Bioinformatics and Systems Biology
Suraj Sharma


Bioinformatics and Systems Biology (BSysBio) is working at two different locations: The main part of the group is a subgroup of the Microorganisms and Plants research group at UIT. The other part of the group is affiliated with the Department of Clinical Sciences at the University of Bergen and part of the Clinical Center of Excellence NeuroSysMed. BSySBio focuses on the development of mathematical models of molecular biological processes and related bioinformatics tools as well as on the development of new approaches for bioinformatics data analysis.



Bioinformatics and systems biology subgroup has received continuous funding from both European (Horizon 2020) and national funding sources (Research Council of Norway (RCN)). Projects with funding of more than 1 Mio. NOK are listed below.

EU H2020

Bioinformatics tools and software

The group has been developing a number of bioinformatics approaches and tools as well as mathematical models. All models are made publicly available through the EBI Biomodels database and bioinformatics tools are released as open software on GitHub.

>Publications since 2012

  1. Sauter, R, Sharma, S, Heiland, I1 Accounting for NAD Concentrations in Genome-Scale Metabolic Models Captures Important Metabolic Alterations in NAD-Depleted Systems Biomolecules 2024 14 (5), 602
  2. Suraj Sharma, Yin-Chen Hsieh, Jörn Dietze, Mathias Bockwoldt, Øyvind Strømland, Mathias Ziegler, Ines Heiland Early evolutionary selection of NAD biosynthesis pathway in bacteria Metabolites 12 (7), 569
  3. Alienke van Pijkeren, Jörn Dietze, .... Ines Heiland, Rainer Bischoff1, Marcel Kwiatkowski1 Combined Metabolic and Chemical (CoMetChem) labeling using stable isotopes–A strategy to reveal site-specific histone acetylation and deacetylation rates by LC-MS Analytical Chemistry  2021 93, 38, 12872–12880
  4. Dietze, J, van Pijkeren, A Ziegler, M, Kwiatkowski, M, Heiland, I Natural isotope correction improves analysis of protein modification dynamics Analytical and Bioanalytical Chemistry 2021413 (30), 7333-7340
  5. M Ziegler, M Monné, A Nikiforov, G Agrimi, I Heiland, (2021) F Palmieri Welcome to the Family: Identification of the NAD+ Transporter of Animal Mitochondria as Member of the Solute Carrier Family SLC25 Biomolecules 11 (6), 880
  6. Panitz et al. Tryptophan metabolism is inversely regulated in the tumor and blood of patients with glioblastoma Theranostics accepted
  7. Mohapatra et al. Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine Production Frontiers in immunology 12, 8
  8. Prentzell et al. G3BPs tether the TSC complex to lysosomes and suppress mTORC1 signalling Cell 2021 184 (3), 655-674. e27
  9. Zupanic, A, Bernstein,HC, Heiland, I Systems Biology: Current status and challenges Cell Mol Life Science 2020
  10. Prentzell et al. G3BP1 tethers the TSC complex to lysosomes and suppresses mTORC1 in the absence of stress granules (preprint available at BioRxiv, submitted to Cell)
  11. Mohapatra SR, Sadik A, Tykocinski LO, Dietze J, Poschet G, Heiland I et al. Hypoxia Inducible Factor 1alpha Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma Frontiers Immunology 2019, 10: 2762 [1]
  12. Clarelli F., Liang, J., Martinecz, A., Heiland, I, Abel zur Wiesch, P. Multi-scale modeling of drug binding kinetics to predict drug efficacy Cell Mol Life Science 2019, online [7]
  13. Bockwoldt, M, Houry, D, Niere, Gossmann, TI, M, Reinhartz, I, Schug, A, Ziegler, M, Heiland, I Identification of evolutionary and kinetic drivers of NAD-dependent signalling PNAS 2019, 116 (32) 15957-15966  [27]
