Data files
1st Announcement 7th Noordwijkerhout Symposium on Pharmocokinetics, Pharmacodynamics and Systems Pharmacology
Uploader: Adriano M. Henney
Contributor: Adriano M. Henney
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 8th Jul 2013 at 13:39
Uploader: Maria Thomas
Contributor: Maria Thomas
Other contributors: Not specified
Version: 1
Scales: Not specified
Nuclear Receptor PPARalpha Regulates Drug Metabolism in Human Liver
Created: 11th Nov 2011 at 15:10  Last updated: 20th Jun 2012 at 15:48
Affymetrix microarray data of primary mouse hepatocytes, comparison of the two types of hepatocytes with high and low insulin affinity
Uploader: Clemens Kreutz
Contributor: Clemens Kreutz, María Matilde Bartolomé Rodríguez
Other contributors: Not specified
Version: 1
Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...
Scales: Cell
The data set was generated from four samples (mice). For each sample, three conditions were measured:
a) unsorted cells
b) sorted cells: low insulin binding type
c) sorted cells: high insuin binding type
Altogether, 4x3 =12 experimental data sets were investigated.
Gene expression profiling was performed using an AffymetrixGeneChip mouse gene 2.0 ST Array (Affymetrix Europe, Wooburn Green, UK).
The probe sequences can be downloaded from the Affymetrix website.
The following files contain probe
...
Created: 27th Mar 2014 at 09:06  Last updated: 26th Jan 2015 at 18:08
Uploader: Seddik Hammad
Contributor: Jan Böttger, Seddik Hammad
Other contributors: Not specified
Version: 1
Projects: C5: Structural changes and functional consequences of the liver lobular/...
Scales: Liver lobule
reconstruction of BC network
Created: 6th Mar 2012 at 11:25  Last updated: 18th Jun 2012 at 13:58
Uploader: Antonia Stank
Contributor: Rebecca Wade
Other contributors: N.J. Bruce, Daria B. Kokh, M. Ozboyaci
Version: 1
Projects: F3: Kinetic data handling
Scales: Cell
Lecture notes from Winterschool in Juelich:
N.J. Bruce, Daria B. Kokh, M. Ozboyaci and Rebecca C. Wade.
Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.
In Computational Trends in Solvation and Transport in Liquids Lecture Notes, volume 28 of IAS Series, (2015) pages 259-280. Eds. Sutmann G., Grotendorst, J., Gompper,G., Marx,D. Schriften des Forschungszentrums Juelich.
https://juser.fz-juelich.de/record/188877/files/IAS-Band-28-V2.pdf
Created: 18th Sep 2015 at 13:48
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: F: Data management, Virtual Liver
Scales: Not specified
Tutorial workshop outline
Created: 13th Aug 2014 at 13:25
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe, Christian Bölling, Hermann-Georg Holzhütter, Matthias König, Sascha Bulik
Other contributors: Not specified
Version: 1
Projects: A: Cellular level
Scales: Cell
Supplement 5 of publication: HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
Created: 4th Mar 2014 at 11:25
Uploader: Bruno Christ
Contributor: Bruno Christ
Other contributors: Not specified
Version: 1
Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase Steatosis
Scales: Liver
Created: 12th Feb 2014 at 16:15  Last updated: 11th Jan 2016 at 08:48
Dynamic network reconstruction identified unexpected gene expression in primary hepatocytes after exchange of culture medium (FOSBE 2007 Contributed Paper)
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 11:49  Last updated: 1st Aug 2011 at 13:43
Uploader: Iryna Ilkavets
Contributor: Frank Herweck, Iryna Ilkavets, Sonja Lukowski, Steven Dooley
Other contributors: Not specified
Version: 1
Projects: B2.1: Hepatic stellate cells as source and target for hepatocellular gro..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., C5: Structural changes and functional consequences of the liver lobular/..., Showcase HGF and Regeneration, Showcase LPS and Inflammation
Scales: Not specified
Von der hepatischen Sternzelle zum 3D-Modell der Leberregeneration
In German, publication in Systembiologie 5, 2012
Created: 31st Oct 2012 at 13:01  Last updated: 10th Jun 2013 at 11:07
Uploader: Sebastian Vlaic
Contributor: Andreas Dräger, Sebastian Vlaic
Other contributors: Michael Weber, Peter Kupfer, Bianca Hoffmann
Version: 2
Projects: A3.6: Transcription factor network and links to metabolism in NAFLD
Scales: Not specified
GRN2SBML
Copyright (c) 2012-2013 Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e.V. - Hans-Knoell-Institut (HKI).
