Ioannis Xenarios received a Ph.D in immunology at the Ludwig Institute of Cancer Research and the Institute of Biochemistry. He worked on the development of the Database of Interacting Proteins (DIP) under the supervision of Prof. David Eisenberg at the University of California Los Angeles. He then became the head of Translational Bioinformatics at Serono (now Merck Serono) where his group developed computational methodologies in the area of proteomics, microarray and genetics. He is one of the Principal investigators of the ENFIN project aiming at providing methods in dynamical systems modeling.
Ioannis Xenarios is UNIL full Professor ad personam, affiliated with the CIG, since August 2010
1: Seguín-Estévez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M,
Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H,
Reith W. Extensive remodeling of DC function by rapid maturation-induced
transcriptional silencing. Nucleic Acids Res. 2014 Aug 7. pii: gku674. [Epub
ahead of print] PubMed PMID: 25104025.
2: Rausell A, Mohammadi P, McLaren PJ, Bartha I, Xenarios I, Fellay J, Telenti A.
Analysis of stop-gain and frameshift variants in human innate immunity genes.
PLoS Comput Biol. 2014 Jul 24;10(7):e1003757. doi: 10.1371/journal.pcbi.1003757.
eCollection 2014 Jul. PubMed PMID: 25058640; PubMed Central PMCID: PMC4110073.
3: Pellissier L, Niculita-Hirzel H, Dubuis A, Pagni M, Guex N, Ndiribe C, Salamin
N, Xenarios I, Goudet J, Sanders IR, Guisan A. Soil fungal communities of
grasslands are environmentally structured at a regional scale in the Alps. Mol
Ecol. 2014 Jul 8. doi: 10.1111/mec.12854. [Epub ahead of print] PubMed PMID:
25041483.
4: Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG,
Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW,
Del Toro N, Perez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O,
Vizcaino JA, Hermjakob H. The mzTab Data Exchange Format: communicating MS-based
proteomics and metabolomics experimental results to a wider audience. Mol Cell
Proteomics. 2014 Jun 30. pii: mcp.O113.036681. [Epub ahead of print] PubMed PMID:
24980485.
5: Roppolo D, Boeckmann B, Pfister A, Boutet E, Rubio MC, Dénervaud-Tendon V,
Vermeer JE, Gheyselinck J, Xenarios I, Geldner N. Functional and Evolutionary
Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family. Plant Physiol.
2014 Jun 11;165(4):1709-1722. [Epub ahead of print] PubMed PMID: 24920445; PubMed
Central PMCID: PMC4119050.
6: Crouse J, Bedenikovic G, Wiesel M, Ibberson M, Xenarios I, Von Laer D, Kalinke
U, Vivier E, Jonjic S, Oxenius A. Type I interferons protect T cells against NK
cell attack mediated by the activating receptor NCR1. Immunity. 2014 Jun
19;40(6):961-73. doi: 10.1016/j.immuni.2014.05.003. Epub 2014 Jun 5. PubMed PMID:
24909889.
7: Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A,
Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium. Genetic
Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert
Manual Curation. Hum Mutat. 2014 Aug;35(8):927-35. doi: 10.1002/humu.22594. Epub
2014 Jun 24. PubMed PMID: 24848695; PubMed Central PMCID: PMC4107114.
8: Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S,
Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin
O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D,
Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD. Fifteen years SIB Swiss
Institute of Bioinformatics: life science databases, tools and support. Nucleic
Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub
2014 May 3. PubMed PMID: 24792157.
9: Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa
S, Nemir M, Sarre A, Johnson R, Dauvillier J, Burdet F, Ibberson M, Guigó R,
Xenarios I, Heymans S, Pedrazzini T. Genome-wide profiling of the cardiac
transcriptome after myocardial infarction identifies novel heart-specific long
non-coding RNAs. Eur Heart J. 2014 Apr 30. [Epub ahead of print] PubMed PMID:
24786300.
10: Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA,
Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L,
Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R,
Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally
coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014
Mar;32(3):223-6. doi: 10.1038/nbt.2839. PubMed PMID: 24727771; PubMed Central
PMCID: PMC3986813.
11: Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM,
Herr W, Hernandez N, Delorenzi M; CycliX Consortium. Quantifying ChIP-seq data: a
spiking method providing an internal reference for sample-to-sample
normalization. Genome Res. 2014 Jul;24(7):1157-68. doi: 10.1101/gr.168260.113.
Epub 2014 Apr 7. PubMed PMID: 24709819; PubMed Central PMCID: PMC4079971.
12: Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios
I, Sanz F. Integrative knowledge management to enhance pharmaceutical R&D. Nat
Rev Drug Discov. 2014 Apr;13(4):239-40. doi: 10.1038/nrd4290. PubMed PMID:
24687050.
