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 (NASH). (NASH), the inflammatory form of NAFLD can follow NAFLD if it goes undetected. LiSyM scientists also investigate liver disease caused by exposure to selected harmful chemicals, drugs and other toxins. In LiSyM, 37 research groups at 23 scientific centers and institutions located around Germany have joined forces to tackle some of the most complex problems of the human body.
Web page: https://www.lisym.org/
Funding details:Federal Ministry of education and Research (BMBF)
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- People (122)
- Projects (13)
- Institutions (38)
- Investigations (11+11)
- Studies (8+23)
- Assays (36+47)
- Data files (214+139)
- Models (10+4)
- SOPs (6+17)
- Publications (302)
- Presentations (103+97)
- Events (61+8)
- Documents (6+185)
- Samples (114+120)
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
In chronic diseases, at some point the liver can suddenly stop functioning. This is called acute-on-chronic liver failure, or ACLF. This is the leading cause of death in liver patients and is often provoked by the use of transcription or freely available drugs or alcohol abuse. For this condition we need an effective treatment quickly. LiSyM-Pillar III researches the factors that contribute significantly to ACLF. What exactly happens then? Are there any early signs that would enable ACLF to be ...
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/pillar-research
Start date: 1st Jan 2016
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Rattus rattus
In one in five people with NAFLD, the functioning liver cells, the hepatocytes, are replaced by connective tissue. Eventually this fibrosis becomes irreversible. In this state the liver is like a ‘scar that never heals’. Through it, the liver loses many of its vital functions. LiSyM-Pillar II wants to know more about which factors promote fibrosis and the conditions under which fibrosis becomes irreversible How can fibrosis be diagnosed as early as possible? Researchers in the pillar are also ...
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/pillar-research
Start date: 1st Jan 2016
Organisms: Mus musculus, Rattus rattus, Rattus norvegicus, Homo sapiens
This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org
Start date: 1st Jan 2016
Organisms: Rattus norvegicus, Rattus rattus, Mus musculus, Homo sapiens
One of the tasks of the healthy liver is to store fat. Yet, at some stage, too much fat makes the liver sick. One critical time point occurs when a healthy fatty liver becomes inflamed and progresses to steatohepatitis, or NASH. LiSyM-Pillar I will identify what events lead to this transition. Does it occur in all parts of the liver? Which molecules indicate that it is taking place? Can the degeneration be stopped or undone - and if so, how?
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/pillar-research/zones-of-the-liver
Start date: 1st Jan 2016
Organisms: Mus musculus, Rattus rattus, Rattus norvegicus, Homo sapiens
Major infrastructure backbone of the whole LiSyM network. It comprises the core management tasks of the program directorate and the scientific project management, as well as the central data management. The data management concept relies on FAIRDOM (http://fair-dom.org) and uses the LiSyM SEEK platform as a major hub for exchanging data, models, SOPs and other information, as well as yellow pages for the projects with its corresponding members, institutions, events, presentations and publications. ...
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/data-management
Start date: 1st Jan 2016
Organisms: Not specified
To investigate the underlying molecular principles of metabolic and morphogenic zonation of the human liver lobule, we generated an integrated epigenetic map across three zones (pericentral, intermediate and periportal) by methylation and transcriptomic analysis of hepatocytes captured by laser micro-dissection. We observe a deep link between epigenetic zonation of human liver and a zonated expression of metabolic and morphogenic pathways: Key transcriptionally zonated enzymes in xenobiotic and ...
Submitter: Mario Brosch
Studies: Integrated epigenetic map across three hepatic zones (pericentral, inte...
Assays: DNA-methylation at binding sites of uniformly expressed transcription fa..., DNA-methylation at binding sites of uniformly expressed transcription fa..., DNA-methylation at binding sites of uniformly expressed transcription fa..., Transcriptomic analysis of hepatocytes ( hepatic zone: intermediate (IZ), Transcriptomic analysis of hepatocytes ( hepatic zone: periportal (PP), Transcriptomic analysis of hepatocytes ; hepatic zone: pericentral (CV)
Snapshots: No snapshots
Liver macrophages (LMs) play a central role in acute and chronic liver pathologies. In our study, we sought to gain further insight into the role of LMs in different liver pathologies and into their characteristics after isolation from liver tissue. Here we will characterize LMs in human liver tissue sections using immunohistochemistry and bioinformatic image analysis. We investigate liver tissues characterized by antiinflammatory LMs which show a homogeneous distribution and increased cell numbers ...
Submitter: Martin Golebiewski
Studies: In vivo and in vitro characterization of primary human macrophages and t...
Assays: Characterization of liver macrophages (LMs) in human liver tissue sections
Snapshots: No snapshots
We face a crisis in reproducibility, where it is impossible to believe most of the computational results shown in conferences and papers. Recent replication efforts and theoretical considerations indicate that most published research findings in biomedical research are wrong. This is especially problematic for the translation of computational models into the clinics. Modelling standards, software, and community initiatives are fundamental for reproducibility in systems biology and systems medicine. ...
Snapshots: No snapshots
Test for SEEK API upload.
Submitter: Matthias König
Studies: PKDB Caffeine Study
Assays: Digitized pharmacokinetics data (Akinyinka2000), Digitized pharmacokinetics data (Amchin1999), Digitized pharmacokinetics data (Blanchard1983a), Digitized pharmacokinetics data (Haller2002), Digitized pharmacokinetics data (Healy1991), Digitized pharmacokinetics data (Hetzler1990), Digitized pharmacokinetics data (Jeppesen1996), Digitized pharmacokinetics data (Kakuda2014), Digitized pharmacokinetics data (Kaplan1997), Digitized pharmacokinetics data (Magnusson2008), Digitized pharmacokinetics data (Oh2012), Digitized pharmacokinetics data (Perera2011), Digitized pharmacokinetics data (Spigset1999a), Digitized pharmacokinetics data (Tanaka2014)
Snapshots: No snapshots
Introduction: The field of pharmacokinetics describe the kinetics of substances administered to the body, consisting of absorption, distribution, metabolization and elimination (ADME) of the substance. An important use case is the testing of liver function via test substances like caffeine, methacetin or galactose in dynamical liver function tests. Understanding the kinetics of test substances and drugs is crucial to evaluate therapeutic outcome and diagnostic value.
Results: Physiologically based ...
Submitter: Matthias König
Studies: PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Compu...
Assays: No Assays
Snapshots: No snapshots
The study comprises 19 human liver biopsy donors divided into the groups normal control (NC = 7012, 7173, 7194, 7279), healthy obese (HO = 6758, 6922, 7213, 7230, 7252), bland steatosis (STEA = 6967, 7137, 7172, 7181, 7251) and early NASH (EARLY = 6610, 7041, 7157, 7188, 7344).
Hepatocytes captured by laser microdissection were obtained from three hepatic zones (pericentral, intermediate and periportal) and subjected to reduced representation bisulfite sequencing and RNA-seq resulting in 114 ...
Submitter: Mario Brosch
Investigation: Epigenomic analysis of micro-dissected human liver
Assays: DNA-methylation at binding sites of uniformly expressed transcription fa..., DNA-methylation at binding sites of uniformly expressed transcription fa..., DNA-methylation at binding sites of uniformly expressed transcription fa..., Transcriptomic analysis of hepatocytes ( hepatic zone: intermediate (IZ), Transcriptomic analysis of hepatocytes ( hepatic zone: periportal (PP), Transcriptomic analysis of hepatocytes ; hepatic zone: pericentral (CV)
Snapshots: No snapshots
Submitter: Alain Becam
Investigation: LiSyM Pillar III: Regeneration and Repair in Ac...
Assays: OpenBIS FILES
Snapshots: No snapshots
Submitter: Alain Becam
Investigation: LiSyM Pillar III: Regeneration and Repair in Ac...
Assays: OpenBIS FILES
Snapshots: No snapshots
Submitter: Alain Becam
Investigation: LiSyM Pillar III: Regeneration and Repair in Ac...
Assays: OpenBIS FILES
Snapshots: No snapshots
In this study, we investigated human LMs in tissue sections as well as isolated from human liver tissues which were characterized both in suspension and in adherent cultures to find out whether the inflammatory state of primary human LMs corresponds to patients and disease characteristics and whather it is possible to maintain the macrophage pattern in suspension as well as in adherent cultures with just a few limitations. (CCA: cholangiocarcinoma, CRLM: colorectal liver metastasis, FNH: focal ...
Submitter: René Hänsel
Investigation: Role of liver macrophages in different liver pa...
