Schneider (Reinhard) GroupPublications
Arena3D: visualizing time-driven phenotypic differences in biological systems.
Secrier, M., Pavlopoulos, G.A., Aerts, J. & Schneider, R.
BMC Bioinformatics. 2012 Mar 22;13(1):45. PubMed
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.
Glaab, E. & Schneider, R.
Bioinformatics. 2012 Feb 1;28(3):446-7. Epub 2011 Nov 28. PubMed
Using graph theory to analyze biological networks.
Pavlopoulos, G.A., Secrier, M., Moschopoulos, C.N., Soldatos, T.G., Kossida, S., Aerts, J., Schneider, R. & Bagos, P.G.
BioData Min. 2011 Apr 28;4:10. PubMed
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.
Satagopam, V.P., Theodoropoulou, M.C., Stampolakis, C.K., Pavlopoulos, G.A., Papandreou, N.C., Bagos, P.G., Schneider, R. & Hamodrakas, S.J.
Database (Oxford). 2010 Aug 5;2010:baq019. Print 2010. PubMed
Reflect: A practical approach to web semantics
O'Donoghue, S.I.; Horn, H.; Pafilis, E.; Haag, S.;, Kuhn, M.; Satagopam, V.P.; Schneider, R., Jensen, L.J.
Journal of Web Semantics, Special Issue: Sp. Iss. SI 2-3 (8) 182-189
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.
Neumann, B., Walter, T., Heriche, J.K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, M.H., Chapuis, C., Gerlich, D.W., Schneider, R., Eils, R., Huber, W., Peters, J.M., Hyman, A.A., Durbin, R., Pepperkok, R. & Ellenberg, J.
Nature. 2010 Apr 1;464(7289):721-7. PubMed
Visualization of omics data for systems biology.
Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. & Gavin, A.C.
Nat Methods. 2010 Mar;7(3 Suppl):S56-68. PubMed
Martini: using literature keywords to compare gene sets.
Soldatos, T.G., O'Donoghue, S.I., Satagopam, V.P., Jensen, L.J., Brown, N.P., Barbosa-Silva, A. & Schneider, R.
Nucleic Acids Res. 2010 Jan;38(1):26-38. Epub 2009 Oct 25. PubMed
Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition.
Marji, J., O'Donoghue, S.I., McClintock, D., Satagopam, V.P., Schneider, R., Ratner, D., J Worman, H., Gordon, L.B. & Djabali, K.
PLoS One. 2010 Jun 15;5(6):e11132. PubMed
Live coverage of scientific conferences using web technologies.
Lister, A.L., Datta, R.S., Hofmann, O., Krause, R., Kuhn, M., Roth, B. & Schneider, R.
PLoS Comput Biol. 2010 Jan 29;6(1):e1000563. PubMed
LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships.
Barbosa-Silva, A., Soldatos, T.G., Magalhaes, I.L., Pavlopoulos, G.A., Fontaine, J.F., Andrade-Navarro, M.A., Schneider, R. & Ortega, J.M.
BMC Bioinformatics. 2010 Feb 1;11:70. PubMed
From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication.
Borner, K., Hermle, J., Sommer, C., Brown, N.P., Knapp, B., Glass, B., Kunkel, J., Torralba, G., Reymann, J., Beil, N., Beneke, J., Pepperkok, R., Schneider, R., Ludwig, T., Hausmann, M., Hamprecht, F., Erfle, H., Kaderali, L., Krausslich, H.G. & Lehmann, M.J.
Biotechnol J. 2009 Dec 10;5(1):39-49. PubMed
Reflect: augmented browsing for the life scientist.
Pafilis, E., O'Donoghue, S.I., Jensen, L.J., Horn, H., Kuhn, M., Brown, N.P. & Schneider, R.
Nat Biotechnol. 2009 Jun;27(6):508-10. PubMed
GIBA: a clustering tool for detecting protein complexes.
Moschopoulos, C.N., Pavlopoulos, G.A., Schneider, R., Likothanassis, S.D. & Kossida, S.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S11. PubMed
jClust: A clustering and visualization toolbox.
Pavlopoulos, G.A., Moschopoulos, C.N., Hooper, S.D., Schneider, R. & Kossida, S.
Bioinformatics. 2009 May 19. PubMed
New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.
Bromberg, Y., Yachdav, G., Ofran, Y., Schneider, R. & Rost, B.
Curr Opin Drug Discov Devel. 2009 May;12(3):408-19. PubMed
OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.
Pavlopoulos, G.A., Pafilis, E., Kuhn, M., Hooper, S.D. & Schneider, R.
Bioinformatics. 2009 Feb 17. PubMed
Arena3D: visualization of biological networks in 3D.
Pavlopoulos, G.A., O'Donoghue, S.I., Satagopam, V.P., Soldatos, T.G., Pafilis, E. & Schneider, R.
BMC Syst Biol. 2008 Nov 28;2(1):104. PubMed
A survey of visualization tools for biological network analysis.
Pavlopoulos GA, G.ap, Wegener AL, A.w & Schneider, R., R.s
BioData Min. 2008 Nov 28;1(1):12. PubMed
SuperTarget and Matador: resources for exploring drug-target relationships.
Gunther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E.G., Gewiess, A., Jensen, L.J., Schneider, R., Skoblo, R., Russell, R.B., Bourne, P.E., Bork, P. & Preissner, R.
Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22. Epub 2007 Oct 16. PubMed
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.
Barbosa-Silva, A., Satagopam, V.P., Schneider, R. & Ortega, J.M.
BMC BIOINFORMATICS 2008 9, 141
Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.
Barbosa-Silva, A., Pafilis, E., Ortega, J.M. & Schneider, R.
Genet Mol Res. 2007 Dec 11;6(4):1142-50. PubMed
Status of text-mining techniques applied to biomedical text.
Erhardt, R.A., Schneider, R. & Blaschke, C.
Drug Discov Today. 2006 Apr;11(7-8):315-25. PubMed
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
Ofran, Y., Punta, M., Schneider, R. & Rost, B.
Drug Discov Today 2005 Nov 1;10(21):1475-82. PubMed
A bioinformatics perspective on proteomics: data storage, analysis, and integration.
Kremer, A., Schneider, R. & Terstappen, G.C.
Biosci Rep 2005 Feb-Apr;25(1-2):95-106. PubMed
Ensemble and UniProt (Swiss-Prot).
Jackson, D., & Schneider, R.
In "Genetics, Genomics, Proteomics and Bioinformatics", Jorde L.B., Little, P. Dunn, M., & Subramaniam (Eds.), John Wiley & Sons, UK
Improving research productivity at a pharmaceutical company.
Ramakrishnan, S., Caruso, A. & Schneider, R.
LION bioscience, White paper, 2002.