Presentations

 

Pdf A 1.2 Detoxification in Hepatocytes Challenged by Steatotic Conditions


Uploader: Anne Bonin

Contributor: Anne Bonin, Hermann-Georg Holzhütter, Jochen Hampe, Jürgen Borlak, Klaus Mauch, Mario Brosch, Ulrich Zanger, Ute Hofmann

Other contributors: Jens Niklas

Scales: Cell

No description specified

Created: 11th Jul 2012 at 09:02


 

Pdf Access to reaction kinetics data: The SABIO-RK database


Uploader: Martin Golebiewski

Contributor: Andreas Weidemann, Elina Wetsch, Jonathan Fuller, Maja Rey, Martin Golebiewski, Michael Martinez, Rebecca Wade, Ulrike Wittig, Wolfgang Müller

Other contributors: Enkhjargal Algaa, Meik Bittkowski, Lenneke Jong, Renate Kania, Lei Shi, Stefan Henrich, Isabel Rojas

Scales: Cell

SABIO-RK is a curated database for biochemical reaction kinetics data. The system offers standardized data manually extracted from the literature or directly submitted from lab experiments. The captured data is standardized by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies.

Created: 9th Jul 2012 at 14:28   Last updated: 16th Jul 2012 at 14:43


 

Tar another test


Uploader: Quyen Nguyen

Contributor: Quyen Nguyen

Other contributors: Not specified

Version: 2

Projects: No Projects

Scales: Not specified

No description specified

Created: 2nd Jun 2016 at 14:54   Last updated: 3rd Jun 2016 at 10:25


 

Pdf Automated Encoding of Gene Regulatory Networks from Inference Tools in SBML


Uploader: Sebastian Vlaic

Contributor: Andreas Dräger, Sebastian Vlaic

Other contributors: Bianca Hoffmann

Scales: Cell

Poster at the GCB2012 in Jena

Created: 23rd Oct 2012 at 12:42   Last updated: 23rd Oct 2012 at 13:18


 

Pdf Bridging Experiments and Modelling: The SABIO-RK Reaction Kinetics Database


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: F3: Kinetic data handling

Scales: Not specified

Talk at the COMBINE 2012 meeting

Created: 9th Oct 2012 at 10:35


 

Pdf Building a liver knowledgebase: ontology-based representation of liver biochemical processes and their evidence


Uploader: Christian Bölling

Contributor: Christian Bölling, Hermann-Georg Holzhütter, Michael Weidlich

Other contributors: Not specified

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Computational approaches to study biochemistry require machine accessible representations of biochemical knowledge. Based on the requirements for assembling, managing and analysing genome-scale constraint-based models of liver metabolism we developed a semantic data model for representation of liver biochemical knowledge. Employing a role-based representation of biochemical processes as molecular events specified in the Web Ontology Language (OWL) we here outline an information model that employs
...

Created: 13th Jul 2012 at 16:24


 

Genericblue ChemSpot


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

ChemSpot is a named entity recognition tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and IUPAC entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It currently achieves an F1 measure of 74.2% on the SCAI corpus.
ChemSpot is released under the Common Public License 1.0.
...

Created: 16th Dec 2013 at 10:23


 

Pdf COMBINE 2011 Programme


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Not specified

No description specified

Created: 21st Oct 2011 at 16:39


 

Pdf COMBINE, what it is, what it could be


Uploader: Martin Golebiewski

Contributor: Nicolas Le Novère

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Not specified

No description specified

Created: 21st Oct 2011 at 16:33   Last updated: 21st Oct 2011 at 16:33


 

Pdf Constructive Algorithms for Modeling Realistic Vascular Structures


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen, Tobias Preusser

Other contributors: Not specified

Scales: Liver

Presentation at ECMTB 2011

Created: 8th Jul 2011 at 09:46   Last updated: 23rd Oct 2013 at 13:58


 

