Mathematical modeling in precision nutrition

V. Skantze, PhD thesis. Chalmers University of Technology, 23 January 2024. Supervisors: M. Jirstrand, R. Landberg; co-supervisors: M. Wallman, C. Brunius.

Analysis and Prediction of Postprandial Metabolic Response to Multiple Dietary Challenges Using Dynamic Mode Decomposition

V. Skantze, M. Jirstrand, C, Brunius, A-S. Sandberg, R. Landberg, M. Wallman. MDPI, Proceedings of The 14th European Nutrition Conference FENS 2023, 91(1), 38, Belgrade, Serbia, 14–17 November 2023.

Analysis and prediction of postprandial metabolic response to multiple dietary challenges using dynamic mode decomposition

V. Skantze, M. Jirstrand, C. Brunius, A-S. Sandberg, R. Landberg, M. Wallman. 3rd Nordic Metabolomics Conference, Poster P40, p. 75. Trondheim, Norway, 18-20 October 2023.

Differential Responders to a Mixed Meal Tolerance Test Associated with Type 2 Diabetes Risk Factors and Gut Microbiota—Data from the MEDGI-Carb Randomized Controlled Trial

V. Skantze, T. Hjorth, M. Wallman, C. Brunius, J. Dicksved, E. A. Pelve, A. Esberg, M. Vitale, R. Giacco, G. Costabile, R. E. Bergia, M. Jirstrand, W. W. Campbell, G. Riccardi, R. Landberg. Nutrients. 2023; 15(20):4369. 15 October 2023.

Plasma Pharmacokinetics of N-Acetylgalactosamine-Conjugated Small-Interfering Ribonucleic Acids (GalNAc-Conjugated siRNAs)

S. Sten, T. Cardilin, M. Antonsson, P. Gennemark. Clinical Pharmacokinetics (2023), 12 October 2023.

ECG-based Assessment and Therapeutic Implications of AV Nodal Conduction Dynamics During Atrial Fibrillation

M. Karlsson, M. Wallman, P. G. Platonov, S. R. Ulimoen, F. Sandberg. Computing in Cardiology (Cinc 2023), Atlanta, USA, 1-4 October 2023.

Effects from large-scale employment of model-predictive control in district heating substations

H. Håkansson, M. Önnheim, E. Gustavsson, M. Jirstrand. Kaiserslautern Applied and Industrial Mathematics Days (KLAIM2023), 25 - 27 September 2023, Abstract No. A20, p.33.

Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens

D. Lund, R. Dirk Coertze, M. Parras-Moltó, F. Berglund, C-F. Flach, A. Johnning, D.G.J. Larsson, E Kristiansson. Communications Biology, 6(1), 812. 3 August 2023.

Model-based Prediction of Progression-Free Survival for Combination Therapies in Oncology

M. Baaz, T. Cardilin, M. Jirstrand. 31st PAGE Meeting, A Coruña, Spain, 27-30 June 2023.

Model-based Prediction of Progression-Free Survival for Combination Therapies in Oncology

M. Baaz, T. Cardlin, M. Jistrand. CPT Pharmacometrics Systems Pharmacology, 10 June 2023.

Replenishing the pipeline: A quantitative approach to optimising the sourcing of new projects

S. J. Wiklund, M. Önnheim, M. Ytterstad. Pharmaceutical Statistics, The Journal of Applied Statistics in the Pharmaceutical Industry. 1 June 2023.

Model-Based Assessment of Combination Therapies – Ranking of Radiosensitizing Agents in Oncology

M. Baaz, T. Cardilin, F. Lignet, A. Zimmermann, S. El Bawab, J. Gabrielsson, M. Jirstrand. BMC Cancer 23, 409 (2023). 6 May 2023.

Model Predictive Control when utilizing LSTM as dynamic models

M. Jung, P. Renato da Costa Mendes, M. Önnheim, E. Gustavsson. Engineering Applications of Artificial Intelligence, Vol. 123, Part B, August 2023, 106226. Online 26 April, 2023.

Outbreak of OXA-48-producing Enterobacteriaceae in a neonatal intensive care unit in Western Sweden

E. T. Hallbäck, A. Johnning, S. Myhrman, M. Studahl, E. Hentz, A. Elfvin, I. Adlerberth, European Journal of Clinical Microbiology & Infectious Diseases, 1-9. 20 March 2023.

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

J. S. Inda-Díaz, D. Lund, M. Parras-Moltó, A. Johnning, J. Bengtsson-Palme, E. Kristiansson. Microbiome, 11(1), 44. 8 March 2023.

Strain-level bacterial typing directly from patient samples using optical DNA mapping

M. Nyblom, A. Johnning, K. Frykholm, M. Wrande, V. Müller, G. Goyal, M. Robertsson, A. Dvirnas, T. Sewunet, S. KK, T. Ambjörnsson, C. G. Giske, L. Sandgren, E. Kristiansson, F. Westerlund. Communications Medicine, 3(1), 31. February 23, 2023

Utilization of convolutional neural networks for H I source finding – Team FORSKA-Sweden approach to SKA Data Challenge 2

H. Håkansson, A. Sjöberg, M. C. Toribio, M. Önnheim, M. Olberg, E. Gustavsson, M. Lindqvist, M. Jirstrand, J. Conway. Astronomy & Astrophysics, Vol 671, March 2023, A39.

Accessing Liver Carcinoma in Pharmacokinetic Profiles of Magnetic Nanoparticles Through a Simple Mathematical Model

D.S. Rodrigues, G.A. Soares, V.A. González-López, A.T. Bezerra, M. Jirstrand, J.R.A. Miranda. In proceedings of the 14th conference on Dynamical Systems Applied to Biology and Natural Sciences (DSABNS23), 5-8 February 2023, Bilbao, Spain.

Antibiotic susceptibility prediction using transformers

J. Inda-Diaz, A. Johnning, A. Sjöberg, A. Lokrantz, M. Jirstrand, M. Hessel, L. Helldal, L. Svensson, E. Kristiansson. Pacific Symposium on Biocomputing (PSB) 2023, January 3-7, Hawaii, USA.

Identification of metabotypes in complex biological data using tensor decomposition

V. Skantze, M. Wallman, A-S. Sandberg, R. Landberg, M. Jirstrand, C. Brunius. Chemometrics and Intelligent Laboratory Systems, December 18 2022.

Model-based Analysis of Temporal Patterns in Atrioventricular Node Conduction during Atrial Fibrillation

M. Karlsson, Licentiate thesis, Lund University, 16 December 2022. Supervisor: F. Sandberg; Co-supervisor: M. Wallman

Online geometry assurance in individualized production by feedback control and model calibration of digital twins

A. Sjöberg, M. Önnheim, O. Frost, C. Cronrath, E. Gustavsson, B. Lennartson, M. Jirstrand. Journal of Manufacturing Systems, 66:71-81, Online December 10, 2022

Drug Dependent Circadian Variations in AV-nodal Properties During Atrial Fibrillation

M. Karlsson, M. Wallman, P. G. Platonov, S. R. Ulimoen, F. Sandberg. Computing in Cardiology. Pre-print.

ECG based assessment of circadian variation in AV-nodal conduction during AF—Influence of rate control drugs

M. Karlsson, M. Wallman, P. G. Platonov, S. R. Ulimoen, F. Sandberg. Frontiers in Physiology, October 4 2022.

An atrioventricular node model incorporating autonomic tone

F. Plappert, M. Wallman, M. Abdollahpur, P. G. Platonov, S. Östenson, F. Sandberg. Frontiers in Physiology 2022, 13. Online 15 September 2022.

