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Selected publications by the core facility users

2023

Bhattacharya, D., Theodoropoulos, J., Nurmi, K., Juutilainen, T., Eklund, K. K., Koivuniemi, R., Kelkka, T., Mustjoki, S. & Lönnberg, T. (2023). Single-cell characterisation of tissue homing CD4+ and CD8+ T cell clones in immune-mediated refractory arthritis. J Immunol (2023) 210 (1_Supplement): 78.10. https://doi.org/10.4049/jimmunol.210.Supp.78.10

Huuhtanen, J., Kasanen, H., Peltola, K., Lönnberg, T., Glumoff, V., Brück, O., … & Mustjoki, S. (2023). Single-cell characterization of anti–LAG-3 and anti–PD-1 combination treatment in patients with melanoma.The Journal of Clinical Investigation, 133(6).

Oras, A., Kallionpää, H., Suomi, T., Koskinen, S., Laiho, A., Elo, L. L., … & Uibo, R. (2023). Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study.Heliyon, 9(2).

Rannikko, H., Bono, P., Hynninen, J., & Hollmén, M. (2023). Bexmarilimab activates human tumor-associated macrophages to support adaptive immune responses in interferon-poor immune microenvironments.Cancer Immunology Research. https://doi.org/10.1158/2326-6066.CIR-23-0350

Suomi, T., Starskaia, I., Kalim, U. U., Rasool, O., Jaakkola, M. K., Grönroos, T., et al. (2023). Gene expression signature predicts rate of type 1 diabetes progression. EBioMedicine, 92. https://doi.org/10.1016/j.ebiom.2023.104625

2022

Kainulainen K, Takabe P, Heikkinen S, Aaltonen N, de la Motte C, Rauhala L, Durst FC, Oikari S, Rahunen E, Ikonen E, Hartikainen JM, Ketola K, Pasonen-Seppänen S. M1 Macrophages Induce Protumor Inflammation in Melanoma Cells through TNFR-NF-kB Signaling. J. Invest. Dermatol. 2022; 142:3041-3051.e10. https://doi.org/10.1016/j.jid.2022.04.024.

Kietz C, Mohan AK, Pollari V, Tuominen IE, Ribeiro PS, Meier P, Meinander A. Drice restrains Diap2-mediated inflammatory signalling and intestinal inflammation. Cell Death Differ. 2022 Jan;29(1):28-39. doi: 10.1038/s41418-021-00832-w. Epub 2021 Jul 14. PMID: 34262145; PMCID: PMC8738736.

Laajala, E., Kalim, U.U., Grönroos, T. et al. Umbilical cord blood DNA methylation in children who later develop type 1 diabetes. Diabetologia. 2022 Jun; 65, 1534–1540. https://doi.org/10.1007/s00125-022-05726-1.

Starskaia, I., Laajala, E., Grönroos, T. et al. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia. 2022 Feb; 65, 844–860. https://doi.org/10.1007/s00125-022-05657-x.

Suomi T, Kalim UU, Rasool O, Laiho A, Kallionpää H, Vähä-Mäkilä M, Nurmio M, Mykkänen J, Härkönen T, Hyöty H, Ilonen J, Veijola R, Toppari J, Knip M, Elo LL, Lahesmaa R. Type 1 Diabetes in Children With Genetic Risk May Be Predicted Very Early With a Blood miRNA. Diabetes Care. 2022 Apr 1;45(4):e77-e79. doi: 10.2337/dc21-2120. PMID: 35134118; PMCID: PMC9016735.

Viiklepp K, Nissinen L, Ojalil M, Riihilä P, Kallajoki M, Meri S, Heino J, Kähäri V-M. C1r Upregulates Production of Matrix Metalloproteinase-13 and Promotes Invasion of Cutaneous Squamous Cell Carcinoma. J. Investig. Dermatol. 2022 May:142(5):1478-1488.e9. https://doi.org/10.1016/j.jid.2021.10.008.

Weldenegodguad M, Kantanen J, Peippo J, Pokharel K. Differences in Adipose Gene Expression Profiles between Male and Female Even Reindeer (Rangifer tarandus) in Sakha (Yakutia). Genes. 2022 Sep; 13(9):1645. https://doi.org/10.3390/genes13091645.