13: Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K; UniProt
Consortium. Expert curation in UniProtKB: a case study on dealing with
conflicting and erroneous data. Database (Oxford). 2014 Mar 12;2014:bau016. doi:
10.1093/database/bau016. Print 2014. PubMed PMID: 24622611; PubMed Central PMCID:
PMC3950660.
14: Claes F, Kuznetsov D, Liechti R, Von Dobschuetz S, Truong BD, Gleizes A,
Conversa D, Colonna A, Demaio E, Ramazzotto S, Larfaoui F, Pinto J, Le Mercier P,
Xenarios I, Dauphin G. The EMPRES-i genetic module: a novel tool linking
epidemiological outbreak information and genetic characteristics of influenza
viruses. Database (Oxford). 2014 Mar 6;2014:bau008. doi: 10.1093/database/bau008.
Print 2014. PubMed PMID: 24608033; PubMed Central PMCID: PMC3945526.
15: Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex
N, Desvergne B; CycliX Consortium. Genome-wide analysis of SREBP1 activity around
the clock reveals its combined dependency on nutrient and circadian signals. PLoS
Genet. 2014 Mar 6;10(3):e1004155. doi: 10.1371/journal.pgen.1004155. eCollection
2014 Mar. PubMed PMID: 24603613; PubMed Central PMCID: PMC3945117.
16: Sankar M, Nieminen K, Ragni L, Xenarios I, Hardtke CS. Automated quantitative
histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary
growth. Elife. 2014 Feb 11;3:e01567. doi: 10.7554/eLife.01567. PubMed PMID:
24520159; PubMed Central PMCID: PMC3917233.
17: Alfaiz AA, Micale L, Mandriani B, Augello B, Pellico MT, Chrast J, Xenarios
I, Zelante L, Merla G, Reymond A. TBC1D7 mutations are associated with
intellectual disability, macrocrania, patellar dislocation, and celiac disease.
Hum Mutat. 2014 Apr;35(4):447-51. doi: 10.1002/humu.22529. PubMed PMID: 24515783.
18: Garg A, Mohanram K, Di Cara A, Degueurce G, Ibberson M, Dorier J, Xenarios I.
Efficient computation of minimal perturbation sets in gene regulatory networks.
Front Physiol. 2013 Dec 17;4:361. doi: 10.3389/fphys.2013.00361. eCollection
2013. PubMed PMID: 24391592; PubMed Central PMCID: PMC3867968.
19: Pellissier L, Pinto-Figueroa E, Niculita-Hirzel H, Moora M, Villard L, Goudet
J, Guex N, Pagni M, Xenarios I, Sanders I, Guisan A. Plant species distributions
along environmental gradients: do belowground interactions with fungi matter?
Front Plant Sci. 2013 Dec 10;4:500. doi: 10.3389/fpls.2013.00500. eCollection
2013. PubMed PMID: 24339830; PubMed Central PMCID: PMC3857535.
20: Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N,
Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M,
Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le
Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model
representation format and infrastructure to foster interactions between
qualitative modelling formalisms and tools. BMC Syst Biol. 2013 Dec 10;7:135.
doi: 10.1186/1752-0509-7-135. PubMed PMID: 24321545; PubMed Central PMCID:
PMC3892043.
21: UniProt Consortium. Activities at the Universal Protein Resource (UniProt).
Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8. doi: 10.1093/nar/gkt1140.
Epub 2013 Nov 18. PubMed PMID: 24253303; PubMed Central PMCID: PMC3965022.
22: Peterson H, Abu Dawud R, Garg A, Wang Y, Vilo J, Xenarios I, Adjaye J.
Qualitative modeling identifies IL-11 as a novel regulator in maintaining
self-renewal in human pluripotent stem cells. Front Physiol. 2013 Oct 28;4:303.
doi: 10.3389/fphys.2013.00303. eCollection 2013. PubMed PMID: 24194720; PubMed
Central PMCID: PMC3809568.
23: Bonzanni N, Garg A, Feenstra KA, Schütte J, Kinston S, Miranda-Saavedra D,
Heringa J, Xenarios I, Göttgens B. Hard-wired heterogeneity in blood stem cells
revealed using a dynamic regulatory network model. Bioinformatics. 2013 Jul
1;29(13):i80-8. doi: 10.1093/bioinformatics/btt243. PubMed PMID: 23813012; PubMed
Central PMCID: PMC3694641.
24: Ibberson M, Bron S, Guex N, Faes-van't Hull E, Ifticene-Treboux A, Henry L,
Lehr HA, Delaloye JF, Coukos G, Xenarios I, Doucey MA. TIE-2 and VEGFR kinase
activities drive immunosuppressive function of TIE-2-expressing monocytes in
human breast tumors. Clin Cancer Res. 2013 Jul 1;19(13):3439-49. doi:
10.1158/1078-0432.CCR-12-3181. Epub 2013 May 6. PubMed PMID: 23649001.
