Achawanantakun R et al (2015) LncRNA-ID: Long non-coding RNA identification using balanced random forests. Bioinform 31(24):3897–3905
Agarwal V et al (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elite 4:e05005
Altesha MA et al (2019) Circular RNA in cardiovascular disease. J Cell Physiol 234(5):5588–5600
[PMID:
30341894]
Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19(7):454–492
[PMID:
18839252]
Amaral PP et al (2011) lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acid Res 39(1):D146–D151
[PMID:
21112873]
Aparicio-Puerta E et al (2019) sRNAbench and sRNAtoolbox 2019: Intuitive fast small RNA profiling and differential expression. Nucleic Acids Res 47(1):W530–W535
[PMID:
31114926]
Backes C et al (2016) miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res 44(W1):W110–W116
[PMID:
27131362]
Baek J et al (2018) LncRNAnet: Long non-coding RNA identification using deep learning. Bioinform 34(22):3889–3897
[DOI:
10.1093/bioinformatics/bty418]
Baek J et al (2018) LncRNAnet: Long non-coding RNA identification using deep learning. Bioinform 34(22):3889–3897
[DOI:
10.1093/bioinformatics/bty418]
Beltran M et al (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial–mesenchymal transition. Genes Dev 22(6):756–769
[PMID:
18347095]
Betel D et al (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11(8):1–14
[DOI:
10.1186/gb-2010-11-8-r90]
Bortolomeazzi M, Gaffo E, Bortoluzzi S (2019) A survey of software tools for microRNA discovery and characterization using RNA-seq. Brief Bioinform. 20(3):918–930
[PMID:
29126230]
Boucheham A et al (2017) IpiRId: Integrative approach for piRNA prediction using genomic and epigenomic data. Plos One 12(6):e0179787
[PMID:
28622364]
Castañeda J et al (2011) piRNAs, transposon silencing, and germline genome integrity. Mutat Res/Fundam Mol Mech Mutagen 714(1–2):95–104
[DOI:
10.1016/j.mrfmmm.2011.05.002]
Chen L et al (2019) Trends in the development of miRNA bioinformatics tools. Brief Bioinform 20(5):1836–1852. https://doi.org/10.1093/bib/bby054
[DOI:
10.1093/bib/bby054]
Chen G, Ning B, Shi T (2019b) Single-cell RNA-seq technologies and related computational data analysis. Front Genet317
Cheng W-C et al (2013) YM500: A small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 41(D1):D285–D294
[PMID:
23203880]
Cheng J, Metge F, Dieterich CJB (2016) Specific Identification and Quantification of Circular RNAs from Sequencing Data. Bioinform 32(7):1094–1096
[DOI:
10.1093/bioinformatics/btv656]
Chiquitto AG et al (2022) Impact of sequencing technologies on long non-coding RNA computational identification. BioRxiv. https://doi.org/10.1101/2022.04.15.488462
Cox DN et al (1998) A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 12(23):3715–3727
[PMID:
9851978]
Cox DN, Chao A, Lin HJD (2000) Piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development 127(3):503–514
[PMID:
10631171]
Dinger ME et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18(9):1433–1445
[PMID:
18562676]
Ernst C, Odom DT, Kutter C (2017) The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun 8(1):1–10
[DOI:
10.1038/s41467-017-01049-7]
Everaert C et al (2017) Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data. Sci Rep 7(1):1–11
[DOI:
10.1038/s41598-017-01617-3]
Fan XN, Zhang SW (2015) lncRNA-MFDL: Identification of human long non-coding RNAs by fusing multiple features and using deep learning. Mol BioSyst 11(3):892–897
[PMID:
25588719]
Fang Y et al (2020) Recent advances on the roles of LncRNAs in cardiovascular disease. J Cell Mol Med 24(21):12246–12257
[PMID:
32969576]
Farrell D (2017) Smallrnaseq: short non coding RNA-seq analysis with Python. Biorxiv :110585. https://doi.org/10.1101/110585