Model predictive control for heating systems when using demand tariffs

H. Håkansson, M. Önnheim, E. Gustavsson, M. Jirstrand. Smart Energy Systems 2022, Aalborg. September 13-14 2022.

Tilt-Induced Changes in RR Series Characteristics: An AV Node Simulation Study

F. Plappert, M. Wallman, P. Platonov, S. Östenson, F. Sandberg. 2022 Computing in Cardiology (CinC), 4-7 September 2022, Tampere, Finland.

Optimizing study design in LPS challenge studies for quantifying drug induced inhibition of TNFα response: Did we miss the prime time?

J. Larsson, E. Hoppe, M. Gautrois, M. Cvijovic, M. Jirstrand. European Journal of Pharmaceutical Sciences, Vol 176, September 1, 2022, 106256.

Optimized scaling of translational factors in oncology: from xenografts to RECIST

M. Baaz, T. Cardilin, F. Lignet, M. Jirstrand. Cancer Chemotherapy and Pharmacology 90, 239-150. August 3 2022.

Utilization of Convolutional Neural Networks for H I Source Finding: Team FORSKA-Sweden approach to SKA Data Challenge 2

H. Håkansson, A. Sjöberg, M. C. Toribio, M. Önnheim, M. Olberg, E. Gustavsson, M. Lindqvist, M. Jirstrand, J. Conway. European Astronomical Society Annual Meeting 2022. Valencia, Spain, 27 June-1 July, 2022.

Identifying Metabotypes from Tensor Data

V. Skantze, M. Wallman, A. Sandberg, R. Landberg, M. Jirstrand, C. Brunius. 18 th International Conference of the Metabolomics Society in Valencia, Spain, June 19-23, 2022.

Joint modeling of Longitudinal and Time-To-Event data – A Comparison of Joint versus Sequential Parameter Estimation

S. Axillus. Master thesis, Chalmers University of Technology, 14 June 2022. Supervisor: T. Cardilin.

Population Analysis of Toxicological Combination Effects

M. Baaz, T. Cardilin, T. Lundh, M. Jirstrand. In Proceedings of The 21st International Symposium on Pollutant Responses In Marine Organisms, PRIMO21, May 22-25 2022, Gothenburg, Sweden.

An integrative pharmacokinetic-cardiovascular physiology modelling approach based on in vivo dog studies including five reference compounds

M. Wallman, J. M. Borghardt, E. Martel, N. Pairet, M. Markert, M. Jirstrand. Journal of Pharmacological and Toxicological Methods, Vol. 115, May-June 2022.

Exposure-response modeling improves selection of radiation and radiosensitizer combinations

T. Cardilin, J. Almquist, M. Jirstrand, A. Zimmermann, F. Lignet, S. El Bawab, J. Gabrielsson. Journal of Pharmacokinetics and Pharmacodynamics 49(2):167-178. April 2022.

Nonlinear Mixed Effects Modeling of Combination Therapies in Oncology

M. Baaz. Licentiate thesis, Chalmers University of Technology, 10 March 2022. Supervisors: M. Jirstrand, T. Cardilin, T. Lundh

Sparse Inversion of Stacked Autoencoder Classification Machines

A. Sarishvili, M. Jirstrand, B. Adrian, A. Wirsen. In proceedings of 7th International Congress on Information and Communication Technology (ICICT 2022), London, UK, 21-24 February, 2022.

A stochastic mixed effects model to assess treatment effects and fluctuations in home-measured peak expiratory flow and the association with exacerbation risk in asthma

J. Leander, M. Jirstrand, U. G. Eriksson, R. Palmér. CPT: Pharmacometrics & Systems Pharmacology, 11(2):212-224. February 2022

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes

D. Lund, N. Kieffer, M. Parras-Moltó, S. Ebmeyer, F. Berglund, A. Johnning, D. G. J. Larsson, E. Kristiansson. Microbial Genomics 8.1: 000770, 27 January 2022.

Changes in RR Series Characteristics During Atrial Fibrillation: An AV Node Simulation Study

F. Plappert, M. Wallman, P. Platonov, F. Sandberg. IEEE Xplore, 2021 Computing in Cardiology (CinC), 10 January 2022.

Combining dense and sparse labeling in optical DNA mapping

E. Torstensson, G. Goyal, A. Johnning, F. Westerlund & T. Ambjörnsson. PLOS ONE, 16(11), 29 November 2021

Plastic Extrusion Process Optimization by Digital Twins

A. Sarishvili, D. Just, K. Moser, A. Wirsen, J. Diemert, M. Jirstrand. Chemie Ingenieur Technik, 10 November 2021.

Stochastic mixed effects modeling of home-measured peak expiratory flow and the association to exacerbation risk in asthma

J. Leander, M. Jirstrand, U.G. Eriksson, R. Palmér. In proceedings of The 12th American Conference of Pharmacometrics (ACoP12) 8-12 November 2021, Virtual.

Non-invasive Characterization of Human AV-Nodal Conduction Delay and Refractory Period During Atrial Fibrillation

M. Karlsson, F. Sandberg, S. R. Ulimoen, M. Wallman. Frontiers in Physiology 28 October 2021.

NLMEModeling: Nonlinear Mixed Effects Modeling of Dynamical Systems

M. Jirstrand. Wolfram Virtual Technology Conference 2021 (WVTC2021), 12-15 October, 2021.

Online and Offline Calibration of Digital Twins in the Smart Assembly 4.0 Framework

A. Sjöberg, M. Önnheim, O. Frost, C. Cronrath, E. Gustavsson, B. Lennartsson, and M. Jirstrand. In Proceedings of Kaiserslautern Applied and Industrial Mathematics Days (KLAIM2021), Abstract No. A39, p.54-55. 11-13 October, 2021.

Exposure-response modeling improves selection of radiation and radiosensitizer combinations

T. Cardilin, J. Almquist, M. Jirstrand, A. Zimmermann, F. Lignet, S. El Bawab, J. Gabrielsson. Journal of Pharmacokinetics and Pharmacodynamics, 8 October 2021

Mixed Effects Modelling and Optimal Design of TNFα Response in LPS Challenge Studies – Methods and Applications in Drug Discovery

J. Larsson, Licentiate thesis, Chalmers University of Technology, 20 September 2021. Supervisors: M. Jirstrand, M. Cvijovic.

Nonlinear Mixed Effects Modeling of Deterministic and Stochastic Dynamical Systems in Wolfram Mathematica

J. Leander, J. Almquist, A. Johnning, J. Larsson, M. Jirstrand. IFAC-PapersOnLine Vol. 54, Issue 7, 2021, Pages 409-414. Online 15 September, 2021.

Non-Invasive Characterization of Atrio-Ventricular Properties During Atrial Fibrillation

M. Karlsson, M. Wallman, S. R. Ulimoen, F. Sandberg. CINC2021, Brno, Czech Republic, 12-15 September 2021.

Evaluation and Optimization of Model-based Translations in Oncology – From Xenografts to RECIST

M. Baaz, T. Cardilin, F, Lignet, M. Jirstrand. Drug/Disease Modelling - Oncology, PAGE 29 (2021) Abstr 9754, 2-7 September 2021.

A second-generation challenge model of TNFa turnover with LPS provocations and drug intervention

J. Larsson, E. Hoppe, M. Gautrois, M. Cvijovic, M. Jirstrand. PAGE 29 (2021): Drug/Disease Modelling - Other Topics, Abstr 9593, 2-7 September 2021.