25: Schmitter D, Wachowicz P, Sage D, Chasapi A, Xenarios I, Simanis, Unser M. A
2D/3D image analysis system to track fluorescently labeled structures in
rod-shaped cells: application to measure spindle pole asymmetry during mitosis.
Cell Div. 2013 Apr 27;8:6. doi: 10.1186/1747-1028-8-6. eCollection 2013. PubMed
PMID: 23622681; PubMed Central PMCID: PMC3693874.
26: Guex N, Iseli C, Syngelaki A, Deluen C, Pescia G, Nicolaides KH, Xenarios I,
Conrad B. A robust second-generation genome-wide test for fetal aneuploidy based
on shotgun sequencing cell-free DNA in maternal blood. Prenat Diagn. 2013
Jul;33(7):707-10. doi: 10.1002/pd.4130. Epub 2013 May 3. PubMed PMID: 23592076.
27: Pagni M, Niculita-Hirzel H, Pellissier L, Dubuis A, Xenarios I, Guisan A,
Sanders IR, Goudet J, Guex N. Density-based hierarchical clustering of
pyro-sequences on a large scale--the case of fungal ITS1. Bioinformatics. 2013
May 15;29(10):1268-74. doi: 10.1093/bioinformatics/btt149. Epub 2013 Mar 28.
PubMed PMID: 23539304; PubMed Central PMCID: PMC3654712.
28: Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios
I. Application of text-mining for updating protein post-translational
modification annotation in UniProtKB. BMC Bioinformatics. 2013 Mar 22;14:104.
doi: 10.1186/1471-2105-14-104. PubMed PMID: 23517090; PubMed Central PMCID:
PMC3660268.
29: Zhang X, Krause KH, Xenarios I, Soldati T, Boeckmann B. Evolution of the
ferric reductase domain (FRD) superfamily: modularity, functional
diversification, and signature motifs. PLoS One. 2013;8(3):e58126. doi:
10.1371/journal.pone.0058126. Epub 2013 Mar 7. PubMed PMID: 23505460; PubMed
Central PMCID: PMC3591440.
30: Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L.
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.
Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129. Epub
2013 Mar 16. PubMed PMID: 23505298; PubMed Central PMCID: PMC3634184.
31: Lew JM, Mao C, Shukla M, Warren A, Will R, Kuznetsov D, Xenarios I, Robertson
BD, Gordon SV, Schnappinger D, Cole ST, Sobral B. Database resources for the
tuberculosis community. Tuberculosis (Edinb). 2013 Jan;93(1):12-7. doi:
10.1016/j.tube.2012.11.003. Epub 2013 Jan 17. Review. PubMed PMID: 23332401;
PubMed Central PMCID: PMC3592388.
32: Bugliani M, Liechti R, Cheon H, Suleiman M, Marselli L, Kirkpatrick C,
Filipponi F, Boggi U, Xenarios I, Syed F, Ladriere L, Wollheim C, Lee MS,
Marchetti P. Microarray analysis of isolated human islet transcriptome in type 2
diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell
dysfunction. Mol Cell Endocrinol. 2013 Mar 10;367(1-2):1-10. doi:
10.1016/j.mce.2012.12.001. Epub 2012 Dec 12. PubMed PMID: 23246353.
33: Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R,
Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U,
Rougemont J, Guex N, Hernandez N, Naef F; CycliX Consortium. Genome-wide RNA
polymerase II profiles and RNA accumulation reveal kinetics of transcription and
associated epigenetic changes during diurnal cycles. PLoS Biol.
2012;10(11):e1001442. doi: 10.1371/journal.pbio.1001442. Epub 2012 Nov 27. PubMed
PMID: 23209382; PubMed Central PMCID: PMC3507959.
34: Masson P, Hulo C, De Castro E, Bitter H, Gruenbaum L, Essioux L, Bougueleret
L, Xenarios I, Le Mercier P. ViralZone: recent updates to the virus knowledge
resource. Nucleic Acids Res. 2013 Jan;41(Database issue):D579-83. doi:
10.1093/nar/gks1220. Epub 2012 Nov 28. PubMed PMID: 23193299; PubMed Central
PMCID: PMC3531065.
35: Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E,
Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A;
UniProt Consortium. HAMAP in 2013, new developments in the protein family
classification and annotation system. Nucleic Acids Res. 2013 Jan;41(Database
issue):D584-9. doi: 10.1093/nar/gks1157. Epub 2012 Nov 27. PubMed PMID: 23193261;
PubMed Central PMCID: PMC3531088.
