Jeppe Vinther – Department of Biology - University of Copenhagen

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Computational and RNA Biology > RNA Biology > Vinther lab > Staff > Jeppe Vinther

CV | ‍Jeppe Vinther | Petersborgvej 4, 3tv | 2100 Copenhagen Ø | +4522840780 | jvinther@bio.ku.dk | jeppevinther@gmail.com | rna.dk/vinther

Personal information

  • Danish citizen.
  • Born on: 22nd of April, 1973 in Randers, Denmark.
  • Pivate status: Married, 2 children (in total 30 weeks of paternity leave).

Scientific focus

  • I am interested in understanding RNA based mechanisms involved in the control of cellular processes, in particular those that are related to disease. Currently, I focus on developing sequencing based methods for improving the prediction of RNA structure and accessibility and making it possible to investigate the regulatory potential of many RNA sequences in parallel. Moreover, I want to contribute to the further development of RNA based therapies that utilize our knowledge of RNA based mechanisms.

Professional experience

Associate Professor | 1/2 2011-current | Department of Biology, University of Copenhagen.

  • Current group: 1 postdoc, 1 PhD students, 2 MSc students and a half time lab technician.
  • Published 5 corresponding author papers, including 2 in NAR and 1 in RNA.
  • Developed method for reducing background in sequencing based RNA probing experiments. Patent application filed by University of Copenhagen.

Assistant Professor | 15/2 2008 -31/1 2011 | Department of Biology, University of Copenhagen.

  • Main driving force behind the application for and establishment of the Center for Computational and Applied Transcriptomics (COAT) funded by the Danish Council for Strategic Research with a 5 million EURO grant.

Postdoc, Arctander Group | 1/2 2005 - 14/2 2008 | Department of Biology, University of Copenhagen.

  • Was appointed groupleader for the group in the period from 1/9 2006 to 14/2 2008, because professor Arctander became ill.
  • Developed first method for identification of miRNA targets using quantitative proteomics.

Visiting Scientist, Galloway Lab | 1/8 2004 - 31/1 2005 | FHCRC, Seattle, USA.

  • Investigated the influence of Nonsense mediated Decay on HPV-16 oncogene expression.

Postdoc, Norrild Lab | 1/6 2003 – 31/7 2004 | Institute of Molecular Pathology, University of Copenhagen.

Education

Ph.d. in Medicine | 14/5 2003 | Faculty of Health, University of Copenhagen

  • Thesis: Influence of the HPV-16 early 3’ UTR on expression of the HPV-16 oncogenes.
  • Supervisor: Bodil Norrild
  • Obtained highly competitive grant for integrated M.Sc.-Ph.D. studies from Faculty of Health.

M.Sc. in Human Biology | 14/6 2000 | Faculty of Health, University of Copenhagen

  • Thesis: Chartacterisation of the Regulation of the HPV-16 E5 Oncoprotein Expression
  • Supervisor: Bodil Norrild
  • Undergraduate studies: Chemical Engineering (Organic Synthesis specialisation), Technical University of Denmark (DTU).

Teaching and supervision experience

Supervison

  • 4 graduated PhD students: Rukov (2011), Olivarius (2014), Kielpinski (2014), Poulsen (2015), 5 graduated MSc students.

Teaching

  • Completed the Higher Education Teaching Programme in 2009, Department of Science Education, University of Copenhagen
  • RNA Biology: course responsible from 2010. Redesigned the course. Good evaluations from students and a steady increase in the number of attending students over the years.
  • Introduction to Bioinformatics: Course responsible from 2011. Good evaluations from students and a steady increase in the number of attending students over the years. Course becomes obligatory for Biochemistry students from 2016.
  • In addition I have taught on the following courses:  Bioinformatics of high throughput analyses, Cellebiologi for biokemikere, Evolutionsbiologi.

Management experience and training

Workpackage leader | 2011-current | Center for Computational and Applied Transcriptomics.

  • Member of the Steering committee and involved in the daily management of the center.

Groupleader | 2006-current | Department of Biology, University of Copehagen.

Management training

  • Project Management module 1 (2011), Implement A/S
  • Group Leader Development Program (2009), Implement A/S, Extensive course over 7 full days providing excellent training in how to lead a research group, both focused on practical and more strategic considerations
  • EMBO Lab Management Course (2007), Heidelberg, Germany.

