A primer on machine learning techniques for genomic applications.
Deep learning
Genomics
Machine learning
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:
07
05
2021
revised:
23
07
2021
accepted:
23
07
2021
entrez:
25
8
2021
pubmed:
26
8
2021
medline:
26
8
2021
Statut:
epublish
Résumé
High throughput sequencing technologies have enabled the study of complex biological aspects at single nucleotide resolution, opening the big data era. The analysis of large volumes of heterogeneous "omic" data, however, requires novel and efficient computational algorithms based on the paradigm of Artificial Intelligence. In the present review, we introduce and describe the most common machine learning methodologies, and lately deep learning, applied to a variety of genomics tasks, trying to emphasize capabilities, strengths and limitations through a simple and intuitive language. We highlight the power of the machine learning approach in handling big data by means of a real life example, and underline how described methods could be relevant in all cases in which large amounts of multimodal genomic data are available.
Identifiants
pubmed: 34429852
doi: 10.1016/j.csbj.2021.07.021
pii: S2001-0370(21)00311-1
pmc: PMC8365460
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
4345-4359Informations 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
Hum Mol Genet. 2018 May 1;27(R1):R40-R47
pubmed: 29590361
Mol Cell. 2015 May 21;58(4):586-97
pubmed: 26000844
Transl Psychiatry. 2018 Dec 13;8(1):276
pubmed: 30546092
Genes (Basel). 2018 Aug 23;9(9):
pubmed: 30142958
Appl Environ Microbiol. 2007 Aug;73(16):5261-7
pubmed: 17586664
Per Med. 2011 May 1;8(3):331-345
pubmed: 23662107
Brief Bioinform. 2019 May 21;20(3):931-951
pubmed: 29186295
Brief Bioinform. 2020 Jul 15;21(4):1209-1223
pubmed: 31243426
BMC Med Genomics. 2013;6 Suppl 1:S10
pubmed: 23369200
Cell Syst. 2020 Dec 16;11(6):640-652.e5
pubmed: 33296684
Nucleic Acids Res. 2017 Sep 29;45(17):e156
pubmed: 28973464
BMC Bioinformatics. 2018 Jan 25;19(1):21
pubmed: 29368597
Cancer Lett. 2013 Nov 1;340(2):284-95
pubmed: 23174106
BMC Bioinformatics. 2015 Jul 10;16:219
pubmed: 26159165
Integr Biol (Camb). 2018 Apr 23;10(4):218-231
pubmed: 29589844
BMC Bioinformatics. 2006 Sep 26;7:419
pubmed: 17002805
Nucleic Acids Res. 2018 May 4;46(8):e50
pubmed: 29408992
Arthritis Rheumatol. 2018 May;70(5):690-701
pubmed: 29468833
PLoS One. 2017 Sep 21;12(9):e0184203
pubmed: 28934234
Artif Intell Med. 2014 Sep;62(1):23-31
pubmed: 24997860
BMC Syst Biol. 2019 Apr 5;13(Suppl 2):27
pubmed: 30952205
Brief Bioinform. 2010 Mar;11(2):181-97
pubmed: 19864250
Annu Rev Genomics Hum Genet. 2008;9:387-402
pubmed: 18576944
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1250-1261
pubmed: 29993697
IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1214-1227
pubmed: 27483460
Genes Dev. 2009 Jun 15;23(12):1379-86
pubmed: 19528315
Phys Biol. 2020 Dec 01;18(1):016003
pubmed: 33049726
BMC Bioinformatics. 2019 Dec 30;20(Suppl 22):715
pubmed: 31888444
Int J Mol Sci. 2020 Sep 02;21(17):
pubmed: 32887275
Comput Methods Programs Biomed. 2019 Jul;176:173-193
pubmed: 31200905
Rev Neurosci. 2020 Aug 27;31(6):681-689
pubmed: 32678803
BMC Bioinformatics. 2020 Nov 7;21(1):505
pubmed: 33160303
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Nat Rev Genet. 2015 Jun;16(6):321-32
pubmed: 25948244
Curr Opin Biotechnol. 2019 Aug;58:161-167
pubmed: 30965188
PLoS Comput Biol. 2019 Apr 11;15(4):e1006937
pubmed: 30973878
J Comput Biol. 2018 Oct;25(10):1091-1105
pubmed: 30052049
BMC Bioinformatics. 2020 Apr 16;21(1):146
pubmed: 32299344
Patterns (N Y). 2020 Aug 17;1(6):100087
pubmed: 33205131
PLoS One. 2020 Nov 5;15(11):e0242028
pubmed: 33152046
Bioinformatics. 2013 Oct 15;29(20):2539-46
pubmed: 23956304
Mediators Inflamm. 2019 Apr 4;2019:7434376
pubmed: 31089324
Nat Med. 2021 Feb;27(2):321-332
pubmed: 33432175
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42
pubmed: 24288368
PLoS One. 2017 Jun 5;12(6):e0178751
pubmed: 28582401
BMC Genomics. 2019 Aug 8;20(1):638
pubmed: 31395005
Front Bioeng Biotechnol. 2015 Jun 25;3:92
pubmed: 26161383
Nat Rev Genet. 2020 Mar;21(3):171-189
pubmed: 31729472
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
Nat Rev Genet. 2017 May;18(5):275-291
pubmed: 28216634
PLoS One. 2019 Jul 16;14(7):e0219682
pubmed: 31310640
J Bioinform Comput Biol. 2019 Jun;17(3):1940007
pubmed: 31288636
Epigenetics. 2017 Jul 3;12(7):505-514
pubmed: 28524769
Microbiome. 2018 May 17;6(1):90
pubmed: 29773078
Quant Biol. 2020 Mar;8(1):78-94
pubmed: 32274259
Sci Rep. 2015 May 19;5:10312
pubmed: 25988841
Front Genet. 2020 Sep 09;11:1016
pubmed: 33033492
Nucleic Acids Res. 2019 Apr 23;47(7):e41
pubmed: 30993345
BMC Bioinformatics. 2019 Aug 22;20(1):433
pubmed: 31438843
PLoS One. 2019 Dec 31;14(12):e0226190
pubmed: 31891941
Nat Biotechnol. 2019 Aug;37(8):852-857
pubmed: 31341288
BMC Med Genomics. 2015 Jun 27;8:33
pubmed: 26112054
PLoS Comput Biol. 2020 Jul 24;16(7):e1008099
pubmed: 32706788