Presentations
Uploader: Quyen Nguyen
Contributor: Quyen Nguyen
Other contributors: Not specified
Version: 2
Projects: No Projects
Scales: Not specified
Created: 2nd Jun 2016 at 14:54  Last updated: 3rd Jun 2016 at 10:25
Uploader: Antonia Stank
Contributor: Antonia Stank, Jonathan Fuller, Michael Martinez, Rebecca Wade
Other contributors: Stefan Henrich, Stefan Richter
Version: 1
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling
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
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Created: 15th Jan 2016 at 13:49
Uploader: Lars Ole Schwen
Contributor: Lars Ole Schwen
Other contributors: Felix Gremse, Markus Krauss, Christoph Niederalt
Version: 1
Projects: C1: The role of blood flow in liver lobule function and morphology, CTU Image Processing, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis
Scales: Cell, Liver lobule, Liver and Organism
Talk at Jena Centre for Bioinformatics, 2014-11-20
Created: 25th Nov 2014 at 17:37
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
Version: 1
Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis
Scales: Cell, Liver lobule, Liver and Organism
Presentation at VPH 2014
Created: 11th Sep 2014 at 09:50
Uploader: Lars Ole Schwen
Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser
Other contributors: Christoph Niederalt, Felix Gremse
Version: 1
Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales
Scales: Cell, Liver lobule and Organism
Talk given at ISGSB 2014 in Durham (UK)
Created: 8th Sep 2014 at 10:03
Uploader: Lars Ole Schwen
Contributor: Lars Ole Schwen, Matthias König, Tobias Preusser
Other contributors: Not specified
Version: 1
Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis
Scales: Cell, Liver lobule, Liver and Organism
Presentation at WCCM-ECCM-ECFD 2014
Created: 25th Jul 2014 at 16:01
Uploader: Lars Ole Schwen
Contributor: Andrea Schenk, Fabian Kiessling, Lars Küpfer, Lars Ole Schwen, Markus Krauß, Tobias Preusser
Other contributors: Christoph Niederalt, Felix Gremse
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
Version: 1
Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis
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
Uploader: Iryna Ilkavets
Contributor: Iryna Ilkavets, Ivan Savora, Martin Golebiewski, Meik Bittkowski, Wolfgang Müller
Other contributors: Not specified
Version: 1
Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, C: Liver lobule level, CTU Confocal microscopy, CTU Drug detoxification, CTU Gene expression profiling, D: Whole organ level, F: Data management, Virtual Liver
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
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.
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Created: 18th Dec 2013 at 12:40
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.
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Created: 16th Dec 2013 at 10:23
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
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Created: 16th Dec 2013 at 10:01
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
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Created: 16th Dec 2013 at 09:53
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
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
Version: 1
Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., C1: The role of blood flow in liver lobule function and morphology, C2: Organization of the sinusoidal system and the liver lobule - referen..., C3: Zonation of metabolism and its regulation
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
Uploader: Clemens Kreutz
Contributor: Andreas Raue, Clemens Kreutz, Jens Timmer, Ursula Klingmüller
Other contributors: Not specified
Version: 1
Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A2.5: Integration of insulin and Wnt signalling in hepatocytes
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
Uploader: Jose Villaveces
Contributor: Bianca Habermann, Jose Villaveces
Other contributors: Rafael C. Jimenez
Version: 1
Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...
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
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Created: 30th Oct 2013 at 10:07  Last updated: 30th Oct 2013 at 10:21
Uploader: Lars Ole Schwen
Contributor: Lars Ole Schwen, Tobias Preusser
Other contributors: Not specified
Version: 1
Projects: D1: Regulation of Blood Flow and Perfusion in the Liver
Scales: Liver
Presentation at ECMTB 2011
Created: 8th Jul 2011 at 09:46  Last updated: 23rd Oct 2013 at 13:58
Uploader: Martin Golebiewski
Contributor: Martin Golebiewski
Other contributors: Not specified
Version: 1
Projects: F3: Kinetic data handling
Scales: Not specified
Created: 9th Sep 2013 at 12:12
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
Created: 8th Jul 2013 at 09:52