Artificial Intelligence for Hospital Health Care: Application Cases and Answers to Challenges in European Hospitals

M. Klumpp, M. Hintze, M. Immonen, F. Ródenas-Rigla, F. Pilati, F. Aparicio-Martínez, D. Çelebi, T. Liebig, M. Jirstrand, O. Urbann, M. Hedman, JA. Lipponen, S. Bicciato, A-P. Radan, B. Valdivieso, W. Thronicke, D. Gunopulos, R. Delgado-Gonzalo. Healthcare. 2021; 9(8):961, 29 July 2021.

Nonlinear Mixed Effects Modeling of Deterministic and Stochastic Dynamical Systems in Wolfram Mathematica

J. Leander, J. Almquist, A. Johnning, J. Larsson, M. Jirstrand. In Proceedings of the 16th IFAC Symposium on System Identification (SYSID 2021), 14 July 2021.

Second-generation TNFα turnover model for improved analysis of test compound interventions in LPS challenge studies

J. Larsson, E. Hoppe, M. Gautrois, M. Cvijovic, M. Jirstrand. European Journal of Pharmaceutical Sciences, Vol. 165, 1 October 2021, 105937. Online 11 July 2021.

Mathematical Model Predicts that Acceleration of Diabetic Wound Healing is Dependent on Spatial Distribution of VEGF-A mRNA (AZD8601)

S.M. Rikard, P.J. Myers, J. Almquist, P. Gennemark, A.C. Bruce, M. Wågberg, R. Fritsche-Danielson, K.M. Hansson, M.J. Lazzara, and S.M. Peirce. Cellular and Molecular Bioengineering, 15 June 2021.

Identification of Robust Metabotypes Associated With Increased Cardiometabolic Disease Risk- an Approach for Improved Prevention Through Precision Nutrition

M. Palmnäs-Bédard, V. Skantze, A. Rastgaard-Hansen, J. Dicksved, J. Halkjaer, A. Tjønneland, C. Brunius, R. Landberg. Current Developments in Nutrition 5 (Supplement_2):604-604, 7 June 2021.

Identifying Metabotypes From Complex Biological Data Using PARAFAC

V. Skantze, M. Wallman, A-S. Sandberg, R. Landberg, M. Jirstrand, C. Brunius. Current Developments in Nutrition 5 (Supplement_2):882-882, 7 June 2021.

Mixed Effects Modeling of Deterministic and Stochastic Dynamical Systems – Methods and Applications in Drug Development

J. Leander, PhD thesis, Chalmers University of Technology, 4 June 2021. Supervisors: M. Jirstrand, M. Cvijovic.

Optimization of additive chemotherapy combinations for an in vitro cell cycle model with constant drug exposures

T. Cardilin, T. Lundh, M. Jirstrand. Mathematical Biosciences, 108595. Online 5 April 2021.

Natural language processing methods for knowledge management – Applying document clustering for fast search and grouping of engineering documents

I.Ö. Arnarsson, O. Frost, E. Gustavsson, M. Jirstrand, J. Malmqvist. Concurrent Engineering, 6 March 2021.

An Integrative Approach for Improved Assessment of Cardiovascular Safety Data

M. Wallman, S. Scheuerer, E. Martel, N. Pairet, M. Jirstrand, J. Gabrielsson. Journal of Pharmacology and Experimental Therapeutics, JPET-AR-2020-000348. 1 March 2021.

OODIDA: On-Board/Off-Board Distributed Real-Time Data Analytics for Connected Vehicles

G. Ulm, S. Smith, A. Nilsson, E. Gustavsson, M. Jirstrand. Data Science and Engineering Vol. 6, pages102–117(2021). 22 January 2021.

Facilitating Rapid Prototyping in the Distributed Data Analytics Platform OODIDA via Active-Code Replacement

G. Ulm, S. Smith, A. Nilsson, E. Gustavsson, M. Jirstrand. Array, Vol. 8, December 2020, 100043.

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes

F. Berglund, M-E. Böhm, A. Martinsson, S. Ebmeyer, T. Österlund, A. Johnning, D.G.J. Larsson, E. Kristiansson. Microbial Genomics 6.11: e000455 , 30 October 2020

An updated phylogeny of the metallo-β-lactamases

F. Berglund, A. Johnning, D. G-J. Larsson, E. Kristiansson. Journal of Antimicrobial Chemotherapy, dkaa392, 2 October 2020

Multi-objective constrained Bayesian optimization for structural design

A. Mathern, O. Skogby Steinholtz, A. Sjöberg, M. Önnheim, K. Ek, R. Rempling, E. Gustavsson, M. Jirstrand. Structural and Multidisciplinary Optimization, 24 September 2020.

S-RASTER: contraction clustering for evolving data streams

G. Ulm, S. Smith, A. Nilsson, E. Gustavsson, M. Jirstrand. Journal of Big Data Vol. 7, Article number: 62, 13 August 2020.

Training Multi-Tasking Neural Networks using ADMM: Analyzing Autoencoder-Based Semi-Supervised Learning

H. Håkansson. Master thesis, Chalmers University of Technology, 10 June 2020. Supervisors: E. Gustavsson, M. Önnheim, A. Sjöberg

Modeling of Combination Therapy to Support Drug Discovery in Oncology

T. Cardilin, PhD thesis, Chalmers University of Technology, 4 June 2020. Supervisors: M. Jirstrand, T. Lundh, J. Gabrielsson.

Active-Code Replacement in the OODIDA Data Analytics Platform

G. Ulm, E. Gustavsson, M. Jirstrand, "Euro-Par 2019: Parallel Processing Workshops", LNCS 11997, pp. 715-719. 29 May 2020.

Model‐based analysis reveals a sustained and dose‐dependent acceleration of wound healing by VEGF‐A mRNA (AZD8601)

J. Almquist, M. Rikard, M. Wågberg, A. C. Bruce, P. Gennemark et al. CPT: Pharmacometrics & Systems Pharmacology (PSP), 21 May 2020.

Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

V. Müller, M. Nyblom, A. Johnning, M. Wrande, A. Dvirnas, S. KK, C. G. Giske, T. Ambjörnsson, L. Sandegren, E. Kristiansson, F. Westerlund. ACS Infectious Diseases 2020, 6, 5, 1076–1084, 15 April 2020.

Modeling industrial engineering change processes using the design structure matrix for sequence analysis: a comparison of multiple projects

Í Arnarsson, E. Gustavsson, M. Jirstrand, J. Malmqvist. Design Science, 6, E6, 16 March 2020.

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping

R. Karlsson, A. Thorsell, M. Gomila, F. Salvà-Serra, H. E. Jakobsson, L. Gonzales-Siles, D. Jaén-Luchoro, S. Skovbjerg, J. Fuchs, A. Karlsson, F. Boulund, A. Johnning, E. Kristiansson, E. R.B. Moore. Molecular & Cellular Proteomics, Vol. 19, Issue 3, P518-528. 1 March 2020.

The tumor static exposure (TSE) concept & utility: Application to combination treatment of radiation and radiosensitizing agent in tumor xenograft experiments

S. El Bawab, T. Cardilin, M. Jirstrand, A. Zimmermann, F. Lignet, J. Gabrielsson. In proceedings of the 44th Congress of the European-Society-for-Medical-Oncology (ESMO), Barcelona, Spain, September 2019.

