Olga Krebs
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project (http://www.sysmo-db.org) I was responsible for metadata design (SEEK), conceptual and logical modelling of experimental data (JERM), now our team continue this work as FAIRDOM project (http://fair-dom.org/).
SEEK ID: https://seek.lisym.org/people/8
Location:
Germany
ORCID:
https://orcid.org/0000-0003-3540-0402
Joined: 27th Apr 2017
Expertise: big data, Systems Biology, Genetics, wet lab
Tools: SEEK, openBis, Protege, Copasi, JWS online RightFiled
Project roles
Project administrator
- LiSyM network
- LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)
- LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF)
- LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)
- LiSyM PALs
- LiSyM Core Infrastructure and Management (LiSyM-PD)
- LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi)
- LiSyM-Krebs Partnering
- Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM)
- Forschungsnetzwerk LiSyM-Krebs
- SMART-NAFLD
- DEEP-HCC network
- C-TIP-HCC network
Asset housekeeper
- LiSyM network
- LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)
- LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF)
- LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)
- LiSyM PALs
- LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi)
- LiSyM-Krebs Partnering
Their tagsLiSyM PALs (HITS gGmbH) ; LiSyM network (HITS gGmbH) ; LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI) (HITS gGmbH) ; LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF) (HITS gGmbH) ; LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP) (HITS gGmbH) ; LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi) (HITS gGmbH) ; LiSyM Core Infrastructure and Management (LiSyM-PD) (HITS gGmbH) ; LiSyM-Krebs Partnering (HITS gGmbH) ; Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM) (HITS gGmbH) ; Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF) (HITS gGmbH) ; The Hedgehog Signalling Pathway (LiSyM-JGMMS) (HITS gGmbH) ; Forschungsnetzwerk LiSyM-Krebs (HITS gGmbH) ; SMART-NAFLD (HITS gGmbH) ; DEEP-HCC network (HITS gGmbH) ; C-TIP-HCC network (HITS gGmbH)
Related items
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
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/
Forschungsnetzwerk zur Früherkennung und Prävention- LiSyM-Krebs
Ein Netzwerk von Klinikern, Wissenschaftlern und Datenmanagern hat sich zur Aufgabe gemacht, Methoden zu entwickeln, um Patienten mit einem hohen Risiko für ein Leberkarzinom frühzeitig, in Vorstadien der Tumorentwicklung, identifizieren zu können. Gemeinsam bilden sie das „Systemmedizinische Forschungsnetzwerk zur Früherkennung und Prävention von Leberkrebs“, LiSym-Krebs, das vom Bundesministerium für Bildung und Forschung ...
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
Public web page: Not specified
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
Public web page: Not specified
SMART-NAFLD : A Systems Medicine Approach to Early Detection and Prevention of Hepatocellular Carcinoma in Non-Alcoholic Fatty Liver Disease
The massive increase in obesity is leading to an alarming rise in non-alcoholic liver disease (NAFLD). This development will lead to a dramatic increase in liver diseases such as hepatocellular carcinoma (HCC). A particular challenge is that NAFLD-associated HCCs, for reasons still unknown, not only occur in association with advanced liver fibrosis/cirrhosis, ...
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
Public web page: Not specified
C-TIP-HCC- Mechanism-based Multiscale Model to Dissect the Tipping Point from Liver Cirrhosis to Hepatocellular Carcinoma
The ultimate goal of the C-TIP-HCC is a „mechanistic multiscale model to describe dynamic changes in regenerative nodes across a tipping point (TIP) towards development in patients with cirrhosis to facilitate early monitoring and intervention“ and facilitate intervention“. To achieve this, we will conduct in-depth studies on cirrhotic regenerative nodes.
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
Public web page: Not specified
This generic project is intended to be a forum for all LiSyM partner and external stakeholders interested in participating in the BMBF initiative LiSyM-Krebs.
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
In this study, we characterize Western diet-induced phenotypic changes in murine 392 hepatocytes and employ dynamic pathway modelling to resolve the underlying molecular 393 mechanisms resulting in altered intracellular signal transduction and enhanced proliferation 394 of WD hepatocytes.
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
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
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
Download
Isolation of primary mouse hepatocytes
Creators: Ina Biermayer, Ursula Klingmüller
Submitter: Olga Krebs
This SOP - Standard Operating Procedure for Sample Collection and Preservation of Blood and Endometrial Tissue were developed at NIH University of California San Francisco Human Endometrial Tissue and DNA Bank by Elizabeth Sheldonand, Ramsey A McIntire
Creators: Olga Krebs, Martin Golebiewski, Elizabeth Sheldonand, Ramsey A McIntire
Submitter: Olga Krebs
Abstract (Expand)
Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers
Date Published: 29th Jun 2020
Publication Type: Journal
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 3rd Dec 2016
Publication Type: Not specified
Poster presentation at SBMC 2018 (Bremen)
Creators: Martin Golebiewski, Olga Krebs, Hadas Leonov, Wolfgang Müller, Stuart Owen, Maja Rey, Natalie Stanford, Andreas Weidemann, Ulrike Wittig, Katy Wolstencroft, Jacky L. Snoep, Carole Goble
Submitter: Martin Golebiewski
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
Kickoff Meeting SMART- NAFLD 1.12.2021 - 2.12.2021
Heidelberg, Bioquant 7th Floor Greenier Room
Start Date: 1st Dec 2021
End Date: 2nd Dec 2021
Event Website: Not specified
Country: Germany
City: Heidelberg
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
