Katrine Højholt Iversen
Main PostDoc project
Detection of human genomics variants with graph genomes
The current human reference genome is a linear representation of a composite genome and therefore does not contain information about the variants that have previously been identified in other human genomes. In a graph-genome, the reference genome and genetic variants are integrated into a graph structure and a single genome therefore represents a path through this graph. One benefit of the variant graph is that they are much better at detecting structural variation. This is largely because the variation is present in the graph-genome making it much easier for the short reads to match compared to when the variation is not present (as in the standard reference genome).
In this project we want to investigate the possibility of using the genome graph for detection of genetic variation in the Danish National Genome Center setup. We will create a Danish genome graph from variation identified in the Danish population and add in SVs from the Danish, Swedish, and Icelandic population. Furthermore, we will add genetic variation data representing other minorities in Denmark.
Short profile
In 2014 I was involved in a project focusing on infective endocarditis caused by Mitis group streptococcus. This subject became my main focus in my ph.d. project, which was initiated in 2015. My main interest is to solve biological questions using bioinformatics. During my ph.d. project I was involved in several different projects, among others the investigation of ancient DNA and genomic comparisons of bacteria that has caused human infections. The majority of my ph.d. was conducted at Technical University of Denmark with Simon Rasmussen as my supervisor. In 2018 I was affiliated University of Copenhagen, where I briefly worked in Tom Gilbert group at the Natural History Museum of Denmark and later joined Simon Rasmussens Lab at the Novo Nordisk Foundation Center for Protein Research. In 2020 I defended my ph.d., and was hired in a one-year PostDoc position shared between Novo Nordisk Foundation Center for Protein Research and Danish National Genome Center.
Brief CV
- 01/2020–present: PostDoc at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark and Danish National Genome Center.
- 12/2015–12/2019: Ph.d. student at DTU
- 08/2016–08/2017: Maternity leave
- 08/2015–10/2015: Research assistant at Klinisk Mikrobiologi, Slagelse Sygehus, Denmark
- 08/2012–05/2015: Master in Systems Biology at Technical University of Denmark
- 10/2013–07/2014: Maternity leave
- 01/2013–05/2013: Exchange stay for 1 semester at Lund University, Sweden
- 08/2009–06/2012: Bachelor in Biotechnology at Technical University of Denmark
Teaching and supervision
In 2013 I worked as a teaching assistant at the DTU diploma course “Biotechnology and process design” which included assistance in the laboratory and with theoretically exercises. In 2016, 2018 and 2019 I assisted in the DTU master course “Next Generation Sequencing Analysis” where I assisted during the exercises and helped the examination and grade the students. In 2017 and 2018 I assisted in the DTU master course “Metagenomics and Microbiome Analysis”. I assisted during the exercises and helped the examination and grade the students. From November to December 2017 I became course responsible for “Metagenomics and Microbiome Analysis”.
Grants
I 2015 I received a grant, covering 1/3 of my ph.d. salary from Hjerteforeningen 15-R99-A6040-22951
Publications
“Similar genomic patterns of clinical infective en- docarditis and oral isolates of Streptococcus san- guinis and Streptococcus gordonii” Katrine Højholt Iversen, Louise Hesselbjerg Rasmussen, Kosai Al-Nakeeb, Jose Juan Almagro Armenteros, Christian Salg ̊ard Jensen, Rimtas Dargis, Ok- sana Lukjancenko, Ulrik Stenz Justesen, Claus Moser, Flemming S. Rosenvinge, Xiaohui Chen Nielsen, Jens Jørgen Christensen, and Simon Rasmussen. Scientific Reports, 2020 doi: 10.1038/s41598-020-59549-4
