Selected publications and reference material

BTS scientists have many years of experience in computational systems biology. Selected references for the different product areas and services are listed below.

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 2012  -  2011  - 2010  - 2009  - 2008  - 2007  - 2006 - 2005 - 2004 - 2003 

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2012  -  top of page

Meyer M, Schneckener S, Ludewig B, Kuepfer L, Lippert J.
Using expression data for quantification of active processes in physiologically-based pharmacokinetic modeling.
Drug Metab Dispos. 2012 Jan 31. [Epub ahead of print]

Holzhütter HG, Drasdo D, Preusser T, Lippert J, Henney AM.
The virtual liver: a multidisciplinary, multilevel challenge for systems biology.
Wiley Interdiscip Rev Syst Biol Med. 2012 Jan 13. doi: 10.1002/wsbm.1158. [Epub ahead of print]

Kuepfer L, Lippert J, Eissing T.
Multiscale mechanistic modeling in pharmaceutical research and development.
Adv Exp Med Biol. 2012;736:543-61.

 

2011  -  top of page

Thelen K, Coboeken K, Willmann S, Dressman JB, Lippert J.
Evolution of a detailed physiological model to simulate the gastrointestinal transit and absorption process in humans, Part 2: Extension to describe performance of solid dosage forms.
J Pharm Sci. 2011 Nov 28. doi: 10.1002/jps.22825. [Epub ahead of print]

Müller FJ, Schuppert A.
Few inputs can reprogram biological networks.
Nature; 478:E4, doi:10.1038/nature10543

Schneckener S, Arden NS, Schuppert A.
Quantifying stability in gene list ranking across microarray derived clinical biomarkers.
BMC Med Gen 2011, 4:73, doi:10.1186/1755-8794-4-73.

Thelen K, Coboeken, K, Willmann S, Burghaus R, Dressman JB, Lippert J. 
Evolution of a detailed physiological model to simulate the gastrointestinal transit and absorption process in humans, Part 1: Oral solutions.
J Pharm Sci, DOI: 10.1002/jps.22726. [Epub ahead of print]

Dressman JB, Thelen K, Willmann S.
An update on computational oral absorption simulation.
 Expert Opin Drug Metab Toxicol. 2011 Sep 23. [Epub ahead of print]

Ummanni R, Mundt F, Pospisil H, Venz S, Scharf C, Barett C, Fälth M, Köllermann J, Walther R, Schlomm T, Sauter G, Bokemeyer C, Sültmann H, Schuppert A, Brümmendorf TH, Balabanov S.
Identification of clinically relevant protein targets in prostate cancer with 2D-DIGE coupled mass spectrometry and systems biology network platform.
PLoS One. 2011 Feb 11;6(2):e16833.

Dickmann F, Falkner J, Gunia W, Hampe J, Hausmann M, Herrmann A, Kepper N, Knoch TA, Lauterbach S, Lippert J, Peter K, Schmitt E, Schwardmann U, Solodenko J, Sommerfeld D, Steinke T, Weisbecker A, Sax U.
Solutions for biomedical grid computing—Case studies from the D-Grid project Services@MediGRID.
J Comp Sci, in press, doi:10.1016/j.jocs.2011.06.006  

Kersting G, Willmann S, Würthwein G, Lippert J, Boos J, Hempel G.
Physiologically based pharmacokinetic modelling of high- and low-dose etoposide: from adults to children.
Cancer Chemother Pharmacol. 2011 Jul 26. [Epub ahead of print]

Schuppert A. 
Efficient reengineering of meso-scale topologies for functional networks in biomedical applications.
J Math Ind. 2011; 1:6 doi:10.1186/2190-5983-1-6

Görlitz L, Gao Z, Schmitt W.
Statistical Analysis of Chemical Transformation Kinetics using Markov-Chain Monte-Carlo Methods. 
Environ Sci Technol. 2011; 45(10): 4429-4437, doi: 10.1021/es104218h.

