Wordprocessing Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice

Authors: K. Abshagen, M. Konig, A. Hoppe, I. Muller, M. Ebert, H. Weng, H. G. Holzhutter, U. M. Zanger, J. Bode, B. Vollmar, M. Thomas, S. Dooley

PubMed ID: 26589287

Date Published: 20th Nov 2015

Scales: Cell, Liver lobule and Liver

Abstract (Expand)

BACKGROUND: Disrupted bile secretion leads to liver damage characterized by inflammation, fibrosis, eventually cirrhosis, and hepatocellular cancer. As obstructive cholestasis often progresses insidiously, ...

Created: 23rd Nov 2015 at 07:41


Wordprocessing Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events

Authors: Jürgen Borlak, Prashant Singh, Giuseppe Gazzana

PubMed ID: 25872475

Date Published: 25th Feb 2015

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

Journal: BMC Genomics

Citation: BMC Genomics 16: 124

Scales: Cell

Abstract (Expand)

Hepatocellular carcinoma (HCC) is on the rise and the sixth most common cancer worldwide. To combat HCC effectively research is directed towards its early detection and the development of targeted ...

Created: 5th May 2015 at 13:29


Wordprocessing Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Authors: Michael Hucka, David P. Nickerson, Gary D. Bader, Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le Novère

DOI: 10.3389/fbioe.2015.00019

Date Published: 24th Feb 2015

Projects: F1: The data management system, Virtual Liver

Journal: Front. Bioeng. Biotechnol.

Citation: Front. Bioeng. Biotechnol. 3

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s ...

Created: 25th Feb 2015 at 12:58   Last updated: 25th Feb 2015 at 13:01


Wordprocessing Pathological implications of cadherin zonation in mouse liver

Authors: M. Hempel, A. Schmitz, S. Winkler, O. Kucukoglu, S. Bruckner, C. Niessen, B. Christ

PubMed ID: 25687506

Date Published: 17th Feb 2015

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

Journal: Cell Mol Life Sci

Citation: Cell Mol Life Sci. 2015 Jul;72(13):2599-612. doi: 10.1007/s00018-015-1861-y. Epub 2015 Feb 17.

Scales: Liver lobule

Abstract (Expand)

Both acute and chronic liver diseases are associated with ample re-modeling of the liver parenchyma leading to functional impairment, which is thus obviously the cause or the consequence of the disruption ...

Created: 11th Nov 2015 at 11:12


Wordprocessing Pregnane X receptor activation and silencing promote steatosis of human hepatic cells by distinct lipogenic mechanisms

Authors: Andreas Bitter, Petra Rümmele, Kathrin Klein, Benjamin A Kandel, Jessica K Rieger, Andreas K Nüssler, Ulrich M Zanger, Michael Trauner, Matthias Schwab, Oliver Burk

PubMed ID: 25182422

Date Published: 3rd Sep 2014

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

In addition to its well-characterized role in the regulation of drug metabolism and transport by xenobiotics, pregnane X receptor (PXR) critically impacts on lipid homeostasis. In mice, both ligand-dependent ...

Created: 5th Dec 2014 at 12:44


Wordprocessing Predicting idiosyncratic drug-induced liver injury - some recent advances

Authors: Minjun Chen, Jürgen Borlak, Weida Tong

PubMed ID: 24857265

Date Published: 27th May 2014

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

Journal: Expert Rev Gastroenterol Hepatol

Citation: Expert Rev Gastroenterol Hepatol : 1-3

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) is a major challenge for the pharmaceutical industry, regulatory authorities, and clinicians. It is usually categorized into 'intrinsic' and 'idiosyncratic', ...

Created: 28th Jun 2014 at 16:40


Wordprocessing 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

Authors: Seddik Hammad, Stefan Hoehme, Adrian Friebel, Iris von Recklinghausen, Amnah Othman, Brigitte Begher-Tibbe, Raymond Reif, Patricio Godoy, Tim Johann, Amruta Vartak, Klaus Golka, Petru O. Bucur, Eric Vibert, Rosemarie Marchan, Bruno Christ, Steven Dooley, Christoph Meyer, Iryna Ilkavets, Uta Dahmen, Olaf Dirsch, Jan Böttger, Rolf Gebhardt, Dirk Drasdo, Jan G. Hengstler

