Ioannis Xenarios

Publications | Phd and Masters theses

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160 publications

In press | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1994 |
 
HumaReC Project: Digital New Testament and Continuous Data Publishing (Poster)
Schulthess Sara, Chasapi Anastasia, Xenarios Ioannis, Sankar Martial, Clivaz Claire dans Jakacki Diane, Sinclair Stefan, Sinatra Michael (eds.) DH2017 Proceedings, Montréal, Erudit.
 
Gene expression across mammalian organ development.
Cardoso-Moreira M., Halbert J., Valloton D., Velten B., Chen C., Shao Y., Liechti A., Ascenção K., Rummel C., Ovchinnikova S. et al., 2019/07. Nature, 571 (7766) pp. 505-509. Peer-reviewed.
Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes.
Khamis A., Canouil M., Siddiq A., Crouch H., Falchi M., Bulow M.V., Ehehalt F., Marselli L., Distler M., Richter D. et al., 2019/06. Molecular Metabolism, 24 pp. 98-107. Peer-reviewed.
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.
Deforges J., Reis R.S., Jacquet P., Sheppard S., Gadekar V.P., Hart-Smith G., Tanzer A., Hofacker I.L., Iseli C., Xenarios I. et al., 2019/05. Plant Physiology, 180 (1) pp. 305-322. Peer-reviewed.
DynaStI: A Dynamic Retention Time Database for Steroidomics.
Codesido S., Randazzo G.M., Lehmann F., González-Ruiz V., García A., Xenarios I., Liechti R., Bridge A., Boccard J., Rudaz S., 2019/04/30. Metabolites, 9 (5) p. 85. Peer-reviewed.
Navigating in vitro bioactivity data by investigating available resources using model compounds.
Ilmjärv S., Augsburger F., Bolleman J.T., Liechti R., Bridge A.J., Sandström J., Jaquet V., Xenarios I., Krause K.H., 2019/04/29. Scientific data, 6 (1) p. 45. Peer-reviewed.
 
Genome-wide identification of microRNAs regulating the human prion protein.
Pease D., Scheckel C., Schaper E., Eckhardt V., Emmenegger M., Xenarios I., Aguzzi A., 2019/03. Brain pathology, 29 (2) pp. 232-244. Peer-reviewed.
Differential regulation of RNA polymerase III genes during liver regeneration.
Yeganeh M., Praz V., Carmeli C., Villeneuve D., Rib L., Guex N., Herr W., Delorenzi M., Hernandez N., CycliX consortium, 2019/02/28. Nucleic Acids Research, 47 (4) pp. 1786-1796. Peer-reviewed.
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.
Famiglietti M.L., Estreicher A., Breuza L., Poux S., Redaschi N., Xenarios I., Bridge A., UniProt Consortium, 2019/01/01. Database, 2019. Peer-reviewed.
 
Toward unrestricted use of public genomic data.
Amann R.I., Baichoo S., Blencowe B.J., Bork P., Borodovsky M., Brooksbank C., Chain PSG, Colwell R.R., Daffonchio D.G., Danchin A. et al., 2019. Science, 363 (6425) pp. 350-352. Peer-reviewed.
Updates in Rhea: SPARQLing biochemical reaction data.
Lombardot T., Morgat A., Axelsen K.B., Aimo L., Hyka-Nouspikel N., Niknejad A., Ignatchenko A., Xenarios I., Coudert E., Redaschi N. et al., 2019. Nucleic Acids Research, 47 (D1) pp. D596-D600. Peer-reviewed.
Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.
Egli A., Blanc D.S., Greub G., Keller P.M., Lazarevic V., Lebrand A., Leib S., Neher R.A., Perreten V., Ramette A. et al., 2018/12/03. Swiss medical weekly, 148 pp. w14693. Peer-reviewed.
 
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.
Mylonas R., Beer I., Iseli C., Chong C., Pak H.S., Gfeller D., Coukos G., Xenarios I., Müller M., Bassani-Sternberg M., 2018/12. Molecular & cellular proteomics, 17 (12) pp. 2347-2357. Peer-reviewed.
A systems genetics resource and analysis of sleep regulation in the mouse.
Diessler S., Jan M., Emmenegger Y., Guex N., Middleton B., Skene D.J., Ibberson M., Burdet F., Götz L., Pagni M. et al., 2018/08. PLoS biology, 16 (8) pp. e2005750. Peer-reviewed.
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
Lee K., Famiglietti M.L., McMahon A., Wei C.H., MacArthur JAL, Poux S., Breuza L., Bridge A., Cunningham F., Xenarios I. et al., 2018/08. PLoS computational biology, 14 (8) pp. e1006390. Peer-reviewed.
 
Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.
Tanyi J.L., Bobisse S., Ophir E., Tuyaerts S., Roberti A., Genolet R., Baumgartner P., Stevenson B.J., Iseli C., Dangaj D. et al., 2018/04/11. Science translational medicine, 10 (436) pp. NA. Peer-reviewed.
Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer.
Bobisse S., Genolet R., Roberti A., Tanyi J.L., Racle J., Stevenson B.J., Iseli C., Michel A., Le Bitoux M.A., Guillaume P. et al., 2018/03/15. Nature communications, 9 (1) p. 1092. Peer-reviewed.
Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes.
Solimena M., Schulte A.M., Marselli L., Ehehalt F., Richter D., Kleeberg M., Mziaut H., Knoch K.P., Parnis J., Bugliani M. et al., 2018/03. Diabetologia, 61 (3) pp. 641-657. Peer-reviewed.
KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis.
Gueneau L., Fish R.J., Shamseldin H.E., Voisin N., Tran Mau-Them F., Preiksaitiene E., Monroe G.R., Lai A., Putoux A., Allias F. et al., 2018/01/04. American journal of human genetics, 102 (1) pp. 116-132. Peer-reviewed.
Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer.
Faget J., Groeneveld S., Boivin G., Sankar M., Zangger N., Garcia M., Guex N., Zlobec I., Steiner L., Piersigilli A. et al., 2017/12/12. Cell reports, 21 (11) pp. 3190-3204. Peer-reviewed.
 
Low number of fixed somatic mutations in a long-lived oak tree.
Schmid-Siegert E., Sarkar N., Iseli C., Calderon S., Gouhier-Darimont C., Chrast J., Cattaneo P., Schütz F., Farinelli L., Pagni M. et al., 2017/12. Nature plants, 3 (12) pp. 926-929. Peer-reviewed.
 
MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.
Martín-Campos T., Mylonas R., Masselot A., Waridel P., Petricevic T., Xenarios I., Quadroni M., 2017/08/04. Journal of proteome research, 16 (8) pp. 3092-3101. Peer-reviewed.
Local auxin production underlies a spatially restricted neighbor-detection response in <i>Arabidopsis</i>.
Michaud O., Fiorucci A.S., Xenarios I., Fankhauser C., 2017/07/11. Proceedings of the National Academy of Sciences of the United States of America, 114 (28) pp. 7444-7449. Peer-reviewed.
Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for <i>Elovl2</i> in glucose-induced insulin secretion.
Cruciani-Guglielmacci C., Bellini L., Denom J., Oshima M., Fernandez N., Normandie-Levi P., Berney X.P., Kassis N., Rouch C., Dairou J. et al., 2017/04. Molecular metabolism, 6 (4) pp. 340-351. Peer-reviewed.
Plasma Dihydroceramides Are Diabetes Susceptibility Biomarker Candidates in Mice and Humans.
Wigger L., Cruciani-Guglielmacci C., Nicolas A., Denom J., Fernandez N., Fumeron F., Marques-Vidal P., Ktorza A., Kramer W., Schulte A. et al., 2017/02/28. Cell reports, 18 (9) pp. 2269-2279. Peer-reviewed.
Updates in Rhea - an expert curated resource of biochemical reactions.
Morgat A., Lombardot T., Axelsen K.B., Aimo L., Niknejad A., Hyka-Nouspikel N., Coudert E., Pozzato M., Pagni M., Moretti S. et al., 2017/01/04. Nucleic acids research, 45 (D1) pp. D415-D418. Peer-reviewed.
MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering.
Kostyrko K., Neuenschwander S., Junier T., Regamey A., Iseli C., Schmid-Siegert E., Bosshard S., Majocchi S., Le Fourn V., Girod P.A. et al., 2017. Biotechnology and Bioengineering, 114 (2) pp. 384-396. Peer-reviewed.
TIE-2 expressing monocytes in human cancers.
Turrini R., Pabois A., Xenarios I., Coukos G., Delaloye J.F., Doucey M.A., 2017. Oncoimmunology, 6 (4) pp. e1303585. Peer-reviewed.
Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.
Kohnen M.V., Schmid-Siegert E., Trevisan M., Petrolati L.A., Sénéchal F., Müller-Moulé P., Maloof J., Xenarios I., Fankhauser C., 2016/12. The Plant cell, 28 (12) pp. 2889-2904. Peer-reviewed.
Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors.
Artois J., Newman S.H., Dhingra M.S., Chaiban C., Linard C., Cattoli G., Monne I., Fusaro A., Xenarios I., Engler R. et al., 2016/07/25. Scientific reports, 6 p. 30316. Peer-reviewed.
 
West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1.
Alfaiz A.A., Müller V., Boutry-Kryza N., Ville D., Guex N., de Bellescize J., Rivier C., Labalme A., des Portes V., Edery P. et al., 2016/07. European journal of human genetics, 24 (7) pp. 1001-1008. Peer-reviewed.
 
Analysis of the dynamic co-expression network of heart regeneration in the zebrafish.
Rodius S., Androsova G., Götz L., Liechti R., Crespo I., Merz S., Nazarov P.V., de Klein N., Jeanty C., González-Rosa J.M. et al., 2016/05/31. Scientific reports, 6 p. 26822. Peer-reviewed.
Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways.
Crippa S., Nemir M., Ounzain S., Ibberson M., Berthonneche C., Sarre A., Boisset G., Maison D., Harshman K., Xenarios I. et al., 2016. Cardiovascular Research, 110 (1) pp. 73-84. Peer-reviewed.
Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation.
Dhingra M.S., Artois J., Robinson T.P., Linard C., Chaiban C., Xenarios I., Engler R., Liechti R., Kuznetsov D., Xiao X. et al., 2016. eLife, 5 pp. e19571. Peer-reviewed.
Identification of a novel PPARβ/δ/miR-21-3p axis in UV-induced skin inflammation.
Degueurce G., D'Errico I., Pich C., Ibberson M., Schütz F., Montagner A., Sgandurra M., Mury L., Jafari P., Boda A. et al., 2016. EMBO Molecular Medicine, 8 (8) pp. 919-936. Peer-reviewed.
Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics.
Loviglio M.N., Beck C.R., White J.J., Leleu M., Harel T., Guex N., Niknejad A., Bi W., Chen E.S., Crespo I. et al., 2016. Genome medicine, 8 (1) p. 105. Peer-reviewed.
Identifying biological mechanisms for favorable cancer prognosis using non-hypothesis-driven iterative survival analysis.
Crespo I., Götz L., Liechti R., Coukos G., Doucey M.A., Xenarios I., 2016. NPJ systems biology and applications, 2 p. 16037. Peer-reviewed.
 
