List of works by Chris T. Evelo

2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

scientific article

A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma

scientific article published on 26 April 2022

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

scientific article published on 7 November 2017

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

A Study on the Interaction between Hydroxylamine Analogues and Oxyhemoglobin in Intact Erythrocytes

scientific article (publication date: August 2000)

A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

scientific article published on 01 February 2019

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

scientific article published on 15 January 2021

A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences

scientific article (publication date: 2010)

A data fusion pipeline for generating and enriching Adverse Outcome Pathway descriptions

scientific article published on 15 November 2017

A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

A formalization of one of the main claims of “Overlap of vitamin A and vitamin D target genes with CAKUT-related processes” by Ozisik et al. 20211

scientific article published on 22 March 2022

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

scientific article

A pathway approach to investigate the function and regulation of SREBPs

scientific article published on 21 March 2013

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

scientific article

A systematic review of large scale and heterogeneous gene array data in heart failure

scientific article

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

scientific article

Acknowledging contributions to online expert assistance

Acknowledging contributions to online expert assistance

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

article by Mark D Wilkinson et al published 19 March 2019 in Scientific Data

Advancing food, nutrition, and health research in Europe by connecting and building research infrastructures in a DISH-RI: Results of the EuroDISH project

article

Adverse outcome pathways: opportunities, limitations and open questions

scientific article published on 19 October 2017

Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

scientific article (publication date: 8 February 2011)

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

scientific article

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions

scientific article published on 10 March 2009

Answering biological questions: querying a systems biology database for nutrigenomics

scientific article

Applying linked data approaches to pharmacology: Architectural decisions and implementation ⬇️

scientific article

Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue

scientific article published on 31 May 2021

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

scientific article published on 21 February 2019

Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice.

scientific article

Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

scientific article

Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio

scientific article (publication date: December 2008)

Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus-A Co-expression Network Based Analysis

Biological effect monitoring

scientific article published on January 1992

Biological effect monitoring of occupational exposure to 1,3-dichloropropene: effects on liver and renal function and on glutathione conjugation

scientific article (publication date: March 1991)

Biologically relevant effects of mRNA amplification on gene expression profiles

scientific article

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

scientific article (publication date: October 2010)

Blunted nutrient-response pathways in adipose tissue following high fat meals in men with metabolic syndrome: A randomized postprandial transcriptomic study

scientific article published on 27 August 2020

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

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

scientific article published on 05 May 2020

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

journal article from 'Molecular Systems Biology' published in 2021

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

scientific article (publication date: 3 February 2010)

Changes in blood glutathione concentrations, and in erythrocyte glutathione reductase and glutathione S-transferase activity after running training and after participation in contests

scientific article (publication date: 1992)

Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate

scientific article

Community curation on WikiPathways: How we assist knowledge collection

Comparison of metabolic states using genome-scale metabolic models

scientific article published on 08 November 2021

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

Connecting the Human Variome Project to nutrigenomics

scientific article

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

scientific article (publication date: 2014)

Current systems biology approaches in hazard assessment of nanoparticles

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

scientific article published on 14 June 2018

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

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

scientific article (publication date: 2013)

Cysteine adducts of human haemoglobin measured by isoelectric focusing in polyacrylamide gels with a non-linear pH gradient

scientific article (publication date: 4 September 1987)

Decreased glutathione content and glutathione S-transferase activity in red blood cells of coal miners with early stages of pneumoconiosis

scientific article (publication date: July 1993)

Development of a software package for computer simulations: the use of a sorted event list for reduction of calculation times

scientific article (publication date: July 1993)

Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases

Differential valine metabolism in adipose tissue of low and high fat-oxidizing obese subjects

scientific article (publication date: October 2007)

Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool

scientific article published in January 2024

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

scientific article published on 12 February 2020

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

Effect of Vitamin E on Glutathione-Dependent Enzymes

scientific article (publication date: 2003)

