Search Results - "Lund, Riikka J"

Genetic and epigenetic stability of human pluripotent stem cells by Lund, Riikka J., Närvä, Elisa, Lahesmaa, Riitta

“…Key Points Recent studies that exploit novel high-resolution genome-wide approaches have reported frequent accumulation of genomic and epigenomic alterations…”
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Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data by Smolander, Johannes, Khan, Sofia, Singaravelu, Kalaimathy, Kauko, Leni, Lund, Riikka J, Laiho, Asta, Elo, Laura L

“…Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method…”
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DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer by Lund, Riikka J., Huhtinen, Kaisa, Salmi, Jussi, Rantala, Juha, Nguyen, Elizabeth V., Moulder, Robert, Goodlett, David R., Lahesmaa, Riitta, Carpén, Olli

“…High-grade serous ovarian cancer is the most common ovarian cancer type. Although the combination of surgery and platinum-taxane chemotherapy provide an…”
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LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis by Malonzo, Maia H, Halla-Aho, Viivi, Konki, Mikko, Lund, Riikka J, Lähdesmäki, Harri

“…DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency…”
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Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming by Elo, Laura L., Järvenpää, Henna, Tuomela, Soile, Raghav, Sunil, Ahlfors, Helena, Laurila, Kirsti, Gupta, Bhawna, Lund, Riikka J., Tahvanainen, Johanna, Hawkins, R. David, Orešič, Matej, Lähdesmäki, Harri, Rasool, Omid, Rao, Kanury V., Aittokallio, Tero, Lahesmaa, Riitta

“…Dissecting the molecular mechanisms by which T helper (Th) cells differentiate to effector Th2 cells is important for understanding the pathogenesis of…”
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Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity by Hrdlickova, Barbara, Kumar, Vinod, Kanduri, Kartiek, Zhernakova, Daria V, Tripathi, Subhash, Karjalainen, Juha, Lund, Riikka J, Li, Yang, Ullah, Ubaid, Modderman, Rutger, Abdulahad, Wayel, Lähdesmäki, Harri, Franke, Lude, Lahesmaa, Riitta, Wijmenga, Cisca, Withoff, Sebo

“…Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID),…”
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Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases by Valensisi, Cristina, Andrus, Colin, Buckberry, Sam, Doni Jayavelu, Naresh, Lund, Riikka J., Lister, Ryan, Hawkins, R. David

“…We currently lack a comprehensive understanding of the mechanisms underlying neural tube formation and their contributions to neural tube defects (NTDs)…”
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Placental DNA methylation marks are associated with maternal depressive symptoms during early pregnancy by Lund, Riikka J., Kyläniemi, Minna, Pettersson, Nina, Kaukonen, Riina, Konki, Mikko, Scheinin, Noora M., Karlsson, Linnea, Karlsson, Hasse, Ekholm, Eeva

“…Maternal depressive symptoms during pregnancy are a significant risk factor for adverse developmental and health outcomes of the offspring. The molecular…”
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Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease by Konki, Mikko, Malonzo, Maia, Karlsson, Ida K, Lindgren, Noora, Ghimire, Bishwa, Smolander, Johannes, Scheinin, Noora M, Ollikainen, Miina, Laiho, Asta, Elo, Laura L, Lönnberg, Tapio, Röyttä, Matias, Pedersen, Nancy L, Kaprio, Jaakko, Lähdesmäki, Harri, Rinne, Juha O, Lund, Riikka J

“…Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling…”
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Genome-Wide Identification of Novel Genes Involved in Early Th1 and Th2 Cell Differentiation by Lund, Riikka J, Loytomaki, Maritta, Naumanen, Tiina, Dixon, Craig, Chen, Zhi, Ahlfors, Helena, Tuomela, Soile, Tahvanainen, Johanna, Scheinin, Joonas, Henttinen, Tiina, Rasool, Omid, Lahesmaa, Riitta

“…Th cell subtypes, Th1 and Th2, are involved in the pathogenesis or progression of many immune-mediated diseases, such as type 1 diabetes and asthma,…”
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RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells by Lund, Riikka J., Rahkonen, Nelly, Malonzo, Maia, Kauko, Leni, Emani, Maheswara Reddy, Kivinen, Virpi, Närvä, Elisa, Kemppainen, Esko, Laiho, Asta, Skottman, Heli, Hovatta, Outi, Rasool, Omid, Nykter, Matti, Lähdesmäki, Harri, Lahesmaa, Riitta

“…POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms not known in…”
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Early Target Genes of IL-12 and STAT4 Signaling in Th Cells by Lund, Riikka J, Chen, Zhi, Scheinin, Joonas, Lahesmaa, Riitta

“…IL-12 signaling through STAT4 is essential for induction of optimal levels of IFN-gamma production and commitment of Th1 cells. The molecular mechanism that…”
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Umbilical cord blood DNA methylation in children who later develop type 1 diabetes by Laajala, Essi, Kalim, Ubaid Ullah, Grönroos, Toni, Rasool, Omid, Halla-aho, Viivi, Konki, Mikko, Kattelus, Roosa, Mykkänen, Juha, Nurmio, Mirja, Vähä-Mäkilä, Mari, Kallionpää, Henna, Lietzén, Niina, Ghimire, Bishwa R., Laiho, Asta, Hyöty, Heikki, Elo, Laura L., Ilonen, Jorma, Knip, Mikael, Lund, Riikka J., Orešič, Matej, Veijola, Riitta, Lähdesmäki, Harri, Toppari, Jorma, Lahesmaa, Riitta

“…Aims/hypothesis Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim…”
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Activation of Plasmacytoid Dendritic Cells in Colon-Draining Lymph Nodes during Citrobacter rodentium Infection Involves Pathogen-Sensing and Inflammatory Pathways Distinct from Conventional Dendritic Cells by Toivonen, Raine, Kong, Lingjia, Rasool, Omid, Lund, Riikka J, Lahesmaa, Riitta, Hänninen, Arno

“…Dendritic cells (DCs) bear the main responsibility for initiation of adaptive immune responses necessary for antimicrobial immunity. In the small intestine,…”
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Decorin in Human Colon Cancer: Localization In Vivo and Effect on Cancer Cell Behavior In Vitro by Nyman, Marie C., Sainio, Annele O., Pennanen, Mirka M., Lund, Riikka J., Vuorikoski, Sanna, Sundström, Jari T. T., Järveläinen, Hannu T.

“…Decorin is generally recognized as a tumor suppressing molecule. Nevertheless, although decorin has been shown to be differentially expressed in malignant…”
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Kinetics and STAT4‐ or STAT6‐mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells by Lund, Riikka J., Ylikoski, Emmi K., Aittokallio, Tero, Nevalainen, Olli, Lahesmaa, Riitta

“…Many genes implicated in Th1 and Th2 differentiation have been identified in both human and mouse. However, the functional roles and hierarchy of these factors…”
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Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells by Konki, Mikko, Pasumarthy, Kalyan, Malonzo, Maia, Sainio, Annele, Valensisi, Cristina, Söderström, Mirva, Emani, Maheswara Reddy, Stubb, Aki, Närvä, Elisa, Ghimire, Bishwa, Laiho, Asta, Järveläinen, Hannu, Lahesmaa, Riitta, Lähdesmäki, Harri, Hawkins, R. David, Lund, Riikka J.

“…Epigenomic regulation is likely to be important in the maintenance of genomic integrity of human pluripotent stem cells, however, the mechanisms are unknown…”
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High-throughput karyotyping of human pluripotent stem cells by Lund, Riikka J, Nikula, Tuomas, Rahkonen, Nelly, Närvä, Elisa, Baker, Duncan, Harrison, Neil, Andrews, Peter, Otonkoski, Timo, Lahesmaa, Riitta

“…Genomic integrity of human pluripotent stem cell (hPSC) lines requires routine monitoring. We report here that novel karyotyping assay, utilizing bead-bound…”
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Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases by Lund, Riikka J, Emani, Maheswara Reddy, Barbaric, Ivana, Kivinen, Virpi, Jones, Mark, Baker, Duncan, Gokhale, Paul, Nykter, Matti, Lahesmaa, Riitta, Andrews, Peter W

“…Genomic abnormalities may accumulate in human embryonic stem cells (hESCs) during in vitro maintenance. Characterization of the mechanisms enabling survival…”
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Expression of human pim family genes is selectively up‐regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation by Aho, Teija L. T., Lund, Riikka J., Ylikoski, Emmi K., Matikainen, Sampsa, Lahesmaa, Riitta, Koskinen, Päivi J.

“…Summary Cytokines are the most important inducers of T helper (Th) cell differentiation. Interleukin‐12 (IL‐12) and interferon‐α (IFN‐α) are responsible for…”
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