209 related articles for article (PubMed ID: 34606413)
1. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.
Radecki P; Uppuluri R; Deshpande K; Aviran S
RNA Biol; 2021 Oct; 18(sup1):521-536. PubMed ID: 34606413
[TBL] [Abstract][Full Text] [Related]
2. Dawn of the in vivo RNA structurome and interactome.
Kwok CK
Biochem Soc Trans; 2016 Oct; 44(5):1395-1410. PubMed ID: 27911722
[TBL] [Abstract][Full Text] [Related]
3. Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.
Pan X; Rijnbeek P; Yan J; Shen HB
BMC Genomics; 2018 Jul; 19(1):511. PubMed ID: 29970003
[TBL] [Abstract][Full Text] [Related]
4. RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.
Pan X; Shen HB
BMC Bioinformatics; 2017 Feb; 18(1):136. PubMed ID: 28245811
[TBL] [Abstract][Full Text] [Related]
5. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.
Ledda M; Aviran S
Genome Biol; 2018 Mar; 19(1):28. PubMed ID: 29495968
[TBL] [Abstract][Full Text] [Related]
6. DotAligner: identification and clustering of RNA structure motifs.
Smith MA; Seemann SE; Quek XC; Mattick JS
Genome Biol; 2017 Dec; 18(1):244. PubMed ID: 29284541
[TBL] [Abstract][Full Text] [Related]
7. Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.
Li YE; Xiao M; Shi B; Yang YT; Wang D; Wang F; Marcia M; Lu ZJ
Genome Biol; 2017 Sep; 18(1):169. PubMed ID: 28886744
[TBL] [Abstract][Full Text] [Related]
8. A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data.
Polishchuk M; Paz I; Kohen R; Mesika R; Yakhini Z; Mandel-Gutfreund Y
Methods; 2017 Apr; 118-119():73-81. PubMed ID: 28274760
[TBL] [Abstract][Full Text] [Related]
9. Discovering sequence and structure landscapes in RNA interaction motifs.
Adinolfi M; Pietrosanto M; Parca L; Ausiello G; Ferrè F; Helmer-Citterich M
Nucleic Acids Res; 2019 Jun; 47(10):4958-4969. PubMed ID: 31162604
[TBL] [Abstract][Full Text] [Related]
10. ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller D; Krestel R; Ohler U; Vingron M; Marsico A
Nucleic Acids Res; 2017 Nov; 45(19):11004-11018. PubMed ID: 28977546
[TBL] [Abstract][Full Text] [Related]
11. Understanding the transcriptome through RNA structure.
Wan Y; Kertesz M; Spitale RC; Segal E; Chang HY
Nat Rev Genet; 2011 Aug; 12(9):641-55. PubMed ID: 21850044
[TBL] [Abstract][Full Text] [Related]
12. Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction.
Su Y; Luo Y; Zhao X; Liu Y; Peng J
PLoS Comput Biol; 2019 Sep; 15(9):e1007283. PubMed ID: 31483777
[TBL] [Abstract][Full Text] [Related]
13. Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS.
Chorostecki U; Willis JR; Saus E; Gabaldon T
Methods Mol Biol; 2021; 2284():51-62. PubMed ID: 33835437
[TBL] [Abstract][Full Text] [Related]
14. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
Corley M; Flynn RA; Lee B; Blue SM; Chang HY; Yeo GW
Mol Cell; 2020 Dec; 80(5):903-914.e8. PubMed ID: 33242392
[TBL] [Abstract][Full Text] [Related]
15. Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Zhang C; Lee KY; Swanson MS; Darnell RB
Nucleic Acids Res; 2013 Aug; 41(14):6793-807. PubMed ID: 23685613
[TBL] [Abstract][Full Text] [Related]
16. Motif Discovery from CLIP Experiments.
Pietrosanto M; Ausiello G; Helmer-Citterich M
Methods Mol Biol; 2021; 2284():43-50. PubMed ID: 33835436
[TBL] [Abstract][Full Text] [Related]
17. SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.
Dotu I; Adamson SI; Coleman B; Fournier C; Ricart-Altimiras E; Eyras E; Chuang JH
PLoS Comput Biol; 2018 Mar; 14(3):e1006078. PubMed ID: 29596423
[TBL] [Abstract][Full Text] [Related]
18. Structural imprints in vivo decode RNA regulatory mechanisms.
Spitale RC; Flynn RA; Zhang QC; Crisalli P; Lee B; Jung JW; Kuchelmeister HY; Batista PJ; Torre EA; Kool ET; Chang HY
Nature; 2015 Mar; 519(7544):486-90. PubMed ID: 25799993
[TBL] [Abstract][Full Text] [Related]
19. mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins.
Weyn-Vanhentenryck SM; Zhang C
Methods Mol Biol; 2016; 1421():215-26. PubMed ID: 26965268
[TBL] [Abstract][Full Text] [Related]
20. Decoding the RNA structurome.
Lu Z; Chang HY
Curr Opin Struct Biol; 2016 Feb; 36():142-8. PubMed ID: 26923056
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