Effect of supplementation with an 80:20cis9,trans11 conjugated linoleic acid blend on the human platelet proteome

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

scientific article published on 20 September 2017

Erythrocyte antioxidant defense response against cigarette smoking in humans--the glutathione S-transferase vulnerability.

scientific article published in January 2005

Erythrocyte glutathione S transferase as a marker of oxidative stress at birth

scientific article

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Exploring pathway interactions in insulin resistant mouse liver

scientific article (publication date: 15 August 2011)

Exploring the cellular network of metabolic flexibility in the adipose tissue.

scientific article published on 5 July 2018

Exposing WikiPathways as Linked Open Data

Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations

scientific article published in 2023

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

Fasting induces a biphasic adaptive metabolic response in murine small intestine

scientific article

Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets

scientific article

Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

scientific article (publication date: December 2009)

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

scientific article published in 2018

From nanotechnology to nanomedicine: applications to cancer research

scientific article published on October 2010

GO-Elite: a flexible solution for pathway and ontology over-representation

scientific article

Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress

scientific article published on 7 February 2006

Gene profiling in atherosclerosis reveals a key role for small inducible cytokines: validation using a novel monocyte chemoattractant protein monoclonal antibody.

scientific article

Gene profiling of cathepsin K deficiency in atherogenesis: profibrotic but lipogenic.

scientific article

Gene promoter DNA methylation patterns have a limited role in orchestrating transcriptional changes in the fetal liver in response to maternal folate depletion during pregnancy

scientific article published on 02 May 2016

Genetic deficiency of human class mu glutathione S-transferase isoenzymes in relation to the urinary excretion of the mercapturic acids of Z- and E-1,3-dichloropropene.

scientific article published in January 1991

Genetic variation in thioredoxin interacting protein (TXNIP) is associated with hypertriglyceridaemia and blood pressure in diabetes mellitus.

scientific article published on 22 March 2007

Glutathione depletion in human erythrocytes and rat liver: a study on the interplay between bioactivation and inactivation functions of liver and blood

Glutathione depletion in human erythrocytes as an indicator for microsomal activation of cyclophosphamide and 3-hydroxyacetanilide

scientific article (publication date: 12 November 1993)

High oxygen treatment during preparation of children for open-heart surgery leads to a decrease in total antioxidant capacity.

scientific article

History of rare diseases and their genetic causes - a data driven approach

Hydroxylamine Treatment Increases Glutathione-Protein and Protein-Protein Binding in Human Erythrocytes

scientific article (publication date: December 1997)

Hypochlorous acid is a potent inhibitor of GST P1-1.

scientific article

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3.

scientific article published on 26 October 2016

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

scientific article published on 01 January 2019

Identification of novel ER-alpha target genes in breast cancer cells: gene- and cell-selective co-regulator recruitment at target promoters determines the response to 17beta-estradiol and tamoxifen

scientific article

Impact of supervised gene signatures of early hypoxia on patient survival

scientific article published on 25 May 2007

In vitro haematotoxic effects of three methylated hydroxylamines

scientific article published on 01 January 1997

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

scientific article

Influence of glutathione on the formation of cysteine alkylation products in human hemoglobin

scientific article

Influence of oxygen supply on liver condition and elimination of dimethylacetamide in the isolated perfused rat liver

Inhibition of human glutathione S-transferase P1-1 by tocopherols and alpha-tocopherol derivatives

scientific article published in July 2001

Inhibition of various glutathione S-transferase isoenzymes by RRR-alpha-tocopherol

scientific article

Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes

article

Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes

scientific article published on 25 March 2019

Integrated visualization of a multi-omics study of starvation in mouse intestine

scientific article

Integrated visualization of a multi-omics study of starvation in mouse intestine

scientific article published on 28 March 2014

Integration among databases and data sets to support productive nanotechnology: challenges and recommendations ⬇️

journal article published in 2018

Integrative multiomics analysis of human atherosclerosis reveals a serum response factor-driven network associated with intraplaque hemorrhage

scientific article published on 01 June 2021

Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells

scientific article published on 15 August 2015

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

scientific article published on 21 December 2018

Introducing WikiPathways to link molecular pathways to adverse outcome pathways to support regulatory risk assessment

scientific article

Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts

scientific article

Kinetics of the formation and secretion of the aniline metabolite 4-aminophenol and its conjugates by isolated rat hepatocytes

scientific article (publication date: 1984)

