1 B. MaherENCODE: the human encyclopaedia Nature, 489 (7414) (2012), pp. 46-48

2 J.L. Rinn, H.Y. ChangGenome regulation by long noncoding RNAs Annu Rev Biochem, 81 (2012), pp. 145-166

3 R.A. Boon, N. Jaé, L. Holdt, et al.Long noncoding RNAs: from clinical genetics to therapeutic targets? J Am Coll Cardiol, 67 (10) (2016), pp. 1214-1226

4 J. Ponjavic, C.P. Ponting, G. LunterFunctionality or transcriptional noise? evidence for selection within long noncoding RNAs Genome Res, 17 (5) (2007), pp. 556-565

5 P. Kapranov, G. St Laurent, T. Raz, et al.The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA BMC Biol, 8 (2010), p. 149

6 M.B. Clark, A. Choudhary, M.A. Smith, et al.The dark matter rises: the expanding world of regulatory RNAs Essays Biochem, 54 (2013), pp. 1-16

7 P.J. Batista, H.Y. ChangLong noncoding RNAs: cellular address codes in development and disease Cell, 152 (6) (2013), pp. 1298-1307

8 L. Stojic, M. Niemczyk, A. Orjalo, et al.Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions Nat Commun, 7 (2016), Article 10406

9 I. Martianov, A. Ramadass, A. Serra Barros, et al.Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript Nature, 445 (7128) (2007), pp. 666-670

10 V. Tripathi, J.D. Ellis, Z. Shen, et al.The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation Mol Cell, 39 (6) (2010), pp. 925-938

11 W. Zhuo, Y. Liu, S. Li, et al.Long noncoding RNA GMAN, up-regulated in gastric cancer tissues, is associated with metastasis in patients and promotes translation of ephrin A1 by competitively binding GMAN-AS Gastroenterology, 156 (3) (2019), pp. 676-691

12 I. Ulitsky, D.P. BartellincRNAs: genomics, evolution, and mechanisms Cell, 154 (1) (2013), pp. 26-46

13 J.R. Prensner, A.M. ChinnaiyanThe emergence of lncRNAs in cancer biology Cancer Discov, 1 (5) (2011), pp. 391-407

14 M. Melé, K. Mattioli, W. Mallard, et al.Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs Genome Res, 27 (1) (2017), pp. 27-37

15 S. Jiang, S.J. Cheng, L.C. Ren, et al.An expanded landscape of human long noncoding RNA Nucleic Acids Res, 47 (15) (2019), pp. 7842-7856

16 M. Schlackow, T. Nojima, T. Gomes, et al.Distinctive patterns of transcription and RNA processing for human lincRNAs Mol Cell, 65 (1) (2017), pp. 25-38

17 J.S. MattickA new paradigm for developmental biology J Exp Biol, 210 (Pt 9) (2007), pp. 1526-1547

18 G. St Laurent III, C. WahlestedtNoncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci, 30 (12) (2007), pp. 612-621

19 C. Trapnell, A. Roberts, L. Goff, et al.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat Protoc, 7 (3) (2012), pp. 562-578

20 B. Langmead, C. Trapnell, M. Pop, et al.Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol, 10 (3) (2009), p. R25

21 D. Kim, B. Langmead, S.L. SalzbergHISAT: a fast spliced aligner with low memory requirements Nat Methods, 12 (4) (2015), pp. 357-360

22 M. Pertea, D. Kim, G.M. Pertea, et al.Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Nat Protoc, 11 (9) (2016), pp. 1650-1667

23 M. Pertea, G.M. Pertea, C.M. Antonescu, et al.StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nat Biotechnol, 33 (3) (2015), pp. 290-295

24 M.G. Grabherr, B.J. Haas, M. Yassour, et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome Nat Biotechnol, 29 (7) (2011), pp. 644-652

25 B.J. Haas, A. Papanicolaou, M. Yassour, et al.De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis Nat Protoc, 8 (8) (2013), pp. 1494-1512

26 B.H. You, S.H. Yoon, J.W. NamHigh-confidence coding and noncoding transcriptome maps Genome Res, 27 (6) (2017), pp. 1050-1062

27 R. Leman, P. Gaildrat, G. Le Gac, et al.Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort Nucleic Acids Res, 46 (15) (2018), pp. 7913-7923

28 A. Moles-Fernández, L. Duran-Lozano, G. Montalban, et al.Computational tools for splicing defect prediction in breast/ovarian cancer genes: how efficient are they at predicting RNA alterations? Front Genet, 9 (2018), p. 366

29 A. Tiulpakov, N. Zubkova, N. Makretskaya, et al.Minigene splicing assessment of 20 novel synonymous and intronic glucokinase gene variants identified in patients with maturity-onset diabetes of the young Hum Mutat, 41 (1) (2020), pp. 129-132

30 S. Monger, M. Troup, E. Ip, et al.Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants Bioinformatics, 35 (21) (2019), pp. 4405-4407

31 J.M. Rodriguez, P. Maietta, I. Ezkurdia, et al.APPRIS: annotation of principal and alternative splice isoforms Nucleic Acids Res, 41 (Database issue) (2013), pp. D110-D117

32 M. Garber, M.G. Grabherr, M. Guttman, et al.Computational methods for transcriptome annotation and quantification using RNA-seq Nat Methods, 8 (6) (2011), pp. 469-477

33 M. Guttman, M. Garber, J.Z. Levin, et al.Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Nat Biotechnol, 28 (5) (2010), pp. 503-510

34 H. Kawaji, M. Lizio, M. Itoh, et al.Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing Genome Res, 24 (4) (2014), pp. 708-717

35 C.H. Jan, R.C. Friedman, J.G. Ruby, et al.Formation, regulation and evolution of Caenorhabditis elegans 3’UTRs Nature, 469 (7328) (2011), pp. 97-101

36 M. Kim, B.H. You, J.W. NamGlobal estimation of the 3' untranslated region landscape using RNA sequencing Methods, 83 (2015), pp. 111-117

37 Z. Huang, E.C. TeelingExUTR: a novel pipeline for large-scale prediction of 3'-UTR sequences from NGS data BMC Genom, 18 (1) (2017), p. 847

38 Y.N. Kang, D.P. Lai, H.S. Ooi, et al.Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast Mol Genet Genom, 290 (1) (2015), pp. 217-224

39 L. Kong, Y. Zhang, Z.Q. Ye, et al.CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine Nucleic Acids Res, 35 (Web Server issue) (2007), pp. W345-W349

40 M.F. Lin, I. Jungreis, M. KellisPhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions Bioinformatics, 27 (13) (2011), pp. i275-i282

41 L. Wang, H.J. Park, S. Dasari, et al.CPAT: coding-Potential Assessment Tool using an alignment-free logistic regression model Nucleic Acids Res, 41 (6) (2013), p. e74

