Publications

    Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease. Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ. Clin Epigenetics. 2019 Sep 2;11(1):130.

    Early Detection of Peripheral Blood Cell Signature in Children Developing β-Cell Autoimmunity at a Young Age. Kallionpää H, Somani J, Tuomela S, Ullah U, de Albuquerque R, Lönnberg T, Komsi E, Siljander H, Honkanen J, Härkönen T, Peet A, Tillmann V, Chandra V, Anagandula MK, Frisk G, Otonkoski T, Rasool O, Lund R, Lähdesmäki H, Knip M, Lahesmaa R. Diabetes. 2019 Oct;68(10):2024-2034.

    LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis. Maia Aisha Honculada Malonzo, Viivi Halla-Aho, Mikko Konki, Riikka Lund, Harri Lähdesmäki. BioRxiv. 2018. doi: https://doi.org/10.1101/444711.

    Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter. Lund RJ, Osmala M, Malonzo M, Lukkarinen M, Leino A, Salmi J, Vuorikoski S, Turunen R, Vuorinen T, Akdis C, Lähdesmäki H, Lahesmaa R, Jartti T. Allergy. 2018 Aug;73(8):1735-1740.

    The impact of probiotic supplementation during pregnancy on DNA methylation of obesity-related genes in mothers and their children. Vähämiko S, Laiho A, Lund R, Isolauri E, Salminen S, Laitinen K. Eur J Nutr. 2018 Jan 3.

    Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements. Pasumarthy KP, Jayavelu ND, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. Stem Cell Rep. 2017 Sept 12;9:1-17.

    Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. Cell Rep. 2017 Aug 8;20(6):1448-1462.

    RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R. Stem Cell Rep. 2017 09 May;8(5):1442–1454.

    DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Lund RJ, Huhtinen K, Salmi J, Rantala J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. Sci Rep. 2017 May 4;7(1):1469.

    Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund R. Stem Cell Res. 2016 Nov;17(3):498-503.

    Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ. Sci Rep. 2016 Feb 25;6:22190.

    Decorin in Human Colon Cancer: Localization In Vivo and Effect on Cancer Cell Behavior In Vitro. Nyman MC, Sainio AO, Pennanen MM, Lund RJ, Vuorikoski S, Sundström JT, Järveläinen HT. J Histochem Cytochem. 2015 Sep;63(9):710-20.

    The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Emani MR, Närvä E, Stubb A, Chakroborty D, Viitala M, Rokka A, Rahkonen N, Moulder R, Denessiouk K, Trokovic R, Lund R, Elo LL, Lahesmaa R. Stem Cell Reports. 2015 Mar 10;4(3):519-28.

    Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. Kumar H, Lund R, Laiho A, Lundelin K, Ley RE, Isolauri E, Salminen S. MBio. 2014 Dec 16;5(6). pii: e02113-14.

    Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. Hrdlickova B, Kumar V, Kanduri K, Zhernakova DV, Tripathi S, Karjalainen J, Lund RJ, Li Y, Ullah U, Modderman R, Abdulahad W, Lähdesmäki H, Franke L, Lahesmaa R, Wijmenga C, Withoff S. Genome Med. 2014 Oct 28;6(10):88.

    Notch signaling regulates the differentiation of neural crest from human pluripotent stem cells. Noisa P, Lund C, Kanduri K, Lund R, Lähdesmäki H, Lahesmaa R, Lundin K, Chokechuwattanalert H, Otonkoski T, Tuuri T, Raivio T. J Cell Sci. 2014 May 1;127(Pt 9):2083-94.

    Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels. Närvä E, Pursiheimo JP, Laiho A, Rahkonen N, Emani MR, Viitala M, Laurila K, Sahla R, Lund R, Lähdesmäki H, Jaakkola P, Lahesmaa R. PLoS One. 2013 Nov 13;8(11):e78847.

    Lack of decorin expression by human bladder cancer cells offers new tools in the therapy of urothelial malignancies. Sainio A, Nyman M, Lund R, Vuorikoski S, Boström P, Laato M, Boström PJ, Järveläinen H. PLoS One. 2013 Oct 11;8(10):e76190.

    A novel feeder-free culture system for human pluripotent stem cell culture and induced pluripotent stem cell derivation. Vuoristo S, Toivonen S, Weltner J, Mikkola M, Ustinov J, Trokovic R, Palgi J, Lund R, Tuuri T, Otonkoski T. PLoS One. 2013 Oct 2;8(10):e76205.

    ESTOOLS Data@Hand: human stem cell gene expression resource. Kong L, Aho KL, Granberg K, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Närvä E, Yli-Harja O, Andrews PW, Nykter M, Lahesmaa R, Roos C, Autio R. Nat Methods. 2013 Sep;10(9):814-5.

    Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases. Lund RJ, Emani MR, Barbaric I, Kivinen V, Jones M, Baker D, Gokhale P, Nykter M, Lahesmaa R, Andrews PW. Stem Cell Res. 2013 Nov;11(3):1022-36.

    Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Immunity. 2013 Jun 27;38(6):1271-84.

    Genetic and epigenetic stability of human pluripotent stem cells. Lund RJ, Närvä E, Lahesmaa R. Nat Rev Genet. 2012 Oct;13(10):732-44. Review.

    High-throughput karyotyping of human pluripotent stem cells. Lund RJ, Nikula T, Rahkonen N, Närvä E, Baker D, Harrison N, Andrews P, Otonkoski T, Lahesmaa R. Stem Cell Res. 2012 Nov;9(3):192-5.

    RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R. Stem Cells. 2012 Mar;30(3):452-60.

    Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Elo LL, Järvenpää H, Tuomela S, Raghav S, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. Immunity. 2010 Jun 25;32(6):852-62.