166 entries « 4 of 4 »

2010

Marz, Manja; Vanzo, Nathalie; Stadler, Peter F

Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history Journal Article

In: J Bioinform Comput Biol, vol. 8, no. 1, pp. 1–17, 2010.

Abstract | Links | BibTeX | Tags: evolution, RNA structure, splicing

Dalloul, Rami A; Long, Julie A; Zimin, Aleksey V; Aslam, Luqman; Beal, Kathryn; Blomberg, Le Ann; Bouffard, Pascal; Burt, David W; Crasta, Oswald; Crooijmans, Richard P M A; Cooper, Kristal; Coulombe, Roger A; De, Supriyo; Delany, Mary E; Dodgson, Jerry B; Dong, Jennifer J; Evans, Clive; Frederickson, Karin M; Flicek, Paul; Florea, Liliana; Folkerts, Otto; Groenen, Martien A M; Harkins, Tim T; Herrero, Javier; Hoffmann, Steve; Megens, Hendrik-Jan; Jiang, Andrew; Jong, Pieter; Kaiser, Pete; Kim, Heebal; Kim, Kyu-Won; Kim, Sungwon; Langenberger, David; Lee, Mi-Kyung; Lee, Taeheon; Mane, Shrinivasrao; Marcais, Guillaume; Marz, Manja; McElroy, Audrey P; Modise, Thero; Nefedov, Mikhail; Notredame, Cédric; Paton, Ian R; Payne, William S; Pertea, Geo; Prickett, Dennis; Puiu, Daniela; Qioa, Dan; Raineri, Emanuele; Ruffier, Magali; Salzberg, Steven L; Schatz, Michael C; Scheuring, Chantel; Schmidt, Carl J; Schroeder, Steven; Searle, Stephen M J; Smith, Edward J; Smith, Jacqueline; Sonstegard, Tad S; Stadler, Peter F; Tafer, Hakim; Tu, Zhijian Jake; Tassell, Curtis P Van; Vilella, Albert J; Williams, Kelly P; Yorke, James A; Zhang, Liqing; Zhang, Hong-Bin; Zhang, Xiaojun; Zhang, Yang; Reed, Kent M

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis Journal Article

In: PLoS Biol, vol. 8, 2010.

Abstract | Links | BibTeX | Tags: alignment, annotation, assembly, DNA / genomics, ncRNAs

Yusuf, Dilmurat; Marz, Manja; Stadler, Peter F; Hofacker, Ivo L

Bcheck: a wrapper tool for detecting RNase P RNA genes Journal Article

In: BMC Genomics, vol. 11, pp. 432, 2010.

Abstract | Links | BibTeX | Tags: annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software

Donath, Alexander; Findeiß, Sven; Hertel, Jana; Marz, Manja; Otto, Wolfgang; Schulz, Christine; Stadler, Peter F.; Wirth, Stefan

Noncoding RNA Incollection

In: Evolutionary Genomics and Systems Biology, pp. 251-293, John Wiley & Sons, Ltd, 2010, ISBN: 9780470570418.

Abstract | Links | BibTeX | Tags: ncRNAs

2009

Marz, Manja; Stadler, Peter F

Comparative analysis of eukaryotic U3 snoRNA Journal Article

In: RNA Biol, vol. 6, pp. 503–507, 2009.

Abstract | Links | BibTeX | Tags: ncRNAs, RNA structure

Copeland, Claudia S; Marz, Manja; Rose, Dominic; Hertel, Jana; Brindley, Paul J; Santana, Clara Bermudez; Kehr, Stephanie; Attolini, Camille Stephan-Otto; Stadler, Peter F

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum Journal Article

In: BMC Genomics, vol. 10, pp. 464, 2009.

Abstract | Links | BibTeX | Tags: annotation, ncRNAs, RNA structure

Marz, Manja; Donath, Alexander; Verstraete, Nina; Nguyen, Van Trung; Stadler, Peter F; Bensaude, Olivier

Evolution of 7SK RNA and its protein partners in metazoa Journal Article

In: Mol Biol Evol, vol. 26, no. 12, pp. 2821–2830, 2009.