42 L. Sun, H. Luo, D. Bu, et al.Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts Nucleic Acids Res, 41 (17) (2013), p. e166

43 A. Li, J. Zhang, Z. ZhouPLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme BMC Bioinf, 15 (1) (2014), p. 311

44 J. Zhao, X. Song, K. WanglncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts Sci Rep, 6 (2016), Article 34838

45 J.C. Guo, S.S. Fang, Y. Wu, et al.CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition Nucleic Acids Res, 47 (W1) (2019), pp. W516-W522

46 X. Tong, S. LiuCPPred: coding potential prediction based on the global description of RNA sequence Nucleic Acids Res, 47 (8) (2019), p. e43

47 Y. Zhang, C. Jia, M.J. Fullwood, et al.DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction Briefings Bioinf, 22 (2) (2021), pp. 2073-2084

48 T. Kondo, S. Plaza, J. Zanet, et al.Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis Science, 329 (5989) (2010), pp. 336-339

49 B.R. Nelson, C.A. Makarewich, D.M. Anderson, et al.A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle Science, 351 (6270) (2016), pp. 271-275

50 N. Rion, M.A. RüeggLncRNA-encoded peptides: more than translational noise? Cell Res, 27 (5) (2017), pp. 604-605

51 P. Wu, Y. Mo, M. Peng, et al.Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA Mol Cancer, 19 (1) (2020), p. 22

52 Y. Chen, L. Ho, V. TergaonkarsORF-Encoded MicroPeptides: new players in inflammation, metabolism, and precision medicine Cancer Lett, 500 (2021), pp. 263-270

53 C.T. Flower, L. Chen, H.J. Jung, et al.An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla Physiol Genom, 52 (10) (2020), pp. 485-491

54 B. Wang, J. Hao, N. Pan, et al.Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell J Proteonomics, 230 (2021), Article 103965

55 B. Bonilauri, F.B. Holetz, B. DallagiovannaLong non-coding RNAs associated with ribosomes in human adipose-derived stem cells: from RNAs to microproteins Biomolecules, 11 (11) (2021), p. 1673

56 Y. Hao, L. Zhang, Y. Niu, et al.SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci Briefings Bioinf, 19 (4) (2018), pp. 636-643

57 M.P. Dragomir, G.C. Manyam, L.F. Ott, et al.FuncPEP: a database of functional peptides encoded by non-coding RNAs Noncoding RNA, 6 (4) (2020), p. 41

58 H. Liu, X. Zhou, M. Yuan, et al.ncEP: a manually curated database for experimentally validated ncRNA-encoded proteins or peptides J Mol Biol, 432 (11) (2020), pp. 3364-3368

59 Y. Huang, J. Wang, Y. Zhao, et al.cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function Nucleic Acids Res, 49 (D1) (2021), pp. D65-D70

60 T. Liu, J. Wu, Y. Wu, et al.LncPep: a resource of translational evidences for lncRNAs Front Cell Dev Biol, 10 (2022), Article 795084

61 D. Lv, Z. Chang, Y. Cai, et al.TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome Nucleic Acids Res, 50 (D1) (2022), pp. D413-D420

62 X. Luo, Y. Huang, H. Li, et al.SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients Nucleic Acids Res, 50 (D1) (2022), pp. D1373-D1381

63 V. Olexiouk, G. MenschaertUsing the sORFs.Org database Curr Protoc Bioinformatics, 65 (1) (2019), p. e68

64 M.A. Brunet, J.F. Lucier, M. Levesque, et al.OpenProt 2021:deeper functional annotation of the coding potential of eukaryotic genomes Nucleic Acids Res, 49 (D1) (2021), pp. D380-D388

65 S.A. Choteau, A. Wagner, P. Pierre, et al.MetamORF: A repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses Database (Oxford), 2021 (2021), Article baab032

66 A.Z.X. Leong, P.Y. Lee, M.A. Mohtar, et al.Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures J Biomed Sci, 29 (1) (2022), p. 19

67 M.K. Iyer, Y.S. Niknafs, R. Malik, et al.The landscape of long noncoding RNAs in the human transcriptome Nat Genet, 47 (3) (2015), pp. 199-208

68 C. Howald, A. Tanzer, J. Chrast, et al.Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome Genome Res, 22 (9) (2012), pp. 1698-1710

69 Y. Liao, G.K. Smyth, W. ShifeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features Bioinformatics, 30 (7) (2014), pp. 923-930

70 S. Anders, P.T. Pyl, W. HuberHTSeq: a Python framework to work with high-throughput sequencing data Bioinformatics, 31 (2) (2015), pp. 166-169

71 J. Kawai, A. Shinagawa, K. Shibata, et al.Functional annotation of a full-length mouse cDNA collection Nature, 409 (6821) (2001), pp. 685-690

72 M. Seki, M. Narusaka, A. Kamiya, et al.Functional annotation of a full-length Arabidopsis cDNA collection Science, 296 (5565) (2002), pp. 141-145

73 P. Kapranov, J. Drenkow, J. Cheng, et al.Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays Genome Res, 15 (7) (2005), pp. 987-997

74 J. Lagarde, B. Uszczynska-Ratajczak, J. Santoyo-Lopez, et al.Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq) Nat Commun, 7 (2016), Article 12339

75 T.R. Mercer, D.J. Gerhardt, M.E. Dinger, et al.Targeted RNA sequencing reveals the deep complexity of the human transcriptome Nat Biotechnol, 30 (1) (2011), pp. 99-104

76 L. Zhu, J. Zhong, X. Jia, et al.Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology Nucleic Acids Res, 44 (2) (2016), pp. 730-743

77 P. Giesselmann, B. Brändl, E. Raimondeau, et al.Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing Nat Biotechnol, 37 (12) (2019), pp. 1478-1481

78 D. Sharon, H. Tilgner, F. Grubert, et al.A single-molecule long-read survey of the human transcriptome Nat Biotechnol, 31 (11) (2013), pp. 1009-1014

79 J. Lagarde, B. Uszczynska-Ratajczak, S. Carbonell, et al.High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing Nat Genet, 49 (12) (2017), pp. 1731-1740

80 A.M. Wenger, P. Peluso, W.J. Rowell, et al.Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome Nat Biotechnol, 37 (10) (2019), pp. 1155-1162

81 J. Ding, X. Adiconis, S.K. Simmons, et al.Systematic comparison of single-cell and single-nucleus RNA-sequencing methods Nat Biotechnol, 38 (6) (2020), pp. 737-746

82 M. Hong, S. Tao, L. Zhang, et al.RNA sequencing: new technologies and applications in cancer research J Hematol Oncol, 13 (1) (2020), p. 166

