A. Altenhoff

Most-cited papers

1. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

   Nai-Hui Zhou, Yuxiang Jiang, T. Bergquist, Alexandra J. Lee +163 more

   2019Genome Biology451 citations Open access

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2. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

   A. Altenhoff, C. Dessimoz

   2009PLoS Comput. Biol.421 citations Open access

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3. The Aquila Digital Community The Aquila Digital Community

   Tal Yuxiang Jiang, Ronnen Oron, W. Clark, Asma R. Bankapur +144 more

   246 citations

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4. Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

   A. Altenhoff, R. Studer, M. Robinson-Rechavi, C. Dessimoz

   2012PLoS Comput. Biol.231 citations Open access

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5. OMA 2011: orthology inference among 1000 complete genomes

   A. Altenhoff, Adrian Schneider, G. Gonnet, C. Dessimoz

   2010Nucleic Acids Res.227 citations Open access

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6. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

   A. Altenhoff, N. Glover, Clément-Marie Train, Klara Kaleb +9 more

   2017Nucleic Acids Res.215 citations Open access

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7. Standardised Benchmarking in the Quest for Orthologs

   A. Altenhoff, B. Boeckmann, S. Capella-Gutiérrez, D. Dalquen +23 more

   2016Nature Methods215 citations Open access

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8. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

   A. Altenhoff, N. Skunca, N. Glover, Clément-Marie Train +8 more

   2014Nucleic Acids Res.215 citations Open access

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9. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

   A. Altenhoff, Clément-Marie Train, K. J. Gilbert, Ishita Mediratta +8 more

   2020Nucleic Acids Res.202 citations Open access

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10. Quality assessment of gene repertoire annotations with OMArk

    Yannis Nevers, Alex Warwick Vesztrocy, Victor Rossier, Clément-Marie Train +3 more

    2024Nature Biotechnology167 citations Open access

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11. OMA standalone: orthology inference among public and custom genomes and transcriptomes

    A. Altenhoff, Jeremy Levy, M. Zarowiecki, Bartlomiej Tomiczek +7 more

    2018bioRxiv158 citations Open access

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12. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Yuxiang Jiang, T. Oron, W. Clark, Asma R. Bankapur +143 more

    2016Genome Biology155 citations Open access

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13. Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

    A. Altenhoff, M. Gil, G. Gonnet, C. Dessimoz

    2013PLoS ONE153 citations Open access

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14. Inferring orthology and paralogy.

    A. Altenhoff, C. Dessimoz

    2012Methods in molecular biology147 citations Open access

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15. Quality of Computationally Inferred Gene Ontology Annotations

    N. Skunca, A. Altenhoff, C. Dessimoz

    2012PLoS Comput. Biol.126 citations Open access

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16. A gridded hourly precipitation dataset for Switzerland using rain‐gauge analysis and radar‐based disaggregation

    M. Wüest, C. Frei, A. Altenhoff, M. Hagen +2 more

    2010111 citations Open access

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17. Linkage of atmospheric blocks and synoptic-scale Rossby waves: a climatological analysis

    A. Altenhoff, O. Martius, M. Croci‐Maspoli, C. Schwierz +1 more

    2008100 citations Open access

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18. Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

    Clément-Marie Train, N. Glover, G. Gonnet, A. Altenhoff +1 more

    2017Bioinform.86 citations Open access

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19. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem

    A. Altenhoff, Alex Warwick Vesztrocy, Charles Bernard, Clément-Marie Train +8 more

    2023Nucleic Acids Research82 citations Open access

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20. Read2Tree: scalable and accurate phylogenetic trees from raw reads

    D. Dylus, A. Altenhoff, Sina Majidian, F. Sedlazeck +1 more

    2022bioRxiv67 citations Open access

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21. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

    D. Dylus, A. Altenhoff, Sina Majidian, F. Sedlazeck +1 more

    2023Nature Biotechnology49 citations Open access

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22. Distinct evolutionary strategies in the GGPPS family from plants

    D. Coman, A. Altenhoff, S. Zoller, W. Gruissem +1 more

    2014Frontiers in Plant Science49 citations Open access

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23. The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

    D. Dalquen, A. Altenhoff, G. Gonnet, C. Dessimoz

    2013PLoS ONE48 citations Open access

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24. The Quest for Orthologs benchmark service and consensus calls in 2020

    A. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, D. Emms +19 more

    2020Nucleic Acids Res.44 citations Open access

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25. Inferring Orthology and Paralogy.

