Arnaud Kerhornou

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2ranked-venue papers

1as first author

1since 2021 · last 2023

0000-0002-2890-295XORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 2 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing

2 papers

Bioinformatics and computational biology · 100%

Topics — the 5 heaviest of 6, each with the papers that count most for it

Topic	Weight	Papers	Last	Evidence papers
Bioinformatics and computational biology › protein analysis › protein bioinformatics protein annotation	0.7	1	2023	Annotation of biologically relevant ligands in UniProtKB using ChEBI · Bioinform. 2023
Bioinformatics and computational biology gene regulation	0.1	1	2007	BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations · Bioinform. 2007
Bioinformatics and computational biology › gene regulation promoter analysis	0.1	1	2007	BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations · Bioinform. 2007
Bioinformatics and computational biology › gene regulation › transcription factor binding site prediction transcription factor binding site analysis	0.1	1	2007	BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations · Bioinform. 2007
Bioinformatics and computational biology web services	0.0	1	2007	BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations · Bioinform. 2007

Methods — techniques the papers use, named apart from their topics

ontology-based annotation · 0.7SPARQL querying · 0.7web services · 0.1gene clustering · 0.1

Year	Publication	Venue	Position
2023	Annotation of biologically relevant ligands in UniProtKB using ChEBI abstract MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant interactions between protein sequences and structures and small molecule ligands. RESULTS: We structured the data model for cognate ligand binding site annotations in UniProtKB and performed a complete reannotation of all cognate ligand binding sites using stable unique identifiers from ChEBI, which we now use as the reference vocabulary for all such annotations. We developed improved search and query facilities for cognate ligands in the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that ChEBI provides. AVAILABILITY AND IMPLEMENTATION: Binding site annotations for cognate ligands described using ChEBI are available for UniProtKB protein sequence records in several formats (text, XML and RDF) and are freely available to query and download through the UniProt website (www.uniprot.org), REST API (www.uniprot.org/help/api), SPARQL endpoint (sparql.uniprot.org/) and FTP site (https://ftp.uniprot.org/pub/databases/uniprot/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny 0002, Tunca Dogan, Thankgod Ebenezer, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra 0004, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen E. Ross, C. R. Vinayaka, Qinghua Wang 0003	Bioinform.	34
2007	BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations abstract UNLABELLED: Here we present a computational protocol to analyze the promoter regions of a given set of co-expressed genes, and its implementation through the use of Web services technologies. This protocol aims to cluster a set of co-regulated genes in subsets of genes showing similar configurations of transcription factor binding sites. All the steps of this protocol have been developed as web services that are compliant with BioMoby specifications. AVAILABILITY: {http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi}. SUPPLEMENTARY INFORMATION: Supplementary data are available at {http://genome.imim.es/webservices/} Arnaud Kerhornou, Roderic Guigó	Bioinform.	1