DEEP-HCC - Detailed Analysis of the Spatial Organization of the Development of Hepatocellular Carcinoma
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
SEEK ID: https://seek.lisym.org/projects/18
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus
FAIRDOM PALs: No PALs for this Project
Project created: 1st Dec 2021
Related items
- People (35)
- Programmes (1)
- Institutions (15)
- Investigations (1+3)
- Studies (6+3)
- Assays (10+8)
- Data files (1+1)
- Models (3)
- SOPs (2+6)
- Publications (35)
- Presentations (1+27)
- Events (2+4)
- Documents (7+8)
- Sample types (0+3)
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
Projects: LiSyM network, LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), SMART-NAFLD, Forschungsnetzwerk LiSyM-Krebs, DEEP-HCC network, C-TIP-HCC network
Institutions: German Cancer Research Center (DKFZ), Division of Systems Biology of Signal Transduction, HITS gGmbH
Program management team LiSyM-Cancer (project and communications manager)
Former PhD student in LiSyM, at DKFZ Heidelberg in the group of Ursula Klingmüller
(née Schmitt)
Projects: LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM PALs, LiSyM network, LiSyM-Krebs Partnering, Forschungsnetzwerk LiSyM-Krebs, DEEP-HCC network
Institutions: Zentrum für Informationsdienste und Hochleistungsrechnen (ZIH), Technische Universität Dresden
https://orcid.org/0000-0003-0137-5106LiSyM-Krebs ist ein nationales Forschungsnetz zur Früherkennung und Prävention von Leberkrebs, das unter Verwendung des systemmedizinischen Forschungsansatzes die komplexen, dynamischen Prozesse der Krankheitsprogression analysiert, um ausgehend von den Erkenntnissen aus dem Forschungsnetz LiSyM die Entstehung von Leberkrebs besser zu verstehen, vorherzusagen und im besten Fall sogar zu verhindern. LiSyM-Krebs setzt die erfolgreichen Forschungsaktivitäten der BMBF-Vorgängerprogramme ...
Projects: LiSyM-Krebs Partnering, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, DEEP-HCC network, C-TIP-HCC network
Web page: https://www.lisym-cancer.org
LiSyM-Cancer project data for integration into public repositories based on
Submitter: Olga Krebs
Studies: GENOMICS/TRANSCRIPTOMICS, METABOLOMICS, OTHER OMICS DATA, Several proteomics experimental data
Assays: DNA sequence data, RNA sequence data, Western blot
Snapshots: No snapshots
Several proteomics experimental data
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: Western blot
Snapshots: No snapshots
OTHER OMICS DATA
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
Snapshots: No snapshots
METABOLOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
Snapshots: No snapshots
GENOMICS/TRANSCRIPTOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: DNA sequence data, RNA sequence data
Snapshots: No snapshots
Documents submitted to BMBF
Submitter: Olga Krebs
Investigation: 1 hidden item
Assays: Meeting minutes 2021, Meeting minutes 2022
Snapshots: No snapshots
Project proposals
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Meeting minutes 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Meeting minutes 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Project deliverables 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Project deliverables 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Primary hepatocytes from a preclinical mouse model fed with high-sugar and high-fat diet are used to develop a data-based mathematical model that identifies the basal phosphorylation rate of the tyrosine kinase receptor MET as the main dysregulated parameter driving fatty liver disease.
Creators: Sebastian Burbano De Lara, Ursula Klingmüller
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The model studies the influence of hepatocyte–sinusoid alignment (HSA), i.e. the orientation of the division plane such that daughter hepatocytes align with nearby sinusoids, on the shape of tumor nodules in liver lobules. It employs the structure of the model ‘Liver Regeneration from CCl4’ (https://seek.lisym.org/models/19).
Originally, Höhme et al. (https://doi.org/10.1007/s11538-017-0375-1) employed a center-based model. Here, the model is encoded in the standardized language MorpheusML. ...
Creators: Diego Jahn, Michael Kücken, Lutz Brusch
Submitter: Diego Jahn
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
In the experimental paradigm of CCl4 intoxication of mice, hepatocytes around the central vein (located in the center of an idealized hexagonal liver lobule) are dying and are subsequently replaced by new hepatocytes, largely through activation of proliferation in the remaining hepatocytes.
Alignment of daughter hepatocytes along the orientation of the closest sinusoid, a process which is named hepatocyte-sinusoid alignment (HSA), was proposed by Höhme et al. (https://doi.org/10.1073/pnas.0909374107) ...
