Publications by authors named "Adrian Altenhoff"

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EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.
Charles Bernard, Yannis Nevers, Naga Bhushana Rao Karampudi, Kimberly J Gilbert, Clément Train, Adrian Altenhoff

Nat Ecol Evol· October 2025

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OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.
Ali Yazdizadeh Kharrazi, Adrian M Altenhoff, Nikolai Romashchenko, Christophe Dessimoz, Sina Majidian

J Mol Evol· September 2025

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Annotation matters: the effect of structural gene annotation on orthology inference.
Silvia Prieto-Baños, Yannis Nevers, Adrian Altenhoff, Alex Warwick Vesztrocy, Christophe Dessimoz

Bioinformatics· July 2025

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Orthology inference at scale with FastOMA.
Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, Adrian M Altenhoff

Nat Methods· February 2025

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Quality assessment of gene repertoire annotations with OMArk.
Yannis Nevers, Alex Warwick Vesztrocy, Victor Rossier, Clément-Marie Train, Adrian Altenhoff

Nat Biotechnol· January 2025

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A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.
Jerven Bolleman, Vincent Emonet, Adrian Altenhoff, Amos Bairoch, Marie-Claude Blatter

Gigascience· January 2025

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New developments for the Quest for Orthologs benchmark service.
Adrian Altenhoff, Yannis Nevers, Vinh Tran, Dushyanth Jyothi, Maria Martin

NAR Genom Bioinform· December 2024

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DrosOMA: the Orthologous Matrix browser.
Antonin Thiébaut, Adrian M Altenhoff, Giulia Campli, Natasha Glover, Christophe Dessimoz

F1000Res· March 2024

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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J Sedlazeck, Christophe Dessimoz

Nat Biotechnol· January 2024

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OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Adrian M Altenhoff, Alex Warwick Vesztrocy, Charles Bernard, Clement-Marie Train, Alina Nicheperovich

Nucleic Acids Res· January 2024

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Read2Tree: scalable and accurate phylogenetic trees from raw reads.
David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J Sedlazeck, Christophe Dessimoz

bioRxiv· December 2022

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The Quest for Orthologs orthology benchmark service in 2022.
Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Adrian Altenhoff

Nucleic Acids Res· July 2022

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OMAMO: orthology-based alternative model organism selection.
Alina Nicheperovich, Adrian M Altenhoff, Christophe Dessimoz, Sina Majidian

Bioinformatics· May 2022

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OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Adrian M Altenhoff, Clément-Marie Train, Kimberly J Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias

Nucleic Acids Res· January 2021

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The Quest for Orthologs benchmark service and consensus calls in 2020.
Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover

Nucleic Acids Res· July 2020

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Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the packages for R and Python.
Klara Kaleb, Alex Warwick Vesztrocy, Adrian Altenhoff, Christophe Dessimoz

F1000Res· June 2020

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How to build phylogenetic species trees with OMA.
David Dylus, Yannis Nevers, Adrian M Altenhoff, Antoine Gürtler, Christophe Dessimoz

F1000Res· June 2020

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Inferring Orthology and Paralogy.
Adrian M Altenhoff, Natasha M Glover, Christophe Dessimoz

Methods Mol Biol· January 2020

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, Adrian Altenhoff

Genome Biol· November 2019

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iHam and pyHam: visualizing and processing hierarchical orthologous groups.
Clément-Marie Train, Miguel Pignatelli, Adrian Altenhoff, Christophe Dessimoz

Bioinformatics· July 2019

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OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Adrian M Altenhoff, Jeremy Levy, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy

Genome Res· July 2019

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Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.
Ivana Piližota, Clément-Marie Train, Adrian Altenhoff, Henning Redestig, Christophe Dessimoz

Bioinformatics· April 2019

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Assigning confidence scores to homoeologs using fuzzy logic.
Natasha M Glover, Adrian Altenhoff, Christophe Dessimoz

PeerJ· January 2019

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Gearing up to handle the mosaic nature of life in the quest for orthologs.
Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff

Bioinformatics· January 2018

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The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Adrian M Altenhoff, Natasha M Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy

Nucleic Acids Res· January 2018

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