Jon Bråte

Jon Bråte

Biologist

CV Jon Bråte

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Senior Researcher at the Norwegian Institute of Public Health (NIPH)

Date of birth: 12.03.1983
Nationality: Norwegian
NIPH profile: https://www.fhi.no/en/about/departments-and-centres/virology/jon-brate/
GitHub: https://github.com/jonbra
ORCID: https://orcid.org/0000-0003-0490-1175

Current and previous positions

Period Position Institution
2024 – present Senior Researcher Norwegian Institute of Public Health, Norway
2022 – 2025 Associate Professor University of Oslo, Norway
2020 – 2024 Researcher Norwegian Institute of Public Health, Norway
2020 – 2021 Senior Lecturer Department of Biosciences, University of Oslo, Norway
2015 – 2019 Researcher Department of Biosciences, University of Oslo, Norway
2012 – 2015 Post Doc Department of Biosciences, University of Oslo, Norway

Education

Period Degree Institution
2008 – 2012 PhD Department of Biology, University of Oslo, Norway
2006 – 2008 Master of Science Department of Molecular Biosciences, University of Oslo, Norway
2003 – 2006 Bachelor of Science Department of Molecular Biosciences, University of Oslo, Norway

Additional education

  • PRINCE2 7 Foundation Project Management course (2024)
  • Project Management for Post Docs by Institute for Co-creative Leadership, Ltd. (2013)
  • Development Program in Leadership by Institute for Co-creative Leadership, Ltd. (2012)
  • Courses in communication, teamwork and leadership by Scandinavian Training Design (2008 – 2009)

Visiting researcher & collaborations

  • Visiting researcher at the lab of Iñaki Ruiz-Trillo, Institute de Biologia Evolutiva, Barcelona, Spain (2014)
  • Visiting researcher at the lab of Maja Adamska, Sars Centre, Bergen, Norway (2012)
  • Exchanging PhD at the lab of Mikhail Matz, University of Texas at Austin, USA (2010)

Grants and projects

Year Grant
2025 Frances and Augustus Newman Foundation: Analysis of viral agents in childhood leukemia (£14,000). My role is to help design lab and bioinformatics protocols, as well as identification of viral agents in sequence data.
2025 European Commission: European Reference Laboratory (EURL) for food and waterborne viruses, 2026–2032 (€3.25 million). My role is to implement tools for virus surveillance based on whole genome sequence data.
2023 Research Council of Norway (RCN): SICKSOIL: Linking Microbes, Organic Matter and Sick Soil Syndrome (€266,000). My role is to investigate the diversity of viruses in various soil environments.
2022 ErC EU4Health: Development of NGS and bioinformatics tools for increased preparedness against infectious diseases (€1 million).
2021 ErC HERA Incubator: Method development and improved preparedness for future Covid-19 variants (€1.8 million).
2019 RCN: Financial support for ERC Consolidator Grant application (€51,000).
2019 Invited to interview for ErC Starting Grant (June 2019).
2018 UNIFOR: Small grant for purchasing scientific equipment (€2,900).
2017 RCN: Mobility grant for PhD-students. Funding for my PhD student to stay at the lab of Iñaki Ruiz-Trillo at the Institut de Biologia Evolutiva, Barcelona, Spain (€5,800).
2017 Norwegian Academy of Science and Letters: Centre for Advanced Study (2019–2020). Part of an international consortium of evolutionary biologists granted a two-year project on the concept of Evolvability.
2014 RCN: Young Research Talent grant (2015–2018). Three-year personal grant including salary for a PhD-student (total €786,000), for studying the role of non-coding RNAs in the evolution of animals (project nr. 240284).
2014 RCN: Mobility grant for post docs. Funding for a research stay in the lab of Iñaki Ruiz-Trillo at the Institut de Biologia Evolutiva, Barcelona, Spain (€9,500).
2011 RCN: Personal Post Doc grant (2012–2015). Three-year personal grant (total €408,000) for studying the role of non-coding RNAs in the evolution of multicellularity (project nr. 213707).
2009 Molecular Life Science, UiO: Mobility grant for PhD-students. Visiting the lab of Mikhail Matz at the University of Texas at Austin (€2,800).

