with FFGC coauthors

2017

  • 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. RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Stem Cell Rep. 2017 09 May;8(5):1442–1454. IF:7.023 [NGS, qPCR]
  • Lund RJ, Huhtinen K, Salmi J, Rantala J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Sci Rep. 2017 May 4;7(1):1469. IF:5.228 [NGS, qPCR]

2016

  • Salomäki-Myftari H, Vähätalo LH, Ailanen L, Pietilä S, Laiho A, Hänninen A, Pursiheimo JP, Munukka E, Rintala A, Savontaus E, Pesonen U, Koulu M. Neuropeptide Y Overexpressing Female and Male Mice Show Divergent Metabolic but Not Gut Microbial Responses to Prenatal Metformin Exposure. PLoS One. 2016 Sep 28;11(9):e0163805. doi: 10.1371/journal.pone.0163805. IF: 3.057 [Bioinformatics]
  • Mokkala K, Röytiö H, Munukka E, Pietilä S, Ekblad U, Rönnemaa T, Eerola E, Laiho A, Laitinen K. Gut Microbiota Richness and Composition and Dietary Intake of Overweight Pregnant Women Are Related to Serum Zonulin Concentration, a Marker for Intestinal Permeability. J Nutr. 2016 Sep;146(9):1694-700. doi: 10.3945/jn.116.235358.  IF: 3.740 [Bioinformatics]
  • Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund RJ. Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Stem Cell Res. 2016 Sep 24;17(3):498-503. doi: 10.1016/j.scr.2016.09.025. IF: 3.892 [NGS, qPCR]
  • Toivonen R, Kong L, Rasool O, Lund RJ, Lahesmaa R, Hänninen A. 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. J Immunol. 2016 Jun 1;196(11):4750-9. IF: 4.985 [NGS]
  • 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. Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Sci Rep. 2016 Feb 25;6:22190. IF: 5.578 [NGS]
  • Vehniäinen ER, Bremer K, Scott JA, Junttila S, Laiho A, Gyenesei A, Hodson PV, Oikari AO. Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos. Environ Toxicol Pharmacol. 2016 Jan;41:95-102. doi: 10.1016/j.etap.2015.11.015.  IF: 2.47 [Microarrays]

2015

  • Babu M, Durga Devi T, Mäkinen P, Kaikkonen M, Lesch HP, Junttila S, Laiho A, Ghimire B, Gyenesei A, Ylä-Herttuala S. Differential Promoter Methylation of Macrophage Genes Is Associated With Impaired Vascular Growth in Ischemic Muscles of Hyperlipidemic and Type 2 Diabetic Mice: Genome-Wide Promoter Methylation Study. Circ Res. 2015 Jul 17;117(3):289-99. IF: 11.019 [NGS]
  • Nyman MC, Sainio AO, Pennanen MM, Lund RJ, Vuorikoski S, Sundström JT, Järveläinen HT. Decorin in Human Colon Cancer: Localization In Vivo and Effect on Cancer Cell Behavior In Vitro. J Histochem Cytochem. 2015 Sep;63(9):710-20. IF: 1.959 [meDNA-qPCR]
  • Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. Identification of global regulators of T-helper cell lineage specification. Genome Med. 2015 Nov 20;7(1):122. IF: 5.809 [microarrays, NGS]
  • 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. The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports. 2015 Mar 10;4(3):519-28. IF: 5.365 [microarrays]
  • Budzyńska PM, Niemelä M, Sarapulov AV, Kyläniemi MK, Nera KP, Junttila S, Laiho A, Mattila PK, Alinikula J, Lassila O. IRF4 Deficiency Leads to Altered BCR Signalling Revealed by Enhanced PI3K Pathway, Decreased SHIP Expression and Defected Cytoskeletal Responses. Scand J Immunol. 2015 Nov;82(5):418-28. IF: 1.739 [microarrays, qPCR]
  • Vehniäinen ER, Bremer K, Scott JA, Junttila S, Laiho A, Gyenesei A, Hodson PV, Oikari AO. Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos. Environ Toxicol Pharmacol. 2015 Nov 28;41:95-102. IF: 2.084
  • Fischer D, Laiho A, Gyenesei A, Sironen A. Identification of Reproduction-Related Gene Polymorphisms Using Whole Transcriptome Sequencing in the Large White Pig Population. G3 (Bethesda). 2015 Apr 27;5(7):1351-60. IF: 3.198 [NGS]
  • Heikinheimo K, Kurppa KJ, Laiho A, Peltonen S, Berdal A, Bouattour A, Ruhin B, Catón J, Thesleff I, Leivo I, Morgan PR. Early dental epithelial transcription factors distinguish ameloblastoma from keratocystic odontogenic tumor. J Dent Res. 2015 Jan;94(1):101-11. IF: 4.139 [microarrays]
  • Salminen TS, Vesala L, Laiho A, Merisalo M, Hoikkala A, Kankare M. Seasonal gene expression kinetics between diapause phases in Drosophila virilis group species and overwintering differences between diapausing and non-diapausing females. Sci Rep. 2015 Jun 11;5:11197. IF: 5.578 [microarrays]
  • Koskinen A, Lehtoranta L, Laiho A, Laine J, Kääpä P, Soukka H. Maternal diabetes induces changes in the umbilical cord gene expression. Placenta. 2015 Jul;36(7):767-74. IF: 3.285 [Microarrays]