On Chow-Liu Forest Based Regularization of Deep Belief Networks

A. Sarishvili, A. Wirsen, M. Jirstrand. In Proceedings of the 28th International Conference on Artificial Neural Networks 2019, Munich, Germany, 17-19 September, 2019.

Architecture-aware Bayesian Optimization for Neural Network Tuning

A. Sjöberg, M. Önnheim, E. Gustavsson, M. Jirstrand. In Proceedings of the 28th International Conference on Artificial Neural Networks 2019, Munich, Germany, 17-19 September, 2019.

Reinforcement Learning informed by optimal control

M. Önnheim, P. Andersson, E. Gustavsson, M. Jirstrand. In Proceedings of the 28th International Conference on Artificial Neural Networks 2019, Munich, Germany, 17-19 September, 2019.

Federated Learning of Deep Neural Decision Forests

A. Sjöberg, E. Gustavsson, A. C. Koppisetty, M. Jirstrand. In Proceedings of the Fifth International Conference on Machine Learning, Optimization, and Data Science 2019, Siena, Italy, 10-13 September, 2019.

Active-Code Replacement in the OODIDA Data Analytics Platform

G. Ulm, E. Gustavsson, M. Jirstrand. The 25th International Conference on Parallel and Distributed Computing (Euro-Par 2019), University of Göttingen, Göttingen, Germany, 26-30 August, 2019.

Supporting Knowledge Re-Use with Effective Searches of Related Engineering Documents – A Comparison of Search Engine and Natural Language Processing-Based Algorithms

Í. Ö. Arnarsson, O. Frost, E. Gustavsson; D. Stenholm, M. Jirstrand, J. Malmqvist. In proceedings of the 22nd International Conference on Engineering Design (ICED2019), Delft, The Netherlands, 5-8 August 2019.

Tumor Static Exposure for anticancer combinations in early drug discovery

T. Cardilin, M. Jirstrand, F. Lignet, S. El Bawab, J. Gabrielsson. In proceedings of the 28th PAGE meeting, Stockholm,Sweden , 11-14 June, 2019.

A challenge model of TNFα turnover with LPS provocations and drug intervention

F. Held, E. Hoppe, M. Cvijovic, M. Jirstrand, J. Gabrielsson. In proceedings of the 28th PAGE meeting, Stockholm,Sweden, 11-14 June, 2019.

Parameter Estimation for Nonlinear Mixed Effects Models Implemented in Mathematica

J. Leander, J. Almquist, H. K. Ólafsdóttir, A. Johnning, M. Jirstrand. Workshop on Modelling in Biology and Medicine, Gothenburg, Sweden, 9-10 May 2019.

Modeling long-term tumor growth and kill after combinations of radiation and radiosensitizing agents

T. Cardilin, J. Almquist, M. Jirstrand, A. Zimmermann, F. Lignet, S. El Bawab, J. Gabrielsson. Cancer Chemotherapy and Pharmacology, Vol. 83, Issue 6, pp 1159–1173. June 2019.

Functional Federated Learning in Erlang (ffl-erl)

G. Ulm, E. Gustavsson, M. Jirstrand. Silva J. (eds) Functional and Constraint Logic Programming. WFLP 2018. Lecture Notes in Computer Science, vol 11285. Springer, Cham. Online 16 March, 2019.

Challenge model of TNFα turnover at varying LPS and drug provocations

F. Held, E. Hoppe, M. Cvijovic, M. Jirstrand, J. Gabrielsson. J Pharmacokinet Pharmacodyn, P 1-18. 18 February 2019.

Modelling of oscillatory cortisol response in horses using a Bayesian population approach for evaluation of dexamethasone suppression test protocols

F. Held, C. Ekstrand, M. Cvijovic, J. Gabrielsson, M. Jirstrand. J Pharmacokinet Pharmacodyn. 23 January, 2019.

Dose-Response-Time Data Analysis: An Underexploited Trinity

J. Gabrielsson, R. Andersson, M. Jirstrand, S. Hjorth. Pharmacol Rev. 2019 Jan;71(1):89-122.

Modelling of drug-effect on time-varying biomarkers

F. Held. Licentiate thesis, Chalmers University of Technology, 23 November 2018. Supervisors: M. Jirstrand, J. Gabrielsson, M. Cvijovic ,E. Hoppe.

Challenging the dose-response-time data approach: Analysis of a complex system

R. Andersson, M. Jirstrand, J. Almquist, J. Gabrielsson. Eur J Pharm Sci. 2019 Feb 1;128:250-269. Online 17 November, 2018.

A Performance Evaluation of Federated Learning Algorithms

A. Nilsson, S. Smith, G. Ulm, E. Gustavsson, M. Jirstrand. The 2nd Workshop on Distributed Infrastructures for Deep Learning (DIDL 2018). Rennes, France. 10 December, 2018

BAgger: A Bayesian Algorithm for Safe and Query-efficient Imitation Learning

C. Cronrath, E. Jorge, J. Moberg, M. Jirstrand, B. Lennartson. IROS 2018 Workshop on Machine Learning in Robot Motion Planning October 5, 2018, Madrid, Spain.

Functional Federated Learning in Erlang (ffl-erl)

G. Ulm, E. Gustavsson, M. Jirstrand. The 26th International Workshop on Functional and Logic Programming (WFLP 2018), Frankfurt am Main, Germany, 6 September 2018.

Evaluation and translation of combination therapies in oncology

T. Cardilin, J. Almquist, M. Jirstrand, J. Gabrielsson. European Journal of Pharmacology, Vol. 834, 5 September 2018, p 327-336.

Exact Gradients Improve Parameter Estimation in Nonlinear Mixed Effects Models with Stochastic Dynamics

H. K. Olafsdottir, J. Leander, J. Almquist, M. Jirstrand. AAPS J (2018) 20: 88. Online 1 August, 2018.

A Comparative Study of Black-box Optimization Algorithms for Tuning of Hyper-Parameters in Deep Neural Networks

O. Skogby Steinholtz and J. Söderström. Master thesis, Chalmers University of Technology, May 2018.

Evaluating the Performance of Federated Learning: A Case Study of Distributed Machine Learning with Erlang

A. Nilsson and S. Smith. Master thesis, Chalmers University of Technology, May 2018.

Investigation of sparse clinical sampling in light of baseline oscillations and between-individual variability using pharmacokinetic/pharmacodynamic modelling

F. Held, C. Ekstrand, J. Gabrielsson, M. Jirstrand. 14th International Congress of the European Association for Veterinary Pharmacology and Toxicology (EAVPT), Wroclaw, Poland, 24-27 June 2018.

Root Cause Analysis of Failures and Quality Deviations in Manufacturing Using Machine Learning

A. Lokrantz, E. Gustavsson, M. Jirstrand. In proceedings of the 51st CIRP Conference on Manufacturing Systems, Stockholm, Sweden, 16-18 May 2018.

Analysis of engineering change requests using Markov Chains

Í. Ö. Arnarsson, E. Gustavsson, J. Malmqvist, M. Jirstrand. DS 92: Proceedings of the DESIGN 2018 15th International Design Conference, p. 523-532. Dubrovnik, Croatia, 21-24 May, 2018.

Reinforcement learning in real-time geometry assurance

E. Jorge, L. Brynte, C. Cronrath, O. Wigström, K. Bengtsson, E. Gustavsson, B. Lennartson, M. Jirstrand. In proceedings of the 51st CIRP Conference on Manufacturing Systems, Stockholm, Sweden, 16-18 May 2018.