Commissions of trust

  • CAS Fellow: Fellow at the Centre for Advanced Study (CAS) at the Norwegian Academy of Science and Letters (2019–2020).
  • Marie Curie evaluator: European Commission’s Marie Sklodowska-Curie Individual Fellowships (2016–2018).
  • National Science Centre of Poland, grant reviewer: Reviewed a research proposal for the SONATA BIS-13 call (2023).
  • Peder Sather Center reviewer: Reviewer for the UC Berkeley Peder Sather Center grants (2019).
  • Board member, Department of Biology, University of Oslo, Norway (2012).
  • Peer reviewer for Molecular Biology and Evolution, Scientific Reports, Proceedings of the Royal Society: Biological Sciences, BMC Plant Biology, Algal Research, European Journal of Protistology, Aquatic Microbial Ecology, Genes, IJMS and Applied and Environmental Microbiology.
  • PhD evaluation committee (2017): External referee evaluating a PhD thesis for public defense. Institut de Ciències del Mar, ICM-CSIC, Spain.
  • Hiring committees: Served on several hiring committees for PhD and Post Doc fellowships at UiO and UiB.

Supervision of graduate students

Main supervisor: Marlene Elise Sivertsen (master, 2026 - present), Therese Lothe (master, 2026 – present), Eugenia Giovanna Grande (master, 2023 – 2025), Ina J. Andresen (PhD, 2015 – 2021), Arthur A. H. Blørstad (PhD, 2016 – 2019†), Hengyi Zhu (master, 2018 – 2019), Alexander H. Løvestad (master, 2015 – 2017), Shruti Mehrotra (master, 2015 – 2018).

Co-supervisor: Tengel Hvidsten Tjersland (2022 – 2025), Peter Arnesen (master, 2019 – present*), Renate M. Alling (master, 2017 – 2019), Øyvind S. Gulbrandsen (master, 2016 – 2018), Eirik Høye (master, 2015 – 2016), Line L. Røsæg (master, 2014 – 2016), Andreas Evenstad (master, 2014 – 2017), Ina J. Andresen (master, 2014 – 2015), Anders K. Krabberød (master, 2008 – 2010), Dan K. Ree (master, 2008 – 2010).

†Deceased. *Not finished.

Teaching

  • Bioinformatics for Molecular Biology (MBV-INF4410/9410): Organized and lead the course; lectures and computer labs in genomics/transcriptomics data analysis, Unix/command line, Python and R programming.
  • Bioinformatics (BIOS3010): Teaching Unix, molecular phylogenetics and NGS analysis.
  • Genetics and Developmental Biology (BIOS3601): Echinoderm development, animal organogenesis and Evo-Devo.
  • Special curriculum on the Evolution of Multicellularity (2016): Organized a special curriculum for four students (one master and three PhD). Formed curriculum and participated in oral examinations and grading.
  • Molecular Biology and Biological Methods (BIO2140): Organized the course in 2015; teaching wet labs and computer labs in environmental sequencing and transcriptomics. 2009–2011: supervised colloquia and wet labs in molecular biology.
  • Elementary Biology (BIO1000): 2008–2010: supervised lab work in genetics and phylogeny.
  • Classification and Phylogeny (BIO4210): 2008: supervised lab work in molecular phylogenetic methods.

