Publications

 

Wordprocessing A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule


Authors: K. Meyer, O. Ostrenko, G. Bourantas, H. Morales-Navarrete, N. Porat-Shliom, F. Segovia-Miranda, H. Nonaka, A. Ghaemi, J. M. Verbavatz, L. Brusch, I. Sbalzarini, Y. Kalaidzidis, R. Weigert, M. Zerial

PubMed ID: 28330614

Date Published: 24th Mar 2017

Projects: Showcase LIAM (Liver Image Analysis Based Model)

Journal: Cell Syst

Citation: Cell Syst. 2017 Mar 15. pii: S2405-4712(17)30052-2. doi: 10.1016/j.cels.2017.02.008.

Scales: Liver lobule

Abstract (Expand)

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its ...

Created: 25th Jul 2017 at 13:19


 

Wordprocessing Activating and Inhibitory Functions of WNT/β-catenin in the Induction of Cytochromes P450 by Nuclear Receptors in HepaRG Cells


Authors: Maria Thomas, Christine Bayha, Silvia Vetter, Ute Hofmann, Michael Schwarz, Ulrich M Zanger, Albert Braeuning

PubMed ID: 25824487

Date Published: 1st Apr 2015

Scales: Cell

Abstract (Expand)

The WNT/β-catenin signaling pathway has been identified as an important endogenous regulator of hepatic cytochrome P450 (CYP) expression in mouse liver. In particular, it is involved in the regulation ...

Created: 7th Apr 2015 at 14:00


 

Wordprocessing A Quick Guide for Building a Successful Bioinformatics Community


Authors: Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

DOI: 10.1371/journal.pcbi.1003972

Date Published: 5th Feb 2015

Projects: No Projects

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 11(2) : e1003972

Scales: Not specified

Abstract (Expand)

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role ...

Created: 9th Feb 2015 at 13:55   Last updated: 9th Feb 2015 at 14:06


 

Wordprocessing A Systematic Comparison of the Impact of Inflammatory Signaling on ADME Gene Expression and Activity in Primary Human Hepatocytes and HepaRG Cells


Authors: Marcus Klein, Maria Thomas, Ute Hofmann, Daniel Seehofer, Georg Damm, Ulrich M Zanger

PubMed ID: 25480923

Date Published: 7th Dec 2014

Scales: Not specified

Abstract (Expand)

Inflammatory processes are associated with compromised metabolism and elimination of drugs in the liver, largely mediated by proinflammatory cytokines, such as interleukin-6 (IL-6). The HepaRG cell ...

Created: 7th Dec 2014 at 10:17


 

Wordprocessing Algorithmically generated rodent hepatic vascular trees in arbitrary detail


Authors: Lars Ole Schwen, Weiwei Wei, Felix Gremse, Josef Ehling, Lei Wang, Uta Dahmen, Tobias Preusser

DOI: 10.1016/j.jtbi.2014.10.026

Date Published: 1st Nov 2014

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: Journal of Theoretical Biology

Citation: Journal of Theoretical Biology

Scales: Liver

Abstract (Expand)

Physiologically realistic geometric models of the vasculature in the liver are indispensable for modelling hepatic blood flow, the main connection between the liver and the organism. Current in vivo ...

Created: 17th Nov 2014 at 10:07   Last updated: 17th Nov 2014 at 10:12


 

Wordprocessing Adenoviral overexpression of Lhx2 attenuates cell viability but does not preserve the stem cell like phenotype of hepatic stellate cells


Authors: Berit Genz, Maria Thomas, Brigitte M Pützer, Marcin Siatkowski, Georg Fuellen, Brigitte Vollmar, Kerstin Abshagen

PubMed ID: 24995995

Date Published: 6th Jul 2014

Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. :

Scales: Cell

Abstract (Expand)

Hepatic stellate cells (HSC) are well known initiators of hepatic fibrosis. After liver cell damage, HSC transdifferentiate into proliferative myofibroblasts, representing the major source of extracellular ...

Created: 7th Jul 2014 at 20:27


 

Wordprocessing A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models


Authors: A. Ryll, J. Bucher, A. Bonin, S. Bongard, E. Gonçalves, J. Saez-Rodriguez, J. Niklas, S. Klamt

DOI: 10.1016/j.biosystems.2014.07.002

Date Published: 1st Jul 2014

Scales: Cell

Abstract (Expand)

Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling ...

Created: 6th Aug 2014 at 07:36   Last updated: 6th Aug 2014 at 07:50


 

Wordprocessing A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model


Authors: Minjun Chen, Chun-Wei Tung, Qiang Shi, Lei Guo, Leming Shi, Hong Fang, Jürgen Borlak, Weida Tong

PubMed ID: 24958025

Date Published: 11th Jun 2014

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Arch. Toxicol.

Citation: Arch. Toxicol. 88(7): 1439-49

Scales: Cell

Abstract (Expand)

Drug-induced liver injury (DILI) is a major cause of drug failures in both the preclinical and clinical phase. Consequently, improving prediction of DILI at an early stage of drug discovery will reduce ...

Created: 28th Jun 2014 at 16:37


 

Wordprocessing A Novel Mitochondrial MAVS/Caspase-8 Platform Links RNA Virus-Induced Innate Antiviral Signaling to Bax/Bak-Independent Apoptosis


Authors: Souhayla El Maadidi, Laura Faletti, Birgit Berg, Christin Wenzl, Katrin Wieland, Zhijian J Chen, Ulrich Maurer, Christoph Borner

PubMed ID: 24391214

Date Published: 3rd Jan 2014

Projects: No Projects

Journal: J. Immunol.

Citation: J. Immunol. 192(3): 1171-83

Scales: Not specified

Abstract (Expand)

Semliki Forest virus (SFV) requires RNA replication and Bax/Bak for efficient apoptosis induction. However, cells lacking Bax/Bak continue to die in a caspase-dependent manner. In this study, we show ...

Created: 22nd Jan 2014 at 15:15


 

Wordprocessing A multi-scale model of hepcidin promoter regulation reveals factors controlling systemic iron homeostasis


Authors: Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U Muckenthaler, Stefan Legewie

PubMed ID: 24391488

Date Published: 2nd Jan 2014

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 10(1): e1003421

Scales: Cell

Abstract (Expand)

Systemic iron homeostasis involves a negative feedback circuit in which the expression level of the peptide hormone hepcidin depends on and controls the iron blood levels. Hepcidin expression is regulated ...

Created: 14th Jan 2014 at 11:56


 

Wordprocessing A fat option for the pig: Hepatocytic differentiated mesenchymal stem cells for translational research


Authors: Sandra Brückner, Hans-Michael Tautenhahn, Sandra Winkler, Peggy Stock, Matthias Dollinger, Bruno Christ

PubMed ID: 24200501

Date Published: 4th Nov 2013

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

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. 321(2): 267-75

Scales: Cell and Liver

Abstract (Expand)

Study background: Extended liver resection is the only curative treatment option of liver cancer. Yet, the residual liver may not accomplish the high metabolic and regenerative capacity needed, which ...

Created: 10th Feb 2014 at 17:22


 

Wordprocessing ABCC11/MRP8 polymorphisms affect 5-fluorouracil-induced severe toxicity and hepatic expression


Authors: Tarek Magdy, Rudolf Arlanov, Stefan Winter, Thomas Lang, Kathrin Klein, Yu Toyoda, Toshihisa Ishikawa, Matthias Schwab, Ulrich M Zanger

PubMed ID: 24024896

Date Published: 13th Sep 2013

Scales: Not specified

Abstract (Expand)

Because 5-fluorodeoxyuridine monophosphate (5-FdUMP), an anabolic active metabolite of 5-fluorouracil (5-FU), is a substrate of MRP8 (encoded by ABCC11), we investigated whether ABCC11 polymorphisms ...

Created: 8th Jan 2014 at 14:01


 

Wordprocessing A theoretical study of lipid accumulation in the liver-implications for nonalcoholic fatty liver disease


Authors: J Schleicher, R Guthke, U Dahmen, O Dirsch, H G Holzhuetter, S Schuster

PubMed ID: 23999488

Date Published: 4th Sep 2013

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Biochim. Biophys. Acta

Citation: Biochim. Biophys. Acta 1841(1): 62-69

Scales: Cell

Abstract (Expand)

A hallmark of the nonalcoholic fatty liver disease is the accumulation of lipids. We developed a mathematical model of the hepatic lipid dynamics to simulate the fate of fatty acids in hepatocytes. Our ...

Created: 23rd Oct 2013 at 14:55   Last updated: 24th Oct 2013 at 16:14


 

Wordprocessing Assessment of hepatic detoxification activity: proposal of an improved variant of the (13)c-methacetin breath test


Authors: Hermann-Georg Holzhütter, Johan Friso Lock, Pouria Taheri, Sascha Bulik, Andrean Goede, Martin Stockmann

PubMed ID: 23967104

Date Published: 15th Aug 2013

Scales: Not specified

Abstract (Expand)

Breath tests based on the administration of a (13)C-labeled drug and subsequent monitoring of (13)CO2 in the breath (quantified as DOB - delta over baseline) liberated from the drug during hepatic ...

Created: 9th Sep 2013 at 15:13   Last updated: 24th Oct 2013 at 16:14


 

Wordprocessing Apoptosis induced by the fungal pathogen gliotoxin requires a triple phosphorylation of Bim by JNK


Authors: A Geissler, F Haun, D O Frank, K Wieland, M M Simon, M Idzko, R J Davis, U Maurer, C Borner

PubMed ID: 23832115

Date Published: 5th Jul 2013

Projects: No Projects

Journal: Cell Death Differ.

Citation: Cell Death Differ. 20(10): 1317-29

Scales: Not specified

Abstract (Expand)

We previously reported that gliotoxin (GT), the major virulence factor of the mold Aspergillus fumigatus causing invasive aspergillosis (IA) in immunocompromised patients, induces apoptosis in a ...

Created: 22nd Jan 2014 at 15:18


 

Wordprocessing Alkyne lipids as substrates for click chemistry-based in vitro enzymatic assays


Authors: Anne Gaebler, Robin Milan, Leon Straub, Dominik Hoelper, Lars Kuerschner, Christoph Thiele

PubMed ID: 23709689

Date Published: 23rd May 2013

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

Journal: J. Lipid Res.

Citation: J. Lipid Res. 54(8): 2282-90

Scales: Not specified

Abstract (Expand)

Click chemistry is evolving as a powerful tool in biological applications because it allows the sensitive and specific detection of compounds with alkyne or azido groups. Here we describe the use of ...

Created: 6th Jan 2014 at 11:19


 

Wordprocessing A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs


Authors: Philip Stegmaier, Alexander Kel, Edgar Wingender, Jürgen Borlak

DOI: 10.1371/journal.pcbi.1002958

Date Published: 21st Mar 2013

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 9(3) : e1002958

Scales: Cell

Abstract (Expand)

Algorithmic comparison of DNA sequence motifs is a problem in bioinformatics that has received increased attention during the last years. Its main applications concern characterization of potentially ...

Created: 28th Mar 2013 at 11:59   Last updated: 24th Oct 2013 at 16:14


 

Wordprocessing A community-driven global reconstruction of human metabolism


Authors: Ines Thiele, Neil Swainston, Ronan M T Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K Aurich, Hulda Haraldsdottir, Monica L Mo, Ottar Rolfsson, Miranda D Stobbe, Stefan G Thorleifsson, Rasmus Agren, Christian Bölling, Sergio Bordel, Arvind K Chavali, Paul Dobson, Warwick B Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon J Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le Novère, Naglis Malys, Alexander Mazein, Jason A Papin, Nathan D Price, Evgeni Selkov, Martin I Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes H G M van Beek, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans V Westerhoff, Douglas B Kell, Pedro Mendes, Bernhard Ø Palsson

PubMed ID: 23455439

Date Published: 3rd Mar 2013

Scales: Not specified

Abstract (Expand)

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', ...

Created: 19th Mar 2013 at 12:53   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Abnormal body iron distribution and erythropoiesis in a novel mouse model with inducible gain of iron regulatory protein (IRP)-1 function


Authors: D Casarrubea, L Viatte, T Hallas, A Vasanthakumar, R S Eisenstein, K Schümann, M W Hentze, B Galy

PubMed ID: 23455710

Date Published: 1st Mar 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: J. Mol. Med.

Citation: J. Mol. Med. 91(7): 871-81

Scales: Not specified

Abstract (Expand)

Disorders of iron metabolism account for some of the most common human diseases. Cellular iron homeostasis is maintained by iron regulatory proteins (IRP)-1 and 2 through their binding to cis-regulatory ...

Created: 14th Jan 2014 at 14:40


 

Wordprocessing A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induced Liver Injury


Authors: Yuping Wang, Zhi Lin, Zhichao Liu, Stephen Harris, Reagan Kelly, Jie Zhang, Weigong Ge, Minjun Chen, Jürgen Borlak, Weida Tong

PubMed ID: 23395088

Date Published: 12th Feb 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Am. J. Pathol.

Citation: Am. J. Pathol. 182(4): 1180-7

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) may present any morphologic characteristic of acute or chronic liver disease with no standardized terminology in place. Defining lexemes of DILI histopathology would ...

Created: 5th Mar 2013 at 16:36   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk


Authors: Juan G Diaz Ochoa, Joachim Bucher, Alexandre R R Péry, José M Zaldivar Comenges, Jens Niklas, Klaus Mauch

PubMed ID: 23346056

Date Published: 22nd Jan 2013

Projects: No Projects

Journal: Front Pharmacol

Citation: Front Pharmacol 3: 204

Scales: Not specified

Abstract (Expand)

In this study, we focus on a novel multi-scale modeling approach for spatiotemporal prediction of the distribution of substances and resulting hepatotoxicity by combining cellular models, a 2D liver ...

Created: 4th Feb 2013 at 11:46   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing A Mechanistic, Model-Based Approach to Safety Assessment in Clinical Development


Authors: J Lippert, M Brosch, O von Kampen, M Meyer, H.-U Siegmund, C Schafmayer, T Becker, B Laffert, L Goerlitz, S Schreiber, PJ Neuvonen, M Niemi, J Hampe, L Kuepfer

DOI: 10.1038/psp.2012.22

Date Published: 2013

Projects: G3: Clinical Translation to Pharmaceutical Drug Development, G: Clinical translation

Journal: CPT: pharmacomet. syst. pharmacol.

Citation: CPT: pharmacomet. syst. pharmacol. 2(1) : e21

Scales: Not specified

Abstract:

Not specified

Created: 28th Jan 2013 at 09:55   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes


Authors: Federico Pinna, Sven Sahle, Katharina Beuke, Michaela Bissinger, Selcan Tuncay, Lorenz A D'Alessandro, Ralph Gauges, Andreas Raue, Jens Timmer, Ursula Klingmüller, Peter Schirmacher, Ursula Kummer, Kai Breuhahn

PubMed ID: 23293603

Date Published: 31st Dec 2012

Scales: Cell and Intercellular

Abstract (Expand)

The cytokine tumor necrosis factor-alpha (TNFα) is one of the key factors during the priming phase of liver regeneration as well as in hepatocarcinogenesis. TNFα activates the nuclear factor ...

Created: 16th Jan 2013 at 08:49   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing A rapid screening assay to search for phosphorylated proteins in tissue extracts


Authors: Ignazio Garaguso, Juergen Borlak

PubMed ID: 23166814

Date Published: 15th Nov 2012

Projects: CTU Proteomics

Journal: PLoS ONE

Citation: PLoS ONE 7(11): e50025

Scales: Not specified

Abstract (Expand)

Reversible protein phosphorylation is an essential mechanism in the regulation of diverse biological processes, nonetheless is frequently altered in disease. As most phosphoproteome studies are based ...

Created: 14th Dec 2012 at 19:18   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing A variational approach to parameter estimation in ordinary differential equations


Authors: Daniel Kaschek, Jens Timmer

PubMed ID: 22892133

Date Published: 14th Aug 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 99

Scales: Cell

Abstract (Expand)

ABSTRACT: BACKGROUND: Ordinary differential equations are widely-used in the field of systems biology andchemical engineering to model chemical reaction networks. Numerous techniques havebeen developed ...

Created: 29th Oct 2012 at 10:50   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing A General Theoretical Framework to Infer Endosomal Network Dynamics from Quantitative Image Analysis


Authors: Lionel Foret, Jonathan E. Dawson, Roberto Villaseñor, Claudio Collinet, Andreas Deutsch, Lutz Brusch, Marino Zerial, Yannis Kalaidzidis, Frank Jülicher

DOI: 10.1016/j.cub.2012.06.021

Date Published: 1st Aug 2012

Scales: Intercellular

Abstract (Expand)

Background: Endocytosis allows the import and distribution of cargo into a series of endosomes with distinct morphological and biochemical characteristics. Our current understanding of endocytic cargo ...

Created: 21st Sep 2012 at 14:35   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Analysis of drug metabolism activities in a miniaturized liver cell bioreactor for use in pharmacological studies


Authors: Stefan A Hoffmann, Ursula Müller-Vieira, Klaus Biemel, Daniel Knobeloch, Sandra Heydel, Marc Lübberstedt, Andreas K Nüssler, Tommy B Andersson, Jörg C Gerlach, Katrin Zeilinger

PubMed ID: 22688505

Date Published: 13th Jun 2012

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen...

Journal: Biotechnology and bioengineering

Citation: Biotechnol. Bioeng. 109(12): 3172-81

Scales: Intercellular

Abstract (Expand)

Based on a hollow fiber perfusion technology with internal oxygenation, a miniaturized bioreactor with a volume of 0.5 mL for in vitro studies was recently developed. Here, the suitability of this novel ...

Created: 24th Aug 2012 at 11:07   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes


Authors: Jérémy Huard, Stephanie Mueller, Ernst D Gilles, Ursula Klingmüller, Steffen Klamt

PubMed ID: 22443451

Date Published: 27th Mar 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., E1: Integration on the cellular level

Journal: The FEBS journal

Citation: FEBS J. 279(18): 3290-313

Scales: Intercellular

Abstract (Expand)

During liver regeneration, quiescent hepatocytes re-enter the cell cycle to proliferate and compensate for lost tissue. Multiple signals including hepatocyte growth factor, epidermal growth factor, ...

Created: 18th Jul 2012 at 09:45   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing A hypothetical model of cargo-selective rab recruitment during organelle maturation


Authors: Bernd Binder, Hermann-Georg Holzhütter

PubMed ID: 22328341

Date Published: 14th Feb 2012

Projects: A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc...

Journal: Cell Biochem. Biophys.

Citation: Cell Biochem. Biophys. 63(1): 59-71

Scales: Cell

Abstract (Expand)

Rabs constitute a group of small GTPases that confer directionality to intracellular vesicle transport by promoting on the membrane of transport vesicles in the formation of specific protein complexes ...

Created: 18th Jul 2012 at 13:01   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins


Authors: Katrin Luckert, Taranjit S Gujral, Marina Chan, Mark Sevecka, Thomas O Joos, Peter K Sorger, Gavin Macbeath, Oliver Pötz

PubMed ID: 22234610

Date Published: 12th Jan 2012

Projects: CTU Protein Arrays

Journal: Sci Signal

Citation: Sci Signal 5(206): pl1

Scales: Not specified

Abstract (Expand)

A system-wide analysis of cell signaling requires detecting and quantifying many different proteins and their posttranslational modification states in the same cellular sample. Here, we present Protocols ...

Created: 27th Nov 2012 at 13:16   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Analysis and Algorithmic Generation of Hepatic Vascular Systems


Authors: Lars Ole Schwen, Tobias Preusser

DOI: 10.1155/2012/357687

Date Published: 2012

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: International Journal of Hepatology

Citation: International Journal of Hepatology 2012(3) : 1

Scales: Liver

Abstract (Expand)

A proper geometric model of the vascular systems in the liver is crucial for modeling blood flow, the connection between the organ and the rest of the organism. In vivo imaging does not provide sufficient ...

Created: 27th Sep 2012 at 16:42   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing A Lattice-gas Cellular Automaton Model for in Vitro Sprouting Angiogenesis


Authors: C. Mente, I. Prade, L. Brusch, G. Breier, A. Deutsch

DOI: 10.5506/APhysPolBSupp.5.99

Date Published: 20th Dec 2011

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., D4: Regeneration and Liver Size

Journal: Acta Phys. Pol. B

Citation: Acta Phys. Pol. B Proc. Suppl. 5(1) : 99

Scales: Not specified

Abstract (Expand)

The mechanisms of sprout formation and branching during sprouting angiogenesis are only partially understood and mostly attributed to nonlocal signals mediated by the heterogeneous distribution of ...

Created: 23rd Oct 2012 at 15:55   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Adiponectin upregulates hepatocyte CMKLR1 which is reduced in human fatty liver


Authors: Josef Wanninger, Sabrina Bauer, Kristina Eisinger, Thomas S Weiss, Roland Walter, Claus Hellerbrand, Andreas Schäffler, Akiko Higuchi, Kenneth Walsh, Christa Buechler

PubMed ID: 22118966

Date Published: 18th Nov 2011

Projects: CTU SOP Human Hepatocytes, Show cases

Journal: Mol. Cell. Endocrinol.

Citation: Mol. Cell. Endocrinol. 349(2): 248-54

Scales: Cell and Liver

Abstract (Expand)

Chemokine-like receptor 1 (CMKLR1) ligands chemerin and resolvin E1 are suggested to have a role in non-alcoholic fatty liver disease (NAFLD). Here, expression of CMKLR1 in liver cells and NAFLD was ...

