Index

Anamaria Elek

Contact

Carrer del Bruc 107, 08009 Barcelona, Spain

+34 671 743 750

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Experience

2024 - present Bioinformatician Centre for Genomic Regulation (Barcelona, ES)

  • Bioinformatician for the Biodiversity Cell Atlas project.
  • Setting up computational pipelines for analysis and integration of single cell RNA-seq data from different species and technologies.

2019 - 2024 PhD Student Centre for Genomic Regulation (Barcelona, ES)

  • PhD student in Comparative regulatory genomics group (Sebé-Pedrós lab)
  • Modeling cell type evolution using single-cell and chromatin profiling approaches

2019 Bioinformatician The Institute of Cancer Research (London, UK)

  • Bioinformatician in Genomics Facility
  • Development and maintenance of computational pipelines for the analysis of next-generation sequencing data.

Education

2019 - present PhD in Biomedicine Universitat Pompeu Fabra (Barcelona, ES)

  • Project: Modeling cell type evolution using single-cell and chromatin profiling approaches

2016 - 2018 Master’s degree in molecular biology University of Zagreb (Zagreb, HR)

  • Thesis: coRdon: an R package for codon usage analysis and prediction of gene expressivity

2013 - 2016 Bachelor’s degree in molecular biology University of Zagreb (Zagreb, HR)

  • Thesis: Structure and dynamics of the spliceosome

Publications

Levy, S., Elek, A., Grau-Bové, X., Menéndez-Bravo, S., Iglesias, M., Tanay, A., Mass, T., & Sebé-Pedrós, A. (2021). A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell, 184(11), 2973–2987.e18. https://doi.org/10.1016/j.cell.2021.04.005

Najle, S. R., Grau-Bové, X., Elek, A., Navarrete, C., Cianferoni, D., Chiva, C., Cañas-Armenteros, D., Mallabiabarrena, A., Kamm, K., Sabidó, E., Gruber-Vodicka, H., Schierwater, B., Serrano, L., & Sebé-Pedrós, A. (2023). Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell, 186(21):4676-4693.e29. https://doi.org/10.1016/j.cell.2023.08.027

Li, Y., Slavik, K. M., Toyoda, H. C., Morehouse, B. R., de Oliveira Mann, C. C., Elek, A., Levy, S., Wang, Z., Mears, K. S., Liu, J., Kashin, D., Guo, X., Mass, T., Sebé-Pedrós, A., Schwede, F., & Kranzusch, P. J. (2023). cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell, 20;186(15):3261-3276.e20. https://doi.org/10.1016/j.cell.2023.05.038

Miguel-Escalada, I., Maestro, M. A., Balboa, D., Elek, A., Bernal, A., Bernardo, E., Grau, V., Garcia-Hurtado, J., Sebé-Pedrós, A., & Ferrer, J. (2022). Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster. Developmental Cell, 57(16), 1922–1936.e9. https://doi.org/10.1016/j.devcel.2022.07.014

Garcı́a-Castro, H., Kenny, N. J., Iglesias, M., Álvarez-Campos, P., Mason, V., Elek, A.., Schönauer, A., Sleight, V. A., Neiro, J., Aboobaker, A., Permanyer, J., Irimia, M., Sebé-Pedrós, A., & Solana, J. (2021). ACME dissociation: A versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02302-5

Elek, A., Kuzman, M., & Vlahovicek, K. (2018). CoRdon: Codon usage analysis and prediction of gene expressivity. R Package. https://doi.org/10.18129/B9.BIOC.CORDON

Roje, B., Elek, A., Palada, V., Bom, J., Iljazović, A., Šimić, A., Sušak, L., Vilović, K., Strowig, T., Vlahoviček, K., & Terzić, J. (2020). Microbiota alters urinary bladder weight and gene expression. Microorganisms, 8(3), 421. https://doi.org/10.3390/microorganisms8030421

Skills

R programming | Python | Linux/BASH | HPC computing | Git versioning | Docker

Awards

2021 Best poster award EMBO | EMBL Symposium: The Identity and Evolution of Cell Types (virtual)

Volunteering

2020 - 2022 NGSchool bioinformatics summer school (educational)

  • I worked on scientific program and participants selection for the summer school.
  • I taught two webinars (on R programming and single cell RNA-seq) and mentored of a hackathon team of 10 people (RNA-seq analysis project).
  • I also led the project of developing NGSchool website (https://ngschool.eu/).

2021 Introduction to Machine Learning CRG Internal Training Course (educational)

  • I held a lecture and a workshop on feature selection and dimensionality reduction.

Training

2018 NGSchool: Nanopore sequencing & personalised medicine bioinformatics summer school (Lublin, PL)

2017 VBC Summer School molecular biology summer school (Vienna, AT)