Bioinformatics experience

  • Genomic epidemiology: Phylogenetic and phylogeographic analyses of virus genome data using Nextstrain, NextClade, TreeTime and BEAST.
  • Genomics: Genome assemblers for short- and long-read data (Spades, Canu, Flye). Quality assessment (coverage, k-mer analysis, Kraken2, MetaBAT, BUSCO).
  • Transcriptomics: Quality control (MultiQC, Trimmomatic), de novo assembly (Trinity), reference assembly (HISAT2, PASA), small RNA mapping (Bowtie1, MirDeep2), gene quantification (RSEM, HTSeq, Cufflinks).
  • Comparative transcriptomics: Differential gene expression (DESeq2, edgeR), GO-enrichment, orthology comparisons, co-expression analysis (WGCNA, Clust).
  • Molecular phylogeny: Multiple sequence alignment (Muscle, Mafft), model selection (ModelTest), phylogenetic analysis (RAxML, Phylobayes, MrBayes).
  • Gene identification and annotation: Homology searches (Blast), gene prediction (Augustus), annotation (Transdecoder, InterProScan), ortholog/paralog detection.
  • Protein structure analysis: Evolutionary comparisons using ConSurf and Phyre2; visualization in PyMOL.
  • Programming: Extensive experience with Unix/command line, Python, Perl and R.
  • Workflow managers: Nextflow pipelines for genome assembly and virus analysis, deployable locally or on HPC.
  • High-performance computing (HPC): Deploying pipelines and running large batch jobs on SLURM systems such as Abel/Saga at UiO; experience managing large NGS datasets.
  • Workflow development and version control: Experience with Git, GitHub, and collaborative workflow development.

Publications

Peer-reviewed research papers

Bråte, J., Instefjord, K. H., Alfsnes, K. and Stene-Johansen, K. 2026. HCVTyper: A Nextflow pipeline for hepatitis C virus genome assembly, genotyping and antiviral resistance detection. Access Microbiology. doi: 10.1099/acmi.0.001193.v1. Under review

Bråte, J., Grande, E. G., Pedersen, B. N., Frengen, T. G. and Stene-Johansen, K. 2026. Evaluation of a multiplexed tiling PCR scheme for whole-genome amplification of hepatitis B virus using Oxford Nanopore sequencing. bioRxiv. doi: 10.64898/2026.03.28.714721.

Zhu, H. and Bråte, J. 2025. Identification and Functional Characterization of microRNAs in Ichthyosporea. F1000Research. https://doi.org/10.12688/f1000research.162501.1. Awaiting peer review

Garcia, I., Bråte, J., Fossum, E., Rohringer, A., Moen, L. V., Hungnes, O., Fjære, O., Zaragkoulias, K. and Bragstad, K. 2024. Recombinant SARS-CoV-2 Delta/Omicron BA.5 emerging in an immunocompromised long-term infected COVID-19 patient. Scientific Reports. https://doi.org/10.1038/s41598-024-75241-3.

Ondracka, A., Dudin, O. and Bråte, J. 2023. Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica. F1000Research. doi: 10.12688/f1000research.133935.1.

Moen, L. V., Vollan, H. S., Bråte, J., Hungnes, O. and Bragstad, K. 2022. Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63. Viruses. doi: 10.3390/v14122734.

Osnes, N. M., Alfsnes, K., Bråte, J., Llorente, G. I., Riis, K. R., Instefjord, H. K., Elshaug, H., Vollan, S. H., Moen, L. V., Pedersen, N. B., Caugant, A. D., Stene-Johansen, K., Hungnes, O., Bragstad, K., Brynildsrud, O., Eldholm, V. 2021. The Impact of Global Lineage Dynamics, Border Restrictions and Emergence of the B.1.1.7 Lineage on the SARS-CoV-2 Epidemic in Norway. Virus Evolution. doi: 10.1093/ve/veab086.

Andresen, I. J., Orr, R. J. S., Shalchian-Tabrizi, K. and Bråte, J. 2021. Compartmentalization of mRNAs in the giant, unicellular green alga Acetabularia acetabulum. Scientific Reports. doi: 10.1016/j.algal.2021.102440.

Andresen, I. J., Orr, R. J. S., Krabberød, A. K., Shalchian-Tabrizi, K. and Bråte, J. 2021. Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum. Scientific Reports. doi: 10.1038/s41598-021-92092-4.

