DoRC: Discovery of rare cells from ultra-large scRNA-seq data

Xiang Chen; Fang Xiang Wu; Jin Chen; Min Li

doi:10.1109/BIBM47256.2019.8983250

DoRC: Discovery of rare cells from ultra-large scRNA-seq data

Xiang Chen
, Fang Xiang Wu
, Jin Chen
, Min Li

Internal Medicine

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Scopus citations

Abstract

The advent of droplet-based transcriptomics platforms has enabled parallel screening over thousands or millions of cells. One of the challenging issues is to identify the rare cells from the ultra-large scRNA-seq data. Existing algorithms to find rare cells are time consuming or memory-exhausting. We propose an efficient and accurate method, Discovery of Rare Cells (DoRC). The rareness scores generated by DoRC can help biologists focus the downstream analyses only on a fraction of expression profiles within ultra-large scRNA-seq data. We also demonstrate the efficacy of DoRC in delineating human blood dendritic cell sub-types using ∼68k single-cell expression profiles of human blood cells. DoRC can recover artificially planted rare cells and is sensitive to cell type identities as well.

Original language	English
Title of host publication	Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019
Editors	Illhoi Yoo, Jinbo Bi, Xiaohua Tony Hu
Pages	111-116
Number of pages	6
ISBN (Electronic)	9781728118673
DOIs	https://doi.org/10.1109/BIBM47256.2019.8983250
State	Published - Nov 2019
Event	2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 - San Diego, United States Duration: Nov 18 2019 → Nov 21 2019

Publication series

Name	Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

Conference

Conference	2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019
Country/Territory	United States
City	San Diego
Period	11/18/19 → 11/21/19

Bibliographical note

Publisher Copyright:
© 2019 IEEE.

Funding

We would like to thank Dr Aashi Jindal for fruitful discussions. This work is supported in part by the National Natural Science Foundation of China under Grants (No.61622213, No.61732009), the 111 Project (No.B18059) and the Hunan Provincial Science and Technology Program (2018WK4001).

Funders	Funder number
National Natural Science Foundation of China (NSFC)	61622213, 61732009
Hunan Provincial Science and Technology Department	2018WK4001
Higher Education Discipline Innovation Project

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

anomaly detection
isolation forest
rare cells
scRNA-seq
transcriptomics

ASJC Scopus subject areas

Biochemistry
Biotechnology
Molecular Medicine
Modeling and Simulation
Health Informatics
Pharmacology (medical)
Public Health, Environmental and Occupational Health

Access to Document

10.1109/BIBM47256.2019.8983250

Cite this

Chen, X., Wu, F. X., Chen, J., & Li, M. (2019). DoRC: Discovery of rare cells from ultra-large scRNA-seq data. In I. Yoo, J. Bi, & X. T. Hu (Eds.), Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 (pp. 111-116). Article 8983250 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019). https://doi.org/10.1109/BIBM47256.2019.8983250

Chen, Xiang ; Wu, Fang Xiang ; Chen, Jin et al. / DoRC : Discovery of rare cells from ultra-large scRNA-seq data. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. editor / Illhoi Yoo ; Jinbo Bi ; Xiaohua Tony Hu. 2019. pp. 111-116 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

@inproceedings{a97bc52d83ee4576a11266bb2a045349,

title = "DoRC: Discovery of rare cells from ultra-large scRNA-seq data",

abstract = "The advent of droplet-based transcriptomics platforms has enabled parallel screening over thousands or millions of cells. One of the challenging issues is to identify the rare cells from the ultra-large scRNA-seq data. Existing algorithms to find rare cells are time consuming or memory-exhausting. We propose an efficient and accurate method, Discovery of Rare Cells (DoRC). The rareness scores generated by DoRC can help biologists focus the downstream analyses only on a fraction of expression profiles within ultra-large scRNA-seq data. We also demonstrate the efficacy of DoRC in delineating human blood dendritic cell sub-types using ∼68k single-cell expression profiles of human blood cells. DoRC can recover artificially planted rare cells and is sensitive to cell type identities as well.",

