Research output per year
Research output per year
Personal profile
Profile
Please see my group website, https://www.healthtech.dtu.dk/protein-sorting
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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Dive into the research topics where Henrik Nielsen is active. These topic labels come from the works of this person. Together they form a unique fingerprint.
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
Publications
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DeepLoc 2.1: multi-label membrane protein type prediction using protein language models
Ødum, M. T., Teufel, F., Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Winther, O. & Nielsen, H., 2024, In: Nucleic Acids Research. 6 p., gkae237.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile90 Downloads (Orbit) -
Predicting the subcellular location of prokaryotic proteins with DeepLocPro
Moreno, J., Nielsen, H., Winther, O. & Teufel, F., 2024, In: Bioinformatics. 40, 12, 5 p., btae677.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile12 Downloads (Orbit) -
Protein Sorting Prediction
Nielsen, H., 2024, Bacterial Secretion Systems: Methods and Protocols. 2 ed. Springer, Vol. 2715. p. 27-63 (Methods in molecular biology (Clifton, N.J.)).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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SignalP: The Evolution of a Web Server
Nielsen, H., Teufel, F., Brunak, S. & von Heijne, G., 2024, Protein Bioinformatics. Springer, Vol. 2836. p. 331-367 (Methods in molecular biology (Clifton, N.J.), Vol. 2836).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects
Ferrer Florensa, A., Almagro Armenteros, J. J., Nielsen, H., Aarestrup, F. M. & Clausen, P. T. L. C., 2024, In: NAR Genomics and Bioinformatics. 6, 3, 10 p., lqae106.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile12 Downloads (Orbit)
Projects
- 6 Finished
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Modeling of biological sequences for prediction and characterization of pathogenicity using deep learning
Ferrer Florensa, A. (PhD Student), Aarestrup, F. M. (Main Supervisor), Almagro Armenteros, J. J. (Supervisor) & Nielsen, H. (Supervisor)
15/04/2022 → 14/04/2025
Project: PhD
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Protein sorting in pathogenic unicellular eukaryotes
Almagro Armenteros, J. J. (PhD Student), Nielsen, H. (Main Supervisor), Winther, O. (Supervisor), Marcatili, P. (Examiner), Boomsma, W. (Examiner) & Rost, B. (Examiner)
Technical University of Denmark
01/12/2016 → 20/02/2020
Project: PhD
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Isolation and characterization of bacteriaophages with therapeutic potential
Villarroel, J. (PhD Student), Nielsen, M. (Main Supervisor), Kilstrup, M. (Supervisor), Larsen, M. V. (Supervisor), Nielsen, H. (Examiner), Lavigne, R. (Examiner) & Nielsen, D. S. (Examiner)
Technical University of Denmark
01/12/2013 → 28/02/2018
Project: PhD
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Molecular Evolution of Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV)
Oliveira, R. G. (PhD Student), Pedersen, A. G. (Main Supervisor), Nielsen, H. (Examiner), Hurst, L. D. (Examiner) & Schierup, M. (Examiner)
01/09/2003 → 02/07/2008
Project: PhD
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Biological Sequence Analysis
Brunak, S. (Project Manager), Sorgenfrei Blom, N. (Project Participant), Boesen, L. (Project Participant), Gorodkin, J. (Project Participant), Hansen, J. (Project Participant), Knudsen, S. (Project Participant), Krogh, A. S. (Project Participant), Pedersen, A. G. (Project Participant), Rapacki, K. (Project Participant), Stærfeldt, H. H. (Project Participant), Keiding, J. (Project Participant), Nielsen, H. (Project Participant), Dahlin, K. B. (Project Participant), Larsen, T. S. (Project Participant), Gupta, R. (Project Participant), Andersen, C. A. (Project Participant), Worning, P. (Project Participant), Workman, C. (Project Participant), Jarmer, H. Ø. (Project Participant), Ussery, D. (Project Participant) & Jensen, L. J. (Project Participant)
01/01/1998 → 31/08/2003
Project: Research
Activities
- 13 Conference presentations
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Protein language models and the semiotic language of Signal Peptides
Rodrigues, M. V. (Guest lecturer), Emmeche, C. (Guest lecturer) & Nielsen, H. (Guest lecturer)
1 Aug 2023Activity: Talks and presentations › Conference presentations
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SignalP 6.0: A practical application of a protein language model
Nielsen, H. (Guest lecturer)
11 Aug 2023Activity: Talks and presentations › Conference presentations
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DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
Nielsen, H. (Guest lecturer)
27 Jul 2023Activity: Talks and presentations › Conference presentations
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Practical applications of language models in protein science
Nielsen, H. (Guest lecturer)
30 Nov 2022Activity: Talks and presentations › Conference presentations
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Signal peptide prediction: from plain neural networks to language models
Nielsen, H. (Guest lecturer)
24 Jun 2021Activity: Talks and presentations › Conference presentations
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