Ppt Crosstalk of glucagon- and interleukin 6-signaling at the promoter of the gluconeogenic key control enzyme phosphoenolpyruvate carboxykinase


Uploader: Bruno Christ

Contributor: Bruno Christ

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

The expression of phosphoenolpyruvate carboxykinase 1 (PCK1) is stimulated by glucagon via cAMP-dependent activation and enhancement of binding of the transcription factor CREB to the CRE element in the PCK1 promoter. In primary cultured rat hepatocytes the pro-inflammatory cytokine interleukin-6 (IL6) inhibited the expression of PCK1 although the mode of action remained unclear so far. Binding of IL6 to its receptor initiates phosphorylation of several tyrosine residues of gp130 by Janus kinases
...

Created: 27th Jul 2012 at 14:39


 

Pdf Dynamic network reconstruction identified unexpected gene expression in primary hepatocytes after exchange of culture medium (FOSBE 2007 Poster)


Uploader: Data From HepatoSys

Contributor: Data From HepatoSys, Reinhard Guthke, Rolf Gebhardt, Sebastian Zellmer, Wolfgang Schmidt-Heck

Other contributors: Not specified

Version: 1

Projects: HepatoSys

Scales: Not specified

Primary hepatocytes were exposed to a stimulus by exchanging culture medium, thereby simulating changes in the blood composition. The expression of genes at different time points was recorded. Differentially expressed genes were clustered using fuzzy c-means algorithm into five groups. The arcs of the possible network were identified using the NetGenerator algorithm under the restriction of biological knowledge. The analysis was restricted to the main metabolic pathways of hepatocytes. The reverse
...

Created: 1st Aug 2011 at 11:54   Last updated: 1st Aug 2011 at 13:41


 

Pdf Extended Feature Set for Chemical Named Entity Recognition and Indexing


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber, Philippe Thomas

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

The BioCreative IV CHEMDNER Task provides participants with the opportunity to compare their methods for chemical named entity recognition (NER) and indexing in a controlled environment. We contributed to this task with our previous conditional random field based system [1] extended by a number of novel general and domain-speci c features. For the latter, we used features derived from two existing chemical NER systems, ChemSpot [2] and OSCAR [3], as well as various external resources. In this
...

Created: 16th Dec 2013 at 10:01


 

Pdf GTC Bio - Protein-protein interaction October 23rd-25th Invited talk


Uploader: Jonathan Fuller

Contributor: Jonathan Fuller

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Invited talk abstract:

Recent successes have challenged the widely held belief that protein-protein interactions (PPIs) are 'undruggable'. We show that binding pockets defining PPIs and those that define protein-ligand interactions of currently marketed drugs are markedly different. In the case of PPIs, drug discovery methods that simultaneously target several small pockets at the protein-protein interface are likely to increase the chances of success in this new and important field of therapeutics.
...

Created: 18th Dec 2013 at 12:40


 

Ppt Highlight 1: Steven Dooley - Imaging and data generation of liver inflammation and fibrosis


Uploader: Iryna Ilkavets

Contributor: Anastasia Bachmann, Dirk Drasdo, Frank Herweck, Iryna Ilkavets, Jan Georg Hengstler, Stefan Höhme, Steven Dooley

Other contributors: Hamed Alborzy

Scales: Liver lobule

No description specified

Created: 8th Sep 2011 at 13:17   Last updated: 10th Jun 2013 at 17:53


 

Pdf How to prepare an input for the Portal?