36: Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation
of metabolites and biochemical reactions for metabolic networks. Brief Bioinform.
2014 Jan;15(1):123-35. doi: 10.1093/bib/bbs058. Epub 2012 Nov 19. PubMed PMID:
23172809; PubMed Central PMCID: PMC3896926.
37: Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N,
Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L,
Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey
P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown
NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B,
Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM,
Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A,
Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G,
Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P,
Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán
P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S,
Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering
RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A,
Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J,
Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind
S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan
R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong
EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED,
Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken
K, Howe D, Westerfield M. Gene Ontology annotations and resources. Nucleic Acids
Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov
17. PubMed PMID: 23161678; PubMed Central PMCID: PMC3531070.
38: Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret
L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Res.
2013 Jan;41(Database issue):D344-7. doi: 10.1093/nar/gks1067. Epub 2012 Nov 17.
PubMed PMID: 23161676; PubMed Central PMCID: PMC3531220.
39: Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud
S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V,
Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios
I, Stockinger H. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res.
2012 Jul;40(Web Server issue):W597-603. doi: 10.1093/nar/gks400. Epub 2012 May
31. PubMed PMID: 22661580; PubMed Central PMCID: PMC3394269.
40: Hornitschek P, Kohnen MV, Lorrain S, Rougemont J, Ljung K, López-Vidriero I,
Franco-Zorrilla JM, Solano R, Trevisan M, Pradervand S, Xenarios I, Fankhauser C.
Phytochrome interacting factors 4 and 5 control seedling growth in changing light
conditions by directly controlling auxin signaling. Plant J. 2012
Sep;71(5):699-711. doi: 10.1111/j.1365-313X.2012.05033.x. Epub 2012 Jun 22.
PubMed PMID: 22536829.
41: Jungo F, Bougueleret L, Xenarios I, Poux S. The UniProtKB/Swiss-Prot Tox-Prot
program: A central hub of integrated venom protein data. Toxicon. 2012 Sep
15;60(4):551-7. doi: 10.1016/j.toxicon.2012.03.010. Epub 2012 Mar 23. PubMed
PMID: 22465017; PubMed Central PMCID: PMC3393831.
42: Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A,
Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C,
Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ,
Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L,
Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H. Protein interaction data
curation: the International Molecular Exchange (IMEx) consortium. Nat Methods.
2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012
Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert
[corrected to Hancock, Robert E W]. PubMed PMID: 22453911; PubMed Central PMCID:
PMC3703241.
43: Canella D, Bernasconi D, Gilardi F, LeMartelot G, Migliavacca E, Praz V,
Cousin P, Delorenzi M, Hernandez N; CycliX Consortium. A multiplicity of factors
contributes to selective RNA polymerase III occupancy of a subset of RNA
polymerase III genes in mouse liver. Genome Res. 2012 Apr;22(4):666-80. doi:
10.1101/gr.130286.111. Epub 2012 Jan 27. PubMed PMID: 22287103; PubMed Central
PMCID: PMC3317149.
44: Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H,
Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G,
Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix
I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL,
Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A,
Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA,
Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.
Toward interoperable bioscience data. Nat Genet. 2012 Jan 27;44(2):121-6. doi:
10.1038/ng.1054. PubMed PMID: 22281772; PubMed Central PMCID: PMC3428019.
45: Kapur K, Schüpbach T, Xenarios I, Kutalik Z, Bergmann S. Comparison of
strategies to detect epistasis from eQTL data. PLoS One. 2011;6(12):e28415. doi:
10.1371/journal.pone.0028415. Epub 2011 Dec 19. PubMed PMID: 22205949; PubMed
Central PMCID: PMC3242756.
46: Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, Harshman K,
Guipponi M, Bukach O, Zoete V, Michielin O, Muehlethaler K, Speiser D, Beckmann
JS, Xenarios I, Halazonetis TD, Jongeneel CV, Stevenson BJ, Antonarakis SE. Exome
sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.
Nat Genet. 2011 Dec 25;44(2):133-9. doi: 10.1038/ng.1026. PubMed PMID: 22197931.
47: Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de
Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C.
Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res.
2012 Jan;40(Database issue):D754-60. doi: 10.1093/nar/gkr1126. Epub 2011 Dec 1.
PubMed PMID: 22135291; PubMed Central PMCID: PMC3245052.
48: Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ,
Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane
M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet
E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti
L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J,
Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M,
Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S,
Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I,
Apweiler R. The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 2012
Jan;40(Database issue):D565-70. doi: 10.1093/nar/gkr1048. Epub 2011 Nov 28.
PubMed PMID: 22123736; PubMed Central PMCID: PMC3245010.
49: UniProt Consortium. Reorganizing the protein space at the Universal Protein
Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. doi:
10.1093/nar/gkr981. Epub 2011 Nov 18. PubMed PMID: 22102590; PubMed Central
PMCID: PMC3245120.