Burghaus R, Coboeken K, Gaub T, Kuepfer L, Sensse A, Siegmund H, Weiss W, Mueck W, Lippert J.  
Evaluation of the Efficacy and Safety of Rivaroxaban Using a Computer Model for Blood Coagulation. 
PLoS ONE 6(4): e17626. doi:10.1371/journal.pone.0017626. 

Eissing T, Kuepfer L, Becker C, Block M, Coboeken K, Gaub T, Goerlitz L, Jaeger J, Loosen R, Ludewig B, Meyer M, Niederalt C, Sevestre M, Siegmund H, Solodenko J, Thelen K, Telle U, Weiss W, Wendl T, Willmann S, Lippert J. 
A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks.
Front Physio 2:4. doi: 10.3389/fphys.2011.00004. 2011.

 

2010  -  top of page

Kuepfer L.
Towards whole-body systems physiology.
Mol Syst Biol. 6:409; 2010.

Görlitz L, Loosen R, Mrziglod T.
Topology optimization of artificial neural networks using L1-penalization.
Proceedings of 20. Workshop Computational Intelligence. 2010; pp.  80-87.

Willmann S, Thelen K, Becker C, Dressman JB, Lippert J.
Mechanism-based prediction of particle size-dependent dissolution and absorption: Cilostazol pharmacokinetics in dogs.
Eur J Pharm Biopharm. 2010 Jun 8. [Epub ahead of print]

Mohammed Y, Sax U, Dickmann F, Lippert J, Solodenko J, von Voigt G, Smith M, Rienhoff O.
On transferring the grid technology to the biomedical community.
Stud Health Technol Inform. 2010;159:28-39.

Schneckener S, Görlitz L, Ellinger-Ziegelbauer H, Ahr HJ, Schuppert A.
An elastic network model to identify characteristic stress response genes. 
Comp Biol Chem. 2010; 34(3): 193-202.

Blank LM, Kuepfer L.
Metabolic flux distributions: genetic information, computational predictions, and experimental validation. 
Appl Microbiol Biotechnol. 2010;86(5):1243-55.

 

2009  -  top of page

Thelen K, Jantratid E, Dressman JB, Lippert J, Willmann S.
Analysis of nifedipine absorption from soft gelatin capsules using PBPK modeling and biorelevant dissolution testing. 
J Pharm Sci. 2009; advance online publication. 

Willmann S, Edginton AN, Coboeken K, Ahr G, Lippert J.
Risk to the Breast-Fed Neonate From Codeine Treatment to the Mother: A Quantitative Mechanistic Modeling Study. 
Clin Pharmacol Ther. 2009; advance online publication. 

Radszuweit M, Block M, Hengstler JG, Schöll E, Drasdo D. 
Comparing the growth kinetics of cell populations in two and three dimensions. 
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 May; 79(5 Pt 1):051907. Epub 2009 May 12.

Willmann S, Edginton AN, Kleine-Besten M, Jantratid E, Thelen K, Dressman JB.
Whole-Body Physiologically-Based Pharmacokinetic Population Modelling of Oral Drug Administration: Inter-Individual Variability of Cimetidine Absorption. 
J Pharm Pharmacol. 2009; 61, 891-899. 

Thelen K, Dressman JB.
Cytochrome P450-mediated metabolism in the human gut wall.
J Pharm Pharmacol. 2009 May;61(5):541-58.

Edginton AN, Ahr G, Willmann S, Stass H.
Defining the Role of Macrophages in Local Moxifloxacin Tissue Concentrations using Biopsy Data and Whole-Body Physiologically Based Pharmacokinetic Modelling.
Clin Pharmacokinet. 2009; 48(3): 181-187.

Becker C, Dressman JB,  Junginger HE, Kopp S, Midha KK, Shah VP, Stavchansky S, Barends DM.
Biowaiver monographs for immediate release solid oral dosage forms: Rifampicin.
J Pharm Sci. 2009 Jan 21. [Epub ahead of print]

Eissing T, Chaves M, Allgöwer F.
Live and let die—A systems biology view on cell death.
Comp Chem Eng. 2009; 33(3): 583-589. 

