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List of works by Martina Summer-Kutmon

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The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

scientific article published on 10 November 2017
WikiPathways: building research communities on biological pathways

scientific article (publication date: 2012)
WikiPathways: capturing the full diversity of pathway knowledge

research paper from 2016 about the WikiPathways database
PathVisio 3: an extendable pathway analysis toolbox

scientific article
A resource to explore the discovery of rare diseases and their causative genes

scientific article
Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis

scientific article (publication date: 2013)
CyTargetLinker app update: A flexible solution for network extension in Cytoscape

scientific article published on 14 June 2018
WikiPathways: connecting communities

scientific article published on 19 November 2020
A pathway approach to investigate the function and regulation of SREBPs

scientific article published on 21 March 2013
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

scientific article
WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

scientific article (publication date: 11 September 2014)
Reactome from a WikiPathways Perspective

scientific article (publication date: May 2016)
From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

scientific article published in 2018
Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways

scientific article
A network biology workflow to study transcriptomics data of the diabetic liver

scientific article published on November 15, 2014
The systems biology format converter

scientific article
Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010
Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D.

scientific article published on 12 December 2017
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

scientific article
CyTargetLinker app update: A flexible solution for network extension in Cytoscape

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

January 2021 scholarly article
Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

scientific article
Exploring the cellular network of metabolic flexibility in the adipose tissue

scientific article published on 5 July 2018
Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

scientific article published on 21 February 2019
Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells

scientific article published on 15 August 2015
Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

journal article from 'Molecular Systems Biology' published in 2021
Integrated visualization of a multi-omics study of starvation in mouse intestine

scientific article
TCA Cycle

metabolic pathway (mus musculus)
Integrative multiomics analysis of human atherosclerosis reveals a serum response factor-driven network associated with intraplaque hemorrhage

scientific article published on 01 June 2021
Integrated visualization of a multi-omics study of starvation in mouse intestine

scientific article published on 28 March 2014
A protocol for adding knowledge to Wikidata, a case report

scientific article published on 07 April 2020
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma

scientific article published on 14 June 2019
Pathway information extracted from 25 years of pathway figures

scientific article published on 09 November 2020
Managing biological data in pathways and networks

doctoral thesis
Glycolysis and Gluconeogenesis

metabolic pathway (mus musculus)
Logical modelling reveals the PDC-PDK interaction as the regulatory switch driving metabolic flexibility at the cellular level

scientific article published on 09 September 2019
Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology
Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus-A Co-expression Network Based Analysis

A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

scientific article published on 01 February 2019
Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression

article
Ten simple rules for creating reusable pathway models for computational analysis and visualization

scientific article published on 19 August 2021
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension

scientific article published on 01 April 2020
Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding

scientific article published on 01 January 2019
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models

scientific article published on 12 February 2020

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