Model-Free Functional MRI Analysis Using Topographic Independent Component Analysis. - Anke Meyer-Bäse; Thomas D. Otto; Thomas Martinetz; Dorothee Auer; Axel Wismüller (ESANN, 2003)

Efficient algorithms for finding sills in digital topographic maps. - Thomas D. Otto; Andreas M. Thurnherr (Comput. Geosci., 2007)

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). - Thomas D. Otto; Leonardo H. F. Gomes; Marcelo Alves-Ferreira; Antonio Basílio de Miranda; Wim M. Degrave (BMC Bioinform., 2008)

AnEnPi: identification and annotation of analogous enzymes. - Thomas D. Otto; Ana Carolina R. Guimarães; Wim M. Degrave; Antonio Basílio de Miranda (BMC Bioinform., 2008)

ABACAS: algorithm-based automatic contiguation of assembled sequences. - Samuel A. Assefa; Thomas M. Keane; Thomas D. Otto; Chris Newbold; Matthew Berriman (Bioinform., 2009)

BamView: viewing mapped read alignment data in the context of the reference sequence. - Tim Carver; Ulrike Böhme; Thomas D. Otto; Julian Parkhill; Matthew Berriman (Bioinform., 2010)

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. - Thomas D. Otto; Marcos Catanho; Cristian Tristão; Márcia Bezerra; Renan Mathias Fernandes; Guilherme Steinberger Elias; Alexandre Capeletto Scaglia; Bill Bovermann; Viktors Berstis; Sérgio Lifschitz; Antonio Basílio de Miranda; Wim M. Degrave (Bioinform., 2010)

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. - Thomas D. Otto; Mandy Sanders; Matthew Berriman; Chris Newbold (Bioinform., 2010)

Design and Implementation of ProteinWorldDB. - Sérgio Lifschitz; Carlos Juliano M. Viana; Cristian Tristão; Marcos Catanho; Wim M. Degrave; Antonio Basílio de Miranda; Márcia Bezerra; Thomas D. Otto (BSB, 2012)

BamView: visualizing and interpretation of next-generation sequencing read alignments. - Tim Carver; Simon R. Harris; Thomas D. Otto; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Briefings Bioinform., 2013)

IVA: accurate de novo assembly of RNA virus genomes. - Martin Hunt; Astrid Gall; Swee Hoe Ong; Jacqui Brener; Bridget Ferns; Philip J. R. Goulder; Eleni Nastouli; Jacqueline A. Keane; Paul Kellam; Thomas D. Otto (Bioinform., 2015)

Companion: a web server for annotation and analysis of parasite genomes. - Sascha Steinbiss; Fatima Silva-Franco; Brian P. Brunk; Bernardo Foth; Christiane Hertz-Fowler; Matthew Berriman; Thomas D. Otto (Nucleic Acids Res., 2016)

Varia: a tool for prediction, analysis and visualisation of variable genes. - Gavin Mackenzie; Rasmus W. Jensen; Thomas Lavstsen; Thomas D. Otto (BMC Bioinform., 2022)

Using topic modeling to detect cellular crosstalk in scRNA-seq. - Alexandrina Pancheva; Helen Wheadon; Simon Rogers; Thomas D. Otto (PLoS Comput. Biol., 2022)

peaks2utr: a robust Python tool for the annotation of 3′ UTRs. - William Haese-Hill; Kathryn Crouch; Thomas D. Otto (Bioinform., 2023)

From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA). - José Luis Ruiz; Susanne Reimering; Juan David Escobar-Prieto; Nicolas M. B. Brancucci; Diego F. Echeverry; Abdirahman I Abdi; Matthias Marti; Elena Gómez-Díaz; Thomas D. Otto (Briefings Bioinform., 2023)