2014

  • Noisa P, Lund C, Kanduri K, Lund R, Lähdesmäki H, Lahesmaa R, Lundin K, Chokechuwattanalert H, Otonkoski T, Tuuri T, Raivio T. Notch signaling regulates  the differentiation of neural crest from human pluripotent stem cells. J Cell Sci. (IF 5.32) 2014 May 1;127(Pt 9):2083-94.

  • Laiho A, Elo LL. A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments. PLoS One. (IF 3.534) 2014 Dec 26;9(12):e115964.
  • Heikinheimo K, Kurppa KJ, Laiho A, Peltonen S, Berdal A, Bouattour A, Ruhin B, Catón J, Thesleff I, Leivo I, Morgan PR. Early Dental Epithelial Transcription Factors Distinguish Ameloblastoma from Keratocystic Odontogenic Tumor. J Dent Res. (IF 4.144) 2014 Nov 14.
  • Kumar H, Lund R, Laiho A, Lundelin K, Ley RE, Isolauri E and Salminen S. Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole Genome Methylation Analysis. MBio. (IF: 6.88) 2014 Dec 16;5(6).
  • 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. Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. Genome Med. (IF: 4.94) 2014 Oct 28;6(10):88.
  • Osterback R, Koskinen S, Merilahti P, Pursiheimo JP, Blomqvist S, Roivainen M, Laiho A, Susi P, Waris M. Genome Sequence of Coxsackievirus A6, Isolated during a Hand-Foot-and-Mouth Disease Outbreak in Finland in 2008. Genome Announc. (IF 5.31) 2014 Oct 16;2
  • A. Sironen, D. Fischer, A. Laiho, A. Gyenesei and J. Vilkki. A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs. Animal Genetics. (IF 2.21) Volume 45, Issue 4, August 2014, Pages: 500–507.
  • Toivonen RK, Emani R, Munukka E, Rintala A, Laiho A, Pietilä S, Pursiheimo JP, Soidinsalo P, Linhala M, Eerola E, Huovinen P, Hänninen A. Fermentable fibres condition colon microbiota and promote diabetogenesis in NOD mice. Diabetology.  (IF 3.71) 2014 Jul 17.
  • Halimaa P, Lin YF, Ahonen VH, Blande D, Clemens S, Gyenesei A, Häikiö E, Kärenlampi SO, Laiho A, Aarts MG, Pursiheimo JP, Schat H, Schmidt H, Tuomainen MH, Tervahauta AI. Gene expression differences between Noccaea caerulescens ecotypes help to identify candidate genes for metal phytoremediation. Environ Sci Technol. (IF 5.48) 2014 Mar 18;48(6):3344-53.
  • Pavicic W, Nieminen TT, Gylling A, Pursiheimo JP, Laiho A, Gyenesei A, Järvinen HJ, Peltomäki P. Promoter-specific alterations of APC are a rare cause for mutation-negative familial adenomatous polyposis. Genes Chromosomes Cancer. (IF 3.84) 2014 Oct;53(10):857-64.
  • Martiskainen H, Viswanathan J, Nykänen NP, Kurki M, Helisalmi S, Natunen T, Sarajärvi T, Kurkinen KM, Pursiheimo JP, Rauramaa T, Alafuzoff I, Jääskeläinen JE, Leinonen V, Soininen H, Haapasalo A, Huttunen HJ, Hiltunen M. Transcriptomics and mechanistic elucidation of Alzheimer’s disease risk genes in the in the brain and in vitro models. Neurobiol Aging. 2014 Sep 6. pii: S0197-4580(14)00598-3. IF 4.85. [microarrays]

2013

  • Junttila S, Laiho A, Gyenesei A, Rudd S. Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. BMC Genomics. 2013 Dec 10;14:870.
  • Mohazab L, Koivisto L, Jiang G, Kytömäki L, Haapasalo M, Owen GR, Wiebe C, Xie Y, Heikinheimo K, Yoshida T, Smith CE, Heino J, Häkkinen L, McKee MD, Larjava H. Critical role for αvβ6 integrin in enamel biomineralization. J Cell Sci. 2013 Feb 1;126(Pt 3):732-44.
  • Seyednasrollah F, Laiho A, Elo LL. Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform. 2013 Dec 2. [Epub ahead of print] PMID: 24300110
  • Hyytiäinen H, Juntunen P, Scott T, Kytömäki L, Venho R, Laiho A, Junttila S, Gyenesei A, Revez J, Hänninen ML. Effect of ciprofloxacin exposure on DNA repair mechanisms in Campylobacter jejuni. Microbiology. 2013 Dec;159(Pt 12):2513-23.
  • Sittig E, Kauko O, Salmenniemi U, Laiho A, Kairisto V, Johansson J, Itala-Remes M, Westermarck J (2013) Novel molecular markers for acute myeloid leukaemia disease activity. Eur J Cancer 49:S840-S840.
  • Närvä E, Pursiheimo JP, Laiho A, Rahkonen N, Emani MR, Viitala M, Laurila K, Sahla R, Lund R, Lähdesmäki H, Jaakkola P, Lahesmaa R. Continuous Hypoxic Culturing of Human Embryonic Stem Cells Enhances SSEA-3 and MYC Levels. PLoS One. 2013 Nov 13;8(11):e78847.
  • 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. ESTOOLS Data@Hand: human stem cell gene expression resource. Nat Methods. 2013 Aug;10(9):814-5. *Equal contribution.
  • Rantanen K*, Pursiheimo JP* , Högel H, Sundström J, Jaakkola PM. p62/SQSTM1 regulates hypoxia response by attenuating PHD3 activity through aggregate sequestration and enhanced degradation. J.Cell Science, accepted. *equal contribution
  • Kämäläinen A, Viswanathan J, Natunen T, Helisalmi S, Kauppinen T, Pikkarainen M, Pursiheimo JP, Alafuzoff I, Kivipelto M, Haapasalo A, Soininen H, Herukka SK, Hiltunen M. GRN Variant rs5848 Reduces Plasma and Brain Levels of Granulin in Alzheimer’s Disease Patients. J Alzheimers Dis. 2013 Jan 1;33(1):23-7.
  • Laiho A, Kotaja N, Gyenesei A, Sironen A. Transcriptome profiling of the murine testis during the first wave of spermatogenesis. PLoS One. 2013 Apr 17;8(4):e61558. doi: 10.1371/journal.pone.0061558.
  • Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Global Chromatin State Analysis Reveals Lineage-Specific Enhancers during the Initiation of Human T helper 1 and T helper 2 Cell Polarization. Immunity. 2013 Jun 27;38(6):1271-84. doi: 10.1016/j.immuni.2013.05.011.
  • Lund R, Emani MR, Barbaric I, Kivinen V, Jones M, Baker D, Gokhale P, Nykter M, Lahesmaa R, Andrews PW. Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases. Stem Cell Research. 2013 Nov;11(3):1022-1036
  • Teittinen KJ, Laiho A, Uusimäki A, Pursiheimo JP, Gyenesei A, Lohi O. Expression of small nucleolar RNAs in leukemic cells.Cell Oncol (Dordr). 2013 Feb;36(1):55-63. doi: 10.1007/s13402-012-0113-5.
  • Natunen T, Parrado AR, Helisalmi S, Pursiheimo JP, Sarajärvi T, Mäkinen P, Kurkinen KM, Mullin K, Alafuzoff I, Haapasalo A, Bertram L, Soininen H, Tanzi RE, Hiltunen M. Elucidation of the BACE1 regulating factor GGA3 in Alzheimer’s disease. J Alzheimers Dis. (IF 3.612) 2013;37(1):217-32.
  • Rantanen K, Pursiheimo JP, Högel H, Miikkulainen P, Sundström J, Jaakkola PM. p62/SQSTM1 regulates cellular oxygen sensing by attenuating PHD3 activity through aggregate sequestration and enhanced degradation. J Cell Sci. (IF 5.3) 2013 Mar 1;126(Pt 5):1144-54.
  • Kämäläinen A, Viswanathan J, Natunen T, Helisalmi S, Kauppinen T, Pikkarainen M, Pursiheimo JP, Alafuzoff I, Kivipelto M, Haapasalo A, Soininen H, Herukka SK, Hiltunen M. GRN variant rs5848 reduces plasma and brain levels of granulin in Alzheimer’s disease patients. J Alzheimers Dis. (IF 3.612) 2013;33(1):23-7.
  • Natunen T, Martiskainen H, Sarajärvi T, Helisalmi S, Pursiheimo JP, Viswanathan J, Laitinen M, Mäkinen P, Kauppinen T, Rauramaa T, Leinonen V, Alafuzoff I, Haapasalo A, Soininen H, Hiltunen M. Effects of NR1H3 genetic variation on the expression of liver X receptor alpha and the progression of Alzheimer’s disease. PLoS One. (IF 3.534) 2013 Nov 20;8(11):e80700.

