Scientific Project Manager at Luxembourg Centre for Systems Biomedicine, University of Luxembourg http://lcsb.uni.lu
SEEK ID: https://fairdomhub.org/people/665
Locations:
Germany
,
Luxembourg
ORCID:
https://orcid.org/0000-0003-1473-370X
Joined: 29th May 2016
Expertise: Data Management, Molecular Biology, Systems Biology, Curation
Tools: SBGN, CellDesigner, MIRIAM, SBML, Data Science
Related items
- Programmes (3)
- Projects (3)
- Institutions (3)
- Models (27)
- Publications (2)
- Presentations (1)
- Documents (5)
The Disease Maps Project is designed as a large-scale community effort. It is a network of groups that work together in order to better understand disease mechanisms. The project exchanges best practices, share information, develop tools to make it easier for all the involved groups to achieve their goals.
Projects: COVID-19 Disease Map
Web page: https://disease-maps.org
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
Web page: http://www.denbi.de
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, FUNCEMM, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE, IDIM, Sampling vicinity of industrial settings for pathogens and GMO identification, RNA-seq data for paper, RNA-seq data, Academic Scientific Research Group, SYLOBIO, 3T3 murine fibroblast as feeder-layer, Comparative Analysis of decell efficiency and structural integrity of vessels for tissue engineering aplications, Raman Data, Alters-Krebs-Korrelation anhand der Patienteneingänge 2024, Cassava Gates Curation, GWI-HDMT stemcells, HubMOL, test, Lipopeptide research @ VIB, PRIN 2022 - High-resolution study of translational dynamics in human epithelial stem cells, Automated Hepatic Vessel Segmentation in Whole-Slide Images Using U-Net Variants with Attention and SE Blocks, Diverse Metabolic Control of Phosphoglucomutases by Bisphosphorylated Sugars in Heterotrophic Bacteria, GENBioDORA, Preclinical Imaging and Testing Core at MIT Koch Institute, Ultrasound Guided Injection Protocol Development, BullNet, TERRACOTA, B.Ed Colleges in Bangalore, LIRA, reNEW, Cross-Feeding B.theta, Surgery Analyzer, Pseudomonas aeruginosa and its vesicles, FAIRe Tests BMDS, LabscriptAI, Principais cânceres que afetam mulheres no Brasil, DKDM: Diabetic Kidney Disease Map, NGID, Transforming Marine Waste into Sustainable Value_WASTE2TASTE
Web page: Not specified
Chronic kidney disease (CKD) affects around 9% of the global population and is the 12th leading cause of death (GBD Chronic Kidney Disease Collaboration 2020). Diabetic kidney disease (DKD) is the most common form of CKD, responsible for nearly half of all end-stage renal disease (ESRD) cases (Samsu 2021). Despite its high burden, progress in developing effective therapies has been slow, largely due to limited understanding of the underlying molecular mechanisms.
DKD is driven by complex and ...
Programme: Independent Projects
Public web page: https://disease-maps.io/diabetickidneydisease
Start date: 1st Oct 2023
Organisms: Homo sapiens
The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.
Programme: Disease Maps
Public web page: http://doi.org/10.17881/covid19-disease-map
ROR ID: Not specified
Department: Not specified
Country: Luxembourg
City: Luxembourg
Web page: https://wwwde.uni.lu/lcsb
ROR ID: https://ror.org/036x5ad56
Department: Systems Biomedicine Center
Country: Luxembourg
City: Luxembourg
Web page: https://www.uni.lu
NLRP3 inflammasome activation
Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Thrombotic complications and coagulopathy in COVID-19
Creators: Goar Frischmann, Gisela Fobo, Corinna Montrone
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Kynurenine synthesis pathway
Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
TGF beta signalling
Creator: Francesco Messina
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The role of the interaction between the SARS-CoV-2 Spike protein and the renin-angiotensin pathway, in particular human ACE2 in pulmonary blood pressure regulation
Creators: Enrico Glaab, Andreas Ruepp, Corinna Montrone, Gisela Fobo
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The Interferon-lambda (IFNL) map describes the action of the drug candidate IFNL on intra- and intercellular signal transduction under SARS-CoV-2.
Creators: Marius Rameil, Vanessa Nakonecnij, Marta Conti
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The relation of the interferon 2 pathway and SARS-CoV-2.
Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The pathway of heme metabolism under COVID-19, involving Orf3a and Orf9c
Creators: Julia Somers, Emek Demir
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The impact of SARS-CoV-2 on the apoptosis pathway
Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The pathways focused on SARS-CoV infections curated in Reactome. These pathways are work-in-progress.
Creators: Marc Gillespie, Robin Haw, Peter D'Eustachio
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
Interactions of Nsp4 and Nsp6 proteins of SARS-CoV-2.
Creators: Arnau Montagud, Miguel Ponce-de-Leon
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Organism: Severe acute respiratory syndrome coronavirus 2
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Interactions of the SARS-CoV-2 Orf3a with human proteins, especially in the context of the HOPS Complex.
Creator: Muhammad Naveez
Submitter: Marek Ostaszewski
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A diagram of Nsp9 interactions.
