Emerging artificial intelligence applications in Spatial Transcriptomics analysis.

Artificial intelligence Deep learning Machine learning Spatial transcriptomics

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:
2022
Historique:
received: 17 03 2022
revised: 28 05 2022
accepted: 28 05 2022
entrez: 29 6 2022
pubmed: 30 6 2022
medline: 30 6 2022
Statut: epublish

Résumé

Spatial transcriptomics (ST) has advanced significantly in the last few years. Such advancement comes with the urgent need for novel computational methods to handle the unique challenges of ST data analysis. Many artificial intelligence (AI) methods have been developed to utilize various machine learning and deep learning techniques for computational ST analysis. This review provides a comprehensive and up-to-date survey of current AI methods for ST analysis.

Identifiants

pubmed: 35765645
doi: 10.1016/j.csbj.2022.05.056
pii: S2001-0370(22)00212-4
pmc: PMC9201012
doi:

Types de publication

Journal Article Review

Langues

eng

Pagination

2895-2908

Informations de copyright

© 2022 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

Science. 2016 Jul 1;353(6294):78-82
pubmed: 27365449
Front Genet. 2021 Mar 23;12:636743
pubmed: 33833776
Nat Methods. 2018 Nov;15(11):932-935
pubmed: 30377364
Sci Rep. 2020 Nov 2;10(1):18802
pubmed: 33139755
Nat Methods. 2021 Nov;18(11):1352-1362
pubmed: 34711971
Nat Methods. 2018 May;15(5):339-342
pubmed: 29553578
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
Bioinformatics. 2021 Jul 02;:
pubmed: 34213536
Nature. 2019 Apr;568(7751):235-239
pubmed: 30911168
Nat Commun. 2020 Apr 29;11(1):2084
pubmed: 32350282
Genome Biol. 2020 Dec 10;21(1):300
pubmed: 33303016
Nucleic Acids Res. 2021 May 21;49(9):e50
pubmed: 33544846
Bioinformatics. 2021 Jun 24;:
pubmed: 34165490
Science. 2015 Apr 24;348(6233):aaa6090
pubmed: 25858977
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
Nat Biotechnol. 2022 Apr;40(4):476-479
pubmed: 34845373
Nat Biotechnol. 2022 Apr 21;:
pubmed: 35449415
Commun Biol. 2020 Oct 9;3(1):565
pubmed: 33037292
Nat Methods. 2021 Nov;18(11):1282-1283
pubmed: 34711969
Bioinformatics. 2021 Jul 12;37(Suppl_1):i299-i307
pubmed: 34252941
Cell. 2020 Nov 12;183(4):1103-1116.e20
pubmed: 33098772
Nat Methods. 2020 Feb;17(2):159-162
pubmed: 31819264
Science. 2017 Oct 13;358(6360):194-199
pubmed: 28860209
Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):11046-51
pubmed: 27625426
Nat Biotechnol. 2021 Nov;39(11):1375-1384
pubmed: 34083791
Nature. 2021 Aug;596(7871):211-220
pubmed: 34381231
Nat Methods. 2020 Feb;17(2):193-200
pubmed: 31988518
Science. 2018 Jul 27;361(6400):
pubmed: 29930089
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Science. 2019 Apr 5;364(6435):89-93
pubmed: 30948552
Nat Commun. 2021 Sep 6;12(1):5283
pubmed: 34489425
Nat Biotechnol. 2022 May;40(5):661-671
pubmed: 35027729
Nat Biotechnol. 2019 Jun;37(6):685-691
pubmed: 31061482
Nat Commun. 2021 Feb 17;12(1):1088
pubmed: 33597522
Cell. 2019 Jun 13;177(7):1873-1887.e17
pubmed: 31178122
Genome Biol. 2022 Apr 14;23(1):97
pubmed: 35422018
Nat Methods. 2018 Dec;15(12):1053-1058
pubmed: 30504886
Science. 2018 Nov 16;362(6416):
pubmed: 30385464
Nucleic Acids Res. 2022 Jun 10;50(10):e57
pubmed: 35191503
Nat Methods. 2022 Jun;19(6):662-670
pubmed: 35577954
Adv Neural Inf Process Syst. 2019 Dec;32:9240-9251
pubmed: 32265580
Nature. 2019 Dec;576(7785):132-137
pubmed: 31748748
Nat Biotechnol. 2021 Mar;39(3):313-319
pubmed: 33288904
Nat Neurosci. 2021 Mar;24(3):425-436
pubmed: 33558695
BMC Genomics. 2020 Jul 14;21(1):482
pubmed: 32664861
Neuron. 2017 May 17;94(4):745-746
pubmed: 28521128
Nat Biotechnol. 2020 Mar;38(3):333-342
pubmed: 31932730
Nat Genet. 2021 Sep;53(9):1334-1347
pubmed: 34493872
Bioinformatics. 2020 Apr 1;36(7):2293-2294
pubmed: 31808789
Nucleic Acids Res. 2020 Oct 9;48(18):e107
pubmed: 32955565
Nat Commun. 2018 Jun 20;9(1):2419
pubmed: 29925878
Genome Biol. 2021 Mar 8;22(1):78
pubmed: 33685491
Nat Methods. 2021 Nov;18(11):1342-1351
pubmed: 34711970
Nat Biotechnol. 2008 Mar;26(3):317-25
pubmed: 18278033
BMC Bioinformatics. 2021 Aug 9;22(1):397
pubmed: 34372758
Nucleic Acids Res. 2022 Apr 22;50(7):e42
pubmed: 35253896
Brief Bioinform. 2021 Sep 2;22(5):
pubmed: 33480403
Nat Commun. 2022 Apr 1;13(1):1739
pubmed: 35365632
Nat Methods. 2018 May;15(5):343-346
pubmed: 29553579
Nat Biotechnol. 2022 Apr;40(4):517-526
pubmed: 33603203
Nat Protoc. 2020 Apr;15(4):1484-1506
pubmed: 32103204
Sci Rep. 2022 Mar 8;12(1):4133
pubmed: 35260632
Genome Biol. 2022 Mar 25;23(1):83
pubmed: 35337374
Cell. 2022 May 12;185(10):1777-1792.e21
pubmed: 35512705
Genome Biol. 2021 May 10;22(1):145
pubmed: 33971932
Nat Biotechnol. 2015 May;33(5):495-502
pubmed: 25867923

Auteurs

Yijun Li (Y)

Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.

Stefan Stanojevic (S)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Lana X Garmire (LX)

Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Classifications MeSH