A new method for modeling protein evolution. - Tobias Müller 001; Rainer Spang; Martin Vingron (German Conference on Bioinformatics, 1999)

Modeling Amino Acid Replacement. - Tobias Müller 001; Martin Vingron (J. Comput. Biol., 2000)

Non-symmetric score matrices and the detection of homologous transmembrane proteins. - Tobias Müller 001; Sven Rahmann; Marc Rehmsmeier (ISMB (Supplement of Bioinformatics), 2001)

Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. - Tobias Müller 001; Sven Rahmann; Thomas Dandekar; Matthias Wolf 002 (German Conference on Bioinformatics, 2003)

Gaussian Mixture Density Estimation Applied to Microarray Data. - Christine Steinhoff; Tobias Müller 001; Ulrike A. Nuber; Martin Vingron (IDA, 2003)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. - Torsten Crass; Iris Antes; Rico Basekow; Peer Bork; Christian Buning; Maik Christensen; Holger Claussen 002; Christian Ebeling; Peter Ernst; Valérie Gailus-Durner; Karl-Heinz Glatting; Rolf Gohla; et al. (Bioinform., 2004)

Annotating significant pairs of transcription factor binding sites in regulatory DNA. - Katja Rateitschak; Tobias Müller 001; Martin Vingron (Silico Biol., 2004)

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. - Joachim Friedrich; Thomas Dandekar; Matthias Wolf 002; Tobias Müller 001 (Bioinform., 2005)

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. - Matthias Wolf 002; Joachim Friedrich; Thomas Dandekar; Tobias Müller 001 (Silico Biol., 2005)

Modelling interaction sites in protein domains with interaction profile hidden Markov models. - Torben Friedrich; Birgit Pils; Thomas Dandekar; Jörg Schultz; Tobias Müller 001 (Bioinform., 2006)

4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. - Philipp N. Seibel; Tobias Müller 001; Thomas Dandekar; Jörg Schultz; Matthias Wolf 002 (BMC Bioinform., 2006)

The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. - Jörg Schultz; Tobias Müller 001; Marco Achtziger; Philipp N. Seibel; Thomas Dandekar; Matthias Wolf 002 (Nucleic Acids Res., 2006)

Deep Metazoan Phylogeny. - Daniel Gerlach; Matthias Wolf 002; Thomas Dandekar; Tobias Müller 001; Andreas Pokorny; Sven Rahmann (Silico Biol., 2007)

Identifying functional modules in protein-protein interaction networks: an integrated exact approach. - Marcus T. Dittrich; Gunnar W. Klau; Andreas Rosenwald; Thomas Dandekar; Tobias Müller 001 (ISMB, 2008)

ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. - Matthias Wolf 002; Benjamin Ruderisch; Thomas Dandekar; Jörg Schultz; Tobias Müller 001 (Bioinform., 2008)

Two-point concentration in random geometric graphs. - Tobias Müller 001 (Comb., 2008)

Improper colouring of (random) unit disk graphs. - Ross J. Kang; Tobias Müller 001; Jean-Sébastien Sereni (Discret. Math., 2008)

Lower bounding the boundary of a graph in terms of its maximum or minimum degree. - Tobias Müller 001; Attila Pór; Jean-Sébastien Sereni (Discret. Math., 2008)

The ITS2 Database II: homology modelling RNA structure for molecular systematics. - Christian Selig; Matthias Wolf 002; Tobias Müller 001; Thomas Dandekar; Jörg Schultz (Nucleic Acids Res., 2008)

Acyclic and Frugal Colourings of Graphs. - Ross J. Kang; Tobias Müller 001 (CTW, 2009)

Identifying and Locating-Dominating Codes in (Random) Geometric Networks. - Tobias Müller 001; Jean-Sébastien Sereni (Comb. Probab. Comput., 2009)

Conditioning of Random Conic Systems Under a General Family of Input Distributions. - Raphael Hauser; Tobias Müller 001 (Found. Comput. Math., 2009)

Circular choosability is rational. - Tobias Müller 001; Robert J. Waters (J. Comb. Theory B, 2009)

Circular choosability. - Frédéric Havet; Ross J. Kang; Tobias Müller 001; Jean-Sébastien Sereni (J. Graph Theory, 2009)

Dot Product Representations of Planar Graphs. - Ross J. Kang; Tobias Müller 001 (GD, 2010)

The Number of Bits Needed to Represent a Unit Disk Graph. - Colin McDiarmid; Tobias Müller 001 (WG, 2010)

BioNet: an R-Package for the functional analysis of biological networks. - Daniela Beisser; Gunnar W. Klau; Thomas Dandekar; Tobias Müller 001; Marcus T. Dittrich (Bioinform., 2010)

Acyclic dominating partitions. - Louigi Addario-Berry; Ross J. Kang; Tobias Müller 001 (J. Graph Theory, 2010)

The ITS2 Database III - sequences and structures for phylogeny. - Christian Koetschan; Frank Förster; Alexander Keller 006; Tina Schleicher; Benjamin Ruderisch; Roland Schwarz 002; Tobias Müller 001; Matthias Wolf 002; Jörg Schultz (Nucleic Acids Res., 2010)

On the chromatic number of random geometric graphs. - Colin McDiarmid; Tobias Müller 001 (Comb., 2011)

Dot Product Representations of Planar Graphs. - Ross J. Kang; László Lovász 001; Tobias Müller 001; Edward R. Scheinerman (Electron. J. Comb., 2011)

Graphs with Four Boundary Vertices. - Tobias Müller 001; Attila Pór; Jean-Sébastien Sereni (Electron. J. Comb., 2011)

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer - Christine Staiger; Sidney Cadot; R. Kooter; Marcus T. Dittrich; Tobias Müller 001; Gunnar W. Klau; Lodewyk F. A. Wessels (CoRR, 2011)

Frugal, acyclic and star colourings of graphs. - Ross J. Kang; Tobias Müller 001 (Discret. Appl. Math., 2011)

Counting disk graphs. - Colin McDiarmid; Tobias Müller 001 (Electron. Notes Discret. Math., 2011)

Disjoint Hamilton cycles in the random geometric graph. - Tobias Müller 001; Xavier Pérez-Giménez; Nicholas C. Wormald (J. Graph Theory, 2011)

Robustness and accuracy of functional modules in integrated network analysis. - Daniela Beisser; Stefan Brunkhorst; Thomas Dandekar; Gunnar W. Klau; Marcus T. Dittrich; Tobias Müller 001 (Bioinform., 2012)

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. - Daniela Beisser; Markus A. Grohme; Joachim Kopka; Marcus Frohme; Ralph O. Schill; Steffen Hengherr; Thomas Dandekar; Gunnar W. Klau; Marcus T. Dittrich; Tobias Müller 001 (BMC Syst. Biol., 2012)

Cops and Robbers on Geometric Graphs. - Andrew Beveridge; Andrzej Dudek; Alan M. Frieze; Tobias Müller 001 (Comb. Probab. Comput., 2012)

Sphere and Dot Product Representations of Graphs. - Ross J. Kang; Tobias Müller 001 (Discret. Comput. Geom., 2012)

Induced Matchings in Subcubic Planar Graphs. - Ross J. Kang; Matthias Mnich; Tobias Müller 001 (SIAM J. Discret. Math., 2012)

A counterexample to a conjecture of Grünbaum on piercing convex sets in the plane. - Tobias Müller 001 (Discret. Math., 2013)

Integer realizations of disk and segment graphs. - Colin McDiarmid; Tobias Müller 001 (J. Comb. Theory B, 2013)

Integer Representations of Convex Polygon Intersection Graphs. - Tobias Müller 001; Erik Jan van Leeuwen; Jan van Leeuwen (SIAM J. Discret. Math., 2013)

Arrangements of Pseudocircles and Circles. - Ross J. Kang; Tobias Müller 001 (Discret. Comput. Geom., 2014)

The number of disk graphs. - Colin McDiarmid; Tobias Müller 001 (Eur. J. Comb., 2014)

Maker-breaker games on random geometric graphs. - Andrew Beveridge; Andrzej Dudek; Alan M. Frieze; Tobias Müller 001; Milos Stojakovic (Random Struct. Algorithms, 2014)

A threshold for the Maker-Breaker clique game. - Tobias Müller 001; Milos Stojakovic (Random Struct. Algorithms, 2014)

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. - Mohammed El-Kebir; Hayssam Soueidan; Thomas Hume; Daniela Beisser; Marcus T. Dittrich; Tobias Müller 001; Guillaume Blin; Jaap Heringa; Macha Nikolski; Lodewyk F. A. Wessels; Gunnar W. Klau (Bioinform., 2015)

Chasing robbers on percolated random geometric graphs. - Anshui Li; Tobias Müller 001; Pawel Pralat (Contributions Discret. Math., 2015)

On the Largest Component of a Hyperbolic Model of Complex Networks. - Michel Bode; Nikolaos Fountoulakis; Tobias Müller 001 (Electron. J. Comb., 2015)

On r-dynamic coloring of grids. - Ross J. Kang; Tobias Müller 001; Douglas B. West (Discret. Appl. Math., 2015)

The acquaintance time of (percolated) random geometric graphs. - Tobias Müller 001; Pawel Pralat (Eur. J. Comb., 2015)

The probability of connectivity in a hyperbolic model of complex networks. - Michel Bode; Nikolaos Fountoulakis; Tobias Müller 001 (Random Struct. Algorithms, 2016)

The critical probability for confetti percolation equals 1/2. - Tobias Müller 001 (Random Struct. Algorithms, 2017)

Theoretical analysis of beaconless geocast protocols in 1D. - Joachim Gudmundsson; Irina Kostitsyna; Maarten Löffler; Tobias Müller 001; Vera Sacristán; Rodrigo I. Silveira (ANALCO, 2018)

The first order convergence law fails for random perfect graphs. - Tobias Müller 001; Marc Noy (Electron. Notes Discret. Math., 2018)

Logical limit laws for minor-closed classes of graphs. - Peter Heinig; Tobias Müller 001; Marc Noy; Anusch Taraz (J. Comb. Theory B, 2018)

The critical probability for Voronoi percolation in the hyperbolic plane tends to 1/2. - Benjamin T. Hansen; Tobias Müller 001 (Random Struct. Algorithms, 2022)

Limiting probabilities of first order properties of random sparse graphs and hypergraphs. - Lázaro Alberto Larrauri; Tobias Müller 001; Marc Noy (Random Struct. Algorithms, 2022)

Component Games on Random Graphs. - Rani Hod; Michael Krivelevich; Tobias Müller 001; Alon Naor; Nicholas C. Wormald (Comb., 2022)