Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes von Donath, Alexander, Jühling, Frank, Al-Arab, Marwa, Bernhart, Stephan H, Reinhardt, Franziska, Stadler, Peter F, Middendorf, Martin, Bernt, Matthias

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Proteinortho: detection of (co-)orthologs in large-scale analysis von Lechner, Marcus, Findeiss, Sven, Steiner, Lydia, Marz, Manja, Stadler, Peter F, Prohaska, Sonja J

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Genetic aspects of mitochondrial genome evolution von Bernt, Matthias, Braband, Anke, Schierwater, Bernd, Stadler, Peter F.

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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data von Jühling, Frank, Kretzmer, Helene, Bernhart, Stephan H, Otto, Christian, Stadler, Peter F, Hoffmann, Steve

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Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks von Holdt, Lesca M, Hoffmann, Steve, Sass, Kristina, Langenberger, David, Scholz, Markus, Krohn, Knut, Finstermeier, Knut, Stahringer, Anika, Wilfert, Wolfgang, Beutner, Frank, Gielen, Stephan, Schuler, Gerhard, Gäbel, Gabor, Bergert, Hendrik, Bechmann, Ingo, Stadler, Peter F, Thiery, Joachim, Teupser, Daniel

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Design of Artificial Riboswitches as Biosensors von Findeiß, Sven, Etzel, Maja, Will, Sebastian, Mörl, Mario, Stadler, Peter F

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ViennaRNA Package 2.0 von Lorenz, Ronny, Bernhart, Stephan H, Höner Zu Siederdissen, Christian, Tafer, Hakim, Flamm, Christoph, Stadler, Peter F, Hofacker, Ivo L

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Sound–meaning association biases evidenced across thousands of languages von Blasi, Damián E., Wichmann, Søren, Hammarström, Harald, Stadler, Peter F., Christiansen, Morten H.

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The primary transcriptome of the major human pathogen Helicobacter pylori von Sharma, Cynthia M., Hoffmann, Steve, Darfeuille, Fabien, Reignier, Jérémy, Findeiß, Sven, Sittka, Alexandra, Chabas, Sandrine, Reiche, Kristin, Hackermüller, Jörg, Reinhardt, Richard, Stadler, Peter F., Vogel, Jörg

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RNAalifold: improved consensus structure prediction for RNA alignments von Bernhart, Stephan H, Hofacker, Ivo L, Will, Sebastian, Gruber, Andreas R, Stadler, Peter F

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Lacking alignments? The next-generation sequencing mapper segemehl revisited von Otto, Christian, Stadler, Peter F, Hoffmann, Steve

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Optimisation via encodings: a renormalisation group perspective von Klemm, Konstantin, Mehta, Anita, Stadler, Peter F

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The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations von Hellmuth, Marc, Stadler, Peter F., Wieseke, Nicolas

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Fast mapping of short sequences with mismatches, insertions and deletions using index structures von Hoffmann, Steve, Otto, Christian, Kurtz, Stefan, Sharma, Cynthia M, Khaitovich, Philipp, Vogel, Jörg, Stadler, Peter F, Hackermüller, Jörg

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Orthology detection combining clustering and synteny for very large datasets von Lechner, Marcus, Hernandez-Rosales, Maribel, Doerr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K, Prohaska, Sonja J, Stadler, Peter F

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An updated human snoRNAome von Jorjani, Hadi, Kehr, Stephanie, Jedlinski, Dominik J, Gumienny, Rafal, Hertel, Jana, Stadler, Peter F, Zavolan, Mihaela, Gruber, Andreas R

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From modular decomposition trees to rooted median graphs von Bruckmann, Carmen, Stadler, Peter F., Hellmuth, Marc

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Ryūtō: network-flow based transcriptome reconstruction von Gatter, Thomas, Stadler, Peter F

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LocARNA-P: accurate boundary prediction and improved detection of structural RNAs von Will, Sebastian, Joshi, Tejal, Hofacker, Ivo L, Stadler, Peter F, Backofen, Rolf

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Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more von Gatter, Thomas, Stadler, Peter F

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