I am currently working as a research scientist in the population genetics group at the Institute of Marine Research (IMR). Before my employment here, I held a position as a research scientist at the Department of Informatics, University of Bergen. Starting in 2016, I have a part-time engagement as an associate professor at the University of Bergen, with teaching and research responsibilities. The autumn of 2016, I will teach Inf283, a course in machine learning.
| Academic degrees | University | Year | |
|---|---|---|---|
| siv.ing/cand.scient | (M.Sc.) | University of Bergen | 1996 |
| dr.scient. | (Ph.D.) | University of Bergen | 2004 |
After completing my M.Sc., I worked for some years in consulting and industry, doing document management, systems administration, and software development.
Scientific qualifications
Including two recently submitted manuscripts, I have 30 publications, 16 as first author. On additional 7 publications I am second author, on three of these I was main supervisor for the Ph.D. candidate which had first authorship. On the other four I had substantial input on bioinformatics methods, performed bioinformatics analysis, and/or participated in the overall design. According to Google Scholar, I currently have 745 citations, my h-index is 11, and my i10-index is 12.
The majority of my work has been in the fields of genomics and transcriptomics, where I have performed analysis. I have been part of several large projects, including the cod genome project and the salmon louse genome project, and I have developed new methods and implemented several software utilities for analysis.
I am currently working in population genomics, where my most recent work is on the population structure of the minke whale. Recently, I have developed a novel method for predicting SNPs that combines effect size and confidence, and a simple, yet effective method for identifying sex chromosomes from sequence data alone.
I have a very broad field of interest and in addition to my core work in genomics, transcriptomics, and population genomics, I have worked with more basic computer science. I have worked with functional programming, in particular the Haskell programming language, where I have a small contribution to the language standard, the Haskell 2010 report. I am coordinating the Biohaskell effort, building a foundation for implementing bioinformatics tools in Haskell. This interest has led to several publications, and I am now collaborating with researchers in Leipzig and Vienna on publishing an article on a web server implementing my method for transitive alignments.
I am generally interested in algorithms and data structures, and I believe I was the first to publish methods using Bloom filters for bioinformatics, as well as some of the earliest publications on using k-mer indexing and de Bruijn graphs for sequence analysis.
I have been involved in data management and other technical support, and I have developed an innovative system for scientific data storage, search, and retrieval. This resulted in a paper in 2013.
I am often asked to perform grading duties for university exams or to referee M.Sc. theses. Below is a list of activities the last three years; previously, I have graded M.Sc. theses at the University of Agder and Norwegian University of Science and Technology in Trondheim.
| Exam | Institution | Year |
|---|---|---|
| M.Sc, T. K. Thoresen | UiO | 2015 |
| Inf283 - Machine learning | UiB | 2015 |
| M.Sc, R. Cañadas | UiB | 2014 |
| Inf280 - Bioinformatics | UiB | 2013 |
Related activities
Supervision, teaching
I have supervised two Ph.D. students, I was main supervisor for S. Balzer (2013) and co-supervised A. Sharma (not finished). I have co-supervised several M.Sc. students.
I have participated in Google's Summer of Code program, and in the summer of 2014, I supervised S. Berkmeier in Leipzig. She worked on ../posts/transalign, successfully optimizing its performance. She is currently developing a web site around this tool.
I have organized the journal club for the population genetics group at IMR. This involved setting up the schedule, and I exploited empty slots (e.g., due to cancellations) with my own talks. In addition, I occasionally give talks, mainly at the IMR or the University of Bergen.
I have formal training in teaching and leadership from the military, where I was NCO in the Royal Norwegian Coastal Artillery, where I attended the Officer's School in Drøbak, and then worked as an instructor.
This year, I have a part-time position at the Department of Informatics, University of Bergen. This includes teaching and supervision duties, and this autumn, I will teach a course in machine learning.
Scientific management experience
I have been project leader in two projects at IMR. The Norwegian Marine Genome Center was an early effort at organizing marine molecular data and building infrastructure for working with them. I was project leader for a project working on the salmon louse genome, where I was main supervisor for a Ph.D. student.
Currently, I am WP leader in an internally funded project developing resources for data management and analysis. This WP involves people from several departments at the IMR.
As the population genetics group did not have an active journal club, in 2014, I took the initiative to and organized weekly meetings where group members presented either their own work or a published paper, for criticism and discussion.
External funding
Most grant proposals at IMR are biology oriented, and as such, bioinformatics is often limited to a supporting role. Many proposals list me as WP leader, responsible for bioinformatics analysis. I also write my own, more technologically oriented proposals. I have participated in the following recent grant proposals and applications:
| Application | Proposer | Program | Year | Funded |
|---|---|---|---|---|
| MarIntNet | K. Malde | EU COST Action | 2016 | ? |
| DeepMarine | K. Malde | FriNaTek | ? | |
| DeepMarine | K. Malde | FriNaTek | 2015 | |
| SlippingBehavior | N. O. Handegard | FHF | yes | |
| EcoDeep | N. O. Handegard | Marinforsk | ||
| OPTISORT | Ø. Skaala | FORNY | ||
| EcoVocal | N. O. Handegard | Marinforsk | ||
| MAME | K. Malde | FriMedBio | 2014 | |
| EvoLouse | R. Skern | FriBio | ||
| Short Circuit | K. Malde | HFSP | ||
| Haddock-6161 | S. Meier | VISTA | 2013 | yes |
| NYPROOF | S. Meier | Havet og Kysten |
In addition, I have participated in the planning and development of several large/infrastructure proposals Digital Life, Elixir, and NMDC.
