Personal profile
Short presentation
My area of research is network biology and I am particularly interested in the integration, analysis and visualization of omics data towards a more comprehensive understanding of human diseases. Furthermore, I have been actively involved in the development and maintenance of our group resources, in particular, the stringApp for Cytoscape. I also enjoy teaching about network biology methods and tools at various educational levels.
CV
Current position
05/2025–present: Data scientist, Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
Previous positions
- 05/2020–05/2025: Assistant Professor, NNF Center for Protein Research, University of Copenhagen, Denmark
- 05/2016–05/2020: PostDoc researcher, NNF Center for Protein Research and Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark
- 01/2010–05/2016: Research scientist, Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Germany
- 03/2013–05/2013: Research scientist, Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, USA
Education
- PhD (Dr. rer. nat), Max Planck Institute for Informatics and Saarland University, Germany (June 2016)
- Masters (M. Sc.) in Bioinformatics, Saarland University, Germany (Nov 2009)
- Bachelor (B.S.) in Computational Molecular Biology, Saarland University, Germany (Oct 2007)
Research Awards
- Conference travel fellowship for ISMB/ECCB 2015
- BioVis 2013 data contest overall favorite (IEEE BioVis 2013, Atlanta, US)
- Travel grant of the Boehringer Ingelheim Fonds for a 3-month research visit at UCSF, USA (March - May 2013)
- Conference travel fellowships for VIZBI 2010
- Conference travel fellowships for ECCB10
Teaching
- Bioinformatics and Systems Biology, MSc Human Biology, University of Copenhagen, Denmark (yearly since 2016)
- Bioinformatics analysis of gene expression data, PhD course, University of Copenhagen, Denmark (yearly since 2019)
- Translational Discovery Omics II, BRIDGE PostDoc course, University of Copenhagen, Denmark (yearly since 2021)
- Cytoscape/STRING Workshops, PhD/PostDoc level, at different universities in Denmark (yearly since 2017)
- Big Data Analytics and Machine Learning I, BRIDGE PostDoc course, University of Copenhagen, Denmark (yearly in 2019-2020)
- EMBO Practical Course on Computational analysis of protein-protein interactions, PhD/PostDoc course, different locations (yearly 2011-2019)
Fields of interest
Network biology, Computational Proteomics, Medical bioinformatics, Structural biology
Education/Academic qualification
Bioinformatics, PhD (Dr. rer. nat.), Max Planck Institute for Informatics
Award Date: 6 Jun 2016
Bioinformatics, Master of Science (M. Sc.), Saarland University
Award Date: 16 Nov 2009
Collaborations and top research areas from the last five years
Research output
-
A ligand-receptor interactome of the bone tumor microenvironment in multiple myeloma bone pain
Barakat, A., Doncheva, N. T., Prado, J., Moll, L., Jensen, J. L., Daz-Delcastillo, M., Novak, I., Eijkelkamp, N., Jensen, L. J. & Heegaard, A. M., 2025, In: Pain. 166, 12, p. 2831-2850Research output: Contribution to journal › Journal article › Research › peer-review
-
PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways
Moortele, T. V., Verschaffelt, P., Huang, Q., Doncheva, N. T., Holstein, T., Jachmann, C., Dawyndt, P., Martens, L., Mesuere, B. & Van Den Bossche, T., 2025, In: Molecular and Cellular Proteomics. 24, 3, 10 p., 100918.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile1 Citation (Scopus)8 Downloads (Pure) -
The STRING database in 2025: protein networks with directionality of regulation
Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M. E., Huang, Q., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J. & Von Mering, C., 2025, In: Nucleic Acids Research. 53, D1, p. D730-D737 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile287 Citations (Scopus)41 Downloads (Pure) -
Understanding Data Analysis Steps in Mass-Spectrometry-Based Proteomics Is Key to Transparent Reporting
Doncheva, N. T., Schwammle, V. & Locard-Paulet, M., 2025, In: Journal of Proteome Research. 24, 10, p. 4965−4976Research output: Contribution to journal › Journal article › Research › peer-review
1 Citation (Scopus) -
A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates
Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., Rykær, M., Jensen, L. J., Christophorou, M. A. & Nielsen, M. L., 2024, In: Nature Structural and Molecular Biology. 31, 6, p. 977–995 34 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile23 Citations (Scopus)35 Downloads (Pure) -
Functional Analysis of MS-Based Proteomics Data: From Protein Groups to Networks
Locard-Paulet, M., Doncheva, N. T., Morris, J. H. & Jensen, L. J., 2024, In: Molecular and Cellular Proteomics. 23, 12, 14 p., 100871.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile5 Citations (Scopus)6 Downloads (Pure) -
Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement
Batth, T. S., Locard-Paulet, M., Doncheva, N. T., Lopez Mendez, B., Jensen, L. J. & Olsen, J. V., 2024, In: Nature Communications. 15, 1, 17 p., 8923.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile15 Citations (Scopus)18 Downloads (Pure) -
Alteration of microglial metabolism and inflammatory profile contributes to neurotoxicity in a hiPSC-derived microglia model of frontotemporal dementia 3
Haukedal, H., Syshøj Lorenzen, S., Westi, E. W., Corsi, G., Gadekar, V. P., McQuade, A., Davtyan, H., Doncheva, N. T., Schmid, B., Chandrasekaran, A., Seemann, E. S., Cirera, S., Blurton-Jones, M., Meyer, M., Gorodkin, J., Aldana, B. & Freude, K., 2023, In: Brain, Behavior, and Immunity. 113, p. 353-373Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile5 Citations (Scopus)118 Downloads (Pure)