Publications

oncogenomics_publications#2

 

Read more about our research from the publications below. For complete list of publications, see the PubMed link.

Selected publications

  • Pehkonen H, Lento M, von Nandelstadh P, Filippou A, Grénman R, Lehti K, Monni O. Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton. Cell Commun Signal  2018;16:41. doi: 10.1186/s12964-018-0253-y.

  • Lepikhova T, Karhemo PR, Louhimo R, Yadav B, Murumägi A, Kulesskiy E, Kivento M, Sihto H, Grénman R, Syrjänen SM, Kallioniemi O, Aittokallio T, Wennerberg K, Joensuu H, Monni O. Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy. Mol Cancer Ther 2018 Jul 3. [Epub ahead of print] doi: 10.1158/1535-7163.MCT-17-0733.

  • Pehkonen H, von Nandelstadh P, Karhemo P-R, Lepikhova T, Grenman R, Lehti K, Monni O. Liprin-alpha 1 is a regulator of vimentin intermediate filament network in the cancer cell adhesion machinery. Sci Rep  2016; 6:24486. doi: 10.1038/srep24486.

  • Marques E, Englund JI, Tervonen TA, Virkunen E, Laakso M, Myllynen M, Mäkelä A, Ahvenainen M, Lepikhova T, Monni O, Hautaniemi S, Klefström J. Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers. Oncogene 2015; 35:1386-98. doi: 10.1038/onc.2015.196.

  • Heinonen H, Lepikhova T, Sahu B, Pehkonen H, Pihlajamaa P, Louhimo R, Gao P, Wei GH, Hautaniemi S, Jänne OA, Monni O. Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer. Int J Cancer 2015; 137:2374-83. doi: 10.1002/ijc.29616.

  • Hickman JA, Graeser R, de Hoogt R, Vidic S, Brito C, Gutekunst M, van der Kuip H; IMI PREDECT Consortium. Three-dimensional models of cancer for pharmacology and cancer cell biology: capturing tumor complexity in vitro/ex vivo. Biotechnol J 2014; 9:1115-1128. doi: 10.1002/biot.201300492. Review. 

  • Louhimo R, Lepikhova T, Monni O, Hautaniemi S. Comparative analysis of algorithms for integration of copy number and gene expression data. Nat Methods, advanced online publication, 2012 Feb; 9(4):351-5. doi: 10.1038/nmeth.1893.

  • Chen P, Lepikhova T, Hu Y, Monni O, Hautaniemi S. Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants. Nucleic Acids Res 2011; 39(18):e123. doi: 10.1093/nar/gkr513.

  • Junnila S, Kokkola A, Karjalainen-Lindsberg ML, Puolakkainen P, Monni O. Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines. BMC Cancer 2010; 10:73. doi: 10.1186/1471-2407-10-73.

  • Dancau AM, Wuth L, Waschow M, Holst F, Krohn A, Choschzick M, Terracciano L, Politis S, Kurtz S, Lebeau A, Friedrichs K, Wencke K, Monni O, Simon R. PPFIA1 and CCND1 are frequently coamplified in breast cancer. Genes Chromosomes Cancer 2010; 49:1-8. doi: 10.1002/gcc.20713.

  • Junnila S, Kokkola A, Mizuguchi T, Hirata K, Karjalainen-Lindsberg ML, Puolakkainen P, Monni O. Gene expression analysis identifies over-expression of CXCL1, SPARC, SPP1, and SULF1 in gastric cancer. Genes Chromosomes Cancer 2010; 49:28-39. doi: 10.1002/gcc.20715.

  • Mäkitie AM, Monni O. Molecular profiling of laryngeal cancer. Expert Rev Anticancer Ther. 2009; 9:1251-1260. doi: 10.1586/era.09.102.

  • Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, Hautaniemi S, Monni O. Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics 9:348, 2008. doi: 10.1186/1471-2164-9-348.

  • Myllykangas S, Junnila S, Kokkola A, Autio R, Scheinin I, Karjalainen-Lindsberg M-L, Kiviluoto T, Hollmén J, Knuutila S, Puolakkainen P, Monni O. Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes. Int J Cancer 123:817-825, 2008. doi: 10.1002/ijc.23574.

  • Järvinen AK, Autio R, Kilpinen S, Saarela M, Leivo I, Grénman R, Mäkitie AA, Monni O. High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx. Genes Chromosomes Cancer 47:500-509, 2008. doi: 10.1002/gcc.20551.

  • Järvinen AK, Autio R, Haapa-Paananen S, Wolf M, Saarela M, Leivo I, Grénman R, Kallioniemi O, Mäkitie AA, Monni O. Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene 2006; 25:6997-7008. Supplementary material.

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

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

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

  • Bärlund M, Monni O, Weaver DJ., 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 2002; 35:311-317. 

  • 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. P Natl Acad Sci USA 2001; 98:5711-5716. 

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