114 related articles for article (PubMed ID: 31856671)
1. IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.
Gelhausen R; Will S; Hofacker IL; Backofen R; Raden M
J Bioinform Comput Biol; 2019 Oct; 17(5):1940009. PubMed ID: 31856671
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs.
King AM; Vanderpool CK; Degnan PH
mSphere; 2019 Jan; 4(1):. PubMed ID: 30700509
[TBL] [Abstract][Full Text] [Related]
4. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
Busch A; Richter AS; Backofen R
Bioinformatics; 2008 Dec; 24(24):2849-56. PubMed ID: 18940824
[TBL] [Abstract][Full Text] [Related]
5. Prediction of consensus RNA secondary structures including pseudoknots.
Witwer C; Hofacker IL; Stadler PF
IEEE/ACM Trans Comput Biol Bioinform; 2004; 1(2):66-77. PubMed ID: 17048382
[TBL] [Abstract][Full Text] [Related]
6. Dynamic programming algorithms for RNA structure prediction with binding sites.
Poolsap U; Kato Y; Akutsu T
Pac Symp Biocomput; 2010; ():98-107. PubMed ID: 19908362
[TBL] [Abstract][Full Text] [Related]
7. Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Huang FW; Qin J; Reidys CM; Stadler PF
Bioinformatics; 2009 Oct; 25(20):2646-54. PubMed ID: 19671692
[TBL] [Abstract][Full Text] [Related]
8. Detecting RNA-RNA interactions in E. coli using a modified CLASH method.
Liu T; Zhang K; Xu S; Wang Z; Fu H; Tian B; Zheng X; Li W
BMC Genomics; 2017 May; 18(1):343. PubMed ID: 28468647
[TBL] [Abstract][Full Text] [Related]
9. Structure and Interaction Prediction in Prokaryotic RNA Biology.
Wright PR; Mann M; Backofen R
Microbiol Spectr; 2018 Apr; 6(2):. PubMed ID: 29676245
[TBL] [Abstract][Full Text] [Related]
10. An assessment of bacterial small RNA target prediction programs.
Pain A; Ott A; Amine H; Rochat T; Bouloc P; Gautheret D
RNA Biol; 2015; 12(5):509-13. PubMed ID: 25760244
[TBL] [Abstract][Full Text] [Related]
11. Simultaneous prediction of RNA secondary structure and helix coaxial stacking.
Shareghi P; Wang Y; Malmberg R; Cai L
BMC Genomics; 2012 Jun; 13 Suppl 3(Suppl 3):S7. PubMed ID: 22759616
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.
Vazquez-Anderson J; Mihailovic MK; Baldridge KC; Reyes KG; Haning K; Cho SH; Amador P; Powell WB; Contreras LM
Nucleic Acids Res; 2017 May; 45(9):5523-5538. PubMed ID: 28334800
[TBL] [Abstract][Full Text] [Related]
14. A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.
Ebrahimi P; Kaur S; Baronti L; Petzold K; Chen AA
Methods; 2019 Jun; 162-163():96-107. PubMed ID: 31059830
[TBL] [Abstract][Full Text] [Related]
15. RnaPredict--an evolutionary algorithm for RNA secondary structure prediction.
Wiese K; Deschenes A; Hendriks A
IEEE/ACM Trans Comput Biol Bioinform; 2008; 5(1):25-41. PubMed ID: 18245873
[TBL] [Abstract][Full Text] [Related]
16. SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.
Tsang HH; Wiese KC
IEEE/ACM Trans Comput Biol Bioinform; 2010; 7(4):727-40. PubMed ID: 21030739
[TBL] [Abstract][Full Text] [Related]
17. Using temperature effects to predict the interactions between two RNAs.
Ganjtabesh M; Montaseri S; Zare-Mirakabad F
J Theor Biol; 2015 Jan; 364():98-102. PubMed ID: 25218429
[TBL] [Abstract][Full Text] [Related]
18. Computational prediction of sRNAs and their targets in bacteria.
Backofen R; Hess WR
RNA Biol; 2010; 7(1):33-42. PubMed ID: 20061798
[TBL] [Abstract][Full Text] [Related]
19. Real time kinetic studies of the interaction between folded antisense and target RNAs using surface plasmon resonance.
Nordgren S; Slagter-Jäger JG; Wagner GH
J Mol Biol; 2001 Jul; 310(5):1125-34. PubMed ID: 11502000
[TBL] [Abstract][Full Text] [Related]
20. Novel and efficient RNA secondary structure prediction using hierarchical folding.
Jabbari H; Condon A; Zhao S
J Comput Biol; 2008 Mar; 15(2):139-63. PubMed ID: 18312147
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]