Ioannis Xénarios

37.2k citations

171 papers · 14.3k indexed · 7 hit papers · h-index 52

Molecular Biology top 0.2%
- Genomics and Phylogenetic Studies 31
- Bioinformatics and Genomic Networks 28
- Microbial Metabolic Engineering and Bioproduction 22
- RNA and protein synthesis mechanisms 16
- Gene Regulatory Network Analysis 16
- Metabolomics and Mass Spectrometry Studies 11
- Machine Learning in Bioinformatics 10
- Gene expression and cancer classification 10
Computational Theory and Mathematics top 0.2%
Plant Science top 1%
Immunology top 2%
Genetics top 1%

Co-authors: David Eisenberg Lydie Bougueleret Alan Bridge Edward M. Marcotte Edouard de Castro Luis Mendoza Beatrice Cuche Lorenzo Cerutti
Cited by: Molecular Biology Computational Theory and Mathematics Plant Science
Journals: Nature (1 paper)Cell (1 paper)Proceedings of the National Academy of Sciences (3 papers)
Partner nations: Switzerland United States United Kingdom

In The Last Decade

Ioannis Xénarios

165 papers receiving 14.0k citations

Hit Papers

7 papers align trajectories log scale

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

2015 Methods in molecular biology
2012 Nucleic Acids Research
2012 The Plant Journal
2011 Nucleic Acids Research
2002 Nucleic Acids Research
2000 Nucleic Acids Research
2000 Nature

Peers

Countries citing papers authored by Ioannis Xénarios

Since Specialization

Citations

This map shows the geographic impact of Ioannis Xénarios's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ioannis Xénarios with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ioannis Xénarios more than expected).

Fields of papers citing papers by Ioannis Xénarios

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ioannis Xénarios. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ioannis Xénarios. The network helps show where Ioannis Xénarios may publish in the future.

