Publications

 

Wordprocessing Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics


Authors: M. G. Mooij, A. T. Nies, C. A. Knibbe, E. Schaeffeler, D. Tibboel, M. Schwab, S. N. de Wildt

PubMed ID: 26410689

Date Published: 28th Sep 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacokinet

Citation: Clin Pharmacokinet. 2015 Sep 26.

Scales: Not specified

Abstract (Expand)

Membrane transporters play an essential role in the transport of endogenous and exogenous compounds, and consequently they mediate the uptake, distribution, and excretion of many drugs. The clinical ...

Created: 17th Dec 2015 at 11:53


 

Wordprocessing Drug-Induced liver injury: interactions between drug properties and host factors


Authors: Minjun Chen, Ayako Suzuki, Jürgen Borlak, Raúl J Andrade, M Isabel Lucena

PubMed ID: 25912521

Date Published: 29th Apr 2015

Scales: Not specified

Abstract (Expand)

Idiosyncratic drug-induced liver injury (DILI) is a common cause for drug withdrawal from the market and although infrequent, DILI can result in serious clinical outcomes including acute liver failure ...

Created: 5th May 2015 at 09:06


 

Wordprocessing Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling


Authors: Lorenza A. D’Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller

DOI: 10.1371/journal.pcbi.1004192

Date Published: 23rd Apr 2015

Scales: Cell

Abstract (Expand)

Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations ...

Created: 5th May 2015 at 13:29   Last updated: 22nd May 2015 at 08:57


 

Wordprocessing Dysregulated serum response factor triggers formation of hepatocellular carcinoma


Authors: Stefan Ohrnberger, Abhishek Thavamani, Albert Braeuning, Daniel B. Lipka, Milen Kirilov, Robert Geffers, Stella E. Authenrieth, Michael Römer, Andreas Zell, Michael Bonin, Michael Schwarz, Günther Schütz, Peter Schirmacher, Christoph Plass, Thomas Longerich, Alfred Nordheim

DOI: 10.1002/hep.27539

Date Published: 1st Mar 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Hepatology

Citation: Hepatology 61(3) : 979

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

The ubiquitously expressed transcriptional regulator serum response factor (SRF) is controlled by both Ras/MAPK (mitogen-activated protein kinase) and Rho/actin signaling pathways, which are frequently ...

Created: 14th Dec 2015 at 15:12   Last updated: 14th Dec 2015 at 15:15


 

Wordprocessing Data collection as a barrier to personalized medicine


Authors: David Zakim, Matthias Schwab

PubMed ID: 25479798

Date Published: 2nd Dec 2014

Projects: G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Trends Pharmacol. Sci.

Citation: Trends Pharmacol. Sci. 36(2): 68-71

Scales: Not specified

Abstract (Expand)

Basic life science research holds the promise of personalizing medical care. However, translation steps from the laboratory to the bedside are not trivial. Results from clinical research are difficult ...

Created: 7th Apr 2015 at 14:54


 

Wordprocessing Data extraction for the reaction kinetics database SABIO-RK


Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

DOI: 10.1016/j.pisc.2014.02.004

Date Published: 1st May 2014

Projects: F3: Kinetic data handling

Journal: Perspectives in Science

Citation: Perspectives in Science 1(1-6) : 33

Scales: Not specified

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting ...

Created: 3rd Feb 2015 at 10:55   Last updated: 3rd Feb 2015 at 11:03


 

Wordprocessing Determinants of Cell-to-Cell Variability in Protein Kinase Signaling


Authors: Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie

PubMed ID: 24339758

Date Published: 5th Dec 2013

Scales: Not specified

Abstract (Expand)

Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein ...

Created: 20th Jan 2014 at 16:29


 

Wordprocessing Dynamics of VEGF matrix-retention in vascular network patterning


Authors: A Köhn-Luque, W de Back, Y Yamaguchi, K Yoshimura, M A Herrero, T Miura

DOI: 10.1088/1478-3975/10/6/066007

Date Published: 1st Dec 2013

Scales: Intercellular

Abstract (Expand)

Vascular endothelial growth factor (VEGF) is a central regulator of blood vessel morphogenesis, although its role in patterning of endothelial cells into vascular networks is not fully understood. It ...

Created: 24th Jan 2014 at 13:54   Last updated: 24th Jan 2014 at 13:57


 

Wordprocessing Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs


Authors: Ioannis N Melas, Regina Samaga, Leonidas G Alexopoulos, Steffen Klamt

PubMed ID: 24039561

Date Published: 5th Sep 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 9(9): e1003204

Scales: Cell

Abstract (Expand)

Cross-referencing experimental data with our current knowledge of signaling network topologies is one central goal of mathematical modeling of cellular signal transduction networks. We present a new ...

Created: 13th Dec 2013 at 17:20


 

Wordprocessing DNA methylation of the SLC16A3 promoter regulates expression of the human lactate transporter MCT4 in renal cancer with consequences for clinical outcome


Authors: Pascale Fisel, Stephan Kruck, Stefan Winter, Jens Bedke, Jörg Hennenlotter, Anne T Nies, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Matthias Schwab, Elke Schaeffeler

PubMed ID: 23881922

Date Published: 23rd Jul 2013

Scales: Not specified

Abstract (Expand)

The monocarboxylate transporter 4 (MCT4) is a metabolic target in tumor biology because it mediates lactate transport across membranes resulting in antiapoptotic effects. Cell experiments support the ...