50: Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A,
Bougueleret L, Xenarios I, Viari A. UniPathway: a resource for the exploration
and annotation of metabolic pathways. Nucleic Acids Res. 2012 Jan;40(Database
issue):D761-9. doi: 10.1093/nar/gkr1023. Epub 2011 Nov 18. PubMed PMID: 22102589;
PubMed Central PMCID: PMC3245108.
51: Gene Ontology Consortium. The Gene Ontology: enhancements for 2011. Nucleic
Acids Res. 2012 Jan;40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. Epub
2011 Nov 18. PubMed PMID: 22102568; PubMed Central PMCID: PMC3245151.
52: Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y. Visualization and
quality assessment of de novo genome assemblies. Bioinformatics. 2011 Dec
15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569. Epub 2011 Oct 12. PubMed
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53: Garg A, Mohanram K, De Micheli G, Xenarios I. Implicit methods for
qualitative modeling of gene regulatory networks. Methods Mol Biol.
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54: Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C. Conceptual framework
and pilot study to benchmark phylogenomic databases based on reference gene
trees. Brief Bioinform. 2011 Sep;12(5):423-35. doi: 10.1093/bib/bbr034. Epub 2011
Jul 7. PubMed PMID: 21737420; PubMed Central PMCID: PMC3178055.
55: Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly
JF, Notredame C. T-Coffee: a web server for the multiple sequence alignment of
protein and RNA sequences using structural information and homology extension.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. doi: 10.1093/nar/gkr245.
Epub 2011 May 9. PubMed PMID: 21558174; PubMed Central PMCID: PMC3125728.
56: Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Quadroni M,
Waridel P, Gaillard M, Pidoux M, Rapin B, Rivolta C, Xenarios I, Simpson AJ,
Antonarakis SE, Beckmann JS, Jongeneel CV, Iseli C, Stevenson BJ. Network-guided
analysis of genes with altered somatic copy number and gene expression reveals
pathways commonly perturbed in metastatic melanoma. PLoS One. 2011 Apr
8;6(4):e18369. doi: 10.1371/journal.pone.0018369. PubMed PMID: 21494657; PubMed
Central PMCID: PMC3072964.
57: Sankar M, Osmont KS, Rolcik J, Gujas B, Tarkowska D, Strnad M, Xenarios I,
Hardtke CS. A qualitative continuous model of cellular auxin and brassinosteroid
signaling and their crosstalk. Bioinformatics. 2011 May 15;27(10):1404-12. doi:
10.1093/bioinformatics/btr158. Epub 2011 Mar 30. PubMed PMID: 21450717.
58: Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK,
Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih
CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED,
Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi
SV, Heinze J, Goodisman MA, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios
I, Shoemaker D, Keller L. The genome of the fire ant Solenopsis invicta. Proc
Natl Acad Sci U S A. 2011 Apr 5;108(14):5679-84. doi: 10.1073/pnas.1009690108.
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59: UniProt Consortium. Ongoing and future developments at the Universal Protein
Resource. Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. doi:
10.1093/nar/gkq1020. Epub 2010 Nov 4. PubMed PMID: 21051339; PubMed Central
PMCID: PMC3013648.
60: Gordon V, Bhadel S, Wunderlich W, Zhang J, Ficarro SB, Mollah SA, Shabanowitz
J, Hunt DF, Xenarios I, Hahn WC, Conaway M, Carey MF, Gioeli D. CDK9 regulates AR
promoter selectivity and cell growth through serine 81 phosphorylation. Mol
Endocrinol. 2010 Dec;24(12):2267-80. doi: 10.1210/me.2010-0238. Epub 2010 Oct 27.
PubMed PMID: 20980437; PubMed Central PMCID: PMC2999477.
61: Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le
Mercier P. ViralZone: a knowledge resource to understand virus diversity. Nucleic
Acids Res. 2011 Jan;39(Database issue):D576-82. doi: 10.1093/nar/gkq901. Epub
2010 Oct 14. PubMed PMID: 20947564; PubMed Central PMCID: PMC3013774.
62: Liechti R, Csárdi G, Bergmann S, Schütz F, Sengstag T, Boj SF, Servitja JM,
Ferrer J, Van Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL,
Marselli L, Bugliani M, Marchetti P, Lucas S, Holm C, Jongeneel CV, Xenarios I.
EuroDia: a beta-cell gene expression resource. Database (Oxford). 2010 Oct
12;2010:baq024. doi: 10.1093/database/baq024. PubMed PMID: 20940178; PubMed
Central PMCID: PMC2963318.
