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Ines Heiland

Department of Arctic and Marine Biology

Job description:

Prof. for Molecular Biology and Bioinformatics

Research interests

Mathematical simulations are an important tool in physics and engineering, but its application to biology and medicine is still in its infancy. However, as our knowledge of the molecular basis of biological processes is progressing, mathematical modelling is increasingly used to understand the complexity of living organisms.

We use existing biochemical data to built dynamic models of metabolisms and dynamic molecular processes. The resulting models can be used to understand the basis of diseases and guide the development of drugs. We work in close collaboration with experimental groups, which is advantageous, as model building is always an iterative process of simulation and experimental verification of model hypothesis. It furthermore guides the developement of our models and usually defines the aim of the model.

Research projects

Simulation of circadian rhythms

Most organisms employ circadian clocks to anticipate daily variations in their natural environments. Circadian clocks are self-sustained oscillators that can be entrained by external time cues like light–dark or temperature cycles to match local time. The rhythm persists in the absence of such stimuli with a period of approximately 24 h. Thus, circadian clocks are generally thought to resemble limit-cycle oscillators.

In recent years we have studied the entrainment characteristics of circadian oscillators. Most previous studies have focused on the entrainment by light-dark cycles but much less is known about the entrainment by temperature or feeding cycles. Temperature permanently influences all processes within an organism. Thus, it is difficult to study temperature regulation of circadian clocks separately by in vivo experiments. Although the clock can be entrained by temperature cycles, its free-running period is relatively constant within a broad range of physiological temperatures. This phenomenon is called temperature compensation. We unraveled the relation between temperature compensation and temperature entrainment of circadian clocks recently and have shown that temperature compensation ensures temperature entrainment at e.g. seasonal changing mean temperatures.

We have furthermore started to study the mechanisms of feeding entrainment of circadian clocks. Although it has been known for decades that the clock of peripheral tissues can be set by feeding entrainment.  Recently, significant advances have been made to elucidate the molecular mechanisms behind this process. We use this data to recosntruct a dynamic model of metabolic regulation of circadian clocks.

Bioinformatic analysis and simulation of Tryptophan- and NAD-Metabolism

Tryptophan is an essential amino acid for protein biosynthesis and the precursor of serotonin, melatonin, NAD and kynurenate as well as the neurotoxins quinolinic acid (QA) and 3-hydroxy-kynurenine (3HK). Changes in tryptophan metabolism have been found in several neurodegenerative diseases such as Parkinsons’s and Huntington’s disease, in AIDS-dementia and various kinds of cancer. Furthermore, changes in serotonin levels are the basis of several gastrointestinal disorders. Serotonin is furthermore known as important regulator of the metabolism. Melatonin which is synthesized from serotonin in a light-sensitive and circadian clock regulated manner, is itself an important regulator of our sleep-wake cycle and changes in its synthesis are the basis of e.g. the delayed sleep phase syndrom.

NAD is equally important as metabolite of redox-reactions and as signaling molecule. NAD is required for DNA-damage repair and the NAD-dependent deacetylase (sirtuins) seem to play an important role in ageing and in the metabolic regulation of circadian clocks. As these enzymes consume NAD cellular NAD-pools need to be constantly replenished.



Sept/2015 - Prof. for molecular biology and  bioinformatics at the Department of arctic and marine biology

Dec/2012 - Sept/2015 Assoc. Prof. for molceular bioinformatics at the Department of arctic and marine biology

2008 - 2012
Postdoctoral researcher and junior group leader at the Friedrich Schiller University Jena, Department of Bioinformatics
Project: Modelling and simulation of circadiane rhythms and dynamic metabolic processes

2005 - 2006
Postdoctoral reseracher at the FSU Jena Department of General Botany
Project: Data evaluation of large scale proteome projects of C. reinhardtii

2004 - 2005
Postdoctoral researcher at the Ruhr University Bochum Laboratory of Systems Biochemistry
Project: Characterisation of the Pex3p-Complexes of Saccharomyces cerevisiae



2003 - 2004 Ruhr Universit Bochum, Laboratory of Systems Biochemistry
2001 - 2002 Department of Biochemistry, Free University Berlin

I have done my PhD-thesis in the group of Prof. Ralf Erdmann. The title of my work was: "Investigating peroxisomal membrane biogenesis". I have defended my PhD thesis at the 19th of November in 2004 at the FU Berlin.