Linking microarray reporters with protein functions

scientific article

Liver damage after coal-tar treatment does not prevent induction of glutathione S-transferases in rat liver

scientific article (publication date: 1989)

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

MECP2 variation in Rett syndrome - an overview of current coverage of genetic and phenotype data within existing databases

scholarly article from 2018

Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse

article

Maternal folate depletion during early development and high fat feeding from weaning elicit similar changes in gene expression, but not in DNA methylation, in adult offspring

scientific article published on 8 December 2016

Measuring impact in online resources with the CInumber (the CitedIn Number for online impact)

Microarray profiling of human white adipose tissue after exogenous leptin injection.

scientific article published on March 2006

Mining biological pathways using WikiPathways web services

scientific article

Molecular pathways involved in prostate carcinogenesis: insights from public microarray datasets

scientific article (publication date: 2012)

Myocardial and Serum Galectin-3 Expression Dynamics Marks Post-Myocardial Infarction Cardiac Remodelling

scientific article published on 19 December 2016

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data ⬇️

article published in 2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Nature Europe site should highlight most productive countries.

scientific article (publication date: 10 June 2010)

Network Analysis of Genome-Wide Association Studies for Chronic Obstructive Pulmonary Disease in the Context of Biological Pathways

scientific article published on 01 December 2019

New insights in Rett syndrome using pathway analysis for transcriptomics data

scientific article

No reduction of alpha-tocopherol quinone by glutathione in rat liver microsomes

scientific article

Only the glutathione dependent antioxidant enzymes are inhibited by haematotoxic hydroxylamines

Only the glutathione dependent antioxidant enzymes are inhibited by haematotoxic hydroxylamines

scientific article published on 01 October 1998

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

scientific article

Open PHACTS: semantic interoperability for drug discovery ⬇️

scientific article (publication date: November 2012)

OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment

Organ-Specific Gene Expression Changes in the Fetal Liver and Placenta in Response to Maternal Folate Depletion.

scientific article published on 22 October 2016

Overlap of vitamin A and vitamin D target genes with CAKUT-related processes

scientific article, version 1

Overlap of vitamin A and vitamin D target genes with CAKUT-related processes

publication published on 18 May 2021

Oxidative effects in human erythrocytes caused by some oximes and hydroxylamine

scientific article (publication date: April 1998)

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity

scientific article published on 2 March 2023

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

scientific article from 2022

PathVisio 3: an extendable pathway analysis toolbox

scientific article

Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D.

scientific article published on 12 December 2017

Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism

scientific article

Physiologically based toxicokinetic modeling of 1,3-butadiene lung metabolism in mice becomes more important at low doses

scientific article (publication date: November 1993)

Prader-Willi Syndrome and Angelman Syndrome: Visualisation of the molecular pathways for two chromosomal disorders.

scientific article published on 9 February 2018

Presenting and exploring biological pathways with PathVisio

scientific article

Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression

article

Protein profiling of 3T3-L1 adipocyte differentiation and (tumor necrosis factor ?-mediated) starvation

scientific article (publication date: February 2005)

Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

scientific article

Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

scientific article (publication date: November 2016)

Reactome from a WikiPathways Perspective

scientific article (publication date: May 2016)

Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols

scientific article (publication date: 22 July 2009)

Reliable Granular References to Changing Linked Data

conference proceedings article

Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes

Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes

scientific article (publication date: 25 November 2016)