63: Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Le Mercier P, Bairoch A,
Xenarios I. OpenFluDB, a database for human and animal influenza virus. Database
(Oxford). 2010 Jul 6;2010:baq004. doi: 10.1093/database/baq004. PubMed PMID:
20624713; PubMed Central PMCID: PMC2911839.
64: Schüpbach T, Xenarios I, Bergmann S, Kapur K. FastEpistasis: a high
performance computing solution for quantitative trait epistasis. Bioinformatics.
2010 Jun 1;26(11):1468-9. doi: 10.1093/bioinformatics/btq147. Epub 2010 Apr 7.
PubMed PMID: 20375113; PubMed Central PMCID: PMC2872003.
65: Dominiczak AF, Herget-Rosenthal S, Delles C, Fliser D, Fournier I, Graber A,
Girolami M, Holmes E, Lang F, Molina F, Nicholson J, Remuzzi G, Rossing P,
Rudolph KL, Wolkenhauer O, Xenarios I, Zubarev R, Zubov D, Vlahou A, Schanstra
JP. Systems biology to battle vascular disease. Nephrol Dial Transplant. 2010
Apr;25(4):1019-22. doi: 10.1093/ndt/gfq025. Epub 2010 Feb 3. PubMed PMID:
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66: Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I. Animal Toxins:
How is Complexity Represented in Databases? Toxins (Basel). 2010 Feb;2(2):262-82.
doi: 10.3390/toxins2020262. Epub 2010 Feb 21. PubMed PMID: 22069583; PubMed
Central PMCID: PMC3202812.
67: Guex N, Migliavacca E, Xenarios I. Multiple imputations applied to the DREAM3
phosphoproteomics challenge: a winning strategy. PLoS One. 2010 Jan
18;5(1):e8012. doi: 10.1371/journal.pone.0008012. PubMed PMID: 20090915; PubMed
Central PMCID: PMC2807461.
68: Santuari L, Pradervand S, Amiguet-Vercher AM, Thomas J, Dorcey E, Harshman K,
Xenarios I, Juenger TE, Hardtke CS. Substantial deletion overlap among divergent
Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
Genome Biol. 2010 Jan 12;11(1):R4. doi: 10.1186/gb-2010-11-1-r4. PubMed PMID:
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69: Hinz U; UniProt Consortium. From protein sequences to 3D-structures and
beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci. 2010
Apr;67(7):1049-64. doi: 10.1007/s00018-009-0229-6. Epub 2009 Dec 31. Review.
PubMed PMID: 20043185; PubMed Central PMCID: PMC2835715.
70: Gene Ontology Consortium. The Gene Ontology in 2010: extensions and
refinements. Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi:
10.1093/nar/gkp1018. Epub 2009 Nov 17. PubMed PMID: 19920128; PubMed Central
PMCID: PMC2808930.
71: Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.
ENFIN--A European network for integrative systems biology. C R Biol. 2009
Nov;332(11):1050-8. doi: 10.1016/j.crvi.2009.09.003. Review. PubMed PMID:
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72: UniProt Consortium. The Universal Protein Resource (UniProt) in 2010. Nucleic
Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846. Epub 2009
Oct 20. PubMed PMID: 19843607; PubMed Central PMCID: PMC2808944.
73: Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L,
Telenti A. Evolutionary trajectories of primate genes involved in HIV
pathogenesis. Mol Biol Evol. 2009 Dec;26(12):2865-75. doi: 10.1093/molbev/msp197.
Epub 2009 Sep 2. PubMed PMID: 19726537.
74: Bugliani M, Masini M, Liechti R, Marselli L, Xenarios I, Boggi U, Filipponi
F, Masiello P, Marchetti P. The direct effects of tacrolimus and cyclosporin A on
isolated human islets: A functional, survival and gene expression study. Islets.
2009 Sep-Oct;1(2):106-10. doi: 10.4161/isl.1.2.9142. PubMed PMID: 21099257.
75: Garg A, Mohanram K, Di Cara A, De Micheli G, Xenarios I. Modeling
stochasticity and robustness in gene regulatory networks. Bioinformatics. 2009
Jun 15;25(12):i101-9. doi: 10.1093/bioinformatics/btp214. PubMed PMID: 19477975;
PubMed Central PMCID: PMC2687968.
76: Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig
M. MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC
Bioinformatics. 2009 May 18;10:151. doi: 10.1186/1471-2105-10-151. PubMed PMID:
19450266; PubMed Central PMCID: PMC2694794.
77: Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J. The
Microbe browser for comparative genomics. Nucleic Acids Res. 2009 Jul;37(Web
Server issue):W296-9. doi: 10.1093/nar/gkp268. Epub 2009 Apr 30. PubMed PMID:
19406928; PubMed Central PMCID: PMC2703916.