“A 5700 year-old human genome and oral microbiome from chewed birch pitch” Theis ZT Jensen, Jonas Niemann, Katrine Højholt Iversen*, Anna K Fotakis, Shyam Gopalakrishnan, Åshild J. Vågene, Mikkel Winther Pedersen, Mikkel H S Sinding, Martin R Ellegaard, Morten E Allentoft, Liam T Lanigan, Alberto J Taurozzi, Sofie Holtsmark Nielsen, Michael W Dee, Martin N Mortensen, Mads C Christensen, Søren A Sørensen, Matthew J Collins, M Thomas P Gilbert, Martin Sikora, Simon Rasmussen, and Hannes Schroeder. Nature Communications, 10:5520, December 2019 doi: 10.1038/s41467-019-13549-9
“Population genomics of the Viking world”
Ashot Margaryan, Daniel Lawson, Martin Sikora, Fernando Racimo, Simon Rasmussen, Ida Moltke, Lara Cassidy, Emil Jørsboe, Andrés Ingason, Mikkel Pedersen, Thorfinn Korneliussen, Helene Wilhelmson, Magdalena Bús, Peter de Barros Damgaard, RuiMartiniano, Gabriel Renaud, Claude Bh ́erer, J. Víctor Moreno-Mayar, Anna Fotakis, Marie Allen, Martyna Molak, Enrico Cappellini, Gabriele Scorrano, Alexandra Buzhilova, Allison Fox, Anders Albrechtsen, Berit Schütz, Birgitte Skar, Caroline Arcini, Ceri Falys, Charlotte Hedenstierna Jonson, Dariusz B laszczyk, Denis Pezhemsky, Gordon Turner-Walker, Hildur Gestsdóottir, Inge Lundstrøm, Ingrid Gustin, Ingrid Mainland, Inna Potekhina, Italo Muntoni, Jade Cheng, Jesper Stenderup, Jilong Ma, Julie Gib-son, Jüri Peets, Jörgen Gustafsson, Katrine Iversen, Linzi Simpson, Lisa Strand, Louise Loe, Maeve Sikora, Marek Florek, Maria Vretemark, Mark Redknap, Monika Bajka, Tamara Pushkina, Morten Søvsø, Natalia Grigoreva, Tom Christensen, Ole Kastholm,Otto Uldum, Pasquale Favia, Per Holck, Raili Allmäe, Sabine Sten, Símun Arge, Sturla Ellingvåg, Vayacheslav Moiseyev, Wieslaw Bogdanowicz, Yvonne Magnusson, LudovicOrlando, Daniel Bradley, Marie Louise Jørkov, Jette Arneborg, Niels Lynnerup, NeilPrice, M. Thomas Gilbert, Morten Allentoft, Jan Bill, Søren Sindbæk, Lotte Hedeager, Kristian Kristiansen, Rasmus Nielsen, Thomas Werge, and Eske Willerslev.
Type: Working paper in Biorxiv, July 2019.
doi: 10.1101/703405
“The first horse herders and the impact of early Bronze Age steppe expansions into Asia” de Barros Damgaard, Peter ; Martiniano, Rui ; Kamm, Jack ; Moreno-Mayar, J Víctor ; Kroonen, Guus ; Peyrot, Michaël ; Barjamovic, Gojko ; Rasmussen, Simon ; Zacho, Claus ; Baimukhanov, Nurbol ; Zaibert, Victor ; Merz, Victor ; Biddanda, Arjun ; Merz, Ilja ; Loman, Valeriy ; Evdokimov, Valeriy ; Usmanova, Emma ; Hemphill, Brian ; Seguin-Orlando, Andaine; Yediay, Fulya Eylem ; Ullah, Inam ; Sjögren, Karl-Göran ; Iversen, Katrine Højholt ; Choin, Jeremy ; de la Fuente, Constanza ; Ilardo, Melissa ; Schroeder, Hannes ; Moiseyev, Vyacheslav ; Gromov, Andrey ; Polyakov, Andrei ; Omura, Sachihiro ; Senyurt, Süleyman Yücel ; Ahmad, Habib ; McKenzie, Catriona ; Margaryan, Ashot ; Hameed, Abdul ; Samad, Abdul ; Gul, Nazish ; Khokhar, Muhammad Hassan ; Goriunova, O I ; Bazaliiskii, Vladimir I ; Novembre, John ; Weber, Andrzej W ; Orlando, Ludovic ; Allentoft, Morten E ; Nielsen, Rasmus ; Kristiansen, Kristian ; Sikora, Martin ; Outram, Alan K ; Durbin, Richard ; Willerslev, Eske Science, vol: 360, issue: 6396, June 2018 dpi: 10.1126/science.aar7711
“Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes.” Derya Carkaci, Katrine Højholt, Xiaohui Chen Nielsen, Rimtas Dargis, Simon Rasmussen,Ole Skovgaard, Kurt Fuursted, Paal Skytt Andersen, Marc Stegger, and Jens Jørgen Christensen. In: Microbial Pathogenesis, 112:327–340, November 2017. doi: 10.1016/j.micpath.2017.09.042
“In silico assessment of virulence factors in strains of Streptococcus oralis and Streptococcus mitis isolated from patients with Infective Endocarditis”
Louise H. Rasmussen, Katrine Højholt, Rimtas Dargis, Jens Jørgen Christensen, OleSkovgaard, Ulrik S. Justesen, Flemming S. Rosenvinge, Claus Moser, Oksana Lukjancenko, Simon Rasmussen, and Xiaohui C. Nielsen†.
Journal of Medical Microbiology, 66(9):1316–1323, September 2017.
doi: 10.1099/jmm.0.000573
“Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci.” L. H. Rasmussen, R. Dargis, K. Højholt, J. J. Christensen, O. Skovgaard, U. S. Justesen, F. S. Rosenvinge, C. Moser, O. Lukjancenko, S. Rasmussen, and X. C. Nielsen. European Journal of Clinical Microbiology & Infectious Diseases,3 5(10):1615–1625, October 2016. doi: 10.1007/s10096-016-2700-2