2021

Laine A, Nagelli SG, Farrington C, Butt U, Cvrljevic AN, Vainonen JP, Feringa FM, Grönroos TJ, Gautam P, Khan S, Sihto H, Qiao X, Pavic K, Connolly DC, Kronqvist P, Elo LL, Maurer J, Wennerberg K, Medema RH, Joensuu H, Peuhu E, de Visser K, Narla G, Westermarck J. CIP2A Interacts with TopBP1 and Drives Basal-Like Breast Cancer Tumorigenesis. Cancer Res. 2021 Aug 15;81(16):4319-4331. doi: 10.1158/0008-5472.CAN-20-3651. Epub 2021 Jun 18. PMID: 34145035; PMCID: PMC8373817.

Virtakoivu R, Rannikko JH, Viitala M, Vaura F, Takeda A, Lönnberg T, Koivunen J, Jaakkola P, Pasanen A, Shetty S, de Jonge MJA, Robbrecht D, Ma YT, Skyttä T, Minchom A, Jalkanen S, Karvonen MK, Mandelin J, Bono P, Hollmén M. Systemic Blockade of Clever-1 Elicits Lymphocyte Activation Alongside Checkpoint Molecule Downregulation in Patients with Solid Tumors: Results from a Phase I/II Clinical Trial. Clin Cancer Res. 2021 Aug 1;27(15):4205-4220.

Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. Circ Res. 2021 Jul 9;129(2):240-258. doi: 10.1161/CIRCRESAHA.121.318971.

Iftakhar-E-Khuda I, Pessia A, Zheng S, Kankainen M, Kontro M, Karikoski M, Laurila J, Gerke H, Tadayon S, Hollmén M, Tang J, Imhof BA, Salmi M, Jalkanen S. Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation. Cell Mol Life Sci. 2021 Dec;78(23):7851-7872. doi: 10.1007/s00018-021-03977-6. IF: 9.261

Raita Y, Toivonen L, Schuez-Havupalo L, Karppinen S, Waris M, Hoffman KL, Camargo CA Jr, Peltola V, Hasegawa K. Maturation of nasal microbiota and antibiotic exposures during early childhood: a population-based cohort study. Clin Microbiol Infect. 2021 Feb;27(2):283.e1-283.e7. doi: 10.1016/j.cmi.2020.05.033. Epub 2020 Jun 4. PMID: 32505584. IF: 8.067

Stenroos P, Pirttimäki T, Paasonen J, Paasonen E, Salo RA, Koivisto H, Natunen T, Mäkinen P, Kuulasmaa T, Hiltunen M, Tanila H, Gröhn O. Isoflurane affects brain functional connectivity in rats 1 month after exposure. Neuroimage. 2021 Jul 1;234:117987. doi: 10.1016/j.neuroimage.2021.117987. Epub 2021 Mar 21. PMID: 33762218. IF: 6.556

Spinelli L, Marchingo JM, Nomura A, Damasio MP, Cantrell DA. Phosphoinositide 3-Kinase p110 Delta Differentially Restrains and Directs Naïve Versus Effector CD8+ T Cell Transcriptional Programs. Front Immunol. 2021 Jun 18;12:691997. doi: 10.3389/fimmu.2021.691997. PMID: 34220851; PMCID: PMC8250422. IF: 6.429

Wiberg RAW, Tyukmaeva V, Hoikkala A, Ritchie MG, Kankare M. Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana. Mol Ecol. 2021 Aug;30(15):3783-3796. doi: 10.1111/mec.16003. IF: 6.185

Eichin D, Pessia A, Takeda A, Laakkonen J, Bellmann L, Kankainen M, Imhof BA, Stoitzner P, Tang J, Salmi M, Jalkanen S. CD73 contributes to anti-inflammatory properties of afferent lymphatic endothelial cells in humans and mice. Eur J Immunol. 2021 Jan;51(1):231-246. doi: 10.1002/eji.201948432. Epub 2020 Oct 29. PMID: 32970335; PMCID: PMC7821194. IF: 5.532

Lund RJ, Kyläniemi M, Pettersson N, Kaukonen R, Konki M, Scheinin NM, Karlsson L, Karlsson H, Ekholm E. Placental DNA methylation marks are associated with maternal depressive symptoms during early pregnancy. Neurobiol Stress. 2021 Jul 31;15:100374. doi: 10.1016/j.ynstr.2021.100374. PMID: 34401410; PMCID: PMC8353413. IF: 5.441