Created: 30th Jan 2014 at 17:18


 

Wordprocessing A methionine-choline-deficient diet elicits NASH in the immunodeficient mouse featuring a model for hepatic cell transplantation


Authors: Sandra Pelz, Peggy Stock, Sandra Brückner, Bruno Christ

PubMed ID: 22108588

Date Published: 13th Nov 2011

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

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. 318(3): 276-87

Scales: Cell, Liver lobule and Liver

Abstract (Expand)

Non-alcoholic staetohepatitis (NASH) is associated with fat deposition in the liver favoring inflammatory processes and development of fibrosis, cirrhosis and finally hepatocellular cancer. In Western ...

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


 

Wordprocessing Applications and trends in systems biology in biochemistry


Authors: Katrin Hübner, Sven Sahle, Ursula Kummer

PubMed ID: 21707921

Date Published: 26th Jul 2011

Projects: HepatoSys, Virtual Liver

Journal: FEBS J.

Citation: FEBS J. 278(16): 2767-857

Scales: Cell

Abstract (Expand)

Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated ...

Created: 30th Aug 2012 at 13:14   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing A simple TLC-MALDI method to monitor oxidation products of phosphatidylcholines and -ethanolamines


Authors: A. Bischoff, M. Eibisch, B. Fuchs, R. Süss, M. Schürenberg, D. Suckau, J. Schiller

DOI: 10.1556/AChrom.23.2011.2.13

Date Published: 1st Jun 2011

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

Journal: Acta Chromatographica

Citation: Acta Chromatographica 23(2) : 365

Scales: Not specified

Abstract (Expand)

The analysis of lipid/phospholipid oxidation products is of primary importance. Although there are established HPLC and LC/MS techniques, it is shown here for the first time that the combination of ...

Created: 23rd Jun 2011 at 17:24   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes


Authors: Joachim Bucher, Stephan Riedmaier, Anke Schnabel, Katrin Marcus, Gabriele Vacun, Thomas S Weiss, Wolfgang E Thasler, Andreas K Nüssler, Ulrich M Zanger, Matthias Reuss

PubMed ID: 21548957

Date Published: 6th May 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: BMC Syst Biol

Citation: BMC Syst Biol 5: 66

Scales: Not specified

Abstract (Expand)

The individual character of pharmacokinetics is of great importance in the risk assessment of new drug leads in pharmacological research. Amongst others, it is severely influenced by the properties and ...

Created: 31st Jan 2012 at 11:59   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing Addressing parameter identifiability by model-based experimentation


Authors: A Raue, C Kreutz, T Maiwald, U Klingmuller, J Timmer

PubMed ID: 21405200

Date Published: 17th Mar 2011

Scales: Cell and Intercellular

Abstract (Expand)

Mathematical description of biological processes such as gene regulatory networks or signalling pathways by dynamic models utilising ordinary differential equations faces challenges if the model ...

Created: 18th Jul 2012 at 09:24   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing ABCB1 single-nucleotide polymorphisms determine tacrolimus response in patients with ulcerative colitis


Authors: K R Herrlinger, H Koc, S Winter, A Teml, E F Stange, K Fellermann, P Fritz, M Schwab, E Schaeffeler

PubMed ID: 21289623

Date Published: 2nd Feb 2011

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Clin. Pharmacol. Ther.

Citation: Clin. Pharmacol. Ther. 89(3): 422-8

Scales: Not specified

Abstract (Expand)

Tacrolimus (Tac) is effective in the treatment of steroid-refractory ulcerative colitis (UC); however, nonresponse and unpredictable side effects are major limitations. Because Tac response in patients ...

Created: 18th Jul 2012 at 12:30   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing A comparison of sampling strategies for histological image analysis


Authors: André Homeyer, Uta Dahmen, Hai Huang, Andrea Schenk, Olaf Dirsch, HorstK Hahn

DOI: 10.4103/2153-3539.92034

Date Published: 2011

Projects: D4: Regeneration and Liver Size

Journal: J Pathol Inform

Citation: J Pathol Inform 2(2) : 11

Scales: Liver

Abstract (Expand)

Histological image analysis methods often employ machine-learning classifiers in order to adapt to the huge variability of histological images. To train these classifiers, the user must select samples ...