Scientific leadership

  • Editor for: Genetics Research, Cambridge University Press.
  • Reviewer for: Swedish Research Council, ERC Advanced Grants, Canada First Research Excellence Fund, Nature Methods, Nucleic Acids Research, RNA, Trends in Genetics, Oncogene, Molecular Biology and Evolution, PLOS One.
  • In the PhD assessment committee for 6 students (University of Copenhagen and Aarhus University)

Publications

ResearcherID: researcherid.com/rid/A-8172-2012
ORCID: orcid.org/0000-0002-3847-3853

  • Reviewed articles: 17, Sum of the Times Cited: 371, h-index: 10 (based on ISI ResearcherID: A-8172-2012).
  • As corresponding author: 3 Nucleic Acids Research, 1 RNA Journal, 1 Trends in Genetics, 1 BMC Genomics, 1 Methods in Enzymology, 1 Methods in molecular biology.
  • 1 Patent application: WO2015021990-A1: Analyzing structure of RNA polynucleotides by allowing for selection of full length cDNA.

Poulsen LD, Kielpinski LJ, Salama SR, Krogh A, Vinther J. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. RNA 2015 PubMed link

Vinther J, Kielpinski LJ, Poulsen LD, Patent WO_2015_021990_A1: RNA Probing Methods and Reagents.

Kielpinski LJ, Sidiropoulos, N, Vinther J. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools. Methods in Enzymology, in press.

Kielpinski LJ, Vinther J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res. 2014 42(8):e70. PubMed link

Kielpinski LJ, Boyd M, Sandelin A, Vinther J. Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing. Methods Mol Biol. 2013;1038:213-31

Rukov JL, Wilentzik R, Jaffe I, Vinther J, Shomron N. Pharmaco-miR: linking microRNAs and drug effects. Brief Bioinform. 2013 Jan 31

Rukov JL, Vinther J, Shomron N. Pharmacogenomics genes show varying perceptibility to microRNA regulation. Pharmacogenet Genomics. 2011 May;21(5):251-62.

Glahder JA, Kristiansen K, Durand M, Vinther J, Norrild B. The early noncoding region of human papillomavirus type 16 is regulated by cytoplasmic polyadenylation factors. Virus Res. 2010 May;149(2):217-23. Epub 2010 Feb 8.

Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J. Quantitative regulation of alternative splicing in evolution and development. Bioessays. 2009 Jan;31(1):40-50. Review.

Rosenstierne MW, Vinther J, Mittler G, Larsen L, Mann M, Norrild B. Conserved CPEs in the p53 3' untranslated region influence mRNA stability and protein synthesis. Anticancer Res. 2008 Sep-Oct;28(5A):2553-9.

Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW. Origin of introns by 'intronization' of exonic sequences. Trends Genet. 2008 Aug;24(8):378-81.

Gardner PP, Vinther J. Mutation of miRNA target sequences during human evolution. Trends Genet. 2008 Jun;24(6):262-5.

Boyerinas B, Park SM, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter ME. Identification of let-7-regulated oncofetal genes. Cancer Res. 2008 Apr 15;68(8):2587-91.

Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, Roy SW. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol Biol Evol. 2008 Feb;25(2):375-82.

Weile C, Gardner PP, Hedegaard MM, Vinther J. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes. BMC Genomics. 2007 Jul 23;8:244.

Rukov JL, Irimia M, Mørk S, Lund VK, Vinther J, Arctander P. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol. 2007 Apr;24(4):909-17.

Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res. 2006;34(16):e107.

Vinther J, Rosenstierne MW, Kristiansen K, Norrild B. The 3' region of human papillomavirus type 16 early mRNAs decrease expression. BMC Infect Dis. 2005 Oct 14;5:83.

Glahder JA, Hansen CN, Vinther J, Madsen BS, Norrild B. A promoter within the E6 ORF of human papillomavirus type 16 contributes to the expression of the E7 oncoprotein from a monocistronic mRNA. J Gen Virol. 2003 Dec;84(Pt 12):3429-41.

Rosenstierne MW, Vinther J, Hansen CN, Prydsoe M, Norrild B. Identification and characterization of a cluster of transcription start sites located in the E6 ORF of human papillomavirus type 16. J Gen Virol. 2003 Nov;84(Pt 11):2909-20

Vinther J, Norrild B. Clearance of cervical human papillomavirus infections. Int J Cancer. 2003 Mar 20;104(2):255-6. PubMed PMID: 12569584.