Review and gap analysis: molecular pathways leading to fetal alcohol spectrum disorders

scientific article published on 11 June 2018

Role of 1α,25-Dihydroxyvitamin D 3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation

Role of the Rhoa/Rho kinase system in flow-related remodeling of rat mesenteric small arteries in vivo

scientific article

Scientific Lenses to Support Multiple Views over Linked Chemistry Data ⬇️

scientific article

Separation of human haemoglobin alkylated at beta 93 cysteine from its native form by fast protein liquid chromatography

Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

scientific article

Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation

scientific article published on 03 February 2020

Subcutaneous Adipose Tissue and Systemic Inflammation Are Associated With Peripheral but Not Hepatic Insulin Resistance in Humans

scientific article published on 06 September 2019

Systems Biology in ELIXIR: modelling in the spotlight

scientific article published on 31 May 2024

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

scientific article published on 19 August 2021

Ten simple rules to make your publication look better

scientific article

The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework

publication published on 14 February 2022

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

scientific article (publication date: 4 January 2010)

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

scientific article

The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands

scientific article

The FAIR Cookbook - the essential resource for and by FAIR doers

scientific article published on 19 May 2023

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

The Importance of Modularity in Bioinformatics Tools

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

scientific article

The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension

scientific article published on 01 April 2020

The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation

scientific article (publication date: 26 November 2008)

The application of the open pharmacological concepts triple store (Open PHACTS) to support drug discovery research

scientific article published in 2014

The future of food and nutrition in ELIXIR

scientific article published on 25 August 2022

The nutritional phenotype database*. A real data structure for systems biology

scholarly article by Chris T. Evelo published 3 November 2010 in Nature Precedings

The public road to high-quality curated biological pathways

scientific article published in October 2008

The role of bioinformatics in pathway curation

scientific article (publication date: December 2008)

The systems biology format converter

scientific article

Thrombospondin-2 Is Essential for Myocardial Matrix Integrity: Increased Expression Identifies Failure-Prone Cardiac Hypertrophy

scientific article (publication date: 3 September 2004)

Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance

scientific article

Tocotrienols Inhibit Human Glutathione S-Transferase P1-1

scientific article (publication date: August 2002)

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Toxicokinetics of Dimethylacetamide (DMAc) in Rat Isolated Perfused Liver

scientific article (publication date: March 1993)

Toxicological stress indicators in human red blood cells: changes in glutathione and glutathione S-transferase as biological markers for electrophilic and oxidative stress ⬇️

Ph.D. thesis

Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

scientific article

Two Mechanisms for Toxic Effects of Hydroxylamines in Human Erythrocytes: Involvement of Free Radicals and Risk of Potentiation

article

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

scientific article published on 18 April 2022

Up-regulation of CD36/FAT in preadipocytes in familial combined hyperlipidemia

scientific article

Urinary cyclophosphamide assay as a method for biological monitoring of occupational exposure to cyclophosphamide

scientific article (publication date: June 1986)

User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org

scientific article (publication date: July 2013)

Using a data triangle to understand molecular nutrition

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

scientific article

Validating nutrient-related gene expression changes from microarrays using RT(2) PCR-arrays

scientific article

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

scientific article

WikiPathways 2024: next generation pathway database

scientific article published on 6 November 2023

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

scientific article (publication date: 11 September 2014)

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

scientific article published in 2014

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.

WikiPathways: connecting communities ⬇️

scientific article published on 19 November 2020

WikiPathways: pathway editing for the people

Research paper from 2008 about the WikiPathways database.

Wikidata and Scholia as a hub linking chemical knowledge ⬇️

poster presented at 11th International Conference on Chemical Structures

XMetDB: an open access database for xenobiotic metabolism

scientific article

alpha-Tocopherol inhibits human glutathione S-transferase pi.

scientific article

diXa: a data infrastructure for chemical safety assessment

scientific article

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