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Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.
López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W; ICGC MMML-Seq Consortium; Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R. López C, et al. Among authors: stadler pf. Nat Commun. 2019 Mar 29;10(1):1459. doi: 10.1038/s41467-019-08578-3. Nat Commun. 2019. PMID: 30926794 Free PMC article.
Alignment of RNA base pairing probability matrices.
Hofacker IL, Bernhart SH, Stadler PF. Hofacker IL, et al. Among authors: stadler pf. Bioinformatics. 2004 Sep 22;20(14):2222-7. doi: 10.1093/bioinformatics/bth229. Epub 2004 Apr 8. Bioinformatics. 2004. PMID: 15073017
Local RNA base pairing probabilities in large sequences.
Bernhart SH, Hofacker IL, Stadler PF. Bernhart SH, et al. Among authors: stadler pf. Bioinformatics. 2006 Mar 1;22(5):614-5. doi: 10.1093/bioinformatics/btk014. Epub 2005 Dec 20. Bioinformatics. 2006. PMID: 16368769
Partition function and base pairing probabilities of RNA heterodimers.
Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL. Bernhart SH, et al. Among authors: stadler pf. Algorithms Mol Biol. 2006 Mar 16;1(1):3. doi: 10.1186/1748-7188-1-3. Algorithms Mol Biol. 2006. PMID: 16722605 Free PMC article.
RNAs everywhere: genome-wide annotation of structured RNAs.
Athanasius F Bompfünewerer Consortium; Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, Washietl S, Will S. Athanasius F Bompfünewerer Consortium, et al. Among authors: stadler pf. J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25. doi: 10.1002/jez.b.21130. J Exp Zool B Mol Dev Evol. 2007. PMID: 17171697 Review.
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
Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF. Langenberger D, et al. Among authors: stadler pf. Bioinformatics. 2009 Sep 15;25(18):2298-301. doi: 10.1093/bioinformatics/btp419. Epub 2009 Jul 6. Bioinformatics. 2009. PMID: 19584066
595 results