04/2011 - 05/2011 Computational Biology Unit, Uni Reserach, Bergen, Norway

03/2004 - 04/2004 Biological school of sciences, C. Stirling Group, Manchester University, England

06/1999 - 07/1999 Department of Organic Chemistry, S. Oscarsons Group, Arhenius Laboratories, Stockholm University, Sweden


Undergraduate Studies in Biochemistry

1995 - 1997 Friedrich Schiller University Jena
1997 - 2000
Free University Berlin

Awards and distinctions

2015  "50 years FEBS"  Education Training Award
09/2011 ISGSB Travel grant
03/2009 FEBS YTF-Grant
2001 - 2003 PhD-Scolarship of the Boehringer Ingelheim Fonds


Home page / Social Media

Blog / Website: http://users.minet.uni-jena.de/~iheiland/english.html

Publications in CRIStin

  • Dewi, Dyah L; Mohapatra, Soumya R; Cabañes, Saioa Blanco; Adam, Isabell; Patterson, Luis F Somarribas; Berdel, Bianca; Kahloon, Masroor; Thürmann, Loreen; Loth, Stefanie; Heilmann, Katharina; Weichenhan, Dieter; Mucke, Oliver; Heiland, Ines; Wimberger, Pauline; Kuhlmann, Jan Dominik; Kellner, Karl-Heinz; Schott, Sarah; Plass, Christoph; Platten, Michael; Gerhäuser, Clarissa; Trump, Saskia; Opitz, Christiane A.. Suppression of indoleamine-2, 3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer. Oncoimmunology 2017; Volum 6 (2). ISSN 2162-402X.s doi: 10.1080/2162402X.2016.1274477.

  • Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines. SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics 2017; Volum 18:314. ISSN 1471-2105.s 1 - 8.s doi: 10.1186/s12859-017-1722-9.

  • Heiland, Ines; Thedieck, K. Nutrigenomics: Toward a cross-disciplinary understanding of nutrient-driven networks in health and disease: What can we learn from the study of cross-talk in complex protein kinase and metabolic networks?. Aktuelle Ernãhrungsmedizin 2015; Volum 40 (2). ISSN 0341-0501.s 88 - 92.s doi: 10.1055/s-0034-1387602.

  • Opitz, Christiane A.; Heiland, Ines. Dynamics of NAD-metabolism: everything but constant. Biochemical Society Transactions 2015; Volum 43 (6). ISSN 0300-5127.s 1127 - 1132.s doi: 10.1042/BST20150133.

  • Wencke, Walter; Ketelsen, Bernd; Emmanuel, Gaquerel; Baldwin, Ian T.; Sang-Gyu, Kim; Heiland, Ines. Improving the accuracy of expression data analysis in time course experiments using resampling. (fulltekst) BMC Bioinformatics 2014; Volum 15. ISSN 1471-2105.s doi: 10.1186/s12859-014-0352-8.

  • Schäuble, Sascha; Stavrum, Anne-Kristin; Puntervoll, Pål; Schuster, Stefan; Heiland, Ines. Effect of substrate competition in kinetic models of metabolic networks. (fulltekst) FEBS Letters 2013; Volum 587 (17). ISSN 0014-5793.s 2818 - 2824.s doi: 10.1016/j.febslet.2013.06.025.

  • Stavrum, Anne-Kristin; Heiland, Ines; Schuster, Stefan; Puntervoll, Pål; Ziegler, Mathias. Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. Journal of Biological Chemistry 2013; Volum 288 (48). ISSN 0021-9258.s 34555 - 34566.s doi: 10.1074/jbc.M113.474908.

  • Schmeisser, Kathrin; Mannsfeld, Johannes; Kuhlow, Doreen; Weimer, Sandra; Priebe, Steffen; Heiland, Ines; Birringer, Marc; Groth, Marco; Segref, Alexandra; Kanfi, Yariv; Price, Nathan L.; Schmeisser, Sebastian; Schuster, Stefan; Pfeiffer, Andreas F. H.; Guthke, Reinhard; Platzer, Matthias; Hoppe, Torsten; Haim, Cohen Y; Zarse, Kim; Sinclair, David A; Ristow, Michael. Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nature Chemical Biology 2013; Volum 9 (11). ISSN 1552-4450.s 693 - 700.s doi: 10.1038/nchembio.1352.

