Publications

Pre-prints

6. N. Welkenhuysen, L. Österberg, S.Persson, S. Hohmann, M. CvijovicLocalization and phosphorylation in the Snf1 network is controlled by two independent pathwaysbioRxiv (2021), doi.org/10.1101/2021.06.14.448401

5. L. Österberg, I. Domenzain, J.Münch, J.Nielsen, S. Hohmann, M. Cvijovic, A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. bioRxiv (2020), doi.org/10.1101/2020.09.11.290817

4. B. Schnitzer, J. Borgqvist, M.Cvijovic, The Synergy of Damage Repair and Retention Promotes Rejuvenation and Prolongs Healthy Lifespans in Cell Lineages. bioRxiv (2020), doi.org/10.1101/2020.03.24.005116

3. J.Borgqvist, A.Malik, C. Lundholm, A. Logg, P. Gerlee, M. Cvijovic, Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability.bioRxiv (2020),

2. F. Ohlsson*, J.Borgqvist*,  M.Cvijovic Symmetry structures in dynamic models of biochemical systems. bioRxiv (2020), doi:https://doi.org/10.1101/2020.01.27.922005  (*equal contribution)

1. J. Borgqvist, N. Welkenhuysen, M. Cvijovic Repair, resilience and asymmetric segregation of damage in the context of replicative ageing: it is a balancing act. bioRxiv (2019), doi 10.1101/446302

Publications

35. L. Österberg, I. Domenzain, J.Münch, J.Nielsen, S. Hohmann, M. Cvijovic, A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism (2021) PLoS Comput Biol 17(4): e1008891. https://doi.org/10.1371/journal.pcbi.1008891

34. A.Polster, L.Öhman, J.Tap, M. Derrien, B. Le Nevé, J. Sundin, H. Törnblom, M. Cvijovic, M. Simrén A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome (2021) Scientific Reports 11:5521 https://doi.org/10.1038/s41598-021-84686-9

33. J.Borgqvist, A.Malik, C. Lundholm, A. Logg, P. Gerlee, M. Cvijovic Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability (2021) npj Systems Biology and Applications 7:13 https://doi.org/10.1038/s41540-021-00173-x

32. B. Schnitzer, J. Borgqvist, M.Cvijovic The Synergy of Damage Repair and Retention Promotes Rejuvenation and Prolongs Healthy Lifespans in Cell Lineages. (2020) PLoS Comput Biol 16(10):e1008314 https://doi.org/10.1371/journal.pcbi.1008314

31. F. Ohlsson, J.Borgqvist,  M.Cvijovic Symmetry structures in dynamic models of biochemical systems (2020) Royal Society Interface Vol 17 Issue 168 https://doi.org/10.1098/rsif.2020.0204

30. S. Persson, N. Welkenhysen, S. Shashkova, M Cvijovic Fine-tuning of energy levels regulates SUC2 via a SNF1-dependent feedback loop (2020) Front.  Physiol. 11:954 https://doi.org/10.3389/fphys.2020.00954

29. G. Schmidt, N. Welkenhuysen, T. Ye, M.Cvijovic, S. Hohmann Mig1 localization exhibits biphasic behavior which is controlled by both metabolic and regulatory roles of the sugar kinases 295, 1489–1500 (2020) Mol Genet Genomics  https://doi.org/10.1007/s00438-020-01715-4

28. J. Borgqvist, N. Welkenhuysen, M. Cvijovic Synergistic effects of repair, resilience and retention of damage determine the conditions for replicative ageing. Scientific Reports 10(1556) (2020) https://doi.org/10.1038/s41598-020-58444-2

27. Q.Ali, R.Dainese, M.Cvijovic Adaptive damage retention mechanism enables healthier yeast population. Journal of Theoretical Biology (2019) https://doi.org/10.1016/j.jtbi.2019.04.005

