Tue Kjærgaard Nielsen

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About me:

I am a molecular microbiologist with a special interest in 3rd generation sequencing (Nanopore) and bioinformatics. I apply these methods to study how mobile genetic elements (MGEs) affect microbial evolution. This includes important traits such as degradation of xenobiotics (e.g. PFAS), resistance to antibiotics and virulence traits. 

Current research topics:

• PFAS degradation by microorganisms:
  • What genes and enzymes are involved?
  • How do bacteria handle fluoride (from PFAS) toxicity?
  • Are PFAS truly "forever chemicals"?
• Improving the accuracy of antibiotic resistance prediction by analyzing the genetic context of antibiotic resistance genes.
• Investigating how non-resistance genes become resistance determinants by interactions with MGEs.
• Detecting and analyzing exotic DNA modifications of bacteriophages using Nanopore sequencing.
• Virulence traits of plant pathogens associated with MGEs.
• Detection and quantification of the activity of MGEs in single bacterial genomes using new lab and bioinformatics techniques.

Teaching and supervision:

Lecturer and co-organizer on MSc course "Applied Microbiology" LBIK10180U

Lecturer on courses "Synthetic Biology" LBIK10207U,  "Microbiology" NPLB14012U, "Bioinformatik: metoder og anvendelse" NPLB24004U, "Project in Experimental Molecular Biology" NPLB17004U

Organizer and teacher on several courses on DNA/RNA extraction, sequencing, qPCR, and bioinformatics at Zealand Academy of Technologies and Business.

Supervisor of Postdoc, guest PhDs, MSc, BSc, and project students.

Previous organizer and main teacher on PhD courses in microbial bioinformatics. 

Key words:

PFAS, bioinformatics, antibiotic resistance genes, mobile genetic elements, 3rd generation sequencing, Nanopore, Illumina, bacteriophages, plasmids, xenobiotics, antibiotics.

 

If you are interested in working with me on your BSc or MSc thesis project or wish to collaborate on future projects please feel free to contact me at tkn@plen.ku.dk. 

Udvalgte publikationer

1. Udgivet

   Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs.

   Nielsen, Tue Kjærgaard & Hansen, Lars Hestbjerg, jul. 2024, bioRxiv.

   Publikation: Working paper › Preprint › Forskning

2. Udgivet

   Antibiotic resistance genes are differentially mobilized according to resistance mechanism

   Nielsen, Tue Kjærgaard, Browne, Patrick Denis & Hansen, Lars Hestbjerg, 2022, I: GigaScience. 11, 17 s., giac072.

   Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

3. Udgivet

   Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software

   Nielsen, Tue Kjærgaard, Forero Junco, Laura Milena, Kot, Witold, Moineau, S., Hansen, Lars Hestbjerg & Riber, Leise, 2023, I: Molecular Ecology. 32, 6, s. 1236-1247 12 s.

   Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt