Landscapes: Complex Optimization Problems and Biopolymer Structures. - Peter Schuster 002; Peter F. Stadler (Comput. Chem., 1994)

Random walks and orthogonal functions associated with highly symmetric graphs. - Peter F. Stadler (Discret. Math., 1995)

Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. - Jan Cupal; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 1996)

Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. - Ivo L. Hofacker; Martijn A. Huynen; Peter F. Stadler; Paul E. Stolorz (KDD, 1996)

Bio-molecular Shapes and Algebraic Structures. - Christian M. Reidys; Peter F. Stadler (Comput. Chem., 1996)

Canonical approximation of fitness landscapes. - Robert Happel; Peter F. Stadler (Complex., 1996)

Base Pairing Probabilities in a Complete HIV-1 RNA. - Martijn A. Huynen; Alan S. Perelson; W. A. Vieira; Peter F. Stadler (J. Comput. Biol., 1996)

Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. - Jan Cupal; Christoph Flamm; Alexander Renner; Peter F. Stadler (ISMB, 1997)

Algebraic Theory of Recombination Spaces. - Peter F. Stadler; Günter P. Wagner (Evol. Comput., 1997)

Amplitude Spectra of Fitness Landscapes. - Wim Hordijk; Peter F. Stadler (Adv. Complex Syst., 1998)

Minimal Cycle Bases of Outerplanar Graphs. - Josef Leydold; Peter F. Stadler (Electron. J. Comb., 1998)

Combinatorics of RNA Secondary Structures. - Ivo L. Hofacker; Peter Schuster 002; Peter F. Stadler (Discret. Appl. Math., 1998)

Conserved secondary structures in hepatitis B virus DNA. - Roman R. Stocsits; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 1999)

An efficient potential for protein sequence design. - G. Weberndorfer; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 1999)

Call for proposals. - Eric Bonabeau; Peter F. Stadler (Adv. Complex Syst., 1999)

RNA In Silico The Computational Biology of RNA Secondary Structures. - Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (Adv. Complex Syst., 1999)

Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. - Ivo L. Hofacker; Peter F. Stadler (Comput. Chem., 1999)

RNA Shape Space Topology. - Jan Cupal; Stephan Kopp; Peter F. Stadler (Artif. Life, 2000)

Interchangeability of Relevant Cycles in Graphs. - Petra M. Gleiss; Josef Leydold; Peter F. Stadler (Electron. J. Comb., 2000)

Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. - Martin Fekete; Ivo L. Hofacker; Peter F. Stadler (J. Comput. Biol., 2000)

Relevant cycles in Chemical reaction Networks. - Petra M. Gleiss; Peter F. Stadler; Andreas Wagner; David A. Fell (Adv. Complex Syst., 2001)

Glassy States in a shaken Sandbox. - Peter F. Stadler; Anita Mehta; Jean-Marc Luck (Adv. Complex Syst., 2001)

Neutrality in fitness landscapes. - Christian M. Reidys; Peter F. Stadler (Appl. Math. Comput., 2001)

Stochastic pairwise alignments. - Ulrike Mückstein; Ivo L. Hofacker; Peter F. Stadler (ECCB, 2002)

Minimum cycle bases of product graphs. - Wilfried Imrich; Peter F. Stadler (Australas. J Comb., 2002)

Landscapes on spaces of trees. - Oliver Bastert; Daniel N. Rockmore; Peter F. Stadler; Gottfried Tinhofer (Appl. Math. Comput., 2002)

Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. - Bärbel M. R. Stadler; Peter F. Stadler (J. Chem. Inf. Comput. Sci., 2002)

Combinatorial Landscapes. - Christian M. Reidys; Peter F. Stadler (SIAM Rev., 2002)

Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. - Gil Benkö; Christoph Flamm; Peter F. Stadler (ECAL, 2003)

Design of multi-stable nucleid acid sequences. - Ingrid G. Abfalter; Christoph Flamm; Peter F. Stadler (German Conference on Bioinformatics, 2003)

Molecular Replicator Dynamics. - Bärbel M. R. Stadler; Peter F. Stadler (Adv. Complex Syst., 2003)

Circuit bases of strongly connected digraphs. - Petra M. Gleiss; Josef Leydold; Peter F. Stadler (Discuss. Math. Graph Theory, 2003)

Barrier Trees on Poset-Valued Landscapes. - Peter F. Stadler; Christoph Flamm (Genet. Program. Evolvable Mach., 2003)

A Graph-Based Toy Model of Chemistry. - Gil Benkö; Christoph Flamm; Peter F. Stadler (J. Chem. Inf. Comput. Sci., 2003)

Minimum cycle bases of Halin graphs. - Peter F. Stadler (J. Graph Theory, 2003)

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)

Conserved RNA Pseudoknots. - C. Thurner; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 2004)

The Partition Function Variant of Sankoff's Algorithm. - Ivo L. Hofacker; Peter F. Stadler (International Conference on Computational Science, 2004)

Alignment of RNA base pairing probability matrices. - Ivo L. Hofacker; Stephan H. Bernhart; Peter F. Stadler (Bioinform., 2004)

Prediction of locally stable RNA secondary structures for genome-wide surveys. - Ivo L. Hofacker; Barbara Priwitzer; Peter F. Stadler (Bioinform., 2004)

Conserved RNA secondary structures in viral genomes: a survey. - Ivo L. Hofacker; Peter F. Stadler; Roman R. Stocsits (Bioinform., 2004)

Counterexamples in Chemical Ring Perception. - Franziska Berger; Christoph Flamm; Petra M. Gleiss; Josef Leydold; Peter F. Stadler (J. Chem. Inf. Model., 2004)

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

Prediction of Consensus RNA Secondary Structures Including Pseudoknots. - Christina Witwer; Ivo L. Hofacker; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Editorial. - Olaf Breidbach; Jürgen Jost; Peter F. Stadler; Michael S. Weingarten (Theory Biosci., 2004)

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

Simon-Ando decomposability and fitness landscapes. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Lee Altenberg (Theory Biosci., 2004)

Aggregation of variables and system decomposition: Applications to fitness landscape analysis. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Joachim Hermisson (Theory Biosci., 2004)

CelloS: A Multi-level Approach to Evolutionary Dynamics. - Camille Stephan-Otto Attolini; Peter F. Stadler; Christoph Flamm (ECAL, 2005)

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. - Gil Benkö; Christoph Flamm; Peter F. Stadler (ECAL, 2005)

Non-coding RNAs in Ciona intestinalis. - Kristin Missal; Dominic Rose; Peter F. Stadler (ECCB/JBI, 2005)

Neutral Networks of Interacting RNA Secondary Structures. - Camille Stephan-Otto Attolini; Peter F. Stadler (Adv. Complex Syst., 2005)

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)

Multiple sequence alignments of partially coding nucleic acid sequences. - Roman R. Stocsits; Ivo L. Hofacker; Claudia Fried; Peter F. Stadler (BMC Bioinform., 2005)

