Publications. Since 2005 


Ghallab, A., Henkel, S.G., Cellière, G., Driesch, D., Hoehme, S., Hofmann, U., Zellmer, S., Godoy, P., Sachinidis, A., Blaszkewicz, M., Reif, R., Marchan, R., Kuepfer, L., Häussinger, D., Drasdo, D., Gebhardt, R., Hengstler, J.G.

Model guided identification and therapeutic implications of an ammonia sink mechanism.

Journal of Hepatology (accepted) 

van Liedekerke, P., Palm, M., Jagiella, N., Drasdo, D.

Simulating tissue mechanics with Agent Based Models: concepts and perspectives.

Computational Particle Mechanics (accepted) 

Jagiella, N., Mueller, B., Mueller, M., Vignon-Clementel, I., Drasdo, D.

Inferring growth control mechanisms in growing multi-cellular spheroids of NSCLC cells from spatial-temporal image data.

PLoS Comput. Biol. (accepted) 

Müller, B., Bovet, M., Yin, Y., Stichel, D., Malz, M., González-Vallinas, M., Middleton, A., Ehemann, V., Schmitt, J., Muley, T., Meister, M., Herpel, E., Singer, S., Warth, A., Schirmacher, P., Drasdo, D., Matthäus, F., Breuhahn, K.

Concomitant expression of far upstream element (FUSE) binding protein (FBP) interacting repressor (FIR) and its splice variants induce migration and invasion of non-small cell lung cancer (NSCLC) cells

Journal of Pathology (accepted)

D’Alessandro, L., Hoehme, S., Drasdo, D., Klingmüller, U.

Unraveling liver complexity from molecular to organ level: Challenges and perspectives.

Progress in Biophysics and Molecular Biology, 117 1, 78–86

Friebel, A., Neitsch, J., Johann, T., Hammad, S., Hengstler, JG., Drasdo, D., Hoehme, S.

TiQuant: Software for tissue analysis, quantification and surface reconstruction.

Bioinformatics 2015. doi: 10.1093/bioinformatics/btv346



Drasdo, D., Bode, J., Dahmen, U., Dirsch, O., Dooley, S., Gebhardt, R., Ghallab, A., Godoy, P., Häussinger, D., Hammad, S., Hoehme, S., Holzhütter, HG., Klingmüller, U., Kuepfer, L., Timmer, J., Zerial, M., Hengstler, JG.

The virtual liver: state of the art and future perspectives.

Arch Toxicol 2014, Editorial: doi: 10.1007/s00204-014-1384-6

Bertaux, F., Stoma, S., Drasdo, D., Batt, G.

Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance.

PLoS Comput Biol 10(10): e1003893. doi: 10.1371/journal.pcbi.1003893

 Drasdo, D.Hoehme, S., Hengstler, JG.

How predictive quantitative modeling of tissue organization can inform liver disease pathogenesis.

Journal of Hepatology, Volume 61, Issue 4, October 2014, pp 951-956

Wolkenhauer, O., Auffray, C., Brass, O., Clairambault, J., Deutsch, A., Drasdo, D., Gervasio, F., Preziosi, L., Maini, P., Marciniak-Czochra, A., Kossow, C., Kuepfer, L., Rateitschak, K., Ramis-Conde, I., Ribba, B., Schuppert, A., Smallwood, R., Stamatakos, G., Winter, F., Byrne, H.

Enabling multiscale modeling in systems medicine.

Genome Medicine 2014, 6:21. doi:10.1186/gm538

Hammad, S., Hoehme, S., Friebel, A., von Recklinghausen, I., Othman, A., Begher-Tibbe, B., Reif, R., Godoy, P., Johann, T., Vartak, A., Golka, K., Bucur, P.O., Vibert, E., Marchan, R., Christ, B., Dooley, S., Meyer, C., Ilkavets, I., Dahmen, U., Dirsch, O., Böttger, J., Gebhardt, R., Drasdo, D., Hengstler, JG.

Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis.

Archives of Toxicology, Vol. 88 (5), pp 1161-1183; doi:10.1007/s00204-014-1243-5

 Schliess, F., Hoehme, S., Henkel, S., Ghallab, A., Driesch, D., Böttger, J., Guthke, R., Pfaff, M., Hengstler, JG., Gebhardt, R., Häussinger, D., Drasdo*, D., Zellmer*, S. (*corresponding authors) (2014)

Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration.

Hepatology 2014, doi:10.1002/hep.27136

López Alfonso, J.C., Jagiella, N., Núñez, L., Herrero, M.A., and Drasdo, D. (2014)

Estimating Dose Paining Effects Radiotherapy: A Mathematical Model.

PLoS One, 9(2): e89380. doi:10.1371/journal.pone.0089380



Tang, Min; Vauchelet, Nicolas; Cheddadi, Ibrahim, Vignon-Clementel, Irene, Drasdo, Dirk and Perthame, Benoit. (2013)

Composite waves for a cell population system modeling tumor growth and invasion.

