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Strain details
Name | Provider name | Provider's strain ID | Genotypes | Phenotypes | Synonym | Comments | Based on |
---|---|---|---|---|---|---|---|
MCF-7 | Opitz lab | MCF-7 | wild-type | wild-type | Not specified | The cells were sent to CHAB from Opitz lab and STR profiled to confirm their identity. Their mutational pattern was analysed by panel DNA sequencing as described in file "MESI-STRATcells.docx". | Not specified |
GM03417 t(14:21) fibroblasts | Coriell Institute | GM03417 | wild-type | wild-type | Not specified | Mosaic t(14,21) translocation | Not specified |
Related items
- Programmes (62)
- Projects (67)
- Assays (18+18)
- Strains (2)
- Models (28+17)
- Publications (10)
- Samples (0+1)
The Snoep Lab’s core research efforts are in Computational Systems Biology; a combined experimental, modeling and theoretical approach to quantitatively understand the functional behavior of Biological Systems resulting from the characteristics of their components. Our main focus is on metabolism, of human pathogens such as Plasmodium falciparum, Mycobacterium tuberculosis, but also of breast cancer cell lines, and on modelling disease states such as glucose homeostatis in type 2 diabetes, and ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, Glucose metabolism in cancer cell lines
Web page: http://www.sun.ac.za/english/faculty/science/biochemistry/research/snoep-group
The Snoep Lab’s core research efforts are in Computational Systems Biology; a combined experimental, modeling and theoretical approach to quantitatively understand the functional behavior of Biological Systems resulting from the characteristics of their components. Our main focus is on metabolism, of human pathogens such as Plasmodium falciparum, Mycobacterium tuberculosis, but also of breast cancer cell lines, and on modelling disease states such as glucose homeostatis in type 2 diabetes, and ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, Glucose metabolism in cancer cell lines
Web page: http://www.sun.ac.za/english/faculty/science/biochemistry/research/snoep-group
The Snoep Lab’s core research efforts are in Computational Systems Biology; a combined experimental, modeling and theoretical approach to quantitatively understand the functional behavior of Biological Systems resulting from the characteristics of their components. Our main focus is on metabolism, of human pathogens such as Plasmodium falciparum, Mycobacterium tuberculosis, but also of breast cancer cell lines, and on modelling disease states such as glucose homeostatis in type 2 diabetes, and ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, Glucose metabolism in cancer cell lines
Web page: http://www.sun.ac.za/english/faculty/science/biochemistry/research/snoep-group
Background. RB1 is a paradigm gene for heritable cancer. Almost all RB1 mutation-carriers develop retinoblastoma (heritable-Rb-patient) during childhood and many heritable-Rb-survivors develop second primary malignancies (SPMs; notably sarcomas and melanomas) throughout life, which are often fatal. To date, no standard protocols are available for early detection of SPMs. Recently, blood-based cancer tests have opened up encouraging new possibilities for surveillance. We have developed novel ...
Projects: NIRBTEST
Web page: Not specified
RNA-Seq projects from SECARNA
Projects: Investigation of the activity of antisense oligonucleotides targeting multiple genes
Web page: Not specified
The principal research aim of iPLACENTA is to improve our ability to study, model and visualise the placenta. This will contribute to developing diagnostic tests and therapies for pregnancy complications such as preeclampsia and intrauterine growth restriction (IUGR). Placental defects are thought to be the cause of many major pregnancy complications, such as preeclampsia and intra-uterine growth restriction. Preeclampsia affects between 5 and 8 out of every 100 pregnant women and claims the lives ...
Projects: Molecular characterization and angiogenic properties of extracellular vesicles in healthy and preeclamptic amniotic fluid, Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved, Comparative Proteome Profile of Placental Sub-anatomical regions, The deregulated interplay of complement system and antioxidant activity as a driver of adverse pregnancy outcomes
Web page: https://www.iplacenta.eu/
Projects: Mass spectrometry proteomics for biomarker discovery, TEAD-(YAP) structure, function and inhibition, Thymidylate synthase dimer dissociation
Web page: Not specified
This page is dedicated to the bioinformatics analysis and computational modelling related to Covid-19 disease map pathways.
Projects: Covid-19 Interferon pathway modelling and analysis
Web page: Not specified
We develop macrophage logical models to represent the activation/polarization of this immune cell. Interactions are manually curated with available macrophage literature. The models are mainly built and analyzed in GINsim. But other resources are used to integrate specific pathways or small modules (CasQ software) and to analyze the logical models (CoLoMoTo Notebooks).
Projects: C19DM - Macrophage logical model
Web page: Not specified
We used the Neo4j graph database approach to integrate the content of the COVID-19 Disease Map diagrams to efficiently access, query and manage the content of these diagrams and enable communication with external resources, such as Reactome and Recon, that already provide support via a similar environment.
Projects: C19DM-Neo4j
Web page: Not specified
nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...
Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Web page: https://www.nfdi4health.de
nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...
Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Web page: https://www.nfdi4health.de
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 main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...
Projects: SysVirDrug, SysMilk, SysMetEx, MetApp, IMOMESIC, WineSys, CropClock, SYSTERACT, XyloCut, RootBook, ROBUSTYEAST, LEANPROT, ErasysApp Funders
Web page: https://www.cobiotech.eu/about-cobiotech/erasysapp
The main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...
Projects: SysVirDrug, SysMilk, SysMetEx, MetApp, IMOMESIC, WineSys, CropClock, SYSTERACT, XyloCut, RootBook, ROBUSTYEAST, LEANPROT, ErasysApp Funders
Web page: https://www.cobiotech.eu/about-cobiotech/erasysapp
Projects: Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Projects: Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
The RNA Systems Biology Lab Programme compiles the different research projects developed in our lab. The RNA Systems Biology Lab is a collaborative research lab headed by PIs Margarida Gama-Carvalho and Francisco Pinto at the Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, and integrates the BioSystems and Integrative Sciences Institute (BioISI) Gene Expression and Regulation Group, headed by Margarida Gama-Carvalho. Our research brings together computational ...
Projects: CF transcriptome, miRiAD - exploring the role of microRNAs in T cell function and anti-viral defence, ComPASs - Common Pathways in Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA), LungCARD - Blood test for clinical therapy guidance of non-small cell lung cancer patients, UnCentre - Unlocking satellite DNA and centromere structure in vertebrate chromosomes, Mapping Disease Modules Overlaps in Biological Networks
Web page: Not specified
Up-regulation of glycolytic flux (glucose to lactate conversion), also known as the “Warburg effect”, has been associated with 90% of cancers. We implemented a systems biology approach in order to improve the overall understanding of the “Warburg effect” as well as identifying drug targets within the glycolytic pathway.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Homo sapiens
Developing a placenta on a chip
Programme: Independent Projects
Public web page: https://www.iplacenta.eu/
Start date: 1st Jan 2018
End date: 31st May 2022
Organisms: Homo sapiens
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.
Programme: e:med
Public web page: Not specified
Organisms: Homo sapiens
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Organisms: Homo sapiens
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Organisms: Homo sapiens
Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Start date: 1st Mar 2020
End date: 24th Mar 2023
Organisms: Homo sapiens
IMOMESIC - Integrating Modelling of Metabolism and Signalling towards an Application in Liver Cancer
One of the most challenging questions in cancer research is currently the interconnection of metabolism and signalling. An understanding of mechanisms that facilitate the physiological shift towards a proliferative metabolism in cancer cells is considered a major upcoming topic in oncology and is a key activity for future drug development. Due to the complexity of interrelations, a systems biology ...
Programme: ERASysAPP
Public web page: Not specified
Organisms: Homo sapiens
This project bundles information about COVID-19 related studies and tools in Germany. It intends to provide an information hub for the different initiatives, their aims, their processes, standards and study protocols, as well as their available data and metadata. It is initiated by the German National Research Data Infrastructure for Personal Health Data (nfdi4health), a consortium that plans to establish a concept for a federated research data infrastructure for personal health data in Germany. ...
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Homo sapiens
This project aims to characterise the mechanisms through which microRNAs and small non-coding RNAs act to regulate cellular processes focusing on Naïve CD4 T cell activation and viral replication - namely HIV - and to explore their potential use as a therapeutic co-adjuvant agents or targets.
Organisms: Homo sapiens
Programme: RNA Systems Biology Lab
Public web page: http://flysmals.campus.ciencias.ulisboa.pt
Organisms: Drosophila melanogaster, Homo sapiens
to complete
Programme: Independent Projects
Public web page: Not specified
Organisms: Homo sapiens
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to ...
