Affiliation: University of Tampere
YlipÃ¤Ã¤ A, Kivinummi K, Kohvakka A, Annala M, Latonen L, Scaravilli M, et al
. Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer. Cancer Res. 2015;75:4026-31 pubmed publisher
..Furthermore, they establish PCAT5 as a novel oncogenic lncRNA in ERG-positive prostate cancers, with implications for defining CRPC biomarkers and new therapeutic interventions. ..
Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, et al
. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018;9:1176 pubmed publisher
..Our proteogenomic analysis uncovers robustness against genomic and transcriptomic aberrations during prostate cancer progression, and significantly extends understanding of prostate cancer disease mechanisms. ..
Marttila S, Kananen L, HÃ¤yrynen S, JylhÃ¤vÃ¤ J, Nevalainen T, Hervonen A, et al
. Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression. BMC Genomics. 2015;16:179 pubmed publisher
Lin J, Kramna L, Autio R, Hyoty H, Nykter M, Cinek O. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics. 2017;18:378 pubmed publisher
..Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source. ..
Ampuja M, Rantapero T, Rodriguez Martinez A, Palmroth M, Alarmo E, Nykter M, et al
. Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. BMC Genomics. 2017;18:68 pubmed publisher
..We identified and experimentally validated downstream regulators of BMP4 signaling that relate to the different in vitro phenotypes and thus demonstrate that the downstream BMP4 response is regulated in a cell type-specific manner. ..
Lehtinen B, Raita A, Kesseli J, Annala M, Nordfors K, Yli Harja O, et al
. Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas. BMC Cancer. 2017;17:310 pubmed publisher
..Further studies are warranted to evaluate whether ependymoma patients with high FGFR3 and/or FGFR1 expression could benefit from treatment with FGFR inhibitor based therapeutic approaches currently under evaluation in clinical trials. ..
Afyounian E, Annala M, Nykter M. Segmentum: a tool for copy number analysis of cancer genomes. BMC Bioinformatics. 2017;18:215 pubmed publisher
..Segmentum is an accurate, user-friendly tool for somatic copy number analysis of tumor samples. We demonstrate that this tool is suitable for the analysis of large cohorts, such as the TCGA dataset. ..