Minimum path bases and relevant paths. - Petra M. Gleiss; Josef Leydold; Peter F. Stadler (Networks, 2005)

Fast and reliable prediction of noncoding RNAs. - Stefan Washietl; Ivo L. Hofacker; Peter F. Stadler (Proc. Natl. Acad. Sci. USA, 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)

MATH/CHEM/COMP 2004 Contributions. - Ante Graovac; Peter F. Stadler (Theory Biosci., 2005)

Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Joachim Hermisson (Theory Biosci., 2005)

Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. - Axel Mosig; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 2006)

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. - Jana Hertel; Peter F. Stadler (ISMB (Supplement of Bioinformatics), 2006)

Visualization of Lattice-Based Protein Folding Simulations. - Sebastian Potzsch; Gerik Scheuermann; Peter F. Stadler; Michael T. Wolfinger; Christoph Flamm (IV, 2006)

Partition function and base pairing probabilities of RNA heterodimers. - Stephan H. Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2006)

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

New journal: Algorithms for Molecular Biology. - Burkhard Morgenstern; Peter F. Stadler (Algorithms Mol. Biol., 2006)

Local RNA base pairing probabilities in large sequences. - Stephan H. Bernhart; Ivo L. Hofacker; Peter F. Stadler (Bioinform., 2006)

Memory efficient folding algorithms for circular RNA secondary structures. - Ivo L. Hofacker; Peter F. Stadler (Bioinform., 2006)

Thermodynamics of RNA-RNA binding. - Ulrike Mückstein; Hakim Tafer; Jörg Hackermüller; Stephan H. Bernhart; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 2006)

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. - Christian V. Forst; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BMC Bioinform., 2006)

A prime factor theorem for a generalized direct product. - Wilfried Imrich; Peter F. Stadler (Discuss. Math. Graph Theory, 2006)

Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. - Axel Mosig; Katrin Sameith; Peter F. Stadler (Genom. Proteom. Bioinform., 2006)

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. - Paul Wei-Che Hsu; Hsien-Da Huang; Sheng-Da Hsu; Li-Zen Lin; Ann-Ping Tsou; Ching-Ping Tseng; Peter F. Stadler; Stefan Washietl; Ivo L. Hofacker (Nucleic Acids Res., 2006)

Visualization of Barrier Tree Sequences. - Christian Heine 002; Gerik Scheuermann; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (IEEE Trans. Vis. Comput. Graph., 2006)

Saddles and Barrier in Landscapes of Generalized Search Operators. - Christoph Flamm; Ivo L. Hofacker; Bärbel M. R. Stadler; Peter F. Stadler (FOGA, 2007)

Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. - Axel Mosig; Peter Menzel; Peter F. Stadler (German Conference on Bioinformatics, 2007)

Homology Search with Fragmented Nucleic Acid Sequence Patterns. - Axel Mosig; Julian J.-L. Chen; Peter F. Stadler (WABI, 2007)

RNAstrand: reading direction of structured RNAs in multiple sequence alignments. - Kristin Reiche; Peter F. Stadler (Algorithms Mol. Biol., 2007)

CREx: inferring genomic rearrangements based on common intervals. - Matthias Bernt; Daniel Merkle; Kai Ramsch; Guido Fritzsch; Marleen Perseke; Detlef Bernhard; Martin Schlegel; Peter F. Stadler; Martin Middendorf (Bioinform., 2007)

Progressive multiple sequence alignments from triplets. - Matthias Kruspe; Peter F. Stadler (BMC Bioinform., 2007)

U7 snRNAs: A Computational Survey. - Manja Marz; Axel Mosig; Bärbel M. R. Stadler; Peter F. Stadler (Genom. Proteom. Bioinform., 2007)

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. - Sebastian Will; Kristin Reiche; Ivo L. Hofacker; Peter F. Stadler; Rolf Backofen (PLoS Comput. Biol., 2007)

Towards theoretical formalisms. - Olaf Breidbach; Jürgen Jost; Peter F. Stadler (Theory Biosci., 2007)

Evolution of the vertebrate Y RNA cluster. - Axel Mosig; Guofeng Meng; Bärbel M. R. Stadler; Peter F. Stadler (Theory Biosci., 2007)

The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. - Marleen Perseke; Thomas Hankeln; Bettina Weich; Guido Fritzsch; Peter F. Stadler; Olle Israelsson; Detlef Bernhard; Martin Schlegel (Theory Biosci., 2007)

Visualization of Barrier Tree Sequences Revisited. - Christian Heine 002; Gerik Scheuermann; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (Visualization in Medicine and Life Sciences, 2008)

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. - Ulrike Mückstein; Hakim Tafer; Stephan H. Bernhart; Maribel Hernandez-Rosales; Jörg Vogel 002; Peter F. Stadler; Ivo L. Hofacker (BIRD, 2008)

FRANz: Fast Reconstruction of Wild Pedigrees. - Markus Riester; Peter F. Stadler; Konstantin Klemm (German Conference on Bioinformatics, 2008)

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)

SnoReport: computational identification of snoRNAs with unknown targets. - Jana Hertel; Ivo L. Hofacker; Peter F. Stadler (Bioinform., 2008)

RNAalifold: improved consensus structure prediction for RNA alignments. - Stephan H. Bernhart; Ivo L. Hofacker; Sebastian Will; Andreas R. Gruber; Peter F. Stadler (BMC Bioinform., 2008)

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

Duplicated RNA genes in teleost Fish genomes. - Dominic Rose; Julian Jöris; Jörg Hackermüller; Kristin Reiche; Qiang Li; Peter F. Stadler (J. Bioinform. Comput. Biol., 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)

Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. - Peter Menzel; Jan Gorodkin; Peter F. Stadler (GCB, 2009)

A Topological Approach to Chemical Organizations. - Gil Benkö; Florian Centler; Peter Dittrich; Christoph Flamm; Bärbel M. R. Stadler; Peter F. Stadler (Artif. Life, 2009)

A note on quasi-robust cycle bases. - Philipp-Jens Ostermeier; Marc Hellmuth; Josef Leydold; Konstantin Klemm; Peter F. Stadler (Ars Math. Contemp., 2009)

Partition function and base pairing probabilities for RNA-RNA interaction prediction. - Fenix W. D. Huang; Jing Qin 006; Christian M. Reidys; Peter F. Stadler (Bioinform., 2009)

Structural profiles of human miRNA families from pairwise clustering. - Bogumil Kaczkowski; Elfar Torarinsson; Kristin Reiche; Jakob Hull Havgaard; Peter F. Stadler; Jan Gorodkin (Bioinform., 2009)

Evidence for human microRNA-offset RNAs in small RNA sequencing data. - David Langenberger; Clara Bermudez-Santana; Jana Hertel; Steve Hoffmann; Philipp Khaitovich; Peter F. Stadler (Bioinform., 2009)

FRANz: reconstruction of wild multi-generation pedigrees. - Markus Riester; Peter F. Stadler; Konstantin Klemm (Bioinform., 2009)

