I Xenarios - PMC

Filip Claes, Dmitry Kuznetsov, Robin Liechti, Sophie Von Dobschuetz, Bao Dinh Truong, Anne Gleizes, Daniele Conversa, Alessandro Colonna, Ettore Demaio, Sabina Ramazzotto, Fairouz Larfaoui, Julio Pinto, Philippe Le Mercier, Ioannis Xenarios, Gwenaelle Dauphin

Database (Oxford) 2014; 2014: bau008. Published online 2014 Mar 6. doi: 10.1093/database/bau008

PMCID:: PMC3945526

Abstract Article PDF–695K

Select item 45266544.

An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation

Anastasia Chasapi, Paulina Wachowicz, Anne Niknejad, Philippe Collin, Andrea Krapp, Elena Cano, Viesturs Simanis, Ioannis Xenarios

PLoS One. 2015; 10(8): e0134214. Published online 2015 Aug 5. doi: 10.1371/journal.pone.0134214

PMCID:: PMC4526654

Abstract Article PDF–3.0M

Select item 43591635.

Angiogenic Activity of Breast Cancer Patients’ Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches

Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene-Treboux, Eveline Faes-van’t Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, Francois Majo, Michäel Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnès Doucey

PLoS Comput Biol. 2015 Mar; 11(3): e1004050. Published online 2015 Mar 13. doi: 10.1371/journal.pcbi.1004050

PMCID:: PMC4359163

Abstract Article PDF–5.7M

Select item 76934946.

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

Anne Gleizes, Florian Laubscher, Nicolas Guex, Christian Iseli, Thomas Junier, Samuel Cordey, Jacques Fellay, Ioannis Xenarios, Laurent Kaiser, Philippe Le Mercier

Viruses. 2020 Nov; 12(11): 1248. Published online 2020 Nov 1. doi: 10.3390/v12111248

PMCID:: PMC7693494

Abstract Article PDF–2.4M

Select item 65722607.

DynaStI: A Dynamic Retention Time Database for Steroidomics

Santiago Codesido, Giuseppe Marco Randazzo, Fabio Lehmann, Víctor González-Ruiz, Arnaud García, Ioannis Xenarios, Robin Liechti, Alan Bridge, Julien Boccard, Serge Rudaz

Metabolites. 2019 May; 9(5): 85. Published online 2019 Apr 30. doi: 10.3390/metabo9050085

PMCID:: PMC6572260

Abstract Article PDF–2.4M

Select item 54908038.

Bacterial Virus Ontology; Coordinating across Databases

Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H. Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

Viruses. 2017 Jun; 9(6): 126. Published online 2017 May 23. doi: 10.3390/v9060126

PMCID:: PMC5490803

Abstract Article PDF–3.9M

Select item 32028129.

Animal Toxins: How is Complexity Represented in Databases?

Florence Jungo, Anne Estreicher, Amos Bairoch, Lydie Bougueleret, Ioannis Xenarios

Toxins (Basel) 2010 Feb; 2(2): 262–282. Published online 2010 Feb 21. doi: 10.3390/toxins2020262

PMCID:: PMC3202812

Abstract Article PDF–648K

Select item 369464110.

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens

Bioinformatics. 2013 Jul 1; 29(13): i80–i88. Published online 2013 Jun 19. doi: 10.1093/bioinformatics/btt243

PMCID:: PMC3694641

Abstract Article PDF–971K

Select item 353108811.

HAMAP in 2013, new developments in the protein family classification and annotation system

Ivo Pedruzzi, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Edouard de Castro, Delphine Baratin, Béatrice A. Cuche, Lydie Bougueleret, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios, Alan Bridge, the UniProt Consortium

Nucleic Acids Res. 2013 Jan; 41(Database issue): D584–D589. Published online 2012 Nov 26. doi: 10.1093/nar/gks1157

PMCID:: PMC3531088

Abstract Article PDF–5.5M

Select item 519916012.

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu

Database (Oxford) 2016; 2016: baw161. Published online 2016 Dec 26. doi: 10.1093/database/baw161

PMCID:: PMC5199160

Abstract Article PDF–367K

Select item 407997113.

