Frédéric B. Bastian

Most-cited papers

1. Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

   Frédéric B. Bastian, G. Parmentier, Julien Roux, S. Moretti +2 more

   2008Data Integration in the Life Sciences190 citations Open access

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2. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

   Frédéric B. Bastian, Julien Roux, A. Niknejad, A. Comte +19 more

   2020bioRxiv178 citations Open access

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3. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

   M. Haendel, J. Balhoff, Frédéric B. Bastian, D. Blackburn +14 more

   2014Journal of Biomedical Semantics160 citations Open access

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4. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

   Frédéric B. Bastian, M. Chibucos, P. Gaudet, M. Giglio +8 more

   2015Database J. Biol. Databases Curation56 citations Open access

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5. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

   Hayley M Dingerdissen, Frédéric B. Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi +11 more

   2020JCO Clinical Cancer Informatics46 citations Open access

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6. Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools

   Frédéric B. Bastian, A. Cammarata, Sara Carsanaro, H. Detering +9 more

   2024Nucleic Acids Research33 citations Open access

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7. BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

   Andrea Komljenovic, Julien Roux, Julien Wollbrett, M. Robinson-Rechavi +1 more

   2016F1000Research33 citations Open access

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8. Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy

   G. Parmentier, Frédéric B. Bastian, M. Robinson-Rechavi

   2010Bioinform.25 citations Open access

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9. vHOG, a multispecies vertebrate ontology of homologous organs groups

   A. Niknejad, A. Comte, G. Parmentier, Julien Roux +2 more

   2012Bioinform.22 citations Open access

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10. 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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11. 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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12. INODE

    S. Amer-Yahia, Georgia Koutrika, Frédéric B. Bastian, Theofilos Belmpas +24 more

    2021SIGMOD record12 citations

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13. Uncovering hidden duplicated content in public transcriptomics data

    Marta Rosikiewicz, A. Comte, A. Niknejad, M. Robinson-Rechavi +1 more

    2013Database J. Biol. Databases Curation12 citations Open access

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14. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

    P. Gaudet, C. Arighi, Frédéric B. Bastian, A. Bateman +24 more

    2012Database J. Biol. Databases Curation11 citations Open access

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15. Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets

    T. M. de Farias, Tatsuya Kushida, A. Sima, C. Dessimoz +3 more

    2023SWAT4HCLS4 citations

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16. Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

    Tarcisio Mendes de Farias, Julien Wollbrett, M. Robinson-Rechavi, Frédéric B. Bastian

    2022GigaScience4 citations Open access

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17. Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

    Tatsuya Kushida, T. M. de Farias, A. Sima, Christophe Dessimoz +3 more

    2023bioRxiv3 citations Open access

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18. Robust data-driven gene expression inference for RNA-seq using curated intergenic regions

    Alessandro Brandulas Cammarata, Sara S. Fonseca Costa, Marta Rosikiewicz, Julien Roux +3 more

    2026bioRxiv2 citations Open access

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19. The Expression Comparison Tool in Bgee

    M. Robinson-Rechavi, Valentine Rech de Laval, Frédéric B. Bastian, Julien Wollbrett +1 more

    20202 citations

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20. gene-ontology: Initial zenodo release

    D. Himmelstein, S. Baranzini, Frédéric B. Bastian, C. Greene +1 more

    20152 citations

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21. STARGEO: expression signatures for disease using crowdsourced GEO annotation

    D. Himmelstein, Frédéric B. Bastian, D. Hadley, C. Greene

    20152 citations Open access

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22. Creation and unification of development and life stage ontologies for animals

    A. Niknejad, C. Mungall, David Osumi-Sutherland, M. Robinson-Rechavi +1 more

    20221 citations

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23. dhimmel/bgee v1.0: Anatomy-specific gene expression in humans from Bgee

    D. Himmelstein, Frédéric B. Bastian, S. Baranzini

    20161 citations

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24. Tissue-specific gene expression resources

    D. Himmelstein, Frédéric B. Bastian

    20151 citations Open access

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25. Compiling Gene Ontology annotations into an easy-to-use format

    D. Himmelstein, C. Greene, V. Malladi, Frédéric B. Bastian

    20151 citations Open access

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26. Bgee: a database for the study of gene expression evolution

    Frédéric B. Bastian, A. Comte, Walid H. Gharib, M. Porta +10 more

    20101 citations

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27. Boosting interoperability: towards an increasingly reusable bioinformatics knowledge base

    T. M. de Farias, Julien Wollbrett, M. Robinson-Rechavi, Frédéric B. Bastian

    2023arXiv.org0 citations Open access

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28. Integration of single-cell with bulk RNA-Seq to provide a unified view of gene expression and analysis tools in Bgee

    Frédéric B. Bastian, Sara S. Fonseca Costa, A. Niknejad, Julien Wollbrett +2 more

    20210 citations Open access

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29. OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery

    Amanda Bell, R. Mazumder, D. Crichton, Vijay K. Shanker +9 more

    2019American Medical Informatics Association Annual Symposium0 citations

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30. Abstract 2463: Prototype open-access biomarker knowledgebase for genetic tests for breast cancer

    D. Baker, Natalie Abrams, Amanda Bell, M. Colbert +13 more

    2019Bioinformatics, Convergence Science, and Systems Biology0 citations

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31. Accessing and manipulating curated and annotated gene expression data in R with BgeeDB

    Andrea Komljenovic, Julien Roux, Julien Wollbrett, Bgee Team +2 more

    20170 citations Open access

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32. Bgee database: creating knowledge from gene expression

    Frédéric B. Bastian, Amina Echchiki, Andrea Komljenovic, S. Moretti +6 more

    20170 citations Open access

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33. Bgee: Database and R Package for Retrieving the Preferred Anatomical Expression Localization of a List of Genes, or of a Single Gene, in Animals.

    Frédéric B. Bastian

    20170 citations

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34. Workshop slides presenting Gene enrichment of anatomical structures using TopAnat

    M. Robinson-Rechavi, Frédéric B. Bastian

    20160 citations Open access

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35. The Bgee database: gene expression data in animals

    Valentine Rech de Laval, Frédéric B. Bastian, Julien Roux, A. Niknejad +4 more

    20160 citations

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36. Processing GTEx for tissue-specific gene expression

    D. Himmelstein, C. Mungall, Frédéric B. Bastian

    20150 citations Open access

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37. Curation effort in the Bgee database

    A. Niknejad, M. Robinson-Rechavi, Frédéric B. Bastian

    20140 citations

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38. Taxon-wide curation of homology relations between anatomical structures

    A. Niknejad, M. Robinson-Rechavi, Frédéric B. Bastian

    20140 citations

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39. Analysis of gene expression patterns in animals

    Frédéric B. Bastian

    20110 citations

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40. Generating Homology Relationships by Alignment of Anatomical Ontologies

    Frédéric B. Bastian, G. Parmentier, M. Robinson-Rechavi

    20090 citations Open access

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41. L'évolution de l'ornement en coquille sous la période rocaille á Strasbourg au XVIII siécle

    Frédéric B. Bastian

    20090 citations

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42. THE GENOTYPE TISSUE EXPRESSION (GTEX) PROJECT COMMUNITY MEETING ENHANCING THE USAGE OF HUMAN GENOMICS FOR THE BENEFIT OF ALL 01

    R. Guigó, K. Ardlie, Helen M. Moore, Abhi Rao +71 more

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