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Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Will S, et al. Among authors: stadler pf. PLoS Comput Biol. 2007 Apr 13;3(4):e65. doi: 10.1371/journal.pcbi.0030065. Epub 2007 Feb 22. PLoS Comput Biol. 2007. PMID: 17432929 Free PMC article.
Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77-i78). ...
Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missa …
Structured RNAs in the ENCODE selected regions of the human genome.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. Washietl S, et al. Among authors: stadler pf. Genome Res. 2007 Jun;17(6):852-64. doi: 10.1101/gr.5650707. Genome Res. 2007. PMID: 17568003 Free PMC article.
Computational RNomics of drosophilids.
Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Rose D, et al. Among authors: stadler pf. BMC Genomics. 2007 Nov 8;8:406. doi: 10.1186/1471-2164-8-406. BMC Genomics. 2007. PMID: 17996037 Free PMC article.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. Geis M, et al. Among authors: stadler pf. J Mol Biol. 2008 May 23;379(1):160-73. doi: 10.1016/j.jmb.2008.02.064. Epub 2008 Mar 6. J Mol Biol. 2008. PMID: 18440024
Structural profiles of human miRNA families from pairwise clustering.
Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J. Kaczkowski B, et al. Among authors: stadler pf. Bioinformatics. 2009 Feb 1;25(3):291-4. doi: 10.1093/bioinformatics/btn628. Epub 2008 Dec 4. Bioinformatics. 2009. PMID: 19059941
Duplicated RNA genes in teleost fish genomes.
Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF. Rose D, et al. Among authors: stadler pf. J Bioinform Comput Biol. 2008 Dec;6(6):1157-75. doi: 10.1142/s0219720008003886. J Bioinform Comput Biol. 2008. PMID: 19090022
Evolution of vault RNAs.
Stadler PF, Chen JJ, Hackermüller J, Hoffmann S, Horn F, Khaitovich P, Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K. Stadler PF, et al. Mol Biol Evol. 2009 Sep;26(9):1975-91. doi: 10.1093/molbev/msp112. Epub 2009 Jun 2. Mol Biol Evol. 2009. PMID: 19491402
595 results