  • Heiland, Ines; Kaleta, Christoph. Stoffwechselanalyse: Neue Wege im Labyrinth entdecken. Laborwelt 2012; Volum 4. ISSN 1611-0854.s 30 - 32.

  • Gossmann, Toni Ingolf; Afanasyeva, Arina; Bockwoldt, Mathias; Heiland, Ines; Chris, Cooney. Human intrinsically long disordered protein regions are frequent targets of positive selection. Annual Meeting of the Society for Molecular Biology and Evolution 2017 2017-07-02 - 2017-07-06 2017.

  • Bockwoldt, Mathias; Heiland, Ines. Phylogenetic Analysis of NAD biosynthesis and consumption. NBS contact meeting 2016-01-21 - 2016-01-23 2016.

  • Sauter, Roland; Heiland, Ines. Metabolic Modeling of Marine Biomass Conversion. 1st annual BioCat Meeting 2016-06-12 - 2016-06-14 2016.

  • Heiland, Ines; Bockwoldt, Mathias; Puntervoll, Pål; Schäuble, Sascha; Stavrum, Anne-Kristin. Tissue specific models of Trp- and NAD-metabolism — insights into metabolic crosstalk.. 2016 Conference on Computational Modelling with COPASI 2016-05-12 - 2016-05-13 2016.

  • Bockwoldt, Mathias; Heiland, Ines; Toni, Gossmann; Ziegler, Mathias. Phylogenetic and simulation-based analysis of NAD metabolism. ISGSB 2016 2016-10-04 - 2016-10-07 2016.

  • Heiland, Ines; Bockwoldt, Mathias; Stavrum, Anne-Kristin; Puntervoll, Pål; Ziegler, Mathias. Tissue specific models of Tryptohan-metabolism — insights into metabolic crosstalk. COPASI User conference 2016-05-12 - 2016-05-13 2016.

  • Elliss, Carolyn; Rattei, Thomas; Heiland, Ines. 50 Years of FEBS´ Education Training Awards. (fulltekst) FEBS News 2015; Volum 2015 (2).s 15 - 16.

  • Bockwoldt, Mathias; Heiland, Ines. Use of resampling to improve accuracy of data analysis in time course experiments. European Biological Rhythms Sociecty Congress and World Congress of Chronobiology 2015-08-02 - 2015-08-06 2015.

  • Bockwoldt, Mathias; Heiland, Ines. Phylogenetic Analysis of NAD biosynthesis and consumption. Norbis Annual Meeting 2015-10-28 - 2015-10-30 2015.

  • Bockwoldt, Mathias; Stavrum, Anne-Kristin; Gossmann, Toni I.; Ziegler, Mathias; Heiland, Ines. Dynamics of NAD-metabolism - everything but constant. Metabolic Pathway Analysis (omtale) 2015-06-08 - 2015-06-12 2015.

  • Heiland, Ines; Brandes, Susanne; Stavrum, Anne-Kristin; Bodenstein, Christian; Ziegler, Mathias. NAD-metabolism and the circadian clock -- Unraveling contradictions. Advanced Lecture Course on Systems Biology 2014-03-02 - 2014-03-08 2014.

  • Heiland, Ines. Chemo Informatik: Was hat Tryptophan mit Krebs und Parkinson zu tun?. Chemie in unserer Zeit 2014; Volum 48 (3). ISSN 0009-2851.s 164 - 166.s doi: 10.1002/ciuz.201480013.

  • Walter, Wencke; Gaquerel, Emmanuel; Baldwin, Ian T.; Kim, Sang-Gyu; Heiland, Ines. Improving the analysis of high throughput time course data using modelling based approaches. SocBin Bioinformatics 2014-06-11 - 2014-06-13 2014.

  • Stavrum, Anne-Kristin; Heiland, Ines; Schuster, Stefan; Puntervoll, Pål; Ziegler, Mathias. Predicting pathological metabolic changes using a kinetic model of tryptophan metabolism. Advanced Lecture Course on Systems Biology 2014-03-02 - 2014-03-08 2014.

  • Heiland, Ines. Metabolic modelling: From networks to dynamics and back. Workshop on Visualization in Biology 2013-09-19 - 2013-09-19 2013.

  • Heiland, Ines; Brandes, Susanne; Stavrum, Anne-Kristin; Bodenstein, Christian; Ziegler, Mathias. NAD-metabolism and the circadian clock. Gordon Conference Chronobiology 2013-07-14 - 2013-07-19 2013.

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