Reference publications by MediSapiens Team

  • Eldfors S, Kuusanmäki H, Kontro M, Majumder MM, Parsons A, Edgren H, Pemovska T, Kallioniemi O, Wennerberg K, Gökbuget N, Burmeister T, Porkka K, Heckman CA - Idelalisib sensitivity and mechanisms of disease progression in relapsed TCF3-PBX1 acute lymphoblastic leukemia.(2016).
     
  • Kangaspeska S, Hultsch S, Jaiswal A, Edgren H, Mpindi JP, Eldfors S, Brück O, Aittokallio T, Kallioniemi O. - Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer.(2016).
     
  • Tumiati M, Munne PM, Edgren H, Eldfors S, Hemmes A, Kuznetsov SG. - Rad51c- and Trp53-double-mutant mouse model reveals common features of homologous recombination-deficient breast cancers.(2016).
     
  • Werner S, Brors B, Eick J, Marques E, Pogenberg V, Parret A, Kemming D, Wood AW, Edgren H, Neubauer H, Streichert T, Riethdorf S, Bedi U, Baccelli I, Jücker M, Eils R, Fehm T, Trumpp A, Johnsen SA, Klefström J, Wilmanns M, Müller V, Pantel K, Wikman H. - Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic Acid-induced 2.(2015).
     
  • Koskinen, P., Törönen, P., Nokso-Koivisto, J. & Holm, L. PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. Bioinformatics (2015).
     
  • Andersson E, Eldfors S, Edgren H, Ellonen P, Väkevä L, Ranki A, Mustjoki S. - Novel TBL1XR1, EPHA7 and SLFN12 mutations in a Sezary syndrome patient discovered by whole exome sequencing (2014).
     
  • Løvf, M. et al. A novel transcript, VNN1-AB, as a biomarker for colorectal cancer. Int J Cancer 135, 2077–2084 (2014).
     
  • Andersson, E. et al. Novel TBL1XR1, EPHA7 and SLFN12 mutations in a Sezary syndrome patient discovered by whole exome sequencing. Exp. Dermatol. 23, 366–368 (2014).
     
  • Oghabian, A., Kilpinen, S., Hautaniemi, S. & Czeizler, E. Biclustering methods: biological relevance and application in gene expression analysis. PLoS One 9, e90801 (2014).
     
  • Kontro, M. et al. Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia. Leukemia 28, 1738–1742 (2014).
     
  • Kontro M, Kuusanmäki H, Eldfors S, Burmeister T, Andersson EI, Bruserud O, Brümmendorf TH, Edgren H, Gjertsen BT, Itälä-Remes M, Lagström S, Lohi O, Lundán T, Martí JM, Majumder MM, Parsons A, Pemovska T, Rajala H, Vettenranta K, Kallioniemi O, Mustjoki S, Porkka K, Heckman CA.- Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia (2014).
     
  • Pemovska, T. et al. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov 3, 1416–1429 (2013).
     
  • Högnäs, G. et al. Aneuploidy facilitates oncogenic transformation via specific genetic alterations, including Twist2 upregulation. Carcinogenesis 34, 2000–2009 (2013).
     
  • Garcia, H. et al. Facilitates chromatin transcription complex is an ‘accelerator’ of tumor transformation and potential marker and target of aggressive cancers. Cell Rep 4, 159–173 (2013).
     
  • Turpeinen, H. et al. Minor histocompatibility antigens as determinants for graft-versus-host disease after allogeneic haematopoietic stem cell transplantation. Int. J. Immunogenet. 40, 495–501 (2013).
     
  • Kilpinen, L. et al. Extracellular membrane vesicles from umbilical cord blood-derived MSC protect against ischemic acute kidney injury, a feature that is lost after inflammatory conditioning. J Extracell Vesicles 2, (2013).
     
  • Suominen, M. I. et al. Survival benefit with radium-223 dichloride in a mouse model of breast cancer bone metastasis. J Natl Cancer Inst 105, 908–916 (2013).
     
  • Sahlberg, K. K. et al. The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells. Mol Oncol 7, 392–401 (2013).
     
  • Radivojac, P. et al. A large-scale evaluation of computational protein function prediction. Nat Methods 10, 221–227 (2013).
     