83 T. Barrett, D.B. Troup, S.E. Wilhite, et al.NCBI GEO: archive for functional genomics data sets: 10 years on Nucleic Acids Res, 39 (2011), pp. D1005-D1010 Database issue

84 J. Barretina, G. Caponigro, N. Stransky, et al.The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Nature, 483 (7391) (2012), pp. 603-607

85 C. Cummins, A. Ahamed, R. Aslam, et al.The European nucleotide archive in 2021 Nucleic Acids Res, 50 (D1) (2022), pp. D106-D110

86 M. Frenkel-Morgenstern, A. Gorohovski, V. Lacroix, et al.ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data Nucleic Acids Res, 41 (2013), pp. D142-D151 Database issue

87 Y. Yu, H. Zhang, Y. Long, et al.Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ∼45 000 plant public RNA-Seq libraries Plant Biotechnol J, 20 (5) (2022), pp. 806-808

88 A. Frankish, M. Diekhans, I. Jungreis, et al.Gencode 2021 Nucleic Acids Res, 49 (D1) (2021), pp. D916-D923

89 X.C. Quek, D.W. Thomson, J.L.V. Maag, et al.lncRNAdb v2.0:expanding the reference database for functional long noncoding RNAs Nucleic Acids Res, 43 (2015), pp. D168-D173 Database issue

90 L. Zhao, J. Wang, Y. Li, et al.NONCODEV6:an updated database dedicated to long non-coding RNA annotation in both animals and plants Nucleic Acids Res, 49 (D1) (2021), pp. D165-D171

91 M. Pertea, A. Shumate, G. Pertea, et al.CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise Genome Biol, 19 (1) (2018), p. 208

92 I. Abugessaisa, J.A. Ramilowski, M. Lizio, et al.FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs Nucleic Acids Res, 49 (D1) (2021), pp. D892-D898

93 M.N. Cabili, C. Trapnell, L. Goff, et al.Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses Genes Dev, 25 (18) (2011), pp. 1915-1927

94 J. Liu, C. Jung, J. Xu, et al.Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis Plant Cell, 24 (11) (2012), pp. 4333-4345

95 H. Wang, P.J. Chung, J. Liu, et al.Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Genome Res, 24 (3) (2014), pp. 444-453

96 H. Luo, D. Bu, L. Sun, et al.Identification and function annotation of long intervening noncoding RNAs Briefings Bioinf, 18 (5) (2017), pp. 789-797

97 B. Zhou, B. Ji, K. Liu, et al.EVLncRNAs 2.0:an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments Nucleic Acids Res, 49 (D1) (2021), pp. D86-D91

98 Z. Li, L. Liu, S. Jiang, et al.LncExpDB: an expression database of human long non-coding RNAs Nucleic Acids Res, 49 (D1) (2021), pp. D962-D968

99 P.J. Volders, J. Anckaert, K. Verheggen, et al.LNCipedia 5:towards a reference set of human long non-coding RNAs Nucleic Acids Res, 47 (D1) (2019), pp. D135-D139

100 L. Liu, Z. Li, C. Liu, et al.LncRNAWiki 2.0:a knowledgebase of human long non-coding RNAs with enhanced curation model and database system Nucleic Acids Res, 50 (D1) (2022), pp. D190-D195

101 L. Ma, J. Cao, L. Liu, et al.LncBook: a curated knowledgebase of human long non-coding RNAs Nucleic Acids Res, 47 (D1) (2019), pp. D128-D134

102 M. Hou, X. Tang, F. Tian, et al.AnnoLnc: a web server for systematically annotating novel human lncRNAs BMC Genom, 17 (1) (2016), p. 931

103 L. Ke, D.C. Yang, Y. Wang, et al.AnnoLnc2:the one-stop portal to systematically annotate novel lncRNAs for human and mouse Nucleic Acids Res, 48 (W1) (2020), pp. W230-W238

104 C. Park, N. Yu, I. Choi, et al.lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs Bioinformatics, 30 (17) (2014), pp. 2480-2485

105 L.L. Zheng, J.H. Li, J. Wu, et al.deepBase v2.0:identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data Nucleic Acids Res, 44 (D1) (2016), pp. D196-D202

106 I. Abugessaisa, H. Shimoji, S. Sahin, et al.FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki Database (Oxford), 2016 (2016), p. baw105

107 Y. Zhang, D. Bu, P. Huo, et al.ncFANs v2.0:an integrative platform for functional annotation of non-coding RNAs Nucleic Acids Res, 49 (W1) (2021), pp. W459-W468

108 J. Chen, J. Zhang, Y. Gao, et al.LncSEA: a platform for long non-coding RNA related sets and enrichment analysis Nucleic Acids Res, 49 (D1) (2021), pp. D969-D980

109 B.M. Bolstad, R.A. Irizarry, M. Åstrand, et al.A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics, 19 (2) (2003), pp. 185-193

110 A. Mortazavi, B.A. Williams, K. McCue, et al.Mapping and quantifying mammalian transcriptomes by RNA-seq Nat Methods, 5 (7) (2008), pp. 621-628

111 S. Anders, W. HuberDifferential expression analysis for sequence count data Genome Biol, 11 (10) (2010), p. R106

112 Y. Lin, K. Golovnina, Z.X. Chen, et al.Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster BMC Genom, 17 (2016), p. 28

113 K. Kadota, J. Ye, Y. Nakai, et al.ROKU: a novel method for identification of tissue-specific genes BMC Bioinf, 7 (2006), p. 294

114 F.M. Cavalli, R. Bourgon, W. Huber, et al.SpeCond: a method to detect condition-specific gene expression Genome Biol, 12 (10) (2011), p. R101

115 E. Forouzmand, N.D.L. Owens, I.L. Blitz, et al.Developmentally regulated long non-coding RNAs in Xenopus tropicalis Dev Biol, 426 (2) (2017), pp. 401-408

116 Z. Tang, Y. Wu, Y. Yang, et al.Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa Sci Rep, 7 (2017), Article 43166

117 A.C. Bester, J.D. Lee, A. Chavez, et al.An integrated genome-wide CRISPRa approach to functionalize lncRNAs in drug resistance Cell, 173 (3) (2018), pp. 649-664.e20

118 J.M. Stuart, E. Segal, D. Koller, et al.A gene-coexpression network for global discovery of conserved genetic modules Science, 302 (5643) (2003), pp. 249-255

119 M. Weber, H. Teeling, S. Huang, et al.Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics ISME J, 5 (5) (2011), pp. 918-928

120 L. Dai, J. Li, Z. Dong, et al.Temporal expression and functional analysis of long non-coding RNAs in colorectal cancer initiation J Cell Mol Med, 23 (6) (2019), pp. 4127-4138

121 C.K. Yu, T. Xu, R.K. Assoian, et al.Mining the stiffness-sensitive transcriptome in human vascular smooth muscle cells identifies long noncoding RNA stiffness regulators Arterioscler Thromb Vasc Biol, 38 (1) (2018), pp. 164-173

122 H. Liu, Y. Sun, H. Tian, et al.Characterization of long non-coding RNA and messenger RNA profiles in laryngeal cancer by weighted gene co-expression network analysis Aging, 11 (22) (2019), pp. 10074-10099

123 H.G. Xiong, H. Li, Y. Xiao, et al.Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma J Exp Clin Cancer Res, 38 (1) (2019), p. 278

124 P. Liu, X. Xie, A. Yang, et al.Melatonin regulates breast cancer progression by the lnc010561/miR-30/FKBP3 axis Mol Ther Nucleic Acids, 19 (2020), pp. 765-774

125 W.S. Yang, T.Y. Lin, L. Chang, et al.HIV-1 tat interacts with a kaposi's sarcoma-associated herpesvirus reactivation-upregulated antiangiogenic long noncoding RNA, LINC00313, and antagonizes its function J Virol, 94 (3) (2020) e01280-19

126 K. Berns, E.M. Hijmans, J. Mullenders, et al.A large-scale RNAi screen in human cells identifies new components of the p53 pathway Nature, 428 (6981) (2004), pp. 431-437

127 M. Boutros, A.A. Kiger, S. Armknecht, et al.Genome-wide RNAi analysis of growth and viability in Drosophila cells Science, 303 (5659) (2004), pp. 832-835

128 J. Seiler, M. Breinig, M. Caudron-Herger, et al.The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance Nucleic Acids Res, 45 (9) (2017), pp. 5458-5469

129 A.L. Jackson, J. Burchard, J. Schelter, et al.Widespread siRNA off-target transcript silencing mediated by seed region sequence complementarity RNA, 12 (7) (2006), pp. 1179-1187

130 C.J. Echeverri, P.A. Beachy, B. Baum, et al.Minimizing the risk of reporting false positives in large-scale RNAi screens Nat Methods, 3 (10) (2006), pp. 777-779

131 L. Cong, F.A. Ran, D. Cox, et al.Multiplex genome engineering using CRISPR/Cas systems Science, 339 (6121) (2013), pp. 819-823

132 T. Wang, J.J. Wei, D.M. Sabatini, et al.Genetic screens in human cells using the CRISPR-Cas9 system Science, 343 (6166) (2014), pp. 80-84

133 O. Shalem, N.E. Sanjana, E. Hartenian, et al.Genome-scale CRISPR-Cas9 knockout screening in human cells Science, 343 (6166) (2014), pp. 84-87

134 S. Konermann, M.D. Brigham, A.E. Trevino, et al.Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex Nature, 517 (7536) (2015), pp. 583-588

135 Y. Zhou, S. Zhu, C. Cai, et al.High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells Nature, 509 (7501) (2014), pp. 487-491

136 S. Chen, N.E. Sanjana, K. Zheng, et al.Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis Cell, 160 (6) (2015), pp. 1246-1260

137 H. Koike-Yusa, Y. Li, E.P. Tan, et al.Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library Nat Biotechnol, 32 (3) (2014), pp. 267-273

138 W. Chen, G. Zhang, J. Li, et al.CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs Nucleic Acids Res, 47 (D1) (2019), pp. D63-D68

139 W. Li, H. Xu, T. Xiao, et al.MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens Genome Biol, 15 (12) (2014), p. 554

140 W. Li, J. Köster, H. Xu, et al.Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR Genome Biol, 16 (2015), p. 281

141 B. Wang, M. Wang, W. Zhang, et al.Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute Nat Protoc, 14 (3) (2019), pp. 756-780

142 H.H. Jeong, S.Y. Kim, M.W.C. Rousseaux, et al.Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives Genome Res, 29 (6) (2019), pp. 999-1008

143 A.A. Diaz, H. Qin, M. Ramalho-Santos, et al.HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis Nucleic Acids Res, 43 (3) (2015), Article e16

144 T.P. Daley, Z. Lin, X. Lin, et al.CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens Genome Biol, 19 (1) (2018), p. 159

145 R.M. Meyers, J.G. Bryan, J.M. McFarland, et al.Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells Nat Genet, 49 (12) (2017), pp. 1779-1784

146 F. Allen, F. Behan, A. Khodak, et al.JACKS: joint analysis of CRISPR/Cas9 knockout screens Genome Res, 29 (3) (2019), pp. 464-471

147 S. Bodapati, T.P. Daley, X. Lin, et al.A benchmark of algorithms for the analysis of pooled CRISPR screens Genome Biol, 21 (1) (2020), p. 62

148 S. Zhu, W. Li, J. Liu, et al.Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library Nat Biotechnol, 34 (12) (2016), pp. 1279-1286

149 J. Joung, J.M. Engreitz, S. Konermann, et al.Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood Nature, 548 (7667) (2017), pp. 343-346

150 S. Covarrubias, E.K. Robinson, B. Shapleigh, et al.CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter J Biol Chem, 292 (51) (2017), pp. 20911-20920

151 P. Cai, A.B.C. Otten, B. Cheng, et al.A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis Genome Res, 30 (1) (2020), pp. 22-34

152 S.J. Liu, M.A. Horlbeck, S.W. Cho, et al.CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells Science, 355 (6320) (2017), Article aah7111

153 R. Esposito, N. Bosch, A. Lanzós, et al.Hacking the cancer genome: profiling therapeutically actionable long non-coding RNAs using CRISPR-Cas9 screening Cancer Cell, 35 (4) (2019), pp. 545-557

154 A. Goyal, K. Myacheva, M. Groß, et al.Challenges of CRISPR/Cas9 applications for long non-coding RNA genes Nucleic Acids Res, 45 (3) (2017), p. e12

155 Y. Liu, Z. Cao, Y. Wang, et al.Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites Nat Biotechnol, 36 (2018), pp. 1203-1210

156 C. Wang, T. Lu, G. Emanuel, et al.Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization Proc Natl Acad Sci USA, 116 (22) (2019), pp. 10842-10851

157 A. Dixit, O. Parnas, B. Li, et al.Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens Cell, 167 (7) (2016), pp. 1853-1866

158 B. Adamson, T.M. Norman, M. Jost, et al.A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response Cell, 167 (7) (2016), pp. 1867-1882

159 D.A. Jaitin, A. Weiner, I. Yofe, et al.Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-seq Cell, 167 (7) (2016), pp. 1883-1896

160 P. Datlinger, A.F. Rendeiro, C. Schmidl, et al.Pooled CRISPR screening with single-cell transcriptome readout Nat Methods, 14 (3) (2017), pp. 297-301

161 M.J. Lawson, D. Camsund, J. Larsson, et al.In situ genotyping of a pooled strain library after characterizing complex phenotypes Mol Syst Biol, 13 (10) (2017), p. 947

162 G. Emanuel, J.R. Moffitt, X. ZhuangHigh-throughput, image-based screening of pooled genetic-variant libraries Nat Methods, 14 (12) (2017), pp. 1159-1162

163 A. Wroblewska, M. Dhainaut, B. Ben-Zvi, et al.Protein barcodes enable high-dimensional single-cell CRISPR screens Cell, 175 (4) (2018), pp. 1141-1155

164 S. Zhu, Z. Cao, Z. Liu, et al.Guide RNAs with embedded barcodes boost CRISPR-pooled screens Genome Biol, 20 (1) (2019), p. 20

165 G. Michlits, M. Hubmann, S.H. Wu, et al.CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens Nat Methods, 14 (12) (2017), pp. 1191-1197

166 B. Schmierer, S.K. Botla, J. Zhang, et al.CRISPR/Cas9 screening using unique molecular identifiers Mol Syst Biol, 13 (10) (2017), p. 945

167 A.H. Smits, F. Ziebell, G. Joberty, et al.Biological plasticity rescues target activity in CRISPR knock outs Nat Methods, 16 (11) (2019), pp. 1087-1093

168 M.A. El-Brolosy, Z. Kontarakis, A. Rossi, et al.Genetic compensation triggered by mutant mRNA degradation Nature, 568 (7751) (2019), pp. 193-197

169 O.O. Abudayyeh, J.S. Gootenberg, P. Essletzbichler, et al.RNA targeting with CRISPR-Cas13 Nature, 550 (7675) (2017), pp. 280-284

170 C. Zhang, S. Konermann, N.J. Brideau, et al.Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d Cell, 175 (1) (2018), pp. 212-223

171 H.H. Wessels, A. Méndez-Mancilla, X. Guo, et al.Massively parallel Cas13 screens reveal principles for guide RNA design Nat Biotechnol, 38 (6) (2020), pp. 722-727

172 E. Lauretti, K. Dabrowski, D. PraticòThe neurobiology of non-coding RNAs and Alzheimer's disease pathogenesis: pathways, mechanisms and translational opportunities Ageing Res Rev, 71 (2021), Article 101425

173 C.A. Hartana, Y. Rassadkina, C. Gao, et al.Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers J Clin Invest, 131 (9) (2021), Article 146136

174 L. Xia, X. Wang, L. Liu, et al.lnc-BAZ2B promotes M2 macrophage activation and inflammation in children with asthma through stabilizing BAZ2B pre-mRNA J Allergy Clin Immunol, 147 (3) (2021), pp. 921-932

175 N. Liu, M. Kataoka, Y. Wang, et al.LncRNA LncHrt preserves cardiac metabolic homeostasis and heart function by modulating the LKB1-AMPK signaling pathway Basic Res Cardiol, 116 (1) (2021), p. 48

176 P. Yu, J. Guo, J. Li, et al.lncRNA-H19 in fibroblasts promotes wound healing in diabetes Diabetes, 71 (7) (2022), pp. 1562-1578

177 R. Liu, X. Li, W. Zhu, et al.Cholangiocyte-derived exosomal long noncoding RNA H19 promotes hepatic stellate cell activation and cholestatic liver fibrosis Hepatology, 70 (4) (2019), pp. 1317-1335

178 J. Li, L. Han, P. Roebuck, et al.TANRIC: an interactive open platform to explore the function of lncRNAs in cancer Cancer Res, 75 (18) (2015), pp. 3728-3737

179 S. Ning, J. Zhang, P. Wang, et al.Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers Nucleic Acids Res, 44 (D1) (2016), pp. D980-D985

180 Z. Bao, Z. Yang, Z. Huang, et al.LncRNADisease 2.0:an updated database of long non-coding RNA-associated diseases Nucleic Acids Res, 47 (D1) (2019), pp. D1034-D1037

181 Y. Gao, X. Li, S. Shang, et al.LincSNP 3.0:an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements Nucleic Acids Res, 49 (D1) (2021), pp. D1244-D1250

182 L. Ning, T. Cui, B. Zheng, et al.MNDR v3.0:mammal ncRNA-disease repository with increased coverage and annotation Nucleic Acids Res, 49 (D1) (2021), pp. D160-D164

183 S.J. Liu, H.X. Dang, D.A. Lim, et al.Long noncoding RNAs in cancer metastasis Nat Rev Cancer, 21 (7) (2021), pp. 446-460

184 M. Winkle, S.M. El-Daly, M. Fabbri, et al.Noncoding RNA therapeutics - challenges and potential solutions Nat Rev Drug Discov, 20 (8) (2021), pp. 629-651

185 A.M. Schmitt, H.Y. ChangLong noncoding RNAs in cancer pathways Cancer Cell, 29 (4) (2016), pp. 452-463

186 D. HanahanHallmarks of cancer: new dimensions Cancer Discov, 12 (1) (2022), pp. 31-46

187 A. Lanzós, J. Carlevaro-Fita, L. Mularoni, et al.Discovery of cancer driver long noncoding RNAs across 1112 tumour genomes: new candidates and distinguishing features Sci Rep, 7 (2017), Article 41544

188 E. Dai, F. Yang, J. Wang, et al.ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance Bioinformatics, 33 (24) (2017), pp. 4010-4011

189 Q. Dong, F. Li, Y. Xu, et al.RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data Briefings Bioinf, 21 (6) (2020), pp. 2167-2174

190 W. Jiang, Y. Qu, Q. Yang, et al.D-lnc: a comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression RNA Biol, 16 (11) (2019), pp. 1586-1591

191 P. Wang, Q. Guo, Y. Qi, et al.LncACTdb 3.0:an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine Nucleic Acids Res, 50 (D1) (2022), pp. D183-D189

192 Y. Gao, S. Shang, S. Guo, et al.Lnc2Cancer 3.0:an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data Nucleic Acids Res, 49 (D1) (2021), pp. D1251-D1258

193 M. Yang, H. Lu, J. Liu, et al.lncRNAfunc: a knowledgebase of lncRNA function in human cancer Nucleic Acids Res, 50 (D1) (2022), pp. D1295-D1306

194 X. Teng, X. Chen, H. Xue, et al.NPInter v4.0:an integrated database of ncRNA interactions Nucleic Acids Res, 48 (D1) (2020), pp. D160-D165

195 J. Graf, M. KretzFrom structure to function: route to understanding lncRNA mechanism Bioessays, 42 (12) (2020), Article e2000027