Sequence assembly. - K. Scheibye-Alsing; Steve Hoffmann; A. Frankel; Peter Jensen; Peter F. Stadler; Y. Mang; Niels Tommerup; M. J. Gilchrist; A.-B. Nygård; Susanna Cirera; Claus B. Jørgensen; Merete Fredholm; et al. (Comput. Biol. Chem., 2009)

Preface. - Andreas W. M. Dress; Bülent Karasözen; Peter F. Stadler; Gerhard-Wilhelm Weber (Discret. Appl. Math., 2009)

A note on fundamental, non-fundamental, and robust cycle bases. - Konstantin Klemm; Peter F. Stadler (Discret. Appl. Math., 2009)

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

Approximate graph products. - Marc Hellmuth; Wilfried Imrich; Werner Klöckl; Peter F. Stadler (Eur. J. Comb., 2009)

Local Algorithms for the Prime Factorization of Strong Product Graphs. - Marc Hellmuth; Wilfried Imrich; Werner Klöckl; Peter F. Stadler (Math. Comput. Sci., 2009)

tRNAdb 2009: compilation of tRNA sequences and tRNA genes. - Frank Jühling; Mario Mörl; Roland K. Hartmann; Mathias Sprinzl; Peter F. Stadler; Joern Pütz (Nucleic Acids Res., 2009)

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. - Steve Hoffmann; Christian Otto; Stefan Kurtz; Cynthia M. Sharma; Philipp Khaitovich; Jörg Vogel 002; Peter F. Stadler; Jörg Hackermüller (PLoS Comput. Biol., 2009)

Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). - Karen E. Chambers; Ryan McDaniell; Jeremy D. Raincrow; Maya Deshmukh; Peter F. Stadler; Chi-hua Chiu (Theory Biosci., 2009)

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

In Silico Evolution of Early Metabolism. - Alexander Ullrich; Christoph Flamm; Markus Rohrschneider; Peter F. Stadler (ALIFE, 2010)

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

Visual Network Analysis of Dynamic Metabolic Pathways. - Markus Rohrschneider; Alexander Ullrich; Andreas Kerren; Peter F. Stadler; Gerik Scheuermann (ISVC (1), 2010)

Session Introduction. - Rolf Backofen; Hamidreza Chitsaz; Ivo L. Hofacker; Süleyman Cenk Sahinalp; Peter F. Stadler (Pacific Symposium on Biocomputing, 2010)

RNAz 2.0: Improved Noncoding RNA Detection. - Andreas R. Gruber; Sven Findeiß; Stefan Washietl; Ivo L. Hofacker; Peter F. Stadler (Pacific Symposium on Biocomputing, 2010)

Identification and Classification of Small RNAs in Transcriptome Sequence Data. - David Langenberger; Clara Bermudez-Santana; Peter F. Stadler; Steve Hoffmann (Pacific Symposium on Biocomputing, 2010)

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

Evolution of the Long Non-coding RNAs MALAT1 and MENbeta/epsilon. - Peter F. Stadler (BSB, 2010)

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. - Christian Arnold; Peter F. Stadler (Algorithms Mol. Biol., 2010)

Target prediction and a statistical sampling algorithm for RNA-RNA interaction. - Fenix W. D. Huang; Jing Qin 006; Christian M. Reidys; Peter F. Stadler (Bioinform., 2010)

RNAsnoop: efficient target prediction for H/ACA snoRNAs. - Hakim Tafer; Stephanie Kehr; Jana Hertel; Ivo L. Hofacker; Peter F. Stadler (Bioinform., 2010)

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. - Mario Fasold; Peter F. Stadler; Hans Binder (BMC Bioinform., 2010)

Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. - Manja Marz; Nathalie Vanzo; Peter F. Stadler (J. Bioinform. Comput. Biol., 2010)

The primary transcriptome of the major human pathogen Helicobacter pylori. - Cynthia M. Sharma; Steve Hoffmann; Fabien Darfeuille; Jérémy Reignier; Sven Findeiß; Alexandra Sittka; Sandrine Chabas; Kristin Reiche; Jörg Hackermüller; Richard Reinhardt; Peter F. Stadler; Jörg Vogel 002 (Nat., 2010)

Visualization of Graph Products. - Stefan Jänicke; Christian Heine 002; Marc Hellmuth; Peter F. Stadler; Gerik Scheuermann (IEEE Trans. Vis. Comput. Graph., 2010)

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

MicroRNA or Not MicroRNA? - David Langenberger; Sebastian Bartschat; Jana Hertel; Steve Hoffmann; Hakim Tafer; Peter F. Stadler (BSB, 2011)

In Silico Evolution of Early Metabolism. - Alexander Ullrich; Markus Rohrschneider; Gerik Scheuermann; Peter F. Stadler; Christoph Flamm (Artif. Life, 2011)

ViennaRNA Package 2.0. - Ronny Lorenz; Stephan H. Bernhart; Christian Höner zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2011)

Fast local fragment chaining using sum-of-pair gap costs. - Christian Otto; Steve Hoffmann; Jan Gorodkin; Peter F. Stadler (Algorithms Mol. Biol., 2011)

PLEXY: efficient target prediction for box C/D snoRNAs. - Stephanie Kehr; Sebastian Bartschat; Peter F. Stadler; Hakim Tafer (Bioinform., 2011)

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. - Peter Menzel; Peter F. Stadler; Jan Gorodkin (Bioinform., 2011)

Topology and prediction of RNA pseudoknots. - Christian M. Reidys; Fenix W. D. Huang; Jørgen E. Andersen; Robert C. Penner; Peter F. Stadler; Markus E. Nebel (Bioinform., 2011)

Computational discovery of human coding and non-coding transcripts with conserved splice sites. - Dominic Rose; Michael Hiller; Katharina Schutt; Jörg Hackermüller; Rolf Backofen; Peter F. Stadler (Bioinform., 2011)

A folding algorithm for extended RNA secondary structures. - Christian Höner zu Siederdissen; Stephan H. Bernhart; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 2011)

Fast accessibility-based prediction of RNA-RNA interactions. - Hakim Tafer; Fabian Amman; Florian Eggenhofer; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 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)

Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2011)

RNApredator: fast accessibility-based prediction of sRNA targets. - Florian Eggenhofer; Hakim Tafer; Peter F. Stadler; Ivo L. Hofacker (Nucleic Acids Res., 2011)

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. - Mario Fasold; David Langenberger; Hans Binder; Peter F. Stadler; Steve Hoffmann (Nucleic Acids Res., 2011)

A Visual Cross-Database Comparison of Metabolic Networks. - Markus Rohrschneider; Peter F. Stadler; Gerik Scheuermann (ISVC (2), 2012)

RNA Folding Algorithms with G-Quadruplexes. - Ronny Lorenz; Stephan H. Bernhart; Fabian Externbrink; Jing Qin 006; Christian Höner zu Siederdissen; Fabian Amman; Ivo L. Hofacker; Peter F. Stadler (BSB, 2012)