Uploader: Iryna Ilkavets

Contributor: Iryna Ilkavets, Ivan Savora, Martin Golebiewski, Meik Bittkowski, Wolfgang Müller

Other contributors: Not specified

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

The Portal:
6 dimensions to organize content
easy information about difficult topics
quick and easy to publish the input
visibility to the public, colleagues and funders
presentation of the work of group

Created: 8th May 2014 at 15:24


 

Pdf ICSB Tutorial: SABIO-RK - Reaction Kinetics Database


Uploader: Martin Golebiewski

Contributor: Martin Golebiewski

Other contributors: Not specified

Version: 1

Projects: F3: Kinetic data handling

Scales: Not specified

No description specified

Created: 9th Sep 2013 at 12:12


 

Pdf ICSB workshop programme


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

No description specified

Created: 8th Jul 2013 at 09:52


 

Pdf IL-1 and IL-6 Signalling: Logical Modelling and Hepatocellular Specification (POSTER presented at 4th SBMC 2012, July 09-11 in Leipzig)


Uploader: Anke Ryll

Contributor: Anke Ryll, Leonidas G. Alexopoulos, Regina Samaga, Steffen Klamt

Other contributors: Fred Schaper

Scales: Cell

No description specified

Created: 11th Jul 2012 at 10:48   Last updated: 29th Nov 2012 at 10:36


 

Pdf Impact of high free fatty acid load on metabolic fluxes in the central energy metabolism of acute steatotic hepatocytes


Uploader: Anne Bonin

Contributor: Anne Bonin, Carlo Thiel, Klaus Mauch, Madlen Matz-Soja, Rolf Gebhardt, Ute Hofmann

Other contributors: Stefanie Mangin, Joachim Bucher, Stephanie Kopacz,

Scales: Cell

No description specified

Created: 11th Jul 2012 at 09:10   Last updated: 11th Jul 2012 at 09:13


 

Pdf Introduction to Iron Homeostasis - popular science level


Uploader: Christoph Metzendorf

Contributor: Christoph Metzendorf, Martina Muckenthaler

Other contributors: Not specified

Scales: Cell, Intercellular, Liver and Organism

A short introduction to the molecular basics of regulation of iron homeostasis

Created: 20th Sep 2012 at 14:52


 

Pdf Kinetic model of fast insulin signalling in hepatocytes


Uploader: Bernd Binder

Contributor: Bernd Binder

Other contributors: Not specified

Scales: Not specified

We investigate the influence of insulin, glucagon and epinephrine on the core metabolism of hepatocytes by means of a kinetic model. These hormones induce significant alterations in certain metabolic activities of key enzymes like Glycogen synthase and Glycogen phosphorylase. Insulin is the primary anabolic hormone promoting the storage of energy by stimulating, for example, the glycogen synthesis. The effect of Glucagon and epinephrine are opposite that of insulin. They cause the liver to convert
...

Created: 23rd Jul 2012 at 14:31   Last updated: 25th Jul 2012 at 14:01


 

Pdf Kinetic model of fast insulin signalling in hepatocytes


Uploader: Bernd Binder

Contributor: Bernd Binder

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Cell

We investigate the influence of insulin, glucagon and epinephrine on the core metabolism of hepatocytes by means of a kinetic model. These hormones induce significant alterations in certain metabolic activities of key enzymes like Glycogen synthase and Glycogen phosphorylase. Insulin is the primary anabolic hormone promoting the storage of energy by stimulating, for example, the glycogen synthesis. The effect of Glucagon and epinephrine are opposite that of insulin. They cause the liver to convert
...

Created: 12th Jul 2012 at 12:51   Last updated: 17th Jul 2012 at 14:06


 

Pdf Kinetic Modelling of Carbohydrate & Lipid Metabolism in Human Hepatocytes


Uploader: Matthias König

Contributor: Hermann-Georg Holzhütter, Matthias König, Nikolaus Berndt

Other contributors: Not specified

Scales: Cell and Liver

Motivation
The central carbon metabolism of the liver enables the remarkable homeostasis of numerous plasma metabolites under a wide variety of nutritional regimes and physiological states. Examples are the synthesis of glucose by gluconeogenesis and synthesis of ketone-body from fatty acids under fasting conditions or the postprandial storage of glucose and lipids in terms of glycogen and triglycerides.

Results
In order to better understand the regulatory mechanism accounting for the switch
...

