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Dr. E. (Evelien) Jongepier

Bioinformatician
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Institute for Biodiversity and Ecosystem Dynamics
Bezoekadres
  • Science Park 904
  • Kamernummer: C4.204
Postadres
  • Postbus 94240
    1090 GE Amsterdam
Contactgegevens
  • Profiel

    As the bioinformatician of the Institute for Biodiversity and Ecosystem Dynamics, I am part of the Research Priority Area Systems Biology of the University of Amsterdam. We are interested in unraveling the ecological and evolutionary dynamics of complex biological systems. By integrating multi-omics and meta-omics data derived from next- and third-generation sequencing technologies, we aim to elucidate the genomic basis of species interactions and the environmental drivers of community dynamics. 

    Research

    Working on a project basis, I guide and support scientists, postdocs and PhD-students from IBED with bioinformatic analyses of their -omics data. Depending on project needs, my contribtion can consist of advise on experimental design and analyses, development and benchmarking of bioinformatics pipelines, analyses and integration of sequencing data, and / or facilitating open science through the publication of data and tools. If your project needs support in e.g. comparative -omics, population -omics or meta -omics? - Please don't hesitate to contact me!

    Education

    To ensure that cutting-edge bioinformatic approaches are also embedded in the IBED curriculum, I develop teaching material for practicals and assignments. In addition, I offer on-demand workshops in bioinformatic methods for students and scientists, such as the analyses of amplicon sequencing data using QIIME2. As a board member of the Amsterdam Science Park Study Group, I contribute to Data and Software Carpentry courses. If you want to propose a topic for a workshop, please don't hesitate to contact me!

    Infrastructure

    To meet the high computational needs of bioinformatics research, IBED has access to several High Performance Computer clusters, including Genseq and Lisa. I maintain the IBED accounts, and help with installing programs and running analyses on the GenSeq cluster. In addition, I provide SystemAdmin support for Linux machines at IBED. To ensure that IBED is ready for increasing demands for FAIR research data storage, I am involved in the iRODS pilot of SURF.

  • Curriculum vitae

    Work experience

    Since 2019           

     

    		 Bioinformatician 
    Institute for Biodiversity and Ecosystem Dynamics,
    University of Amsterdam, The Netherlands.

    2016 - 2019

     

    		 Postdoctoral researcher in comparative insect genomics
    Molecular Evolution and Bioinformatics group at the Institute for Evolution and Biodiversity
    University of Münster, Germany.

    2015 - 2016

     

    		 Postdoctoral researcher & lecturer in ant genomics
    Evolutionary Biology Group at the Institute for Zoology,
    Johannes Gutenberg University Mainz, Germany.


    Education

    2011 - 2015           

    		 PhD in Evolutionary Biology - Johannes Gutenberg University Mainz.
    Awarded Summa Cum Laude

    2007 - 2011

    		 Master of Science in Ecology and Evolution - Rijksuniversiteit Groningen.                                   
    Top programme Evolutionary Ecology

     

  • Publicaties

    2021

    • Ahn, A-C., Jongepier, E., Schuurmans, J. M., Rijpstra, W. I. C., Sinninghe Damsté, J. S., Galinski, E. A., Roman, P., Sorokin, D., & Muyzer, G. (2021). Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes. mSystems, 6(2), [e01202-20]. https://doi.org/10.1128/mSystems.01202-20 [details]
    • Ford, A. K., Visser, P. M., van Herk, M. J., Jongepier, E., & Bonito, V. (2021). First insights into the impacts of benthic cyanobacterial mats on fish herbivory functions on a nearshore coral reef. Scientific Reports, 11, [7147]. https://doi.org/10.1038/s41598-021-84016-z [details]
    • Jongepier, E., Séguret, A., Labutin, A., Feldmeyer, B., Gstöttl, C., Foitzik, S., Heinze, J., & Bornberg-Bauer, E. (2021). Convergent loss of chemoreceptors across independent origins of slave-making in ants. Molecular Biology and evolution. https://doi.org/10.1093/molbev/msab305
    • Scharf, I., Stoldt, M., Libbrecht, R., Höpfner, A. L., Jongepier, E., Kever, M., & Foitzik, S. (2021). Social isolation causes downregulation of immune and stress response genes and behavioural changes in a social insect. Molecular Ecology, 30(10), 2378-2389. https://doi.org/10.1111/mec.15902 [details]
    • Stoldt, M., Klein, L., Beros, S., Butter, F., Jongepier, E., Feldmeyer, B., & Foitzik, S. (2021). Parasite presence induces gene expression changes in an ant host related to immunity and longevity. Genes, 12(1), [95]. https://doi.org/10.3390/genes12010095
    • Xiong, X., Kelkar, Y. D., Geden, C. J., Zhang, C., Wang, Y., Jongepier, E., Martinson, E. O., Verhulst, E. C., Gadau, J., Werren, J. H., & Wang, X. (2021). Long-Read Assembly and Annotation of the Parasitoid Wasp Muscidifurax raptorellus, a Biological Control Agent for Filth Flies. Frontiers in Genetics, 12, [748135]. https://doi.org/10.3389/fgene.2021.748135

    2020

    • Gstöttl, C., Stoldt, M., Jongepier, E., Bornberg-Bauer, E., Feldmeyer, B., Heinze, J., & Foitzik, S. (2020). Comparative analyses of caste, sex, and developmental stage-specific transcriptomes in two Temnothorax ants. Ecology and Evolution, 10(10), 1-11. https://doi.org/10.1002/ece3.6187

    2019

    • Hartke, J., Schell, T., Jongepier, E., Schmidt, H., Sprenger, P. P., Paule, J., Bornberg-Bauer, E., Schmitt, T., Menzel, F., Pfenninger, M., & Feldmeyer, B. (2019). Hybrid Genome Assembly of a Neotropical Mutualistic Ant. Genome Biology and Evolution, 11(8), 2306-2311. https://doi.org/10.1093/gbe/evz159
    • Kaur, R., Stoldt, M., Jongepier, E., Feldmeyer, B., Menzel, F., Bornberg-Bauer, E., & Foitzik, S. (2019). Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite. Philosophical Transactions of the Royal Society B - Biological Sciences, 374(1769). https://doi.org/10.1098/rstb.2018.0192

    2018

    • Bornberg-Bauer, E., Harrison, M. C., & Jongepier, E. (2018). The first cockroach genome and its significance for understanding development and the evolution of insect eusociality. Journal of Experimental Zoology. Part B Molecular and Development Evolution, 330(5), 251-253. https://doi.org/10.1002/jez.b.22826.
    • Grueter, C., Jongepier, E., & Foitzik, S. (2018). Insect societies fight back: the evolution of defensive traits against social parasites. Philosophical Transactions of the Royal Society B - Biological Sciences, 373(1751). https://doi.org/10.1098/rstb.2017.0200
    • Harrison, M. C., Arning, N., Kremer, L. P. M., Ylla, G., Belles, X., Bornberg-Bauer, E., Huylmans, A. K., Jongepier, E., Piulachs, M. D., Richards, S., & Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology. Part B Molecular and Development Evolution, 330(5), 254-264. https://doi.org/10.1002/jez.b.22824
    • Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., Childers, C. P., Dinh, H., Doddapaneni, H., Dugan, S., Gowin, J., Greiner, C., Han, Y., Hu, H., Hughes, D. S. T., Huylmans, A. K., Kemena, C., Kremer, L. P. M., Lee, S. L., ... Bornberg-Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology & Evolution, 2(3), 557-566. https://doi.org/10.1038/s41559-017-0459-1
    • Jongepier, E., Kemena, C., Lopez-Ezquerra, A., Belles, X., Bornberg-Bauer, E., & Korb, J. (2018). Remodeling of the juvenile hormone pathway through caste-biased gene expression and positive selection along a gradient of termite eusociality. Journal of Experimental Zoology. Part B Molecular and Development Evolution, 330(5), 296-304. https://doi.org/10.1002/jez.b.22805

    2016

    • Jongepier, E., & Foitzik, S. (2016). Ant recognition cue diversity is higher in the presence of slavemaker ants. Behavioral Ecology, 27(1), 304-311. https://doi.org/10.1093/beheco/arv153
    • Jongepier, E., & Foitzik, S. (2016). Fitness costs of worker specialization for ant societies. Proceedings of the Royal Society B-Biological Sciences, 283(1822). https://doi.org/10.1098/rspb.2015.2572
    • Negroni, M. A., Jongepier, E., Feldmeyer, B., Kramer, B. H., & Foitzik, S. (2016). Life history evolution in social insects: a female perspective. Current Opinion in Insect Science, 16, 51-57. https://doi.org/10.1016/j.cois.2016.05.008

    2015

    • Beros, S., Jongepier, E., Hagemeier, F., & Foitzik, S. (2015). The parasite's long arm: a tapeworm parasite induces behavioural changes in uninfected group members of its social host. Proceedings of the Royal Society B-Biological Sciences, 282(1819). https://doi.org/10.1098/rspb.2015.1473
    • Jongepier, E., Kleeberg, I., & Foitzik, S. (2015). The ecological success of a social parasite increases with manipulation of collective host behaviour. Journal of Evolutionary Biology, 28(12), 2152-2162. https://doi.org/10.1111/jeb.12738
    • Kleeberg, I., Jongepier, E., Job, S., & Foitzik, S. (2015). Geographic Variation in Social Parasite Pressure Predicts Intraspecific but not Interspecific Aggressive Responses in Hosts of a Slavemaking Ant. Ethology, 121(7), 694-702. https://doi.org/10.1111/eth.12384

    2014

    • Jongepier, E., Kleeberg, I., Job, S., & Foitzik, S. (2014). Collective defence portfolios of ant hosts shift with social parasite pressure. Proceedings of the Royal Society B-Biological Sciences, 281(1791), [20140225]. https://doi.org/10.1098/rspb.2014.0225
    • Kleeberg, I., Pamminger, T., Jongepier, E., Papenhagen, M., & Foitzik, S. (2014). Forewarned is forearmed: aggression and information use determine fitness costs of slave raids. Behavioral Ecology, 25(5), 1058-1063. https://doi.org/10.1093/beheco/aru084
    • Seifert, B., Kleeberg, I., Feldmeyer, B., Pamminger, T., Jongepier, E., & Foitzik, S. (2014). Temnothorax pilagens sp. n. - a new slave-making species of the tribe Formicoxenini from North America (Hymenoptera, Formicidae). ZooKeys, 368, 65-77. https://doi.org/10.3897/zookeys.368.6423

    2012

    • Kureck, I. M., Jongepier, E., Nicolai, B., & Foitzik, S. (2012). No inbreeding depression but increased sexual investment in highly inbred ant colonies. Molecular Ecology, 21(22), 5613-5623. https://doi.org/10.1111/mec.12060
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Nevenwerkzaamheden
    • Hogeschool Leiden Bioinformatica
      Opleidings Advies Commissie
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