196 A. Kotar, H.N. Foley, K.M. Baughman, et al.Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods Methods, 183 (2020), pp. 93-107

197 O. Solomon, A. Di Segni, K. Cesarkas, et al.RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure Nat Commun, 8 (1) (2017), p. 1440

198 J.G. Underwood, A.V. Uzilov, S. Katzman, et al.FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing Nat Methods, 7 (12) (2010), pp. 995-1001

199 J.B. Lucks, S.A. Mortimer, C. Trapnell, et al.Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) Proc Natl Acad Sci U S A, 108 (27) (2011), pp. 11063-11068

200 Z. Ouyang, M.P. Snyder, H.Y. ChangSeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data Genome Res, 23 (2) (2013), pp. 377-387

201 R. Delli Ponti, S. Marti, A. Armaos, et al.A high-throughput approach to profile RNA structure Nucleic Acids Res, 45 (5) (2017), p. e35

202 X. Wen, L. Gao, X. Guo, et al.lncSLdb: a resource for long non-coding RNA subcellular localization Database, 2018 (2018), pp. 1-6

203 D. Mas-Ponte, J. Carlevaro-Fita, E. Palumbo, et al.LncATLAS database for subcellular localization of long noncoding RNAs RNA, 23 (7) (2017), pp. 1080-1087

204 T. Cui, Y. Dou, P. Tan, et al.RNALocate v2.0:an updated resource for RNA subcellular localization with increased coverage and annotation Nucleic Acids Res, 50 (D1) (2022), pp. D333-D339

205 M. Zeng, Y. Wu, C. Lu, et al.DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding Briefings Bioinf, 23 (1) (2022), p. bbab360

206 X.D. FuNon-coding RNA: a new frontier in regulatory biology Natl Sci Rev, 1 (2) (2014), pp. 190-204

207 J.A. West, C.P. Davis, H. Sunwoo, et al.The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites Mol Cell, 55 (5) (2014), pp. 791-802

208 J.M. Engreitz, A. Pandya-Jones, P. McDonel, et al.The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome Science, 341 (6147) (2013), Article 1237973

209 J. Engreitz, E.S. Lander, M. GuttmanRNA antisense purification (RAP) for mapping RNA interactions with chromatin Methods Mol Biol, 1262 (2015), pp. 183-197

210 M.D. Simon, C.I. Wang, P.V. Kharchenko, et al.The genomic binding sites of a noncoding RNA Proc Natl Acad Sci USA, 108 (51) (2011), pp. 20497-20502

211 C. Chu, K. Qu, F.L. Zhong, et al.Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions Mol Cell, 44 (4) (2011), pp. 667-678

212 J. Sun, W. Li, Y. Sun, et al.A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies Nucleic Acids Res, 42 (15) (2014), pp. 9588-9601

213 X. Li, B. Zhou, L. Chen, et al.GRID-seq reveals the global RNA-chromatin interactome Nat Biotechnol, 35 (10) (2017), pp. 940-950

214 B. Sridhar, M. Rivas-Astroza, T.C. Nguyen, et al.Systematic mapping of RNA-chromatin interactions in vivo Curr Biol, 27 (4) (2017), pp. 602-609

215 J. Lin, Y. Wen, S. He, et al.Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding Nat Protoc, 14 (3) (2019), pp. 795-818

216 C.C. Kuo, S. Hänzelmann, N. Sentürk Cetin, et al.Detection of RNA-DNA binding sites in long noncoding RNAs Nucleic Acids Res, 47 (6) (2019), p. e32

217 F.A. Buske, D.C. Bauer, J.S. Mattick, et al.Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci Bioinformatics, 29 (15) (2013), pp. 1895-1897

218 F.A. Buske, D.C. Bauer, J.S. Mattick, et al.Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data Genome Res, 22 (7) (2012), pp. 1372-1381

219 T. Wongsurawat, P. Jenjaroenpun, C.K. Kwoh, et al.Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity Nucleic Acids Res, 40 (2) (2012), p. e16

220 P. Jenjaroenpun, T. Wongsurawat, S.P. Yenamandra, et al.QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences Nucleic Acids Res, 43 (W1) (2015), pp. W527-W534

221 G. Terai, J. Iwakiri, T. Kameda, et al.Comprehensive prediction of lncRNA-RNA interactions in human transcriptome BMC Genom, 17 (Suppl 1) (2016), p. 12

222 J.M. Engreitz, K. Sirokman, P. McDonel, et al.RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites Cell, 159 (1) (2014), pp. 188-199

223 J.G.A. Aw, Y. Shen, A. Wilm, et al.In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation Mol Cell, 62 (4) (2016), pp. 603-617

224 G. Kudla, S. Granneman, D. Hahn, et al.Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast Proc Natl Acad Sci U S A, 108 (24) (2011), pp. 10010-10015

225 Z. Lu, Q.C. Zhang, B. Lee, et al.RNA duplex map in living cells reveals higher-order transcriptome structure Cell, 165 (5) (2016), pp. 1267-1279

226 T.C. Nguyen, X. Cao, P. Yu, et al.Mapping RNA-RNA interactome and RNA structure in vivo by MARIO Nat Commun, 7 (2016), Article 12023

227 E. Sharma, T. Sterne-Weiler, D. O'Hanlon, et al.Global mapping of human RNA-RNA interactions Mol Cell, 62 (4) (2016), pp. 618-626

228 J.H. Li, S. Liu, H. Zhou, et al.starBase v2.0:decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data Nucleic Acids Res, 42 (Database issue) (2014), pp. D92-D97

229 I.V. Antonov, E. Mazurov, M. Borodovsky, et al.Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools Briefings Bioinf, 20 (2) (2019), pp. 551-564

230 B. Li, N. Huang, S. Wei, et al.lncRNA TUG1 as a ceRNA promotes PM exposure-induced airway hyper-reactivity J Hazard Mater, 416 (2021), Article 125878

231 P. Wang, Q. Guo, Y. Hao, et al.LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution Nucleic Acids Res, 49 (D1) (2021), pp. D125-D133

232 G.Y. Liu, G.N. Zhao, X.F. Chen, et al.The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster Nucleic Acids Res, 44 (6) (2016), pp. 2613-2627

233 V.B. O'Leary, S.V. Ovsepian, L.G. Carrascosa, et al.PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation in response to low-dose irradiation Cell Rep, 11 (3) (2015), pp. 474-485

234 M.D. Huang, W.M. Chen, F.Z. Qi, et al.Long non-coding RNA TUG1 is up-regulated in hepatocellular carcinoma and promotes cell growth and apoptosis by epigenetically silencing of KLF2 Mol Cancer, 14 (2015), p. 165

235 M. Kretz, Z. Siprashvili, C. Chu, et al.Control of somatic tissue differentiation by the long non-coding RNA TINCR Nature, 493 (7431) (2013), pp. 231-235

236 A. Salameh, A.K. Lee, M. Cardó-Vila, et al.PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3 Proc Natl Acad Sci U S A, 112 (27) (2015), pp. 8403-8408

237 J. Chen, S. Ke, L. Zhong, et al.Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice Biochem Pharmacol, 152 (2018), pp. 94-103

238 J.H. Li, S. Liu, L.L. Zheng, et al.Discovery of protein-lncRNA interactions by integrating large-scale CLIP-seq and RNA-seq datasets Front Bioeng Biotechnol, 2 (2014), p. 88

239 C. Chu, Q.C. Zhang, S.T. da Rocha, et al.Systematic discovery of xist RNA binding proteins Cell, 161 (2) (2015), pp. 404-416

240 C.A. McHugh, M. GuttmanRAP-MS: a method to identify proteins that interact directly with a specific RNA molecule in cells Methods Mol Biol, 1649 (2018), pp. 473-488

241 H.P. Chu, A. Minajigi, Y. Chen, et al.iDRiP for the systematic discovery of proteins bound directly to noncoding RNA Nat Protoc, 16 (7) (2021), pp. 3672-3694

242 Y.C.T. Yang, C. Di, B. Hu, et al.CLIPdb: a CLIP-seq database for protein-RNA interactions BMC Genom, 16 (1) (2015), p. 51

243 D. Cirillo, M. Blanco, A. Armaos, et al.Quantitative predictions of protein interactions with long noncoding RNAs Nat Methods, 14 (1) (2016), pp. 5-6

244 M. Ge, A. Li, M. WangA bipartite network-based method for prediction of long non-coding RNA-protein interactions Dev Reprod Biol, 14 (1) (2016), pp. 62-71

245 H. Hu, L. Zhang, H. Ai, et al.HLPI-Ensemble: prediction of human lncRNA-protein interactions based on ensemble strategy RNA Biol, 15 (6) (2018), pp. 797-806

246 F. Agostini, D. Cirillo, B. Bolognesi, et al.X-inactivation: quantitative predictions of protein interactions in the Xist network Nucleic Acids Res, 41 (1) (2013), p. e31

247 Y. Yao, S. Jin, H. Long, et al.RNAe: an effective method for targeted protein translation enhancement by artificial non-coding RNA with SINEB2 repeat Nucleic Acids Res, 43 (9) (2015), p. e58

248 T.K. Kim, M. Hemberg, J.M. GrayEnhancer RNAs: a class of long noncoding RNAs synthesized at enhancers Cold Spring Harbor Perspect Biol, 7 (1) (2015), Article a018622

249 T.K. Kim, M. Hemberg, J.M. Gray, et al.Widespread transcription at neuronal activity-regulated enhancers Nature, 465 (7295) (2010), pp. 182-187

250 Z. Zhang, J.H. Lee, H. Ruan, et al.Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer Nat Commun, 10 (1) (2019), p. 4562

251 Z. Zhang, W. Hong, H. Ruan, et al.HeRA: an atlas of enhancer RNAs across human tissues Nucleic Acids Res, 49 (D1) (2021), pp. D932-D938

252 L.J. Core, J.J. Waterfall, J.T. LisNascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science, 322 (5909) (2008), pp. 1845-1848

253 D.B. Mahat, H. Kwak, G.T. Booth, et al.Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) Nat Protoc, 11 (8) (2016), pp. 1455-1476

254 T. Chu, E.J. Rice, G.T. Booth, et al.Chromatin Run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme Nat Genet, 50 (11) (2018), pp. 1553-1564

255 J.P. Smith, A.B. Dutta, K.M. Sathyan, et al.PEPPRO: quality control and processing of nascent RNA profiling data Genome Biol, 22 (1) (2021), p. 155

256 K.F. Au, H. Jiang, L. Lin, et al.Detection of splice junctions from paired-end RNA-seq data by SpliceMap Nucleic Acids Res, 38 (14) (2010), pp. 4570-4578

257 K. Wang, D. Singh, Z. Zeng, et al.MapSplice: accurate mapping of RNA-seq reads for splice junction discovery Nucleic Acids Res, 38 (18) (2010), p. e178

258 T.D. Wu, S. NacuFast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics, 26 (7) (2010), pp. 873-881

259 A. Dobin, C.A. Davis, F. Schlesinger, et al.STAR: ultrafast universal RNA-seq aligner Bioinformatics, 29 (1) (2013), pp. 15-21

260 D. Kim, G. Pertea, C. Trapnell, et al.TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol, 14 (4) (2013), p. R36

261 H. LiMinimap2:pairwise alignment for nucleotide sequences Bioinformatics, 34 (18) (2018), pp. 3094-3100

262 H. LiNew strategies to improve minimap2 alignment accuracy Bioinformatics, 37 (23) (2021), pp. 4572-4574

263 B. Liu, Y. Liu, J. Li, et al.deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index Genome Biol, 20 (1) (2019), p. 274

264 M.T. Parker, K. Knop, G.J. Barton, et al.2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing Genome Biol, 22 (1) (2021), p. 72

265 W. Li, T. JiangTranscriptome assembly and isoform expression level estimation from biased RNA-Seq reads Bioinformatics, 28 (22) (2012), pp. 2914-2921

266 L. Song, L. FloreaCLASS: constrained transcript assembly of RNA-seq reads BMC Bioinf, 14 (Suppl 5) (2013), p. S14

267 A.I. Tomescu, A. Kuosmanen, R. Rizzi, et al.A novel Min-cost flow method for estimating transcript expression with RNA-Seq BMC Bioinf, 14 (Suppl 5) (2013), p. S15

268 A.M. Mezlini, E.J.M. Smith, M. Fiume, et al.iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data Genome Res, 23 (3) (2013), pp. 519-529

269 L. Maretty, J.A. Sibbesen, A. KroghBayesian transcriptome assembly Genome Biol, 15 (10) (2014), p. 501

270 E. Bernard, L. Jacob, J. Mairal, et al.Efficient RNA isoform identification and quantification from RNA-Seq data with network flows Bioinformatics, 30 (17) (2014), pp. 2447-2455

271 J. Liu, T. Yu, T. Jiang, et al.TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs Genome Biol, 17 (1) (2016), p. 213

272 L. Song, S. Sabunciyan, L. FloreaCLASS2:accurate and efficient splice variant annotation from RNA-seq reads Nucleic Acids Res, 44 (10) (2016), p. e98

273 S. Canzar, S. Andreotti, D. Weese, et al.CIDANE: comprehensive isoform discovery and abundance estimation Genome Biol, 17 (2016), p. 16