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Nicolas Bonhoure, Gergana Bounova, David Bernasconi, Viviane Praz, Fabienne Lammers, Donatella Canella, Ian M. Willis, Winship Herr, Nouria Hernandez, Mauro Delorenzi, The CycliX Consortium, Nouria Hernandez, Mauro Delorenzi, Bart Deplancke, Béatrice Desvergne, Nicolas Guex, Winship Herr, Felix Naef, Jacques Rougemont, Ueli Schibler, Teemu Andersin, Pascal Cousin, Federica Gilardi, Pascal Gos, Fabienne Lammers, Sunil Raghav, Dominic Villeneuve, Roberto Fabbretti, Volker Vlegel, Ioannis Xenarios, Eugenia Migliavacca, Viviane Praz, Fabrice David, Yohan Jarosz, Dmitry Kuznetsov, Robin Liechti, Olivier Martin, Julien Delafontaine, Julia Cajan, Kyle Gustafson, Irina Krier, Marion Leleu, Nacho Molina, Aurélien Naldi, Leonor Rib, Laura Symul, Gergana Bounova

Genome Res. 2014 Jul; 24(7): 1157–1168. doi: 10.1101/gr.168260.113

PMCID:: PMC4079971

Abstract Article PDF–1.6M

Select item 391723314.

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

Martial Sankar, Kaisa Nieminen, Laura Ragni, Ioannis Xenarios, Christian S Hardtke

eLife. 2014; 3: e01567. Published online 2014 Feb 11. doi: 10.7554/eLife.01567

PMCID:: PMC3917233

Abstract Article PDF–3.6M

Select item 669413215.

HENA, heterogeneous network-based data set for Alzheimer’s disease

Elena Sügis, Jerome Dauvillier, Anna Leontjeva, Priit Adler, Valerie Hindie, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Herault, Jean-Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xenarios, Jaak Vilo, Michel Simonneau, Hedi Peterson

Sci Data. 2019; 6: 151. Published online 2019 Aug 14. doi: 10.1038/s41597-019-0152-0

PMCID:: PMC6694132

Abstract Article PDF–2.8M

Select item 610728516.

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources

Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu

PLoS Comput Biol. 2018 Aug; 14(8): e1006390. Published online 2018 Aug 13. doi: 10.1371/journal.pcbi.1006390

PMCID:: PMC6107285

Abstract Article PDF–1.3M

Select item 339426917.

ExPASy: SIB bioinformatics resource portal

Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gabor Csardi, Edouard de Castro, Séverine Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger, Aurélien Grosdidier, Céline Hernandez, Vassilios Ioannidis, Dmitry Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger

Nucleic Acids Res. 2012 Jul; 40(Web Server issue): W597–W603. Published online 2012 May 31. doi: 10.1093/nar/gks400

PMCID:: PMC3394269

Abstract Article PDF–5.9M

Select item 268796818.

Modeling stochasticity and robustness in gene regulatory networks

Abhishek Garg, Kartik Mohanram, Alessandro Di Cara, Giovanni De Micheli, Ioannis Xenarios

Bioinformatics. 2009 Jun 15; 25(12): i101–i109. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp214

PMCID:: PMC2687968

Abstract Article PDF–974K

Select item 331714919.

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

Donatella Canella, David Bernasconi, Federica Gilardi, Gwendal LeMartelot, Eugenia Migliavacca, Viviane Praz, Pascal Cousin, Mauro Delorenzi, Nouria Hernandez, The CycliX Consortium, Nouria Hernandez, Mauro Delorenzi, Bart Deplancke, Béatrice Desvergne, Nicolas Guex, Winship Herr, Felix Naef, Jacques Rougemont, Ueli Schibler, Bart Deplancke, Nicolas Guex, Winship Herr, Nicolas Guex, Teemu Andersin, Pascal Cousin, Federica Gilardi, Pascal Gos, Gwendal Le Martelot, Fabienne Lammers, Donatella Canella, Federica Gilardi, Sunil Raghav, Roberto Fabbretti, Arnaud Fortier, Li Long, Volker Vlegel, Ioannis Xenarios, Eugenia Migliavacca, Viviane Praz, Nicolas Guex, Felix Naef, Jacques Rougemont, Fabrice David, Yohan Jarosz, Dmitry Kuznetsov, Robin Liechti, Olivier Martin, Frederick Ross, Lucas Sinclair, Julia Cajan, Irina Krier, Marion Leleu, Eugenia Migliavacca, Nacho Molina, Aurélien Naldi, Guillaume Rey, Laura Symul, Nicolas Guex, Felix Naef, Jacques Rougemont, David Bernasconi, Mauro Delorenzi, Teemu Andersin, Donatella Canella, Federica Gilardi, Gwendal Le Martelot, Fabienne Lammers, Sunil Raghav

