Peer-reviewed publications
2012 (1)
Li-Thiao-Té S, Schwikowski B (2012) Feature Detection with Controlled Error Rates in LC/MS Images, Journal of Computational Biology, accepted for publication
2011 (3)
Schwikowski B (2011) From genes to regulatory circuits (Des Gènes aux circuits de régulation). Biofutur 30(323): 53
Elo LL, Schwikowski B (2011) Mining proteomic data for biomedical research. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Bochet P, Rugheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B (2011) Fragmentation-free LC-MS can identify hundreds of proteins. Proteomics 11(1): 22-32
2010 (4)
Rügheimer F (2010) Using Enriched Ontology Structure for Improving Statistical Models of Gene Annotation Sets. In Information Processing and Management of Uncertainty in Knowledge-Based Systems. Applications. Vol. 81, pp 55-64. Heidelberg: Springer
Besenbacher S, Schwikowski B, Stoye J (2010) Indexing and Searching a Mass Spectrometry Database. In Algorithms and Applications, Elomaa T, Mannila H, Orponen P (eds), Vol. 6060, pp 62-76. New York: Springer
Mazurie A, Bonchev D, Schwikowski B, Buck GA (2010) Evolution of metabolic network organization. BMC Syst Biol 4: 59
Cerqueira FR, Graber A, Schwikowski B, Baumgartner C (2010) MUDE: A new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification. J Proteome Res 9(5): 2265–2277
2009 (2)
Clement-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S (2009) Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics 25(19): 2617-2618
Schussler O, Coirault C, Louis-Tisserand M, Al-Chare W, Oliviero P, Menard C, Michelot R, Bochet P, Salomon DR, Chachques JC, Carpentier A, Lecarpentier Y (2009) Use of arginine-glycine-aspartic acid adhesion peptides coupled with a new collagen scaffold to engineer a myocardium-like tissue graft. Nat Clin Pract Cardiovasc Med 6(3): 240-249
2008 (6)
Splendiani A (2008) RDFScape: Semantic Web meets systems biology. BMC Bioinformatics 9 Suppl 4: S6
Vandenbogaert M, Li-Thiao-Te S, Kaltenbach HM, Zhang R, Aittokallio T, Schwikowski B (2008) Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics 8(4): 650-672
Tuikkala J, Elo LL, Nevalainen OS, Aittokallio T (2008) Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics 9(1): 202
Mazurie A, Bonchev D, Schwikowski B, Buck GA (2008) Phylogenetic distances are encoded in networks of interacting pathways. Bioinformatics 24(22): 2579-2585
Elo L, Filén S, Lahesmaa R, Aittokallio T (2008) Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Transactions on Computational Biology and Bioinformatics
Tafelmeyer P, Laurent C, Lenormand P, Rousselle JC, Marsollier L, Reysset G, Zhang R, Sickmann A, Stinear TP, Namane A, Cole ST (2008) Comprehensive proteome analysis of Mycobacterium ulcerans and quantitative comparison of mycolactone biosynthesis. Proteomics: Epub 9 Jul 2008
2007 (11)
Roberts SB, Mazurie AJ, Buck GA (2007) Integrating genome-scale data for gene essentiality prediction. Chem Biodivers 4(11): 2618-2630
Ochs MF, Peterson AJ, Kossenkov A, Bidaut G (2007) Incorporation of gene ontology annotations to enhance microarray data analysis. Methods Mol Biol 377: 243-254
Abraham I, Abraham R, Desolneux A, Li-Thiao-Te S (2007) Significant edges in the case of non-stationary Gaussian noise. Pattern Recognition 40(11): 3277-3291
Zhang R, Huang GB, Sundararajan N, Saratchandran P (2007) Multi-category classification using an Extreme Learning Machine for microarray gene expression cancer diagnosis. IEEE/ACM Trans Comput Biol Bioinform 4(3): 485-495
Elo LL, Jarvenpaa H, Oresic M, Lahesmaa R, Aittokallio T (2007) Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23(16): 2096-2103
Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P (2007) The genopolis microarray database. BMC Bioinformatics 8 Suppl 1: S21
Zhang R, Huang GB, Sundararajan N, Saratchandran P (2007) Improved GAP-RBF Network for Classification Problems. Neurocomputing 70: 3011-3018
Vähämaa H, Ojala P, Pahikkala T, Nevalainen OS, Lahesmaa R, Aittokallio T (2007) Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments. Electrophoresis 28(6): 879-893
Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T (2007) GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics 23(3): 394-396
Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, Paulovich A, Schwikowski B (2007) Assessing bias in experiment design for large-scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics 6: 1741-1748
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 (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2(10): 2366-2382
2006 (8)
Aittokallio T, Schwikowski B (2006) Graph-based methods for analysing networks in cell biology. Brief Bioinform 7(3): 243-255
Regnier M, Vandenbogaert M (2006) Comparison of statistical significance criteria. J Bioinform Comput Biol 4(2): 537-551
Splendiani A (2006) Semantic browsing of pathway ontologies and biological networks with RDFScape. In Managing and Mining Genome Information: Frontiers in Bioinformatics, Blazewicz J, Freytag JC, Vingron M (eds). Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany
Elo L, Lahesmaa R, Aittokallio T (2006) Inference of gene co-expression networks by integrative analysis across microarray experiments. Journal of Integrative Bioinformatics 3(Proc of the 3rd Integrative Bioinformatics Workshop)
Elo LL, Katajamaa M, Lund R, Oresic M, Lahesmaa R, Aittokallio T (2006) Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays. Omics 10(3): 369-380
Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2006) A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics 7: 484
Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B (2006) Signal Maps for Mass Spectrometry-based Comparative Proteomics. Mol Cell Proteomics 5(3): 423-432
Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M, Jr. (2006) Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol 2(1): e4
2005 (4)
Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R (2005) ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 5(16): 4096-4106
Cline MS, Blume J, Cawley S, Clark TA, Hu JS, Lu G, Salomonis N, Wang H, Williams A (2005) ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics 21 Suppl 1: i107-i115
Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T (2005) Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. BMC Bioinformatics 6(1): 154
Christmas R, Avila-Campillo I, Bolouri H, Schwikowski B, Anderson M, Kelley BP, Landys N, Workman C, Ideker T, Cerami E, Sheridan R, Bader GD, Sander C (2005) Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Am Assoc Cancer Res Educ : 12-16
2004 (2)
Reiss DJ, Schwikowski B (2004) Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics 20 Suppl 1: I274-I282
Ben-Dor A, Hartman T, Karp RM, Schwikowski B, Sharan R, Yakhini Z (2004) Towards optimally multiplexed applications of universal arrays. J Comput Biol 11(2-3): 476-492
Original Cytoscape reference
Shannon P, Markiel A, Ozier O, Baliga N, Amin N, Ramage D, Schwikowski B, Ideker T (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res' 13(11): 2498-2504