2012

  • Levula M, Oksala N, Airla N, Zeitlin R, Salenius JP, Järvinen O, Venermo M, Partio T, Saarinen J, Somppi T, Suominen V, Virkkunen J, Hautalahti J, Laaksonen R, Kähönen M, Mennander A, Kytömäki L, Soini JT, Parkkinen J, Pelto-Huikko M, Lehtimäki T. Genes involved in systemic and arterial bed dependent atherosclerosis–Tampere Vascular study. Plos One. 2012;7(4):e33787. Epub 2012 Apr 11.
  • Vesala L, Salminen TS, Laiho A, Hoikkala A, Kankare M. Cold tolerance and cold-induced modulation of gene expression in two Drosophila virilis group species with different distributions. Insect Mol Biol. 2012 Feb;21(1):107-18.
  • Teittinen KJ, Grönroos T, Parikka M, Junttila S, Uusimäki A, Laiho A, Korkeamäki H, Kurppa K, Turpeinen H, Pesu M, Gyenesei A, Rämet M, Lohi O. SAP30L (Sin3A-associated protein 30-like) is involved in regulation of cardiac development and hematopoiesis in zebrafish embryos. J Cell Biochem. 2012 Dec;113(12):3843-52.
  • Junttila S, Rudd S. Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data. BMC Genomics. 2012 Oct 30;13:575
  • Laiho A, Kiraly A, Gyenesei A. GeneFuncster: A Web Tool for Gene Functional Enrichment Analysis and Visualisation. In volume of Computational System Biology, Lecture Notes in Computer Science series.
  • Gyenesei A, Moody J, Laiho A, Semple CA, Haley CS, Wei WH. BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies. Nucleic Acids Research 2012, 40:W628-32
  • Gyenesei A, Moody J, Semple CA, Haley CS, Wei WH. High-throughput analysis of epistasis in genome-wide association studies with BiForce. Bioinformatics 2012, 28(15):1957-64
  • Kiraly A, Laiho A, Gyenesei A. Biclustering of high-throughput gene expression data with BiclusterMiner. IEEE 12th International Conference on Data Mining Workshops, 2012, pp:131-138
  • Wei WH, Hemani G, Gyenesei A, Vitart V, Navarro P, Hayward C, Cabrera CP, Huffman JE, Knott SA, Hicks AA, Rudan I, Pramstaller PP, Wild SH, Wilson JF, Campbell H, Hastie ND, Wright AF, Haley CS. Genome-wide analysis of epistasis in body mass index using multiple human populations. European Journal of  Human Genetics 2012, 20(8):857-62
  • Lund RJ, Nikula T, Rahkonen N, Närvä E, Baker D, Harrison N, Andrews P, Otonkoski T, Lahesmaa R. High-throughput karyotyping of human pluripotent stem cells. Stem Cell Res. 2012 Nov;9(3):192-5.
  • Närvä E*, Rahkonen N*, Emani MR*, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R. RNA-Binding Protein L1TD1 Interacts with LIN28 via RNA and is Required for Human Embryonic Stem Cell Self-Renewal and Cancer Cell Proliferation. Stem Cells 2012 30(3):452-60. *Equal contribution.
  • Benson MJ, Aijö T, Chang X, Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo JP, Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H, Rao A. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16252-7.