Gulbrandsen, Ø. S., Andresen, I. J., Krabberød, A. K., Bråte, J.* and Shalchian-Tabrizi, K. 2021. Phylogenomic analysis restructures the Ulvophyceae. Journal of Phycology. doi: 10.1111/jpy.13168. *Joint senior author.

Dudin, O., Ondracka, A., Grau-Bové, X., Haraldsen, A. A. B., Toyoda, A., Suga, H., Bråte, J.* and Ruiz-Trillo, I. 2019. A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife. doi: 10.7554/eLife.49801. *Senior author, ncRNA work.

Bråte, J., Fuss, J., Jakobsen, K. S. and Klaveness, D. 2019. A draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Research. doi: 10.12688/f1000research.16734.1.

Bråte, J., Neumann, R. S., Fromm, B., Haraldsen, A. A. B., Tarver, J. E., Suga, H., Donoghue, P. C. J., Peterson, K. J., Ruiz-Trillo, I., Grini, P. and Shalchian-Tabrizi, K. 2018. Unicellular origin of the animal microRNA pathway. Current Biology. 28:1–8. doi: 10.1016/j.cub.2018.08.018.

Krabberød, A. K., Orr, R. J. S., Bråte, J., Kristensen, T., Bjørklund, K. R. and Shalchian-Tabrizi, K. 2017. Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria. Molecular Biology and Evolution. doi: 10.1093/molbev/msx075.

Bråte, J., Adamski, M., Neumann, S. R., Shalchian-Tabrizi, K. and Adamska, M. 2015. Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proc. Royal. Soc. B. doi: 10.1098/rspb.2015.1746.

Leininger, S., Adamski, M., Bergum, B., Guder, C., Liu, J., Laplante, M., Bråte, J., Hoffmann, F., Fortunato, S., Jordal, S., Rapp, H. T. and Adamska, M. 2014. Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nature Communications. 5:3905. doi: 10.1038/ncomms4905.

Bråte, J., Krabberød, A. K., Dolven, J. K., Ose, R. F., Kristensen, T., Bjørklund, K. R. and Shalchian-Tabrizi, K. 2012. Radiolaria associated with large diversity of marine alveolates. Protist. 163(5): 767–777.

Zhao, S., Burki, F., Bråte, J., Keeling, P., Klaveness, D. and Shalchian-Tabrizi, K. 2012. Collodictyon – an ancient lineage in the tree of eukaryotes. Mol Biol Evol. doi: 10.1093/molbev/mss001.

Krabberød, A. K., Bråte, J., Dolven, J. K., Ose, R. F., Klaveness, D., Kristensen, T., Bjørklund, K. and Shalchian-Tabrizi, K. 2011. Radiolaria divided into Polycystina and Spasmaria in combined 18S and 28S rDNA phylogeny. PLoS ONE. 6(8): e23526. doi: 10.1371/journal.pone.0023526.

Klaveness, D., Bråte, J., Patil, V., Shalchian-Tabrizi, K., Kluge, R., Gislerød, H. R. and Jakobsen, K. S. 2011. The 18S and 28S rDNA Identity and Phylogeny of the common lotic Chrysophyte, Hydrurus foetidus. Eur J Phycol. 46(3): 282–291.

Shalchian-Tabrizi, K., Røberg, K. R., Ree, D. K., Klaveness, D. and Bråte, J. 2011. Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences. J Euk Microbiol. 58. doi: 10.1111/j.1550-7408.2011.00547.x.

Bråte, J., Klaveness, D., Rygh, T., Jakobsen, K. S. and Shalchian-Tabrizi, K. 2010. Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiology. 10:168. doi: 10.1186/1471-2180-10-168.

Bråte, J., Logares, R., Berney, C., Ree, D. K., Klaveness, D., Jakobsen, K. S. and Shalchian-Tabrizi, K. 2010. Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME Journal. doi: 10.1038/ismej.2010.39.

