Steinn Gudmundsson
Professor in the Department of Computer Science
Research interests
Optimization in systems biology, metabolic engineering, machine learning, medical applications of pattern recognition
Teaching
2023 Analysis of algorithms (part)
2022 Introduction to Data Science (part), Formal languages and computability, Introduction to Deep Learning
2021 Machine learning, Analysis of algorithms (part)
2020 Machine learning, Software Development A, Computer Science Seminar for Undergraduates
2019 Machine learning, Discrete structures in mathematics
2018 Machine learning, Mathematics and scientific computing, Introduction to systems biology
2017 Algorithms, logic and complexity, Introduction to systems biology, Nonlinear optimization (part)
2016 Algorithms, logic and complexity, Introduction to systems biology, Formal languages and computability, Optimization in systems biology
2015 Algorithms, logic and complexity, Introduction to systems biology, Formal languages and computability
2014 Discrete structures in mathematics
2013 Software development, Discrete structures in mathematics
2012 Discrete structures in mathematics, Nonlinear optimization, Software development
2011 Discrete structures in mathematics, Nonlinear optimization, Software development, Optimization in systems biology
2010 Operations research, Reliability of systems, Engineering optimization (part)
Education
2010 PhD in Computer Science, University of Iceland
1998 MSc in Engineering, Technical University of Denmark
1996 CSc in Mechanical Engineering, University of Iceland
Publications
Ana Borovac, Thomas P Runarsson, Gardar Thorvardsson and Steinn Gudmundsson, Calibration of Automatic Seizure Detection Algorithms. IEEE Signal Processing in Medicine and Biology Symposium 2022.
(pdf)
Ana Borovac, Thomas P Runarsson, Gardar Thorvardsson, Steinn Gudmundsson. Neonatal seizure detection algorithms: The effect of channel count,
Current Directions in Biomedical Engineering 8 (2), 604-607, 2022.
(open access)
Ana Borovac, Steinn Gudmundsson, Gardar Thorvardsson, Saeed M Moghadam, Päivi Nevalainen, Nathan Stevenson, Sampsa Vanhatalo, Thomas P Runarsson.
Ensemble learning using individual neonatal data for seizure detection. IEEE Journal of Translational Engineering in Health and Medicine, 10:1-11, 2022.
(open access)
Ana Borovac, Steinn Gudmundsson, Gardar Thorvardsson, Thomas P Runarsson.
Influence of human-expert labels on a neonatal seizure detector based on a convolutional neural network. NeurIPS Data-centric AI Workshop 2021.
(open access)
Steinn Gudmundsson and Juan Nogales. Recent advances in model-assisted metabolic engineering.
Current Opinion in Systems Biology, 28:100392, 2021.
(pdf)
Sigurdur Karvelsson, Qiong Wang, Bylgja Hilmarsdottir, Arnar Sigurdsson, Siver Moestue, Gunhild Maelandsmo, Skarphedinn Halldorsson,
Steinn Gudmundsson, Ottar Rolfsson. Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer.
npj Syst Biol Appl 7, 36, 2021.
(open access)
Thordis Kristjansdottir, Gudmundur O. Hreggvidsson, Sigmar K. Stefansson, Elisabet. E. Gudmundsdottir, Snaedis H. Bjornsdottir, Olafur H. Fridjonsson, Eva N. Karlsson,
Justin Vanhalst, Birkir Reynisson, Steinn Gudmundsson.
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus,
bioRxiv 2021.
Thordis Kristjansdottir, Emanuel YC Ron, Daniel Molins-Delgado, Olafur H Fridjonsson, Charlotta Turner, Snaedis H Bjornsdottir,
Steinn Gudmundsson, Ed WJ van Niel, Eva Nordberg Karlsson, Gudmundur O Hreggvidsson.
Engineering the carotenoid biosynthetic pathway in Rhodothermus marinus for lycopene production. Metabolic Engineering Communications, 2020.
(open access)
Kjartan Palsson, Steinn Gudmundsson, Sachin Shetty. Analysis of the impact of cyber events for cyber insurance.