Programme: LiSyM - Systems Medicine of the Liver
Public web page: https://livermetabolism.com
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes
Programme: e:Bio
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus
Hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival in malaria patients. In this project we aim to test to what extent the metabolic activity of Plasmodium falciparum contributes to a changed glucose metabolism in malaria patients. The approach is to start with detailed bottom up models for the parasite and then merge these with more coarse grained models at the whole body level.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Plasmodium falciparum, Homo sapiens
Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat
Submitter: Olga Krebs
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Investigation: Creating data sheet template for 'omics data
Organisms: Saccharomyces cerevisiae, Homo sapiens : MCF-7 (wild-type / wild-type) (batch)
SOPs: No SOPs
Data files: Excel sheet template : concentrations of intrac..., The FAIR Guiding Principles for scientific data...
Snapshots: No snapshots
Data digitized from publication.
Hetzler1990 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Hetzler1990), PNG (Hetzler1990)
Snapshots: No snapshots
Data digitized from publication.
Magnusson2008 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Magnusson2008), PNG (Magnusson2008)
Snapshots: No snapshots
Data digitized from publication.
Perera2011 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Perera2011), PNG (Perera2011)
Snapshots: No snapshots
Data digitized from publication.
Tanaka2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Tanaka2014), PNG (Tanaka2014)
Snapshots: No snapshots
Data digitized from publication.
Blanchard1983a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Blanchard1983a), PNG (Blanchard1983a)
Snapshots: No snapshots
Data digitized from publication.
Kaplan1997 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Kaplan1997), PNG (Kaplan1997)
Snapshots: No snapshots
Data digitized from publication.
Amchin1999 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Amchin1999), PNG (Amchin1999)
Snapshots: No snapshots
Data digitized from publication.
Haller2002 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Haller2002), PNG (Haller2002)
Snapshots: No snapshots
Data digitized from publication.
Kakuda2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Kakuda2014), PNG (Kakuda2014)
Snapshots: No snapshots
Data digitized from publication.
Akinyinka2000 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Akinyinka2000), PNG (Akinyinka2000)
Snapshots: No snapshots
Data digitized from publication.
Healy1991 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Healy1991), PNG (Healy1991)
Snapshots: No snapshots
Data digitized from publication.
Oh2012 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Oh2012), PNG (Oh2012)
Snapshots: No snapshots
Data digitized from publication.
Jeppesen1996 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Jeppesen1996), PNG (Jeppesen1996)
Snapshots: No snapshots
Data digitized from publication.
Spigset1999a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Organisms: Homo sapiens
SOPs: No SOPs
Data files: CSV (Spigset1999a), PNG (Spigset1999a)
Snapshots: No snapshots
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Organisms: Homo sapiens
Models: Calibrated comprehensive model of ROS management, Calibrated comprehensive model of ROS managemen..., Detailed model of ROS management
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Arnau Montagud
Biological problem addressed: Gene Regulatory Network
Investigation: PhysiBoSS-COVID: the Boolean modelling of COVID...
Organisms: Homo sapiens
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Arnau Montagud
Biological problem addressed: Gene Regulatory Network
Investigation: PhysiBoSS-COVID: the Boolean modelling of COVID...
Organisms: Homo sapiens
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Margarida Gama-Carvalho
Provider Name: Coriell Institute
Provider's strain ID: GM03417
Organism: Homo sapiens
Genotypes: wild-type
Phenotypes: wild-type
Comment: Mosaic t(14,21) translocation
Submitter: Pamela Riemer
Provider Name: Opitz lab
Provider's strain ID: MCF-7
Organism: Homo sapiens
Genotypes: wild-type
Phenotypes: wild-type
Comment: The cells were sent to CHAB from Opitz lab and STR profiled to confirm their identity. Their mutational pattern was analysed by panel DNA sequencing as described in file "MESI-STRATcells.docx".
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: Andreas Ruepp, Corinna Montrone, Gisela Fobo, Enrico Glaab
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: Emek Demir, Julia Somers
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: Peter D'Eustachio, Marc Gillespie, Robin Haw
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
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: Barbara Brauner, Cristobal Monraz, Inna Kuperstein
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
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
Interactions of the SARS-CoV-2 E protein with human proteins in the context of histone acetylation.
Creator: Francesco Messina
Submitter: Marek Ostaszewski
Model type: Not specified
Model format: Not specified
Environment: Not specified
Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, entry, translation, transcription, replication, assembly and release.
Creators: Marcio Acencio, Alexander Mazein
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
A diagram of JNK pathway in COVID-19.
