Computational strategies for single-cell multi-omics integration.
Clustering
Integration
Multi-omics
Single-cell
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2021
2021
Historique:
received:
19
02
2021
revised:
23
04
2021
accepted:
24
04
2021
entrez:
24
5
2021
pubmed:
25
5
2021
medline:
25
5
2021
Statut:
epublish
Résumé
Single-cell omics technologies are currently solving biological and medical problems that earlier have remained elusive, such as discovery of new cell types, cellular differentiation trajectories and communication networks across cells and tissues. Current advances especially in single-cell multi-omics hold high potential for breakthroughs by integration of multiple different omics layers. To pair with the recent biotechnological developments, many computational approaches to process and analyze single-cell multi-omics data have been proposed. In this review, we first introduce recent developments in single-cell multi-omics in general and then focus on the available data integration strategies. The integration approaches are divided into three categories: early, intermediate, and late data integration. For each category, we describe the underlying conceptual principles and main characteristics, as well as provide examples of currently available tools and how they have been applied to analyze single-cell multi-omics data. Finally, we explore the challenges and prospective future directions of single-cell multi-omics data integration, including examples of adopting multi-view analysis approaches used in other disciplines to single-cell multi-omics.
Identifiants
pubmed: 34025945
doi: 10.1016/j.csbj.2021.04.060
pii: S2001-0370(21)00172-0
pmc: PMC8114078
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
2588-2596Informations de copyright
© 2021 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
J Mol Cell Cardiol. 2020 May;142:80-92
pubmed: 32205182
Nat Methods. 2017 Sep;14(9):865-868
pubmed: 28759029
Nature. 2012 Oct 4;490(7418):61-70
pubmed: 23000897
IEEE Trans Image Process. 2017 Feb 08;26(6):3016-3027
pubmed: 28186894
Front Oncol. 2015 Mar 10;5:53
pubmed: 25806353
Nat Commun. 2019 Jan 28;10(1):470
pubmed: 30692544
Nat Methods. 2015 Jun;12(6):519-22
pubmed: 25915121
Bioinformatics. 2020 Feb 15;36(4):1159-1166
pubmed: 31501851
Nat Genet. 2022 Oct;54(10):1514-1526
pubmed: 36138229
Proteomics. 2017 Feb;17(3-4):
pubmed: 28128880
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7723-7728
pubmed: 29987051
Hum Brain Mapp. 2020 Sep;41(13):3807-3833
pubmed: 32592530
Elife. 2017 Dec 05;6:
pubmed: 29206104
Sci Rep. 2020 Aug 12;10(1):13654
pubmed: 32788601
Nat Biotechnol. 2017 Oct;35(10):936-939
pubmed: 28854175
Trends Biotechnol. 2020 Sep;38(9):1007-1022
pubmed: 32818441
Trends Immunol. 2019 Nov;40(11):1011-1021
pubmed: 31645299
Genome Biol. 2017 Jul 24;18(1):138
pubmed: 28738873
Cell Res. 2016 Mar;26(3):304-19
pubmed: 26902283
Genome Biol. 2015 Aug 21;16:172
pubmed: 26294014
Biotechniques. 2015 Oct 01;59(4):209-12, 214, 216 passim
pubmed: 26458549
Sci Data. 2019 Oct 31;6(1):256
pubmed: 31672995
Nat Commun. 2021 Jan 4;12(1):31
pubmed: 33397893
Nat Commun. 2021 Feb 23;12(1):1247
pubmed: 33623021
Nat Cell Biol. 2018 Jul;20(7):847-858
pubmed: 29915357
PLoS Comput Biol. 2017 Oct 16;13(10):e1005781
pubmed: 29036190
Nat Methods. 2020 Jan;17(1):11-14
pubmed: 31907462
Neuron. 2019 Apr 3;102(1):143-158.e7
pubmed: 30770253
Cell. 2020 Nov 12;183(4):1103-1116.e20
pubmed: 33098772
Cell Rep. 2020 Dec 1;33(9):108438
pubmed: 33264626
Nat Commun. 2018 Nov 19;9(1):4877
pubmed: 30451828
Nat Methods. 2014 Aug;11(8):817-820
pubmed: 25042786
Nat Med. 2020 May;26(5):792-802
pubmed: 32405060
Nat Rev Genet. 2015 Dec;16(12):716-26
pubmed: 26460349
