Publications
Selected examples
Placental DNA methylation marks are associated with maternal depressive symptoms during early pregnancy. Lund RJ, Kyläniemi M, Pettersson N, Kaukonen R, Konki M, Scheinin NM, Karlsson L, Karlsson H, Ekholm E. Neurobiol Stress. 2021 Jul 31;15:100374.
Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data. Smolander J, Khan S, Singaravelu K, Kauko L, Lund RJ, Laiho A, Elo LL. BMC Genomics. 2021 May 17;22(1):357.
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities. Mehtonen J, Teppo S, Lahnalampi M, Kokko A, Kaukonen R, Oksa L, Bouvy-Liivrand M, Malyukova A, Mäkinen A, Laukkanen S, Mäkinen PI, Rounioja S, Ruusuvuori P, Sangfelt O, Lund R, Lönnberg T, Lohi O, Heinäniemi M. Genome Med. 2020 Nov 20;12(1):99.
Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression. Kaukonen D, Kaukonen R, Polit L, Hennessy BT, Lund R, Madden SF. BMC Med Genomics. 2020 Jul 3;13(1):92
Plasma cell-free DNA methylation marks for episodic memory impairment: a pilot twin study. Konki M, Lindgren N, Kyläniemi M, Venho R, Laajala E, Ghimire B, Lahesmaa R, Kaprio J, Rinne JO & Lund RJ. Sci Rep 10, 14192 (2020).
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.
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.
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.
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.
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.