Creator: Daniela Börnigen
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Abstract (Expand)
Authors: Mitsuhiro Odaka, Morgan Magnin, Katsumi Inoue
Date Published: 11th Feb 2022
Publication Type: Journal
DOI: 10.21203/rs.3.rs-1300133/v1
Citation: [Preprint]
Abstract (Expand)
Authors: Hans V. Westerhoff, Alexey N. Kolodkin
Date Published: 1st Dec 2020
Publication Type: Journal
DOI: 10.1038/s41540-020-0138-8
Citation: npj Syst Biol Appl 6(1),18
Abstract (Expand)
Authors: A. N Kolodkin, R. P. Sharma, A. M. Colangelo, A. Ignatenko, F. Martorana, D. Jennen, J. J. Briede, N. Brady, M. Barberis, T. D. G. A. Mondeel, M. Papa, V. Kumar, B. Peters, A. Skupin, L. Alberghina, R. Balling, H. V. Westerhoff
Date Published: 26th Oct 2020
Publication Type: Journal
PubMed ID: 33106503
Citation: NPJ Syst Biol Appl. 2020 Oct 26;6(1):34. doi: 10.1038/s41540-020-00150-w.
Abstract
Authors: Michael Getz, Yafei Wang, Gary An, Maansi Asthana, Andrew Becker, Chase Cockrell, Nicholson Collier, Morgan Craig, Courtney L. Davis, James R. Faeder, Ashlee N. Ford Versypt, Tarunendu Mapder, Juliano F. Gianlupi, James A. Glazier, Sara Hamis, Randy Heiland, Thomas Hillen, Dennis Hou, Mohammad Aminul Islam, Adrianne L. Jenner, Furkan Kurtoglu, Caroline I. Larkin, Bing Liu, Fiona Macfarlane, Pablo Maygrundter, Penelope A Morel, Aarthi Narayanan, Jonathan Ozik, Elsje Pienaar, Padmini Rangamani, Ali Sinan Saglam, Jason Edward Shoemaker, Amber M. Smith, Jordan J.A. Weaver, Paul Macklin
Date Published: 5th Apr 2020
Publication Type: Journal
DOI: 10.1101/2020.04.02.019075
Citation: biorxiv;2020.04.02.019075v4,[Preprint]
Abstract (Expand)
Authors: A. Montagud, P. Traynard, L. Martignetti, E. Bonnet, E. Barillot, A. Zinovyev, L. Calzone
Date Published: 19th Jul 2019
Publication Type: Journal
PubMed ID: 29237040
Citation: Brief Bioinform. 2019 Jul 19;20(4):1238-1249. doi: 10.1093/bib/bbx163.
Abstract
Authors: Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone
Date Published: 1st Apr 2019
Publication Type: Journal
DOI: 10.1093/bioinformatics/bty766
Citation: Bioinformatics 35(7):1188-1196
Abstract (Expand)
Authors: G. Stoll, B. Caron, E. Viara, A. Dugourd, A. Zinovyev, A. Naldi, G. Kroemer, E. Barillot, L. Calzone
Date Published: 15th Jul 2017
Publication Type: Journal
PubMed ID: 28881959
Citation: Bioinformatics. 2017 Jul 15;33(14):2226-2228. doi: 10.1093/bioinformatics/btx123.
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Authors: M. Poenisch, P. Metz, H. Blankenburg, A. Ruggieri, J. Y. Lee, D. Rupp, I. Rebhan, K. Diederich, L. Kaderali, F. S. Domingues, M. Albrecht, V. Lohmann, H. Erfle, R. Bartenschlager
Date Published: 8th Jan 2015
Publication Type: Not specified
PubMed ID: 25569684
Citation: PLoS Pathog. 2015 Jan 8;11(1):e1004573. doi: 10.1371/journal.ppat.1004573. eCollection 2015 Jan.
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Authors: G. Stoll, E. Viara, E. Barillot, L. Calzone
Date Published: 29th Aug 2012
Publication Type: Journal
PubMed ID: 22932419
Citation: BMC Syst Biol. 2012 Aug 29;6:116. doi: 10.1186/1752-0509-6-116.
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Authors: Alexey Kolodkin, Raju Prasad Sharma, Anna Maria Colangelo, Andrew Ignatenko, Francesca Martorana, Danyel Jennen, Jacco J. Briede, Nathan Brady, Matteo Barberis, Thierry D.G.A. Mondeel, Michele Papa, Vikas Kumar, Bernhard Peters, Alexander Skupin, Lilia Alberghina, Rudi Balling, Hans V. Westerhoff
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/647776
Citation: Design principles of ROS dynamic networks relevant to precision therapies for age-related diseases 74 : 324