Frith MC, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genetics 13(8):894–897
[DOI:
10.1038/sj.ejhg.5201459]
Fu Q et al (2018) Single-cell non-coding RNA in embryonic development. Single Cell Biomed :19–32. https://doi.org/10.1007/978-981-13-0502-3_3
Gao Y, Zhang J, Zhao F (2018) Circular RNA identification based on multiple seed matching. Brief Bioinform 19(5):803–810
[PMID:
28334140]
Gawronski KA, Kim J (2017) Single cell transcriptomics of noncoding RNAs and their cell-specificity. Wiley Interdiscip Rev RNA 8(6):e1433
[DOI:
10.1002/wrna.1433]
Ge M et al (2016) A bipartite network-based method for prediction of long non-coding RNA–protein interactions. Genomics Proteomics Bioinformatics 14(1):62–71
Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14(11):699–712
[PMID:
24105322]
Geles K et al (2021) WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data. F1000Res 10:1. https://doi.org/10.12688/f1000research.27868.3
Giroux P et al (2020) miRViz: A novel webserver application to visualize and interpret microRNA datasets. Nucleic Acids Res 48(W1):W252–W261
[PMID:
32319523]
Gong Y et al (2021) Bioinformatics analysis of long non-coding RNA and related diseases: An overview. Front Genet 12:813873. https://doi.org/10.3389/fgene.2021.813873
Guttman M et al (2010) Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5):503–510
[PMID:
20436462]
Hagemann-Jensen M et al (2018) Small-seq for single-cell small-RNA sequencing. Nat Protoc 13(10):2407–2424
[PMID:
30250291]
Han BW et al (2015) piPipes: A set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-Seq, Degradome-and CAGE-Seq, ChIP-Seq and genomic DNA sequencing. Bioinformatics 31(4):593–595
[PMID:
25342065]
Han S et al (2019) LncFinder: An integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. Brief Bioinform 20(6):2009–2027
[PMID:
30084867]
Hauptman N, Glavač D (2013) Long non-coding RNA in cancer. Int J Mol Sci 14(3):4655–4669
[PMID:
23443164]
Hinger SA et al (2018) Diverse long RNAs are differentially sorted into extracellular vesicles secreted by colorectal cancer cells. Cell Rep 25(3):715–725
[PMID:
30332650]
Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16(2):71–84
[PMID:
25554358]
Hu X et al (2020) Integration of single-cell multi-omics for gene regulatory network inference. Comput Struct Biotechnol J 18:1925–1938
[PMID:
32774787]
Huarte M (2015) The emerging role of lncRNAs in cancer. Nat Med 21(11):1253–1261
[PMID:
26540387]
Hwang B, Lee JH, Bang D (2018) Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med 50(8):1–14
[PMID:
30416196]
Iyer MK et al (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47(3):199–208
[PMID:
25599403]
Jarroux J, Morillon A, Pinskaya M (2017) History, discovery, and classification of lncRNAs. Adv Exp Med Biol 1008:1-46
Jensen S et al (2020) Conserved small nucleotidic elements at the origin of concerted piRNA biogenesis from genes and lncRNAs. Cells 9(6):1491
[PMID:
32570966]
Jurka J (2000) Repbase update: a database and an electronic journal of repetitive elements. Trend Genet 16(9):418–420
[DOI:
10.1016/S0168-9525(00)02093-X]
Karunanithi S, Simon M, Schulz MHJP (2019) Automated Analysis of Small RNA Datasets with RAPID. PeerJ 7:e6710
[PMID:
30993044]
Kato M, Carninci P (2020) Genome-wide technologies to study RNA–chromatin interactions. Noncoding RNA 6(2):20
[PMID:
32471183]
Kawai J et al (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409(6821):685–689
[PMID:
11217851]
Kertesz M et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39(10):1278–1284
[PMID:
17893677]
Li D et al (2016) A genetic algorithm-based weighted ensemble method for predicting transposon-derivedd piRNAs. BMC Bioinform 17(1):1–11
[DOI:
10.1186/s12859-016-1206-3]
Li Z, Zhu X, Huang S (2020) Extracellular vesicle long non-coding RNAs and circular RNAs: Biology, functions and applications in cancer. Cancer Lett 489:111–120
[PMID:
32561417]
Liu X, Ding J, Gong J (2014) piRNA identification based on motif discovery. Mol BioSyst 10(12):3075–3080
[PMID:
25230731]
Liu Q et al (2021) Small Noncoding RNA Discovery and Profiling with sRNAtools Based on High-Throughput Sequencing. Brief Bioinform 22(1):463–473
[PMID:
31885040]
Liu Z et al (2021) DEBKS: A tool to detect differentially expressed circular RNA
Liu S et al (2019) PredLnc-GFStack: A global sequence feature based on a stacked ensemble learning method for predicting lncRNAs from transcripts. Genes (Basel) 10(9):672
Lorenzi L et al (2019) Long noncoding RNA expression profiling in cancer: Challenges and opportunities. Genes Chromosom Cancer 58(4):191–199
[PMID:
30461116]
Luginbühl J, Sivaraman DM, Shin JW (2017) The essentiality of non-coding RNAs in cell reprogramming. Noncoding RNA Res 2(1):74–82
[PMID:
30159423]
Ma L, Bajic VB, Zhang Z (2013) On the classification of long non-coding RNAs. RNA Biol 10(6):924–933
[>PMCID:
]
Matsumoto H et al (2017) SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Bioinformatics 33(15):2314–2321
[PMID:
28379368]
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: Insights into functions. Nat Rev Genet 10(3):155–159
[PMID:
19188922]
Mohankumar S, Patel T (2016) Extracellular vesicle long noncoding RNA as potential biomarkers of liver cancer. Brief Funct Genomics 15(3):249–256
[PMID:
26634812]
Monga I, Banerjee I (2019) Computational identification of piRNAs using features based on rna sequence, structure, thermodynamic and physicochemical properties. Curr Genom 20(7):508–518
[DOI:
10.2174/1389202920666191129112705]
Mortazavi A et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628
[PMID:
18516045]
Nielsen MM, Pedersen JS (2021) miRNA activity inferred from single cell mRNA expression. Sci Rep 11(1):1–8
[DOI:
10.1038/s41598-021-88480-5]
Pan X, Xiong K (2015) PredcircRNA: Computational classification of circular RNA from other long non-coding RNA using hybrid features. Mol Biosyst 11(8):2219–2226
[PMID:
26028480]
Pan Q et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40(12):1413–1415
[PMID:
18978789]
Pasmant E et al (2007) Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Can Res 67(8):3963–3969
[DOI:
10.1158/0008-5472.CAN-06-2004]
Pogorelcnik R et al (2018) sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data. Mobile DNA 9(1):1–6
[DOI:
10.1186/s13100-018-0130-7]
Quillet A et al (2020) Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation. Front Genet 10:1330
[PMID:
32047509]
Ramos TA et al (2021) RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction. F1000Res 10:323. https://doi.org/10.12688/f1000research.52350.2
Riffo-Campos ÁL, Riquelme I, Brebi-Mieville P (2016) Tools for sequence-based miRNA target prediction: What to choose? Int J Mol Sci 17(12):1987
[PMID:
27941681]
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166
[PMID:
22663078]
Rocchi A et al (2020) MicroRNAs: An update of applications in forensic science. Diagnostics 11(1):32
[PMID:
33375374]
Ru Y et al (2014) The multiMiR R package and database: Integration of microRNA–target interactions along with their disease and drug associations. Nucleic Acids Res 42(17):e133–e133
[PMID:
25063298]
Sablok G et al (2013) isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett 587(16):2629–2634
[PMID:
23831580]
Shi J et al (2021) PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol 23(4):424–436
[PMID:
33820973]
Song X et al (2016) Circular RNA profile in gliomas revealed by identification toolUROBORUS. Nucleic Acids Res 44(9):e87–e87
