Thomas Gatter

According to our database, Thomas Gatter authored at least 13 papers between 2016 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data.

Nora Beier, Thomas Gatter, Jakob L. Andersen, Peter F. Stadler

Algorithms Mol. Biol., December, 2026

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, December, 2025

TRAMbio: a flexible python package for graph rigidity analysis of macromolecules.

Nicolas Handke, Thomas Gatter, Franziska Reinhardt, Peter F. Stadler

BMC Bioinform., December, 2025

<tt>SynKit</tt> : A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis.

Tieu-Long Phan, Marcos E. González Laffitte, Klaus Weinbauer, Daniel Merkle, Jakob Lykke Andersen, Rolf Fagerberg, Thomas Gatter, Peter F. Stadler

J. Chem. Inf. Model., 2025

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, September, 2024

2021

New Algorithms for Fast and Economic Assembly: Advances in Transcriptome and Genome Assembly

Thomas Gatter

PhD thesis, 2021

Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more.

Thomas Gatter, Peter F. Stadler

Bioinform., 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

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

Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data.

Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, Peter F. Stadler

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

2019

Ryūtō: network-flow based transcriptome reconstruction.

Thomas Gatter, Peter F. Stadler

BMC Bioinform., 2019

2016

Tools and data services registry: a community effort to document bioinformatics resources.

Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Res., 2016

Integrating Pareto Optimization into Dynamic Programming.

Thomas Gatter, Robert Giegerich, Cédric Saule

Algorithms, 2016