Minimum cycle bases of lexicographic products. - Marc Hellmuth; Philipp-Jens Ostermeier; Peter F. Stadler (Ars Math. Contemp., 2012)

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. - David Langenberger; Sachin Pundhir; Claus Thorn Ekstrøm; Peter F. Stadler; Steve Hoffmann; Jan Gorodkin (Bioinform., 2012)

Fast and sensitive mapping of bisulfite-treated sequencing data. - Christian Otto; Peter F. Stadler; Steve Hoffmann (Bioinform., 2012)

Addendum: topology and prediction of RNA pseudoknots. - Christian M. Reidys; Fenix W. D. Huang; Jørgen E. Andersen; Robert C. Penner; Peter F. Stadler; Markus E. Nebel (Bioinform., 2012)

From event-labeled gene trees to species trees. - Maribel Hernandez-Rosales; Marc Hellmuth; Nicolas Wieseke; Katharina T. Huber; Vincent Moulton; Peter F. Stadler (BMC Bioinform., 2012)

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2012)

Diagonalized Cartesian products of s-prime graphs are s-prime. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Discret. Math., 2012)

Symmetric circular matchings and RNA folding. - Ivo L. Hofacker; Christian M. Reidys; Peter F. Stadler (Discret. Math., 2012)

The Cartesian product of hypergraphs. - Lydia Ostermeier; Marc Hellmuth; Peter F. Stadler (J. Graph Theory, 2012)

A Survey on Hypergraph Products. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Math. Comput. Sci., 2012)

Hidden treasures in unspliced EST data. - Jan Engelhardt; Peter F. Stadler (Theory Biosci., 2012)

Atom Mapping with Constraint Programming. - Martin Mann; Feras Nahar; Heinz Ekker; Rolf Backofen; Peter F. Stadler; Christoph Flamm (CP, 2013)

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. - Rolf Backofen; Markus Fricke; Manja Marz; Jing Qin 006; Peter F. Stadler (WABI, 2013)

The Trouble with Long-Range Base Pairs in RNA Folding. - Fabian Amman; Stephan H. Bernhart; Gero Doose; Ivo L. Hofacker; Jing Qin 006; Peter F. Stadler; Sebastian Will (BSB, 2013)

ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation. - Wosley Arruda; Célia Ghedini Ralha; Tainá Raiol; Marcelo M. Brigido; Maria Emília M. T. Walter; Peter F. Stadler (BSB, 2013)

How to Multiply Dynamic Programming Algorithms. - Christian Höner zu Siederdissen; Ivo L. Hofacker; Peter F. Stadler (BSB, 2013)

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. - Sebastian Will; Michael F. Siebauer; Steffen Heyne; Jan Engelhardt; Peter F. Stadler; Kristin Reiche; Rolf Backofen (Algorithms Mol. Biol., 2013)

Relations between graphs. - Jan Hubicka; Jürgen Jost; Yangjing Long; Peter F. Stadler; Ling Yang (Ars Math. Contemp., 2013)

Square Property, Equitable Partitions, and Product-like Graphs - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (CoRR, 2013)

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. - Jakob L. Andersen; Tommy Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle; Peter F. Stadler (Entropy, 2013)

On the Complexity of Reconstructing Chemical Reaction Networks. - Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Philipp Peters; Peter F. Stadler (Math. Comput. Sci., 2013)

The RNAsnp web server: predicting SNP effects on local RNA secondary structure. - Radhakrishnan Sabarinathan; Hakim Tafer; Stefan E. Seemann; Ivo L. Hofacker; Peter F. Stadler; Jan Gorodkin (Nucleic Acids Res., 2013)

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. - Ronny Lorenz; Stephan H. Bernhart; Jing Qin 006; Christian Höner zu Siederdissen; Andrea Tanzer; Fabian Amman; Ivo L. Hofacker; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

The correlation of genome size and DNA methylation rate in metazoans. - Marcus Lechner; Manja Marz; Christian Ihling; Andrea Sinz; Peter F. Stadler; Veiko Krauss (Theory Biosci., 2013)

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (FMMB, 2014)

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)

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. - Sebastian Will; Peter F. Stadler (WABI, 2014)

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. - Hugo W. Schneider; Sebastian Bartschat; Gero Doose; Lucas Maciel 001; Erick Pizani; Marcelo Bassani; Fernando Araripe Torres; Sebastian Will; Tainá Raiol; Marcelo M. Brigido; Maria Emília Telles Walter; Peter F. Stadler (BSB, 2014)

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

Atom mapping with constraint programming. - Martin Mann; Feras Nahar; Norah Schnorr; Rolf Backofen; Peter F. Stadler; Christoph Flamm (Algorithms Mol. Biol., 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)

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. - Jing Qin 006; Markus Fricke; Manja Marz; Peter F. Stadler; Rolf Backofen (Algorithms Mol. Biol., 2014)

Convex cycle bases. - Marc Hellmuth; Josef Leydold; Peter F. Stadler (Ars Math. Contemp., 2014)

snoStrip: a snoRNA annotation pipeline. - Sebastian Bartschat; Stephanie Kehr; Hakim Tafer; Peter F. Stadler; Jana Hertel (Bioinform., 2014)

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. - Marcel Kucharík; Ivo L. Hofacker; Peter F. Stadler; Jing Qin 006 (Bioinform., 2014)

Challenges in RNA virus bioinformatics. - Manja Marz; Niko Beerenwinkel; Christian Drosten; Markus Fricke; Dmitrij Frishman; Ivo L. Hofacker; Dieter Hoffmann; Martin Middendorf; Thomas Rattei; Peter F. Stadler; Armin Töpfer (Bioinform., 2014)

Lacking alignments? The next-generation sequencing mapper segemehl revisited. - Christian Otto; Peter F. Stadler; Steve Hoffmann (Bioinform., 2014)

TSSAR: TSS annotation regime for dRNA-seq data. - Fabian Amman; Michael T. Wolfinger; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler; Sven Findeiß (BMC Bioinform., 2014)

Simulation of gene family histories. - Maribel Hernandez-Rosales; Nicolas Wieseke; Marc Hellmuth; Peter F. Stadler (BMC Bioinform., 2014)

Algorithmic Cheminformatics (Dagstuhl Seminar 14452). - Wolfgang Banzhaf; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 2014)

Unique square property, equitable partitions, and product-like graphs. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Discret. Math., 2014)

Generic strategies for chemical space exploration. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Int. J. Comput. Biol. Drug Des., 2014)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. - Juliane C. Dohm; André E. Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; et al. (Nat., 2014)

Rugged and Elementary Landscapes. - Konstantin Klemm; Peter F. Stadler (Theory and Principled Methods for the Design of Metaheuristics, 2014)

The relaxed square property. - Marc Hellmuth; Tilen Marc; Lydia Ostermeier; Peter F. Stadler (Australas. J Comb., 2015)