Modeling of radiation therapy and radiosensitizing agents in tumor xenografts

T. Cardilin, J. Almquist, M. Jirstrand, F. Lignet, A. Zimmermann, S. El Bawab, J. Gabrielsson. PAGE 27 (2018) Abstr 8654. Montreux, Switzerland, May 2018.

Kinetic Models in Life Science — Contributions to Methods and Applications

J. Almquist, PhD thesis, Chalmers University of Technology, supervisors M. Jirstrand, J. Nielsen, 15 December 2017.

Model-based Evaluation of Radiation and Radiosensitizing Agents in Oncology

T. Cardilin, J. Almquist, M. Jirstrand, A. Zimmermann, S. El Bawab, J. Gabrielsson. CPT: Pharmacometrics & Systems Pharmacology, November 2017.

Overexpressing Cell Systems are a Competitive Option to Primary Adipocytes when Predicting In Vivo Potency of Dual GPR81/GPR109A Agonists

J. Almquist, D. Hovdal, C. Ahlström, O. Fjellström, P. Gennemark, M. Sundqvist. European Journal of Pharmaceutical Sciences, Available online 24 November 2017.

Functional Federated Learning in Erlang

G. Ulm, E. Gustavsson, M. Jirstrand. The 5th Swedish Workshop on Data Science (SweDS 2017), December 12-13, 2017, University of Gothenburg, Gothenburg, Sweden

Quantitative Assessment of Drug Delivery to Tissues and Association with Phospholipidosis: A Case Study with Two Structurally Related Diamines in Development

I. Loryan, E. Hoppe, K. Hansen, F. Held, A. Kless , K. Linz, V. Marossek, B. Nolte, P. Ratcliffe, D. Saunders, R. Terlinden, A. Wegert, A. Welbers, O. Will, M. Hammarlund-Udenaes. Mol. Pharmaceutics, 2017, 14 (12), pp 4362–4373, November 3, 2017.

Extending existing structural identifiability analysis methods to mixed-effects models

D. L. I. Janzén, M. Jirstrand, M. J. Chappell, N. D. Evans. Mathematical Biosciences, Vol 295, January 2018, Pages 1-10. Online 26 October 2017.

Exact Gradients Improve Parameter Estimation in Nonlinear Mixed Effects Models with Stochastic Dynamics

H. K. Ólafsdóttir, J. Leander, J. Almquist, M. Jirstrand. In proceedings of The 8th American Conference of Pharmacometrics (ACoP8), October 2017, Fort Lauderdale, USA.

Multiple computational modeling approaches for prediction of wound healing dynamics following pharmacologic intervention

S. M. Rikard, J. Almquist, A. Lundahl, K. M. Hansson, R. Fritsche-Danielson, K. R. Chien, S. M. Pierce. Biomedical Engineering Society (BMES) annual meeting, Phoenix, AZ, USA, 11-14 October 2017.

Contraction Clustering (RASTER): A Big Data Algorithm for Density-Based Clustering in Constant Memory and Linear Time

G. Ulm, E. Gustavsson, M. Jirstrand. The 3rd International Conference on Machine Learning, Optimization and Big Data (MOD 2017), September 14 - 17, 2017, Volterra, Italy

Dose-response-time data analysis

R. Andersson. PhD thesis, University of Warwick. supervisors J. Gabrielsson, M. Jirstrand, M. J. Chappell, N. D. Evans, August 2017.

Purely Functional Federated Learning in Erlang

G. Ulm, E. Gustavsson, and M. Jirstrand. The 29th Symposium on Implementation and Application of Functional Languages (IFL 2017), August 30 - September 1, 2017, University of Bristol, Bristol, United Kingdom.

Characterisation of human AV-nodal properties using a network model

M. Wallman, F. Sandberg. Medical & Biological Engineering & Computing, pp 1-13. 13 July 2017 (Epub ahead of print).

Design analytics is the answer, but what questions would product developers like to have answered?

I.Ö. Arnarsson, E. Gustavsson, J. Malmqvist, M. Jirstrand. ICED17: 21st International Conference on Engineering Design.

Modeling of free fatty acid dynamics: insulin and nicotinic acid resistance under acute and chronic treatments

R. Andersson, T. Kroon, J. Almquist, M. Jirstrand, N. D. Oakes, N.D. Evans, M.J. Chappel, J. Gabrielsson. Journal of Pharmacokinetics and Pharmacodynamics, June 2017, Volume 44, Issue 3, pp 203–222.

Assessment of cardiotoxic effects from ion channel assay data

M. Wallman, I. Jacobson, M. Jirstrand. Poster, Advances in Cell Based Screening 2017, 10-11 May, AstraZeneca, Mölndal, Sweden

Hemostatic effects of the ticagrelor antidote MEDI2452 in pigs treated with ticagrelor on a background of aspirin

S. Pehrsson, K.J. Johansson, A. Janefeldt, A-S Sandinge, S. Maqbool, J. Goodman, J. Sanchez, J. Almquist, P. Gennemark, S. Nylander. J Thromb Haemost 2017; 15: 1213–22. 11 May 2017.

Structural identifiability and indistinguishability in mixed-effects models

D. Janzén. PhD thesis, University of Warwick, supervisors M. J. Chappell, N. D. Evans, M. Jirstrand, December 2016.

Learning to Play Guess Who? and Inventing a Grounded Language as a Consequence

E. Jorge, M. Kågebäck, E. Gustavsson. In proceedings of Deep Reinforcement Learning Workshop, NIPS 2016, Barcelona, Spain, December 2016.

Parameter identifiability of fundamental pharmacodynamic models

L. Bergenholm, D. Janzen, M. Jirstrand, J. Parkinson, J. Yates, N.D. Evans, M.J. Chappell. Frontiers in Physiology, section Computational Physiology and Medicine. 5 December, 2016.

Inventing a Grounded Language by Playing Guess Who? – Creating a Communication Protocol with Deep Multi-Agent Reinforcement Learning

E. Jorge. Master thesis, Chalmers University of Technology and University of Gothenburg, supervisors M. Kågebäck and E. Gustavsson, examinator R. Jörnsten, November 2016.

Data-driven modeling of combination therapy in oncology

T. Cardilin. Licentiate thesis, Chalmers University of Technology and University of Gothenburg, supervisors M. Jirstrand, T. Lundh and J. Gabrielsson, September 2016.

Tumor Static Concentration Curves in Combination Therapy

T. Cardilin, J. Almquist, M. Jirstrand et al. The AAPS Journal, pp 1–12. Online 28 September, 2016.

Third generation turnover model – Nicotinic acid-induced adaptation of insulin and free fatty acids

R. Andersson, T. Kroon, J. Almquist, M. Jirstrand, N.D. Oakes, J. Gabrielsson. In proceedings of the UK Quantitative Systems Pharmacology Network 1st Exchange Workshop, September 5-7, 2016, Surrey, UK.

Towards big-data analysis of deviation and error reports in product development projects

Í.Ö. Arnarsson, J. Malmqvist, E. Gustavsson, M. Jirstrand. In proceedings of NordDesign 2016, Trondheim, Norway, 10 – 12 August, 2016.

Sensitivity-based Gradients for Parameter Estimation in Nonlinear Mixed Effects Models with Deterministic and Stochastic Dynamics

H K Òlafsdóttir. Master thesis, Chalmers University of Technology, supervisor J. Almquist, June, 2016.