This program is free software; you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation, Version 3.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
...
Created: 15th Apr 2013 at 10:59  Last updated: 1st Nov 2013 at 13:36
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 22nd Jul 2014 at 11:43
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 22nd Jul 2014 at 11:44
Uploader: Martin Golebiewski
Contributor: Peter Hunter
Other contributors: Not specified
Version: 1
Projects: Virtual Liver
Scales: Not specified
Created: 2nd Jul 2013 at 11:54
In vitro KD of Rab5all for 5 days followed by 30 min DiI-LDL uptake. Strong effect on LDL internalization upon Rab5 loss
Uploader: Konstantina Diamantara
Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B3: Intercellular communication through cell adhesion
Scales: Not specified
Created: 28th Feb 2014 at 11:31  Last updated: 11th Jan 2016 at 15:18
Uploader: Konstantina Diamantara
Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B3: Intercellular communication through cell adhesion
Scales: Cell, Intercellular and Liver
Created: 28th Feb 2014 at 11:27  Last updated: 11th Jan 2016 at 15:18
Uploader: Konstantina Diamantara
Contributor: Anja Zeigerer, Hidenori Nonaka, Konstantina Diamantara, Marino Zerial
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B3: Intercellular communication through cell adhesion
Scales: Cell, Intercellular and Liver
Created: 28th Feb 2014 at 11:23  Last updated: 11th Jan 2016 at 15:18
Uploader: Konstantina Diamantara
Contributor: Anja Zeigerer, Jerome Gilleron, Konstantina Diamantara
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...
Scales: Not specified
Created: 11th Dec 2013 at 10:35  Last updated: 11th Jan 2016 at 15:18
Uploader: Iryna Ilkavets
Contributor: Bianca Habermann, Jose Villaveces
Other contributors: Not specified
Version: 1
Projects: A1: Cellular metabolism, A3: Crosslinking signalling metabolism and hepatocyte polarisation
Scales: Cell
KEGGViewer is an open-source tool freely available at the BioJS Registry. Renders a KEGGML file and displays a KEGG pathway.
Created: 19th Jun 2015 at 09:34
Uploader: Maria Thomas
Contributor: Andreas Dräger, Andreas Zell, Marcus Klein, Maria Thomas, Roland Keller, Thomas Joos, Ulrich Zanger, Ute Metzger, Wolfgang E. Thasler
Other contributors: Not specified
Version: 1
Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes
Scales: Not specified
Contains all experimental data used for the study "Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy logic modeling" by Keller and colleagues.
Created: 6th Oct 2015 at 13:16
Uploader: Jonathan Fuller
Contributor: Jonathan Fuller, Michael Martinez, Rebecca Wade
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling
Scales: Not specified
LigDig is a web application for investigating ligand-protein interactions. LigDig can be used to query structural and functional properties. LigDig can be accessed at http://mcm.h-its.org/ligdig
Created: 17th Jan 2014 at 15:21  Last updated: 6th Dec 2014 at 18:09
Uploader: Madlen Matz-Soja
Contributor: Madlen Matz-Soja, Rolf Gebhardt, Wolfgang Schmidt-Heck
Other contributors: Not specified
Version: 2
Projects: A1: Cellular metabolism
Scales: Cell
Transgenic mice with a conditional hepatocyte-specific deletion of the Smoothened gene after adolescence were characterized for alterations in gene expression via microarrays.
Created: 20th Oct 2015 at 09:10  Last updated: 3rd May 2017 at 11:12
Uploader: Andreas Dräger
Contributor: Andreas Dräger
Other contributors: Not specified
Version: 1
Scales: Not specified
The project A3.4 will create a combined model that containes metabolism, gene regulation and signal transduction with main focus on the influence of the nuclear receptors PXR, CAR, and PPARa. To this end, information is gathered from HepatoNet1, TRANSFAC, and Ingenuity aiming at creating an overal model, which will be equipped with kinetic information subsequently. In project B.5 a model of IL6 signal transduction that links of STAT3 and MAPK (ERK) to ADME genes is created using TRANSFAC, Ingenuity,
...