Geneva Papers on Risk and Insurance - Issues and Practice, 2020.
(pdf)
Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J Canalejo, Estrella Duque, Jonathan Monk, Adam M Feist, Juan Luis Ramos, Wei Niu, Bernhard O Palsson.
High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.
Environmental microbiology, 22:1 255-269, 2020.
(open access)
Freyr Johannsson, James .T. Yurkovich, Steinn Gudmundsson, Olafur. E. Sigurjonsson, Ottar. Rolfsson.
Temperature dependence of platelet metabolism. bioRxiv 2019.
Thordis Kristjansdottir, Elleke F. Bosma, Filipe Branco dos Santos, Emre Ozdemir, Markus J. Herrgaard, Lucas Franca, Bruno Sommer Ferreira,
Alex T. Nielsen, Steinn Gudmundsson.
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory.
Microbial Cell Factories, 18(186), 2019. (pdf)
Weiqi Fu, Steinn Gudmundsson, Kristine Wichuk, Sirus Palsson, Bernhard O. Palsson, Kourosh Salehi-Ashtiani, Sigurdur Brynjolfsson.
Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris.
Science of the Total Environment, 654:275–283, 2019.
(pdf, supporting material)
Kristian Jensen, Steinn Gudmundsson, Markus J. Herrgard. Enhancing Metabolic Models with Genome-Scale Experimental Data.
In: Systems Biology (N. Rajewsky, S. Jurga and J. Barciszewski eds), RNA Technologies,
Springer 2018. (pdf)
Freyr Johannsson, Steinn Gudmundsson, Giuseppe Paglia, Sveinn Gudmundsson, Bernhard Palsson, Olafur E. Sigurjonsson,
Ottar Rolfsson. Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution.
Biochemical Journal, 475:13 2225-2240, 2018.
(pdf, supporting material)
Emanuel Ron, Merichel Plaza, Thordis Kristjansdottir, Roya Sardari, Snaedis Bjornsdottir, Steinn Gudmundsson,
Gudmundur Oli Hreggvidsson, Charlotta Turner, Ed van Niel, Eva Nordberg Karlsson. Characterization of carotenoids
in Rhodothermus marinus. MicrobiologyOpen 7:1, 2018. (open access)
Konstantinos Vavitsas, Emil Ostergaard Rue, Lara Kristin Stefansdottir, Thiyagarajan Gnanasekaran, Andreas Blennow, Christoph Crocoll,
Steinn Gudmundsson and Poul Erik Jensen. Responses of Synechocystis sp. PCC 6803 to heterologous biosynthetic pathways. Microbial Cell Factories 16(1), 2017. (pdf)
Juan Nogales, Steinn Gudmundsson, Estrella Duque, Juan Luis Ramos and Bernhard O. Palsson.
Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness.
bioRxiv 2017.
Steinn Gudmundsson, Lucia Agudo and Juan Nogales. Applications of genome-scale metabolic models of microalgae
and cyanobacteria in biotechnology. In Microalgae-Based Biofuels and Bioproducts (R. Munoz and C. Gonzales eds.)
Elsevier 2017. (pdf)
Skarphedinn Halldorsson, Neha Rohatgi, Manuela Magnusdottir, Kumari Sonal Choudhary, Thorarinn Guðjónsson, Erik Knutsen, Anna Barkovskaya,
Bylgja Hilmarsdottir, Maria Perander, Gunhild M. Mælandsmo, Steinn Gudmundsson and Óttar Rolfsson.
Metabolic re-wiring of isogenic breast epithelial cell lines following epithelial to mesenchymal transition.
Cancer letters 396(28):117-129, 2017.
Ottar Rolfsson, Ólafur E Sigurjonsson, Manuela Magnusdottir, Freyr Johannsson, Giuseppe Paglia, Steinn Gudmundsson, Aarash Bordbar, Sirus Palsson, Sigurdur Brynjólfsson, Sveinn Gudmundsson and Bernhard Palsson.
Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism.
Vox Sanguinis 112(4):326-335, 2017.