Unraveling the pharmacokinetic interaction of ticagrelor and MEDI2452 (Ticagrelor antidote) by mathematical modeling

J. Almquist, M. Penney, S. Pehrsson, A-S Sandinge, A. Janefeldt, S. Maqbool, S. Madalli, J. Goodman, S. Nylander, P. Gennemark. CPT: Pharmacometrics & Systems Pharmacology (Online 16 June, 2016).

Modelling Transferability in Active Acoustic Spectroscopy

M. Gyllenhammar. Master thesis, Chalmers University of Technology, supervisor F. Ekstedt, June, 2016.

Analysis and visualization for production flow of a pharmaceutical pilot plant with a high product variety

A. Ingelström, C. Klang. Bachelor thesis, Chalmers University of Technology, supervisor C. Dudas, June 2016.

Unravelling the pharmacokinetic interaction of ticagrelor and MEDI2452 (ticagrelor-antidote) using mouse data

P. Gennemark, M. Penney, S. Pehrsson, A-S Sandinge, A. Janefeldt, S. Maqbool, S. Madalli, J. Goodman, S. Nylander, J. Almquist. In proceedings from the 25th PAGE meeting, Lisboa, Portugal, 7-10 June, 2016.

Three novel approaches to structural identifiability analysis in mixed-effects models

D. L.I. Janzén, M. Jirstrand, M. J. Chappell, N. D. Evans. Computer Methods and Programs in Biomedicine, Online 6 May, 2016.

Extending the Tumor Static Concentration curve to average doses – a combination therapy example using radiation therapy

T. Cardilin, A. Zimmerman, M. Jirstrand, J. Almquist, S. El Bawab, J. Gabrielsson. In proceedings from the 25th PAGE meeting, Lisboa, Portugal, 7-10 June, 2016.

The Laplace multi-axial response model for fatigue analysis

J. Karlsson, K. Podgórski, I. Rychlik. International Journal of Fatigue, Vol 85, pages 11–17, April 2016.

Investigating a Novel Activation-Repolarisation Time Metric to Predict Localised Vulnerability to Reentry Using Computational Modelling

Y.R. Hill, N. Child, B. Hanson, M. Wallman, R. Coronel, G. Plank, C.A. Rinaldi, J. Gill, N.P. Smith, P. Taggart, M. Bishop (2016), PLoS One, 11(3), e0149342, 2 March, 2016.

Dose-response-time modelling: Second-generation turnover model with integral feedback control

R. Andersson, M. Jirstrand, L. Peletier, M. J. Chappell, N. D. Evans, J. Gabrielsson. European Journal of Pharmaceutical Sciences, Vol 81, 1 January 2016, 189–200

Two approaches to study structural identifiability analysis in mixed-effects models

D. L. I. Janzén, M. Jirstrand, M.J. Chappell, and N.D. Evans. Proceedings of Pharmacokinetics UK (PKUK) 2015, November 2015, Chester, UK.

Characterization of AV‐nodal Properties during Atrial Fibrillation using a Multilevel Modelling Approach

M. Wallman, F. Sandberg. Proceedings of Computing in Cardiology Conference (CinC) 2015. 7-9 September 2015, Nice, France

Dose-response-time modelling: Second generation turnover model with integral feedback control

R. Andersson, M. Jirstrand, L. Peletier, M. J. Chappell, N. D. Evans, J. Gabrielsson. Proceedings of the 24th Annual meeting of the Population Approach Group in Europe, 2-5 June 2015, Crete, Greece.

Modeling and Analysis of Tumor Growth Inhibition for Combination Therapy using Tumor Static Concentration Curves

T. Cardilin, A. Sostelly, J. Gabrielsson, S. El Bawab, C. Amendt, M. Jirstrand. Proceedings of the 24th Annual meeting of the Population Approach Group in Europe, 2-5 June 2015, Crete, Greece

Investigate graph and network algorithms in transport vehicle GPS data to detect and quantify hubs and flow

C. Dudas, C. Engström, J. Karlsson, F. Nellros, L. Qi-Gautier, S. Silvestrov, J. Ulke. Swedish study group Mathematics in Industry, September 4, 2015.

Sensitivity Equations Provide More Robust Gradients and Faster Computation of the FOCE Approximation to the Population Likelihood

J. Almquist, J. Leander, M. Jirstrand. Proceedings of the 24th Annual meeting of the Population Approach Group in Europe, 2-5 June 2015, Crete, Greece

Bile canalicular dynamics in hepatocyte sandwich cultures

R. Reif, J. Karlsson, G. Günther, L. Beattie, D. Wrangborg, S. Hammad, B. Begher-Tibbe, A. Vartak, S. Melega. P.M. Kaye, J.G. Hengstler, M. Jirstrand. Archives of Toxicology, August 18, 2015, Journal no. 204

Structural Identifiability in Mixed-Effects Models: Two different approaches

D. Janzén, M. Jirstrand, N.D. Evans, M. Chappell In proceedings of the 9th IFAC Symposium on Biological and Medical Systems, August 2015, Berlin, Germany.

A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast

J. Almquist, L. Bendrioua, C. Beck Adiels, M. Goksör, S. Hohmann, M. Jirstrand. PLOS ONE, April 20, 2015.

Using sensitivity equations for computing gradients of the FOCE and FOCEI approximations to the population likelihood

J. Almquist, J. Leander, M. Jirstrand, Journal of Pharmacokinetics and Pharmacodynamics, June 2015, 42:3, 191-209.

Mixed Effects Modeling Using Stochastic Differential Equations: Illustrated by Pharmacokinetic Data of Nicotinic Acid in Obese Zucker Rats

J. Leander, J. Almquist, C. Ahlström, J. Gabrielsson, M. Jirstrand, The AAPS Journal, 2015, doi:10.1208/s12248-015-9718-8

Structural Identifiability in mixed-effects models

D. Janzén, J. Yates, M. Jirstrand, N.D. Evans, and M.J. Chappell. In proceedings of PKUK 2014, November 2014, Bath, UK.

Structural Identifiability Analysis of Large Models of Dynamical Systems

J. Karlsson, M. Anguelova, and M. Jirstrand. In proceedings of PKUK 2014, November 5-7, 2014, Bath, UK.

Dose-response-time data analysis of nicotinic acid-induced changes in non-esterified fatty acids in rats

R. Andersson, M. Jirstrand, and J. Gabrielsson. In proceedings of PKUK 2014, November 2014, Bath, UK.

Input estimation in nonlinear dynamical systems for model – based drug discovery using optimal control techniques

M. Trägårdh, M.J. Chappell, N.D. Evans, M. Jirstrand, J. Gabrielsson, and P. Gennemark. In proceedings of PKUK 2014, November 2014, Bath, UK.

A Computational Investigation into the Effect of Infarction on Clinical Human Electrophysiology Biomarkers

L. Cardone-Noott, A. Bueno-Orovio, A. Mincholé, K. Burrage, M. Wallman, N. Zemzemi, E. Dall’Armellina, B. Rodriguez, In proceedings from CinC 2014 Cambridge, MA, USA, 7-10 September 2014.

Contributions to nonlinear mixed-effects modeling

J. Leander, Licentiate thesis, Chalmers University of Technology, supervisors M. Jirstrand and T. Lundh, examiner B. Wennberg, September 2014.

Joint Feedback Analysis Modeling of Nonesterified Fatty Acids in Obese Zucker Rats and Normal Sprague–Dawley Rats after Different Routes of Administration of Nicotinic Acid

S. Tapani, J. Almquist, J. Leander, C. Ahlström, L. A. Peletier, M. Jirstrand, J. Gabrielsson. Journal of Pharmaceutical Sciences, August, 2014, 103(8), 2571–2584.