  • Nikolaev, S. I. et al. A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas. Cancer Res 72, 6279–6289 (2012).
     
  • Högnäs, G. et al. Cytokinesis failure due to derailed integrin traffic induces aneuploidy and oncogenic transformation in vitro and in vivo. Oncogene 31, 3597–3606 (2012).
     
  • Vainio, P. et al. Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer. Prostate 72, 789–802 (2012).
     
  • Pollari, S. et al. Heparin-like polysaccharides reduce osteolytic bone destruction and tumor growth in a mouse model of breast cancer bone metastasis. Mol Cancer Res 10, 597–604 (2012).
     
  • Mamo, A. et al. An integrated genomic approach identifies ARID1A as a candidate tumor-suppressor gene in breast cancer. Oncogene 31, 2090–2100 (2012).
     
  • Nykyri, J. et al. Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. PLoS Pathog. 8, e1003013 (2012).
     
  • Koskela, H. L. M. et al. Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med 366, 1905–1913 (2012).
     
  • Kangaspeska, S. et al. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One 7, e48745 (2012).
     
  • Tollenaere, C. et al. SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection. PLoS One 7, e52492 (2012).
     
  • Ojala, K., Kilpinen, S. & Kallioniemi, O. Abstract 2984: A comprehensive bioinformatic analysis of the representativity of 460 cancer cell lines as model systems for 88 different clinical cancer types. in Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2984 (2012). doi:10.1158/1538-7445.AM2012-2984
     
  • Magnusson, K. et al. SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas. Am J Surg Pathol 35, 937–948 (2011).
     
  • Turpeinen, H. et al. Identification of proprotein convertase substrates using genome-wide expression correlation analysis. BMC Genomics 12, 618 (2011).
     
  • Pollari, S. et al. Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis. Breast Cancer Res Treat 125, 421–430 (2011).
     
  • Edgren, H., Kangaspeska, S. & Kallioniemi, O. KRAS oncogene rearrangements and gene fusions: unexpected rare encounters in late-stage prostate cancers. Cancer Discov 1, 12–13 (2011).
     
  • Östling, P. et al. Systematic analysis of microRNAs targeting the androgen receptor in prostate cancer cells. Cancer Res 71, 1956–1967 (2011).
     
  • Seppälä, E. H. et al. LGI2 truncation causes a remitting focal epilepsy in dogs. PLoS Genet. 7, e1002194 (2011).
     
  • Ojala, K. A., Kilpinen, S. K. & Kallioniemi, O. P. Classification of unknown primary tumors with a data-driven method based on a large microarray reference database. Genome Med 3, 63 (2011).
     
  • Edgren, H. et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 12, R6 (2011).
     
  • Kallio, H. et al. Characterization of non-specific cytotoxic cell receptor protein 1: a new member of the lectin-type subfamily of F-box proteins. PLoS One 6, e27152 (2011).
     
  • Mpindi, J.-P. et al. GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets. PLoS One 6, e17259 (2011).
     
  • Kilpinen, S., Ojala, K. & Kallioniemi, O. Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. BioData Mining (2010).
     
  • Wolf, M. et al. Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication. BMC Cancer 10, 181 (2010).
     
  • Main, H. et al. Interactions between Notch- and hypoxia-induced transcriptomes in embryonic stem cells. Exp Cell Res 316, 1610–1624 (2010).
     
  • Rantala, J. K. et al. Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2. Neoplasia 12, 877–888 (2010).
     
  • Kilpinen, S., Ojala, K. & Kallioniemi, O. Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One 5, e15068 (2010).
     
  • McBride, D. J. et al. Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes Chromosomes Cancer 49, 1062–1069 (2010).
     
  • Sugiyama, N. et al. Fibroblast growth factor receptor 4 regulates tumor invasion by coupling fibroblast growth factor signaling to extracellular matrix degradation. Cancer Res 70, 7851–7861 (2010).
     
  • Kilpinen, S., Ojala, K. & Kallioniemi, O. Analysis of gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One (2010).
     
  • Leo, J. C. et al. First analysis of a bacterial collagen-binding protein with collagen Toolkits: promiscuous binding of YadA to collagens may explain how YadA interferes with host processes. Infect. Immun. 78, 3226–3236 (2010).
     