Created: 25th Jun 2011 at 11:23  Last updated: 12th Jan 2016 at 08:13
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: Virtual Liver
Scales: Not specified
Workshop outline
Created: 18th Jul 2014 at 11:48
Uploader: Matthias König
Contributor: Matthias König
Other contributors: Not specified
Version: 1
Projects: A: Cellular level
Scales: Not specified
Experimental data digitized from publication figure.
Twenty-four-hour endocrine and metabolic profiles following consumption of high-fructose corn syrup-, sucrose-, fructose-, and glucose-sweetened beverages with meals.
Stanhope KL, Griffen SC, Bair BR, Swarbrick MM, Keim NL, Havel PJ.
Am J Clin Nutr. 2008 May;87(5):1194-203.
PMID: 18469239
http://www.ncbi.nlm.nih.gov/pubmed/18469239
Created: 30th Jun 2015 at 07:18
Programme
German Conference on Bioinformatics 2012
Satellite Workshop
Organ-oriented Systems Biology
Uploader: Dominik Driesch
Contributor: Dominik Driesch
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 1st Nov 2012 at 16:44
Uploader: Iryna Ilkavets
Contributor: Bianca Habermann, Jose Villaveces
Other contributors: Not specified
Version: 1
Projects: A1: Cellular metabolism, A2: Integration of Signalling Pathways in Hepatocellular Response, A3: Crosslinking signalling metabolism and hepatocyte polarisation
Scales: Cell
PsicquicGraph, a BioJS component to visualize molecular inteactions from PSICQUIC servers. PsicquicGraph is freely available at the BioJS Registry for download and enhancement. Instructions on how to use the tool are available here http://goo.gl/kDaIgZ and the source code can be found at http://github.com/biojs/biojs and DOI:10.5281/zenodo.7709
Created: 19th Jun 2015 at 09:46
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 22nd Jul 2014 at 11:41
Uploader: Antonia Stank
Contributor: Rebecca Wade
Other contributors: Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling
Scales: Cell
SDA7 can be used to carry out Brownian dynamics simulations of the diffusional association in a continuum aqueous solvent of two solute molecules, e.g. proteins, or of a solute molecule to an inorganic surface. SDA7 can also be used to simulate the diffusion of multiple proteins, in dilute or concentrated solutions, e.g., to study the effects of macromolecular crowding.
Created: 18th Sep 2015 at 14:51
Uploader: Lorenza D'Alessandro
Contributor: No Contributor
Other contributors: Not specified
Version: 1
Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...
Scales: Not specified
Created: 28th Nov 2012 at 08:58  Last updated: 28th Nov 2012 at 09:07
Uploader: Iryna Ilkavets
Contributor: Christian Bölling, Hermann-Georg Holzhütter, Michael Weidlich
Other contributors: Not specified
Version: 1
Projects: F2: The Liver Knowledge Base (LKB)
Scales: Not specified
SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques. Link to the project is given.