Willmann S.
Das In-silico-Child. Können Computer-Simulationen klinisch-pharmakokinetische Studien ersetzten?
Pharm Unserer Zeit. 2009; 38(1): 62-67.

 

2008  -  top of page

Edginton AN, Willmann S.
Physiology-based simulations of a pathological condition: prediction of pharmacokinetics in patients with liver cirrhosis.
Clin Pharmacokinet. 2008; 47(11): 743-752.

Edginton AN, Theil FP, Schmitt W, Willmann S.
Whole body physiologically-based pharmacokinetic models: their use in clinical drug development.
Expert Opin Drug Metab Toxicol. 2008;4(9): 1143-1152.

Loizou G, Spendiff M, Barton HA, Bessems J, Bois FY, d'Yvoire MB, Buist H, Clewell HJ 3rd, Meek B, Gundert-Remy U, Goerlitz G, Schmitt W.
Development of good modelling practice for physiologically based pharmacokinetic models for use in risk assessment: the first steps.
Regul Toxicol Pharmacol. 2008; 50(3):400-11.

Dressman JB, Thelen K, Jantratid E.
Towards Quantitative Prediction of Oral Drug Absorption.
Clin Pharmacokinet. 2008; 47(10): 655-67.

Becker C, Dressman JB, Amidon GL, Junginger HE, Kopp S, Midha KK, Shah VP, Stavchansky S, Barends DM.
Biowaiver monographs for immediate release solid oral dosage forms: Pyrazinamide.
J Pharm Sci. 2008; 97(9): 3709-20.

Granero GE, Longhi MR, Becker C, Junginger HE, Kopp S, Midha KK, Shah VP, Stavchansky S, Dressman JB, Barends DM.
Biowaiver monographs for immediate release solid oral dosage forms: Acetazolamide.
J Pharm Sci. 2008; 97(9): 3691-9.

Becker C, Dressman JB, Amidon GL, Junginger HE, Kopp S, Midha KK, Shah VP, Stavchansky S, Barends DM.
Biowaiver monographs for immediate release solid oral dosage forms: ethambutol dihydrochloride.
J Pharm Sci. 2008; 97(4): 1350-60.

Schmitt W.
General approach for the calculation of tissue to plasma partition coefficients. 
Toxicol In Vitro. 2008; 22(2): 457-67. 

Waldherr S, Eissing T, Allgöwer F.
Feedback during Life and Death of a Cell: Approaches for Systems Theoretical Analysis.
Automatisierungstechnik. 2008; 56(5): 233-240.

Chaves M, Eissing T, Allgöwer F.
Bistable biological systems: a characterization through local compact input-to-state stability. 
IEEE Trans Aut Cont. 2008; 53(1): 87-100.

 

2007  -  top of page

Willmann S, Höhn K, Edginton A, Sevestre M, Solodenko J, Weiss W, Lippert J, Schmitt W.
Development of a physiology-based whole-body population model for assessing the influence of individual variability on the pharmacokinetics of drugs. 
J Pharmacokinet Pharmacodyn. 2007; 34(3): 401-431. 

Bucholz R, Lippert J.
Von der Einzelzelle zum Organismus, vom Computermodell zum Bioreaktor - Verfahrenstechnik in der medizinischen Forschung.
Chem Ing Tech, 79(9):1384:1385. 

Vossen M, Sevestre M, Niederalt C, Jang IJ, Willmann S, Edginton AN.
Dynamically simulating the interaction of midazolam and the CYP3A4 inhibitor itraconazole using individual coupled whole-body physiologically-based pharmacokinetic (WB-PBPK) models.
Theor Biol Med Model. 2007, 4: 13. 

Willmann S, Edginton AN, Dressman JB. 
Development and validation of a physiology-based model for the prediction of oral absorption in monkeys. 
Pharm Res. 2007; 24(7): 1275-1282.

Kuepfer L, Peter M, Sauer U, Stelling J.
Ensemble modeling for analysis of cell signaling dynamics.
Nat Biotechnol. 2007; 25(9): 1001-1006.

Schuetz R, Kuepfer L, Sauer U.
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.
Mol Syst Biol. 2007; 3: 119.