Weldenegodguad M, Pokharel K, Niiranen L, Soppela P, Ammosov I, Honkatukia M, Lindeberg H, Peippo J, Reilas T, Mazzullo N, Mäkelä KA, Nyman T, Tervahauta A, Herzig KH, Stammler F, Kantanen J. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun Biol. 2021 Oct 7;4(1):1170. doi: 10.1038/s42003-021-02703-z. PMID: 34620965; PMCID: PMC8497613. IF: 5.49

Mäkinen H, van Oers K, Eeva T, Ruuskanen S. The effect of experimental lead pollution on DNA methylation in a wild bird population. Epigenetics. 2021 Aug 9:1-17.  IF: 4.918

Huusko JM, Tiensuu H, Haapalainen AM, Pasanen A, Tissarinen P, Karjalainen MK, Zhang G, Christensen K, Ryckman KK, Jacobsson B, Murray JC, Kingsmore SF, Hallman M, Muglia LJ, Rämet M. Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth. Sci Rep. 2021 Aug 24;11(1):17115. doi: 10.1038/s41598-021-96374-9. IF: 4.380.

Smolander J, Khan S, Singaravelu K, Kauko L, Lund RJ, Laiho A, Elo LL. Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data. BMC Genomics. 2021 May 17;22(1):357. doi: 10.1186/s12864-021-07686-z. PMID: 34000988; PMCID: PMC8130438. IF: 3.969.

Ahmad F, Debes PV, Pukk L, Kahar S, Hartikainen H, Gross R, Vasemägi A. Know your enemy – transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology. 2021 May;148(6):726-739. doi: 10.1017/S003118202100010X. Epub 2021 Jan 22. PMID: 33478602; PMCID: PMC8056827. IF: 3.243

Morrill A, Kaunisto KM, Mlynarek JJ, Sippola E, Vesterinen EJ, Forbes MR. Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ. 2021 Dec 17;9:e12634. doi: 10.7717/peerj.12634. PMID: 35003931; PMCID: PMC8686731. IF: 2.984

Bikash B, Vilja S, Mitchell L, Keith Y, Mikael I, Mikko MK, Jarmo N. Differential regulation of undecylprodigiosin biosynthesis in the yeast-scavenging Streptomyces strain MBK6. FEMS Microbiol Lett. 2021 May 6;368(8):fnab044. doi: 10.1093/femsle/fnab044. PMID: 33881506; PMCID: PMC8102152. IF: 2.51

Buchacher T, Honkimaa A, Välikangas T, Lietzén N, Hirvonen MK, Laiho JE, Sioofy-Khojine AB, Eskelinen EL, Hyöty H, Elo LL, Lahesmaa R. Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells. iScience. 2021 Dec 18;25(1):103653. doi: 10.1016/j.isci.2021.103653. PMID: 35024587; PMCID: PMC8728469. IF: 1.805

2020

Kim D, Park G, Huuhtanen J, et al. Somatic mTOR mutation in clonally expanded T lymphocytes associated with chronic graft versus host disease. Nat Commun. 2020;11(1):2246. Published 2020 May 7. doi:10.1038/s41467-020-16115-w. IF: 11.880

Pokharel K, Weldenegodguad M, Popov R, et al. Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions. Anim Genet. 2019;50(3):217‐227. doi:10.1111/age.12783

Pokharel K, Peippo J, Weldenegodguad M, Honkatukia M, Li MH, Kantanen J. Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep. Genes (Basel). 2020;11(4):415. Published 2020 Apr 10. doi:10.3390/genes11040415

Toivonen L, Schuez-Havupalo L, Karppinen S, et al. Antibiotic treatments during infancy, changes in nasal microbiota, and asthma development: Population-based cohort study [published online ahead of print, 2020 Mar 14]. Clin Infect Dis. 2020;ciaa262. doi:10.1093/cid/ciaa262

Grönroos T, Mäkinen A, Laukkanen S, et al. Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia. Sci Rep. 2020;10(1):2043. Published 2020 Feb 6. doi:10.1038/s41598-020-58970-z