A simple data-adaptive probabilistic variant calling model. - Steve Hoffmann; Peter F. Stadler; Korbinian Strimmer (Algorithms Mol. Biol., 2015)

Evolution of 3'UTR-associated RNAs. - Jan Engelhardt; Peter F. Stadler (BMC Bioinform., 2015)

Support for Eschenmoser's Glyoxylate Scenario. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2015)

Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s. - Marc Hellmuth; Adrian Fritz; Nicolas Wieseke; Peter F. Stadler (CoRR, 2015)

The Grid Property and Product-Like Hypergraphs. - Lydia Ostermeier; Peter F. Stadler (Graphs Comb., 2015)

Knowledge-based reasoning to annotate noncoding RNA using multi-agent system. - Wosley Arruda; Daniel S. Souza; Célia Ghedini Ralha; Maria Emília M. T. Walter; Tainá Raiol; Marcelo M. Brigido; Peter F. Stadler (J. Bioinform. Comput. Biol., 2015)

Spiders can be Recognized by Counting Their Legs. - Sarah Berkemer; Ricardo Régis Cavalcante Chaves; Adrian Fritz; Marc Hellmuth; Maribel Hernandez-Rosales; Peter F. Stadler (Math. Comput. Sci., 2015)

Connectivity Spaces. - Bärbel M. R. Stadler; Peter F. Stadler (Math. Comput. Sci., 2015)

Product Grammars for Alignment and Folding. - Christian Höner zu Siederdissen; Ivo L. Hofacker; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

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)

A Software Package for Chemically Inspired Graph Transformation. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2016)

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. - Christoph Flamm; Daniel Merkle; Peter F. Stadler; Uffe Thorsen (ICGT, 2016)

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)

RNA folding with hard and soft constraints. - Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (Algorithms Mol. Biol., 2016)

Pseudoknots in RNA folding landscapes. - Marcel Kucharík; Ivo L. Hofacker; Peter F. Stadler; Jing Qin 006 (Bioinform., 2016)

SHAPE directed RNA folding. - Ronny Lorenz; Dominik Luntzer; Ivo L. Hofacker; Peter F. Stadler; Michael T. Wolfinger (Bioinform., 2016)

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. - João Victor de Araújo Oliveira; Fabrizio Costa; Rolf Backofen; Peter F. Stadler; Maria Emília Telles Walter; Jana Hertel (BMC Bioinform., 2016)

Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events. - Marc Hellmuth; Maribel Hernandez-Rosales; Yangjing Long; Peter F. Stadler (CoRR, 2016)

The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations. - Marc Hellmuth; Peter F. Stadler; Nicolas Wieseke (CoRR, 2016)

Read mapping. - Steve Hoffmann; Peter F. Stadler (it Inf. Technol., 2016)

Associativity and Non-Associativity of Some Hypergraph Products. - Richard H. Hammack; Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Math. Comput. Sci., 2016)

Algebraic dynamic programming for multiple context-free grammars. - Maik Riechert; Christian Höner zu Siederdissen; Peter F. Stadler (Theor. Comput. Sci., 2016)

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

Chemical Graph Transformation with Stereo-Information. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2017)

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (WABI, 2017)

Algebraic Dynamic Programming on Trees. - Sarah Berkemer; Christian Höner zu Siederdissen; Peter F. Stadler (Algorithms, 2017)

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. - Marwa Al Arab; Matthias Bernt; Christian Höner zu Siederdissen; Kifah Tout; Peter F. Stadler (Algorithms Mol. Biol., 2017)

Tractable RNA-ligand interaction kinetics. - Felix Kühnl; Peter F. Stadler; Sebastian Will (BMC Bioinform., 2017)

An Intermediate Level of Abstraction for Computational Systems Chemistry. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2017)

Merging Modules is equivalent to Editing P4's. - Marc Hellmuth; Adrian Fritz; Nicolas Wieseke; Peter F. Stadler (CoRR, 2017)

A Survey on Hypergraph Products (Erratum). - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (CoRR, 2017)

Reconstructing Gene Trees From Fitch's Xenology Relation. - Manuela Geiß; John Anders; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

Phylogenomics with Paralogs. - Marc Hellmuth; Nicolas Wieseke; Marcus Lechner; Hans-Peter Lenhof; Martin Middendorf; Peter F. Stadler (CoRR, 2017)

Topological Representation of the Transit Sets of k-Point Crossover Operators. - Manoj Changat; Prasanth G. Narasimha-Shenoi; Ferdoos Hossein Nezhad; Matjaz Kovse; Shilpa Mohandas; Abisha Ramachandran; Peter F. Stadler (CoRR, 2017)

Algorithmic Cheminformatics (Dagstuhl Seminar 17452). - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 2017)

Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. - Ali M. Yazbeck; Kifah R. Tout; Peter F. Stadler; Jana Hertel (J. Integr. Bioinform., 2017)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

Design of Artificial Riboswitches as Biosensors. - Sven Findeiß; Maja Etzel; Sebastian Will; Mario Mörl; Peter F. Stadler (Sensors, 2017)

A short note on undirected Fitch graphs. - Marc Hellmuth; Yangjing Long; Manuela Geiß; Peter F. Stadler (Art Discret. Appl. Math., 2018)

Split-inducing indels in phylogenomic analysis. - Alexander Donath; Peter F. Stadler (Algorithms Mol. Biol., 2018)

Superbubbles revisited. - Fabian Gärtner; Lydia Müller; Peter F. Stadler (Algorithms Mol. Biol., 2018)

Coordinate systems for supergenomes. - Fabian Gärtner; Christian Höner zu Siederdissen; Lydia Müller; Peter F. Stadler (Algorithms Mol. Biol., 2018)

Time-consistent reconciliation maps and forbidden time travel. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2018)

Axiomatic characterization of transit functions of hierarchies. - Manoj Changat; Ferdoos Hossein Nezhad; Peter F. Stadler (Ars Math. Contemp., 2018)

ceRNAs in plants: computational approaches and associated challenges for target mimic research. - Alexandre Rossi Paschoal; Irma Lozada-Chávez; Douglas Silva Domingues; Peter F. Stadler (Briefings Bioinform., 2018)

Accurate mapping of tRNA reads. - Anne Hoffmann 002; Jörg Fallmann; Elisa Vilardo; Mario Mörl; Peter F. Stadler; Fabian Amman (Bioinform., 2018)

Alignments as Compositional Structures. - Sarah J. Berkemer; Christian Höner zu Siederdissen; Peter F. Stadler (CoRR, 2018)

Finding the K best synthesis plans. - Rolf Fagerberg; Christoph Flamm; Rojin Kianian; Daniel Merkle; Peter F. Stadler (J. Cheminformatics, 2018)

Partially Local Multi-way Alignments. - Nancy Retzlaff; Peter F. Stadler (Math. Comput. Sci., 2018)

