My research interests span a wide range of topics around the intersection of biology and computational science. Broadly speaking, my research has been a mixture of coarse-grained and detailed modeling, often involving gene regulatory networks, and development of algorithms and open source software.  

Since the beginning of my research career, I have worked with Boolean gene regulatory network models, the HP model of protein folding, stem cell regulation, circadian clocks in plants, plant-pathogen interactions, evolutionary algorithms, degradation of soil organic matter by fungi and methods for processing spectroscopic imaging data. Most of this research has been cross-disciplinary in nature, and I have participated in two interdisciplinary themes: bio-inspired energy conversion and synthetic biology.  

The building blocks of my research are things like ODE systems, graph algorithms, parameter optimization and more recently also iterative data processing algorithms and machine learning. My current work is focused on software and algorithms for vibrational spectroscopy imaging in the OCTAVVS project, and as well as biological and medical applications. 

As an applications expert at CIPA, the Correlative Image Processing and Analysis software infrastructure at LU, I provide researchers with services within my field of expertise, in particular regarding 2D spectroscopic data processing. Feel free to contact me about developing, combining and visualizing steps such as data loading, pre-processing, dimensionality reduction and AI classification. 

A few relevant links

For a more useful overview of my publications, see my publication list on Google Scholar.

I currently teach on two courses:

• BERN05/EXTQ01 Theoretical biophysics (in Canvas)
• BERN06 Systems biology (in Canvas)

Selected software projects:

• OCTAVVS – preprocessing and analysis of vibrational spectroscopy data.
• BASE – BioArray Software Environment: Microarray data and analysis platform.

Group members and students, present and past

• Syahril Siregar, Postdoc 2018–2020 
• Adriaan Merlevede, PhD student 2015–2020 
• Tomas Martin-Bertelsen, Postdoc 2014–2019 
• Karl Fogelmark, PhD student 2011–2016
• Ruijue ‘Jerry’ Huang, MSc project 2023
• Sofia Andersson, MSc project 2022 
• Dejan Stančević, BSc project 2021–2022 
• Eric Kull, BSc project 2018–2019 
• Stephan Pissot, MSc project 2019–2020
• Sebastian Hutteri, BSc project 2018–2019
• Henrik Åhl, Summer/BSc projects 2015–2016 

Brief CV 

• 2001 MSc, Physics, Lund University. 
• 2007 PhD, Theoretical physics, Lund University.
• 2007 Postdoc, Millar lab, School of Biological Sciences, University of Edinburgh.
• 2008–2010 HFPS Cross-Disciplinary Fellowship at University of Edinburgh.
• 2010–2011 Postdoc, CBBP, Astronomy and Theoretical Physics, Lund University.
• 2011–2015 Postdoctoral Research Fellow, CBBP, Astronomy and Theoretical Physics, Lund University.
• 2015–2022 Researcher, CBBP, Astronomy and Theoretical Physics, Lund University.
• 2022 Associate professor, Theoretical Physics specialising in Computational Biology, Lund University.
• 2023– Researcher, CBBP, Centre for Environmental and Climate Science, Lund University.