    A. Altenhoff, N. Glover, C. Dessimoz

    2019Methods in molecular biology36 citations Open access

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26. Gearing up to handle the mosaic nature of life in the quest for orthologs

    K. Forslund, Cécile Pereira, S. Capella-Gutiérrez, Alana Sousa da Silva +63 more

    2017Bioinform.36 citations Open access

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27. A stochastic boundary forcing for dissipative particle dynamics

    A. Altenhoff, J. Walther, P. Koumoutsakos

    2007Journal of Computational Physics35 citations Open access

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28. The Quest for Orthologs orthology benchmark service in 2022

    Yannis Nevers, T. Jones, Dushyanth Jyothi, Bethan Yates +35 more

    2022Nucleic Acids Res.33 citations Open access

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29. iHam and pyHam: visualizing and processing hierarchical orthologous groups

    Clément-Marie Train, M. Pignatelli, A. Altenhoff, C. Dessimoz

    2018Bioinform.32 citations Open access

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30. Orthology inference at scale with FastOMA

    Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy +5 more

    2024bioRxiv30 citations Open access

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31. Multifaceted quality assessment of gene repertoire annotation with OMArk

    Yannis Nevers, Victor Rossier, Clément-Marie Train, A. Altenhoff +2 more

    2022bioRxiv20 citations Open access

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32. New developments for the Quest for Orthologs benchmark service

    A. Altenhoff, Yannis Nevers, Vinh Tran, Dushyanth Jyothi +17 more

    2024NAR Genomics and Bioinformatics16 citations Open access

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33. Annotation matters: the effect of structural gene annotation on orthology inference

    Silvia Prieto-Baños, Yannis Nevers, A. Altenhoff, Alex Warwick Vesztrocy +2 more

    2025Bioinform.15 citations Open access

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34. The SIB Swiss Institute of Bioinformatics Semantic Web of data

    Adrian Amos Parit Delphine Frederic Jerven Alan Frédéric Altenhoff Bairoch Bansal Baratin Bastian Bolleman*, A. Altenhoff, A. Bairoch, Parit Bansal +35 more

    2023Nucleic Acids Research15 citations Open access

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35. How to build phylogenetic species trees with OMA

    D. Dylus, Yannis Nevers, A. Altenhoff, Antoine Gürtler +2 more

    2020F1000Research13 citations Open access

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36. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

    H. Stockinger, A. Altenhoff, Konstantin Arnold, A. Bairoch +20 more

    2014Nucleic Acids Res.13 citations Open access

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37. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python

    Klara Kaleb, A. Vesztrocy, A. Altenhoff, C. Dessimoz

    2019F1000Research10 citations Open access

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38. DrosOMA: the Drosophila Orthologous Matrix browser

    Antonin Thiébaut, A. Altenhoff, Giulia Campli, N. Glover +2 more

    2023F1000Research9 citations Open access

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39. Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology

    L. D. Wittwer, Ivana Pilizota, A. Altenhoff, C. Dessimoz

    2014PeerJ9 citations Open access

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40. A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications

    Jerven T. Bolleman, Vincent Emonet, A. Altenhoff, A. Bairoch +13 more

    2024GigaScience7 citations Open access

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41. Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

    B. Boeckmann, D. Dylus, S. Moretti, A. Altenhoff +7 more

    2017bioRxiv7 citations Open access

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42. Assigning confidence scores to homoeologs using fuzzy logic

    N. Glover, A. Altenhoff, C. Dessimoz

    2019PeerJ6 citations Open access

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43. OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data

    Ali Yazdizadeh Kharrazi, A. Altenhoff, Nikolai Romashchenko, Christophe Dessimoz +1 more

    2025Journal of Molecular Evolution4 citations

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44. EdgeHOG: a method for fine-grained ancestral gene order inference at large scale

    Charles Bernard, Yannis Nevers, Naga Bhushana Rao Karampudi, K. J. Gilbert +5 more

    2025Nature Ecology & Evolution4 citations

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45. OMAMO: orthology-based alternative model organism selection

    Alina Nicheperovich, A. Altenhoff, C. Dessimoz, Sina Majidian

    2022Bioinform.2 citations Open access

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46. Parallel and Scalable Precise Clustering for Homologous Protein Discovery

    Stuart Byma, Akash Dhasade, A. Altenhoff, C. Dessimoz +1 more

    2019bioRxiv2 citations Open access

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47. challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Naihui Zhou, Yuxiang Jiang, T. Bergquist, Alex J. Lee +162 more

    2 citations

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48. PhytClust: Efficient and Optimal Monophyletic Partitioning of Rooted Phylogenetic Trees

    Katyayni Ganesan, Elisa Billard, Tom L. Kaufmann, C. B. Strange +4 more

    2026bioRxiv1 citations Open access

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49. On the state of protein function prediction: a report on the fourth CAFA challenge

    R. Ramola, M. C. De Paolis Kaluza, D. Piovesan, Yi-Su Peng +149 more

    2026bioRxiv1 citations Open access

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50. EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

    Charles Bernard, Yannis Nevers, Naga Bhushana Rao Karampudi, K. J. Gilbert +5 more

    2024bioRxiv1 citations Open access

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