Patterning the insect eye: From stochastic to deterministic mechanisms. - Haleh Ebadi; Michael Perry; Keith Short; Konstantin Klemm; Claude Desplan; Peter F. Stadler; Anita Mehta (PLoS Comput. Biol., 2018)

Phylogenetics beyond biology. - Nancy Retzlaff; Peter F. Stadler (Theory Biosci., 2018)

A General Framework for Exact Partially Local Alignments. - Falco Kirchner; Nancy Retzlaff; Peter F. Stadler (BIOINFORMATICS, 2019)

Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. - Maria Waldl; Sebastian Will; Michael T. Wolfinger; Ivo L. Hofacker; Peter F. Stadler (CIBB, 2019)

Axiomatic characterization of transit functions of weak hierarchies. - Manoj Changat; Prasanth G. Narasimha-Shenoi; Peter F. Stadler (Art Discret. Appl. Math., 2019)

Direct Superbubble Detection. - Fabian Gärtner; Peter F. Stadler (Algorithms, 2019)

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. - Daniel Wiegreffe; Daniel Alexander; Peter F. Stadler; Dirk Zeckzer (Bioinform., 2019)

Automatic curation of large comparative animal MicroRNA datasets. - Ali M. Yazbeck; Peter F. Stadler; Kifah Tout; Jörg Fallmann (Bioinform., 2019)

SSS-test: a novel test for detecting positive selection on RNA secondary structure. - Maria Beatriz Walter Costa; Christian Höner zu Siederdissen; Marko Dunjic; Peter F. Stadler; Katja Nowick (BMC Bioinform., 2019)

Ryūtō: network-flow based transcriptome reconstruction. - Thomas Gatter; Peter F. Stadler (BMC Bioinform., 2019)

flowEMMi: an automated model-based clustering tool for microbial cytometric data. - Joachim Ludwig; Christian Höner zu Siederdissen; Zishu Liu; Peter F. Stadler; Susann Müller (BMC Bioinform., 2019)

Best Match Graphs and Reconciliation of Gene Trees with Species Trees. - Manuela Geiß; Marcos González; Alitzel López Sánchez; Dulce I. Valdivia; Marc Hellmuth; Maribel Hernández-Rosales; Peter F. Stadler (CoRR, 2019)

Hierarchical Colorings of Cographs. - Dulce I. Valdivia; Manuela Geiß; Marc Hellmuth; Maribel Hernández-Rosales; Peter F. Stadler (CoRR, 2019)

Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (CoRR, 2019)

Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected research activities. - Erhard Rahm; Wolfgang E. Nagel; Eric Peukert; René Jäkel; Fabian Gärtner; Peter F. Stadler; Daniel Wiegreffe; Dirk Zeckzer; Wolfgang Lehner (Datenbank-Spektrum, 2019)

The RNA workbench 2.0: next generation RNA data analysis. - Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A. Doyle; Tomas Klingström; Florian Eggenhofer; Peter F. Stadler; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2019)

Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOINFORMATICS, 2020)

Efficient Algorithms for Co-folding of Multiple RNAs. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOSTEC (Selected Papers), 2020)

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. - Thomas Gatter; Sarah von Löhneysen; Polina Drozdova; Tom Hartmann; Peter F. Stadler (WABI, 2020)

Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile. - Manuela M. do Almo; Isabel G. Sousa; Waldeyr Mendes Cordeiro da Silva; Thomas Gatter; Peter F. Stadler; Steve Hoffmann; Andrea Queiroz Maranhão; Marcelo M. Brigido (BSB, 2020)

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. - Waldeyr Mendes Cordeiro da Silva; Daniela P. de Andrade; Jakob L. Andersen; Maria Emília Telles Walter; Marcelo M. Brigido; Peter F. Stadler; Christoph Flamm (BSB, 2020)

Cograph editing: Merging modules is equivalent to editing P_4s. - Adrian Fritz; Marc Hellmuth; Peter F. Stadler; Nicolas Wieseke (Art Discret. Appl. Math., 2020)

Transit sets of -point crossover operators. - Manoj Changat; Prasanth G. Narasimha-Shenoi; Ferdoos Hossein Nezhad; Matjaz Kovse; Shilpa Mohandas; Abisha Ramachandran; Peter F. Stadler (AKCE Int. J. Graphs Comb., 2020)

From pairs of most similar sequences to phylogenetic best matches. - Peter F. Stadler; Manuela Geiß; David Schaller 001; Alitzel López Sánchez; Marcos E. González Laffitte; Dulce I. Valdivia; Marc Hellmuth; Maribel Hernandez-Rosales (Algorithms Mol. Biol., 2020)

Clustering Improves the Goemans-Williamson Approximation for the Max-Cut Problem. - Angel E. Rodriguez-Fernandez; Bernardo A. Gonzalez-Torres; Ricardo Menchaca-Mendez; Peter F. Stadler (Comput., 2020)

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. - David Schaller 001; Manuela Geiß; Peter F. Stadler; Marc Hellmuth (CoRR, 2020)

Indirect Identification of Horizontal Gene Transfer. - David Schaller 001; Manuel Lafond; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (CoRR, 2020)

Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (Discret. Appl. Math., 2020)

Exact-2-relation graphs. - Yangjing Long; Peter F. Stadler (Discret. Appl. Math., 2020)

A probabilistic version of Sankoff's maximum parsimony algorithm. - Gábor Balogh; Stephan H. Bernhart; Peter F. Stadler; Jana Schor (J. Bioinform. Comput. Biol., 2020)

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. - Felipe Borim Corrêa; João Pedro Saraiva; Peter F. Stadler; Ulisses Nunes da Rocha (Nucleic Acids Res., 2020)

Complexity of modification problems for reciprocal best match graphs. - Marc Hellmuth; Manuela Geiß; Peter F. Stadler (Theor. Comput. Sci., 2020)

Average Fitness Differences on NK Landscapes. - Wim Hordijk; Stuart A. Kauffman; Peter F. Stadler (Theory Biosci., 2020)

Are spliced ncRNA host genes distinct classes of lncRNAs? - Rituparno Sen; Jörg Fallmann; Maria Emília M. T. Walter; Peter F. Stadler (Theory Biosci., 2020)

Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards. - Sree Rohit Raj Kolora; Deisy Morselli Gysi; Stefan Schaffer; Rui Faria; Klaus Henle; Peter F. Stadler; Martin Schlegel; Katja Nowick; Marton Szablocs; Annegrett Grimm-Seyfarth (Zenodo, 2020)

Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data. - Mirele C. S. F. Costa; João Victor de Araújo Oliveira; Waldeyr M. C. Silva; Rituparno Sen; Jörg Fallmann; Peter F. Stadler; Maria Emília M. T. Walter (BIOINFORMATICS, 2021)

Cut Vertex Transit Functions of Hypergraphs. - Manoj Changat; Ferdoos Hossein Nezhad; Peter F. Stadler (CALDAM, 2021)

