Literature DB >> 31077114

Supervised Machine Learning with CITRUS for Single Cell Biomarker Discovery.

Hannah G Polikowsky1, Katherine A Drake2.   

Abstract

CITRUS is a supervised machine learning algorithm designed to analyze single cell data, identify cell populations, and identify changes in the frequencies or functional marker expression patterns of those populations that are significantly associated with an outcome. The algorithm is a black box that includes steps to cluster cell populations, characterize these populations, and identify the significant characteristics. This chapter describes how to optimize the use of CITRUS by combining it with upstream and downstream data analysis and visualization tools.

Entities:  

Keywords:  Biomarker discovery; CITRUS; Supervised machine learning; viSNE

Mesh：

Substances：

Year:  2019        PMID： 31077114      PMCID： PMC7458409          DOI： 10.1007/978-1-4939-9454-0_20

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

1.  Significance analysis of microarrays applied to the ionizing radiation response.

Authors:  V G Tusher; R Tibshirani; G Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

2.  Thinking outside the gate: single-cell assessments in multiple dimensions.

Authors:  Pia Kvistborg; Cécile Gouttefangeas; Nima Aghaeepour; Angelica Cazaly; Pratip K Chattopadhyay; Cliburn Chan; Judith Eckl; Greg Finak; Sine Reker Hadrup; Holden T Maecker; Dominik Maurer; Tim Mosmann; Peng Qiu; Richard H Scheuermann; Marij J P Welters; Guido Ferrari; Ryan R Brinkman; Cedrik M Britten
Journal:  Immunity       Date:  2015-04-21       Impact factor: 31.745

3.  Automated identification of stratifying signatures in cellular subpopulations.

Authors:  Robert V Bruggner; Bernd Bodenmiller; David L Dill; Robert J Tibshirani; Garry P Nolan
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-16       Impact factor: 11.205

Review 4.  Mass cytometry: blessed with the curse of dimensionality.

Authors:  Evan W Newell; Yang Cheng
Journal:  Nat Immunol       Date:  2016-07-19       Impact factor: 25.606

5.  High-throughput flow cytometry data normalization for clinical trials.

Authors:  Greg Finak; Wenxin Jiang; Kevin Krouse; Chungwen Wei; Ignacio Sanz; Deborah Phippard; Adam Asare; Stephen C De Rosa; Steve Self; Raphael Gottardo
Journal:  Cytometry A       Date:  2013-12-31       Impact factor: 4.355

6.  Mass Cytometric Analysis Reveals Viable Activated Caspase-3+ Luminal Progenitors in the Normal Adult Human Mammary Gland.

Authors:  David J H F Knapp; Nagarajan Kannan; Davide Pellacani; Connie J Eaves
Journal:  Cell Rep       Date:  2017-10-24       Impact factor: 9.423

7.  Diagnosis of multiple cancer types by shrunken centroids of gene expression.

Authors:  Robert Tibshirani; Trevor Hastie; Balasubramanian Narasimhan; Gilbert Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-14       Impact factor: 11.205

8.  viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.

Authors:  El-ad David Amir; Kara L Davis; Michelle D Tadmor; Erin F Simonds; Jacob H Levine; Sean C Bendall; Daniel K Shenfeld; Smita Krishnaswamy; Garry P Nolan; Dana Pe'er
Journal:  Nat Biotechnol       Date:  2013-05-19       Impact factor: 54.908

Review 9.  TCR zeta-chain downregulation: curtailing an excessive inflammatory immune response.

Authors:  Michal Baniyash
Journal:  Nat Rev Immunol       Date:  2004-09       Impact factor: 53.106

10.  Determinants of response and resistance to CD19 chimeric antigen receptor (CAR) T cell therapy of chronic lymphocytic leukemia.

Authors:  Simon F Lacey; Elena J Orlando; Joseph A Fraietta; Iulian Pruteanu-Malinici; Mercy Gohil; Stefan Lundh; Alina C Boesteanu; Yan Wang; Roddy S O'Connor; Wei-Ting Hwang; Edward Pequignot; David E Ambrose; Changfeng Zhang; Nicholas Wilcox; Felipe Bedoya; Corin Dorfmeier; Fang Chen; Lifeng Tian; Harit Parakandi; Minnal Gupta; Regina M Young; F Brad Johnson; Irina Kulikovskaya; Li Liu; Jun Xu; Sadik H Kassim; Megan M Davis; Bruce L Levine; Noelle V Frey; Donald L Siegel; Alexander C Huang; E John Wherry; Hans Bitter; Jennifer L Brogdon; David L Porter; Carl H June; J Joseph Melenhorst
Journal:  Nat Med       Date:  2018-04-30       Impact factor: 53.440
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  2 in total

1.  Activated but functionally impaired memory Tregs are expanded in slow progressors to type 1 diabetes.

Authors:  Joanne Boldison; Anna E Long; Rachel J Aitken; Isabel V Wilson; Clare Megson; Stephanie J Hanna; F Susan Wong; Kathleen M Gillespie
Journal:  Diabetologia       Date:  2021-10-28       Impact factor: 10.122

Review 2.  CyTOF® for the Masses.

Authors:  Akshay Iyer; Anouk A J Hamers; Asha B Pillai
Journal:  Front Immunol       Date:  2022-04-14       Impact factor: 8.786
  2 in total

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