DEEP-HCC network
OverviewDEEP-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
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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: DEEP-HCC network
Institutions: German Cancer Research Center (DKFZ), Division of Applied Bioinformatics
Projects: DEEP-HCC network, Forschungsnetzwerk LiSyM-Krebs
Institutions: HITS gGmbH
I am an student assistant of the LiSyM-Cancer Project Management. I am currently doing my master's degree in molecular biotechnology at the Heidelberg University.
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/0000-0003-0137-5106
Universitätsklinikum Dresden - Medizinische Klinik I, Bereich Gastroenterologie & Hepatologie
LiSyM-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
Country: 
Germany
City: 69120 Heidelberg
Web page: https://www.dkfz.de/en/applied-bioinformatics/index.php
Country: Germany
City: 69120 Heidelberg
Country: Germany
City: Dresden
Country: Not specified
City: Not specified
Web page: Not specified
Due to increasing incidence and high mortality rates, hepatocellular carcinoma (HCC) is an important health problem worldwide. However, its etiopathology and development are poorly understood. While liver metabolism is organized in spatially specific zones, little is known how the zonation is associated with the onset and propagation of liver diseases. To this end, we applied laser capture microdissection (LCM) technique to excise histologically specific features of liver tissues, healthy and ...
Submitter: Olga Krebs
Studies: GENOMICS/TRANSCRIPTOMICS, METABOLOMICS, OTHER OMICS DATA, Several proteomics experimental data
Assays: DNA sequence data, RNA sequence data, Western blot
Several proteomics experimental data
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: Western blot
OTHER OMICS DATA
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
METABOLOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
GENOMICS/TRANSCRIPTOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: DNA sequence data, RNA sequence data
Documents submitted to BMBF
Submitter: Olga Krebs
Investigation: 1 hidden item
Assays: Meeting minutes 2021, Meeting minutes 2022
Documents submitted to BMBF
Submitter: Olga Krebs
Investigation: 1 hidden item
Assays: Project deliverables 2021, Project deliverables 2022, Project proposals
Project proposals
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Meeting minutes 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Meeting minutes 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Project deliverables 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Project deliverables 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
DMPlaning 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
DMPlaning 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
RNA sequence data
Submitter: Olga Krebs
Assay type: RNA-seq Profiling
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
Study: GENOMICS/TRANSCRIPTOMICS
Western blot
Submitter: Olga Krebs
Assay type: Immune Precipitation
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
DNA sequence data
Submitter: Olga Krebs
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
Study: GENOMICS/TRANSCRIPTOMICS
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: Ursula Klingmüller, Sebastian Burbano de Lara
Submitter: Olga Krebs
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
DownloadIn 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
Empty SOP template based on nature protocol format and reqiremeents
Creator: Olga Krebs
Submitter: Olga Krebs
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
Abstract (Expand)
Authors: Koen Minartz, Tim d'Hondt, Leon Hillmann, Jörn Starruß, Lutz Brusch, Vlado Menkovski
Date Published: 4th Feb 2025
Publication Type: Misc
Abstract (Expand)
Authors: W. Gu, V. de Ledinghen, C. Aube, A. Krag, C. Strassburg, L. Castera, J. Dumortier, M. Friedrich-Rust, S. Pol, I. Grgurevic, Y. Zeleke, M. Praktiknjo, R. Schierwagen, S. Klein, S. Francque, H. Gottfriedova, I. Sporea, P. Schindler, F. Rennebaum, M. J. Brol, M. Schulz, F. E. Uschner, J. Fischer, C. Margini, W. Wang, A. Delamarre, J. Best, A. Canbay, D. J. M. Bauer, B. Simbrunner, G. Semmler, T. Reiberger, J. Boursier, D. N. Rasmussen, V. Vilgrain, A. Guibal, S. Zeuzem, C. Vassord, L. Vonghia, R. Senkerikova, A. Popescu, A. Berzigotti, W. Laleman, M. Thiele, C. Jansen, J. Trebicka
Date Published: 22nd Oct 2024
Publication Type: Journal
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
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
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
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
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
Abstract
Authors: Astrid Ruiz-Margáin, Alessandra Pohlmann, Silke Lanzerath, Melanie Langheinrich, Alejandro Campos-Murguía, Berenice M. Román-Calleja, Robert Schierwagen, Sabine Klein, Frank Erhard Uschner, Maximilian Joseph Brol, Aldo Torre-Delgadillo, Nayelli C. Flores-García, Michael Praktiknjo, Ricardo U. Macías Rodríguez, Jonel Trebicka
Date Published: 1st Aug 2023
Publication Type: Journal
Abstract
Authors: Frank Tacke, Tobias Puengel, Rohit Loomba, Scott L. Friedman
Date Published: 1st Aug 2023
Publication Type: Journal
Abstract (Expand)
Authors: C. Mayer, S. Nehring, M. Kucken, U. Repnik, S. Seifert, A. Sljukic, J. Delpierre, H. Morales-Navarrete, S. Hinz, M. Brosch, B. Chung, T. Karlsen, M. Huch, Y. Kalaidzidis, L. Brusch, J. Hampe, C. Schafmayer, M. Zerial
Date Published: 31st Jul 2023
Publication Type: Journal
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
Creators: Ina Biermayer, Susan Eckerle
Submitter: Maja Rey
Workshop #1 LiSym status seminar March 2023, Dresden “Towards concordant multiomics of liver”
Creators: Andrej Shevchenko, Ursula Klingmüller
Submitter: Olga Krebs
Group picture from Lisym-Cancer Status Seminar 2023
Creators: Olga Krebs, Ina Biermayer, Susan Eckerle
Submitter: Olga Krebs
Creator: Olga Krebs
Submitter: Olga Krebs
Agreement on the Use of Personal Data during LiSyM-Cancer Young Scientists Retreat Date: 07.09. -09.09.2022 Place: Ev. Tagungsstätte Hofgeismar
Creator: Olga Krebs
Submitter: Olga Krebs
Agenda for LiSyM-Cancer status seminar 2022
Creators: Olga Krebs, Wolfgang Müller, Ursula Klingmüller, Ina Biermayer
Submitter: Olga Krebs