Creators: Diego Jahn, Michael Kücken, Lutz Brusch
Submitter: Diego Jahn
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
This model was used in the Modeling Workshop at the 2nd LiSyM-Cancer Status Seminar.
Creator: Lutz Brusch
Submitter: Lutz Brusch
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Empty SOP template based on nature protocol format and reqiremeents
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: LiSyM-Cancer project data for integration into...
Studies: METABOLOMICS, Several proteomics experimental data
Assays: Western blot and 1 hidden item
This protocol details the RNAseq sample preparation starting with mRNA and ending with quality control of finished libraries. This protocol was used specifically for virus mRNA samples related to ORFeome lab group.
Creators: Olga Krebs, Marcia Sanders (marcia_sanders@unc.edu), Anne Beall (aebeall@email.unc.edu
Submitter: Olga Krebs
Investigations: LiSyM-Cancer project data for integration into...
Studies: GENOMICS/TRANSCRIPTOMICS
Assays: RNA sequence data
Abstract (Expand)
Authors: Valentin Blank, Thomas Karlas, Ulf Anderegg, Johannes Wiegand, Josi Arnold, Linnaeus Bundalian, Gabriela‐Diana Le Duc, Christiane Körner, Thomas Ebert, Anja Saalbach
Date Published: 4th May 2024
Publication Type: Journal
DOI: 10.1111/liv.15956
Citation: Liver International,liv.15956
Abstract (Expand)
Authors: Xuan Peng, Željko Janićijević, Sandy Lemm, Sandra Hauser, Michael Knobel, Jens Pietzsch, Michael Bachmann, Larysa Baraban
Date Published: 25th Jan 2024
Publication Type: Journal
Citation: Adv Healthcare Materials,2302609
Abstract (Expand)
Authors: E. Alamoudi, Y. Schalte, R. Muller, J. Starruss, N. Bundgaard, F. Graw, L. Brusch, J. Hasenauer
Date Published: 1st Nov 2023
Publication Type: Journal
PubMed ID: 37947308
Citation: Bioinformatics. 2023 Nov 1;39(11):btad674. doi: 10.1093/bioinformatics/btad674.
Abstract (Expand)
Authors: Reik Löser, Manuela Kuchar, Robert Wodtke, Christin Neuber, Birgit Belter, Klaus Kopka, Lakshmi Santhanam, Jens Pietzsch
Date Published: 15th Sep 2023
Publication Type: Journal
Citation: ChemMedChem 18(18),e202300331
Abstract (Expand)
Authors: Anne Krüger-Genge, Susanne Köhler, Markus Laube, Vanessa Haileka, Sandy Lemm, Karolina Majchrzak, Sarah Kammerer, Christian Schulz, Joachim Storsberg, Jens Pietzsch, Jan-Heiner Küpper, Friedrich Jung
Date Published: 1st Aug 2023
Publication Type: Journal
Citation: Cells 12(15):1965
As a member of LiSyM-Cancer you already have a “profile” in LiSyM SEEK, i.e. your name and mail address is known to the system. You now have to register or in other words create a user name and a password. Download and watch the the short tutorial on how this works.
Creator: Maja Rey
Submitter: Maja Rey
Sessions:
- From single cell analysis to clinical application
- Mechanistic modeling at the cellular scale proposing intervention strategies
- Tissue scale modeling and organ communication in systems medicine
- AI contributions to systems medicine - Diagnosis and therapy monitoring
- The future of systems biology
Start Date: 13th May 2024 (13th May 2024 (Etc/UTC))
End Date: 15th May 2024 (15th May 2024 (Etc/UTC))
Event Website: https://www.lisym-cancer.org/sbmc2024
Country: Germany
City: 04109 Leipzig
Young Scientists Retreat (YSR) will take place from September 7th to 9th in Hofgeismar (close to Kassel) (https://tagungsstaette-hofgeismar.de/). Participation is mandatory for all PhD students, MD students and Postdocs in SMART-NAFLD, C-TIP-HCC and DEEP-HCC
Start Date: 7th Sep 2022
End Date: 9th Sep 2022
Event Website: Not specified
Country: Germany
City: Not specified
Creators: Ina Biermayer, Susan Eckerle
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Ina Biermayer, Susan Eckerle
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Workshop #1 LiSym status seminar March 2023, Dresden “Towards concordant multiomics of liver”
Creators: Andrej Shevchenko, Ursula Klingmüller
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Group picture from Lisym-Cancer Status Seminar 2023
Creators: Olga Krebs, Ina Biermayer, Susan Eckerle
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays