Chris T. A. Evelo

According to our database, Chris T. A. Evelo authored at least 42 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Making PBPK models more reproducible in practice.

Elena Domínguez Romero, Stanislav Mazurenko, Martin Scheringer, Vítor A. P. Martins dos Santos, Chris T. A. Evelo, Mihail Anton, John M. Hancock, Anze Zupanic, María Suárez-Diez

Briefings Bioinform., 2024

2023

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

Ammar Ammar, Rachel Cavill, Chris T. A. Evelo, Egon L. Willighagen

J. Cheminformatics, December, 2023

Managing food and microbiome studies data using Fairspace, a flexible and FAIR data management platform.

Ewelina Grudzien, Eelke van der Horst, Frank van den Bergh, Maria H. Traka, Duncan Ng, Falk Hildebrand, Chris T. A. Evelo, Susan L. M. Coort, Duygu Dede Sener, Elisa Cirillo

Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

2022

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

Ammar Ammar, Rachel Cavill, Chris T. A. Evelo, Egon L. Willighagen

J. Cheminformatics, 2022

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.

Friederike Ehrhart, Chris T. A. Evelo

Data Sci., 2022

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall

Database J. Biol. Databases Curation, 2022

2021

Comparison of metabolic states using genome-scale metabolic models.

Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E. Adriaens, Chris T. A. Evelo, Ilja C. W. Arts

PLoS Comput. Biol., 2021

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

Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. A. Evelo, Alexander R. Pico

PLoS Comput. Biol., 2021

Ten simple rules to make your publication look better.

Friederike Ehrhart, Chris T. A. Evelo

PLoS Comput. Biol., 2021

WikiPathways: connecting communities.

Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N. Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N. Lopes, Friederike Ehrhart, Lauren J. Dupuis, Laurent A. Winckers, Susan L. Coort, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico, Martina Kutmon

Nucleic Acids Res., 2021

2020

The need for standardisation in life science research - an approach to excellence and trust.

Susanne Hollmann, Andreas Kremer, Spela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. A. Evelo, Alina S. Nechyporenko, Marcus Frohme, David Safránek, Babette Regierer, Domenica D'Elia

F1000Research, 2020

FAIR Principles: Interpretations and Implementation Considerations.

Annika Jacobsen, Ricardo de Miranda Azevedo, Nick S. Juty, Dominique Batista, Simon J. Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. A. Evelo, Carole A. Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes

Data Intell., 2020

2018

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Denise N. Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L. Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan A. Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M. T. Eijssen, Chris T. A. Evelo, Alexander R. Pico, Egon L. Willighagen

Nucleic Acids Res., 2018

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

Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. A. Evelo, Susan L. Coort

F1000Research, 2018

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

Friederike Ehrhart, Jonathan Mélius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M. G. Curfs, Chris T. A. Evelo

F1000Research, 2018

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

Tobias Kuhn, Albert Meroño-Peñuela, Alexander Malic, Jorrit H. Poelen, Allen H. Hurlbert, Emilio Centeno Ortiz, Laura I. Furlong, Núria Queralt-Rosinach, Christine Chichester, Juan M. Banda, Egon L. Willighagen, Friederike Ehrhart, Chris T. A. Evelo, Tareq B. Malas, Michel Dumontier

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

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

Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck

J. Cheminformatics, 2017

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

Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck

J. Cheminformatics, 2017

Visualizing Metabolomics Data in Directed Biological Networks.

Ryan A. Miller, Denise N. Slenter, Martina Kutmon, Jonathan Mélius, Georg Summer, Chris T. A. Evelo, Egon L. Willighagen

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

Reliable Granular References to Changing Linked Data.

Tobias Kuhn, Egon L. Willighagen, Chris T. A. Evelo, Núria Queralt-Rosinach, Emilio Centeno, Laura I. Furlong

Proceedings of the Semantic Web - ISWC 2017, 2017

2016

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

Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan A. Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico

PLoS Comput. Biol., 2016

Reactome from a WikiPathways Perspective.

Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo

PLoS Comput. Biol., 2016

WikiPathways: capturing the full diversity of pathway knowledge.

Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan A. Miller, Susan L. Coort, Elisa Cirillo, Bart Smeets, Chris T. A. Evelo, Alexander R. Pico

Nucleic Acids Res., 2016

XMetDB: an open access database for xenobiotic metabolism.

Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. A. Evelo, Nina Jeliazkova

J. Cheminformatics, 2016

The systems biology format converter.

Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gaël Jalowicki, Martina Kutmon, Kedar Nath Natarajan, David Tolnay, Melanie I. Stefan, Chris T. A. Evelo, Nicolas Le Novère

BMC Bioinform., 2016

Finding Drugs with Common Downstream Effects, Using Direction Information in Biological Pathways.

Ryan A. Miller, Jonathan Mélius, Nuno Nunes, Egon L. Willighagen, Peter Woollard, Chris T. A. Evelo

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

2015

PathVisio 3: An Extendable Pathway Analysis Toolbox.

Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo

PLoS Comput. Biol., 2015

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard, Chris T. A. Evelo

BMC Bioinform., 2015

diXa: a data infrastructure for chemical safety assessment.

Diana M. Hendrickx, Hugo J. W. L. Aerts, Florian Caiment, Dominic Clark, Timothy M. D. Ebbels, Chris T. A. Evelo, Hans Gmuender, Dennie G. A. J. Hebels, Ralf Herwig, Jürgen Hescheler, Danyel G. J. Jennen, Marlon J. A. Jetten, Stathis Kanterakis, Hector C. Keun, Vera Matser, John P. Overington, Ekaterina Pilicheva, Ugis Sarkans, Marcelo P. Segura-Lepe, Isaia Sotiriadou, Timo Wittenberger, Clemens Wittwehr, Antonella Zanzi, Jos C. S. Kleinjans

Bioinform., 2015

2014

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

Alasdair J. G. Gray, Paul Groth, Antonis Loizou, Sune Askjaer, Christian Y. A. Brenninkmeijer, Kees Burger, Christine Chichester, Chris T. A. Evelo, Carole A. Goble, Lee Harland, Steve Pettifer, Mark Thompson, Andra Waagmeester, Antony J. Williams

Semantic Web, 2014

Integrated Visualization of a Multi-omics Study of Starvation in Mouse Intestine.

Martijn P. van Iersel, Milka Sokolovic, Kaatje Lenaerts, Martina Kutmon, Freek G. Bouwman, Wouter H. Lamers, Edwin C. M. Mariman, Chris T. A. Evelo

J. Integr. Bioinform., 2014

Scientific Lenses to Support Multiple Views over Linked Chemistry Data.

Colin R. Batchelor, Christian Y. A. Brenninkmeijer, Christine Chichester, Mark Davies, Daniela Digles, Ian Dunlop, Chris T. A. Evelo, Anna Gaulton, Carole A. Goble, Alasdair J. G. Gray, Paul Groth, Lee Harland, Karen Karapetyan, Antonis Loizou, John P. Overington, Steve Pettifer, Jon Steele, Robert Stevens, Valery Tkachenko, Andra Waagmeester, Antony J. Williams, Egon L. Willighagen

Proceedings of the Semantic Web - ISWC 2014, 2014

2013

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

Lars M. T. Eijssen, Magali Jaillard, Michiel E. Adriaens, Stan Gaj, Philip J. de Groot, Michael R. Müller, Chris T. A. Evelo

Nucleic Acids Res., 2013

2012

WikiPathways: building research communities on biological pathways.

Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico

Nucleic Acids Res., 2012

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

Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. A. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis

Bioinform., 2012

Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision.

Christian Y. A. Brenninkmeijer, Chris T. A. Evelo, Carole A. Goble, Alasdair J. G. Gray, Paul Groth, Steve Pettifer, Robert Stevens, Antony J. Williams, Egon L. Willighagen

Proceedings of the Second International Workshop on Linked Science 2012, 2012

The Pharmacology Workspace: A Platform for Drug Discovery.

Alasdair J. G. Gray, Sune Askjaer, Christian Y. A. Brenninkmeijer, Kees Burger, Christine Chichester, James M. Eales, Chris T. A. Evelo, Carole A. Goble, Paul Groth, Lee Harland, Antonis Loizou, Steve Pettifer, Rishi Ramgolam, Mark Thompson, Andra Waagmeester, Antony J. Williams

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011

Exploring pathway interactions in insulin resistant mouse liver.

Thomas Kelder, Lars M. T. Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris T. A. Evelo

BMC Syst. Biol., 2011

2010

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

Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo

BMC Bioinform., 2010

2008

Presenting and exploring biological pathways with PathVisio.

Martijn P. van Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Susan L. Coort, Bruce R. Conklin, Chris T. A. Evelo

BMC Bioinform., 2008

2007

Linking microarray reporters with protein functions.

Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. A. Evelo

BMC Bioinform., 2007

2006

Biologically relevant effects of mRNA amplification on gene expression profiles.

Rachel I. M. van Haaften, Blanche Schroen, Ben J. A. Janssen, Arie van Erk, Jacques J. M. Debets, Hubert J. M. Smeets, Jos F. M. Smits, Arthur van den Wijngaard, Yigal M. Pinto, Chris T. A. Evelo

BMC Bioinform., 2006