Assays: Characterization of liver macrophages (LMs) in human liver tissue sections
Snapshots: No snapshots
Submitter: Seddik Hammad
Assay type: Proteomics
Technology type: FACS
Investigation: Julia/Yan
Study: CCl4 Treatment in mice
Organisms: Mus musculus
SOPs: Sample Collection and Preservation of Blood and...
Data files: Movies for quantification, SAC mice RNA microarray, Supp MM 1, Supp fig 3, Supp fig1, Supp fig2, Supplemental Table 1:, Supplemental Table 2, Supplmentary Materials, Methods, Figures and Ta... and 1 hidden item
Snapshots: No snapshots
Data digitized from publication.
Hetzler1990 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Hetzler1990), PNG (Hetzler1990)
Snapshots: No snapshots
Data digitized from publication.
Spigset1999a Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Spigset1999a), PNG (Spigset1999a)
Snapshots: No snapshots
Data digitized from publication.
Akinyinka2000 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Akinyinka2000), PNG (Akinyinka2000)
Snapshots: No snapshots
Data digitized from publication.
Perera2011 Description
Submitter: Matthias König
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Caffeine investigation
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Perera2011), PNG (Perera2011)
Snapshots: No snapshots
Human RNA-Seq data set GSM2819712 stored in NCBI (GEO)
Creator: Mario Brosch
Submitter: Mario Brosch
Human RNA-Seq data set GSM2819698 stored in NCBI (GEO)
liver tissue sample : 6922_IZ_RNA
Creator: Mario Brosch
Submitter: Mario Brosch
Human RNA-Seq data set GSM2819714 stored in NCBI (GEO)
Creator: Mario Brosch
Submitter: Mario Brosch
Human RNA-Seq data set GSM2819713 stored in NCBI (GEO)
Creator: Mario Brosch
Submitter: Mario Brosch
Human RNA-Seq data set GSM2819711 stored in NCBI (GEO)
Creator: Mario Brosch
Submitter: Mario Brosch
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
not yet calibrated, not yet reduced
Creators: Daniel Lill, Viktor Makarenko
Submitter: Daniel Lill
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
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
The model is adapted from A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 https://doi.org/10.1242/jcs.128926
The model format is MorpheusML that can readily be loaded and run in Morpheus: https://morpheus.gitlab.io
Creator: Lutz Brusch
Submitter: Lutz Brusch
Model type: Ordinary differential equations (ODE)
Model format: MorpheusML
Environment: Morpheus
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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
Creator: Sonja Kleeschulte
Submitter: Sonja Kleeschulte
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Non-parenchymal liver cells are isolated and staining for FACS analysis
Creator: Sonja Kleeschulte
Submitter: Sonja Kleeschulte
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Macrophage staining in paraffin-embedded tissue
Creator: Sonja Kleeschulte
Submitter: Sonja Kleeschulte
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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: S. Chakraborty, G. Andrieux, P. Kastl, L. Adlung, S. Altamura, M. E. Boehm, L. E. Schwarzmuller, Y. Abdullah, M. C. Wagner, B. Helm, H. J. Grone, W. D. Lehmann, M. Boerries, H. Busch, M. U. Muckenthaler, M. Schilling, U. Klingmuller
Date Published: 20th Sep 2022
Publication Type: Journal
PubMed ID: 36130519
Citation: Cell Rep. 2022 Sep 20;40(12):111360. doi: 10.1016/j.celrep.2022.111360.
Abstract (Expand)
Authors: Guangyue Yang, Liping Zhuang, Tiantian Sun, Yee Hui Yeo, Le Tao, Wei Zhang, Wenting Ma, Liu Wu, Zongguo Yang, Yanqin Yang, Dongying Xue, Jie Zhang, Rilu Feng, Ebert Matthias P., Steven Dooley, Ekihiro Seki, Ping Liu, Cheng Liu
Date Published: 9th Jul 2022
Publication Type: Journal
DOI: 10.1155/2022/1048104
Citation: Canadian Journal of Gastroenterology and Hepatology 2022:1-9
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
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
Creator: Xiaoming Hu
Submitter: Xiaoming Hu
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Xiaoming Hu
Submitter: Xiaoming Hu
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Xiaoming Hu
Submitter: Xiaoming Hu
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Small movie explaining how to associate authors to profiles.
Creator: Wolfgang Müller
Submitter: Wolfgang Müller
Investigations: No Investigations
Studies: No Studies
Assays: No Assays