 2011

  • Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, Lahesmaa R, Orkin SH, Rodig SJ, Daley GQ, Rao A. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell. 2011 Feb 4;8(2):200-13
  • Alinikula J, Nera KP, Junttila S, Lassila O. Alternate pathways for Bcl6-mediated regulation of B cell to plasma cell differentiation. Eur J Immunol. 2011 Aug;41(8):2404-13.
  • Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, GYENESEI A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dollé P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biology 2011, 9(1):e1000582

2010

  • Koskinen A, Laiho A, Lukkarinen H, Kääpä P, Soukka H. Maternal Hyperglycemia Modifies Extracellular Matrix Signaling Pathways in Neonatal Rat Lung. Neonatology. 2010 Nov 4;98(4):387-396.
  • Akerfelt M, Vihervaara A, Laiho A, Conter A, Christians ES, Sistonen L, Henriksson E. Heat shock transcription factor 1 localizes to sex chromatin during meiotic repression. J Biol Chem. 2010 Nov 5;285(45):34469-76. 
  • Oksala N, Levula M, Pelto-Huikko M, Kytömäki L, Soini JT, Salenius J, Kähönen M, Karhunen PJ, Laaksonen R, Parkkila S, Lehtimäki T. Carbonic anhydrases II and XII are up-regulated in osteoclast-like cells in advanced human atherosclerotic plaques-Tampere Vascular Study. Ann Med. 2010 Jul;42(5):360-70.
  • Niinisalo P, Oksala N, Levula M, Pelto-Huikko M, Järvinen O, Salenius JP, Kytömäki L, Soini JT, Kähönen M, Laaksonen R, Hurme M, Lehtimäki T. Activation of indoleamine 2,3-dioxygenase-induced tryptophan degradation in advanced atherosclerotic plaques: Tampere vascular study. Ann Med. 2010;42(1):55-63.
  • Kankare M, Salminen T, Laiho A, Vesala L, Hoikkala A. Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study. BMC Ecol. 2010 Feb 1;10:3. 
  • Sirén A, Polvi A, Chahine L, Labuda M, Bourgoin S, Anttonen AK, Kousi M, Hirvonen K, Simola KO, Andermann E, Laiho A, Soini J, Koivikko M, Laaksonen R, Pandolfo M, Lehesjoki AE. Suggestive evidence for a new locus for epilepsy with heterogeneous phenotypes on chromosome 17q. Epilepsy Res. 2010 Jan;88(1):65-75. 

2009

  • Huvila J, Brandt A, Rojas CR, Pasanen S, Talve L, Hirsimäki P, Fey V, Kytömäki L, Saukko P, Carpén O, Soini JT, Grénman S, Auranen A. Gene Expression profiling og endometrial adenocarcinomas reveals increased apolipoprotein E expression in poorly differentiated tumors. Int J Gynecol Cancer. 2009 Oct;19(7):1226-31.
  • Oksala N, Levula M, Airla N, Pelto-Huikko M, Ortiz RM, Järvinen O, Salenius JP, Ozsait B, Komurcu-Bayrak E, Erginel-Unaltuna N, Huovila AP, Kytömäki L, Soini JT, Kähönen M, Karhunen PJ, Laaksonen R, Lehtimäki T. ADAM-9, ADAM-15, and ADAM-17 are upregulated in macrophages in advanced human atherosclerotic plaques in aorta and carotid and femoral arteries–Tampere vascular study. Ann Med. 2009;41(4):279-90.
  • Levula M, Airla N, Oksala N, Hernesniemi JA, Pelto-Huikko M, Salenius JP, Zeitlin R, Järvinen O, Huovila AP, Nikkari ST, Jaakkola O, Ilveskoski E, Mikkelsson J, Perola M, Laaksonen R, Kytömäki L, Soini JT, Kahonen M, Parkkinen J, Karhunen PJ, Lehtimäki T. ADAM8 and its single nucleotide polymorphism 2662 T/G are associated with advanced atherosclerosis and fatal myocardial infarction: Tampere vascular study. Ann Med. 2009 Jul 2:1-11.