DOI: 10.1007/s00204-014-1243-5

Date Published: 1st May 2014

Scales: Liver lobule and Liver


Not specified

Created: 7th Nov 2014 at 15:11   Last updated: 7th Nov 2014 at 15:11


Wordprocessing Potential Roles of Bone Morphogenetic Protein (BMP)-9 in Human Liver Diseases

Authors: Blanca Herrera, Steven Dooley, Katja Breitkopf-Heinlein

PubMed ID: 24670474

Date Published: 29th Mar 2014

Scales: Not specified

Abstract (Expand)

Bone morphogenetic proteins (BMP-2 to BMP-15) belong to the Transforming Growth Factor (TGF)-β superfamily and, besides their well-documented roles during embryogenesis and bone formation, some of them ...

Created: 31st Mar 2014 at 11:18


Wordprocessing PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers

Authors: Jose M Villaveces, Rafael C Jimenez, Bianca H Habermann

PubMed ID: 25075287

Date Published: 13th Feb 2014

Scales: Not specified

Abstract (Expand)

Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks. Many ...

Created: 11th Aug 2014 at 16:31


Wordprocessing Phosphorylation of the Smo tail is controlled by membrane localisation and is dispensable for clustering

Authors: A. P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bokel

DOI: 10.1242/​jcs.128926

Date Published: 11th Oct 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Journal of Cell Science

Citation: Journal of Cell Science 126(20) : 4684

Scales: Cell

Abstract (Expand)

The Hedgehog (Hh) signalling cascade is highly conserved and involved in development and disease throughout evolution. Nevertheless, in comparison with other pathways, our mechanistic understanding of ...

Created: 24th Jan 2014 at 14:15   Last updated: 24th Jan 2014 at 14:21


Wordprocessing Practical quantification of necrosis in histological whole-slide images

Authors: André Homeyer, Andrea Schenk, Janine Arlt, Uta Dahmen, Olaf Dirsch, Horst K Hahn

PubMed ID: 23796718

Date Published: 21st Jun 2013

Projects: CTU Image Processing, D4: Regeneration and Liver Size

Journal: Comput Med Imaging Graph

Citation: Comput Med Imaging Graph 37(4): 313-22

Scales: Liver lobule and Liver

Abstract (Expand)

Since the histological quantification of necrosis is a common task in medical research and practice, we evaluate different image analysis methods for quantifying necrosis in whole-slide images. In a ...

Created: 7th Nov 2013 at 08:56


Wordprocessing Profile likelihood in systems biology

Authors: Clemens Kreutz, Andreas Raue, Daniel Kaschek, Jens Timmer

PubMed ID: 23581573

Date Published: 9th May 2013

Scales: Not specified

Abstract (Expand)

Inferring knowledge about biological processes by a mathematical description is a major characteristic of Systems Biology. To understand and predict system's behavior the available experimental ...

Created: 14th Jan 2014 at 11:37


Wordprocessing Pharmacogenetics of cytochrome P450 2B6 (CYP2B6): advances on polymorphisms, mechanisms, and clinical relevance

Authors: Ulrich M Zanger, Kathrin Klein

PubMed ID: 23467454

Date Published: 5th Mar 2013

Projects: A3.4: Linking signalling to metabolic functions

Journal: Front Genet

Citation: Front Genet 4: 24

Scales: Not specified

Abstract (Expand)

Cytochrome P450 2B6 (CYP2B6) belongs to the minor drug metabolizing P450s in human liver. Expression is highly variable both between individuals and within individuals, owing to non-genetic factors, ...

Created: 8th Jan 2014 at 14:10


Wordprocessing Pharmacogenomics of Cytochrome P450 3A4: Recent Progress Toward the "Missing Heritability" Problem

Authors: Kathrin Klein, Ulrich M Zanger

PubMed ID: 23444277

Date Published: 25th Feb 2013

Scales: Not specified

Abstract (Expand)

CYP3A4 is the most important drug metabolizing enzyme in adult humans because of its prominent expression in liver and gut and because of its broad substrate specificity, which includes drugs from most ...

Created: 8th Jan 2014 at 14:16


Wordprocessing Precise generation of systems biology models from KEGG pathways

Authors: Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell

DOI: 10.1186/1752-0509-7-15

Date Published: 2013

Scales: Cell and Intercellular

Abstract (Expand)

Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG ...