Created: 9th Jul 2012 at 20:15   Last updated: 9th Jul 2012 at 20:20


 

Pdf LigDig : web application


Uploader: Michael Martinez

Contributor: Michael Martinez

Other contributors: Not specified

Version: 1

Projects: F3: Kinetic data handling

Scales: Not specified

Presentation VLN Retreat

Created: 28th Nov 2012 at 09:11


 

Pdf LigDig: a web server for querying ligand–protein interactions


Uploader: Antonia Stank

Contributor: Antonia Stank, Jonathan Fuller, Michael Martinez, Rebecca Wade

Other contributors: Stefan Henrich, Stefan Richter

Scales: Not specified

Background: One of the major challenges in complex multi-disciplinary systems biology projects is to understand and process data from a wide variety of data sources. Computational tools to assist in the analysis of this data are essential.
Method: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is
...

Created: 15th Jan 2016 at 13:49


 

Ppt LPS showcase - Introduction


Uploader: Katja Breitkopf-Heinlein

Contributor: Katja Breitkopf-Heinlein

Other contributors: Not specified

Version: 1

Projects: Showcase LPS and Inflammation

Scales: Not specified

No description specified

Created: 4th Apr 2012 at 12:43   Last updated: 4th Apr 2012 at 13:00


 

Ppt LPS Showcase: Mathematical modelling of LPS induced liver inflammation


Uploader: Katja Breitkopf-Heinlein

Contributor: Iryna Ilkavets, Johannes Bode, Katja Breitkopf-Heinlein, Marcus Klein, Maria Thomas, Steven Dooley, Ulrich Zanger, Ute Albrecht

Other contributors: Not specified

Scales: Cell

This poster presents a sub-section of new results that were created within this Showcase. It's focus is on hepatic stellate cells (HSC). Unexpectedly, LPS reduced expression of the activation marker αSMA and other pro-fibrogenic genes in HSC, a finding which challenges the common hypothesis of LPS being an activator of quiescent HSC.

Created: 10th Jul 2012 at 09:37   Last updated: 25th Jul 2012 at 13:17


 

Pdf Mid-Term Evaluation Introduction


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

No description specified

Created: 28th Jan 2013 at 15:39


 

Ppt MidtermReview Poster Projekt A3.1


Uploader: Sascha Bulik

Contributor: Hermann-Georg Holzhütter, Matthias König, Nikolaus Berndt, Sascha Bulik

Other contributors: Not specified

Scales: Cell

MidtermReview Poster Projekt A3.1

Created: 29th Jan 2013 at 15:12   Last updated: 12th Feb 2013 at 12:07


 

Ppt MidtermReview Poster Projekt E1


Uploader: Sascha Bulik

Contributor: Andreas Hoppe, Andreas Raue, Carsten Conradi, Christian Bölling, Clemens Kreutz, Daniel Kaschek, Hermann-Georg Holzhütter, Jens Timmer, Jeremy Huard, Katharina Waldow, Katrin Kolczyk, Lorenza D'Alessandro, Matthias König, Nikolaus Berndt, René Meyer, Sascha Bulik, Seong-Hwan Rho, Steffen Klamt, Stephanie Müller, Svantje Braun, Thomas Maiwald, Ursula Klingmüller, Ursula Kummer

Other contributors: Ralph Gauges

Scales: Not specified

MidtermReview Poster Projekt E1

Created: 29th Jan 2013 at 15:11   Last updated: 12th Feb 2013 at 12:13


 

Pdf Modeling and simulating the effects of atorvastatin on the central carbon metabolism of rat hepatocytes using SBMLsimulator


Uploader: Stephanie Hoffmann

Contributor: Andreas Dräger, Andreas Zell, Benjamin Kandel, Klaus Mauch, Marcus Klein, Maria Thomas, Roland Keller, Stephanie Hoffmann, Ulrich Zanger, Ute Hofmann

Other contributors: Klaus Maier

Scales: Cell

The cholesterol lowering drug atorvastatin (Lipitor) acts by inhibiting the enzyme HMGCoA reductase, which plays a central role in the production of cholesterol in the liver. To investigate the effects of atorvastatin on the central carbon metabolism and the bile acid synthesis we used rat hepatocyte as a model system and constructed a corresponding model based on HepatoNet1 and literature knowledge, e.g. the KEGG knowledgebase. To gain a high-quality model we fully balanced the model and checked
...