  1. Heberle, AM2, Razquin Navas, P2, … Heiland, I, Sascha Schäuble, Kathrin Thedieck The PI3K and MAPK/p38 pathways control stress granule assembly in a hierarchical manner Life Science Alliance 2019 2 (2) e20180025 [17]
  2. Bockwoldt, M, Heiland, I, Fischer, K The evolution of the plastid phosphate translocator family Planta 2019 accepted DOI: 10.1007/s00425-019-03161-y [4]
  3. Strømland, O, Niere, M, Nikiforov, AA, VanLinden, MR, Heiland, I, Ziegler, M. Keeping the balance in NAD metabolism Biochem Soc Trans, 2019 47 (1), 119-130 [42]
  4. Afanasyeva, A, Bockwoldt, M, CR Cooney, Heiland, I, Gossmann, TI Human long intrinsically disordered protein regions are frequent targets of positive selection Genome research 2018 28 (7), 975-982 [34]
  5. Adam et al. Upregulation of tryptophanyl-tRNA synthethase adapts human cancer cells to nutritional stress caused by tryptophan degradationOcoimunology 2018 7 (12), e1486353[30]
  6. Schäuble, S, Stavrum, AK2, Bockwold, Mt2, Puntervoll, P, Heiland, I SBMLmod: A Python-Based Web Application and Web Service for Efficient Data Integration and Model Simulation BMC Bioinf 2017 18 (1), 314 [4]
  7. Dyah L Dewi et al. Suppression of indoleamine-2, 3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer, 216, Oncoimmunology [18]
  8. Opitz, C and I. Heiland, Dynamics of NAD-metabolism - everything but constant, 2016 Biochem Soc Trans43 (6), 1127-1132 [34]
  9. Walter, W., E. Gaquerel, I.T. Baldwin, S.-G. Kim, and I. Heiland Improving the accuracy of expression data analysis in time course experiments using resampling. 2014 BMC Bioinformatics Oct 25;15(1):35 [5]
  10. Schäuble, S2, A.K. Stavrum2, P. Puntervoll, S. Schuster, and I. Heiland, Effect of substrate competition in kinetic models of metabolic networks. FEBS Lett, 2013. 587(25): p. 2818-24. [37]
  11. Schmeisser, K., J. Mansfeld, D. Kuhlow, S. Weimer, S. Priebe, I. Heiland, M. Birringer, M. Groth, A. Segref, Y. Kanfi, N.L. Price, S. Schmeisser, S. Schuster, A.F. Pfeiffer, R. Guthke, M. Platzer, T. Hoppe, H.Y. Cohen, K. Zarse, D.A. Sinclair, and M. Ristow, Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nat Chem Biol, 2013. 9(11): 693-700 [107]
  12. Stavrum, A.K., I. Heiland, S. Schuster, P. Puntervoll, and M. Ziegler, Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. J Biol Chem, 2013. 288(48): 34555-66. [42]
  13. Bodenstein, C., I. Heiland, and S. Schuster, Temperature compensation and entrainment in circadian rhythms. Phys Biol, 2012. 9(3): p. 036011. X [28]
  14. Gossmann, T.I., M. Ziegler, P. Puntervoll, L.F. de Figueiredo, S. Schuster, and I. Heiland, NAD(+) biosynthesis and salvage -a phylogenetic perspective. FEBS J, 2012. 279(38): 3355-63 [30]
  15. Heiland, I., C. Bodenstein, T. Hinze, O. Weisheit, O. Ebenhoeh, M. Mittag, and S. Schuster, Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii. J Biol Phys, 2012. 38(3): 449-6 [10]
  16. Schäuble, S., K. Klement, S. Marthandan, S. Munch, I. Heiland, S. Schuster, P. Hemmerich, and S. Diekmann, Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts. PLoS One, 2012. 7(8): e42150. [24]


The group engages in different outreach activities. We write popular science articles and short publication release notes on the university website and on the Linkedin page of the group leader. In addition, we have a blog that contains popular science articles about bioinformatics.



Bioinformatics and Systems Biology

Ines Heiland - Dept. of Arctic and Marine BiologyFaculty of Bioscience,Fisheries and Economics
Biologifagbygget Framstedet 39
UiT – The Arctic University of Norway. Tromsø NO-9037, Norway
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