New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach.
Zufferey A., Ibberson M., Reny J.L., Nolli S., Schvartz D., Docquier M., Xenarios I., Sanchez J.C., Fontana P., 2016. Human Genetics, 135 (4) pp. 403-414. Peer-reviewed.
Social networks help to infer causality in the tumor microenvironment.
Crespo I., Doucey M.A., Xenarios I., 2016. Bmc Research Notes, 9 (1) p. 168. Peer-reviewed.
 
Standardized benchmarking in the quest for orthologs.
Altenhoff A.M., Boeckmann B., Capella-Gutierrez S., Dalquen D.A., DeLuca T., Forslund K., Huerta-Cepas J., Linard B., Pereira C., Pryszcz L.P. et al., 2016. Nature Methods, 13 (5) pp. 425-430. Peer-reviewed.
TIE-2-expressing monocytes are lymphangiogenic and associate specifically with lymphatics of human breast cancer.
Bron S., Henry L., Faes-Van't Hull E., Turrini R., Vanhecke D., Guex N., Ifticene-Treboux A., Marina Iancu E., Semilietof A., Rufer N. et al., 2016. Oncoimmunology, 5 (2) pp. e1073882. Peer-reviewed.
 
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.
Boutet E., Lieberherr D., Tognolli M., Schneider M., Bansal P., Bridge A.J., Poux S., Bougueleret L., Xenarios I., 2016. Methods in Molecular Biology, 1374 pp. 23-54. Peer-reviewed.
An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation.
Chasapi A., Wachowicz P., Niknejad A., Collin P., Krapp A., Cano E., Simanis V., Xenarios I., 2015. Plos One, 10 (8) pp. e0134214.
Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN.
Wachowicz P., Chasapi A., Krapp A., Cano Del Rosario E., Schmitter D., Sage D., Unser M., Xenarios I., Rougemont J., Simanis V., 2015. Journal of Cell Science, 128 (4) pp. 741-754.
Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches.
Guex N., Crespo I., Bron S., Ifticene-Treboux A., Faes-Van't Hull E., Kharoubi S., Liechti R., Werffeli P., Ibberson M., Majo F. et al., 2015. PLoS Computational Biology, 11 (3) pp. e1004050. Peer-reviewed.
Cooperative development of logical modelling standards and tools with CoLoMoTo.
Naldi A., Monteiro P.T., Müssel C., Consortium for Logical Models, Tools , Kestler H.A., Kestler H.A., Thieffry D., Xenarios I., Saez-Rodriguez J. et al., 2015. Bioinformatics, 31 (7) pp. 1154-1159. Peer-reviewed.
Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs.
Ounzain S., Micheletti R., Beckmann T., Schroen B., Alexanian M., Pezzuto I., Crippa S., Nemir M., Sarre A., Johnson R. et al., 2015. European Heart Journal, 36 (6) pp. 353-68a. Peer-reviewed.
HAMAP in 2015: updates to the protein family classification and annotation system.
Pedruzzi I., Rivoire C., Auchincloss A.H., Coudert E., Keller G., de Castro E., Baratin D., Cuche B.A., Bougueleret L., Poux S. et al., 2015. Nucleic Acids Research, 43 (Database issue) pp. D1064-D1070.
 
MorphoGraphX: A platform for quantifying morphogenesis in 4D.
Barbier de Reuille P., Routier-Kierzkowska A.L., Kierzkowski D., Bassel G.W., Schüpbach T., Tauriello G., Bajpai N., Strauss S., Weber A., Kiss A. et al., 2015. Elife, 4 p. 05864.
 
Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome.
Dikoglu E., Alfaiz A., Gorna M., Bertola D., Chae J.H., Cho T.J., Derbent M., Alanay Y., Guran T., Kim O.H. et al., 2015. American Journal of Medical Genetics. Part A, 167 (7) pp. 1501-1509. Peer-reviewed.
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B., Marcet-Houben M., Rees J.A., Forslund K., Huerta-Cepas J., Muffato M., Yilmaz P., Xenarios I., Bork P., Lewis S.E. et al., 2015. Genome Biology and Evolution, 7 (7) pp. 1988-1999. Peer-reviewed.
The InterPro protein families database: the classification resource after 15 years.
Mitchell A., Chang H.Y., Daugherty L., Fraser M., Hunter S., Lopez R., McAnulla C., McMenamin C., Nuka G., Pesseat S. et al., 2015. Nucleic Acids Research, 43 (Database issue) pp. D213-D221.
The SwissLipids knowledgebase for lipid biology.
Aimo L., Liechti R., Hyka-Nouspikel N., Niknejad A., Gleizes A., Götz L., Kuznetsov D., David F.P., van der Goot F.G., Riezman H. et al., 2015. Bioinformatics, 31 (17) pp. 2860-2866.
Toward a rational design of combination therapy in cancer.
Doucey M.A., Xenarios I., 2015. Oncoimmunology, 4 (11) pp. e1046674. Peer-reviewed.
TRAL: tandem repeat annotation library.
Schaper E., Korsunsky A., Pečerska J., Messina A., Murri R., Stockinger H., Zoller S., Xenarios I., Anisimova M., 2015. Bioinformatics, 31 (18) pp. 3051-3053. Peer-reviewed.
Updates in Rhea-a manually curated resource of biochemical reactions.
Morgat A., Axelsen K.B., Lombardot T., Alcántara R., Aimo L., Zerara M., Niknejad A., Belda E., Hyka-Nouspikel N., Coudert E. et al., 2015. Nucleic Acids Research, 43 (Database issue) pp. D459-D464. Peer-reviewed.
An integrated ontology resource to explore and study host-virus relationships.
Masson P., Hulo C., de Castro E., Foulger R., Poux S., Bridge A., Lomax J., Bougueleret L., Xenarios I., Le Mercier P., 2014. PLoS One, 9 (9) pp. e108075. Peer-reviewed.
Analysis of stop-gain and frameshift variants in human innate immunity genes.
Rausell A., Mohammadi P., McLaren P.J., Bartha I., Xenarios I., Fellay J., Telenti A., 2014. Plos Computational Biology, 10 (7) pp. e1003757. Peer-reviewed.
Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth.
Sankar M., Nieminen K., Ragni L., Xenarios I., Hardtke C.S., 2014. Elife, 3 pp. e01567. Peer-reviewed.
Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation.
Dornbusch T., Michaud O., Xenarios I., Fankhauser C., 2014. Plant Cell, 26 (10) pp. 3911-3921. Peer-reviewed.
Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing.
Seguín-Estévez Q., Dunand-Sauthier I., Lemeille S., Iseli C., Ibberson M., Ioannidis V., Schmid C.D., Rousseau P., Barras E., Geinoz A. et al., 2014. Nucleic Acids Research, 42 (15) pp. 9641-9655.
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Stockinger H., Altenhoff A.M., Arnold K., Bairoch A., Bastian F., Bergmann S., Bougueleret L., Bucher P., Delorenzi M., Lane L. et al., 2014. Nucleic Acids Research, 42 (Web Server issue) pp. W436-W441. Peer-reviewed.
 
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family 1[C][W]
Roppolo D., Boeckmann B., Pfister A., Boutet E., Rubio M.C., Dénervaud-Tendon V., Vermeer J.E.M., Gheyselinck J., Xenarios I., Geldner N., 2014. Plant Physiology, 165 (4) pp. 1709-1722. Peer-reviewed.
 
Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation.
Famiglietti M.L., Estreicher A., Gos A., Bolleman J., Géhant S., Breuza L., Bridge A., Poux S., Redaschi N., Bougueleret L. et al., 2014. Human Mutation, 35 (8) pp. 927-935.
 
ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Vizcaíno J.A., Deutsch E.W., Wang R., Csordas A., Reisinger F., Ríos D., Dianes J.A., Sun Z., Farrah T., Bandeira N. et al., 2014. Nature Biotechnology, 32 (3) pp. 223-226.
Reconciliation of metabolites and biochemical reactions for metabolic networks.
Bernard T., Bridge A., Morgat A., Moretti S., Xenarios I., Pagni M., 2014. Briefings in Bioinformatics, 15 (1) pp. 123-135.
 
Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps.
Pellissier L., Niculita-Hirzel Hélène, Dubuis A., Pagni M., Guex N., Ndiribe C., Salamin N., Xenarios I., Goudet J., Sanders I.R. et al., 2014. Molecular Ecology, 23 (17) pp. 4274-4290. Peer-reviewed.
 
TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease.
Alfaiz A.A., Micale L., Mandriani B., Augello B., Pellico M.T., Chrast J., Xenarios I., Zelante L., Merla G., Reymond A., 2014. Human Mutation, 35 (4) pp. 447-451.
The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience.
Griss J., Jones A.R., Sachsenberg T., Walzer M., Gatto L., Hartler J., Thallinger G.G., Salek R.M., Steinbeck C., Neuhauser N. et al., 2014. Molecular and Cellular Proteomics, 13 (10) pp. 2765-2775.
Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models.
Rodius S., Nazarov P.V., Nepomuceno-Chamorro I.A., Jeanty C., González-Rosa J.M., Ibberson M., da Costa R.M., Xenarios I., Mercader N., Azuaje F., 2014. BMC Genomics, 15 (1) p. 852.
 
Type I interferons protect T cells against NK cell attack mediated by the activating receptor NCR1.
Crouse J., Bedenikovic G., Wiesel M., Ibberson M., Xenarios I., Von Laer D., Kalinke U., Vivier E., Jonjic S., Oxenius A., 2014. Immunity, 40 (6) pp. 961-973. Peer-reviewed.
 
A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.
Schmitter D., Wachowicz P., Sage D., Chasapi A., Xenarios I., Simanis V., Unser M., 2013. Cell Division, 8 (1) p. 6.
Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Veuthey A.L., Bridge A., Gobeill J., Ruch P., McEntyre J.R., Bougueleret L., Xenarios I., 2013. BMC Bioinformatics, 14 p. 104.
Database resources for the tuberculosis community.
Lew J.M., Mao C., Shukla M., Warren A., Will R., Kuznetsov D., Xenarios I., Robertson B.D., Gordon S.V., Schnappinger D. et al., 2013. Tuberculosis, 93 (1) pp. 12-17. Peer-reviewed.
Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.
Pagni M., Niculita-Hirzel Hélène, Pellissier L., Dubuis A., Xenarios I., Guisan A., Sanders I.R., Goudet J., Guex N., 2013. Bioinformatics, 29 (10) pp. 1268-1274. Peer-reviewed.
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs.
Zhang X., Krause K.H., Xenarios I., Soldati T., Boeckmann B., 2013. PLoS One, 8 (3) pp. e58126.
Gene Ontology Annotations and Resources.
The Gene Ontology Consortium, 2013. Nucleic Acids Research, 41 (D1) pp. D530-D535.
HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I., Rivoire C., Auchincloss A.H., Coudert E., Keller G., de Castro E., Baratin D., Cuche B.A., Bougueleret L., Poux S. et al., 2013. Nucleic Acids Research, 41 (D1) pp. D584-D589.
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.
Bonzanni N., Garg A., Feenstra K.A., Schütte J., Kinston S., Miranda-Saavedra D., Heringa J., Xenarios I., Göttgens B., 2013. Bioinformatics, 29 (13) pp. i80-i88.
 
Microarray analysis of isolated human islet transcriptome in type 2 diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell dysfunction.
Bugliani M., Liechti R., Cheon H., Suleiman M., Marselli L., Kirkpatrick C., Filipponi F., Boggi U., Xenarios I., Syed F. et al., 2013. Molecular and Cellular Endocrinology, 367 (1-2) pp. 1-10. Peer-reviewed.
New and continuing developments at PROSITE.
Sigrist C.J., de Castro E., Cerutti L., Cuche B.A., Hulo N., Bridge A., Bougueleret L., Xenarios I., 2013. Nucleic Acids Research, 41 (D1) pp. D344-D347.
Plant species distributions along environmental gradients: do belowground interactions with fungi matter?
Pellissier L., Pinto-Figueroa E., Niculita-Hirzel Hélène, Moora M., Villard L., Goudet J., Guex N., Pagni M., Xenarios I., Sanders I. et al., 2013. Frontiers In Plant Science, 4 (500) p. 500. Peer-reviewed.
 
Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells.
Peterson H., Abu Dawud R., Garg A., Wang Y., Vilo J., Xenarios I., Adjaye J., 2013. Frontiers in Physiology, 4 p. 303.
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C., Bérenguier D., Keating S.M., Naldi A., van Iersel M.P., Rodriguez N., Dräger A., Büchel F., Cokelaer T., Kowal B. et al., 2013. BMC Systems Biology, 7 p. 135.
 
TIE-2 and VEGFR Kinase Activities Drive Immunosuppressive Function of TIE-2-Expressing Monocytes in Human Breast Tumors.
Ibberson M., Bron S., Guex N., Faes-Van't Hull E., Ifticene-Treboux A., Henry L., Lehr H.A., Delaloye J.F., Coukos G., Xenarios I. et al., 2013. Clinical Cancer Research, 19 (13) pp. 3439-3449. Peer-reviewed.
Update on activities at the Universal Protein Resource (UniProt) in 2013.
The UniProt Consortium, 2013. Nucleic Acids Research, 41 (D1) pp. D43-D47.
ViralZone: recent updates to the virus knowledge resource.
Masson P., Hulo C., De Castro E., Bitter H., Gruenbaum L., Essioux L., Bougueleret L., Xenarios I., Le Mercier P., 2013. Nucleic Acids Research, 41 (Database issue) pp. D579-D583.
Biocurators and biocuration: surveying the 21st century challenges.
Burge S., Attwood T.K., Bateman A., Berardini T.Z., Cherry M., O'Donovan C., Xenarios L., Gaudet P., 2012. Database, 2012 pp. bar059.
 
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.
Nikolaev S.I., Rimoldi D., Iseli C., Valsesia A., Robyr D., Gehrig C., Harshman K., Guipponi M., Bukach O., Zoete V. et al., 2012. Nature Genetics, 44 (2) pp. 133-139.
ExPASy: SIB bioinformatics resource portal.
Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E. et al., 2012. Nucleic Acids Research, 40 pp. W597-W603.
 
Implicit methods for qualitative modeling of gene regulatory networks.
Garg A., Mohanram K., De Micheli G., Xenarios I., 2012. Methods in Molecular Biology, 786 pp. 397-443.
Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis - a novel phenotyping approach using laser scanning
Dornbusch T., Lorrain S., Kuznetsov D., Fortier A., Liechti R., Xenarios I., Fankhauser C., 2012. Functional Plant Biology, 39 (10-11) pp. 860-869.
Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling.
Hornitschek P., Kohnen M.V., Lorrain S., Rougemont J., Ljung K., López-Vidriero I., Franco-Zorrilla J.M., Solano R., Trevisan M., Pradervand S. et al., 2012. Plant Journal, 71 (5) pp. 699-711.
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Orchard S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F.S., Brinkman F. et al., 2012. Nature Methods, 9 (4) pp. 345-350.
Rhea-a manually curated resource of biochemical reactions.
Alcántara R., Axelsen K.B., Morgat A., Belda E., Coudert E., Bridge A., Cao H., de Matos P., Ennis M., Turner S. et al., 2012. Nucleic Acids Research, 40 (Database issue) pp. D754-D760.
The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium, 2012. Nucleic Acids Research, 40 (Database issue) pp. D559-D564.
The UniProt-GO Annotation database in 2011.
Dimmer E.C., Huntley R.P., Alam-Faruque Y., Sawford T., O'Donovan C., Martin M.J., Bely B., Browne P., Mun Chan W., Eberhardt R. et al., 2012. Nucleic Acids Research, 40 (Database issue) pp. D565-D570.
 
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data.
Jungo F., Bougueleret L., Xenarios I., Poux S., 2012. Toxicon, 60 (4) pp. 551-557.
 
Toward interoperable bioscience data.
Sansone S.A., Rocca-Serra P., Field D., Maguire E., Taylor C., Hofmann O., Fang H., Neumann S., Tong W., Amaral-Zettler L. et al., 2012. Nature Genetics, 44 (2) pp. 121-126.
UniPathway: a resource for the exploration and annotation of metabolic pathways.
Morgat A., Coissac E., Coudert E., Axelsen K.B., Keller G., Bairoch A., Bridge A., Bougueleret L., Xenarios I., Viari A., 2012. Nucleic Acids Research, 40 (Database issue) pp. D761-D769.
UniProtKB amid the turmoil of plant proteomics research.
Schneider M., Consortium Consortium, Poux S., 2012. Frontiers in Plant Science, 3 p. 270.
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk.
Sankar M., Osmont K.S., Rolcik J., Gujas B., Tarkowska D., Strnad M., Xenarios I., Hardtke C.S., 2011. Bioinformatics, 27 (10) pp. 1404-1412.
Comparison of Strategies to Detect Epistasis from eQTL Data.
Kapur K., Schüpbach T., Xenarios I., Kutalik Z., Bergmann S., 2011. PLoS One, 6 (12) pp. e28415.
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
Boeckmann B., Robinson-Rechavi M., Xenarios I., Dessimoz C., 2011. Briefings in Bioinformatics, 12 (5) pp. 423-435. Peer-reviewed.
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
Valsesia A., Rimoldi D., Martinet D., Ibberson M., Benaglio P., Quadroni M., Waridel P., Gaillard M., Pidoux M., Rapin B. et al., 2011. PLoS One, 6 (4) pp. e18369. Peer-reviewed.
Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium, 2011. Nucleic Acids Research, 39 (Database issue) pp. D214-D219.
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Di Tommaso P., Moretti S., Xenarios I., Orobitg M., Montanyola A., Chang J.M., Taly J.F., Notredame C., 2011. Nucleic Acids Research, 39 (Web Server issue) pp. W13-W17.
The genome of the fire ant Solenopsis invicta.
Wurm Y., Wang J., Riba-Grognuz O., Corona M., Nygaard S., Hunt B.G., Ingram K.K., Falquet L., Nipitwattanaphon M., Gotzek D. et al., 2011. Proceedings of the National Academy of Sciences of the United States of America, 108 (14) pp. 5679-5684. Peer-reviewed.
ViralZone: a knowledge resource to understand virus diversity.
Hulo C., de Castro E., Masson P., Bougueleret L., Bairoch A., Xenarios I., Le Mercier P., 2011. Nucleic Acids Research, 39 (Suppl 1) pp. D576-D582.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O., Keller L., Falquet L., Xenarios I., Wurm Y., 2011. Bioinformatics, 27 (24) pp. 3425-3426. Peer-reviewed.
Animal Toxins: How is Complexity Represented in Databases?
Jungo F., Estreicher A., Bairoch A., Bougueleret L., Xenarios I., 2010. Toxins, 2 (2) pp. 262-282.
 
CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation.
Gordon V., Bhadel S., Wunderlich W., Zhang J., Ficarro S.B., Mollah S.A., Shabanowitz J., Hunt D.F., Xenarios I., Hahn W.C. et al., 2010. Molecular Endocrinology, 24 (12) pp. 2267-2280. Peer-reviewed.
EuroDia: a beta-cell gene expression resource.
Liechti R., Csárdi G., Bergmann S., Schütz F., Sengstag T., Boj S.F., Servitja J.M., Ferrer J., Van Lommel L., Schuit F. et al., 2010. Database, 2010 pp. baq024.
FastEpistasis: a high performance computing solution for quantitative trait epistasis.
Schüpbach T., Xenarios I., Bergmann S., Kapur K., 2010. Bioinformatics, 26 (11) pp. 1468-1469.
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U., UniProt Consortium, 2010. Cellular and Molecular Life Sciences, 67 (7) pp. 1049-1064.
Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.
Guex N., Migliavacca E., Xenarios I., 2010. PLoS One, 5 (1) pp. e8012. Peer-reviewed.
OpenFluDB, a database for human and animal influenza virus.
Liechti R., Gleizes A., Kuznetsov D., Bougueleret L., Le Mercier P., Bairoch A., Xenarios I., 2010. Database, 2010 pp. baq004.
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
Santuari L., Pradervand S., Amiguet-Vercher A.M., Thomas J., Dorcey E., Harshman K., Xenarios I., Juenger T.E., Hardtke C.S., 2010. Genome Biology, 11 (1) pp. R4.
 
