[1] |
Mercer T R, Dinger M E, Mattick J S 2009 Nat. Rev. Genetics 10 155 DOI: 10.1038/nrg2521
|
[2] |
Geisler S, Coller J 2013 Nat. Rev. Mol. Cell Biol. 14 699 DOI: 10.1038/nrm3679
|
[3] |
|
[4] |
Morris K V, Mattick J S 2014 Nat. Rev. Genetics 15 423 DOI: 10.1038/nrg3722
|
[5] |
|
[6] |
|
[7] |
|
[8] |
|
[9] |
Sponer J, Bussi G, Krepl M, Banas P, Bottaro S, Cunha R A, Gil-Ley A, Pinamonti G, Poblete S, Jurecka P, Walter N G, Otyepka M 2018 Chem. Rev. 118 4177 DOI: 10.1021/acs.chemrev.7b00427
|
[10] |
|
[11] |
|
[12] |
Goodfellow I, Bengio Y, Courville A 2016 Deep learning. Adaptive computation and machine learning Cambridge The MIT Press 197 200
|
[13] |
Silver D, Huang A, Maddison C J, Guez A, Sifre L, van den Driessche G, Schrittwieser J, Antonoglou I, Panneershelvam V, Lanctot M, Dieleman S, Grewe D, Nham H, Kalchbrenner N, Sutskever I, Lillicrap T, Leach M, Kavukcuoglu K, Graepel T, Hassabis D 2016 Nature 529 484 DOI: 10.1038/nature16961
|
[14] |
Alipanahi B, Delong A, Weirauch M T, Frey B J 2015 Nat. Biotech. 33 831 DOI: 10.1038/nbt.3300
|
[15] |
|
[16] |
|
[17] |
|
[18] |
|
[19] |
|
[20] |
|
[21] |
|
[22] |
|
[23] |
|
[24] |
|
[25] |
|
[26] |
|
[27] |
|
[28] |
|
[29] |
|
[30] |
|
[31] |
|
[32] |
|
[33] |
|
[34] |
Frellsen J, Moltke I, Thiim M, Mardia K V, Ferkinghoff-Borg J, Hamelryck T 2009 Plos Comput. Biol. 5 e1000406 DOI: 10.1371/journal.pcbi.1000406
|
[35] |
|
[36] |
|
[37] |
|
[38] |
Theis C, Siederdissen C H, Hofacke I L, Gorodki J 2013 Nuc. Acids Res. 41 9999 DOI: 10.1093/nar/gkt795
|
[39] |
Zirbel C, Roll J, Sweeney B A, Petrov A I, Pirrung M, Leontis N B 2015 Nuc. Acids Res. 43 7504 DOI: 10.1093/nar/gkv651
|
[40] |
Theis C, Zirbel C L, Siederdissen C H, Anthon C, Hofacker I L, Nielsen H, Gorodkin J 2015 PLOS One 10 e0139900 DOI: 10.1371/journal.pone.0139900
|
[41] |
|
[42] |
|
[43] |
|
[44] |
|
[45] |
|
[46] |
|
[47] |
|
[48] |
|
[49] |
|
[50] |
Wang J M, Cieplak P, Li J, Wang J, Cai Q, Hsieh M J, Lei H X, Luo R, Duan Y 2011 J. Phys. Chem. B 115 3100 DOI: 10.1021/jp1121382
|
[51] |
Li Y, Li H, Pickard F C, Narayanan B, Sen F G, Chan M, Sankaranarayanan S, Brooks B R, Roux B 2017 J. Chem. Theory Comput. 13 4492 DOI: 10.1021/acs.jctc.7b00521
|
[52] |
Bereau T, DiStasio R A, Tkatchenko A, Lilienfeld O A 2018 J. Chem. Phys. 148 241706 DOI: 10.1063/1.5009502
|
[53] |
|
[54] |
|
[55] |
|
[56] |
|
[57] |
|
[58] |
Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J 2019 Proteins 87 1011 DOI: 10.1002/prot.v87.12
|
[59] |
Senior A W, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Zidek A, Nelson A, Bridgland A, Penedones H, Petersen S, Simonyan K, Crossan S, Kohli P, Jones D T, Silver D, Kavukcuoglu K, Hassabis D 2019 Nature 577 706 DOI: 10.1038/s41586-019-1923-7
|
[60] |
|
[61] |
Leonardis E D, Lutz B, Ratz S, Cocco S, Monasson R, Schug A, Weigt M 2015 Nuc. Acids Res. 43 10444 DOI: 10.1093/nar/gkv932
|
[62] |
Wang J, Mao K, Zhao Y J, Zeng C, Xiang J, Zhang Y, Xiao Y 2017 Nuc. Acids Res. 45 6299 DOI: 10.1093/nar/gkx386
|
[63] |
Zhao Y, Huang Y, Gong Z, Wang Y, Man J, Xiao Y 2012 Scientific Reports 2 734 DOI: 10.1038/srep00734
|
[64] |
Wang J, Xiao Y 2017 Current Protocols in bioinformatics 57 5 DOI: 10.1002/cpbi.21
|
[65] |
|
[66] |
|
[67] |
|
[68] |
Zhang H, Zhang Q, Ju F, Zhu J, Gao Y, Xie Z, Deng M, Sun S, Zheng W M, Bu D B 2019 BMC Bioinformatics 20 537 DOI: 10.1186/s12859-019-3051-7
|
[69] |
|
[70] |
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki E P, Rivas E, Eddy S R, Bateman A, Finn R D, Petrov A 2018 Nuc. Acids Res. 46 D335 DOI: 10.1093/nar/gkx1038
|
[71] |
Wang J X, Nelson Z K, Tirumala D, Soyer H, Leibo J Z, Munos R, Blundell C, Kumaran D, Botvinick M 2017 arXiv: 1611.05763v3 DOI: 10.1145/3386252
|
[72] |
|
[73] |
Wang Y, Yao Q, Kwok J K, Ni L M 2020 ACM Computing Surveys 53 63 DOI: 10.1145/3386252
|