Integrating Pareto Optimization into Dynamic Programming. - Thomas Gatter; Robert Giegerich; Cédric Saule (Algorithms, 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; et al. (Nucleic Acids Res., 2016)

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

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)

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

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

New Algorithms for Fast and Economic Assembly: Advances in Transcriptome and Genome Assembly - Thomas Gatter (2021)

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)

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)