[PMID:
26873924]
Sun L et al (2015) lncRScan-SVM: A tool for predicting long non-coding RNAs using support vector machine. Plos One 10(10):e0139654
[PMID:
26437338]
Szabo L, Salzman J (2016) Detecting circular RNAs: Bioinformatic and experimental challenges. Nat Rev Genet 17(11):679–692
[PMID:
27739534]
Thind AS et al (2021) Demystifying emerging bulk RNA-Seq applications: The application and utility of bioinformatic methodology. Brief Bioinform 22(6):bbab259
[PMID:
34329375]
Thind AS, Kaur K, Monga I (2022) An overview of databases and tools for lncrna genomics advancing precision medicine. Mach Learn Syst Biol Genomics Health :49–67. https://doi.org/10.1007/978-981-16-5993-5_3
Turki T, Taguchi Y (2020) SCGRNs: Novel supervised inference of single-cell gene regulatory networks of complex diseases. Comput Biol Med 118:103656
[PMID:
32174324]
Uhrig S, Klein H (2019) PingPongPro: A tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data. Bioinform 35(2):335–336
[DOI:
10.1093/bioinformatics/bty578]
Ünsal K, Morgan GT (1995) A novel group of families of short interspersed repetitive elements (SINEs) inXenopus: Evidence of a specific target site for dna-mediated transposition of inverted-repeat SINEs. J Mol Biol 248(4):812–823
[PMID:
7752242]
Uszczynska-Ratajczak B et al (2018) Towards a complete map of the human long non-coding RNA transcriptome. Nat Rev Genet 19(9):535–548
[PMID:
29795125]
Volders PJ et al (2013) LNCipedia: A database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 41(D1):D246–D251
[PMID:
23042674]
Wang J, Wang LJB (2019) Deep learning of the back-splicing code for circular RNA formation. Bioinform 35(24):5235–5242
[DOI:
10.1093/bioinformatics/btz382]
Wang Y et al (2013a) The role of miRNA-29 family in cancer. Eur J Cell Biol 92(3):123–128
[PMID:
23357522]
Wang L et al (2013b) CPAT: Coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res 41(6):e74–e74
[PMID:
23335781]
Wang J et al (2019) piRBase: A comprehensive database of piRNA sequences. Nucleic Acids Res 47(D1):D175–D180
[PMID:
30371818]
Wang J et al (2021) scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses. Nat Commun 12(1):1–11
Wilson JE, Connell JE, Macdonald PM (1996) aubergine enhances oskar translation in the Drosophila ovary. Development 122(5):1631–1639
[PMID:
8625849]
Wucher V et al (2017) FEELnc: A tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res 45(8):e57–e57
[PMID:
28053114]
Xu Y et al (2020) Predicting long non-coding RNAs through feature ensemble learning. BMC Genom 21(13):1–12
Yang Q et al (2019) Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes. Nat Commun 10(1):1–15
Yang C et al (2021) LncADeep performance on full-length transcripts. Nat Mach Intell 3(3):197–198
[DOI:
10.1038/s42256-019-0108-2]
Zeng Q et al (2021) PIWI-interacting RNAs and PIWI proteins in diabetes and cardiovascular disease: Molecular pathogenesis and role as biomarkers. Clin Chim Acta 518:33–37
[PMID:
33746016]
Zhang X-O et al (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26(9):1277–1287
[PMID:
27365365]
Zhang J et al (2020) Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11(1):1–14
Zhao Y, Yuan J, Chen R (2016) NONCODEv4: Annotation of noncoding RNAs with emphasis on long noncoding RNAs. Long Non-Coding RNAs. Springer, pp 243–254
[DOI:
10.1007/978-1-4939-3378-5_19]
Zhao X, Lan Y, Chen D (2022) Exploring long non-coding RNA networks from single cell omics data. Comput Struct Biotechnol J 20:4381–4389. https://doi.org/10.1016/j.csbj.2022.08.003
[DOI:
10.1016/j.csbj.2022.08.003]
Ziemann M, Kaspi A, El-Osta AJR (2016) Evaluation of microRNA alignment techniques. RNA 22(8):1120–1138
[PMID:
27284164]
