Chris T. A. Evelo

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 28

Top Topics

Development Kit

Top Venues

PLoS Comput. Biol.

J. Cheminformatics

Nucleic Acids Res.

Publications

Ammar Ammar, Rachel Cavill, Chris T. A. Evelo, Egon L. Willighagen
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. J. Cheminformatics 15 (1) (2023)
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
Managing food and microbiome studies data using Fairspace, a flexible and FAIR data management platform. SWAT4HCLS (2023)
Friederike Ehrhart, Chris T. A. Evelo
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. Data Sci. 5 (1) (2022)
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 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
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022 (2022) (2022)
Ammar Ammar, Rachel Cavill, Chris T. A. Evelo, Egon L. Willighagen
PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. J. Cheminformatics 14 (1) (2022)
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
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR (2021)
Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E. Adriaens, Chris T. A. Evelo, Ilja C. W. Arts
Comparison of metabolic states using genome-scale metabolic models. PLoS Comput. Biol. 17 (11) (2021)
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
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput. Biol. 17 (8) (2021)
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
WikiPathways: connecting communities. Nucleic Acids Res. 49 (Database-Issue) (2021)
Friederike Ehrhart, Chris T. A. Evelo
Ten simple rules to make your publication look better. PLoS Comput. Biol. 17 (5) (2021)
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
FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2 (1-2) (2020)
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
The need for standardisation in life science research - an approach to excellence and trust. F1000Research 9 (2020)
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. A. Evelo, Susan L. Coort
CyTargetLinker app update: A flexible solution for network extension in Cytoscape. F1000Research 7 (2018)
Tobias Kuhn, Albert Meroño-Peñuela, Alexander Malic, Jorrit H. Poelen, Allen H. Hurlbert, Emilio Centeno, 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
Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. CoRR (2018)
Friederike Ehrhart, Jonathan Mélius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M. G. Curfs, Chris T. A. Evelo
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. F1000Research 7 (2018)
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
Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. eScience (2018)
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
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 46 (Database-Issue) (2018)
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
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminformatics 9 (1) (2017)
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
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminformatics 9 (1) (2017)
Tobias Kuhn, Egon L. Willighagen, Chris T. A. Evelo, Núria Queralt-Rosinach, Emilio Centeno, Laura I. Furlong
Reliable Granular References to Changing Linked Data. ISWC (1) (2017)
Tobias Kuhn, Egon L. Willighagen, Chris T. A. Evelo, Núria Queralt-Rosinach, Emilio Centeno, Laura I. Furlong
Reliable Granular References to Changing Linked Data. CoRR (2017)
Ryan A. Miller, Denise N. Slenter, Martina Kutmon, Jonathan Mélius, Georg Summer, Chris T. A. Evelo, Egon L. Willighagen
Visualizing Metabolomics Data in Directed Biological Networks. SWAT4LS (2017)
Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. A. Evelo, Nina Jeliazkova
XMetDB: an open access database for xenobiotic metabolism. J. Cheminformatics 8 (1) (2016)
Ryan A. Miller, Jonathan Mélius, Nuno Nunes, Egon L. Willighagen, Peter Woollard, Chris T. A. Evelo
Finding Drugs with Common Downstream Effects, Using Direction Information in Biological Pathways. SWAT4LS (2016)
Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan A. Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput. Biol. 12 (6) (2016)
Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo
Reactome from a WikiPathways Perspective. PLoS Comput. Biol. 12 (5) (2016)
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
WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 44 (Database-Issue) (2016)
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
The systems biology format converter. BMC Bioinform. 17 (2016)
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
diXa: a data infrastructure for chemical safety assessment. Bioinform. 31 (9) (2015)
Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard, Chris T. A. Evelo
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. BMC Bioinform. 16 (2015)
Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo
PathVisio 3: An Extendable Pathway Analysis Toolbox. PLoS Comput. Biol. 11 (2) (2015)
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
Scientific Lenses to Support Multiple Views over Linked Chemistry Data. ISWC (1) (2014)
Martijn P. van Iersel, Milka Sokolovic, Kaatje Lenaerts, Martina Kutmon, Freek G. Bouwman, Wouter H. Lamers, Edwin C. M. Mariman, Chris T. A. Evelo
Integrated Visualization of a Multi-omics Study of Starvation in Mouse Intestine. J. Integr. Bioinform. 11 (1) (2014)
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
Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semantic Web 5 (2) (2014)
Lars M. T. Eijssen, Magali Jaillard, Michiel E. Adriaens, Stan Gaj, Philip J. de Groot, Michael R. Müller, Chris T. A. Evelo
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
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
The Pharmacology Workspace: A Platform for Drug Discovery. ICBO (2012)
Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. A. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis
GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinform. 28 (16) (2012)
Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico
WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 40 (Database-Issue) (2012)
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
Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision. LISC@ISWC (2012)
Thomas Kelder, Lars M. T. Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris T. A. Evelo
Exploring pathway interactions in insulin resistant mouse liver. BMC Syst. Biol. 5 (2011)
Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinform. 11 (2010)
Martijn P. van Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Susan L. Coort, Bruce R. Conklin, Chris T. A. Evelo
Presenting and exploring biological pathways with PathVisio. BMC Bioinform. 9 (2008)
Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. A. Evelo
Linking microarray reporters with protein functions. BMC Bioinform. 8 (2007)
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
Biologically relevant effects of mRNA amplification on gene expression profiles. BMC Bioinform. 7 (2006)