246 related articles for article (PubMed ID: 31808801)
1. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.
Miladi M; Sokhoyan E; Houwaart T; Heyne S; Costa F; Grüning B; Backofen R
Gigascience; 2019 Dec; 8(12):. PubMed ID: 31808801
[TBL] [Abstract][Full Text] [Related]
2. Mod-seq: high-throughput sequencing for chemical probing of RNA structure.
Talkish J; May G; Lin Y; Woolford JL; McManus CJ
RNA; 2014 May; 20(5):713-20. PubMed ID: 24664469
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.
Kato Y; Gorodkin J; Havgaard JH
BMC Genomics; 2017 Dec; 18(1):935. PubMed ID: 29197323
[TBL] [Abstract][Full Text] [Related]
5. De novo prediction of structured RNAs from genomic sequences.
Gorodkin J; Hofacker IL; Torarinsson E; Yao Z; Havgaard JH; Ruzzo WL
Trends Biotechnol; 2010 Jan; 28(1):9-19. PubMed ID: 19942311
[TBL] [Abstract][Full Text] [Related]
6. PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering.
Biswas AK; Gao JX
J Bioinform Comput Biol; 2016 Oct; 14(5):1650027. PubMed ID: 27455882
[TBL] [Abstract][Full Text] [Related]
7. RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Miladi M; Junge A; Costa F; Seemann SE; Havgaard JH; Gorodkin J; Backofen R
Bioinformatics; 2017 Jul; 33(14):2089-2096. PubMed ID: 28334186
[TBL] [Abstract][Full Text] [Related]
8. DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.
Yang JH; Qu LH
Methods Mol Biol; 2012; 822():233-48. PubMed ID: 22144203
[TBL] [Abstract][Full Text] [Related]
9. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Lu ZJ; Yip KY; Wang G; Shou C; Hillier LW; Khurana E; Agarwal A; Auerbach R; Rozowsky J; Cheng C; Kato M; Miller DM; Slack F; Snyder M; Waterston RH; Reinke V; Gerstein MB
Genome Res; 2011 Feb; 21(2):276-85. PubMed ID: 21177971
[TBL] [Abstract][Full Text] [Related]
10. BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Videm P; Rose D; Costa F; Backofen R
Bioinformatics; 2014 Jun; 30(12):i274-82. PubMed ID: 24931994
[TBL] [Abstract][Full Text] [Related]
11. RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
Toffano-Nioche C; Ott A; Crozat E; Nguyen AN; Zytnicki M; Leclerc F; Forterre P; Bouloc P; Gautheret D
RNA Biol; 2013 Jul; 10(7):1211-20. PubMed ID: 23884177
[TBL] [Abstract][Full Text] [Related]
12. Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures.
Saito Y; Sato K; Sakakibara Y
BMC Bioinformatics; 2011 Feb; 12 Suppl 1(Suppl 1):S48. PubMed ID: 21342580
[TBL] [Abstract][Full Text] [Related]
13. Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.
Naghdi MR; Smail K; Wang JX; Wade F; Breaker RR; Perreault J
Methods; 2017 Mar; 117():3-13. PubMed ID: 28279853
[TBL] [Abstract][Full Text] [Related]
14. 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]
15. Non-Coding RNA Analysis Using the Rfam Database.
Kalvari I; Nawrocki EP; Argasinska J; Quinones-Olvera N; Finn RD; Bateman A; Petrov AI
Curr Protoc Bioinformatics; 2018 Jun; 62(1):e51. PubMed ID: 29927072
[TBL] [Abstract][Full Text] [Related]
16. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
Will S; Reiche K; Hofacker IL; Stadler PF; Backofen R
PLoS Comput Biol; 2007 Apr; 3(4):e65. PubMed ID: 17432929
[TBL] [Abstract][Full Text] [Related]
17. Computational analysis of RNA structures with chemical probing data.
Ge P; Zhang S
Methods; 2015 Jun; 79-80():60-6. PubMed ID: 25687190
[TBL] [Abstract][Full Text] [Related]
18. BSGatlas: a unified
Geissler AS; Anthon C; Alkan F; González-Tortuero E; Poulsen LD; Kallehauge TB; Breüner A; Seemann SE; Vinther J; Gorodkin J
Microb Genom; 2021 Feb; 7(2):. PubMed ID: 33539279
[TBL] [Abstract][Full Text] [Related]
19. Deep learning predicts short non-coding RNA functions from only raw sequence data.
Noviello TMR; Ceccarelli F; Ceccarelli M; Cerulo L
PLoS Comput Biol; 2020 Nov; 16(11):e1008415. PubMed ID: 33175836
[TBL] [Abstract][Full Text] [Related]
20. PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Seemann SE; Richter AS; Gesell T; Backofen R; Gorodkin J
Bioinformatics; 2011 Jan; 27(2):211-9. PubMed ID: 21088024
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]