Blasco L, Kahala M, Tampio E, Vainio M, Ervasti S, Rasi S. Effect of Inoculum Pretreatment on the Composition of Microbial Communities in Anaerobic Digesters Producing Volatile Fatty Acids. Microorganisms. 2020;8(4):581. Published 2020 Apr 17. doi:10.3390/microorganisms8040581

Khan MM, Ullah U, Khan MH, et al. CIP2A Constrains Th17 Differentiation by Modulating STAT3 Signaling. iScience. 2020;23(3):100947. doi:10.1016/j.isci.2020.100947

Mottola G, Nikinmaa M, Anttila K. Hsp70s transcription-translation relationship depends on the heat shock temperature in zebrafish. Comp Biochem Physiol A Mol Integr Physiol. 2020 Feb;240:110629. doi: 10.1016/j.cbpa.2019.110629. Epub 2019 Nov 29.

2019

Takeda A, Hollmén M, Dermadi D, Pan J, Brulois KF, Kaukonen R, Lönnberg T, Boström P, Koskivuo I, Irjala H, Miyasaka M, Salmi M, Butcher EC, Jalkanen S. Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils. Immunity. 2019 Sep 17;51(3):561-572.e5. doi: 10.1016/j.immuni.2019.06.027. IF: 21.522

Kettunen K, Boström PJ, Lamminen T, Heinosalo T, West G, Saarinen I, Kaipio K,Rantala J, Albanese C, Poutanen M, Taimen P. Personalized Drug SensitivityScreening for Bladder Cancer Using Conditionally Reprogrammed Patient-derivedCells. Eur Urol. 2019 Oct;76(4):430-434. doi: 10.1016/j.eururo.2019.06.016. IF: 17.298

Tadayon S, Dunkel J, Takeda A, Halle O, Karikoski M, Gerke H, Rantakari P, Virtakoivu R, Pabst O, Salmi M, Hollmén M, Jalkanen S. Clever-1 contributes to lymphocyte entry into the spleen via the red pulp. Sci Immunol. 2019 Mar 29;4(33). pii: eaat0297. doi: 10.1126/sciimmunol.aat0297. IF: 10.551

Viitala M, Virtakoivu R, Tadayon S, Rannikko J, Jalkanen S, Hollmén M. Immunotherapeutic Blockade of Macrophage Clever-1 Reactivates the CD8+ T-cell Response against Immunosuppressive Tumors. Clin Cancer Res. 2019 Jun 1;25(11):3289-3303. doi: 10.1158/1078-0432.CCR-18-3016. Epub 2019 Feb 12. IF: 10.199

Toivonen L, Hasegawa K, Waris M, Ajami NJ, Petrosino JF, Camargo CA Jr, Peltola V. Early nasal microbiota and acute respiratory infections during the first years of life. Thorax. 2019 Jun;74(6):592-599. doi: 10.1136/thoraxjnl-2018-212629. Epub 2019 May 10. PMID 31076501 [nasal swab sample processing] IF: 10.307

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. Early Detection of Peripheral Blood Cell Signature in ChildrenDeveloping β-Cell Autoimmunity at a Young Age. Diabetes. 2019Oct;68(10):2024-2034. doi: 10.2337/db19-0287. IF: 7.199

Mäkelä E, Löyttyniemi E, Salmenniemi U, Kauko O, Varila T, Kairisto V,Itälä-Remes M, Westermarck J. Arpp19 Promotes Myc and Cip2a Expression andAssociates with Patient Relapse in Acute Myeloid Leukemia. Cancers (Basel). 2019 Nov 11;11(11). pii: E1774. doi: 10.3390/cancers11111774. IF: 6.102

Durian G, Jeschke V, Rahikainen M, Vuorinen K, Gollan PJ, Brosche M, SalojärviJ, Glawischnig E, Winter Z, Li S, Noctor G, Aro EM, Kangasjärvi J, Overmyer K,Burow M, Kangasjärvi S. PROTEIN PHOSPHATASE 2A-B’γ controls Botrytis cinerearesistance and developmental leaf senescence. Plant Physiol. 2019 Oct 28. pii:pp.00893.2019. doi: 10.1104/pp.19.00893. IF: 6.305

Valanne S, Salminen TS, Järvelä-Stölting M, Vesala L, Rämet M. Immune-inducible non-coding RNA molecule lincRNA-IBIN connects immunity and metabolism in Drosophila melanogaster PLoS Pathog. 2019 Jan 11;15(1):e1007504. doi: 10.1371/journal.ppat.1007504. IF: 6.158