Created: 23rd Feb 2013 at 23:19   Last updated: 24th Oct 2013 at 16:15


Wordprocessing Parameter Estimation, Metabolic Network Modeling

Authors: Andreas Dräger, Hannes Planatscher

DOI: 10.1007/978-1-4419-9863-7_1174

Date Published: 2013

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

Book: Encyclopedia of Systems Biology

Citation: Encyclopedia of Systems Biology : 1627

Scales: Cell

Abstract (Expand)

Metabolic networks can mathematically be modeled as a differential equation system. These models consist of a stoichiometric matrix, a modulation matrix, and a vector of reaction rates. The mathematical ...

Created: 15th Aug 2013 at 23:37   Last updated: 23rd Jul 2015 at 13:38


Wordprocessing Path2Models: large-scale generation of computational models from biochemical pathway maps

Authors: Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère

DOI: 10.1186/1752-0509-7-116

Date Published: 2013

Scales: Cell and Intercellular

Abstract (Expand)

Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de ...

Created: 4th Nov 2013 at 16:48   Last updated: 4th Nov 2013 at 16:54


Wordprocessing Pharmacogenomics: a key component of personalized therapy

Authors: Matthias Schwab, Elke Schaeffeler

PubMed ID: 23194652

Date Published: 29th Nov 2012

Scales: Not specified


Not specified

Created: 5th Dec 2012 at 09:51   Last updated: 24th Oct 2013 at 16:15


Wordprocessing Pattern-formation mechanisms in motility mutants of Myxococcus xanthus

Authors: J. Starruss, F. Peruani, V. Jakovljevic, L. Sogaard-Andersen, A. Deutsch, M. Bar

DOI: 10.1098/rsfs.2012.0034

Date Published: 25th Oct 2012

Scales: Cell, Intercellular and Liver lobule


Not specified

Created: 12th Nov 2012 at 15:43   Last updated: 24th Oct 2013 at 16:15


Wordprocessing PPARA: A Novel Genetic Determinant of CYP3A4 In Vitro and In Vivo

Authors: Kathrin Klein, Maria Thomas, Stefan Winter, Andreas K Nussler, Mikko Niemi, Matthias Schwab, Ulrich M Zanger

PubMed ID: 22510778

Date Published: 18th Apr 2012

Projects: A3.4: Linking signalling to metabolic functions

Journal: Clinical pharmacology and therapeutics

Citation: Clin. Pharmacol. Ther. 91(6): 1044-52

Scales: Not specified

Abstract (Expand)

Interindividual variability in cytochrome P450 3A4 (CYP3A4) is believed to be largely heritable; however, predictive genetic factors have remained scarce. Using a candidate-gene approach in a human ...

Created: 14th May 2012 at 09:40   Last updated: 24th Oct 2013 at 16:16


Wordprocessing Pharmacogenomics of Codeine, Morphine, and Morphine-6-Glucuronide: Model-Based Analysis of the Influence of CYP2D6 Activity, UGT2B7 Activity, Renal Impairment, and CYP3A4 Inhibition

Authors: Thomas Eissing, Jörg Lippert, Stefan Willmann

PubMed ID: 22352453

Date Published: 23rd Feb 2012

Projects: E4: Vertical integration across biological scales, G: Clinical translation

Journal: Mol Diagn Ther

Citation: Mol Diagn Ther 16(1): 43-53

Scales: Organism

Abstract (Expand)

Background and Objective: The analgesic effect of codeine depends on the formation of the opioid metabolites morphine and morphine-6-glucuronide. Different factors have been shown or suspected to affect ...

Created: 1st Mar 2012 at 16:49   Last updated: 24th Oct 2013 at 16:16


Wordprocessing Phosphatidylcholine dimers can be easily misinterpreted as cardiolipins in complex lipid mixtures: a matrix-assisted laser desorption/ionization time-of-flight mass spectrometric study of lipids from hepatocytes

Authors: Mandy Eibisch, Sebastian Zellmer, Rolf Gebhardt, Rosmarie Süss, Beate Fuchs, Jürgen Schiller

PubMed ID: 23657956

Date Published: 30th Sep 2011

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

Journal: Rapid Commun. Mass Spectrom.

Citation: Rapid Commun. Mass Spectrom. 25(18): 2619-26

Scales: Cell and Liver

Abstract (Expand)

The liver is an important organ that is particularly involved in the lipid metabolism of the organism. Thus, high interest is nowadays focused on the lipid composition of the liver and particularly the ...

