PUB - Publikationen an der Universität Bielefeld

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium, Apweiler R, Bateman A, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Alpi E, Antunes R, Arganiska J, Barrera Casanova E, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Mun Chan W, Chavali G, Cibrian-Uhalte E, Da Silva A, De Giorgi M, Fazzini F, Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Zellner H, Corbett M, Donnelly M, van Rensburg P, Goujon M, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Auchincloss A, Axelsen K, Bansal P, Baratin D, Binz PA, Blatter MC, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, de Castro E, Cerutti L, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jungo F, Keller G, Lara V, Lemercier P, Lew J, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka C, Wang Q, Wang Y, Yeh LS, Yerramalla MS, Zhang J., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24253303

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
Barsky A, Gardy JL, Hancock RE, Munzner T., Bioinformatics 23(8), 2007
PMID: 17309895

The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen 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., Nat. Biotechnol. 25(8), 2007
PMID: 17687370

Integration of biological networks and gene expression data using Cytoscape.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD., Nat Protoc 2(10), 2007
PMID: 17947979

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Huang da W, Sherman BT, Lempicki RA., Nat Protoc 4(1), 2009
PMID: 19131956

Cytoscape Web: an interactive web-based network browser.
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD., Bioinformatics 26(18), 2010
PMID: 20656902

Cytoscape 2.8: new features for data integration and network visualization.
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T., Bioinformatics 27(3), 2010
PMID: 21149340

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 FS, Brinkman F, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hancock R, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stumpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H., Nat. Methods 9(4), 2012
PMID: 22453911

Linking proteins to signaling pathways for experiment design and evaluation.
Farkas IJ, Szanto-Varnagy A, Korcsmaros T., PLoS ONE 7(4), 2012
PMID: 22558382

Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.
Michalopoulos I, Pavlopoulos GA, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S., BMC Res Notes 5(), 2012
PMID: 22672625

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23203871

GeneMANIA prediction server 2013 update.
Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q., Nucleic Acids Res. 41(Web Server issue), 2013
PMID: 23794635

NetGestalt: integrating multidimensional omics data over biological networks.
Shi Z, Wang J, Zhang B., Nat. Methods 10(7), 2013
PMID: 23807191

mentha: a resource for browsing integrated protein-interaction networks.
Calderone A, Castagnoli L, Cesareni G., Nat. Methods 10(8), 2013
PMID: 23900247

Sparing of the dystrophin-deficient cranial sartorius muscle is associated with classical and novel hypertrophy pathways in GRMD dogs.
Nghiem PP, Hoffman EP, Mittal P, Brown KJ, Schatzberg SJ, Ghimbovschi S, Wang Z, Kornegay JN., Am. J. Pathol. 183(5), 2013
PMID: 24160322

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24234451

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP., Proc. Natl. Acad. Sci. U.S.A. 102(43), 2005
PMID: 16199517