Created: 9th Mar 2012 at 15:42   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing Automated extraction of DNA and RNA from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression


Authors: Guido Hennig, Mathias Gehrmann, Udo Stropp, Hiltrud Brauch, Peter Fritz, Michel Eichelbaum, Matthias Schwab, Werner Schroth

PubMed ID: 20947696

Date Published: 14th Oct 2010

Projects: No Projects

Journal: Clin. Chem.

Citation: Clin. Chem. 56(12): 1845-53

Scales: Not specified

Abstract (Expand)

There is an increasing need for the identification of both DNA and RNA biomarkers from pathodiagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples for the exploration of individualized therapy ...

Created: 18th Jul 2012 at 12:20   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis


Authors: Carola Huthmacher, Andreas Hoppe, Sascha Bulik, Hermann-Georg Holzhütter

PubMed ID: 20807400

Date Published: 31st Aug 2010

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

Journal: BMC Syst Biol

Citation: BMC Syst Biol 4: 120

Scales: Cell

Abstract (Expand)

Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances ...

Created: 4th Jan 2013 at 10:50   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing A cell-based simulation software for multi-cellular systems


Authors: Stefan Hoehme, Dirk Drasdo

PubMed ID: 20709692

Date Published: 13th Aug 2010

Projects: No Projects

Journal: Bioinformatics

Citation: Bioinformatics 26(20): 2641-2

Scales: Not specified

Abstract (Expand)

CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates ...

Created: 10th Sep 2012 at 17:45   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing Atypical protein kinase C zeta exhibits a proapoptotic function in ovarian cancer


Authors: Irina Nazarenko, Marcel Jenny, Jana Keil, Cornelia Gieseler, Karen Weisshaupt, Jalid Sehouli, Stefan Legewie, Lena Herbst, Wilko Weichert, Silvia Darb-Esfahani, Manfred Dietel, Reinhold Schäfer, Florian Ueberall, Christine Sers

PubMed ID: 20501645

Date Published: 25th May 2010

Scales: Cell

Abstract (Expand)

Intracellular signaling governed by serine/threonine kinases comprises the molecular interface between cell surface receptors and the nuclear transcriptional machinery. The protein kinase C (PKC) family ...

Created: 11th Sep 2012 at 11:39   Last updated: 24th Oct 2013 at 16:20


 

Wordprocessing An update of MALDI-TOF mass spectrometry in lipid research


Authors: Beate Fuchs, Rosmarie Süss, Jürgen Schiller

PubMed ID: 20643161

Date Published: 25th Apr 2010

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

Journal: Prog. Lipid Res.

Citation: Prog. Lipid Res. 49(4): 450-75

Scales: Not specified

Abstract (Expand)

Although matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS)--often but not exclusively coupled with a time-of-flight (TOF) mass analyzer--is primarily established in the ...

Created: 23rd Jun 2011 at 17:13   Last updated: 24th Oct 2013 at 16:20


 

Wordprocessing Automating Mathematical Modeling of Biochemical Reaction Networks


Authors: Andreas Dräger, Adrian Schröder, Andreas Zell

DOI: 10.1007/978-1-4419-5797-9_7

Date Published: 2010

Projects: A3.4: Linking signalling to metabolic functions

Book: Systems Biology for Signaling Networks

Citation: Systems Biology for Signaling Networks : 159

Scales: Not specified

Abstract (Expand)

In this chapter we introduce a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each single step and how to ...

Created: 11th Jul 2011 at 09:40   Last updated: 24th Oct 2013 at 16:20


 

Wordprocessing Analysis of an apoptotic core model focused on experimental design using artificial data


Authors: R Schlatter, H Conzelmann, E D Gilles, O Sawodny, T Sauter

PubMed ID: 19640164

Date Published: 31st Jul 2009

Projects: No Projects

Journal: IET Syst Biol

Citation: IET Syst Biol 3(4): 255-65

Scales: Not specified

Abstract (Expand)

The activation of caspases is a central mechanism in apoptosis. To gain further insights into complex processes like this, mathematical modelling using ordinary differential equations (ODEs) can be a ...

Created: 3rd Dec 2010 at 10:00   Last updated: 24th Oct 2013 at 16:21


 

Wordprocessing Accessible methods for the dynamic time-scale decomposition of biochemical systems


Authors: Irina Surovtsova, Natalia Simus, Thomas Lorenz, Artjom König, Sven Sahle, Ursula Kummer

PubMed ID: 19633098

Date Published: 24th Jul 2009

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 25(21): 2816-23

Scales: Not specified

Abstract (Expand)

The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the ...