26. F. Held, E.Hoppe, M. Cvijovic, M. Jirstrand, J. Gabrielsson Challange model of TNFα turnover at varying LPS and drug provocations.  Journal of Pharamcokinetics and Pharmacodynamics 46, 223-240 (2019) https://doi.org/10.1007/s10928-019-09622-x

25. D. Ognissanti, C. Bjurman, M.Holzmann, E. Theodorsson, M. Petzold, M.Cvijovic, O. Hammarsten  Cardiac troponin T concentrations and patient-specific risk of myocardial infarction using the novel PALfx parameter. Clinical Biochemistry Vol 66 p21-28 (2019) https://doi.org/10.1016/j.clinbiochem.2019.02.003

24. F. Held, S. Ekstrand, M.Cvijovic, J. Gabrielsson, M. Jirstrand Modelling of oscillatory cortisol response in horses using a Bayesian population approach for evaluation of dexamethasone suppression test protocols Journal of Pharamcokinetics and Pharmacodynamics (2019) https://doi.org/10.1007/s10928-018-09617-0

23. N. Welkenhuysen, B.Schnitzer, L. Österberg, M. Cvijovic Robustness of nutrient signalling is maintained by interconnectivity between signal transduction pathways (2019) Front. Physiol. 9:1964  https://doi.org/10.3389/fphys.2018.01964

22. S. Hohmann, M. Cvijovic Focus on resolution Current Opinion in Systems Biology Vol 7 (2018) https://doi.org/10.1016/j.coisb.2018.01.001

21. A. Polster, P. Friberg, V. Gunterberg, L. Öhman, B. Le Nevé, H. Törnblom, M. Cvijovic, M. Simren, Heart Rate Variability characteristics of patients with Irritable Bowel Syndrome and associations with symptoms, Neurogastroenterology & Motility (2018) 30(7):e13320. doi: 10.1111/nmo.13320

20. N. Welkenhuysen, J. Borgqvist, M. Backman, L. Bendrioua, M. Goksör, C. B Adiels, M. Cvijovic, S. Hohmann, Single-cell study links metabolism with nutrient signaling and reveals sources of variability (2017) BMC Systems Biology 11:59 https://doi.org/10.1186/s12918-017-0435-z

19. J. Borgqvist, R. Dainese, M. Cvijovic  Systems biology of ageing (2016) Systems Biology Wiley Biotechnology

18. M. Cvijovic, T.Hofer, J. Acimovic, L. Alberghina, E. Almaas, D. Besozzi, A. Blomberg, T. Bretschneider, M. Cascante, O. Collin, P. de Atauri, C. Depner, R. Dickinson, M. Dobrzynski, C. Fleck, J. Garcia-Ojalvo, D. Gonze, J. Hahn, H. M. Hess, S. Hollmann, M. Krantz, U. Kummer, T. Lundh, G. Martial, V. Martins dos Santos, A. Mauer-Oberthur, B. Regierer, B. Skene, E. Stalidzans, J. Stelling, B. Teusink, C. T. Workman, S. Hohmann, Strategies for structuring interdisciplinary education in Systems Biology A European perspective, (2016) npj Systems Biology and Applications 2:16011 https://doi.org/10.1038/npjsba.2016.11

17. T. Österlund, M. Cvijovic, E. Kristiansson, Integrative analysis of omics data (2016) Systems Biology Wiley Biotechnology

16. X. Yang, Y. Shen, E. Garre, X. Hao, D. Krumlinde, M. Cvijovic, C.Arens, T. Nyström, B. Liu, P. Sunnerhagen, Stress granule-defective mutants deregulate stress responsive transcripts (2014)  PLoS Genet. Vol 10(11) https://doi.org/10.1371/journal.pgen.1004763

15. S. Jia, Q. Yang, X. Hao, L. Larsson, J. Yang, X. Zhu, S. Malmgren-Hill, D. Höglund, M. Cvijovic, J. Fernandez-Rodriguez, J. Grantham, C.M. Gustafsson, B. Liu, T.Nyström, Essential genes of the SIR2 genetic interaction network required for asymmetrical inheritance of protein aggregates (2014) PLoS Genetics Vol 10 (7) https://doi.org/10.1371/journal.pgen.1004763

14. L. Bendrioua, M. Smedh, J. Almquist, M. Cvijovic, M. Jirstrand, M. Goksor, C. B. Adiels, S. Hohmann, Yeast AMP-Activated Protein Kinase Monitors Glucose Concentration Changes as well as Absolute Glucose Levels (2014) J. Biol. Chem 289(18):12863-75 doi: 10.1074/jbc.M114.547976

13. 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 Bridging the gaps in systems biology (2014) Molecular Genetics and Genomics 289(5):727-34  doi: 10.1007/s00438-014-0843-3

12. J. Almquist, M. Cvijovic, V. Hatzimanikatis, J.Nielsen, M. Jirstrand, Kinetic Models in Industrial Biotechnology – Improving Cell Factory Performance (2014) Metabolic Engineering 24C:38-60  https://doi.org/10.1016/j.ymben.2014.03.007

11. K. Wanichthanarak, M. Cvijovic, A. Molt, D. Petranovic yApoptosis: Yeast Apoptosis Database (2013) Database Volume 2013, bat068  https://doi.org/10.1093/database/bat068

10. M. Hernebring, Å. Fredriksson, M. Liljevald, M. Cvijovic, K. Norrman, J. Wiseman, H. Semb, T. Nyström Removal of damaged proteins during ES cell fate specification requires the proteasome activator PA28 (2013) Scientific Reports 3: 1381 https://doi.org/10.1038/srep01381

9. L. Kazemzadeh, M. Cvijovic, D. Petranovic Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations, (2012) Front Physiol 3:446 https://doi.org/10.3389/fphys.2012.00446

8. F. Cuklev, J. Fick, M. Cvijovic, E. Kristiansson, L. Förlin, D.G.J. Larsson Does ketoprofen or diclofenac pose the lowest risk to fish? (2012) J Hazard Mater, 229-230:100-6 https://doi.org/10.1016/j.jhazmat.2012.05.077

7. F. Cuklev, L. Gunnarsson, M. Cvijovic, E. Kristiansson, C. Rutgersson, B. Björlenius D.G.J. Larsson Global hepatic gene expression in rainbow trout exposed to sewage effluents: A comparison of different sewage treatment technologies (2012) Science of the Total Environment, 427-428:106-14 10.1016/j.scitotenv.2012.04.009

6. M. Cvijovic, S. Velasco Bordel, J. Nielsen Mathematical Models of Cell Factories: Moving towards the core of Industrial Biotechnology (2011) Microbial Biotechnology 4(5): 572–584 doi: 10.1111/j.1751-7915.2010.00233.x

5. M. Cvijovic, R.Olivares–Hernández, R. Agren, N.Dahr, W. Vongsangnak, I. Nookaew, K. R. Paril, J. Nielsen BioMet Toolbox: genome-wide analysis of metabolism (2010) Nucleic Acid Research, NAR vol 38 https://doi.org/10.1093/nar/gkq404

4. N. Erjavec*, M. Cvijovic, E. Klipp, T. Nyström Selective benefits of damage partitioning in unicellular systems; effects on robustness, fitness and aging, (2008) PNAS vol 105(48)  (Recommended by Faculty of 1000) https://doi.org/10.1073/pnas.0804550105

3. M. Cvijovic, H. Soueidan*, D. J. Sherman, E. Klipp, M. Nikolski Exploratory simulation of Cell Ageing Using Hierarchical Models, Genome Informatics 21:114-25 (2008)

2. M. Cvijovic, D.Dalevi, E. Bilsland, G.J.L. Kemp, P. Sunnerhagen, Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation (2007) BMC Bioinformatics 8:295 https://doi.org/10.1186/1471-2105-8-295

1. Selpi, C.H. Bryant, G.J.L. Kemp, M. Cvijovic, A First Step towards Learning which uORFs Regulate Gene Expression (2006) Journal of Integrative Bioinformatics, 3(2)