Publications
Work Experience
2015-07-01 – present
Researcher, 80%
Section for epidemiology and bioinformatics, Norwegian Veterinary Institute, Norway
My main work focuses on genomic epidemiology, on one health perspectives on and the spread of antibiotic resistance. I am heavily involved in several Norwegian Research Council projects focusing on the spread of quinolone resistant E. coli in Norwegian wildlife and production animals. I am also developing tools and pipelines for comparative genomics. Together with others at the Institute, I am also in charge of an internal bioinformatics educational program.
2013-07-01 – present
Assistant professor, 20%
Computational Life Science initiative, Department of Informatics, University of Oslo, Norway
My responsibilities within the Computational Life Science initiative is focused on teaching: I co-teach and plan the course INF-BIO5/9121 “High Throughput Sequencing technologies and bioinformatics analysis”, and I also supervise master students and PhD students.
2014-10-01 – 2015-07-01
Bioinformatician, 80%
Dept. of Medical Genetics, Oslo University Hospital, Oslo, Norway
I was part of the High Throughput Sequencing group at the Diagnostics section at the Department of Medical Genetics. This group uses HTS to diagnose genetic diseases in patients. The group develops pipelines for analysis, and also establishes new gene panels that can be analyzed for diagnostic purposes. My main role within this group was to work with the pipeplines, both for patient analysis and with developing it further. I was also involved in maintaining and developing the infrastructure necessary for efficient data processing.
22/1-2013 – 30/9-2014
Bioinformatician, 80%
Norwegian Sequencing Centre, Oslo University Hospital, Oslo, Norway
The Norwegian Sequencing Centre is the national core facility for sequencing in Norway. My responsibilities included Linux system administration and computer maintenance, both hardware and software. I was responsible for planning and setting up new servers and storage solutions and for network maintenance and security.
In addition I maintained and developed analysis software and pipelines, both for internal use and for collaborative projects. I was also involved in the day-to-day sequencing production and delivery process.
21/2-2010 – 21/2/2013
Post doc
Centre for Ecological and Evolutionary Synthesis, UiO, Norway
My work at CEES was primarily centered on the cod genome sequencing project led by Kjetill S. Jakobsen. My contribution to this project was mainly comparative work, with the development of methods for comparing the cod genome to that of other fishes. I was also involved in a metagenomics study of urine from women, a population genetics study for characterizing ecotypes of Cyanobacteria in Norwegian lakes, a study of the characteristics of E.coli colonizing the infant gut, and a project in which we developed methods for establishing genotypes in plants. All of these projects required development of custom analysis pipelines and heavy use of the HPC computer cluster at the University of Oslo.
I also taught an introductory Python course for biologists with 15 attendees, and co-supervised several PhD and master students.
1/5-2009 – 1/3-2010
Assistant professor, 90%
Center for Biological Sequence Analysis, DTU, Denmark
My main project was to locate novel putative chicken colonization genes in the genus Campylobacter by combining information on conservation and KEGG and GO classifications to find genes with similar characteristics to those known to be involved in colonization. This project made heavy use of databases and gene annotation software and was initiated by Med-Vet-Net, a European Network of Excellence focusing on zoonoses and food-borne diseases.
In addition, I assisted in teaching a comparative genomics class to bachelor students, as well as several international workshops on the same subject.
1/5-2009 – 1/1-2012
Researcher, 10%
Department of Informatics, University of Oslo, Norway
I was one of several lecturers in the course “Introduction to Bioinformatics” (INF 4350). I co-supervised two PhD students and two master students, and was involved in the Computational Life Science initiative’s efforts to establish an educational program in bioinformatics.
1/1-2009 – 1/5-2009
Researcher
Department of Informatics, University of Oslo, Norway
I worked on finishing my own projects from my Ph.D., and was also involved in several projects within the group. In one of these, I assisted in the mapping of DNA repair pathways in prokaryotes by mining a DNA repair gene database that had been established within the Rognes group.
2002 – 2008
PhD student with Torbjørn Rognes, Institute of Medical Microbiology, Centre for Molecular Biology and Neuroscience, University of Oslo, Norway
EDUCATION
2002 – 2008
PhD in bioinformatics
Institute of Medical Microbiology, Centre for Molecular Biology and Neuroscience, Faculty of Medicine, University of Oslo, Norway
Title of thesis: “Computational characterization of ribosomal RNAs in prokaryotes“. My thesis advisor was Professor Torbjørn Rognes, in collaboration with Professor David W. Ussery at the Center for Biological Sequence Analysis, DTU, Denmark, where I had a research stay for 3 months in 2004. A major part of my PhD thesis was the development of the program RNAmmer, a program that uses Hidden Markov Models within a perl framework to detect ribosomal RNAs. This program has since been used in many different projects, including the SILVA: Tree of Life project.
1999 – 2002
Master in Molecular Biology
Institute of Molecular Biology, University of Bergen, Norway
Title of thesis: “The topology of pore proteins: Developing tools for making and analyzing topological models for the FomA porins from Fusobacterium nucleatum“. This was a collaborative project between the Department of Informatics and the Institute of Molecular Biology. My advisors were Professors Ingvar Eidhammer (informatics) and Rein Aasland (molecular biology). I implemented a neural network engine which I trained to predict the structure of general diffusion porins. I developed a Java program which used the results the neural networks produced for general diffusion porins to analyze the structure of the FomA protein.
1995 – 1998
Bachelor of Molecular Biology and Informatics, University of Bergen
My main subjects were computer science, chemistry, molecular biology and mathematics.
TEACHING, SUPERVISION AND ADMINISTRATION
I have taught basic bioinformatics skills to bachelor and master students in molecular biology. As a lecturer in INF4350 for two consecutive years, I taught bioinformatic algorithms to computer science master students.
During my employment at the Danish Technical University, I helped teach the course “The Scientific Communication of Comparative Genomics”, where students used comparative genomics to characterize a set of organisms as a training exercise in writing scientific papers and posters. I have also taught variations of this course in week-long workshops both in Petropolis, Brazil (2009) and Rabat, Morocco (2010).
I am at present one of two main course organizers of INF-BIO5/9121 “High Throughput Sequencing technologies and bioinformatics analysis”, and I also teach basic python in MBV3070 “Bioinformatics” and in MBV-INF4410 “Bioinformatics for Molecular Biology”
I have completed a course in pedagogy for university employees organized by the University of Oslo.
I have co-supervised a total of five PhD and two master students. I am currently co-supervising two PhD students who are developing methods for de novo genome assembly, one at the Department of Informatics and the other at the Department of Biosciences. I am also supervising three master student at the Department of Informatics, who are all developing software for analysis of genomic data in various ways.
OTHER EXPERIENCE
I am an authorized Software Carpentry instructor, instructor trainer and member of the board. This foundation aims to teach researchers basic lab skills for scientific computing by teaching two day workshops which include the Unix shell, basic python programming, version control using Git, and basic database handling.
LANGUAGE SKILLS
I am fluent in Norwegian and English, and I am currently learning French.
COMPUTER SKILLS
Python, BioPython, shell scripting (bash), Java and some Perl; version control systems (Git and some SVN), SQL (both MySQL and PostgreSQL), R, Bioconductor, metagenomics analysis software, gene prediction and annotation software, genome assembly and mapping software. Using and managing Unix-like operating systems, including software and hardware maintenance, basic network planning and maintenance, planning and installation of new hardware, computer system and infrastructure design, and software installation and management.