Created: 8th Jan 2014 at 13:25


Wordprocessing Prominent regulatory but weak antigen-presenting cell function of hepatic stellate cells

Authors: Frank A. Schildberg, Christian Kurts, Percy A. Knolle

DOI: 10.1002/hep.24565

Date Published: 2nd Sep 2011

Projects: B4: Regulation of pro-inflammatory stimuli through communication of live...

Journal: Hepatology

Citation: Hepatology 54(3) : 1108

Scales: Not specified


Not specified

Created: 18th Jul 2012 at 17:23   Last updated: 24th Oct 2013 at 16:17


Wordprocessing Paraoxonase (PON1 and PON3) Polymorphisms: Impact on Liver Expression and Atorvastatin-Lactone Hydrolysis

Authors: Stephan Riedmaier, Kathrin Klein, Stefan Winter, Ute Hofmann, Matthias Schwab, Ulrich M Zanger

PubMed ID: 21852972

Date Published: 27th Jul 2011

Scales: Cell

Abstract (Expand)

Atorvastatin δ-lactone, a major, pharmacologically inactive metabolite, has been associated with toxicity. In a previous study we showed that polymorphisms of UGT1A3 influence atorvastatin δ-lactone ...

Created: 27th Jun 2012 at 16:05   Last updated: 24th Oct 2013 at 16:18


Wordprocessing Proton pump inhibitors inhibit metformin uptake by organic cation transporters (OCTs)

Authors: Anne T Nies, Ute Hofmann, Claudia Resch, Elke Schaeffeler, Maria Rius, Matthias Schwab

PubMed ID: 21779389

Date Published: 14th Jul 2011

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

Journal: PLoS ONE

Citation: PLoS ONE 6(7): e22163

Scales: Not specified

Abstract (Expand)

Metformin, an oral insulin-sensitizing drug, is actively transported into cells by organic cation transporters (OCT) 1, 2, and 3 (encoded by SLC22A1, SLC22A2, or SLC22A3), which are tissue specifically ...

Created: 18th Jul 2012 at 13:31   Last updated: 24th Oct 2013 at 16:18


Wordprocessing [Pharmacogenomics: hype or hope?]

Authors: M Schwab, E Schaeffeler, U M Zanger, H Brauch, H K Kroemer

PubMed ID: 21365522

Date Published: 1st Mar 2011

Scales: Cell

Abstract (Expand)

Pharmacogenomics follows the concept of individualized medicine via targeted and tailored therapy for each patient. This is aided by current progress in human genome research that provided the basis ...

Created: 27th Jun 2012 at 16:14   Last updated: 24th Oct 2013 at 16:19


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

Authors: Albert Braeuning, Yasmin Singh, Benjamin Rignall, Albrecht Buchmann, Seddik Hammad, Amnah Othman, Iris von Recklinghausen, Patricio Godoy, Stefan Hoehme, Dirk Drasdo, Jan G Hengstler, Michael Schwarz

PubMed ID: 20886225

Date Published: 1st Oct 2010

Projects: No Projects

Journal: Histochem. Cell Biol.

Citation: Histochem. Cell Biol. 134(5): 469-81

Scales: Not specified

Abstract (Expand)

Signaling through the Wnt/β-catenin pathway is a crucial determinant of hepatic zonal gene expression, liver development, regeneration, and tumorigenesis. Transgenic mice with hepatocyte-specific ...

Created: 10th Sep 2012 at 17:18   Last updated: 24th Oct 2013 at 16:19


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

Authors: Stefan Hoehme, Marc Brulport, Alexander Bauer, Essam Bedawy, Wiebke Schormann, Matthias Hermes, Verena Puppe, Rolf Gebhardt, Sebastian Zellmer, Michael Schwarz, Ernesto Bockamp, Tobias Timmel, Jan G Hengstler, Dirk Drasdo

PubMed ID: 20484673

Date Published: 19th May 2010

Projects: B: Communication of Hepatocytes and Non-Parenchymal Liver Cells

Journal: Proc. Natl. Acad. Sci. U.S.A.

Citation: Proc. Natl. Acad. Sci. U.S.A. 107(23): 10371-6

Scales: Liver lobule

Abstract (Expand)

Only little is known about how cells coordinately behave to establish functional tissue structure and restore microarchitecture during regeneration. Research in this field is hampered by a lack of ...