Created: 10th Jul 2012 at 09:54   Last updated: 17th Jul 2012 at 16:04


 

Pdf Modeling Flow Through Realistic, Algorithmically Generated Vascular Structures in the Liver


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen

Other contributors: Not specified

Scales: Liver

Presentation at 21st International Symposium on Mathematical Programming (ISMP 2012)

Created: 27th Aug 2012 at 12:19


 

Ppt Modelling liver regeneration after hepatocyte transplantation


Uploader: Bruno Christ

Contributor: Bruno Christ, Jan Georg Hengstler, Sandra Brückner, Seddik Hammad

Other contributors: Not specified

Scales: Liver lobule

Question: Liver regeneration is accomplished by the hepatocytes, which restore the liver mass after resection, trauma or toxic exposition provided that the insult does not affect the mitotic response of the hepatocytes. Parenchymal proliferation gives rise to progeny, which take over functional capacity. Yet, only limited knowledge is available on the time-dependent positional impact of regenerating hepatocytes ultimately determing the metabolic power of the liver as a whole. Therefore, it is
...

Created: 27th Jul 2012 at 14:13   Last updated: 27th Jul 2012 at 14:45


 

Pdf Moving Towards a Unified Protein Interaction Network


Uploader: Jose Villaveces

Contributor: Bianca Habermann, Jose Villaveces

Other contributors: Rafael C. Jimenez

Scales: Not specified

The analysis of biological networks for interpreting data is becoming a standard in bioinformatics as it enables us to look at a process from the perspective of pathways and network modules rather than single proteins. To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.
We work on several aspects concerning data integration in protein interaction
...

Created: 30th Oct 2013 at 10:07   Last updated: 30th Oct 2013 at 10:21


 

Zip Multi-Scale Simulation of Heterogeneous Metabolism in Mammalian Livers


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen

Other contributors: Felix Gremse, Markus Krauss, Christoph Niederalt

Scales: Cell, Liver lobule, Liver and Organism

Talk at Jena Centre for Bioinformatics, 2014-11-20

Created: 25th Nov 2014 at 17:37


 

Pdf Multi-Scale Simulation of Zonated Liver Metabolism


Uploader: Lars Ole Schwen

Contributor: Ahmed Ghallab, Andrea Schenk, André Homeyer, Arne Schenk, Fabian Kiessling, Hermann-Georg Holzhütter, Jan Georg Hengstler, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Serene Lee, Tobias Preusser, Uta Dahmen, Ute Hofmann

Other contributors: Felix Gremse, Benjamin Knowles

Scales: Cell, Liver lobule, Liver and Organism

presentation at SBMC2014

Created: 14th May 2014 at 15:30   Last updated: 14th May 2014 at 15:55


 

Genericblue Multiscale Simulation of Zonated Metabolism in Steatotic Livers


Uploader: Lars Ole Schwen

Contributor: André Homeyer, Arne Schenk, Lars Küpfer, Lars Ole Schwen, Michael Schwier, Olaf Dirsch, Tobias Preusser, Uta Dahmen

Other contributors: Felix Gremse

Scales: Cell, Liver lobule, Liver and Organism

Presentation at VPH 2014

Created: 11th Sep 2014 at 09:50


 

Ppt Non-Alcoholic Steatohepatitis (NASH) in immunodeficient mice: A model for xenogenic stem cell transplantation


Uploader: Bruno Christ

Contributor: Bruno Christ, Sandra Brückner

Other contributors: Not specified

Scales: Liver lobule

Question: NASH is a benign liver disease and will progress, if untreated, into fibrosis/cirrhosis and potentially into hepatocellular cancer. Human cell therapy approaches for the treatment of NASH have not been addressed yet. Therefore, the present work aimed at establishing an animal model to evaluate the feasibility of stem cell-derived hepatocytes in NASH.

