This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
SEEK ID: https://seek.lisym.org/projects/13
Public web page: http://www.lisym.org
Organisms: Rattus norvegicus, Rattus rattus, Mus musculus, Homo sapiens
FAIRDOM PALs: Max Lüdemann, Matthias König, Vincent Moser, Matthias Reichert, Lutz Brusch, Christian Hudert, Janine Koehncke, Madlen Matz-Soja
Project start date: 1st Jan 2016
Related items
- People (117)
- Programmes (1)
- Institutions (35)
- Investigations (1+3)
- Studies (1+3)
- Assays (2+8)
- Data files (12+17)
- Models (4)
- SOPs (1+2)
- Publications (74)
- Presentations (43+47)
- Events (55+3)
- Documents (1+16)
Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)
Institutions: University of Freiburg - Institute of Physics, LiSyM programme directorate

Projects: LiSyM network, Forschungsnetzwerk LiSyM-Krebs, LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), DEEP-HCC network
Institutions: HITS gGmbH
Liver Systems Medicine : striving to develop non-invasive methods for diagnosing and treating NAFLD by combining mathematical modeling and biological research. LiSyM, is a multidisciplinary research network, in which molecular and cell biologists, clinical researchers, pharmacologists and experts in mathematical modeling examine the liver in its entirety. LiSyM research focuses on the metabolic liver disease non-alcoholic fatty liver disease (NAFLD), which includes non-alcoholic steatohepatitis ...
Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM PALs, Project Management PTJ, LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)
Web page: https://www.lisym.org/
Upon stimulation of cells with transforming growth factorb(TGF-b),Smad proteins form trimeric complexes and activate a broad spectrum of target genes. It remains unresolved which of the possible Smad complexes are formed in cellular contexts and how these contribute to gene expression. Combining quantitative mass spectrometry with a computational selection strategy, we investigate Smad complexes in the mouse hepatoma cell line Hepa1-6.
Submitter: Olga Krebs
Studies: Study about Smad complexes in liver-derived cells
Assays: Modelling asssay II Lucarelli paper, exp assay I Lucarelli paper
Snapshots: No snapshots
In this study we identify most relevant Smad complexes in liver-derived cells, the contribution of the Smad complexes on target gene expression, and the role of Smad abundance and Smad2 phosphorylation in hepatocellular carcinoma
Submitter: Olga Krebs
Investigation: Investigation of the Smad Protein Complex Forma...
Assays: Modelling asssay II Lucarelli paper, exp assay I Lucarelli paper
Snapshots: No snapshots
exp assay I Lucarelli paper
Submitter: Olga Krebs
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Investigation of the Smad Protein Complex Forma...
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Olga Krebs
Biological problem addressed: Signal Induction
Investigation: Investigation of the Smad Protein Complex Forma...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Creator: Seddik Hammad
Submitter: Seddik Hammad
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Proteomic Quantification of the Metabolic Targets in Tumor vs Adjacent Normal Liver Tissues
Creator: Seddik Hammad
Submitter: Seddik Hammad
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma
Creator: Seddik Hammad
Submitter: Seddik Hammad
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Alain Becam
Submitter: Alain Becam
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Alain Becam
Submitter: Alain Becam
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Taken from https://github.com/Benchmarking-Initiative/Benchmark-Models See the github repository for license Import and execute the model in d2d
Creator: Jens Timmer
Submitter: Daniel Lill
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Not specified
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Taken from https://github.com/Benchmarking-Initiative/Benchmark-Models License according to the github repository's license Import and execute with d2d
Creators: Jens Timmer, Lorenza D'Alessandro, S.Sobotta, A. Raue, J. Vanlier
Submitter: Daniel Lill
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Not specified
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
ODE model describes dynamics of IFNalpha-induced signaling in Huh7.5 cells for a time scale up to 32 hours after stimulation with IFNalpha. The model consists of an IFN receptor model, formation/degradation and cytoplasmic/nuclear shuttling of STAT1-homodimers, STAT1-STAT2-heterodimers and STAT1-STAT2-IRF9 (ISGF3) complexes. On top, formation of feedback proteins STAT1, STAT2, IRF9, USP18, SOCS1, SOCS3 and IRF2 and corresponding influences on IFNalpha signaling dynamics was incorporated. The model ...
Creators: Jens Timmer, Ursula Klingmüller, Daniel Seehofer, Marcus Rosenblatt, Krishna Kumar Tiwari, Frédérique Kok
Submitter: Olga Krebs
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix: Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985
The model format is MorpheusML that can readily be loaded and run in the free and open source software ...
Creator: Lutz Brusch
Submitter: Lutz Brusch
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
The purpose of this document is to define procedures to follow for exchanging the following items between collaboration partners within the LiSyM network: a) Exchanging samples of human origin obtained from a natural person (i.e. a patient or other human subject). b) Exchanging material derived from samples of human origin as defined in a). c) Exchanging associated data describing samples of human origin and derived material as defined in a) and b). d) Exchanging data derived from samples of human ...