Created: 14th Aug 2012 at 08:44   Last updated: 24th Oct 2013 at 16:20


Wordprocessing Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver

Authors: Kathrin Klein, Stefan Winter, Miia Turpeinen, Matthias Schwab, Ulrich M. Zanger

DOI: 10.3389/fphar.2010.00129

Date Published: 2010

Projects: B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Front. Pharmacol.

Citation: Front. Pharmacol. 1

Scales: Not specified

Abstract (Expand)

The human drug metabolizing cytochrome P450 (CYP) 1A2, is one of the major P450 isoforms contributing by about 5–20% to the hepatic P450 pool and catalyzing oxidative biotransformation of up to 10% of ...

Created: 27th Jan 2011 at 14:52   Last updated: 24th Oct 2013 at 16:20


Wordprocessing Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome

Authors: Dawadschargal Bech-Otschir, Annett Helfrich, Cordula Enenkel, Gesa Consiglieri, Michael Seeger, Hermann-Georg Holzhütter, Burkhardt Dahlmann, Peter-Michael Kloetzel

PubMed ID: 19169257

Date Published: 25th Jan 2009

Projects: No Projects

Journal: Nat. Struct. Mol. Biol.

Citation: Nat. Struct. Mol. Biol. 16(2): 219-25

Scales: Not specified

Abstract (Expand)

The 26S proteasome degrades polyubiquitylated (polyUb) proteins by an ATP-dependent mechanism. Here we show that binding of model polyUb substrates to the 19S regulator of mammalian and yeast 26S ...

Created: 4th Jan 2013 at 12:53   Last updated: 24th Oct 2013 at 16:21


Wordprocessing Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting

Authors: M Peifer, J Timmer

PubMed ID: 17441551

Date Published: 20th Apr 2007

Projects: HepatoSys

Journal: IET Syst Biol

Citation: IET Syst Biol 1(2): 78-88

Scales: Not specified

Abstract (Expand)

In silico investigations by simulating dynamical models of biochemical processes play an important role in systems biology. If the parameters of a model are unknown, results from simulation studies can ...

Created: 17th Aug 2012 at 10:29   Last updated: 24th Oct 2013 at 16:23


Wordprocessing Protein Domains of GTPases on Membranes: Do They Rely on Turing’s Mechanism?

Authors: Lutz Brusch, Perla Del Conte-Zerial, Yannis Kalaidzidis, Jochen Rink, Bianca Habermann, Marino Zerial, Andreas Deutsch

DOI: 10.1007/978-0-8176-4558-8_4

Date Published: 2007

Projects: HepatoSys

Book: Mathematical Modeling of Biological Systems, Volume I

Citation: Modeling and Simulation in Science, Engineering and Technology : 33

Scales: Cell

Abstract (Expand)

We evaluate different mechanisms for spatial domain formation of guanosine triphosphatases (GTPases) on cellular membranes. A kinetic model of the basic guanine-nucleotide cycle common to all GTPases ...

Created: 25th Jul 2011 at 17:22   Last updated: 24th Oct 2013 at 16:23


Wordprocessing Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways

Authors: U Klingmüller, A Bauer, S Bohl, P J Nickel, K Breitkopf, S Dooley, S Zellmer, C Kern, I Merfort, T Sparna, J Donauer, G Walz, M Geyer, C Kreutz, M Hermes, F Götschel, A Hecht, D Walter, L Egger, K Neubert, C Borner, M Brulport, W Schormann, C Sauer, F Baumann, R Preiss, S MacNelly, P Godoy, E Wiercinska, L Ciuclan, J Edelmann, K Zeilinger, M Heinrich, U M Zanger, R Gebhardt, T Maiwald, R Heinrich, J Timmer, F von Weizsäcker, J G Hengstler

PubMed ID: 17186705

Date Published: 26th Dec 2006

Projects: HepatoSys

Journal: Syst Biol (Stevenage)

Citation: Syst Biol (Stevenage) 153(6): 433-47

Scales: Cell

Abstract (Expand)

Complex cellular networks regulate regeneration, detoxification and differentiation of hepatocytes. By combining experimental data with mathematical modelling, systems biology holds great promises to ...

Created: 30th Aug 2012 at 12:39   Last updated: 24th Oct 2013 at 16:24

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