Kumari Sonal Choudhary, Neha Rohatgi, Skarphedinn Halldorsson, Eirikur Briem, Thorarinn Gudjonsson, Steinn Gudmundsson and Ottar Rolfsson.
EGFR signal-network reconstruction demonstrates metabolic crosstalk in EMT. PLoS Comput Biol 12(6), 2016.
(open access)
Neha Rohatgi, Steinn Gudmundsson, Ottar Rolfsson. Kinetic analysis of gluconate phosphorylation by human gluconokinase
using isothermal titration calorimetry.
FEBS Letters 589(23):3548–3555, 2015. (pdf)
Tommaso Pacini, Weiqi Fu, Steinn Gudmundsson, Antonio Eugenio Chiaravalle, Sigurdur Brynjolfson, Bernhard Palsson,
Giuseppe Astarita and Giuseppe Paglia. Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS
for the screening of natural pigments.
Analytical Chemistry, 87(5), 2015. (pdf)
Steinn Gudmundsson, Juan Nogales. Cyanobacteria as photosynthetic biocatalysts: A systems biology perspective.
Molecular BioSystems, 11:60-70, 2015. (pdf)
Weiqi Fu, Giuseppe Paglia, Manuela Magnusdottir, Elin A Steinarsdottir, Steinn Gudmundsson, Bernhard O Palsson,
Olafur S Andresson and Sigurdur Brynjolfsson. Effects of abiotic stressors on lutein production in the green
microalga Dunaliella salina. Microbial Cell Factories 13(3), 2014 (pdf)
Juan Nogales, Steinn Gudmundsson, Ines Thiele. Toward systems metabolic engineering in cyanobacteria: Opportunities and bottlenecks.
Bioengineered, 4(3), 2013 (open access)
Juan Nogales, Steinn Gudmundsson, Ines Thiele. An in silico re-design of the metabolism in Thermotoga maritima for increased
biohydrogen production. Int J Hydrogen Energ, 37(17):12205-12218, 2012. (pdf, supporting material)
Juan Nogales, Steinn Gudmundsson, Eric M. Knight, Bernhard O. Palsson and Ines Thiele.
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.
PNAS January 30, 2012. (open access,
version 1.1)
Steinn Gudmundsson, Thomas Philip Runarsson, Sven Sigurdsson. Test-retest reliability and feature selection in physiological time series classification.
Computer Methods and Programs in Biomedicine, 105(1):50-60, 2012 (pdf)
Steinn Gudmundsson, Ines Thiele. Computationally efficient flux variability analysis. BMC Bioinformatics 2010, 11:489.
(pdf, code)
Steinn Gudmundsson, Gudny Lilja Oddsdottir, Tomas Philip Runarsson, Sven Sigurdsson, Eythor Kristjansson.
Detecting fraudulent whiplash claims by support vector machines.
Biomedical Signal Processing and Control, 5(4):311-371, 2010 (pdf)
J. Snaedal, G.H. Johannesson, Th.E. Gudmundsson, S. Gudmundsson, T.H. Pajdak, K. Johnsen.
The use of EEG in Alzheimer's disease, with and without scopolamine - a pilot study.
Clin Neurophysiol. 121(6):836-41, 2010 (pubmed)
Steinn Gudmundsson, Thomas Philip Runarsson, Sven Sigurdsson.
Support vector machines and dynamic time warping for time series. IEEE
International Joint Conference on Neural Networks, 2008 (pdf)
Steinn Gudmundsson, Thomas Philip Runarsson, Sven Sigurdsson, Gudrun
Eiriksdottir and Kristinn Johnsen. Reliability of quantitative EEG features.
Clinical Neurophysiology, 118(10):2162-2171, 2007 (pdf)
Steinn Gudmundsson, Thomas Philip Runarsson and Sven Sigurdsson, Automatic
Sleep Staging using Support Vector Machines with Posterior Probability
Estimates. Proceedings of 2005 International Conference on Computational
Intelligence for Modelling, Control and Automation, Volume 2, 28-30 Nov. pp.
366-372, 2005 (pdf)