Created: 20th Jan 2014 at 14:16


 

Wordprocessing Differently Saturated Fatty Acids Can Be Differentiated by (31)P NMR Subsequent to Derivatization with 2-Chloro-4,4,5,5-tetramethyldioxaphospholane: A Cautionary Note


Authors: Mandy Eibisch, Thomas Riemer, Beate Fuchs, Jürgen Schiller

PubMed ID: 23414224

Date Published: 26th Feb 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: J. Agric. Food Chem.

Citation: J. Agric. Food Chem. 61(11): 2696-700

Scales: Not specified

Abstract (Expand)

The analysis of free fatty acid (FFA) mixtures is a very important but, even nowadays, challenging task. This particularly applies as the so far most commonly used technique-gas chromatography/mass ...

Created: 6th Jan 2014 at 13:54


 

Wordprocessing Direct Transcriptional Regulation of Human Hepatic Cytochrome P450 3A4 (CYP3A4) by Peroxisome Proliferator-Activated Receptor Alpha (PPARα)


Authors: Maria Thomas, Oliver Burk, Britta Klumpp, Benjamin A Kandel, Georg Damm, Thomas S Weiss, Kathrin Klein, Matthias Schwab, Ulrich M Zanger

PubMed ID: 23295386

Date Published: 9th Jan 2013

Scales: Cell

Abstract (Expand)

The nuclear receptor peroxisome proliferator-activated receptor (PPAR)α is primarily known as a regulator of fatty acid metabolism, energy balance, and inflammation, but there is evidence suggesting a ...

Created: 9th Jan 2013 at 15:04   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Distinct dedifferentiation processes affect caveolin-1 expression in hepatocytes


Authors: Christoph Meyer, Johanna Dzieran, Yan Liu, Felizitas Schindler, Stefan Munker, Alexandra Müller, Cédric Coulouarn, Steven Dooley

DOI: 10.1186/1478-811X-11-6

Date Published: 2013

Projects: A3.3: Hepatocyte polarity

Journal: Cell Commun Signal

Citation: Cell Commun Signal 11(1) : 6

Scales: Cell

Abstract:

Not specified

Created: 23rd Jan 2013 at 17:57   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Detecting and investigating substrate cycles in a genome-scale human metabolic network


Authors: Juliane Gebauer, Stefan Schuster, Luís F de Figueiredo, Christoph Kaleta

PubMed ID: 22776428

Date Published: 11th Jul 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: The FEBS journal

Citation: FEBS J. 279(17): 3192-202

Scales: Cell

Abstract (Expand)

Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described in the 1970s occurring in muscles of ...

Created: 1st Aug 2012 at 11:45   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Decreased levels of active SMAD2 correlate with poor prognosis in gastric cancer


Authors: Yijun Wu, Qi Li, Xinhui Zhou, Jiren Yu, Yunchuan Mu, Stefan Munker, Chengfu Xu, Zhe Shen, Roman Müllenbach, Yan Liu, Li Li, Norbert Gretz, Derek Zieker, Jun Li, Kouichi Matsuzaki, Youming Li, Steven Dooley, Honglei Weng

PubMed ID: 22539990

Date Published: 23rd Apr 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., Show cases

Journal: PLoS ONE

Citation: PLoS ONE 7(4): e35684

Scales: Not specified

Abstract (Expand)

TGF-β plays a dual role in the progression of human cancer. During the early stages of carcinogenesis, TGF-β functions as a tumor suppressor. During the late stages of tumor development, however, TGF-β ...

Created: 31st Oct 2012 at 09:13   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Dynamics and feedback loops in the transforming growth factor β signaling pathway


Authors: Katja Wegner, Anastasia Bachmann, Jan-Ulrich Schad, Philippe Lucarelli, Sven Sahle, Peter Nickel, Christoph Meyer, Ursula Klingmüller, Steven Dooley, Ursula Kummer

PubMed ID: 22284904

Date Published: 5th Jan 2012

Projects: HepatoSys, Virtual Liver

Journal: Biophys. Chem.

Citation: Biophys. Chem. 162: 22-34

Scales: Cell

Abstract (Expand)

Transforming growth factor β (TGF-β) ligands activate a signaling cascade with multiple cell context dependent outcomes. Disruption or disturbance leads to variant clinical disorders. To develop ...

Created: 30th Aug 2012 at 13:08   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing DNA methylation is associated with downregulation of the organic cation transporter OCT1 (SLC22A1) in human hepatocellular carcinoma


Authors: Elke Schaeffeler, Claus Hellerbrand, Anne T Nies, Stefan Winter, Stephan Kruck, Ute Hofmann, Heiko van der Kuip, Ulrich M Zanger, Hermann Koepsell, Matthias Schwab

PubMed ID: 22196450

Date Published: 23rd Dec 2011

Scales: Cell

Abstract (Expand)

Organic cation transporters (OCTs) determine not only physiological processes but are also involved in the cellular uptake of anticancer agents. Based on microarray analyses in hepatocellular carcinoma ...