2008

  • Fan YM, Karhunen PJ, Levula M, Ilveskoski E, Mikkelsson J, Kajander OA, Järvinen O, Oksala N, Thusberg J, Vihinen M, Salenius JP, Kytömäki L, Soini JT, Laaksonen R, Lehtimäki T. Expression of sterol regulatory element-binding transcription factor (SREBF) 2 and SREBF cleavage-activating protein (SCAP) in human atheroma and the association of their allelic variants with sudden cardiac death. Thromb J. 2008 Dec 30;6:17
  • Cloke B, Huhtinen K, Fusi L, Kajihara T, Yliheikkilä M, Ho KK, Teklenburg G, Lavery S, Jones MC, Trew G, Kim JJ, Lam EW, Cartwright JE, Poutanen M, Brosens JJ. The androgen and progesterone receptors regulate distinct gene networks and cellular functions in decidualizing endometrium. Endocrinology. 2008 Sep;149(9):4462-74
  • Akerfelt M, Henriksson E, Laiho A, Vihervaara A, Rautoma K, Kotaja N, Sistonen L. Promoter ChIP-chip analysis in mouse testis reveals Y chromosome occupancy by HSF2. Proc. Natl. Acad. Sci. U.S.A. 2008 Aug;105(32):11224-9

2007

  • De Windt A, Rai M, Bernier L, Thelen K, Soini J, Lefebvre C, Chintawar S, Lavigne J, Saarinen L, Kytömäki L, Munzer JS, Lujohann D, Pandolfo M, Davignon J, Seidah NG, Laaksonen R. Gene set enrichment analysis reveals several globally affected pathways due to SKI-1/S1P inhibition in HepG2 cells. DNA Cell Biol. 2007 Nov;26(11):765-72
  • Rodriguez A, Hilvo M, Kytömäki L, Fleming RE, Britton RS, Bacon BR, Parkkila S. Effects of iron loading on muscle: genome-wide mRNA expression profiling in the mouse. BMC Genomics. 2007 ;8():379-0
  • De Windt A, Rai M, Kytömäki L, Thelen KM, Lutjohann D, Bernier L, Davignon J, Soini J, Pandolfo M, Laaksonen R. Gene set enrichment analyses revealed several affected pathways in Niemann-pick disease type C fibroblasts. DNA Cell Biol. 2007 Sep;26(9):665-71
  • Mullin M, Lightfoot K, Clarke R, Miller M, Lahesmaa R, Cantrell D. The RhoA transcriptional program in pre-T cells. FEBS Lett. 2007 Sep;581(22):4309-17
  • Heikkinen E, Kallonen T, Saarinen L, Sara R, King AJ, Mooi FR, Soini JT, Mertsola J, He Q. Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains. PLoS ONE. 2007 ;2(9):0-0

2006

  • Laaksonen R, Katajamaa M, Päivä H, Sysi-Aho M, Saarinen L, Junni P, Lütjohann D, Smet J, Van Coster R, Seppänen-Laakso T, Lehtimäki T, Soini J, Oresic M. A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS ONE. 2006 ;1():0-0
  • Laaksonen R, Katajamaa M, Päivä H, Sysi-Aho M, Saarinen L, Junni P, Lütjohann D, Smet J, Van Coster R, Seppänen-Laakso T, Lehtimäki T, Soini J, Oresic M. A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS ONE. 2006 ;1():0-0
  • Laaksonen R, Katajamaa M, Päivä H, Sysi-Aho M, Saarinen L, Junni P, Lütjohann D, Smet J, Van Coster R, Seppänen-Laakso T, Lehtimäki T, Soini J, Oresic M. A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS One. 2006 Dec 20;1:e97.