keywords = "anomaly detection, isolation forest, rare cells, scRNA-seq, transcriptomics",

author = "Xiang Chen and Wu, \{Fang Xiang\} and Jin Chen and Min Li",

note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 ; Conference date: 18-11-2019 Through 21-11-2019",

year = "2019",

month = nov,

doi = "10.1109/BIBM47256.2019.8983250",

language = "English",

series = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",

pages = "111--116",

editor = "Illhoi Yoo and Jinbo Bi and Hu, \{Xiaohua Tony\}",

booktitle = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",

}

Chen, X, Wu, FX, Chen, J & Li, M 2019, DoRC: Discovery of rare cells from ultra-large scRNA-seq data. in I Yoo, J Bi & XT Hu (eds), Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019., 8983250, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, pp. 111-116, 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, San Diego, United States, 11/18/19. https://doi.org/10.1109/BIBM47256.2019.8983250

DoRC: Discovery of rare cells from ultra-large scRNA-seq data. / Chen, Xiang; Wu, Fang Xiang; Chen, Jin et al.
Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. ed. / Illhoi Yoo; Jinbo Bi; Xiaohua Tony Hu. 2019. p. 111-116 8983250 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - DoRC

T2 - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

AU - Chen, Xiang

AU - Wu, Fang Xiang

AU - Chen, Jin

AU - Li, Min

PY - 2019/11

Y1 - 2019/11

N2 - The advent of droplet-based transcriptomics platforms has enabled parallel screening over thousands or millions of cells. One of the challenging issues is to identify the rare cells from the ultra-large scRNA-seq data. Existing algorithms to find rare cells are time consuming or memory-exhausting. We propose an efficient and accurate method, Discovery of Rare Cells (DoRC). The rareness scores generated by DoRC can help biologists focus the downstream analyses only on a fraction of expression profiles within ultra-large scRNA-seq data. We also demonstrate the efficacy of DoRC in delineating human blood dendritic cell sub-types using ∼68k single-cell expression profiles of human blood cells. DoRC can recover artificially planted rare cells and is sensitive to cell type identities as well.

AB - The advent of droplet-based transcriptomics platforms has enabled parallel screening over thousands or millions of cells. One of the challenging issues is to identify the rare cells from the ultra-large scRNA-seq data. Existing algorithms to find rare cells are time consuming or memory-exhausting. We propose an efficient and accurate method, Discovery of Rare Cells (DoRC). The rareness scores generated by DoRC can help biologists focus the downstream analyses only on a fraction of expression profiles within ultra-large scRNA-seq data. We also demonstrate the efficacy of DoRC in delineating human blood dendritic cell sub-types using ∼68k single-cell expression profiles of human blood cells. DoRC can recover artificially planted rare cells and is sensitive to cell type identities as well.

KW - anomaly detection

KW - isolation forest

KW - rare cells

KW - scRNA-seq

KW - transcriptomics

UR - https://www.scopus.com/pages/publications/85084334342

UR - https://www.scopus.com/pages/publications/85084334342#tab=citedBy

U2 - 10.1109/BIBM47256.2019.8983250

DO - 10.1109/BIBM47256.2019.8983250

M3 - Conference contribution

AN - SCOPUS:85084334342

T3 - Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

SP - 111

EP - 116

BT - Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

A2 - Yoo, Illhoi

A2 - Bi, Jinbo

A2 - Hu, Xiaohua Tony

Y2 - 18 November 2019 through 21 November 2019

ER -

Chen X, Wu FX, Chen J, Li M. DoRC: Discovery of rare cells from ultra-large scRNA-seq data. In Yoo I, Bi J, Hu XT, editors, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. 2019. p. 111-116. 8983250. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019). doi: 10.1109/BIBM47256.2019.8983250

DoRC: Discovery of rare cells from ultra-large scRNA-seq data

Abstract

Publication series

Conference

Bibliographical note

Funding

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this