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LiSyM network

Overview

This comprises the whole LiSyM network

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 created: 8th Jun 2017

Related items

Claire Barbieux

Projects: Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM network

Institutions: Deutsches Krebsforschungszentrum

Richa Batra

Projects: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM network

Institutions: Helmholtz Zentrum München - Institute of Computational Biology

https://orcid.org/0000-0003-3708-0086
Johannes Bausch

Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Early Metabolic Injury (LiSyM-EMI - Pillar I), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), The Hedgehog Signalling Pathway (LiSyM-JGMMS), LiSyM network, LiSyM Scientific Leadership Team

Institutions: University of Freiburg - Institute of Physics, LiSyM programme directorate

https://orcid.org/0000-0002-1003-1682
Ann-Kristin Becker

Projects: Early Metabolic Injury (LiSyM-EMI - Pillar I), LiSyM network

Institutions: University Medicine Greifswald - Institute of Bioinformatics

Marie-Luise Berres

Projects: Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network

Institutions: RWTH Aachen University Hospital - Department of Internal Medicine III

SBMC 2018 Book of Abstracts
LiSyM network
No description specified

Creators: None

Contributor: Martin Golebiewski

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LPS stimulated BMDM (ELISA analysis TNF-alpha)
LiSyM network
No description specified

Creator: Sonja Kleeschulte

Contributor: Sonja Kleeschulte

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Key Visual SBMC 2018 Bremen
LiSyM network
No description specified

Creator: Johannes Bausch

Contributor: Johannes Bausch

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Logo SBMC 2018 Bremen
LiSyM network
No description specified

Creator: Johannes Bausch

Contributor: Johannes Bausch

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Banner SBMC 2018 Bremen
LiSyM network
No description specified

Creator: Johannes Bausch

Contributor: Johannes Bausch

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SOP for the exchange of clinical samples and corresponding data between collaboration partners in LiSyM
LiSyM network

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
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Creators: Martin Golebiewski, Frank Lammert, Wolfgang Müller

Contributor: Martin Golebiewski

Editorial: Systems Biology and Bioinformatics in Gastroenterology and Hepatology
LiSyM network

Abstract

Not specified

Authors: Peter Jansen, Kai Breuhahn, Andreas Teufel, Steven Dooley

Date Published: 22nd Nov 2019

Journal: Front. Physiol.

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating … datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of researchers, and exchanged with others researchers for constructing the models. For this process to run smoothly the data and models must be FAIR-findable, accessible, interoperable, and reusable. In order for data and models to be FAIR they must be structured in consistent and predictable ways, and described sufficiently for other researchers to understand them. Furthermore, these data and models must be shared with other researchers, with appropriately controlled sharing permissions, before and after publication. In this chapter we explore the different data and model standards that assist with structuring, describing, and sharing. We also highlight the popular standards and sharing databases within computational systems biology.

Authors: N. J. Stanford, M. Scharm, P. D. Dobson, Martin Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep

Date Published: 12th Oct 2019

Journal: Methods Mol Biol

Three-dimensional spatially resolved geometrical and functional models of human liver tissue reveal new aspects of NAFLD progression.
Early Metabolic Injury (LiSyM-EMI - Pillar I), LiSyM network

Abstract (Expand)

Early disease diagnosis is key to the effective treatment of diseases. Histopathological analysis of human biopsies is the gold standard to diagnose tissue alterations. However, this approach has low … resolution and overlooks 3D (three-dimensional) structural changes resulting from functional alterations. Here, we applied multiphoton imaging, 3D digital reconstructions and computational simulations to generate spatially resolved geometrical and functional models of human liver tissue at different stages of non-alcoholic fatty liver disease (NAFLD). We identified a set of morphometric cellular and tissue parameters correlated with disease progression, and discover profound topological defects in the 3D bile canalicular (BC) network. Personalized biliary fluid dynamic simulations predicted an increased pericentral biliary pressure and micro-cholestasis, consistent with elevated cholestatic biomarkers in patients' sera. Our spatially resolved models of human liver tissue can contribute to high-definition medicine by identifying quantitative multiparametric cellular and tissue signatures to define disease progression and provide new insights into NAFLD pathophysiology.