Genome Res. 2012 Apr; 22(4): 666–680. doi: 10.1101/gr.130286.111

PMCID:: PMC3317149

Abstract Article PDF–2.0M

Select item 442179420.

MorphoGraphX: A platform for quantifying morphogenesis in 4D

Pierre Barbier de Reuille, Anne-Lise Routier-Kierzkowska, Daniel Kierzkowski, George W Bassel, Thierry Schüpbach, Gerardo Tauriello, Namrata Bajpai, Sören Strauss, Alain Weber, Annamaria Kiss, Agata Burian, Hugo Hofhuis, Aleksandra Sapala, Marcin Lipowczan, Maria B Heimlicher, Sarah Robinson, Emmanuelle M Bayer, Konrad Basler, Petros Koumoutsakos, Adrienne HK Roeder, Tinri Aegerter-Wilmsen, Naomi Nakayama, Miltos Tsiantis, Angela Hay, Dorota Kwiatkowska, Ioannis Xenarios, Cris Kuhlemeier, Richard S Smith

eLife. 2015; 4: e05864. Published online 2015 May 6. doi: 10.7554/eLife.05864

PMCID:: PMC4421794

Abstract Article PDF–5.7M

Did you mean: i enarios (1 items)

<< First< Prev

Page of 27

Next >Last >>

Supplemental Content

Filter your results:

Manage Filters

PMC Images search for I Xenarios

Fig. 3.

T-helper GRN (Mendoza and Xenarios, ).

Modeling stochasticity and robustness in gene regulatory networks

Bioinformatics. 2009 Jun 15;25(12):i101-i109.
Figure IV.18

Network of protein interactions in yeast
(reprinted from D. Eisenberg, E.M. Marcotte, I. Xenarios and T.O. Yeates (2000) “Protein function in the post-genomic era”, Nature, vol. 405, pp. 823‑826, by permission from Macmillan Publishers Ltd, D. Eisenberg and Nature)
Example of an interaction network involving the yeast Sup45 prionprotein. The line of dashes refers to experimental data concerning the interaction of Sup45 with another protein, Sup35. The lines in bold refer to interactions taken from experimental data; while the fine lines refer to predictions, particularly phylogenetic ones.

Challenges for Experimentation on Living Beings at the Dawn of the 21st Century

Discovering Life, Manufacturing Life. 2010 Jun 8 :241-345.
Figure 1

Proteins that bind to TFs influence gene expression. (A) A schematic illustration of regulation of Met3, a gene involved in sulphate assimilation. Shown are its five TFs (Met32, Cbf1, and Gcr2, Ume6 and Tye7) (squares) and proteins binding to these TFs (circles) (; ; ). Considering proteins binding to TFs as transcription co-factors result in 23 proteins regulating MET3 expression. (B) The number of incoming regulatory edges for S. cerevisiae genes. and the number of incoming regulatory edges, considering the TF network alone (squares) and with proteins binding to TF influencing TF activity (circles).

Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae

Bioinform Biol Insights. 2008;2:307-316.
Figure 1

Feasible protein interactions change between tissues. All protein interactions (A) and feasible protein interactions that connect “global genes,” which are expressed in all three tissues, with tissue-specific genes that are expressed in one tissue out of adipose (B), or thyroid (C), or muscle (D). Data of the genes expressed per tissue were extracted from GTEx Portal (Mele et al., ) and limited to genes with 50 counts and above. Data of protein interactions were extracted using MyProteinNet (Basha et al., ) from BioGrid (Chatr-Aryamontri et al., ), DIP (Xenarios et al., ), IntAct (Kerrien et al., ), and MINT (Licata et al., ) databases. Only global genes that have tissue-specific interactions in each of the three tissues are shown.

Human protein interaction networks across tissues and diseases

Front Genet. 2015;6:257.