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
Roles
Project administrator
- LiSyM network
- LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)
- 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)
- Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM)
Asset housekeeper
- LiSyM network
- LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI)
- LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP)
- LiSyM PALs
- LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi)
Programme administrator
Their tagsRelated 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/
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
This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org
Start date: 1st Jan 2016
Disorders of the liver show up through changes in blood tests. These blood tests indicate markers for events taking place in the liver. Usually studies of liver tissue cannot be performed: as liver samples would need to be obtained through a liver biopsy, and this procedure is not without risk, therefore these samples are usually unavailable. Complex metabolism models based on existing and new scientific data can simulate changes in the liver caused by disease. They often reveal unknown relationships ...
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/pillar-research/the-liver-is-very-patient
Start date: 1st Jan 2016
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
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
Dr. Nachiket Vartak (TU University, Dortmund) investigates the role of a particular protein - the GTPase Rab18 - in initiating NAFLD. He tries to influence Rab18 pharmacologically so that NAFLD is not initiated. Vartak also analyzes how bile acids leave the liver. He hopes to find ways to improve the flow of bile in a liver with dysfunctional bile flow.
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/junior-group/the-protein-rab18
Start date: 1st Jan 2016
Dr. Madlen Matz-Soja (University of Leipzig) investigates the importance of a control mechanism - the hedgehog signaling pathway - for fatty liver disease. She has shown that the signaling pathway directs how liver cells in NAFLD accumulate fat. Hedgehog also affects sex hormones in the liver. Therefore, Matz-Soya hopes to clarify why women and men suffer from cirrhosis and liver cancer with varying degrees of frequency.
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org/our-work/junior-group/hedgehog-influences
Start date: 1st Jan 2016
This is a generic project that comprises all LiSyM data management PALs and associated FAIRDOM PALs, as well as the LiSyM data management team. Olga Maja Alain
Programme: LiSyM: Liver Systems Medicine
Public web page: Not specified
Dr. Matthias König (Humboldt University, Berlin) models the human liver on the computer. His simulations show the extent of individual differences in liver function and the external factors influencing it. König has shown that smoking falsifies the result of an important liver test (LiMAx). With his models, drug doses can be calculated so that they can be administered in doses that do not harm the liver.
Programme: LiSyM: Liver Systems Medicine
Public web page: https://livermetabolism.com
Start date: 1st Jan 2016
Submitter: Olga Krebs
Studies: GENOMICS/TRANSCRIPTOMICS, METABOLOMICS, OTHER OMICS DATA, Several proteomics experimental data
Assays: DNA sequence data, RNA sequence data, Western blot
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
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
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...
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
DNA-methylation at binding sites of uniformly expressed transcription factors in human hepatocytes ; hepatic zone: intermediate (IZ)
Submitter: Olga Krebs
Assay type: Methylation Profiling
Technology type: Technology Type
Investigation: Epigenomic analysis of micro-dissected human liver
DNA-methylation at binding sites of uniformly expressed transcription factors in human hepatocytes ; periportal (PP)
Submitter: Olga Krebs
Assay type: Methylation Profiling
Technology type: Technology Type
Investigation: Epigenomic analysis of micro-dissected human liver
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
Experimental assay Human-NAFLD/eNASH Samples for the eNASH category were obtained in patients undergoing bariatric surgery with a BMI > 30 and subgroups defined by liver histology as follows: eNASH samples were characterized by >5% fat, an inflammation grade of at least 1, fibrosis ≤1 and ballooning ≤1.
Image data for this assay available via link to file folder containing image data for listed patient IDs (patientID in a file name) ...
Submitter: Olga Krebs
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Three-dimensional spatially resolved geometrica...
Hepatocyte-controlled availability of activated TGFb reprograms macrophage polarization affecting liver injury and regeneration
Creator: Stephanie Wolf
Submitter: Olga Krebs
External Link
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
Wolf2023Hepatology Communications
Creator: Stephanie Wolf
Submitter: Olga Krebs
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
SOP Western diet mouse housing and feeding
Creator: Ina Biermayer
Submitter: Olga Krebs
Empty SOP template based on nature protocol format and reqiremeents
Creator: Olga Krebs
Submitter: Olga Krebs
Liver is the major site for glycogen storage. Glycogen content can be significantly altered upon disruption of glucose homeostasis in metabolic syndromes, such as diabetes.
Glycogen content can be determined by an acid-hydrolysis method . Basically, glucose, the hydrolysis product of glycogen, is converted into glucose-6- phosphate (G-6-P) by hexokinase in the presence of ATP.
With the supply of NADP, G-6-P is further converted into 6-phosphogluconic acid by G-6-P dehydrogenase (G-6-PDH), while ...
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
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
Agenda Kickoff Meeting SMART-NAFLD 1-2 december 2021 in Heidelberg
Creators: Ursula Klingmüller, Ina Biermayer
Submitter: Olga Krebs
Histopathology of human liver biopsies
PAT.ID (String) *, Diagnosis group (Controlled Vocabulary - Diagnostic groups) *, Age (Real number) ( yr ) , Sex (Controlled Vocabulary - Gender) , Weight (kg) (Real number) , BMI (String) , Diabetes Typ II (String) , Surgery indication (String) , Histology: NAS score (Real number) , Histology: NAS fat (Real number) , Histology: NAS balloning (Real number) , Histology: NAS inflammation (Real number) , Fat (Real number) ( % ) , Fibrosis (Real number) , Blood test: GGT (U/l) (Real number) , Blood test: AP (U/l) (Real number) , Blood test: total bilirubin (µmol/l) (Real number) , Blood test: ALT (U/l) (Real number) , Blood test: AST (U/l) (Real number) , Bile acids: primary (µmol/l) (Real number) , Bile acids: secondary (µmol/l) (Real number) , Bile acids: 2º/1º (Real number) , 3D reconstruction (String)
Not specified