Systems biology to battle vascular disease.
Dominiczak A.F., Herget-Rosenthal S., Delles C., Fliser D., Fournier I., Graber A., Girolami M., Holmes E., Lang F., Molina F. et al., 2010. Nephrology, Dialysis, Transplantation, 25 (4) pp. 1019-1022.
The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium, 2010. Nucleic Acids Research, 38 (Database issue) pp. D331-D335.
The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium, 2010. Nucleic Acids Research, 38 (Database issue) pp. D142-D148.
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.
Martin O., Valsesia A., Telenti A., Xenarios I., Stevenson B.J., 2009. Bioinformatics, 25 (5) pp. 662-663.
 
ENFIN--A European network for integrative systems biology.
Kahlem P., Clegg A., Reisinger F., Xenarios I., Hermjakob H., Orengo C., Birney E., 2009. Comptes Rendus Biologies, 332 (11) pp. 1050-1058.
 
Evolutionary trajectories of primate genes involved in HIV pathogenesis.
Ortiz Millan, Ciuffi Angela, Xenarios Ioannis, Martin Olivier, Patin Etienne, Guex Nicolas, Quintana-Murci Luis, Telenti Amalio, 2009. Molecular Biology and Evolution, 26 (12) pp. 2865-2875.
MIMAS 3.0 is a Multiomics Information Management and Annotation System.
Gattiker A., Hermida L., Liechti R., Xenarios I., Collin O., Rougemont J., Primig M., 2009. BMC Bioinformatics, 10 p. 151.
Modeling stochasticity and robustness in gene regulatory networks.
Garg A., Mohanram K., Di Cara A., De Micheli G., Xenarios I., 2009. Bioinformatics, 25 (12) pp. i101-i109.
 
The direct effects of tacrolimus and cyclosporin A on isolated human islets: A functional, survival and gene expression study.
Bugliani M., Masini M., Liechti R., Marselli L., Xenarios I., Boggi U., Filipponi F., Masiello P., Marchetti P., 2009. Islets, 1 (2) pp. 106-110.
The Microbe browser for comparative genomics.
Gattiker A., Dessimoz C., Schneider A., Xenarios I., Pagni M., Rougemont J., 2009. Nucleic Acids Research, 37 (Web Server issue) pp. W296-W299.
 
Guidelines for reporting the use of mass spectrometry in proteomics.
Taylor C.F., Binz P.A., Aebersold R., Affolter M., Barkovich R., Deutsch E.W., Horn D.M., Hühmer A., Kussmann M., Lilley K. et al., 2008. Nature Biotechnology, 26 (8) pp. 860-861.
Probabilistic base calling of Solexa sequencing data.
Rougemont J., Amzallag A., Iseli C., Farinelli L., Xenarios I., Naef F., 2008. BMC Bioinformatics, 9 pp. 431-.
R-Coffee: a web server for accurately aligning noncoding RNA sequences.
Moretti S., Wilm A., Higgins D.G., Xenarios I., Notredame C., 2008. Nucleic Acids Research, 36 (Web Server issue) pp. W10-W13.
Synchronous versus asynchronous modeling of gene regulatory networks.
Garg A., Di Cara A., Xenarios I., Mendoza L., De Micheli G., 2008. Bioinformatics, 24 (17) pp. 1917-1925.
 
A chemical proteomics approach to phosphatidylinositol 3-kinase signaling in macrophages.
Pasquali C., Bertschy-Meier D., Chabert C., Curchod M.L., Arod C., Booth R., Mechtler K., Vilbois F., Xenarios I., Ferguson C.G. et al., 2007. Molecular and Cellular Proteomics, 6 (11) pp. 1829-1841.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S., Orchard S., Montecchi-Palazzi L., Aranda B., Quinn A.F., Vinod N., Bader G.D., Xenarios I., Wojcik J., Sherman D. et al., 2007. BMC Biology, 5 p. 44.
 
Dynamic simulation of regulatory networks using SQUAD.
Di Cara A., Garg A., De Micheli G., Xenarios I., Mendoza L., 2007. BMC Bioinformatics, 8 p. 462.
 
The minimum information about a proteomics experiment (MIAPE).
Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W. et al., 2007. Nature Biotechnology, 25 (8) pp. 887-893.
 
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P. et al., 2007. Nature Biotechnology, 25 (8) pp. 894-898.
 
A method for the generation of standardized qualitative dynamical systems of regulatory networks.
Mendoza L., Xenarios I., 2006. Theoretical Biology and Medical Modelling, 3 p. 13.
 
Proteomic analysis of the mouse liver mitochondrial inner membrane.
Da Cruz S., Xenarios I., Langridge J., Vilbois F., Parone P.A., Martinou J.C., 2003. Journal of Biological Chemistry, 278 (42) pp. 41566-41571.
 
Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database.
Duan X.J., Xenarios I., Eisenberg D., 2002. Molecular and Cellular Proteomics, 1 (2) pp. 104-116.
 
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.
Xenarios I., Salwínski L., Duan X.J., Higney P., Kim S.M., Eisenberg D., 2002. Nucleic Acids Research, 30 (1) pp. 303-305.
 
Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases.
Robyr D., Suka Y., Xenarios I., Kurdistani S.K., Wang A., Suka N., Grunstein M., 2002. Cell, 109 (4) pp. 437-446.
 
Molecular docking of competitive phosphodiesterase inhibitors.
Dym O., Xenarios I., Ke H., Colicelli J., 2002. Molecular Pharmacology, 61 (1) pp. 20-25.
 
Protein interactions: two methods for assessment of the reliability of high throughput observations.
Deane C.M., Salwiński Ł., Xenarios I., Eisenberg D., 2002. Molecular and Cellular Proteomics, 1 (5) pp. 349-356.
 
Characterization of the human ABCG1 gene: liver X receptor activates an internal promoter that produces a novel transcript encoding an alternative form of the protein.
Kennedy M.A., Venkateswaran A., Tarr P.T., Xenarios I., Kudoh J., Shimizu N., Edwards P.A., 2001. Journal of Biological Chemistry, 276 (42) pp. 39438-39447.
 
Complement facilitates early prion pathogenesis.
Klein M.A., Kaeser P.S., Schwarz P., Weyd H., Xenarios I., Zinkernagel R.M., Carroll M.C., Verbeek J.S., Botto M., Walport M.J. et al., 2001. Nature Medicine, 7 (4) pp. 488-492. Peer-reviewed.
 
DIP: The Database of Interacting Proteins: 2001 update.
Xenarios I., Fernandez E., Salwinski L., Duan X.J., Thompson M.J., Marcotte E.M., Eisenberg D., 2001. Nucleic Acids Research, 29 (1) pp. 239-241.
 
Mining literature for protein-protein interactions.
Marcotte E.M., Xenarios I., Eisenberg D., 2001. Bioinformatics, 17 (4) pp. 359-363.
 
Protein interaction databases.
Xenarios I., Eisenberg D., 2001. Current Opinion in Biotechnology, 12 (4) pp. 334-339.
 
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.
Landgraf R., Xenarios I., Eisenberg D., 2001. Journal of Molecular Biology, 307 (5) pp. 1487-1502.
 
DIP: the database of interacting proteins.
Xenarios I., Rice D.W., Salwinski L., Baron M.K., Marcotte E.M., Eisenberg D., 2000. Nucleic Acids Research, 28 (1) pp. 289-291.
 
Human ERK1 induces filamentous growth and cell wall remodeling pathways in Saccharomyces cerevisiae.
Atienza J.M., Suh M., Xenarios I., Landgraf R., Colicelli J., 2000. Journal of Biological Chemistry, 275 (27) pp. 20638-20646.
 
Localizing proteins in the cell from their phylogenetic profiles.
Marcotte E.M., Xenarios I., van Der Bliek A.M., Eisenberg D., 2000. Proceedings of the National Academy of Sciences of the United States of America, 97 (22) pp. 12115-12120.
 
Protein function in the post-genomic era.
Eisenberg D., Marcotte E.M., Xenarios I., Yeates T.O., 2000. Nature, 405 (6788) pp. 823-826.
 
Interplays between mouse mammary tumor virus and the cellular and humoral immune response.
Acha-Orbea H., Finke D., Attinger A., Schmid S., Wehrli N., Vacheron S., Xenarios I., Scarpellino L., Toellner K.M., MacLennan I.C. et al., 1999. Immunological Reviews, 168 pp. 287-303.
 
Differential reactivity of TCR Vbeta10 alleles to a mouse mammary tumor virus superantigen.
Maillard I., Xenarios I., Diggelmann H., Orbea H.A., 1998. European Journal of Immunology, 28 (10) pp. 3075-3085. Peer-reviewed.
 
Immune response to mouse mammary tumor virus in mice lacking the alpha/beta interferon or the gamma interferon receptor.
Maillard I., Launois P., Xenarios I., Louis J.A., Acha-Orbea H., Diggelmann H., 1998. Journal of Virology, 72 (4) pp. 2638-2646.
 
IL-4 rapidly produced by V beta 4 V alpha 8 CD4+ T cells instructs Th2 development and susceptibility to Leishmania major in BALB/c mice.
Launois P., Maillard I., Pingel S., Swihart K.G., Xénarios I., Acha-Orbea H., Diggelmann H., Locksley R.M., MacDonald H.R., Louis J.A., 1997. Immunity, 6 (5) pp. 541-549. Peer-reviewed.
 
Improving the sensitivity of the sequence profile method.
Lüthy R., Xenarios I., Bucher P., 1994. Protein Science, 3 (1) pp. 139-146.
 
New infectious mammary tumor virus superantigen with V beta-specificity identical to staphylococcal enterotoxin B (SEB).
Luther S., Shakhov A.N., Xenarios I., Haga S., Imai S., Acha-Orbea H., 1994. European Journal of Immunology, 24 (8) pp. 1757-1764.
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