Cell Res. 2017 Aug;27(8):967-988
pubmed: 28621329
PNAS Nexus. 2022 Aug 19;1(4):pgac165
pubmed: 36157595
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Sci Data. 2019 Oct 31;6(1):251
pubmed: 31672978
Elife. 2017 Jun 27;6:
pubmed: 28653622
BMC Med Genomics. 2020 Feb 18;13(1):29
pubmed: 32070336
Nat Methods. 2016 Jan;13(1):9-10
pubmed: 26716558
Bioinformatics. 2021 May 5;37(6):775-784
pubmed: 33098418
Genome Biol. 2020 May 11;21(1):111
pubmed: 32393329
Trends Biotechnol. 2016 Aug;34(8):605-608
pubmed: 27212022
FEMS Microbiol Lett. 2003 Jul 29;224(2):191-5
pubmed: 12892882
Bioinformatics. 2020 Jul 1;36(Suppl_1):i48-i56
pubmed: 32657382
Stat Appl Genet Mol Biol. 2009;8:Article 1
pubmed: 19222376
Trends Genet. 2017 Feb;33(2):155-168
pubmed: 28089370
Proc Natl Acad Sci U S A. 2019 May 14;116(20):9775-9784
pubmed: 31028141
Nucleic Acids Res. 2018 Nov 16;46(20):10546-10562
pubmed: 30295871
Genome Biol. 2016 May 05;17:88
pubmed: 27150361
Bioinformatics. 2009 Nov 15;25(22):2906-12
pubmed: 19759197
Science. 2020 Feb 21;367(6480):
pubmed: 32079746
Bioinformatics. 2012 Dec 15;28(24):3290-7
pubmed: 23047558
Commun Biol. 2020 Jan 21;3(1):37
pubmed: 31965050
Science. 2006 Jul 28;313(5786):504-7
pubmed: 16873662
Nat Biotechnol. 2018 Jan;36(1):70-80
pubmed: 29227469
Ann Appl Stat. 2013 Mar 1;7(1):523-542
pubmed: 23745156
Nat Methods. 2016 Mar;13(3):229-232
pubmed: 26752769
Bioinformatics. 2020 Sep 15;36(18):4789-4796
pubmed: 32592464
PLoS Comput Biol. 2020 Apr 2;16(4):e1007677
pubmed: 32240163
Genome Biol. 2019 Mar 12;20(1):54
pubmed: 30866997
Inf Fusion. 2019 Oct;50:71-91
pubmed: 30467459
Nucleic Acids Res. 2020 Jun 19;48(11):5814-5824
pubmed: 32379315
Nat Cell Biol. 2019 Sep;21(9):1164-1172
pubmed: 31481796
Nat Methods. 2019 Sep;16(9):809-812
pubmed: 31406385
Science. 2018 Sep 28;361(6409):1380-1385
pubmed: 30166440
Nat Commun. 2018 Feb 22;9(1):781
pubmed: 29472610
Nat Rev Genet. 2021 Jan;22(1):3-18
pubmed: 32807900
Bioinformatics. 2016 Jan 1;32(1):1-8
pubmed: 26377073
Nat Biotechnol. 2020 Jun;38(6):737-746
pubmed: 32341560
Front Genet. 2020 Dec 15;11:604790
pubmed: 33384718
BMC Bioinformatics. 2017 Feb 14;18(1):108
pubmed: 28196464
Nucleic Acids Res. 2020 Jan 10;48(1):86-95
pubmed: 31777938
Nat Biotechnol. 2015 Mar;33(3):285-289
pubmed: 25599178
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
Algorithms Bioinform. 2019 Sep 3;143:
pubmed: 34632462
Nat Methods. 2020 Jan;17(1):14-17
pubmed: 31907463
Front Genet. 2020 Nov 04;11:572242
pubmed: 33329710
PLoS One. 2019 May 23;14(5):e0216904
pubmed: 31120942
Proteomics. 2020 Jul;20(13):e1900271
pubmed: 32223079
Bioinformatics. 2019 Jul 15;35(14):i501-i509
pubmed: 31510700
Curr Protoc Cytom. 2016 Jan 06;75:7.45.1-7.45.33
pubmed: 26742656
Exp Mol Med. 2018 Aug 7;50(8):1-14
pubmed: 30089861
Genome Res. 2018 Jan;28(1):75-87
pubmed: 29208629
Brief Bioinform. 2021 Jul 20;22(4):
pubmed: 33200787
Bioinformatics. 2013 Oct 15;29(20):2610-6
pubmed: 23990412
Mol Cell. 2019 Mar 21;73(6):1292-1305.e8
pubmed: 30765193
Nat Biotechnol. 2019 Dec;37(12):1452-1457
pubmed: 31611697
Cell Stem Cell. 2018 Aug 02;23(2):166-179
pubmed: 29754780
Genome Res. 2017 Dec;27(12):2025-2039
pubmed: 29066617
Commun Biol. 2020 Oct 23;3(1):602
pubmed: 33097816
Science. 2000 Dec 22;290(5500):2323-6
pubmed: 11125150
Nat Methods. 2016 Mar;13(3):269-75
pubmed: 26808670
Gigascience. 2020 Oct 30;9(11):
pubmed: 33124660
Nucleic Acids Res. 2018 Jan 4;46(D1):D956-D963
pubmed: 29136207
Bioinformatics. 2015 May 1;31(9):1436-43
pubmed: 25527095
Biostatistics. 2009 Jul;10(3):515-34
pubmed: 19377034
Nature. 2019 May;569(7757):576-580
pubmed: 31092926
Mol Syst Biol. 2018 Jun 20;14(6):e8124
pubmed: 29925568
Blood. 2016 Aug 25;128(8):e20-31
pubmed: 27365425