Methods: Immundeficient Pfp/Rag2-/- mice were fed with a methionine-choline-deficient diet (MCD diet) for up to 5 weeks. Alanine-aminotransferase
...

Created: 27th Jul 2012 at 14:25   Last updated: 27th Jul 2012 at 14:43


 

Pdf Poster - Reconstitution of macrophage population during liver regeneration and impact of their differential activation on hepatocytes function and the regeneration process


Uploader: Stephanie Wolf

Contributor: Stephanie Wolf

Other contributors: Not specified

Scales: Not specified

No description specified

Created: 3rd Jan 2012 at 16:07


 

Pdf Presentation at Rhodes Conference June 2012


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

VLN overview presentation incorporating brief contributions from Drasdo, Zeigerer and Küpfer

Created: 12th Jun 2012 at 10:08


 

Pdf Presentation of HGF Showcase


Uploader: Stefan Höhme

Contributor: Stefan Höhme

Other contributors: Not specified

Scales: Not specified

No description specified

Created: 10th Jul 2012 at 11:24   Last updated: 17th Jul 2012 at 15:28


 

Pdf Presentation: From Hepatocytes to Whole Liver Function: A Multi-scale Model of Human Galactose Metabolism (VLN Retreat 2013)


Uploader: Matthias König

Contributor: Hermann-Georg Holzhütter, Matthias König

Other contributors: Not specified

Scales: Cell and Liver lobule

Overview preliminary results and first version of multi-scale model of human hepatic galactose metabolism.
First simulations of normal state and galactosemias.

See also:
Galactose investigation
http://seek.virtuelle-leber.de/investigations/88
Galactose study
http://seek.virtuelle-leber.de/studies/50
Galactose modelling assay
http://seek.virtuelle-leber.de/assays/71

Created: 3rd Nov 2013 at 15:03   Last updated: 8th Nov 2013 at 11:10


 

Pdf Role-based representation and inference of biochemical processes


Uploader: Christian Bölling

Contributor: Christian Bölling, Hermann-Georg Holzhütter, Michael Weidlich

Other contributors: Michel Dumontier

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Cell

Talk at the 3rd International Conference of Biomedical Ontology (ICBO) 2012, July 21-25, Graz, Austria

Abstract
Computational approaches to study biochemistry require machine accessible representations of biochemical knowledge. Based on the requirements for assembling, managing and analysing genome-scale constraint-based models of liver metabolism we developed a semantic data model for representation of liver biochemical knowledge. Adopting a consistent perspective on biochemical processes
...

Created: 14th Aug 2012 at 14:34   Last updated: 14th Aug 2012 at 14:35


 

Pdf SABIO-RK poster ICSB2012


Uploader: Martin Golebiewski

Contributor: Andreas Weidemann, Elina Wetsch, Lei Shi, Maja Rey, Martin Golebiewski, Ulrike Wittig, Wolfgang Müller

Other contributors: Enkhjargal Algaa, Meik Bittkowski, Lenneke Jong, Renate Kania, Isabel Rojas

Version: 1

Projects: F3: Kinetic data handling

Scales: Not specified

No description specified

Created: 10th Oct 2012 at 16:56


 

Pdf SBMC 2012 Programme & Abstract Book


Uploader: Martin Golebiewski

Contributor: Dirk Drasdo, Rolf Gebhardt

Other contributors: Not specified

Version: 1

Projects: Virtual Liver

Scales: Not specified

No description specified

Created: 9th Jul 2012 at 14:41   Last updated: 9th Jul 2012 at 14:45


 