274 M. Shao, C. KingsfordAccurate assembly of transcripts through phase-preserving graph decomposition Nat Biotechnol, 35 (12) (2017), pp. 1167-1169

275 J. Liu, X. Liu, X. Ren, et al.scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions Bioinformatics, 35 (21) (2019), pp. 4264-4271

276 L. Song, S. Sabunciyan, G. Yang, et al.A multi-sample approach increases the accuracy of transcript assembly Nat Commun, 10 (1) (2019), p. 5000

277 X. Shi, A.F. Neuwald, X. Wang, et al.IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles Bioinformatics, 37 (5) (2021), pp. 650-658

278 D.R. Zerbino, E. BirneyVelvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res, 18 (5) (2008), pp. 821-829

279 T. Namiki, T. Hachiya, H. Tanaka, et al.MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads Nucleic Acids Res, 40 (20) (2012), p. e155

280 J. Liu, G. Li, Z. Chang, et al.BinPacker: packing-based de novo transcriptome assembly from RNA-seq data PLoS Comput Biol, 12 (2) (2016), Article e1004772

281 M.F. Hsieh, C.L. Lu, C.Y. TangClover: a clustering-oriented de novo assembler for Illumina sequences BMC Bioinf, 21 (1) (2020), p. 528

282 X. Shi, X. Wang, A.F. Neuwald, et al.A Bayesian approach for accurate de novo transcriptome assembly Sci Rep, 11 (1) (2021), Article 17663

283 G. Jia, X. Wang, G. XiaoA permutation-based non-parametric analysis of CRISPR screen data BMC Genom, 18 (1) (2017), p. 545

284 Q. Hua, M. Jin, B. Mi, et al.LINC01123, a c-Myc-activated long non-coding RNA, promotes proliferation and aerobic glycolysis of non-small cell lung cancer through miR-199a-5p/c-Myc axis J Hematol Oncol, 12 (1) (2019), p. 91

285 Y. Zhong, L. Yang, F. Xiong, et al.Long non-coding RNA AFAP1-AS1 accelerates lung cancer cells migration and invasion by interacting with SNIP1 to upregulate c-Myc Signal Transduct Targeted Ther, 6 (1) (2021), p. 240

286 X. Qian, J. Yang, Q. Qiu, et al.LCAT3, a novel m6A-regulated long non-coding RNA, plays an oncogenic role in lung cancer via binding with FUBP1 to activate c-MYC J Hematol Oncol, 14 (1) (2021), p. 112

287 Z. Peng, J. Wang, B. Shan, et al.The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1 Mol Cancer, 17 (1) (2018), p. 167

288 J. Kim, H.L. Piao, B.J. Kim, et al.Long noncoding RNA MALAT1 suppresses breast cancer metastasis Nat Genet, 50 (12) (2018), pp. 1705-1715

289 Q. Hu, Y. Ye, L.C. Chan, et al.Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression Nat Immunol, 20 (7) (2019), pp. 835-851

290 D. Huang, J. Chen, L. Yang, et al.NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death Nat Immunol, 19 (10) (2018), pp. 1112-1125

291 J. Wang, S. Xie, J. Yang, et al.The long noncoding RNA H19 promotes tamoxifen resistance in breast cancer via autophagy J Hematol Oncol, 12 (1) (2019), p. 81

292 Z. Wei, L. Chen, L. Meng, et al.LncRNA HOTAIR promotes the growth and metastasis of gastric cancer by sponging miR-1277-5p and upregulating COL5A1 Gastric Cancer, 23 (6) (2020), pp. 1018-1032

293 E. Zhang, X. He, C. Zhang, et al.A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1 Genome Biol, 19 (1) (2018), p. 154

294 Y. Hu, Y. Yu, S. You, et al.Long noncoding RNA MALAT1 regulates autophagy associated chemoresistance via miR-23b-3p sequestration in gastric cancer Mol Cancer, 16 (1) (2017), p. 174

295 Y. Wang, L. He, Y. Du, et al.The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling Cell Stem Cell, 16 (4) (2015), pp. 413-425

296 J.H. Yuan, F. Yang, F. Wang, et al.A long noncoding RNA activated by TGF-β promotes the invasion-metastasis cascade in hepatocellular carcinoma Cancer Cell, 25 (5) (2014), pp. 666-681

297 R. Jiang, J. Tang, Y. Chen, et al.The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion Nat Commun, 8 (2017), Article 15129

298 T. Guo, C. Gong, P. Wu, et al.LINC00662 promotes hepatocellular carcinoma progression via altering genomic methylation profiles Cell Death Differ, 27 (7) (2020), pp. 2191-2205

299 B. Chen, M.P. Dragomir, L. Fabris, et al.The long noncoding RNA CCAT2 induces chromosomal instability through BOP1-AURKB signalin Gastroenterology, 159 (6) (2020), pp. 2146-2162

300 M. Pichler, C. Rodriguez-Aguayo, S.Y. Nam, et al.Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer Gut, 69 (10) (2020), pp. 1818-1831

301 S. Wen, Y. Wei, C. Zen, et al.Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine Mol Cancer, 19 (1) (2020), p. 171

302 J.R. Prensner, M.K. Iyer, A. Sahu, et al.The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex Nat Genet, 45 (11) (2013), pp. 1392-1398

303 C. Chen, Y. Luo, W. He, et al.Exosomal long noncoding RNA LNMAT2 promotes lymphatic metastasis in bladder cancer J Clin Invest, 130 (1) (2020), pp. 404-421

304 Y. Zhan, Z. Chen, S. He, et al.Long non-coding RNA SOX2OT promotes the stemness phenotype of bladder cancer cells by modulating SOX2 Mol Cancer, 19 (1) (2020), p. 25

305 D. Papaioannou, A. Petri, O.M. Dovey, et al.The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia Nat Commun, 10 (1) (2019), p. 5351

306 Y. Ma, G. Guo, T. Li, et al.A novel imatinib-upregulated long noncoding RNA plays a critical role in inhibition of tumor growth induced by Abl oncogenes Mol Cancer, 21 (1) (2022), p. 5

307 H. Li, X. Wang, C. Wen, et al.Long noncoding RNA NORAD, a novel competing endogenous RNA, enhances the hypoxia-induced epithelial-mesenchymal transition to promote metastasis in pancreatic cancer Mol Cancer, 16 (1) (2017), p. 169

308 H. Hu, Y. Wang, X. Ding, et al.Long non-coding RNA XLOC000647 suppresses progression of pancreatic cancer and decreases epithelial-mesenchymal transition-induced cell invasion by down-regulating NLRP3 Mol Cancer, 17 (1) (2018), p. 18

309 Z. Du, X. Wen, Y. Wang, et al.Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network Genome Biol, 22 (1) (2021), p. 233