  • Lund, P., Kilpinen, S., Kallioniemi, O. & Gronemmeyer, H. Oncogene-Dependent Silencing of Tumor-Selective Apoptogenic TRAIL by DNA Hypermethylation is Antagonized by Decitabine. (Submitted) (2009).
     
  • Autio, R. et al. Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics 10 Suppl 1, S24 (2009).
     
  • Koski, T. A. et al. Array comparative genomic hybridization identifies a distinct DNA copy number profile in renal cell cancer associated with hereditary leiomyomatosis and renal cell cancer. Genes Chromosomes Cancer 48, 544–551 (2009).
     
  • Muggerud, A. A. et al. Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell line. BMC Medical Genomics 2, 26 (2009).
     
  • Côme, C. et al. CIP2A is associated with human breast cancer aggressivity. Clin Cancer Res 15, 5092–5100 (2009).
     
  • Brennan, D. J. et al. The transcription factor Sox11 is a prognostic factor for improved recurrence-free survival in epithelial ovarian cancer. Eur J Cancer 45, 1510–1517 (2009).
     
  • Turunen, J. et al. Mitochondrial aspartate/glutamate carrier SLC25A12 gene is associated with autism. Autism Res 1, 189–192 (2008).
     
  • Varjosalo, M. et al. Application of active and kinase-deficient kinome collection for identification of kinases regulating hedgehog signaling. Cell 133, 537–548 (2008).
     
  • Pellinen, T. et al. Integrin trafficking regulated by Rab21 is necessary for cytokinesis. Dev Cell 15, 371–385 (2008).
     
  • Sundvall, M. et al. Role of ErbB4 in breast cancer. J Mammary Gland Biol Neoplasia 13, 259–268 (2008).
     
  • Mattsson, J. M., Laakkonen, P., Kilpinen, S., Stenman, U.-H. & Koistinen, H. Gene expression changes associated with the anti-angiogenic activity of kallikrein-related peptidase 3 (KLK3) on human umbilical vein endothelial cells. Biol. Chem. 389, 765–771 (2008).
     
  • Järvinen, A.-K. et al. 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).
     
  • Kilpinen, S. et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol 9, R139 (2008).
     
  • Wicker, N. et al. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 8, 84 (2007).
     
  • Borgenström, M. et al. O-sulfated bacterial polysaccharides with low anticoagulant activity inhibit metastasis. Semin. Thromb. Hemost. 33, 547–556 (2007).
     
  • Oyajobi, B. O. et al. Detection of myeloma in skeleton of mice by whole-body optical fluorescence imaging. Mol Cancer Ther 6, 1701–1708 (2007).
     
  • Edgren, H. & Kallioniemi, O. Integrated breast cancer genomics. Cancer Cell 10, 453–454 (2006).
     
  • Iljin, K. et al. TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming. Cancer Res 66, 10242–10246 (2006).
     
  • Wolf, M. et al. NMD microarray analysis for rapid genome-wide screen of mutated genes in cancer. Cell. Oncol. 27, 169–173 (2005).
     
  • Berger, J. A. et al. Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5, 194 (2004).
     
  • Jarvinen, A. et al. Are data from different gene expression microarray platforms comparable? Genomics 83, 1164–1168 (2004).
     
  • Kettunen, E. et al. Differentially expressed genes in nonsmall cell lung cancer: expression profiling of cancer-related genes in squamous cell lung cancer. Cancer Genet Cytogenet 149, 98–106 (2004).
     
  • Hautaniemi, S. et al. A novel strategy for microarray quality control using Bayesian networks. Bioinformatics 19, 2031–2038 (2003).
     
  • Nagy, B. et al. Abnormal expression of apoptosis-related genes in haematological malignancies: overexpression of MYC is poor prognostic sign in mantle cell lymphoma. Br J Haematol 120, 434–441 (2003).
     
  • Repo, H. et al. CD14 and TNfa promoter polymorphisms in patients with acute arthritis. Special reference to development of chronic spondyloarthropathy. Scand. J. Rheumatol. 31, 355–361 (2002).