Created: 19th Jun 2015 at 10:19
Supplement to "A Conceptual Mathematical Model of the Dynamic Self-Organisation of Distinct Cellular Organelles"
Uploader: Bernd Binder
Contributor: Bernd Binder
Other contributors: Not specified
Version: 1
Projects: A3.3: Hepatocyte polarity
Scales: Cell
Created: 13th Jan 2014 at 13:08  Last updated: 13th Jan 2014 at 13:15
Uploader: Bernd Binder
Contributor: Bernd Binder
Other contributors: Not specified
Version: 1
Projects: A3.3: Hepatocyte polarity
Scales: Not specified
Created: 13th Jan 2014 at 13:12
Supplementary data to
Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Enzyme protein chain lengths
Created: 10th Jan 2014 at 11:21  Last updated: 16th Jan 2014 at 16:42
Supplementary table 1 to
Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 10th Jan 2014 at 11:20  Last updated: 16th Jan 2014 at 16:43
Supplementary table 2 to
Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 10th Jan 2014 at 11:20  Last updated: 16th Jan 2014 at 16:44
Supplementary table 3 to
Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 10th Jan 2014 at 11:20  Last updated: 16th Jan 2014 at 16:44
Supplementary table 4 to
Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Uploader: Andreas Hoppe
Contributor: Andreas Hoppe
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Created: 10th Jan 2014 at 11:20  Last updated: 16th Jan 2014 at 16:41
Uploader: Meik Bittkowski
Contributor: Martin Golebiewski, Meik Bittkowski
Other contributors: Not specified
Version: 1
Projects: F: Data management
Scales: Not specified
Created: 30th Oct 2013 at 11:07  Last updated: 13th Apr 2016 at 13:33
TGF-β induced hepatocellular Wisp1 is expressed in HCC and drives proliferation of epithelial type cancer cells
Uploader: Iryna Ilkavets
Contributor: Iryna Ilkavets, Steven Dooley
Other contributors: Not specified
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, C5: Structural changes and functional consequences of the liver lobular/..., Showcase HGF and Regeneration
Scales: Cell, Intercellular and Liver lobule
Invited conference talk at Cold Spring Harbour Asia Meeting Shuzou 2012 Liver Metabolism, Diseases & Cancer
Created: 31st Oct 2012 at 12:52  Last updated: 10th Jun 2013 at 11:10
Uploader: Bruno Christ
Contributor: Bruno Christ
Other contributors: Not specified
Version: 1
Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase Steatosis
Scales: Liver
Created: 12th Feb 2014 at 16:18  Last updated: 11th Jan 2016 at 08:50
Uploader: Walter De Back
Contributor: Walter De Back
Other contributors: Not specified
Version: 1
Projects: No Projects
Scales: Not specified
Morpheus XML model of patterning of HUVEC cells in Matrigel culture, based on retention of external VEGF to cell-modified matrix.
As used in reference:
A Köhn-Luque, W de Back, Y Yamaguchi, K Yoshimura, M A Herrero, T Miura (2013) Dynamics of VEGF matrix-retention in vascular network patterning, Physical Biology, 10(6) : 066007, doi: 10.1088/1478-3975/10/6/066007
Created: 24th Jan 2014 at 14:08
Uploader: S. Babak Azimifar
Contributor: Matthias Mann, S. Babak Azimifar
Other contributors: Not specified
Version: 1
Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., C5: Structural changes and functional consequences of the liver lobular/...
Virtual Liver Retreat 2012 (Poster)
Quantitative Proteomics of liver
S. Babak Azimifar, Kirti Sharma, Mara Monetti, Nagarjuna Nagaraj and Matthias Mann*.
*Corresponding author; contact: S. Babak Azimifar (Max Planck Institute of Biochemistry, Martinsried, Germany; Azimifar@biochem.mpg.de).
Despite enormous progress in MS based proteomics, accurate quantification of in vivo proteomic and phosphoproteomic changes such as those in liver remains a challenge. We developed a new strategy which we termed
...
Created: 28th Nov 2012 at 08:35  Last updated: 28th Nov 2012 at 09:28
Uploader: Antonia Stank
Contributor: Jonathan Fuller, Rebecca Wade
Other contributors: Xiaofeng Yu, Michael Martinez, Annika L. Gable, Neil J. Bruce, Stefan Richte
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling
Scales: Cell
webSDA: a web server to simulate macromolecular diffusional association.
Created: 18th Sep 2015 at 14:47  Last updated: 18th Sep 2015 at 14:48
Uploader: Jose Villaveces
Contributor: Jose Villaveces
Other contributors: Not specified
Version: 1
Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C3: Zonation of metabolism and its regulation, C5: Structural changes and functional consequences of the liver lobular/...
Scales: Not specified
The use of biological networks for interpreting data is becoming a standard in bioinformatics analysis. It enables us to look at a process from the perspective of pathways and network modules rather than single genes. Yet, there are still many obstacles when dealing with biological networks, such as protein-protein interaction or genetic networks. Firstly, these type of networks represent binary, rather than complex biological interactions; then, networks are still viewed as ‘static’ and do not
...
Created: 19th Oct 2011 at 16:14  Last updated: 21st Oct 2011 at 11:22