Logares, R., Bråte, J., Heinrich, F., Shalchian-Tabrizi, K. and Bertilsson, S. 2010. Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11). Mol Biol Evol. 27(2): 347–357.

Burki, F., Inagaki, Y., Bråte, J., Archibald, J. M., Keeling, P. J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak, A., Kumar, S., Klaveness, D., Jakobsen, K. S., Pawlowski, J. and Shalchian-Tabrizi, K. 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol. 1: 231–238.

Logares, R., Bråte, J., Bertilsson, S., Clasen, J. L., Shalchian-Tabrizi, K. and Rengefors, K. 2009. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 17(9): 414–422.

Shalchian-Tabrizi, K., Bråte, J., Logares, R., Klaveness, D., Berney, C. and Jakobsen, K. S. 2008. Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Env. Microbiol. 10(10): 2635–2644.

Patil, V., Bråte, J., Shalchian-Tabrizi, K. and Jakobsen, K. S. 2008. Revisiting the phylogenetic position of Synchroma grande. J Euk Microbiol. 56(4): 394–396.

Conferences and meetings

  • Bråte, J. Genomic surveillance of HCV in Norway. Norwegian Consortium of Microbial Genomics. Invited talk. 2024-12-05.
  • Bråte, J. Genome sequencing and surveillance of viruses at FHI (NIPH). Norwegian Bioinformatics Days. 2024-05-28.
  • Bråte, J. SARS-CoV-2 sequencing at the Norwegian Institute of Public Health. Nordic Elixir meeting 2022 on Handling Pandemic Omics Data in the Nordics.
  • Bråte, J. Import og evolusjon av SARS-CoV-2 i Norge. SARS-CoV-2 NGS Workshop at NIPH, Oslo Norway. 2022.
  • Bråte, J. Dyrenes opprinnelse. Bio-konferansen 2019. Invited talk. Norsk Biologforening. Oslo, Norway.
  • Bråte, J. Evolution and development in single-celled eukaryotes. Seminar at the Evolvability Project at the Centre for Advanced Study. 2019. Norwegian Academy of Science and Letters, Oslo, Norway.
  • Bråte, J. Evolution and function of the ichthyosporean miRNA system. 7th Choanoflagellates & Friends Meeting. 2019. Institute of Evolutionary Biology, Barcelona, Spain.
  • Bråte, J. Studying protist evolution using single-cell transcriptomics. Annual CIME/NFM meeting. 2017.
  • Haraldsen, A. A. B., Bråte, J. et al. Pre-metazoan origin of animal microRNAs. EuroEvoDevo 2016. European Society of Evolutionary Developmental Biology, Uppsala, Sweden.
  • Bråte, J. Long non-coding RNAs in the sponge Sycon ciliatum. Origin of multicellularity. Institut de Biologia Evolutiva (UPF-CSIC). Barcelona. 2013.
  • Bråte, J. Regulatorisk RNA – Evolusjon, utvikling og epigenetikk. Konferanse i bioteknologi og etikk for lærere. 2013. Skolelabben, UiO.
  • Bråte, J. 18S+28S phylogeny divides Radiolaria into Polycystina and Spasmaria and supports the Retaria hypothesis. VI European Congress of Protistology. 2011. Berlin, Germany.
  • Bråte, J. Radiolaria revealed as a reservoir of Marine alveolates. VI European Congress of Protistology. 2011. Berlin, Germany.
  • Bråte, J. Diversity of unculturable Radiolaria and their symbionts revealed by 18S rDNA phylogeny. The 18th meeting of the International Society for Evolutionary Protistology 2010. Kanazawa, Japan.
  • Bråte, J. Lake Finsevatn sediment diversity investigated by pyrosequencing. 2nd International Winter Limnology Symposium 2010. Liebenberg, Germany.
  • Bråte, J. Barriers to Dispersal: Few Marine–Freshwater Colonizations Revealed by Environmental Sequencing. NIVA Algesymposium 2008. Oslo, Norway.
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