Jon Bråte

Jon Bråte

Senior Researcher in viral genomics and bioinformatics

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 Department of Virology, 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 Postdoctoral Fellow 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
2026 Norwegian Cancer Society: Viral infection during pregnancy and childhood leukemia. Research project #322391. Total project budget: 13 mill NOK, of which 8 mill NOK in funding.
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: 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 EU4Health: Development of NGS and bioinformatics tools for increased preparedness against infectious diseases (€1 million).
2021 HERA Incubator: Method development and improved preparedness for future Covid-19 variants (€1.8 million).
2019 Research Council of Norway: Financial support for ERC Consolidator Grant application (€51,000).
2019 European Research Council: Invited to interview for ERC Starting Grant (June 2019).
2018 UNIFOR: Small grant for purchasing scientific equipment (€2,900).
2017 Research Council of Norway: 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 Research Council of Norway: 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 Research Council of Norway: 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 Research Council of Norway: 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).

Expert evaluation and peer review

  • Expert evaluator, European Commission: Marie Skłodowska-Curie Actions, Individual Fellowships (2016–2018).
  • Grant reviewer, National Science Centre, Poland: SONATA BIS-13 call (2023).
  • Grant reviewer, Peder Sather Center for Advanced Study, University of California, Berkeley (2019).
  • Peer reviewer for Algal Research, Applied and Environmental Microbiology, Aquatic Microbial Ecology, BMC Biology, BMC Ecology and Evolution, BMC Genomics, BMC Plant Biology, European Journal of Protistology, Genes, Indian Journal of Geo-Marine Sciences, International Journal of Molecular Sciences, iScience, Journal of Applied Phycology, Journal of Phycology, Molecular Biology and Evolution, Pedosphere, PLOS ONE, Proceedings of the Royal Society B, and Scientific Reports. Verified reviews on Web of Science and ORCID.

Commissions of trust

  • CAS Fellow: Fellow at the Centre for Advanced Study (CAS) at the Norwegian Academy of Science and Letters (2019–2020).
  • Board member, Department of Biology, University of Oslo, Norway (2012).
  • 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

Preprints and articles in 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. Access Microbiology. Preprint, under review. doi:10.1099/acmi.0.001232.v1

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. Preprint, under review. doi:10.1099/acmi.0.001193.v2

Zhu, H. and Bråte, J. 2025. Identification and Functional Characterization of microRNAs in Ichthyosporea. F1000Research 14: 319. Version 1; peer review: 1 approved with reservations. doi:10.12688/f1000research.162501.1

Peer-reviewed articles

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 14: 25790. doi: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 12: 542. 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 14(12): 2734. doi:10.3390/v14122734

Osnes, M. N., Alfsnes, K., Bråte, J., Garcia, I., Riis, R. K., Instefjord, K. H., Elshaug, H., Vollan, H. S., Moen, L. V., Pedersen, B. N., Caugant, D. A., Stene-Johansen, K., Hungnes, O., Bragstad, K., Brynildsrud, O. and 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 7(2): veab086. 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. Algal Research 59: 102440. 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 using droplet MDA. Scientific Reports 11: 12820. 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 57(4): 1223–1233. 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 8: e49801. doi:10.7554/eLife.49801 Senior author for the non-coding RNA work.

Bråte, J., Fuss, J., Mehrotra, S., Jakobsen, K. S. and Klaveness, D. 2019. Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Research 8: 401. doi:10.12688/f1000research.16734.3

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. E. and Shalchian-Tabrizi, K. 2018. Unicellular origin of the animal microRNA machinery. Current Biology 28(20): 3288–3295.e5. 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 34(7): 1557–1573. doi:10.1093/molbev/msx075

Bråte, J., Adamski, M., Neumann, R. S., Shalchian-Tabrizi, K. and Adamska, M. 2015. Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proceedings of the Royal Society B: Biological Sciences 282(1821): 20151746. 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. doi:10.1016/j.protis.2012.04.004

Zhao, S., Burki, F., Bråte, J., Keeling, P. J., Klaveness, D. and Shalchian-Tabrizi, K. 2012. Collodictyon—an ancient lineage in the tree of eukaryotes. Molecular Biology and Evolution 29(6): 1557–1568. doi:10.1093/molbev/mss001

Krabberød, A. K., Bråte, J., Dolven, J. K., Ose, R. F., Klaveness, D., Kristensen, T., Bjørklund, K. R. 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. European Journal of Phycology 46(3): 282–291. doi:10.1080/09670262.2011.598950

Shalchian-Tabrizi, K., Reier-Røberg, K., Ree, D. K., Klaveness, D. and Bråte, J. 2011. Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences. Journal of Eukaryotic Microbiology 58(4): 315–318. 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. The ISME Journal 4(9): 1144–1153. 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). Molecular Biology and Evolution 27(2): 347–357. doi:10.1093/molbev/msp239

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 in Microbiology 17(9): 414–422. doi:10.1016/j.tim.2009.05.010

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 Biology and Evolution 1: 231–238. doi:10.1093/gbe/evp022

Patil, V., Bråte, J., Shalchian-Tabrizi, K. and Jakobsen, K. S. 2009. Revisiting the phylogenetic position of Synchroma grande. Journal of Eukaryotic Microbiology 56(4): 394–396. doi:10.1111/j.1550-7408.2009.00389.x

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. Environmental Microbiology 10(10): 2635–2644. doi:10.1111/j.1462-2920.2008.01685.x

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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