CHIN. Ann. Math. Series B, Vol. 34 (2) 295-318

 Godoy, Patricio; Hewitt, Nicola J.; Albrecht, Ute; et al. (2013)

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME.

ARCH. TOXICOL 87 (8) 1315-1530  



Ramis-Conde, I, Dirk Drasdo (2012)

From genotypes to phenotypes: classification of the tumor profiles for different variants of the cadherin adhesion pathway.

Phys. Biol. 2012 June 8; 9(3):36008-36019 

 Dirk Drasdo and Stefan Hoehme (2012)

Predicting the growth pattern of cell populations: pushing, pulling and the effect of an granular and cellular embedding medium.

New Journal of Physics 14, 055025 (37pp)

Holzhütter Hermann-Georg, Dirk Drasdo, Tobias Preusser, Joerg Lippert und Adriano Henney (2012)

The Virtual Liver: A Multidisciplinary, Multi-level Challenge for Systems Biology.

Wiley Interdisciplinary Reviews - Systems Biology and Medicin, Volume 4, Issue 3, Pages 221-235 



 Drasdo, D., Hoehme, S., Hengstler, J. (2011)

A quantiative mathematical modeling approach to liver regeneration.

In Liver Regeneration. Editor: Dieter Häussinger. De Gruyter Berlin/Boston.

 Hoehme, S., Hammad, S., Othman, A., vonRecklinghausen, I., Boettger, J., Gebhardt, R., Dirsch, O., Hengstler, J.G., Drasdo, D. (2011)

Modeling liver regeneration in a virtual lobe.

In proceedings of: Living Imaging 2011 Workshop (LIVIM); December 1 - 2, 2011; IRCAD, Strasbourg, France 

 Drasdo, D., Hoehme, S. Hengstler, J. (2011)

Systems biology to model liver regeneration. 

In Encyclopedia of Systems Biology 

Dubitzky, W.; Wolkenhauer, O.; Yokota, H.; Cho, K.-H. (Eds.), Springer

Hengstler J.G., Gehrmann, M., Hoehme S., Drasdo, D., Stewart, J., Schmidt, M. (2011)

Systems biology, bioinformatics and medicine approaches to cancer progression outcomes

In Cancer Systems Biology, Bioinformatics and Medicine, Cesario, Alfredo; Marcus, Frederick (Eds.), Springer (Read online.)



Hoehme S and Drasdo D. (2010)

A cell-based simulation software for multicellular systems. 

Bioinformatics, 2010 Oct 15;26(20):2641-2.

 A. Braeuning, Y. Singh, B. Rignall, A. Buchmann, S. Hammad, A. Othman, I.v. Recklinghausen, P. Godoy, S. Hoehme, D. Drasdo, J.G. Hengstler, M. Schwarz (2010)

Phenotype and growth behavior of residual β-catenin-positive hepatocytes in livers of β-catenin-deficient mice.

Histochemistry and Cell Biology, 2010 Nov;134(5):469-81. 

 Galle J, Bader A, Grill W, Fuchs B, Kaes JA, Krinner A, Mueller K, Schiller, Schulz R, von Butlar, M, Loeffler M. (2010) 

Stem Cells in Cartilage Repair: State of the Art and Methods to monitor Cell Growth, Differentiation and Cartilage Regeneration.. 

Current Medicinal Chemistry 17: 2274-2291.

Krinner A., Hoffmann M., Loeffler M., Drasdo, D, and Galle J. (2010). 

Individual fates of mesenchymal stem cells in vitro.. 

BMC Systems Biology 4: 73.

 Hoehme, S., Brulport, M., Bauer, A., Bedawy, E., Schormann, W., Gebhardt, R., Zellmer, S., Schwarz, M., Bockamp, E., Timmel, T.G., Hengstler, J.G., and Drasdo, D. (2010). 

Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration. 

Proc. Natl. Acad. Sci. (USA), 107(23), 10371-10376. (Evaluated by Faculty of Biology 1000 as Exceptional)

Wolkenhauer, Olaf; Auffray, Charles; Baltrusch, Simone; Bluthgen, Nils; Byrne, Helen; Cascante, Marta; Ciliberto, Andrea; Dale, Trevor; Drasdo, Dirk; Fell, David; Ferrell, James E Jr; Gallahan, Daniel; Gatenby, Robert; Gunther, Ulrich; Harms, Brian D; Herzel, Hanspeter; Junghanss, Christian; Kunz, Manfred; van Leeuwen, Ingeborg; Lenormand, Philippe; Levi, Francis; Linnebacher, Michael; Lowengrub, John; Maini, Philip K; Malik, Arif; Rateitschak, Katja; Sansom, Owen; Schafer, Reinhold; Schurrle, Karsten; Sers, Christine; Schnell, Santiago; Shibata, Darryl; Tyson, John; Vera, Julio; White, Michael; Zhivotovsky, Boris; Jaster, Robert (2010)

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.

Cancer Research, 70(1) 12-13

Drasdo, D., Jagiella, N., Ramis-Conde, I.,, Vignon-Clementel, I., Weens, W. (2010)

Modeling steps from a benign tumor to an invasive cancer: examples of intrinsically multi-scale problems

In Cell Mechanics: From Single Scale-Based Models To Multiscale Modeling, pp. 379-417, A. Chauviere, L. Preziosi, C. Verdier (Eds.), Chapman & Hall/CRC



 S. Hoehme and D. Drasdo. (2009)  

Biomechanical versus nutrient control: what determines the growth dynamics of mammalian cell populations?  

Mathematical Population Studies, 1547-724X, Volume 17, Issue 3, 2010, 166–187.

 Galle J, Krinner A, Buske P, Drasdo D, Loffler M (2009)

On the impact of single cell biomechanics on the spatio-temporal organization of regenerative tissue.

in World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany IFMBE Proceedings 25/X (ed. Olaf Dössel and Wolfgang C. Schlegel): 185-188. Springer Heidelberg.

 Krinner, A., Zscharnack, M., Bader, A., Drasdo, D., Galle, J. (2009)

The impact of the oxygen environment on mesenchymal stem cell expansion and chondrogenic differentiation.

Cell Proliferation 42: 471-484.

 Radszuweit, M., Block, M., Hengstler, J.G., Schöll, E., Drasdo, D. (2009)

Comparing the growth kinetics of cell populations in two and three dimensions

Phys. Rev. E, 79, 051907 (Article Selected for Virtual Journal of Biological Physics Research and by the Faculty of Biology 1000)

 Ramis-Conde I, Chaplain MA, Anderson AR, Drasdo D. (2009) 

Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis. 

Phys Biol. 2009 Mar 25;6(1):16008 - 16020.

 Byrne, H. and Drasdo, D. (2009)

Individual-based and continuum models of growing cell populations: a comparison.

J. Math. Biol. Apr;58(4-5):657-87. 



Ramis-Conde I.Drasdo D., Anderson ARA, Chaplain MA J. (2008)

Modeling the influence of the E-cadherin-beta-catenin pathway in cancer cell invasion: a multiscale approach.

Biophys. J. 95 , 155-165 (Selected for cover page; recommended by P.Maini with Alexander Fletcher , Faculty of 1000 Biology as state of art example for multi-scale modeling)



 Block, M., Schoell, E. and Drasdo, D. (2007)

Classifying the growth kinetics and surface dynamics in growing cell populations.

Phys. Rev. Lett. Dec 14;99(24):248101-104. (Selected for Virtual Journal of Biological Physics Research)

Rohrschneider M., Scheuermann G., Hoehme, S. and Drasdo D. (2007)

Shape Characterization of Extracted and Simulated Tumor Samples using Topological and Geometric Measures.

IEEE Engineering in Medicine and Biology Society, 2007, 6271-6277.

 Drasdo, D. (2007) 

Center-based Single-cell Models: An Approach to Multi-cellular Organization Based on a Conceptual Analogy to Colloidal Particles. 

In Single-Cell-Based Models in Biology and Medicine, Anderson, A.R.A., Chaplain M.A.J., Rejniak K.A. (Eds), Birkhäuser, Basel

 Hoehme, S., Hengstler J.G., Brulport M., Schäfer M., Bauer A., Gebhardt R. and Drasdo D. (2007) 

Mathematical modelling of liver regeneration after intoxication with CCl4 

Chemico-Biological Interaction, 168, 74-93

Drasdo, D., Hoehme, S. and Block, M. (2007) 

On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models? 

Journal of Statistical Physics, Volume 128, Numbers 1-2, pp. 287-345(59) 



 Galle, J., Aust, G., Schaller, G., Beyer, T. and Drasdo, D. (2006) 

Individual cell-based models of the spatio-temporal organisation of multicellular systems - achievements and limitations 

Cytometry, Cytometry A, 69A, 704-710.

 Missal, K., Cross, M., Drasdo, D. (2006) 

Reverse engineering of gene regulatory networks for incomplete expression data: Transcriptional control of haemopoietic commitment. 

Bioinformatics, Bioinformatics 22(6): 731-738.



Drasdo, D. (2005)

Coarse Graining in Simulated Cell Populations.

Adv. Complex Syst., 2 & 3, 319-363.

Drasdo, D., Kruspe, M. (2005)

Emergence of regulatory networks in simulated evolutionary processes

Adv. Complex Syst., 2 & 3, 285-318.

Galle, J., Loeffler, M. and Drasdo, D. (2005)

Modelling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro.

Biophys. J. 88, 62-75.

Drasdo, D. and Hoehme, S. (2005)

A single-cell-based model of tumor growth in vitro: monolayers and spheroids.

Phys. Biol. 2 133-147. (Selected for cover page)