Publications

How to cite Bgee?

If you find Bgee useful please consider citing:

    Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi.
    The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
    in bioRxiv 2020.05.28.119560.[url] RIS


or choose the publication that best covers the Bgee aspects or components you used in your work from the list of publications below.

How to cite specific components of Bgee?

  • For the BgeeDB R package:
    Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian F.
    BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests.
    in F1000Research. 2018, 5:2748. [url] RIS
  • For UBERON:
    Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.
    Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
    in J Biomed Semantics. (2014): 5:21. [url] RIS

Other publications

  • Hayley M. Dingerdissen, Frederic Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi, Amanda Bell, Nikhita Gogate, Samir Gupta, Evan Holmes, Robel Kahsay, Jonathon Keeney, Heather Kincaid, Charles Hadley King, David Liu, Daniel J. Crichton, Raja Mazumder.
    OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.
    in JCO Clinical Cancer Informatics. 4. 210-220. [url]
  • Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor.
    Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality.
    in Genomics, Proteomics & Bioinformatics. 2020 [url]
  • Marc Robinson-Rechavi, Valentine Rech de Laval, Frédéric B. Bastian, Julien Wollbrett, Bgee Team.
    The Expression Comparison Tool in Bgee.
    in Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era. No commercial publisher | Authors open access book, pp.4.3:1--4.3:4, 2020. [url]
  • Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz.
    Enabling semantic queries across federated bioinformatics databases.
    in Database. Volume 2019, 2019, baz106. [url]
  • Tarcisio Mendes de Farias, Heinz Stockinger, Christophe Dessimoz.
    VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links.
    in On the Move to Meaningful Internet Systems: OTM 2019 Conferences. Lecture Notes in Computer Science. vol 11877. [url]
  • SIB Swiss Institute of Bioinformatics Members.
    TThe SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases.
    in Nucleic Acids Research.Volume 44, Issue D1, 4 January 2016, Pages D27–D37. [url]
  • Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi.
    The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
    in Database.Volume 2015, 2015. [url]
  • Marta Rosikiewicz, Marc Robinson-Rechavi.
    IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.
    in Bioinformatics.Volume 30, Issue 10, 15 May 2014, Pages 1392–1399. [url]
  • Anne Niknejad, Aurélie Comte, Gilles Parmentier, Julien Roux, Frederic B. Bastian, Marc Robinson-Rechavi.
    vHOG, a multispecies vertebrate ontology of homologous organs groups.
    in Bioinformatics.Volume 28, Issue 7, 1 April 2012, Pages 1017–1020. [url]
  • Julien Roux, Marc Robinson-Rechavi.
    An ontology to clarify homology-related concepts.
    in Trends Genet..2010;26(3):99-102. [url]
  • Bastian, Frederic, Parmentier, Gilles, Robinson-Rechavi, Marc.
    Generating Homology Relationships by Alignment of Anatomical Ontologies.
    in Nat Prec (2009).[url]
  • Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M.
    Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species.
    in DILS: Data Integration in Life Sciences. Lecture Notes in Computer Science. 5109:124-131. [url] RIS

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