Created: 30th Aug 2012 at 13:24   Last updated: 24th Oct 2013 at 16:21


 

Wordprocessing A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles


Authors: Bernd Binder, Andrean Goede, Nikolaus Berndt, Hermann-Georg Holzhütter

PubMed ID: 20041124

Date Published: 21st Jul 2009

Projects: A3.3: Hepatocyte polarity

Journal: PLoS ONE

Citation: PLoS ONE 4(12): e8295

Scales: Not specified

Abstract (Expand)

Formation, degradation and renewal of cellular organelles is a dynamic process based on permanent budding, fusion and inter-organelle traffic of vesicles. These processes include many regulatory proteins ...

Created: 4th Feb 2011 at 12:47   Last updated: 24th Oct 2013 at 16:21


 

Wordprocessing A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts


Authors: Nils Blüthgen, Stefan Legewie, Szymon M Kielbasa, Anja Schramme, Oleg Tchernitsa, Jana Keil, Andrea Solf, Martin Vingron, Reinhold Schäfer, Hanspeter Herzel, Christine Sers

PubMed ID: 19154344

Date Published: 12th Jan 2009

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 276(4): 1024-35

Scales: Not specified

Abstract (Expand)

Mitogen-activated protein kinase (MAPK) signaling determines crucial cell fate decisions in most cell types, and mediates cellular transformation in many types of cancer. The activity of MAPK is ...

Created: 11th Sep 2012 at 11:44   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing A minimal circadian clock model


Authors: Ilka M Axmann, Stefan Legewie, Hanspeter Herzel

PubMed ID: 18546474

Date Published: 12th Jun 2008

Projects: HepatoSys

Journal: Genome Inform

Citation: Genome Inform 18: 54-64

Scales: Not specified

Abstract (Expand)

The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Thereby, an internal circadian oscillator drives gene expression in an ...

Created: 11th Sep 2012 at 13:01   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing A mesoscale model of G1/S phase transition in liver regeneration


Authors: Anuradha Chauhan, Stefan Legewie, Pål O Westermark, Stephan Lorenzen, Hanspeter Herzel

PubMed ID: 18339403

Date Published: 1st Feb 2008

Projects: HepatoSys

Journal: J. Theor. Biol.

Citation: J. Theor. Biol. 252(3): 465-73

Scales: Not specified

Abstract (Expand)

The liver regenerates and maintains its function and size after injury by counterbalancing cell death with compensatory cell division. During liver regeneration, injured sites release cytokines, which ...

Created: 11th Sep 2012 at 13:05   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling


Authors: Carola Huthmacher, Christoph Gille, Hermann-Georg Holzhütter

PubMed ID: 17988690

Date Published: 5th Oct 2007

Projects: No Projects

Journal: J. Theor. Biol.

Citation: J. Theor. Biol. 252(3): 456-64

Scales: Not specified

Abstract (Expand)

Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal ...

Created: 4th Jan 2013 at 13:00   Last updated: 24th Oct 2013 at 16:23


 

Wordprocessing An error model for protein quantification


Authors: C Kreutz, M M Bartolome Rodriguez, T Maiwald, M Seidl, H E Blum, L Mohr, J Timmer

PubMed ID: 17768165

Date Published: 3rd Sep 2007

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes

Journal: Bioinformatics

Citation: Bioinformatics 23(20): 2747-53

Scales: Not specified

Abstract (Expand)

MOTIVATION: Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility ...

Created: 10th Dec 2010 at 12:12   Last updated: 24th Oct 2013 at 16:23


 

Wordprocessing Activation of NF-kappaB by IL-1beta blocks IL-6-induced sustained STAT3 activation and STAT3-dependent gene expression of the human gamma-fibrinogen gene


Authors: Ute Albrecht, Xiangping Yang, Rosanna Asselta, Verena Keitel, Maria Luisa Tenchini, Stephan Ludwig, Peter C Heinrich, Dieter Häussinger, Fred Schaper, Johannes G Bode

PubMed ID: 17543500

Date Published: 1st May 2007

Scales: Not specified

Abstract (Expand)

Despite the essential role of the fibrinogen gamma-chain as a blood clotting factor, the fibrinogen gamma-chain contains a number of interaction sites to recruit other factors such as leukocytes important ...

Created: 31st Aug 2012 at 11:47   Last updated: 24th Oct 2013 at 16:23



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