International profile
During my Ph.D., I stayed for three months with Prof. Giegerich at the University of Bielefeld. This resulted in two manuscripts, one published and one unpublished part of my thesis. In 2013/2014 I was a visiting researcher for one year, staying with Prof. Klaus Mayer's group at the Helmholtz Zentrum in Munich.
In 2015, I was invited by Prof. Toonen to visit the University of Honolulu for one week. In additon to giving talks about and discuss my work, I worked with researchers there on methods and analysis, mainly focusing coral population genetics.
I am organizing the Biohaskell community, which is an international effort (the mailing list counts 77 members with 17 different internet domains). I have participated in international workshops, including hackathons organized by the Haskell community and OBF.
Many of my publications have international co-authors. My current grant proposals are an EU COST Action and an RCN FriNaTek research project. The former includes a network of collaborators from eight different countries, the latter involved NOAA and Google as collaborators.
I am often asked to referee for international bioinformatics journals, and have reviewed papers for Bioinformatics, BMC Genomics, ACM Transactions on Computational Biology and Bioinformatics, BMC Research Notes and the Journal of Functional Programming. I have acted as program chair for the RECOMB-CG conference for several years, and have been a session chair at BIOSTEC Bioinformatics.
Administrative experience
In addition to participating in thesis evaluations and grading exams as mentioned previously, I am frequently asked to sit on committees for recruitment. A list of recent activities is given below.
| Position | Institution | Year |
|---|---|---|
| Post doc. | informatics, UiB | 2016 |
| Post doc. | informatics, UiB | 2015 |
| Post doc. | informatics, UiB | 2015 |
| Post doc. | biology, UiB | 2014 |
| Post doc. | IMR | 2014 |
I took the initiative to, and then organized a journal club for the populations genetics group in 2014 and 2015. I have previously helped organize workshops and events of social and academic nature, including the "Bioinformatics in Bergen" workshop.
I was on the board of the car sharing company "Bildeleringen", and chairman of the board at the time when the whole management structure was reorganized. Although not academic in nature, it was instructive in how to manage people through a difficult period. I have co-founded and worked in a small startup internet service provider, Vestnett.
I am currently working to establish an ICES Expert Group on machine learning applications in the marine sciences, to supplement my COST Action proposal. Both of these include substantial administrative work.
Communication
I am active in communicating, but mainly using social networking and other non-traditional channels. As the audience for bioinformatics, statistics, and computer programming is limited, I write about my scientific work on a personal blog.
I participate in various communities, and have contributed to the standardization of the Haskell programming language.
I entered Google's Summer of Code program, and received funding for one student in 2014. The results are published online at the Biohaskell web site, which I also manage.
In 2015, I wrote the chapter in the yearly IMR report ("Havforskingsrapporten"), detailing our results regarding development and spread of pharmaceutical resistance in salmon louse.
Participation in fisheries and aquaculture advisory activities
In many cases, my scientific work is a byproduct of directly supporting advisory activities. This year, I publish two papers based on the Norwegian Minke whale DNA Registry, an important advisory activity the IMR is obliged to maintain. The main objective of this work was to develop genetic markers for management of the minke stocks. Recently, I have used a large fraction of my time on developing similar markers for salmon, which will enable us not only to quantify the amount of genetic introgression in rivers, but if successful, also determine the impact of such introgression on genetic diversity.
As mentioned above, I have written for our internal report ("Havforskningsrapporten"), where we used the salmon louse genome to identify the genetic basis for resistance to emmamectin benzoate, and to determine the spread of resistance genes through the Atlantic.
Recently, IMR was tasked with management, not only of the marine environment and ecosystems, but also of marine scientific data. As the senior bioinformatician at IMR, I have participated in this effort from a bioinformatics perspective. I was project leader for the Norwegian Marine Genome Center, and WP-leader in BIACS, an internal project on integration of molecular data and analysis. I am often tasked with technical support, and have set up and maintain the web sites for the cod genome project and the salmon louse project. I have developed a system for scientific data management, which is both used to organize data internally and which is the basis for the salmon louse web site.
I participate in manhy projects with advisory objectives. Currently, I am working in a project using recent machine learning technology to analyze underwater video recordings. The goal is to understand fish behavior in seines, which will be crucial in reducing mortality from slipping. Another project I work in will develop automatic classification of salmon from video images. This will help us to detect and quantify escaped farmed salmon among the wild populations in rivers, a major concern for aquaculture. Previously, I have worked in a project studying the effect of seismic activity on plankton, where there was concern that oil exploration in sensitive areas could have effects on fish larvae and thus be severely detrimental for important stocks.