Created: 27th Jun 2012 at 15:59   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Distinct functions of the mitogen-activated protein kinase-activated protein (MAPKAP) kinases MK2 and MK3: MK2 mediates lipopolysaccharide-induced signal transducers and activators of transcription 3 (STAT3) activation by preventing negative regulatory effects of MK3


Authors: Christian Ehlting, Natalia Ronkina, Oliver Böhmer, Ute Albrecht, Konrad A Bode, Karl S Lang, Alexey Kotlyarov, Danuta Radzioch, Matthias Gaestel, Dieter Häussinger, Johannes G Bode

PubMed ID: 21586572

Date Published: 17th May 2011

Scales: Cell

Abstract (Expand)

In LPS-treated macrophages, activation of STAT3 is considered to be crucial for terminating the production of inflammatory cytokines. By analyzing the role of MAPK-activated protein kinase (MK) 2 and ...

Created: 31st Aug 2012 at 11:46   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing Does hepatic steatosis affect drug metabolizing enzymes in the liver


Authors: Christa Buechler, Thomas S Weiss

PubMed ID: 21222589

Date Published: 13th Jan 2011

Scales: Liver

Abstract (Expand)

Bioavailability and effects of xenobiotics are dependent on absorption, metabolism and elimination of the respective compounds. Hepatocytes are critically important in drug modification and excretion. ...

Created: 30th Jan 2014 at 17:23


 

Wordprocessing Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets


Authors: Valentina Raia, Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue, Carsten Sticht, Sebastian Bohl, Maria Saile, Peter Möller, Norbert Gretz, Jens Timmer, Fabian Theis, Wolf-Dieter Lehmann, Peter Lichter, Ursula Klingmüller

PubMed ID: 21127196

Date Published: 2nd Dec 2010

Projects: HepatoSys

Journal: Cancer Res.

Citation: Cancer Res. 71(3): 693-704

Scales: Not specified

Abstract (Expand)

Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) share a frequent constitutive activation of JAK (Janus kinase)/STAT signaling pathway. Because of complex, nonlinear ...

Created: 10th Aug 2012 at 09:41   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing Dynamical modeling and multi-experiment fitting with PottersWheel


Authors: Thomas Maiwald, Jens Timmer

PubMed ID: 18614583

Date Published: 9th Jul 2008

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 24(18): 2037-43

Scales: Not specified

Abstract (Expand)

Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. ...

Created: 17th Aug 2012 at 10:13   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing Dynamic pathway modeling: feasibility analysis and optimal experimental design


Authors: Thomas Maiwald, Clemens Kreutz, Andrea C Pfeifer, Sebastian Bohl, Ursula Klingmüller, Jens Timmer

PubMed ID: 18033750

Date Published: 24th Nov 2007

Projects: HepatoSys

Journal: Ann. N. Y. Acad. Sci.

Citation: Ann. N. Y. Acad. Sci. 1115: 212-20

Scales: Not specified

Abstract (Expand)

A major challenge in systems biology is to evaluate the feasibility of a biological research project prior to its realization. Since experiments are animals-, cost- and time-consuming, approaches ...

Created: 17th Aug 2012 at 10:21   Last updated: 24th Oct 2013 at 16:23


 

Wordprocessing Data-based identifiability analysis of non-linear dynamical models


Authors: S Hengl, C Kreutz, J Timmer, T Maiwald

PubMed ID: 17660526

Date Published: 28th Jul 2007

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 23(19): 2612-8

Scales: Not specified

Abstract (Expand)

MOTIVATION: Mathematical modelling of biological systems is becoming a standard approach to investigate complex dynamic, non-linear interaction mechanisms in cellular processes. However, models may ...

Created: 17th Aug 2012 at 10:25   Last updated: 24th Oct 2013 at 16:23


 

Wordprocessing Data-based mathematical modeling of vectorial transport across double-transfected polarized cells


Authors: Kilian Bartholomé, Maria Rius, Katrin Letschert, Daniela Keller, Jens Timmer, Dietrich Keppler

PubMed ID: 17548463

Date Published: 4th Jun 2007

Projects: HepatoSys

Journal: Drug Metab. Dispos.

Citation: Drug Metab. Dispos. 35(9): 1476-81

Scales: Not specified

Abstract (Expand)

Vectorial transport of endogenous small molecules, toxins, and drugs across polarized epithelial cells contributes to their half-life in the organism and to detoxification. To study vectorial transport ...

Created: 25th Jul 2011 at 16:51   Last updated: 24th Oct 2013 at 16:23


 

Wordprocessing Digitoxin metabolism by rat liver microsomes


Authors: A. Schmoldt, H. F. Benthe, G. Haberland

PubMed ID: 10

Date Published: 1st Sep 1975

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Biochem Pharmacol

Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.

Scales: Not specified

Abstract:

Not specified

Created: 17th Nov 2015 at 12:27



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