Henrik Nielsen

Employment

• Technical University of Denmark Center for Biological Sequence Analysis Associate Professor
  2006 - Present
• Technical University of Denmark

Education

• Stockholms Universitet fil.dr. (PhD)
  1996 - 1999
• University of Copenhagen M.Sc.
  1983 - 1993

Projects & Funding

Projects & funding information is unavailable.

Publications (70)

• DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads
  2026 DOI: 10.64898/2026.06.17.732633
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• Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2
  Bioinformatics 2026 DOI: 10.1093/bioinformatics/btag129
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• Bioinformatics Meets Biosemiotics and Signal Peptides Emerge as Dicisigns
  Towards a Biosemiotic Theoretical Biology 2026 DOI: 10.7551/mitpress/16007.003.0020
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• Measuring Meaning of Molecular Motifs
  Biosemiotics 2026 DOI: 10.1007/s12304-026-09637-1
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• Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2
  2025 DOI: 10.1101/2025.04.12.648497
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• NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model
  BMC Bioinformatics 2025 DOI: 10.1186/s12859-025-06220-2
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• Practical Applications of Language Models in Protein Sorting Prediction
  Large Language Models (LLMs) in Protein Bioinformatics 2025 DOI: 10.1007/978-1-0716-4623-6_10
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• SweetBERT
  2025 International Conference on Learning Representations, Singapore, 24/04/2025 2025
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• SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects
  NAR Genomics and Bioinformatics 2024 DOI: 10.1093/nargab/lqae106
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• SignalP
  Protein Bioinformatics 2024 DOI: 10.1007/978-1-0716-4007-4_17
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