2015

  • Aimo L, Liechti R, Hyka-Nouspikel N, Niknejad A, Gleizes A, Gotz L, Kuznetsov D, David FP, van der Goot FG, Riezman H, Bougueleret L, Xenarios I, Bridge A. The SwissLipids knowledgebase for lipid biology. Bioinformatics 2015. (url)
  • Baillie Gerritsen V. Approaching happiness. Protein Spotlight 2015 August. (url)
    • The length of things. Protein Spotlight 2015 June. (url)
    • Another shade of red. Protein Spotlight 2015 May. (url)
    • A question of perspective. Protein Spotlight 2015 April. (url)
    • Taming genes. Protein Spotlight 2015 March. (url)
  • Bhatia P, Baillie Gerritsen V. Becoming two. Protein Spotlight 2015 July. (url)
  • Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford) 2015;2015:bav043. (url)
  • Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 2015;43(Database issue):D213-21. (url)
  • Morgat A, Axelsen KB, Lombardot T, Alcantara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A. Updates in Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res 2015;43(Database issue):D459-64. (url)
  • 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. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 2015;43(Database issue):D1064-70. (url)
  • UniProt C. UniProt: a hub for protein information. Nucleic Acids Res 2015;43(Database issue):D204-12. (url)
  • Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novere N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics 2015;31(11):1875-7. (url)

2014

  • Baillie Gerritsen V. The hidden things. Protein Spotlight 2014 December. (url)
    • The heart of things. Protein Spotlight 2014 November. (url)
    • Moving forward. Protein Spotlight 2014 September. (url)
    • Two’s company. Protein Spotlight 2014 August. (url)
    • It did it its way. Protein Spotlight 2014 July. (url)
    • The senses confused. Protein Spotlight 2014 June. (url)
    • An unusual chemistry. Protein Spotlight 2014 May. (url)
    • On the garden pea. Protein Spotlight 2014 April. (url)
    • A gut’s tale. Protein Spotlight 2014 March. (url)
    • A pain soothed. Protein Spotlight 2014 January. (url)
  • Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 2014;15(1):123-35. (url)
  • Charpilloz C, Veuthey AL, Chopard B, Falcone JL. Motifs tree: a new method for predicting post-translational modifications. Bioinformatics 2014;30(14):1974-82. (url)
  • 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;2014:bau008. (url)
  • Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation. Hum Mutat 2014;35(8):927-35. (url)
  • Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lutteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics 2014;5(1):5. (url)
  • 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;13(4):239-40. (url)
  • Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. An integrated ontology resource to explore and study host-virus relationships. PLoS One 2014;9(9):e108075. (url)
  • Pedersen BP, Ifrim G, Liboriussen P, Axelsen KB, Palmgren MG, Nissen P, Wiuf C, Pedersen CN. Large scale identification and categorization of protein sequences using structured logistic regression. PLoS One 2014;9(1):e85139. (url)
  • Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford) 2014;2014:bau016. (url)
  • Roppolo D, Boeckmann B, Pfister A, Boutet E, Rubio MC, Denervaud-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. (url)
  • Sonnhammer EL, Gabaldon T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs c. Big data and other challenges in the quest for orthologs. Bioinformatics 2014;30(21):2993-8. (url)
  • Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Mercier PL, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, Mering C, 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;42(Web Server issue):W436-41. (url)

2013

  • Baillie Gerritsen V. Something a little different... Protein Spotlight 2013 December. (url)
    • An unexpected turn of events. Protein Spotlight 2013 December. (url)
    • A gait on the wildside. Protein Spotlight 2013 November. (url)
    • About water. Protein Spotlight 2013 October. (url)
    • The geometry of intelligence. Protein Spotlight 2013 August. (url)
    • The root of the problem. Protein Spotlight 2013 July. (url)
    • The intricacy of a smell. Protein Spotlight 2013 July. (url)
    • A case for discomfort. Protein Spotlight 2013 June. (url)
    • The taste of sweet. Protein Spotlight 2013 May. (url)
    • The silence within. Protein Spotlight 2013 March. (url)
    • A wretched tale. Protein Spotlight 2013 January. (url)
  • Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. iAnn: an event sharing platform for the life sciences. Bioinformatics 2013;29(15):1919-1921. (url)
  • 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;41(Database issue):D579-83. (url)
  • Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaino JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled vocabularies and ontologies in proteomics: Overview, principles and practice. Biochim Biophys Acta 2013. (url)
  • Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaino JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013;2013:bat009. (url)
  • 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. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res 2013;41(Database issue):D584-9. (url)
  • Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L. pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics 2013;29(9):1215-7. (url)
  • 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;41(Database issue):D344-7. (url)
  • 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;14:104. (url)
  • 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. (url)