Combining Orthology and Xenology Data in a Common Phylogenetic Tree. - Marc Hellmuth; Mira Michel; Nikolai N. Nøjgaard; David Schaller 001; Peter F. Stadler (BSB, 2021)

Forman-Ricci Curvature for hypergraphs. - Wilmer Leal; Guillermo Restrepo; Peter F. Stadler; Jürgen Jost (Adv. Complex Syst., 2021)

Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (Algorithms, 2021)

LazyB: fast and cheap genome assembly. - Thomas Gatter; Sarah von Löhneysen; Jörg Fallmann; Polina Drozdova; Tom Hartmann; Peter F. Stadler (Algorithms Mol. Biol., 2021)

Heuristic algorithms for best match graph editing. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (Algorithms Mol. Biol., 2021)

A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (Algorithms Mol. Biol., 2021)

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. - Adam Nunn; Christian Otto; Peter F. Stadler; David Langenberger (Briefings Bioinform., 2021)

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. - Adam Nunn; Christian Otto; Peter F. Stadler; David Langenberger (Briefings Bioinform., 2021)

Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more. - Thomas Gatter; Peter F. Stadler (Bioinform., 2021)

A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. - John Anders; Hannes Petruschke; Nico Jehmlich; Sven-Bastiaan Haange; Martin von Bergen; Peter F. Stadler (BMC Bioinform., 2021)

Weighted Consensus Segmentations. - Halima Saker; Rainer Machné; Jörg Fallmann; Douglas B. Murray; Ahmad M. Shahin; Peter F. Stadler (Comput., 2021)

Compatibility of Partitions, Hierarchies, and Split Systems. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (CoRR, 2021)

A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (CoRR, 2021)

Defining Autocatalysis in Chemical Reaction Networks. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2021)

Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (CoRR, 2021)

The Past as a Stochastic Process. - David H. Wolpert; Michael H. Price; Stefani A. Crabtree; Timothy A. Kohler; Jürgen Jost; James Evans; Peter F. Stadler; Hajime Shimao; Manfred D. Laubichler (CoRR, 2021)

Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (Discret. Math. Theor. Comput. Sci., 2021)

Least resolved trees for two-colored best match graphs. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (J. Graph Algorithms Appl., 2021)

Compositional Properties of Alignments. - Sarah J. Berkemer; Christian Höner zu Siederdissen; Peter F. Stadler (Math. Comput. Sci., 2021)

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. - Jonas Coelho Kasmanas; Alexander Bartholomäus; Felipe Borim Corrêa; Tamara L. Tal; Nico Jehmlich; Gunda Herberth; Martin von Bergen; Peter F. Stadler; André Carlos Ponce de Leon Ferreira de Carvalho; Ulisses Nunes da Rocha (Nucleic Acids Res., 2021)

Superbubbles as an empirical characteristic of directed networks. - Fabian Gärtner; Felix Kühnl; Carsten R. Seemann; Christian Höner zu Siederdissen; Peter F. Stadler (Netw. Sci., 2021)

Efficient Laplacian spectral density computations for networks with arbitrary degree distributions. - Grover E. C. Guzman; Peter F. Stadler; André Fujita (Netw. Sci., 2021)

Complexity of modification problems for best match graphs. - David Schaller 001; Peter F. Stadler; Marc Hellmuth (Theor. Comput. Sci., 2021)

Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar. - Dustyn Eggers; Christian Höner zu Siederdissen; Peter F. Stadler (BSB, 2022)

Complete edge-colored permutation graphs. - Tom Hartmann; Max Bannach; Martin Middendorf; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Adv. Appl. Math., 2022)

Whitney's connectivity inequalities for directed hypergraphs. - Anahy Santiago Arguello; Peter F. Stadler (Art Discret. Appl. Math., 2022)

Bi-alignments with affine gaps costs. - Peter F. Stadler; Sebastian Will (Algorithms Mol. Biol., 2022)

BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. - Robson Bonidia; Anderson P. Avila-Santos; Breno Lívio Silva de Almeida; Peter F. Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho (Briefings Bioinform., 2022)

Efficient eigenvalue counts for tree-like networks. - Grover E. C. Guzman; Peter F. Stadler; André Fujita (J. Complex Networks, 2022)

From modular decomposition trees to rooted median graphs. - Carmen Bruckmann; Peter F. Stadler; Marc Hellmuth (Discret. Appl. Math., 2022)

Compatibility of partitions with trees, hierarchies, and split systems. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (Discret. Appl. Math., 2022)

Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy. - Robson Parmezan Bonidia; Anderson P. Avila-Santos; Breno Lívio Silva de Almeida; Peter F. Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho (Entropy, 2022)

What makes a reaction network "chemical"? - Stefan Müller 009; Christoph Flamm; Peter F. Stadler (J. Cheminformatics, 2022)

ExceS-A: an exon-centric split aligner. - Franziska Reinhardt; Peter F. Stadler (J. Integr. Bioinform., 2022)

Generic Context-Aware Group Contributions. - Christoph Flamm; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Hierarchical and modularly-minimal vertex colorings. - Dulce I. Valdivia; Maribel Hernández-Rosales; Manuela Geiß; Peter F. Stadler; Marc Hellmuth (Art Discret. Appl. Math., 2022)

Fitch Graph Completion. - Marc Hellmuth; Peter F. Stadler; Sandhya Thekkumpadan Puthiyaveedu (COCOON (2), 2023)

On the Realisability of Chemical Pathways. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ISBRA, 2023)

Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. - Sarah von Löhneysen; Thomas Spicher; Yuliia Varenyk; Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (ISBRA, 2023)

Annotation-Free Identification of Potential Synteny Anchors. - Karl Käther; Steffen Lemke 002; Peter F. Stadler (IWBBIO (1), 2023)

Optimisation via encodings: a renormalisation group perspective. - Konstantin Klemm; Anita Mehta; Peter F. Stadler (CoRR, 2023)

The Theory of Gene Family Histories. - Marc Hellmuth; Peter F. Stadler (CoRR, 2023)

Chemically inspired Erdős-Rényi oriented hypergraphs. - Angel Garcia-Chung; Marisol Bermúdez-Montaña; Peter F. Stadler; Jürgen Jost; Guillermo Restrepo (CoRR, 2023)

Computational History: Challenges and Opportunities of Formal Approaches. - Jürgen Jost; Roberto Lalli; Manfred D. Laubichler; Eckehard Olbrich; Jürgen Renn; Guillermo Restrepo; Peter F. Stadler; Dirk Wintergrün (J. Soc. Comput., 2023)

Best Match Graphs With Binary Trees. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Quasi-best match graphs. - Annachiara Korchmaros; David Schaller 001; Marc Hellmuth; Peter F. Stadler (Discret. Appl. Math., 2023)

Planar median graphs and cubesquare-graphs. - Carsten R. Seemann; Vincent Moulton; Peter F. Stadler; Marc Hellmuth (Discret. Appl. Math., 2023)