Authors: Fabian Segovia Miranda, H. Morales-Navarrete, Michael Kücken, Vincent Moser, S. Seifert, U. Repnik, Fabian Rost, Mario Brosch, A. Hendricks, S. Hinz, C. Rocken, D. Lutjohann, Y. Kalaidzidis, Clemens Schafmayer, Lutz Brusch, Jochen Hampe, Marino Zerial

Date Published: 2nd Dec 2019

Journal: Nat Med

Benchmark and integration of resources for the estimation of human transcription factor activities
Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network

Abstract (Expand)

The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional … regulatory circuits. Several strategies and data sets have been proposed to link the target genes likely regulated by a TF, each one providing a different level of evidence. The most established ones are (1) manually curated repositories, (2) interactions derived from ChIP-seq binding data, (3) in silico prediction of TF binding on gene promoters, and (4) reverse-engineered regulons from large gene expression data sets. However, it is not known how these different sources of regulons affect the TF activity estimations and, thereby, downstream analysis and interpretation. Here we compared the accuracy and biases of these strategies to define human TF regulons by means of their ability to predict changes in TF activities in three reference benchmark data sets. We assembled a collection of TF–target interactions for 1541 human TFs and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode of interaction with the chromatin, affect the predictions of TF activity. We assessed their coverage and found little overlap on the regulons derived from each strategy and better performance by literature-curated information followed by ChIP-seq data. We provide an integrated resource of all TF–target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.

Authors: Luz Garcia-Alonso, Christian Holland, Mahmoud M. Ibrahim, Denes Turei, Julio Saez-Rodriguez

Date Published: 1st Aug 2019

Journal: Genome Res.

Robustness and applicability of functional genomics tools on scRNA-seq data
Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network

Abstract (Expand)

Many tools have been developed to extract functional and mechanistic insight from bulk transcriptome profiling data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible … to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events, low library sizes and a comparatively large number of samples/cells. It is thus not clear if functional genomics tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. To address this question, we performed benchmark studies on in silico and in vitro single-cell RNA-seq data. We included the bulk-RNA tools PROGENy, GO enrichment and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compared them against the tools AUCell and metaVIPER, designed for scRNA-seq. For the in silico study we simulated single cells from TF/pathway perturbation bulk RNA-seq experiments. Our simulation strategy guarantees that the information of the original perturbation is preserved while resembling the characteristics of scRNA-seq data. We complemented the in silico data with in vitro scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on both the simulated and real data revealed comparable performance to the original bulk data. Additionally, we showed that the TF and pathway activities preserve cell-type specific variability by analysing a mixture sample sequenced with 13 scRNA-seq different protocols. Our analyses suggest that bulk functional genomics tools can be applied to scRNA-seq data, outperforming dedicated single cell tools. Furthermore we provide a benchmark for further methods development by the community.

Authors: Christian Holland, Jovan Tanevski, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Javier Perales-Patón, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Saez-Rodriguez

Date Published: 2019

Journal: Not specified

Participant Abstracts LiSyM Retreat 2020
LiSyM network
No description specified

Creator: Nachiket Vartak

Contributor: Nachiket Vartak

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Hedgehog around the clock
The Hedgehog Signalling Pathway (LiSyM-JGMMS), LiSyM PALs, LiSyM network
No description specified

Creator: Madlen Matz-Soja

Contributor: Madlen Matz-Soja

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Pillar II: Outline poster-Jamboree2019-Leipzig
Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network
No description specified

Creator: Seddik Hammad

Contributor: Seddik Hammad

Pillar III: AG Dooley Poster-Jamboree2019-Leipzig
Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM network
No description specified

Creator: Seddik Hammad

Contributor: Seddik Hammad

AG Dooley Poster- Jamboree2019-Leipzig
Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network
No description specified

Creator: Seddik Hammad

Contributor: Seddik Hammad

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LiSyM Ph.D Postdoc Retreat 2020

Venue : Evangelische Tagungsstätte Hofgeismar, Kassel-Wilhelmshöhe

Start Date: 29th Jan 2020

End Date: 31st Jan 2020

Event Website: http://bit.ly/lisymretreat2020

Country:  DE

City: Hofgeismar

e:Med meeting on Systems Medicine

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:  DE

City: Bonn

21st International Conference on Systems Biology (ICSB 2020)

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.

Start Date: 10th Oct 2020

End Date: 16th Oct 2020

Event Website: http://icsb2020.bioscience-ct.net/

Country:  US

City: Hartford, Connecticut

HARMONY 2020 (Hackathon on Resources for Modeling in Biology)

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
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Start Date: 9th Mar 2020

End Date: 13th Mar 2020

Event Website: http://co.mbine.org/events

Country:  GB

City: Hinxton, Cambridge

COMBINE 2020 (Computational Modeling in Biology Network Meeting)

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
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Start Date: 6th Oct 2020

End Date: 9th Oct 2020

Event Website: http://co.mbine.org/events

Country:  US

City: Farmington, Connecticut

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