Training & Outreach

As training and industry outreach coordinator at NBIS, I help shape how Swedish life scientists and industry partners learn bioinformatics, and I still teach myself.

Industry outreach

I work to make NBIS expertise and training accessible to companies and industry partners, and to build collaborations that connect academia, national infrastructure and industry.

• Opening NBIS training to industry partners
• Bringing NBIS data-analysis expertise to company questions
• Building lasting bridges between academia, infrastructure and industry

Discuss a collaboration

Timeline

2008201020122014201620182020202220242026

Knowledge-based Systems in Bioinformatics2008 · teaching assistant

LUPA Workshop: GWAS in Stratified Populations2011 · course responsible

Statistical Methods in Genetic Mapping2013 · course responsible and teacher

R Programming for Life Scientists2015–2020 · course responsible

RaukR, Advanced R Programming2018 onwards · co-organiser, Visby

13x13 public lecture, Uppsala University2025 · invited speaker

Co-advisor, PhD thesesdefences 2014, 2016, 2020

Examiner, opponent and reviewer2019–2024

Course, workshop or lectureThesis role

Training coordination

• Planning and coordinating NBIS training: courses, workshops and summer schools
• Keeping the training portfolio aligned with what researchers need in practice
• Helping researchers become confident, independent data analysts

RaukR

Since 2018, together with colleagues, I organise RaukR, the Advanced R Programming for Bioinformatics summer school held on the island of Gotland in Visby, Sweden. The course covers writing robust, efficient and reproducible R for life-science data. Course materials and information about upcoming editions are at raukr.nbis.se.

Courses and workshops

• RaukR, Advanced R Programming for Bioinformatics, Visby. Co-organiser, annually since 2018 (raukr.nbis.se).
• R for non-programmers and Advanced R for data scientists. Course leader.
• R Programming for Life Scientists, SciLifeLab course, 2015–2020. Course responsible; teacher in five editions, 2015–2017 (materials from the 2017 Uppsala edition).
• Statistical Methods in Genetic Mapping: An R-based Course, 4 ECTS graduate course, Nov–Dec 2013. Course responsible and teacher.
• LUPA Workshop: GWAS Analyses in Stratified Populations, Uppsala, May 2011. Course responsible.
• Next-Generation Sequencing: Bioinformatics and Data Analysis, PhD-level course. Course responsible.
• Boolean Reasoning, lectures and labs on random forests. Teacher.
• Knowledge-based Systems in Bioinformatics, 2008. Teaching assistant.

Talks and popular science

From mythology to artificial intelligence: a short journey through statistical models (in Swedish: Från mytologi till artificiell intelligens. En kort resa genom statistiska modeller)

Public lecture in the 13x13 series, Uppsala University, 5 November 2025, Humanistiska Teatern. The talk follows how people have tried to understand the world, from myth to modern statistical models and AI: how such models are built, how reliable they are, and what to look out for when a new AI model appears. 13x13 is a series of thirteen free lectures, organised by the Department of Physics and Astronomy, in which Uppsala researchers present their work to a general audience.

Supervision

Examiner, PhD theses

• Martin Dahlö. Approaches for Distributing Large Scale Bioinformatic Analyses. Examiner, Uppsala University, 2021.
• Andrea García-Montaner. Genome evolution of a bee-associated bacterium. Examiner, Uppsala University, 2020.

Opponent, licentiate theses

• Kristiina Ausmees. Efficient computational methods for applications in genomics. Opponent, Uppsala University, 2019.

Subject reviewer, master’s theses

• Yasemin Utkueri. Enhancing cDNA Basecalls for Non-Model Organisms Using Custom Nanopore Models: A Case Study on Krill. Subject reviewer, Uppsala University, 2024.
• Moa Qvarnlöf. The accuracy, reliability, and practicality of Convolutional Neural Networks in classifying ultrasound images for improved breast cancer diagnosis. Subject reviewer, Uppsala University, 2024.

Advisor, PhD theses

• Sharadha Sakthikumar. Characterizing the spectrum of somatic alterations in canine and human cancers. Co-advisor, defended 2020.
• Simon Forsberg. Complex Trait Genetics: Beyond Additivity. Co-advisor, defended 2016.
• Muhammad Ahsan. Identification and evaluation of functional sequences, selective sweeps and candidate mutations within QTL regions regulating growth in chicken. Co-advisor, defended 2014.

Advisor, master’s thesis

• Małgorzata Kauczyńska-Karlsson. Random Forest-based classifiers for prediction of SLE risk from SNP microarray data. Co-supervisor, defended 2006.

Research projects

• Oskar Gauffin. Analysis of time-spatial data on microbehaviour in the domestic dog, 2015–2016.
• Jagoda Jabłońska. Development and application of novel tools for enhanced genome-wide association studies; published in Bioinformatics, 2015.
• Andreas E. Lundberg. A tool for assembly and SNP detection using data from different SOLiD sequencing setups. Supervisor.
• Simon Forsberg. An R package for assessing the impact of mutations on protein function. Supervisor.
• Samuel Lampa. PTMatcher, a web-based tool for predicting post-translational modifications in proteins.