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. - Paul Klemm; Peter F. Stadler; Marcus Lechner (Frontiers Bioinform., 2023)

Tailored machine learning models for functional RNA detection in genome-wide screens. - Christopher Klapproth; Siegfried Zöztsche; Felix Kühnl; Jörg Fallmann; Peter F. Stadler; Sven Findeiß (Zenodo, 2023)

Injective Split Systems. - Marc Hellmuth; Katharina T. Huber; Vincent Moulton; Guillaume E. Scholz; Peter F. Stadler (Graphs Comb., 2023)

Local RNA folding revisited. - Maria Waldl; Thomas Spicher; Ronny Lorenz; Irene K. Beckmann; Ivo L. Hofacker; Sarah von Löhneysen; Peter F. Stadler (J. Bioinform. Comput. Biol., 2023)

Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (SIAM J. Discret. Math., 2023)

RNA interaction format: a general data format for RNA interactions. - Richard A. Schäfer; Dominik Rabsch; Guillaume E. Scholz; Peter F. Stadler; Wolfgang R. Hess; Rolf Backofen; Jörg Fallmann; Björn Voß (Bioinform., 2023)

Clustering systems of phylogenetic networks. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (Theory Biosci., 2023)

Relative timing information and orthology in evolutionary scenarios. - David Schaller 001; Tom Hartmann; Manuel Lafond; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2023)

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. - Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (Algorithms Mol. Biol., 2023)

Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. - Lisa Fiedler; Matthias Bernt; Martin Middendorf; Peter F. Stadler (BMC Bioinform., 2023)

Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. - Ameera Vaheeda Shanavas; Manoj Changat; Marc Hellmuth; Peter F. Stadler (CALDAM, 2024)

REvolutionH-tl: Reconstruction of Evolutionary Histories tool. - José Antonio Ramírez-Rafael; Annachiara Korchmaros; Katia Aviña-Padilla; Alitzel López Sánchez; Andrea Arlette España-Tinajero; Marc Hellmuth; Peter F. Stadler; Maribel Hernández-Rosales (RECOMB-CG, 2024)

Squares in Cycles: Prediction of G-Quadruplexes in Circular RNA Secondary Stuctures. - Ronny Lorenz; Peter F. Stadler (BSB, 2024)

Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss. - Bruno J. Schmidt; Tom Hartmann; Peter F. Stadler (Adv. Appl. Math., 2024)

Directed Transit Functions. - Arun Anil; Manoj Changat; Lekshmi Kamal K. Sheela; Ameera Vaheeda Shanavas; John J. Chavara; Prasanth G. Narasimha-Shenoi; Bruno J. Schmidt; Peter F. Stadler (CoRR, 2024)

Nesting of Touching Polygons. - Carsten R. Seemann; Peter F. Stadler; Marc Hellmuth (CoRR, 2024)

Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean Countries. - André C. P. L. F. de Carvalho; Robson Bonidia; Jude Dzevela Kong; Mariana Dauhajre; Cláudio José Struchiner; Guilherme Tegoni Goedert; Peter F. Stadler; Maria Emília M. T. Walter; Danilo Sipoli Sanches; Troy Day; Marcia Castro; John Edmunds; et al. (CoRR, 2024)

Transit functions and pyramid-like binary clustering systems. - Manoj Changat; Ameera Vaheeda Shanavas; Peter F. Stadler (Discret. Appl. Math., 2024)

Limits of experimental evidence in RNA secondary structure prediction. - Sarah von Löhneysen; Mario Mörl; Peter F. Stadler (Frontiers Bioinform., 2024)

Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. - Sarah von Löhneysen; Thomas Spicher; Yuliia Varenyk; Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (J. Comput. Biol., 2024)

TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success. - Gábor Balogh; Natasha Jorge; Célia Dupain; Maud Kamal; Nicolas Servant; Christophe Le Tourneau; Peter F. Stadler; Stephan H. Bernhart (J. Integr. Bioinform., 2024)

Progressive Multiple Alignment of Graphs. - Marcos E. González Laffitte; Peter F. Stadler (Algorithms, 2024)

Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions. - Marcos E. González Laffitte; Klaus Weinbauer; Tieu-Long Phan; Nora Beier; Nico Domschke; Christoph Flamm; Thomas Gatter; Daniel Merkle; Peter F. Stadler (Symmetry, 2024)

Reaction rebalancing: a novel approach to curating reaction databases. - Tieu-Long Phan; Klaus Weinbauer; Thomas Gärtner 001; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Peter F. Stadler (J. Cheminformatics, 2024)

RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. - John Anders; Peter F. Stadler (J. Integr. Bioinform., 2024)

Core Potentials: The Consensus Segmentation Conjecture. - Anahy Santiago Arguello; Guillaume E. Scholz; Peter F. Stadler (Math. Comput. Sci., 2024)

Integrating High-Throughput RNA-RNA Interaction Data Into RNA Secondary Structure Prediction. - Denis Skibinski; Thomas Spicher; Leonhard Sidl; Paulína Holotová; Yingjie Pan; Maximilian Faissner; Cristian A. Velandia-Huerto; Ronny Lorenz; Maria Waldl; Hua-Ting Yao; Peter F. Stadler (ISBRA (2), 2025)

A Sankoff-Rousseau-Like Algorithm for Minimizing Lateral Gene Transfers and Losses on Single Origin Characters. - Alitzel López Sánchez; Guillaume E. Scholz; Peter F. Stadler; Manuel Lafond (RECOMB-CG, 2025)

Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms. - Marcos E. González Laffitte; Tieu-Long Phan; Peter F. Stadler (WABI, 2025)

Transit functions and clustering systems. - Manoj Changat; Ameera Vaheeda Shanavas; Peter F. Stadler (Art Discret. Appl. Math., 2025)

Primitive, edge-short, isometric, and pantochordal cycles. - Gover E. C. Guzman; Marcos E. González Laffitte; André Fujita; Peter F. Stadler (Art Discret. Appl. Math., 2025)

Pathway Realizability in Chemical Networks. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (J. Comput. Biol., 2025)

SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. - Tieu-Long Phan; Klaus Weinbauer; Marcos E. González Laffitte; Yingjie Pan; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Peter F. Stadler (J. Chem. Inf. Model., 2025)

On the Cut-Vertex and the Interval Transit Functions of Hypergraphs. - Ameera Vaheeda Shanavas; Manoj Changat; Peter F. Stadler (Graphs Comb., 2025)

Assembly in Directed Hypergraphs. - Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2025)

Unbiased anchors for reliable genome-wide synteny detection. - Karl Käther; Andreas Remmel; Steffen Lemke 002; Peter F. Stadler (Algorithms Mol. Biol., 2025)

Crossover operators for molecular graphs with an application to virtual drug screening. - Nico Domschke; Bruno J. Schmidt; Thomas Gatter; Richard Golnik; Paul Eisenhuth; Fabian Liessmann; Jens Meiler; Peter F. Stadler (J. Cheminformatics, 2025)