Pdf SBMC-2012 Poster P1.7: Modelling of Temporal Transcriptional Regulation in Hepatocytes in Response to Cultural Adaptation by State Space Modelling and Granger Causality


Uploader: Wolfgang Schmidt-Heck

Contributor: Wolfgang Schmidt-Heck

Other contributors: Not specified

Scales: Cell

No description specified

Created: 13th Jul 2012 at 09:25   Last updated: 17th Jul 2012 at 16:09


 

Zip Show Case Steatosis - Portal Version


Uploader: Katja Steffi Lerche

Contributor: Hermann-Georg Holzhütter, Iwona Wallach, Katja Steffi Lerche, Rolf Gebhardt

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

No description specified

Created: 25th Feb 2013 at 14:31   Last updated: 25th Feb 2013 at 14:34


 

Ppt Show Case “LPS“: Steven Dooley - Lipopolysaccharide (LPS) induced inflammatory responses of the liver


Uploader: Iryna Ilkavets

Contributor: Anastasia Bachmann, Iryna Ilkavets, Steven Dooley

Other contributors: Not specified

Version: 1

Projects: Showcase LPS and Inflammation

Scales: Not specified

No description specified

Created: 8th Sep 2011 at 13:22   Last updated: 10th Jun 2013 at 17:52


 

Zip Spatially Resolved Simulation of Glucose Metabolism in the Human Liver


Uploader: Lars Ole Schwen

Contributor: Lars Ole Schwen, Matthias König, Tobias Preusser

Other contributors: Not specified

Scales: Cell, Liver lobule, Liver and Organism

Presentation at WCCM-ECCM-ECFD 2014

Created: 25th Jul 2014 at 16:01


 

Zip Spatio-Temporal Simulation of First Pass Drug Perfusion in a Murine Liver


Uploader: Lars Ole Schwen

Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser

Other contributors: Christoph Niederalt, Felix Gremse

Scales: Cell, Liver lobule and Organism

Talk given at ISGSB 2014 in Durham (UK)

Created: 8th Sep 2014 at 10:03


 

Genericblue Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver


Uploader: Lars Ole Schwen

Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser

Other contributors: Christoph Niederalt, Felix Gremse

Scales: Cell, Liver and Organism

Poster for VLN Retreat 2013 in Hünfeld

Created: 23rd Oct 2013 at 14:05   Last updated: 12th Jun 2014 at 09:58


 

Pdf Structuring and Visualization of Data in the Virtual Liver Data Management System


Uploader: Martin Golebiewski

Contributor: Andreas Weidemann, David Shockley, Jonathan Fuller, Lihua An, Martin Golebiewski, Rebecca Wade, Wolfgang Müller

Other contributors: Not specified

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Poster presented at the SBMC 2012

Created: 9th Jul 2012 at 14:13


 

Pdf The Challenges of 21st Century Medicine Demand a Big Science Approach


Uploader: Adriano M. Henney

Contributor: Adriano M. Henney

Other contributors: Not specified

Version: 1

Projects: No Projects

Scales: Not specified

Talk given at the Transatlantic Science Forum meeting in the European Parliament, November 12, 2013 (see http://www.tsciencef.org/event.php?id=2)

Created: 15th Nov 2013 at 15:43


 

Pdf Transcription Factor Networks and Links to Biological Processes in Liver Metabolic Diseases and NAFLD


Uploader: Sebastian Vlaic

Contributor: Sebastian Vlaic

Other contributors: Not specified

Scales: Cell

No description specified

Created: 12th Jul 2012 at 08:29


 

Pdf Transcriptome Response of Rat Liver in response to PPAR-agonists.