Kuepfer L, Sauer U, Parrilo PA.
Efficient classification of complete parameter regions based on semidefinite programming.
BMC Bioinformatics. 2007; 8: 12.

Becker C, Dressman JB, Amidon GL, Junginger HE, Kopp S, Midha KK, Shah VP, Stavchansky S, Barends DM; International Pharmaceutical Federation, Groupe BCS.
Biowaiver monographs for immediate release solid oral dosage forms: isoniazid.
J Pharm Sci. 2007;96(3): 522-31.

Drasdo D, Hoehme S, Block M.
On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models?
J Stat Phys. 2007; 128(1-2): 287-345.

Block M, Schöll E, Drasdo D.
Classifying the expansion kinetics and critical surface dynamics of growing cell populations.
Phys Rev Lett. 2007; 99(24): 248101. 

Eissing T, Waldherr S, Allgöwer F, Scheurich P, Bullinger E.
Steady state and (bi-)stability evaluation of simple protease signalling networks.
BioSystems. 2007; 90(3): 591-601. 

Eissing T, Waldherr S, Allgöwer F, Scheurich P, Bullinger E.
Response to Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores.
Biophys J. 2007; 92(9): 3332-3334.

 

2006  -  top of page

Edginton AN, Schmitt W, Willmann S 
Development and evaluation of a generic physiologically based pharmacokinetic model for children. 
Clin Pharmacokinet. 2006; 45(10): 1013-1034. 

Edginton AN, Schmitt W, Voith B, Willmann S 
A mechanistic approach for the scaling of clearance in children. 
Clin Pharmacokinet. 2006, 45(7): 683-704. 
Erratum in: Clin Pharmacokinet. 2006; 45(11): 1075. 

Edginton AN, Schmitt W, Willmann S 
Application of physiology-based pharmacokinetic and pharmacodynamic modeling to individualized target-controlled propofol infusions. 
Adv Ther. 2006; 23(1): 143-158. 

Edginton AN, Willmann S 
Physiology-based versus allometric scaling of clearance in children; an eliminating process based comparison. 
Paediatr Perinat Drug Ther, 2006; 7 (3): 146-153.

 

2005  -  top of page

Willmann S, Lippert J, Schmitt W. 
From physicochemistry to absorption and distribution: predictive mechanistic modelling and computational tools. 
Expert Opin Drug Metab Toxicol. 2005; 1(1): 159-168. 

Schmitt W, Willmann S 
Physiology-based pharmacokinetic modeling: ready to be used.
Drug Discov Today. 2005; 2(1): 125-132.

Kuepfer L, Sauer U, Blank LM.
Metabolic functions of duplicate genes in Saccharomyces cerevisiae.
Genome Res. 2005; 15(10): 1421-1430.

Blank LM, Kuepfer L, Sauer U.
Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.
Genome Biol. 2005; 6(6): R49. 

Eissing T, Allgöwer F, Bullinger E
Robustness properties of apoptosis models with respect to parameter variations and stochastic influences.
Syst Biol (Stevenage). 2005; 152(4): 221-228.

 

2004  -  top of page

Willmann S, Schmitt W, Keldenich J, Lippert J, Dressman JB. 
A physiological model for the estimation of the fraction dose absorbed in humans. 
J Med Chem. 2004; 47(16): 4022-4031.

Eissing T, Conzelmann H, Gilles ED, Allgöwer F, Bullinger E, Scheurich P.
Bistability analyses of a caspase activation model for receptor-induced apoptosis.
J Biol Chem. 2004; 279(35): 36892-36897.

 

2003  -  top of page

Willmann S, Schmitt W, Keldenich J, Dressman JB. 
A physiologic model for simulating gastrointestinal flow and drug absorption in rats.
Pharm Res. 2003; 20(11): 1766-1771. 

Willmann S, Lippert J, Sevestre M, Solodenko J, Fois F, Schmitt W 
PK-Sim^®: a physiologically based pharmacokinetic ‘whole-body’ model. 
Biosilico. 2003; 1 (4): 121-124.