Kinetic models in industrial biotechnology – Improving cell factory performance

J. Almquist, M. Cvijovic, V. Hatzimanikatis, J. Nielsen, M. Jirstrand. Metabolic Engineering, July, 2014, 24, 38-60.

Probabilistic Computational Assessment of Arrhythmic Risk in Post-Myocardial Infarction Human Ventricles

M. Wallman, A. Bueno-Orovio, B. Rodriguez, Heart Rhythm 35th Annual Scientific Session, San Francisco, USA, Jun 2014.

Mixed-Effects Modeling Using Stochastic Differential Equations – Application to Pharmacokinetic Modeling

J. Leander, J. Almquist, C. Ahlström, J. Gabrielsson, M. Jirstrand, 23rd PAGE meeting, Alicante, Spain, June 2014.

An Imaging System for Semantic Image Segmentation

S. Pfreundschuh, Master thesis, Chalmers University of Technology, supervisor J. Karlsson, examiner T. Gebäck, June 2014.

Yeast AMP-Activated Protein Kinase Monitors Glucose Concentration Changes as well as Absolute Glucose Levels

L. Bendrioua, M. Smedh, J. Almquist, M. Cvijovic, M. Jirstrand, M. Goksör, C. Adiels, and S. Hohmann. The Journal of Biological Chemistry, May 2, 2014, 289, 12863-12875.

A Mechanistic Lung-Disposition Model for Real-time Simulation of Pharmacokinetics and Pharmacodynamics for Pulmonary Drug Delivery

E. Boger, M. Fridén, U.G. Eriksson, M. Jirstrand, J. Gabrielsson, 7th Noordwijkerhout Symposium on Pharmacokinetics, Pharmacodynamics and Systems Pharmacology, Noordwijkerhout, The Neatherlands, April 2014.

Dose-Response-Time Modelling, Input Estimation and Structural Identiability as tools for Systems Pharmacology

M. Trägårdh, D. Janzén, R. Andersson, N. Evans, M. Jirstrand, J. Gabrielsson, L.A. Peletier, P. Gennemark, J. Yates, M. Chappell, 7th Noordwijkerhout Symposium on Pharmacokinetics, Pharmacodynamics and Systems Pharmacology, Noordwijkerhout, The Neatherlands, April 2014.

Bridging the gaps in systems biology

M. Cvijovic, J. Almquist, J. Hagmar, S. Hohmann, H.-M. Kaltenbach, E. Klipp, M. Krantz, P. Mendes, S. Nelander, J. Nielsen, A. Pagnani, N. Przulj, A. Raue, J. Stelling, S. Stoma, F. Tobin, J.A.H. Wodke, R. Zecchina, M. Jirstrand. Molecular Genetics and Genomics, 2014, 289(5), 727-734.

Laplace model for multi-axial responses in fatigue analysis of a cultivator frame

J. Karlsson, P. Krzysztof, I. Rychlik, Proceedings of the 3rd International Commercial Vehicle Technology Symposium (CVT 2014), Shaker Verlag, 2014, 141-150.

Comparison of approaches for parameter identifiability analysis of biological systems

A. Raue, J. Karlsson, M.P. Saccomani, M. Jirstrand, J. Timmer, Bioinformatics, May 2014, 30(10), 1440-8.

Maxsim2—Real-time interactive simulations for computer-assisted teaching of pharmacokinetics and pharmacodynamics

J. Gabrielsson, K. Andersson, G. Tobin, C. Ingvast-Larsson, and M. Jirstrand. Computer Methods and Programs in Biomedicine. December 2013, 113(3):815-829.

Laplace moving average model for multi-axial responses applied to fatigue analysis of a cultivator

M. Kvarnström , K. Podgórski, I. Rychlik. Probabilistic Engineering Mechanics, October 2013, 34, 12–25.

Computational probabilistic quantification of pro-arrhythmic risk from scar and left-to-right heterogeneity in the human ventricles

M. Wallman, A. Bueno-Orovio, B. Rodriguez. Computing in Cardiology Conference (CinC), 2013. pp.711,714, 22-25 Sept. 2013

Computational Methods for Estimation of Cardiac Electrophysiological Conduction Parameters in a Patient Specific Setting

M. Wallman, PhD thesis, University of Oxford, supervisor B. Rodriguez, September 2013.

Cellular Proton Buffer Capacity Revisited: A Study in Xenopus Oocytes

M. Dietrich, J. Almquist, J. Hauth, M. Jirstrand, P. Lang, J.W. Deitmer, 92nd Annual Meeting of the German Physiological Society, Heidelberg, Germany, 2013.

Towards Quantifying the Thymic Dysfunction State in Mouse Models of Inflammatory Bowel Disease

A. Jansson, A.-K. Pernestig, P. Nilsson, M. Jirstrand, E. Hultgren-Hörnquist, Inflammatory Bowel Diseases, March 1, 2013, 19(4), 881-8.

A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model

A. Krengel, J. Hauth, M.-R. Taskinen, M. Adiels, and M. Jirstrand. BMC Systems Biology, January 19, 2013, 7:8.

Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration

R. Meyer, L. D`Alessandro, S. Kar, B. Kramer, B. She, D. Kaschek, B. Hahn, D. Wrangborg, J. Karlsson, M. Kvarnstrom, M. Jirstrand, W.-D. Lehmann, J. Timmer, T. Höfer, U. Klingmüller, Frontiers in Physiology. 2012, 3, 451.

An Efficient Method for Structural Identifiability Analysis of Large Dynamic Systems

J. Karlsson, M. Anguelova, and M. Jirstrand. 16th IFAC Symposium on System Identification (SYSID 2012), 2012, Brussels, Belgium, July 11-13, 2012.

Contrast enhancement, denoising and fusion in dark video for applications in automobile safety

N. Jungenfelt, T. Raski, Master thesis, Chalmers University of Technology, supervisors J. Karlsson, M. Kvarnström, examiner T. McKelvey, June 2012.

A Comparative Study of Graph-Based, Eikonal, and Monodomain Simulations for the Estimation of Cardiac Activation Times

M. Wallman, N. P. Smith, B. Rodriguez, IEEE Transactions on Biomedical Engineering, Vol. 59, No. 6, N/A, 06.2012, p. 1739-1748.

Minimal Output Sets for Identifiability

M. Anguelova, J. Karlsson, and M. Jirstrand. Mathematical Biosciences, May 16, 2012, 239, 1, 139–153.

Optimal Posterior Density Approximation for Bearings-Only Tracking

M. R. Morelande, L. Svensson, J. Hagmar, and M. Jirstrand. 37th International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Kyoto, Japan, March 25-30, 2012.

Investigations of a compartmental model for leucine kinetics using non-linear mixed effects models with ordinary and stochastic differential equations

M. Berglund, M. Sunnåker, M. Adiels, M. Jirstrand, and B. Wennberg. Mathematical Medicine and Biology, 30 September 2011.

A Method for Zooming of Nonlinear Models of Biochemical Systems

M. Sunnåker, G. Cedersund, M. Jirstrand. BMC Systems Biology, September 7, 2011, 5, 140.

Optimal parameterization of posterior densities using homotopy

J. Hagmar, M. Jirstrand, L. Svensson, M. Morelande. Information Fusion (FUSION), 2011 Proceedings of the 14th International Conference, July 2011, pages 1-8.