Creators: Noriko Hiroi, Yusuke Hiki, Takahiro G. Yamada, Akira Funahashi
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Orf10 of SARS-CoV-2 and its interaction with the Cul2 pathway.
Creators: Jan Hasenauer, Leonard Schmiester, Paul Stapor
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Pyrimidine deprivation and immune response related to human coronavirus infection
Creators: Zsolt Bocskei, Franck Augé, Anna Niarakis
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The mechanisms of the Electron Transport Chain under COVID-19, including Nsp7, Nsp8 and Orf9c
Creator: Julia Scheel
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
SARS-CoV-2 impact on the ER stress
Creators: Cristobal Monraz, Inna Kuperstein, Barbara Brauner
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
COVID-19 Causal Networks: The SIGNOR team has curated the causal relationships that, according to available evidence, are likely to be relevant for the COVID-19 pathology. The perturbations caused by viral infection are integrated into the cell networks. Evidence obtained using related human coronaviruses diseases such as SARS and MERS are also mapped to the networks. Most of these are indirect relationships as few mechanistic details are clarified to date. As new evidence will be published, it ...
Creators: Luana Licata, Marta Iannuccelli, University of Rome Tor Vergata, IT
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: Not specified
Environment: Not specified
Pathway: Assembly of the Replication Transcription Complex and Transcription
Creators: Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
Organism: Severe acute respiratory syndrome coronavirus 2
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotinate and nicotinamide, and purine metabolism.
Creators: Alina Renz, Andreas Dräger
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
All authors
Abstract (Expand)
Authors: M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, A. Orta-Resendiz, V. Singh, S. S. Aghamiri, M. L. Acencio, E. Glaab, A. Ruepp, G. Fobo, C. Montrone, B. Brauner, G. Frishman, L. C. Monraz Gomez, J. Somers, M. Hoch, S. Kumar Gupta, J. Scheel, H. Borlinghaus, T. Czauderna, F. Schreiber, A. Montagud, M. Ponce de Leon, A. Funahashi, Y. Hiki, N. Hiroi, T. G. Yamada, A. Drager, A. Renz, M. Naveez, Z. Bocskei, F. Messina, D. Bornigen, L. Fergusson, M. Conti, M. Rameil, V. Nakonecnij, J. Vanhoefer, L. Schmiester, M. Wang, E. E. Ackerman, J. E. Shoemaker, J. Zucker, K. Oxford, J. Teuton, E. Kocakaya, G. Y. Summak, K. Hanspers, M. Kutmon, S. Coort, L. Eijssen, F. Ehrhart, D. A. B. Rex, D. Slenter, M. Martens, N. Pham, R. Haw, B. Jassal, L. Matthews, M. Orlic-Milacic, A. Senff Ribeiro, K. Rothfels, V. Shamovsky, R. Stephan, C. Sevilla, T. Varusai, J. M. Ravel, R. Fraser, V. Ortseifen, S. Marchesi, P. Gawron, E. Smula, L. Heirendt, V. Satagopam, G. Wu, A. Riutta, M. Golebiewski, S. Owen, C. Goble, X. Hu, R. W. Overall, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, C. Vega, V. Groues, M. Vazquez, P. Porras, L. Licata, M. Iannuccelli, F. Sacco, A. Nesterova, A. Yuryev, A. de Waard, D. Turei, A. Luna, O. Babur, S. Soliman, A. Valdeolivas, M. Esteban-Medina, M. Pena-Chilet, K. Rian, T. Helikar, B. L. Puniya, D. Modos, A. Treveil, M. Olbei, B. De Meulder, S. Ballereau, A. Dugourd, A. Naldi, V. Noel, L. Calzone, C. Sander, E. Demir, T. Korcsmaros, T. C. Freeman, F. Auge, J. S. Beckmann, J. Hasenauer, O. Wolkenhauer, E. L. Wilighagen, A. R. Pico, C. T. Evelo, M. E. Gillespie, L. D. Stein, H. Hermjakob, P. D'Eustachio, J. Saez-Rodriguez, J. Dopazo, A. Valencia, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider
Date Published: 19th Oct 2021
Publication Type: Journal
PubMed ID: 34664389
Citation: Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387.
All authors
Abstract
Authors: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic‐Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean‐Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban‐Medina, Maria Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez‐Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider
Date Published: 1st Oct 2021
Publication Type: Journal
Citation: Mol Syst Biol 17(10)
This document outlines next steps in biocuration of COVID-19 Disease Map diagrams.
The document is based on the preprint "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms" (doi:10.1101/2020.10.26.356014).
Creator: Marek Ostaszewski
Submitter: Marek Ostaszewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This document helps to harmonise the curation efforts for the COVID-19 Disease Map.
Creators: Marek Ostaszewski, Marcio Acencio, Alexander Mazein
Submitters: Martin Golebiewski, Marek Ostaszewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Open listing of contributors to the COVID-19 disease maps
Creator: Marek Ostaszewski
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Presentations and notes from the COVID19 Disease Map curation telephone conferences.
Creator: Marek Ostaszewski
Submitter: Marek Ostaszewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Here we share and organize the literature used to build the components of the COVID-19 DIsease Map
Creator: Marek Ostaszewski
Submitter: Marek Ostaszewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays