Thomas D. Otto

18 papers B 1Journal 16Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Exploring homology detection via k-means clustering of proteins embedded with a large language model.
Bioinform.
Thomas Minotto, Antoine Claessens, Thomas D. Otto
2025 J jnl
TrAGEDy - trajectory alignment of gene expression dynamics.
Bioinform.
Ross F. Laidlaw, Emma M. Briggs, Keith R. Matthews, Amir Madany Mamlouk, Richard McCulloch, Thomas D. Otto
2023 J jnl
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).
Briefings Bioinform.
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
2023 J jnl
peaks2utr: a robust Python tool for the annotation of 3′ UTRs.
Bioinform.
William Haese-Hill, Kathryn Crouch, Thomas D. Otto
2022 J jnl
Using topic modeling to detect cellular crosstalk in scRNA-seq.
PLoS Comput. Biol.
Alexandrina Pancheva, Helen Wheadon, Simon Rogers, Thomas D. Otto
2022 J jnl
Varia: a tool for prediction, analysis and visualisation of variable genes.
BMC Bioinform.
Gavin Mackenzie, Rasmus W. Jensen, Thomas Lavstsen, Thomas D. Otto
2016 J jnl
Companion: a web server for annotation and analysis of parasite genomes.
Nucleic Acids Res.
Sascha Steinbiss, Fatima Silva-Franco, Brian P. Brunk, Bernardo Foth, Christiane Hertz-Fowler, Matthew Berriman, Thomas D. Otto
2015 J jnl
IVA: accurate
Bioinform.
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
2013 J jnl
BamView: visualizing and interpretation of next-generation sequencing read alignments.
Briefings Bioinform.
Tim Carver, Simon R. Harris, Thomas D. Otto, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan
2012 — conf
Design and Implementation of ProteinWorldDB.
BSB
Sérgio Lifschitz, Carlos Juliano M. Viana, Cristian Tristão, Marcos Catanho, Wim M. Degrave, Antonio Basílio de Miranda, Márcia Bezerra, Thomas D. Otto
2010 J jnl
BamView: viewing mapped read alignment data in the context of the reference sequence.
Bioinform.
Tim Carver, Ulrike Böhme, Thomas D. Otto, Julian Parkhill, Matthew Berriman
2010 J jnl
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.
Bioinform.
Thomas D. Otto, Mandy Sanders, Matthew Berriman, Chris Newbold
2010 J jnl
ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.
Bioinform.
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
2009 J jnl
ABACAS: algorithm-based automatic contiguation of assembled sequences.
Bioinform.
Samuel A. Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold, Matthew Berriman
2008 J jnl
AnEnPi: identification and annotation of analogous enzymes.
BMC Bioinform.
Thomas D. Otto, Ana Carolina R. Guimarães, Wim M. Degrave, Antonio Basílio de Miranda
2008 J jnl
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS).
BMC Bioinform.
Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alves-Ferreira, Antonio Basílio de Miranda, Wim M. Degrave
2007 J jnl
Efficient algorithms for finding sills in digital topographic maps.
Comput. Geosci.
Thomas D. Otto, Andreas M. Thurnherr
2003 B conf
Model-Free Functional MRI Analysis Using Topographic Independent Component Analysis.
ESANN
Anke Meyer-Bäse, Thomas D. Otto, Thomas Martinetz, Dorothee Auer, Axel Wismüller