Bärlund, M., Monni, O., Kononen, J., Torhorst, J., Sauter, G., Kallioniemi, O-P., Kallioniemi, A. Multiple genes at 17q23 undergo amplification and overexpression in breast cancer Cancer Res 60, 5340-5344, 2000

Monni, O., Hyman, E., Mousses, S., Bärlund, M., Kallioniemi, A., Kallioniemi, O.P. From chromosomal alterations to target genes for therapy: integrating cytogenetic and functional genomic views of the breast cancer genome. Semin Cancer Biol 11:395-401, 2001

Monni, O., Bärlund, M., Mousses, S., Kononen, J., Sauter, G., Heiskanen, M., Paavola, P., Avela, K., Chen, Y., Bittner, M.L., Kallioniemi, A. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci USA 98:5711-5716, 2001

Kauraniemi, P., Bärlund, M., Monni, O., Kallioniemi, A. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res 61:8235-8240, 2001

Monni O, Hautaniemi S, Kallioniemi O. Geenisirutekniikka ja siihen liittyvä bioinformatiikka. Duodecim 118:1157-1166, 2002

Varis, A., Wolf, M., Monni, O., Vakkari, M.L., Kokkola, A., Moskaluk, C., Frierson Jr, H., Powell, S.M., Knuutila, S., Kallioniemi, A., El-Rifai, W. Targets of gene amplification and overexpression at 17q in gastric cancer. Cancer Res 62:2625-2629, 2002

Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringner M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 62: 6240-6245, 2002

Bärlund, M., Monni, O., Weaver, D.J., Heiskanen, M., Kallioniemi, O-P., Kallioniemi A. Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression and fusion in breast cancer. Genes Chromosom Cancer 35: 311-317, 2002

Hu G, Modrek B, Riise Stensland HM, Saarela J, Pajukanta P, Kustanovich V, Peltonen L, Nelson SF, Lee C. Efficient discovery of single-nucleotide polymorphisms in coding regions of human genes. Pharmacogenomics J. 2:236-242, 2002

Saarela J, Schoenberg Fejzo M, Chen D, Finnila S, Parkkonen M, Kuokkanen S, Sobel E, Tienari PJ, Sumelahti ML, Wikstrom J, Elovaara I, Koivisto K, Pirttila T, Reunanen M, Palotie A, Peltonen L. Fine mapping of a multiple sclerosis locus to 2.5 Mb on chromosome 17q22-q24. Hum Mol Genet. 11:2257-2267, 2002

Hautaniemi S, Edgren H, Vesanen P, Wolf M, Jarvinen AK, Yli-Harja O, Astola J, Kallioniemi O, Monni O. A novel strategy for microarray quality control using Bayesian networks. Bioinformatics. 19: 2031-2038, 2003

Chen DC, Saarela J, Nuotio I, Jokiaho A, Peltonen L, Palotie A. Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping. J Mol Diagn. 5:243-249, 2003

Kauraniemi P, Hautaniemi S, Autio R, Astola J, Monni O, Elkahloun A, Kallioniemi A. Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines. Oncogene 23:1010-1013, 2004

Järvinen, A-K, Hautaniemi, S., Edgren, H., Auvinen, P., Saarela, J., Kallioniemi, O.P., Monni, O. Are data from different gene expression microarray platforms comparable? Genomics 83:1164-1168, 2004

Wolf, M., Mousses, S., Hautaniemi, S., Karhu, R., Huusko, P., Allinen, M., Elkahloun, A., Monni, O., Chen, Y., Kallioniemi, A. and Kallioniemi, O.-P. High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: Impact of copy number on gene expression. Neoplasia 6: 240-247, 2004

Bonetti A, Reunanen K, Finnila S, Koivisto K, Wikstrom J, Sumelahti ML, Pirttila T, Elovaara I, Reunanen M, Saarela J, Peltonen L, Rantamaki T, Tienari PJ. A two-stage study on multiple sclerosis susceptibility and chromosome 2q33. Genes Immun. 5:142-146, 2004

Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen MR, Peltonen L. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nat Genet. 36:371-376, 2004

Solovieva S, Leino-Arjas P, Saarela J, Luoma K, Raininko R, Riihimaki H. Possible association of interleukin 1 gene locus polymorphisms with low back pain. Pain. 109: 8-19, 2004

Järvinen AK, Autio R, Haapa-Paananen S, Wolf M, Saarela M, Grenman R, Leivo I, Kallioniemi O, Makitie AA, Monni O. Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene. 2006 May 22; [Epub ahead of print] Supplementary Material