78: Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. AssociationViewer:
a scalable and integrated software tool for visualization of large-scale
variation data in genomic context. Bioinformatics. 2009 Mar 1;25(5):662-3. doi:
10.1093/bioinformatics/btp017. Epub 2009 Jan 25. PubMed PMID: 19168913; PubMed
Central PMCID: PMC2647839.
79: Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.
Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics. 2008
Oct 13;9:431. doi: 10.1186/1471-2105-9-431. PubMed PMID: 18851737; PubMed Central
PMCID: PMC2575221.
80: Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn
DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA,
Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I,
Zeng R, Julian RK Jr. Guidelines for reporting the use of mass spectrometry in
proteomics. Nat Biotechnol. 2008 Aug;26(8):860-1. doi: 10.1038/nbt0808-860.
PubMed PMID: 18688232.
81: Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G. Synchronous versus
asynchronous modeling of gene regulatory networks. Bioinformatics. 2008 Sep
1;24(17):1917-25. doi: 10.1093/bioinformatics/btn336. Epub 2008 Jul 9. PubMed
PMID: 18614585; PubMed Central PMCID: PMC2519162.
82: Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C. R-Coffee: a web
server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 2008
Jul 1;36(Web Server issue):W10-3. doi: 10.1093/nar/gkn278. Epub 2008 May 15.
PubMed PMID: 18483080; PubMed Central PMCID: PMC2447777.
83: Favre-Kontula L, Sattonnet-Roche P, Magnenat E, Proudfoot AE, Boschert U,
Xenarios I, Vilbois F, Antonsson B. Detection and identification of plasma
proteins that bind GlialCAM using ProteinChip arrays, SELDI-TOF MS, and nano-LC
MS/MS. Proteomics. 2008 Jan;8(2):378-88. doi: 10.1002/pmic.200700564. PubMed
PMID: 18203261.
84: Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L. Dynamic simulation of
regulatory networks using SQUAD. BMC Bioinformatics. 2007 Nov 26;8:462. PubMed
PMID: 18039375; PubMed Central PMCID: PMC2238325.
85: Garg A, Mendoza L, Xenarios I, DeMicheli G. Modeling of multiple valued gene
regulatory networks. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:1398-404. PubMed
PMID: 18002226.
86: Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader
GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A,
Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E,
Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D,
Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the
HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 9;5:44. PubMed
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87: Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M,
Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ,
Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC,
Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S,
Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM,
Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
The minimum information required for reporting a molecular interaction experiment
(MIMIx). Nat Biotechnol. 2007 Aug;25(8):894-8. Review. PubMed PMID: 17687370.
88: Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W,
Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann
M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A,
Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR
3rd, Hermjakob H. The minimum information about a proteomics experiment (MIAPE).
Nat Biotechnol. 2007 Aug;25(8):887-93. Review. PubMed PMID: 17687369.
89: Pasquali C, Bertschy-Meier D, Chabert C, Curchod ML, Arod C, Booth R,
Mechtler K, Vilbois F, Xenarios I, Ferguson CG, Prestwich GD, Camps M, Rommel C.
A chemical proteomics approach to phosphatidylinositol 3-kinase signaling in
macrophages. Mol Cell Proteomics. 2007 Nov;6(11):1829-41. Epub 2007 Jul 7. PubMed
PMID: 17617665.
90: Mendoza L, Xenarios I. A method for the generation of standardized
qualitative dynamical systems of regulatory networks. Theor Biol Med Model. 2006
Mar 16;3:13. PubMed PMID: 16542429; PubMed Central PMCID: PMC1440308.
91: Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A,
Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch
H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker
K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M,
Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C,
Apweiler R. The HUPO PSI's molecular interaction format--a community standard for
the representation of protein interaction data. Nat Biotechnol. 2004
Feb;22(2):177-83. PubMed PMID: 14755292.
92: Da Cruz S, Xenarios I, Langridge J, Vilbois F, Parone PA, Martinou JC.
Proteomic analysis of the mouse liver mitochondrial inner membrane. J Biol Chem.
2003 Oct 17;278(42):41566-71. Epub 2003 Jul 15. PubMed PMID: 12865426.
93: Deane CM, Salwiński Ł, Xenarios I, Eisenberg D. Protein interactions: two
methods for assessment of the reliability of high throughput observations. Mol
Cell Proteomics. 2002 May;1(5):349-56. PubMed PMID: 12118076.
94: Duan XJ, Xenarios I, Eisenberg D. Describing biological protein interactions
in terms of protein states and state transitions: the LiveDIP database. Mol Cell
Proteomics. 2002 Feb;1(2):104-16. PubMed PMID: 12096128.
95: Robyr D, Suka Y, Xenarios I, Kurdistani SK, Wang A, Suka N, Grunstein M.
