Multiple sequence alignment with user-defined constraints. - Burkhard Morgenstern; Sonja J. Prohaska; Nadine Werner; Jan Weyer-Menkhoff; Isabelle Schneider; Amarendran Ramaswami Subramanian; Peter F. Stadler (German Conference on Bioinformatics, 2004)

The Footprint Sorting Problem. - Claudia Fried; Wim Hordijk; Sonja J. Prohaska; Claus R. Stadler; Peter F. Stadler (J. Chem. Inf. Model., 2004)

The duplication of the Hox gene clusters in teleost fishes. - Sonja J. Prohaska; Peter F. Stadler (Theory Biosci., 2004)

Multiple sequence alignment with user-defined constraints at GOBICS. - Burkhard Morgenstern; Nadine Werner; Sonja J. Prohaska; Rasmus Steinkamp; Isabelle Schneider; Amarendran Ramaswami Subramanian; Peter F. Stadler; Jan Weyer-Menkhoff (Bioinform., 2005)

Evolutionary patterns of non-coding RNAs. - Athanasius F. Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L. Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J. Prohaska; Bärbel M. R. Stadler; Peter F. Stadler; et al. (Theory Biosci., 2005)

Multiple sequence alignment with user-defined anchor points. - Burkhard Morgenstern; Sonja J. Prohaska; Dirk Pöhler; Peter F. Stadler (Algorithms Mol. Biol., 2006)

Process flow for classification and clustering of fruit fly gene expression patterns. - Andreas Heffel; Peter F. Stadler; Sonja J. Prohaska; Gerhard Kauer; Jens-Peer Kuska (ICIP, 2008)

Noisy: Identification of problematic columns in multiple sequence alignments. - Andreas W. M. Dress; Christoph Flamm; Guido Fritzsch; Stefan Grünewald; Matthias Kruspe; Sonja J. Prohaska; Peter F. Stadler (Algorithms Mol. Biol., 2008)

SynBlast: Assisting the analysis of conserved synteny information. - Jörg Lehmann; Peter F. Stadler; Sonja J. Prohaska (BMC Bioinform., 2008)

"Genes". - Sonja J. Prohaska; Peter F. Stadler (Theory Biosci., 2008)

Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. - Andreas Heffel; Sonja J. Prohaska; Peter F. Stadler; Gerhard Kauer; Jens-Peer Kuska (Bildverarbeitung für die Medizin, 2009)

Discovering cis-regulatory modules by optimizing barbecues. - Axel Mosig; Türker Bíyíkoglu; Sonja J. Prohaska; Peter F. Stadler (Discret. Appl. Math., 2009)

Defining genes: a computational framework. - Peter F. Stadler; Sonja J. Prohaska; Christian V. Forst; David C. Krakauer (Theory Biosci., 2009)

Quantitative Comparison of Genomic-Wide Protein Domain Distributions. - Arli A. Parikesit; Peter F. Stadler; Sonja J. Prohaska (GCB, 2010)

Detection of Protein Domains in Eukaryotic Genome Sequences. - Arli A. Parikesit; Peter F. Stadler; Sonja J. Prohaska (BSB, 2010)

Phylogenetic Footprinting and Consistent Sets of Local Aligments. - Wolfgang Otto 001; Peter F. Stadler; Sonja J. Prohaska (CPM, 2011)

Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. - Marcus Lechner; Sven Findeiß; Lydia Steiner; Manja Marz; Peter F. Stadler; Sonja J. Prohaska (BMC Bioinform., 2011)

Comparative Detection of Processed Small RNAs in Archaea. - Christian Höner zu Siederdissen; Sarah Berkemer; Fabian Amman; Axel Wintsche; Sebastian Will; Sonja J. Prohaska; Peter F. Stadler (IWBBIO, 2014)

Dynamic Programming for Set Data Types. - Christian Höner zu Siederdissen; Sonja J. Prohaska; Peter F. Stadler (BSB, 2014)

A priori assessment of data quality in molecular phylogenetics. - Bernhard Misof; Karen Meusemann; Björn Marcus von Reumont; Patrick Kück; Sonja J. Prohaska; Peter F. Stadler (Algorithms Mol. Biol., 2014)

Analyzing Chromatin Using Tiled Binned Scatterplot Matrices. - Dirk Zeckzer; Daniel Gerighausen; Lydia Steiner; Sonja J. Prohaska (CoRR, 2014)

The relativity of biological function. - Manfred D. Laubichler; Peter F. Stadler; Sonja J. Prohaska; Katja Nowick (Theory Biosci., 2015)

Algebraic Dynamic Programming over general data structures. - Christian Höner zu Siederdissen; Sonja J. Prohaska; Peter F. Stadler (BMC Bioinform., 2015)

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. - Henrike Indrischek; Nicolas Wieseke; Peter F. Stadler; Sonja J. Prohaska (Algorithms Mol. Biol., 2016)

Design specifications for cellular regulation. - David C. Krakauer; Lydia Müller; Sonja J. Prohaska; Peter F. Stadler (Theory Biosci., 2016)