:  2016

9.  High-dimensional analysis of the murine myeloid cell system.

Authors:  Burkhard Becher; Andreas Schlitzer; Jinmiao Chen; Florian Mair; Hermi R Sumatoh; Karen Wei Weng Teng; Donovan Low; Christiane Ruedl; Paola Riccardi-Castagnoli; Michael Poidinger; Melanie Greter; Florent Ginhoux; Evan W Newell
Journal:  Nat Immunol       Date:  2014-10-12       Impact factor: 25.606

10.  Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples.

Authors:  Andrew Cron; Cécile Gouttefangeas; Jacob Frelinger; Lin Lin; Satwinder K Singh; Cedrik M Britten; Marij J P Welters; Sjoerd H van der Burg; Mike West; Cliburn Chan
Journal:  PLoS Comput Biol       Date:  2013-07-11       Impact factor: 4.475

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  147 in total

1.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

2.  Mass cytometry deep phenotyping of human mononuclear phagocytes and myeloid-derived suppressor cells from human blood and bone marrow.

Authors:  Mikael Roussel; P Brent Ferrell; Allison R Greenplate; Faustine Lhomme; Simon Le Gallou; Kirsten E Diggins; Douglas B Johnson; Jonathan M Irish
Journal:  J Leukoc Biol       Date:  2017-04-11       Impact factor: 4.962

3.  Human Lung Dendritic Cells: Spatial Distribution and Phenotypic Identification in Endobronchial Biopsies Using Immunohistochemistry and Flow Cytometry.

Authors:  Faezzah Baharom; Gregory Rankin; Saskia Scholz; Jamshid Pourazar; Clas Ahlm; Anders Blomberg; Anna Smed-Sörensen
Journal:  J Vis Exp       Date:  2017-01-20       Impact factor: 1.355

Review 4.  Advancing systems immunology through data-driven statistical analysis.

Authors:  Linda E Fong; Andrés R Muñoz-Rojas; Kathryn Miller-Jensen
Journal:  Curr Opin Biotechnol       Date:  2018-04-12       Impact factor: 9.740

5.  High-throughput label-free flow cytometry based on matched-filter compressive imaging.

Authors:  Cong Ba; William J Shain; Thomas G Bifano; Jerome Mertz
Journal:  Biomed Opt Express       Date:  2018-11-12       Impact factor: 3.732

6.  Dimensionality reduction for visualizing single-cell data using UMAP.

Authors:  Etienne Becht; Leland McInnes; John Healy; Charles-Antoine Dutertre; Immanuel W H Kwok; Lai Guan Ng; Florent Ginhoux; Evan W Newell
Journal:  Nat Biotechnol       Date:  2018-12-03       Impact factor: 54.908

7.  Human Blood Monocyte Subsets: A New Gating Strategy Defined Using Cell Surface Markers Identified by Mass Cytometry.

Authors:  Graham D Thomas; Anouk A J Hamers; Catherine Nakao; Paola Marcovecchio; Angela M Taylor; Chantel McSkimming; Anh Tram Nguyen; Coleen A McNamara; Catherine C Hedrick
Journal:  Arterioscler Thromb Vasc Biol       Date:  2017-06-08       Impact factor: 8.311

8.  GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Authors:  Nima Aghaeepour; Erin F Simonds; David J H F Knapp; Robert V Bruggner; Karen Sachs; Anthony Culos; Pier Federico Gherardini; Nikolay Samusik; Gabriela K Fragiadakis; Sean C Bendall; Brice Gaudilliere; Martin S Angst; Connie J Eaves; William A Weiss; Wendy J Fantl; Garry P Nolan
Journal:  Bioinformatics       Date:  2018-12-01       Impact factor: 6.937

Review 9.  Single-Cell Genomics: Approaches and Utility in Immunology.

Authors:  Karlynn E Neu; Qingming Tang; Patrick C Wilson; Aly A Khan
Journal:  Trends Immunol       Date:  2017-01-13       Impact factor: 16.687

10.  Human Monocyte Heterogeneity as Revealed by High-Dimensional Mass Cytometry.

Authors:  Anouk A J Hamers; Huy Q Dinh; Graham D Thomas; Paola Marcovecchio; Amy Blatchley; Catherine S Nakao; Cheryl Kim; Chantel McSkimming; Angela M Taylor; Anh T Nguyen; Coleen A McNamara; Catherine C Hedrick
Journal:  Arterioscler Thromb Vasc Biol       Date:  2019-01       Impact factor: 8.311

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