Modeling and Simulation of Cultivator Load Signals with a Fatigue Damage Perspective

X. Zhao, Master thesis, Chalmers, Supervisor M. Kvarnström, Examiner I. Rychlik, June 2011.

A parameter estimation method for continuous time dynamical systems based on the unscented Kalman filter and maximum likelihood

J. Carlsson, C. Nordheim, Master thesis, Chalmers University of Technology, supervisors J. Hagmar, M. Anguelova, examiner J. Sjöberg, May 2011.

A Kinetic Model of the Monocarboxylate Transporter MCT1 and its Interaction with Carbonic Anhydrase II

J. Almquist, P. Lang, D. Prätzel-Wolters, J. W. Deitmer, M. Jirstrand, and H. M. Becker, Journal of Computer Science & Systems Biology, 3: 107-116, 27 November 2010.

Modeling the Effect of Kv1.5 Block on the Canine Action Potential

J. Almquist, M. Wallman, I. Jacobson, and M. Jirstrand. Biophysical Journal, Volume 99, Issue 9, Pages 2726-2736, 3 November 2010.

Shock-induced arrhythmogenesis in the human heart: A computational modelling study

M.O. Bernabeu, M Wallman, B. Rodriguez. Engineering in Medicine and Biology Society (EMBC), 2010 Annual International Conference of the IEEE , 760,763, Aug. 31 2010-Sept.

Improving Bayesian credibility intervals for classifier error rates using maximum entropy empirical priors

M. G. Gustafsson, M. Wallman, U. Wickenberg, H. Göransson, M. Fryknäs, C.R. Andersson, A. Isaksson. Artificial Intelligence in Medicine, Volume 49, Issue 2, June 2010, Pages 93–104

Biochemical Modeling with Systems Biology Graphical Notation

A. Jansson, M. Jirstrand. Drug Discovery Today, May 2010, 15(9-10), 365-370.

Brownian dynamics simulations in hydrogels using an adaptive time-stepping algorithm

M. Kvarnström, A. Westergård, N. Lorén, M. Nydén. Physical Review, Jan 8, 2009, Epub 79, 016102.

A model reduction approach to the kinetics of the monocarboxylate transporter MCT1 and carbonic anhydrase II

J. Almquist, H. Schmidt, P. Lang, D. Prätzel-Wolters, J. W. Deitmer, M. Jirstrand, and H. M. Becker. The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

Complexity Reduction of Biochemical Rate Expressions

H. Schmidt, M. F. Madsen, S. Danø, G. Cedersund. Bioinformatics, 2008, 24(6), 848-54.

Simulation of Fibrillation in a Realistic Model of Canine Atrial Tissue

M. Wallman, M. Jirstrand, and I. Jacobson. The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

System identification from spatiotemporal cell population data

J. Almquist, M. Sunnåker, J. Hagmar, M. Kvarnström, and M. Jirstrand. The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

Systematic analysis of the RAS/cAMP/PKA signalling pathway using in vivo fluorescence microscopy

K. Bodvard, P. Sliwa, K. Logg, J. Almquist, M. Kvarnström, M. Jirstrand, A. Blomberg and M. Käll. The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

Cross-validation and bootstrapping are unreliable in a small sample classification

A. Isaksson, M. Wallman, H. Göransson, and M.G. Gustafsson. Pattern Recognition Letters, 2008, 29(14), 1960-1965.

Image analysis algorithms for cell contour recognition in budding yeast

M. Kvarnström, K. Logg, A. Diez, K. Bodvard, and M. Käll. Optics Express, 2008, 16, 12943-57.

Automated Image Analysis for Quantification of Protein Localization in Budding Yeast

M. Kvarnström, K. Logg, J. Hagmar, K. Bodvard and M. Käll. The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

Image analysis in nonlinear microscopy

J. Hagmar, C. Brackmann, T, Gustavsson, and A. Enejder. Journal of the Optical Society of America A, 25(9): 2195-2206, 2008.

A Matlab Toolbox for Nonlinear Mixed Effects Modeling – Illustrated with a Model for Lipoprotein Kinetics

M. Sunnåker, M. Berglund, B. Wennberg, M. Adiels, and M. Jirstrand, The 9th Int. Conf. on Systems Biology, Gothenburg, Sweden, August 2008.

Parameter Estimation Methods for Continuous Time Dynamical Systems Given Discrete Time Measurements

N Skaar, Master thesis, Chalmers, supervisor M Jirstrand, examiner B Mehlig, January 2008.

In Silico Simulation of Fibrillation in Canine Atrial Tissue

M. Wallman, M. Jirstrand, L. Gan, and I. Jacobson. In Proceedings of EUFEPS Conference on Optimising Drug Discovery and Development, Basel, Switzerland, Dec 2007.

Development of Parameter Estimation Methods for Biochemical Reaction Systems

P. Zarrineh, Master thesis, Chalmers, supervisor M. Jirstrand, examiner O. Nerman, February 2007.

Systems Biology May Radically Change Healthcare – Individually Based Prediction, Prevention, and Treatment

M. Benson, L.-O. Cardell, S. Hohmann, M. Jirstrand, M. Langston, R. Mobini, and O. Nerman. Läkartidningen, 2007, 104(42), 3037-3041.

Conservation laws and unidentifiability of rate expressions in biochemical models

M. Anguelova, G. Cedersund, M. Johansson, C.J. Franzén, B. Wennberg. IET Systems Biology, July 2007, 1(4), 230-237.

Estimation of centres and radial intensity profiles of spherical nano-particles in digital microscopy

M. Kvarnström and C.A. Glasbey. Biometrical Journal, Apr 2007, Volume 49 (2):300-11.

Development of Automatic Image Analysis Algorithms for Protein Localization Studies in Budding Yeast

K. Logg, M. Kvarnström, A. Diez, K. Bodvard, M. Käll. In D. L. Farkas, R. C. Leif, D. V. Nicolau, editors, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues V, Proceedings of SPIE, February 2007, 6441.

Mathematical Modelling of a Xenopus laevis Oocyte Expressing the NBC and MCT Membrane Transporters – Towards a Better Understanding of the Neuron-Glial Interplay

J. Almquist, N. Lämås, Master thesis, Chalmers, supervisor H. Schmidt, examiners K. Lindgren and C. Breitholtz, February 2007.

Identification of the three-dimensional gel microstructure from transmission electron micrographs

R. Nisslert, M. Kvarnström, N. Lorén, M. Nydén, and M. Rudemo. Journal of Microscopy, Jan 2007, 225(1), 10-21.

New Approaches to Model Reduction of Biochemical Reaction Systems

M. Sunnåker, Master thesis, Chalmers, supervisor H. Schmidt, examiner K. Lindgren, December 2006.

Elimination of the initial value parameters when identifying a system close to a Hopf bifurcation

G. Cedersund. IEE Proceedings - Systems Biology, Nov 2006, Volume 153, Issue 6, p. 448-456.

Core-box Modelling – Theoretical Contributions and Applications to Glucose Homeostasis Related Systems

G. Cedersund, Doctoral thesis, Chalmers, supervisor M. Jirstrand, October 2006.

Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology

H. Schmidt and M. Jirstrand. Bioinformatics, 2006, 22(4), 514-515.

Information Technology in Systems Biology

H. Schmidt, M. Jirstrand, and O. Wolkenhauer. Invited article for it-Information Technology, 2006, 48(3), 133-139.

Evaluation and Development of Methods for Identification of Biochemical Networks

A. Jauhiainen, Master thesis, Linköping University, supervisor M. Jirstrand, January 2005.
Photo credits: Nic McPhee