Microarray deacetylation maps determine genome-wide functions for yeast histone
deacetylases. Cell. 2002 May 17;109(4):437-46. PubMed PMID: 12086601.
96: Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the
Database of Interacting Proteins: a research tool for studying cellular networks
of protein interactions. Nucleic Acids Res. 2002 Jan 1;30(1):303-5. PubMed PMID:
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97: Dym O, Xenarios I, Ke H, Colicelli J. Molecular docking of competitive
phosphodiesterase inhibitors. Mol Pharmacol. 2002 Jan;61(1):20-5. PubMed PMID:
11752202.
98: Xenarios I, Eisenberg D. Protein interaction databases. Curr Opin Biotechnol.
2001 Aug;12(4):334-9. Review. PubMed PMID: 11551460.
99: Kennedy MA, Venkateswaran A, Tarr PT, Xenarios I, Kudoh J, Shimizu N, Edwards
PA. 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. J Biol Chem. 2001 Oct 19;276(42):39438-47. Epub 2001 Aug 10.
Erratum in: J Biol Chem 2002 May 10;277(19):17375. PubMed PMID: 11500512.
100: Marcotte EM, Xenarios I, Eisenberg D. Mining literature for protein-protein
interactions. Bioinformatics. 2001 Apr;17(4):359-63. PubMed PMID: 11301305.
101: Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis
identifies interfaces and functional residue clusters in proteins. J Mol Biol.
2001 Apr 13;307(5):1487-502. PubMed PMID: 11292355.
102: Klein MA, Kaeser PS, Schwarz P, Weyd H, Xenarios I, Zinkernagel RM, Carroll
MC, Verbeek JS, Botto M, Walport MJ, Molina H, Kalinke U, Acha-Orbea H, Aguzzi A.
Complement facilitates early prion pathogenesis. Nat Med. 2001 Apr;7(4):488-92.
PubMed PMID: 11283678.
103: Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. Localizing proteins
in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A. 2000 Oct
24;97(22):12115-20. PubMed PMID: 11035803; PubMed Central PMCID: PMC17303.
104: Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the
post-genomic era. Nature. 2000 Jun 15;405(6788):823-6. Review. PubMed PMID:
10866208.
105: Atienza JM, Suh M, Xenarios I, Landgraf R, Colicelli J. Human ERK1 induces
filamentous growth and cell wall remodeling pathways in Saccharomyces cerevisiae.
J Biol Chem. 2000 Jul 7;275(27):20638-46. PubMed PMID: 10787425.
106: Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM,
Eisenberg D. DIP: The Database of Interacting Proteins: 2001 update. Nucleic
Acids Res. 2001 Jan 1;29(1):239-41. PubMed PMID: 11125102; PubMed Central PMCID:
PMC29798.
107: Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP:
the database of interacting proteins. Nucleic Acids Res. 2000 Jan 1;28(1):289-91.
PubMed PMID: 10592249; PubMed Central PMCID: PMC102387.
108: Acha-Orbea H, Finke D, Attinger A, Schmid S, Wehrli N, Vacheron S, Xenarios
I, Scarpellino L, Toellner KM, MacLennan IC, Luther SA. Interplays between mouse
mammary tumor virus and the cellular and humoral immune response. Immunol Rev.
1999 Apr;168:287-303. Review. PubMed PMID: 10399081.
109: Maillard I, Xenarios I, Diggelmann H, Orbea HA. Differential reactivity of
TCR Vbeta10 alleles to a mouse mammary tumor virus superantigen. Eur J Immunol.
1998 Oct;28(10):3075-85. PubMed PMID: 9808176.
110: Maillard I, Launois P, Xenarios I, Louis JA, Acha-Orbea H, Diggelmann H.
Immune response to mouse mammary tumor virus in mice lacking the alpha/beta
interferon or the gamma interferon receptor. J Virol. 1998 Apr;72(4):2638-46.
PubMed PMID: 9525580; PubMed Central PMCID: PMC109703.
111: Launois P, Maillard I, Pingel S, Swihart KG, Xénarios I, Acha-Orbea H,
Diggelmann H, Locksley RM, MacDonald HR, Louis JA. 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. Immunity. 1997 May;6(5):541-9. PubMed PMID:
9175832.
112: Luther S, Shakhov AN, Xenarios I, Haga S, Imai S, Acha-Orbea H. New
infectious mammary tumor virus superantigen with V beta-specificity identical to
staphylococcal enterotoxin B (SEB). Eur J Immunol. 1994 Aug;24(8):1757-64. PubMed
PMID: 8056034.
113: Lüthy R, Xenarios I, Bucher P. Improving the sensitivity of the sequence
profile method. Protein Sci. 1994 Jan;3(1):139-46. PubMed PMID: 7511453; PubMed
Central PMCID: PMC2142471.