Co-authorship network

The 25 scholars most cited alongside Ioannis Xénarios, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Ioannis Xénarios Line = papers co-authored together Ioannis Xénarios links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria Molecular & Cellular Proteomics ·Jianbo Fu,Vito Riccardo Tomaso Zanotelli,Cédric Howald,Nylsa Chammartin,Ilya Kolpakov,Ioannis Xénarios,D. Sean Froese,Bernd Wollscheid,Patrick G. A. Pedrioli,Sandra Goetze	2025	2
2	Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms mAbs ·Marianne Bachmann Salvy,Luca Santuari,Emanuel Schmid‐Siegert,Nikolaos Lykoskoufis,Ioannis Xénarios,Alaaddin Bulak Arpat	2024	0
3	Improving population scale statistical phasing with whole-genome sequencing data PLoS Genetics ·Rick Wertenbroek,Robin J. Hofmeister,Ioannis Xénarios,Yann Thoma,Olivier Delaneau	2024	0
4	Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing NAR Genomics and Bioinformatics ·Alysha Taylor,Dinis Barros,Nastassia Gobet,Thierry Schuepbach,Branduff McAllister,Lorène Aeschbach,Emma Randall,Evgeniya Trofimenko,Eleanor R. Heuchan,Paula Barszcz,Marc Ciosi,Joanne Morgan,Nathaniel J. Hafford‐Tear,Alice E. Davidson,Thomas H. Massey,Darren G. Monckton,Lesley Jones,REGISTRY Investigators of the European Huntington’s disease network,Ioannis Xénarios,Vincent Dion	2022	7
5	PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling Bioinformatics ·Amel Bekkar,Anita Nasrallah,Nicolas Guex,Lluís Fajas,Ioannis Xénarios,Isabel C. López‐Mejía	2020	4
6	HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes GigaScience ·Jerven Bolleman,Edouard de Castro,Delphine Baratin,Sébastien Géhant,B. A. Cuche,Andrea H Auchincloss,Elisabeth Coudert,Chantal Hulo,Patrick Masson,Ivo Pedruzzi,Catherine Rivoire,Ioannis Xénarios,Nicole Redaschi,Alan Bridge	2020	7
7	Virosaurus A Reference to Explore and Capture Virus Genetic Diversity Viruses ·Anne Gleizes,Florian Laubscher,Nicolas Guex,Christian Iseli,Thomas Junier,Samuel Cordey,Jacques Fellay,Ioannis Xénarios,Laurent Kaiser,Philippe Le Mercier	2020	8
8	Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop Briefings in Bioinformatics ·Anna Niarakis,Martin Kuiper,Marek Ostaszewski,Rahuman S. Malik‐Sheriff,Cristina Casals‐Casas,Denis Thieffry,Tom C. Freeman,Paul D. Thomas,Vasundra Touré,Vincent Noël,Gautier Stoll,Julio Sáez-Rodríguez,Aurélien Naldi,Eugenia Oshurko,Ioannis Xénarios,Sylvain Soliman,Claudine Chaouiya,Tomáš Helikar,Laurence Calzone	2020	13
9	Sleep–wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex Proceedings of the National Academy of Sciences ·Charlotte N. Hor,Jake Yeung,Maxime Jan,Yann Emmenegger,Jeffrey Hubbard,Ioannis Xénarios,Félix Naef,Paul Franken	2019	58
10	Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region Bioinformatics ·Simon Dellicour,Philippe Lemey,Jean Artois,Tommy Tsan‐Yuk Lam,Alice Fusaro,Isabella Monne,Giovanni Cattoli,Dmitry V. Kuznetsov,Ioannis Xénarios,Gwenae͏̈lle Dauphin,Wantanee Kalpravidh,Sophie von Dobschuetz,Filip Claes,Scott H. Newman,Marc A. Suchard,Guy Baele,Marius Gilbert	2019	16
11	Scaling up data curation using deep learning: An application to literature triage in genomic variation resources PLoS Computational Biology ·Kyubum Lee,Maria Livia Famiglietti,Aoife McMahon,Chih-Hsuan Wei,Jacqueline A. L. MacArthur,Sylvain Poux,Lionel Breuza,Alan Bridge,Fiona Cunningham,Ioannis Xénarios,Zhiyong Lu	2018	30
12	Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome* Molecular & Cellular Proteomics ·Roman Mylonas,Ilan Beer,Christian Iseli,Chloé Chong,Huisong Pak,David Gfeller,George Coukos,Ioannis Xénarios,Markus Müller,Michal Bassani‐Sternberg	2018	74
13	Local auxin production underlies a spatially restricted neighbor-detection response in Arabidopsis Proceedings of the National Academy of Sciences ·Olivier Michaud,Anne-Sophie Fiorucci,Ioannis Xénarios,Christian Fankhauser	2017	74
14	Bacterial Virus Ontology; Coordinating across Databases Viruses ·Chantal Hulo,Patrick Masson,Ariane Toussaint,David Osumi-Sutherland,Edouard de Castro,Andrea H Auchincloss,Sylvain Poux,Lydie Bougueleret,Ioannis Xénarios,Philippe Le Mercier	2017	2
15	The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection PLoS ONE ·Chantal Hulo,Patrick Masson,Edouard de Castro,Andrea H Auchincloss,Rebecca E. Foulger,Sylvain Poux,Jane Lomax,Lydie Bougueleret,Ioannis Xénarios,Philippe Le Mercier	2017	7
16	Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation eLife ·Madhur Dhingra,Jean Artois,Timothy P. Robinson,Catherine Linard,Celia Chaiban,Ioannis Xénarios,Robin Engler,Robin Liechti,Dmitry Kuznetsov,Xiangming Xiao,Sophie von Dobschuetz,Filip Claes,Scott H. Newman,Gwenae͏̈lle Dauphin,Marius Gilbert	2016	42
17	Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth The Plant Cell ·Markus V. Kohnen,Emanuel Schmid‐Siegert,Martine Trévisan,Laure Allenbach Petrolati,Fabien Sénéchal,Patricia Müller-Moulé,Julin Maloof,Ioannis Xénarios,Christian Fankhauser	2016	133
18	TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2–Expressing Monocytes in Human Breast Tumors Clinical Cancer Research ·Mark Ibberson,Sylvian Bron,Nicolas Guex,Eveline Faes-van’t Hull,Assia Ifticene‐Treboux,Luc Henry,Hans‐Anton Lehr,Jean-François Delaloye,George Coukos,Ioannis Xénarios,Marie‐Agnès Doucey	2013	32
19	Evolution of the Ferric Reductase Domain (FRD) Superfamily: Modularity, Functional Diversification, and Signature Motifs PLoS ONE ·Xuezhi Zhang,Karl‐Heinz Krause,Ioannis Xénarios,Thierry Soldati,Brigitte Boeckmann	2013	72
20	Localizing proteins in the cell from their phylogenetic profiles Proceedings of the National Academy of Sciences ·Edward M. Marcotte,Ioannis Xénarios,Alexander M. van der Bliek,David Eisenberg	2000	174

About Ioannis Xénarios

Ioannis Xénarios is a scholar working on Molecular Biology, Genetics and Immunology, having authored 171 papers that have together received 14.3k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (31 papers), Bioinformatics and Genomic Networks (28 papers), Microbial Metabolic Engineering and Bioproduction (22 papers), RNA and protein synthesis mechanisms (16 papers), Gene Regulatory Network Analysis (16 papers), Metabolomics and Mass Spectrometry Studies (11 papers), Machine Learning in Bioinformatics (10 papers) and Gene expression and cancer classification (10 papers). The work is most often cited by research in Molecular Biology (10.3k citations), Computational Theory and Mathematics (1.2k citations) and Plant Science (2.0k citations). Ioannis Xénarios has collaborated with scholars based in Switzerland, United States and United Kingdom. Frequent co-authors include David Eisenberg, Lydie Bougueleret, Alan Bridge, Edward M. Marcotte, Edouard de Castro, Luis Mendoza, Beatrice Cuche, Lorenzo Cerutti, Nicolas Hulo and Christian J A Sigrist. Their work appears in journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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