Creators: Martin Golebiewski, Frank Lammert, Wolfgang Müller
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: S. Heming, P. Hansen, A. Vlasov, F. Schworer, S. Schaumann, P. Frolovaite, W. D. Lehmann, J. Timmer, M. Schilling, B. Helm, U. Klingmuller
Date Published: 26th Jan 2023
Publication Type: Journal
PubMed ID: 36699356
Citation: Bioinform Adv. 2022 Jan 17;2(1):vbac004. doi: 10.1093/bioadv/vbac004. eCollection 2022.
Abstract
Authors: Stefan Hoehme, Seddik Hammad, Jan Boettger, Brigitte Begher-Tibbe, Petru Bucur, Eric Vibert, Rolf Gebhardt, Jan G. Hengstler, Dirk Drasdo
Date Published: 2023
Publication Type: Journal
DOI: 10.1016/j.isci.2022.105714
Citation: iScience 26(1):105714
Abstract
Authors: Le Tao, Guangyue Yang, Tiantian Sun, Jie Tao, Chan Zhu, Huimin Yu, Yalan Cheng, Zongguo Yang, Mingyi Xu, Yuefeng Jiang, Wei Zhang, Zhiyi Wang, Wenting Ma, Liu Wu, Dongying Xue, Dongxue Wang, Wentao Yang, Yongjuan Zhao, Shane Horsefield, Bostjan Kobe, Zhe Zhang, Zongxiang Tang, Qigen Li, Qiwei Zhai, Steven Dooley, Ekihiro Seki, Ping Liu, Jianrong Xu, Hongzhuan Chen, Cheng Liu
Date Published: 2023
Publication Type: Journal
DOI: 10.1016/j.jhep.2022.12.031
Citation: Journal of Hepatology,S0168827823000132
Abstract
Authors: Rilu Feng, Kejia Kan, Carsten Sticht, Yujia Li, Shanshan Wang, Hui Liu, Chen Shao, Stefan Munker, Hanno Niess, Sai Wang, Christoph Meyer, Roman Liebe, Matthias P. Ebert, Steven Dooley, Huiguo Ding, Honglei Weng
Date Published: 1st Dec 2022
Publication Type: Journal
DOI: 10.1002/hep.32414
Citation: Hepatology 76(6):1673-1689
Abstract (Expand)
Authors: A. Friebel, T. Johann, D. Drasdo, S. Hoehme
Date Published: 30th Sep 2022
Publication Type: Journal
PubMed ID: 35976110
Citation: Bioinformatics. 2022 Sep 30;38(19):4622-4628. doi: 10.1093/bioinformatics/btac547.
Talk at the Jamboree 2021 about epigenomic map of human liver zonation and loss of zonation in end-stage liver disease
Creators: Mario Brosch, Jochen Hampe, Lutz Brusch, Marino Zerial, Clemens Schafmayer
Submitter: Mario Brosch
Jamboree presentation
Creators: Daniel Lill, Viktor Makarenko, Ursula Klingmüller, Jens Timmer
Submitter: Daniel Lill
Workshop from LiSyM retreat in January 2020. Additional slides devoted to Social Media for Academics. Developed by Peter Krinenberg from https://naturalscience.careers/
Creator: Olga Vvedenskaya
Submitter: Olga Vvedenskaya
We face a reproducibility crisis and computational science, with most published models neither being accessible nor reproducible. The Systems Biology Markup Language (SBML) is the de facto standard format for encoding pathway based models, which provides a means for exchanging process based models between researchers and tools. The talk gives an overview of SBML and SBML-based tools.
Creator: Matthias König
Submitter: Matthias König
ICSB is one of the largest international conferences on systems biology. Since the first conference in Tokyo in 2000, which was organized by Dr. Hiroaki Kitano, it has been held annually in different countries.
Country: United States
City: Hartford, Connecticut
SBMC 2020 was postponed to 10th - 12th of May 2021. Further information will follow soon.
Start Date: 10th May 2021
End Date: 12th May 2021
Event Website: https://sbmc2020.bioquant.uni-heidelberg.de
Country: Germany
City: Heidelberg
The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, systems medicine, synthetic biology and related fields. COMBINE 2020 will be a workshop-style event with invited lectures, oral presentations and posters, but also reserving enough time for afternoon breakout sessions to discuss topics around data and model standardization and integration, as well as harmonization and further ...
Country: United States
City: virtual
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, synthetic biology and related fields. HARMONY is a codefest-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people ...
Start Date: 9th Mar 2020
End Date: 13th Mar 2020
Event Website: http://co.mbine.org/events/HARMONY_2020
Country: United Kingdom
City: Hinxton, Cambridge
e:Med brings together leading scientists and exceptional young researchers from all over Germany in the emerging field of Systems Medicine. Systems medicine uses interdisciplinary systems-oriented research on diseases to create a basis for understanding complex physiological and pathological processes for development of innovative personalized diagnosis, therapies, and preventive measures. Key to the appropriate analysis and possibly to the modelling of Big Data derived from information levels ...
Start Date: 8th Mar 2020
End Date: 10th Mar 2020
Event Website: http://www.sys-med.de/de/meeting/emed-kick-off-2020/
Country: Germany
City: Bonn
Poster for the PhD retreat in Hofgeismar - Svenja Kemmer
Creator: Svenja Kemmer
Submitter: Svenja Kemmer
Investigations: No Investigations
Studies: No Studies
Assays: No Assays