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Molecular evolution of a microRNA cluster.
Tanzer A, Stadler PF. Tanzer A, et al. J Mol Biol. 2004 May 28;339(2):327-35. doi: 10.1016/j.jmb.2004.03.065. J Mol Biol. 2004. PMID: 15136036
The history of this cluster is governed by an initial phase of local (tandem) duplications, a series of duplications of entire clusters and subsequent loss of individual microRNAs from the resulting paralogous clusters. ...
The history of this cluster is governed by an initial phase of local (tandem) duplications, a series of duplications of entire cluste …
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. 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
We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. ...Folding trajectories are modeled at base-pair resolution using the Morgan-Higgs heuristic and a barrier tree-based heuri …
We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of buildin …
Evolution of microRNAs.
Tanzer A, Stadler PF. Tanzer A, et al. Methods Mol Biol. 2006;342:335-50. doi: 10.1385/1-59745-123-1:335. Methods Mol Biol. 2006. PMID: 16957387 Review.
MicroRNAs (miRNAs) form a large class of small regulatory RNAs in eukaryotes. Although they share a common processing pathway and certain structural features, in general, there is no detectable sequence similarity among miRNAs from a given organism. On the ot …
MicroRNAs (miRNAs) form a large class of small regulatory RNAs in eukaryotes. Although they share a common processing pathway …
Evolution of microRNAs located within Hox gene clusters.
Tanzer A, Amemiya CT, Kim CB, Stadler PF. Tanzer A, et al. J Exp Zool B Mol Dev Evol. 2005 Jan 15;304(1):75-85. doi: 10.1002/jez.b.21021. J Exp Zool B Mol Dev Evol. 2005. PMID: 15643628
The expansion of the metazoan microRNA repertoire.
Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF; Students of Bioinformatics Computer Labs 2004 and 2005. Hertel J, et al. BMC Genomics. 2006 Feb 15;7:25. doi: 10.1186/1471-2164-7-25. BMC Genomics. 2006. PMID: 16480513 Free PMC article.
This allows us to reliably identify microRNA clusters that are derived from a common transcript. RESULTS: We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and de …
This allows us to reliably identify microRNA clusters that are derived from a common transcript. RESULTS: We identify three episodes …
Animal snoRNAs and scaRNAs with exceptional structures.
Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF. Marz M, et al. RNA Biol. 2011 Nov-Dec;8(6):938-46. doi: 10.4161/rna.8.6.16603. Epub 2011 Nov 1. RNA Biol. 2011. PMID: 21955586 Free PMC article.
A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throug
A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the no
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.
Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M. Hölzer M, et al. Among authors: tanzer a. Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Sci Rep. 2016. PMID: 27713552 Free PMC article.
Predicting RNA secondary structures from sequence and probing data.
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL. Lorenz R, et al. Among authors: tanzer a. Methods. 2016 Jul 1;103:86-98. doi: 10.1016/j.ymeth.2016.04.004. Epub 2016 Apr 5. Methods. 2016. PMID: 27064083 Free article. Review.
RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles.
Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Hüttenhofer A. Rederstorff M, et al. Nucleic Acids Res. 2010 Jun;38(10):e113. doi: 10.1093/nar/gkq057. Epub 2010 Feb 11. Nucleic Acids Res. 2010. PMID: 20150415 Free PMC article.
As a proof of concept, we applied the RNP method to human Hela cells or total mouse brain, and subjected cDNA libraries, generated from the two model systems, to deep-sequencing. ...Thereby, ncRNAs candidates were mainly located in intergenic as well as intronic regions of …
As a proof of concept, we applied the RNP method to human Hela cells or total mouse brain, and subjected cDNA libraries, generated fr …
Nematode sbRNAs: homologs of vertebrate Y RNAs.
Boria I, Gruber AR, Tanzer A, Bernhart SH, Lorenz R, Mueller MM, Hofacker IL, Stadler PF. Boria I, et al. J Mol Evol. 2010 Apr;70(4):346-58. doi: 10.1007/s00239-010-9332-4. Epub 2010 Mar 27. J Mol Evol. 2010. PMID: 20349053
Stem-bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized noncoding RNAs first described in C. elegans, with a few homologous sequences postulated in C. briggsae. In this study, we report on a comprehensive survey of this ncRNA family in …
Stem-bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized noncoding RNAs first described in C. elegans, with …
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