Uploader: Sebastian Vlaic

Contributor: Jürgen Borlak, Reinhard Guthke, Sebastian Vlaic

Other contributors: Martin Bens

Scales: Cell

No description specified

Created: 23rd Oct 2012 at 13:16


 

Ppt Transplantation of stem cell-derived hepatocytes ameliorate NASH in an immunodeficient mouse model


Uploader: Bruno Christ

Contributor: Bruno Christ, Sandra Brückner

Other contributors: Not specified

Scales: Liver lobule

Question: NASH is a common clinical picture, mostly induced by the Western diet. In the long run NASH is a risk factor for cirrhosis and liver cancer (HCC), which ultimately requires liver transplantation. Because donor organs are limited cell transplantation is a new feasible therapeutic approach. Within this project we asked whether mice suffering from diet-induced NASH would benefit from transplanted adult stem cell-derived hepatocyte-like cells.
Methods: Immunodeficient mice obtained a
...

Created: 27th Jul 2012 at 14:30


 

Pdf Uncertainty of model predictions


Uploader: Clemens Kreutz

Contributor: Andreas Raue, Clemens Kreutz, Jens Timmer, Ursula Klingmüller

Other contributors: Not specified

Scales: Not specified

Poster presented at the VLN Retreat in Hünfeld 2013
A method for statistically assessing uncertainties of model predictions is presented.

Created: 30th Oct 2013 at 11:01


 

Pdf WBI-NER: The impact of domain-specific features on the performance of identifying and classifying mentions of drugs


Uploader: Michael Weidlich

Contributor: Michael Weidlich, Tim Rocktäschel, Ulf Leser

Other contributors: Torsten Huber

Version: 1

Projects: F2: The Liver Knowledge Base (LKB)

Scales: Organism

Named entity recognition (NER) systems are often based on machine learning techniques to reduce the labor-intensive development of hand-crafted extraction rules and domain-dependent dictionaries. Nevertheless, time-consuming feature engineering is often needed to achieve state-of-the-art performance. In this study, we investigate the impact of such domain-specific features on the performance of recognizing and classifying mentions of pharmacological substances. We compare the performance of a
...

Created: 16th Dec 2013 at 09:53


 

Pdf Whole genome array analysis of cultured mouse hepatocytes identifies a JNK pathway mediated Acute Phase Response (APR) signature


Uploader: Agata Widera

Contributor: Agata Widera, Gisela Campos, Jan Georg Hengstler, Patricio Godoy, Reinhard Guthke, Rolf Gebhardt, Steven Dooley, Wolfgang Schmidt-Heck

Other contributors: Katharina Rochlitz, Nils Blüthgen

Scales: Cell

Primary hepatocytes are a fundamental tool to investigate molecular mechanisms in liver physiopathology. Hepatocytes cultured on a 2D collagen
monolayer (CMS for sub-confluent and CMC for confluent) quickly de-differentiate, becoming apoptotic resistant and loosing canalicular polarity,
whereas when cultured on a 3D extracellular matrix (e.g. collagen sandwich, S) they can better sustain a differentiated state and form bile canaliculi
(BC) making the latter system feasible for using hepatocytes
...

Created: 8th Jan 2013 at 11:45   Last updated: 8th Jan 2013 at 12:42


 

Pdf Whole genome array analysis of cultured mouse hepatocytes identifies a JNK pathway mediated Acute Phase Response (APR) signature


Uploader: Agata Widera

Contributor: Agata Widera, Gisela Campos, Jan Georg Hengstler, Patricio Godoy, Reinhard Guthke, Rolf Gebhardt, Steven Dooley, Wolfgang Schmidt-Heck

Other contributors: N. Blüthgen

Version: 2

Projects: No Projects

Scales: Not specified

Background: The liver is an organ acting as a first line of defense against a number of pathological conditions including sepsis via an acute phase response (APR). Primary hepatocytes are a fundamental tool to fully understand the complex circuitry of signal transduction and gene regulation in APR. However, it is known that primary hepatocytes undergo a dedifferentiation process, i.e., apoptotic resistance and epithelial to mesenchymal transition. These alterations are being partly repressed in
...

Created: 25th Jul 2012 at 14:04



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