121 related articles for article (PubMed ID: 30590479)
1. Integration of accessibility data from structure probing into RNA-RNA interaction prediction.
Miladi M; Montaseri S; Backofen R; Raden M
Bioinformatics; 2019 Aug; 35(16):2862-2864. PubMed ID: 30590479
[TBL] [Abstract][Full Text] [Related]
2. ShaKer: RNA SHAPE prediction using graph kernel.
Mautner S; Montaseri S; Miladi M; Raden M; Costa F; Backofen R
Bioinformatics; 2019 Jul; 35(14):i354-i359. PubMed ID: 31510707
[TBL] [Abstract][Full Text] [Related]
3. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y; Shi B; Ding X; Liu T; Hu X; Yip KY; Yang ZR; Mathews DH; Lu ZJ
Nucleic Acids Res; 2015 Sep; 43(15):7247-59. PubMed ID: 26170232
[TBL] [Abstract][Full Text] [Related]
4. SHAPE directed RNA folding.
Lorenz R; Luntzer D; Hofacker IL; Stadler PF; Wolfinger MT
Bioinformatics; 2016 Jan; 32(1):145-7. PubMed ID: 26353838
[TBL] [Abstract][Full Text] [Related]
5. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.
Sahoo S; Świtnicki MP; Pedersen JS
Bioinformatics; 2016 Sep; 32(17):2626-35. PubMed ID: 27153612
[TBL] [Abstract][Full Text] [Related]
6. Experiment-Assisted Secondary Structure Prediction with RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():163-76. PubMed ID: 27665598
[TBL] [Abstract][Full Text] [Related]
7. Carbodiimide reagents for the chemical probing of RNA structure in cells.
Wang PY; Sexton AN; Culligan WJ; Simon MD
RNA; 2019 Jan; 25(1):135-146. PubMed ID: 30389828
[TBL] [Abstract][Full Text] [Related]
8. Direct identification of base-paired RNA nucleotides by correlated chemical probing.
Krokhotin A; Mustoe AM; Weeks KM; Dokholyan NV
RNA; 2017 Jan; 23(1):6-13. PubMed ID: 27803152
[TBL] [Abstract][Full Text] [Related]
9. Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.
Krol A; Westhof E; Bach M; Lührmann R; Ebel JP; Carbon P
Nucleic Acids Res; 1990 Jul; 18(13):3803-11. PubMed ID: 2374709
[TBL] [Abstract][Full Text] [Related]
10. Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting.
Ke Y; Rao J; Zhao H; Lu Y; Xiao N; Yang Y
Bioinformatics; 2020 Nov; 36(17):4576-4582. PubMed ID: 32467966
[TBL] [Abstract][Full Text] [Related]
11. An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data.
Kato Y; Mori T; Sato K; Maegawa S; Hosokawa H; Akutsu T
Bioinformatics; 2017 Jan; 33(2):202-209. PubMed ID: 27663495
[TBL] [Abstract][Full Text] [Related]
12. A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.
Umu SU; Gardner PP
Bioinformatics; 2017 Apr; 33(7):988-996. PubMed ID: 27993777
[TBL] [Abstract][Full Text] [Related]
13. Probing-directed identification of novel structured RNAs.
Vinogradova SV; Sutormin RA; Mironov AA; Soldatov RA
RNA Biol; 2016; 13(2):232-42. PubMed ID: 26732206
[TBL] [Abstract][Full Text] [Related]
14. The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.
Raden M; Müller T; Mautner S; Gelhausen R; Backofen R
BMC Bioinformatics; 2020 Jan; 21(1):15. PubMed ID: 31931703
[TBL] [Abstract][Full Text] [Related]
15. AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.
DiChiacchio L; Sloma MF; Mathews DH
Bioinformatics; 2016 Apr; 32(7):1033-9. PubMed ID: 26589271
[TBL] [Abstract][Full Text] [Related]
16. Determining parameters for non-linear models of multi-loop free energy change.
Ward M; Sun H; Datta A; Wise M; Mathews DH
Bioinformatics; 2019 Nov; 35(21):4298-4306. PubMed ID: 30923811
[TBL] [Abstract][Full Text] [Related]
17. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.
Tang Y; Bouvier E; Kwok CK; Ding Y; Nekrutenko A; Bevilacqua PC; Assmann SM
Bioinformatics; 2015 Aug; 31(16):2668-75. PubMed ID: 25886980
[TBL] [Abstract][Full Text] [Related]
18. Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction.
Montaseri S; Zare-Mirakabad F; Ganjtabesh M
J Bioinform Comput Biol; 2017 Dec; 15(6):1750023. PubMed ID: 29113564
[TBL] [Abstract][Full Text] [Related]
19. Swellix: a computational tool to explore RNA conformational space.
Sloat N; Liu JW; Schroeder SJ
BMC Bioinformatics; 2017 Nov; 18(1):504. PubMed ID: 29157200
[TBL] [Abstract][Full Text] [Related]
20. How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.
Raden M; Miladi M
Methods Mol Biol; 2024; 2726():209-234. PubMed ID: 38780733
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]