Abstract | Links | BibTeX | Tags: evolution, ncRNAs, proteins, RNA structure

Hiller, Michael; Findeiss, Sven; Lein, Sandro; Marz, Manja; Nickel, Claudia; Rose, Dominic; Schulz, Christine; Backofen, Rolf; Prohaska, Sonja J; Reuter, Gunter; Stadler, Peter F

Conserved introns reveal novel transcripts in Drosophila melanogaster Journal Article

In: Genome Res, vol. 19, pp. 1289–1300, 2009.

Abstract | Links | BibTeX | Tags: insects, ncRNAs, RNA structure

Hertel, Jana; Jong, Danielle; Marz, Manja; Rose, Dominic; Tafer, Hakim; Tanzer, Andrea; Schierwater, Bernd; Stadler, Peter F

Non-coding RNA annotation of the genome of Ŧrichoplax adhaerens Journal Article

In: Nucleic Acids Res, vol. 37, no. 5, pp. 1602–1615, 2009.

Abstract | Links | BibTeX | Tags: annotation, ncRNAs

Jones, Thomas A; Otto, Wolfgang; Marz, Manja; Eddy, Sean R; Stadler, Peter F

A survey of nematode SmY RNAs Journal Article

In: RNA Biol, vol. 6, pp. 5–8, 2009.

Abstract | Links | BibTeX | Tags: alignment, ncRNAs, RNA / transcriptomics, RNA structure, splicing

Ingalls, Todd; Martius, Georg; Marz, Manja; Prohaska, Sonja J.

Converting DNA to music: ComposAlign Inproceedings

In: Proceedings of the German Conference on Bioinformatics (GCB 2009), pp. 93-104, 2009.

Abstract | Links | BibTeX | Tags: alignment

2008

Marz, Manja; Kirsten, Toralf; Stadler, Peter F

Evolution of spliceosomal snRNA genes in metazoan animals Journal Article

In: J Mol Evol, vol. 67, pp. 594–607, 2008.

Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure, splicing

Marz, Manja; Mosig, Axel; Stadler, Bärbel M R; Stadler, Peter F

U7 snRNAs: a computational survey Journal Article

In: Genomics Proteomics Bioinformatics, vol. 5, no. 3-4, pp. 187–195, 2008.

Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure

Gruber, Andreas R; Koper-Emde, Dorota; Marz, Manja; Tafer, Hakim; Bernhart, Stephan; Obernosterer, Gregor; Mosig, Axel; Hofacker, Ivo L; Stadler, Peter F; Benecke, Bernd-Joachim

Invertebrate 7SK snRNAs Journal Article

In: J Mol Evol, vol. 66, pp. 107–115, 2008.

Abstract | Links | BibTeX | Tags: evolution, ncRNAs

2007

Washietl, Stefan; Pedersen, Jakob S; Korbel, Jan O; Stocsits, Claudia; Gruber, Andreas R; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Reiche, Kristin; Tanzer, Andrea; Ucla, Catherine; Wyss, Carine; Antonarakis, Stylianos E; Denoeud, France; Lagarde, Julien; Drenkow, Jorg; Kapranov, Philipp; Gingeras, Thomas R; Guigó, Roderic; Snyder, Michael; Gerstein, Mark B; Reymond, Alexandre; Hofacker, Ivo L; Stadler, Peter F

Structured RNAs in the ENCODE selected regions of the human genome Journal Article

In: Genome Res, vol. 17, pp. 852–864, 2007.

Abstract | Links | BibTeX | Tags: annotation, evolution, ncRNAs, RNA structure

2006

Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Fried, Claudia; Tanzer, Andrea; Flamm, Christoph; Hofacker, Ivo L; Stadler, Peter F; 2004, Students Bioinformatics Computer Labs; 2005,

The expansion of the metazoan microRNA repertoire Journal Article

In: BMC Genomics, vol. 7, pp. 25, 2006.

Abstract | Links | BibTeX | Tags: ncRNAs, phylogenetics

166 entries « 4 of 4 »