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Chris T. A. Evelo
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- affiliation: Maastricht University, Department of Bioinformatics, The Netherlands
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2020 – today
- 2023
- [j30]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): 31 (2023) - [c8]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: 171-172 - 2022
- [j29]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). Database J. Biol. Databases Curation 2022(2022) (2022) - [j28]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): 25-27 (2022) - [j27]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): 8 (2022) - 2021
- [j26]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): D613-D621 (2021) - [j25]Friederike Ehrhart
, Chris T. A. Evelo:
Ten simple rules to make your publication look better. PLoS Comput. Biol. 17(5) (2021) - [j24]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) - [j23]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) - [i6]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 abs/2112.07051 (2021) - 2020
- [j22]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): 10-29 (2020) - [i5]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: 1398 (2020)
2010 – 2019
- 2018
- [j21]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): D661-D667 (2018) - [c7]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: 83-92 - [i4]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 abs/1809.06532 (2018) - [i3]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: 743 (2018) - [i2]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: 1390 (2018) - 2017
- [j20]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): 33:1-33:19 (2017) - [j19]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): 53 (2017) - [c6]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: 436-451 - [c5]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 - [i1]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 abs/1708.09193 (2017) - 2016
- [j18]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: 154 (2016) - [j17]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): 47:1-47:8 (2016) - [j16]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): 488-494 (2016) - [j15]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) - [j14]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) - [c4]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 - 2015
- [j13]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): 1505-1507 (2015) - [j12]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: 267:1-267:12 (2015) - [j11]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) - 2014
- [j10]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) - [j9]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): 101-113 (2014) - [c3]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: 98-113 - 2013
- [j8]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): 71-76 (2013) - 2012
- [j7]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): 2209-2210 (2012) - [j6]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): 1301-1307 (2012) - [c2]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 - [c1]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 - 2011
- [j5]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: 127 (2011) - 2010
- [j4]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: 5 (2010)
2000 – 2009
- 2008
- [j3]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) - 2007
- [j2]Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. A. Evelo:
Linking microarray reporters with protein functions. BMC Bioinform. 8 (2007) - 2006
- [j1]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: 200 (2006)
Coauthor Index
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