Konttinen H, Cabral-da-Silva MEC, Ohtonen S, Wojciechowski S, Shakirzyanova A,Caligola S, Giugno R, Ishchenko Y, Hernández D, Fazaludeen MF, Eamen S, Budia MG,Fagerlund I, Scoyni F, Korhonen P, Huber N, Haapasalo A, Hewitt AW, Vickers J,Smith GC, Oksanen M, Graff C, Kanninen KM, Lehtonen S, Propson N, Schwartz MP,Pébay A, Koistinaho J, Ooi L, Malm T. PSEN1ΔE9, APPswe, and APOE4 ConferDisparate Phenotypes in Human iPSC-Derived Microglia. Stem Cell Reports. 2019 Oct8;13(4):669-683. doi: 10.1016/j.stemcr.2019.08.004. IF: 5.499

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. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease. Clin Epigenetics. 2019 Sep2;11(1):130. doi: 10.1186/s13148-019-0729-7. IF: 5.496

Tiensuu H, Haapalainen AM, Karjalainen MK, Pasanen A, Huusko JM, Marttila R, Ojaniemi M, Muglia LJ, Hallman M, Rämet M. Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. PLoS Genet. 2019 Jun 13;15(6):e1008107. doi: 10.1371/journal.pgen.1008107. eCollection 2019 Jun. IF: 5.224

Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M. A multiomic approach to characterize the temporal sequence in Alzheimer’s disease-related pathology. Neurobiol Dis. 2019 Apr;124:454-468. doi: 10.1016/j.nbd.2018.12.009. IF: 5.160

Gubina N, Naudi A, Stefanatos R, Jove M, Scialo F, Fernandez-Ayala DJ,Rantapero T, Yurkevych I, Portero-Otin M, Nykter M, Lushchak O, Navas P, PamplonaR, Sanz A. Essential Physiological Differences Characterize Short- and Long-LivedStrains of Drosophila melanogaster. J Gerontol A Biol Sci Med Sci. 2019 Nov13;74(12):1835-1843. doi: 10.1093/gerona/gly143. IF: 4.711

Rotgers E, Cisneros-Montalvo S, Nurmio M, Toppari J. Retinoblastoma protein represses E2F3 to maintain Sertoli cell quiescence in mouse testis. J Cell Sci. 2019 Jul 15;132(14). pii: jcs229849. doi: 10.1242/jcs.229849. IF: 4.517

Vähämiko S, Laiho A, Lund R, Isolauri E, Salminen S, Laitinen K. The impact ofprobiotic supplementation during pregnancy on DNA methylation of obesity-related genes in mothers and their children. Eur J Nutr. 2019 Feb;58(1):367-377. doi:10.1007/s00394-017-1601-1. IF: 4.449

Miikkulainen P, Högel H, Seyednasrollah F, Rantanen K, Elo LL, Jaakkola PM. Hypoxia-inducible factor (HIF)-prolyl hydroxylase 3 (PHD3) maintains high HIF2A mRNA levels in clear cell renal cell carcinoma. J Biol Chem. 2019 Mar 8;294(10):3760-3771. doi: 10.1074/jbc.RA118.004902. IF: 4.106

Piipponen M, Nissinen L, Riihilä P, Farshchian M, Kallajoki M, Peltonen J, Peltonen S, Kähäri VM. p53-Regulated Long Noncoding RNA PRECSIT Promotes Progression of Cutaneous Squamous Cell Carcinoma via STAT3 Signaling. Am J Pathol. 2019 Dec 12. pii: S0002-9440(19)30856-9. doi: 10.1016/j.ajpath.2019.10.019. IF: 4.069

Ojanen MJT, Uusi-Mäkelä MIE, Harjula SE, Saralahti AK, Oksanen KE, Kähkönen N, Määttä JAE, Hytönen VP, Pesu M, Rämet M. Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio). Sci Rep. 2019 Jan 30;9(1):995. doi: 10.1038/s41598-018-37678-1. IF: 4.011

Yang J, Li X, Cao YH, Pokharel K, Hu XJ, Chen ZH, Xu SS, Peippo J, Honkatukia M, Kantanen J, Li MH. Comparative mRNA and miRNA expression in European mouflon(Ovis musimon) and sheep (Ovis aries) provides novel insights into the geneticmechanisms for female reproductive success. Heredity (Edinb). 2019 Feb;122(2):172-186. doi: 10.1038/s41437-018-0090-1. IF: 3.872

Paatero I, Veikkolainen V, Mäenpää M, Schmelzer E, Belting HG, Pelliniemi LJ, Elenius K. ErbB4 tyrosine kinase inhibition impairs neuromuscular development in zebrafish embryos. Mol Biol Cell. 2019 Jan 15;30(2):209-218. doi: 10.1091/mbc.E18-07-0460. IF: 3.375

Novikova OA, Nazarkina ZK, Cherepanova AV, Laktionov PP, Chelobanov BP, Murashov IS, Deev RV, Pokushalov EA, Karpenko AA, Laktionov PP. Isolation, culturing and gene expression profiling of inner mass cells from stable and vulnerable carotid atherosclerotic plaques. PLoS One. 2019 Jun 26;14(6):e0218892. doi: 10.1371/journal.pone.0218892. IF: 2.776

Stepanova AO, Laktionov PP, Cherepanova AV, Chernonosova VS, Shevelev GY,Zaporozhchenko IA, Karaskov AM, Laktionov PP. General Study and Gene ExpressionProfiling of Endotheliocytes Cultivated on Electrospun Materials. Materials(Basel). 2019 Dec 6;12(24). pii: E4082. doi: 10.3390/ma12244082. IF: 2.728

Lemopoulos A, Prokkola JM, Uusi-Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P,Koljonen ML, Koskiniemi J, Vainikka A. Comparing RADseq and microsatellites forestimating genetic diversity and relatedness – Implications for brown troutconservation. Ecol Evol. 2019 Feb 6;9(4):2106-2120. doi: 10.1002/ece3.4905.eCollection 2019 Feb. IF: 2.4

Pokharel K, Weldenegodguad M, Popov R, Honkatukia M, Huuki H, Lindeberg H,Peippo J, Reilas T, Zarovnyaev S, Kantanen J. Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions. Anim Genet.2019 Jun;50(3):217-227. doi: 10.1111/age.12783. IF: 2.244

2018

Yang J, Li X, Cao YH, Pokharel K, Hu XJ, Chen ZH, Xu SS, Peippo J, Honkatukia M, Kantanen J, Li MH. Comparative mRNA and miRNA expression in European mouflon(Ovis musimon) and sheep (Ovis aries) provides novel insights into the geneticmechanisms for female reproductive success. Heredity (Edinb). 2019Feb;122(2):172-186. doi: 10.1038/s41437-018-0090-1. IF: 3.872

Hänninen A, Toivonen R, Pöysti S, Belzer C, Plovier H, Ouwerkerk JP, Emani R, Cani PD, De Vos WM. Akkermansia muciniphila induces gut microbiota remodellingand controls islet autoimmunity in NOD mice. Gut. 2018 Aug;67(8):1445-1453. doi: 10.1136/gutjnl-2017-314508. IF: 17.016

Ahmad F, Debes PV, Palomar G, Vasemägi A. Association mapping revealscandidate loci for resistance and anaemic response to an emergingtemperature-driven parasitic disease in a wild salmonid fish. Mol Ecol. 2018Mar;27(6):1385-1401. doi: 10.1111/mec.14509. [NGS] IF: 6.131

Lemopoulos A, Uusi-Heikkilä S, Huusko A, Vasemägi A, Vainikka A. Comparison ofMigratory and Resident Populations of Brown Trout Reveals Candidate Genes forMigration Tendency. Genome Biol Evol. 2018 Jun 1;10(6):1493-1503. doi:10.1093/gbe/evy102. [NGS] IF: 3.940

Ozerov MY, Ahmad F, Gross R, Pukk L, Kahar S, Kisand V, Vasemägi A. HighlyContinuous Genome Assembly of Eurasian Perch (Perca fluviatilis) UsingLinked-Read Sequencing. G3 (Bethesda). 2018 Dec 10;8(12):3737-3743. doi:10.1534/g3.118.200768. [NGS] IF: 2.742

Gubina N, Naudi A, Stefanatos R, Jove M, Scialo F, Fernandez-Ayala DJ, Rantapero T, Yurkevych I, Portero-Otin M, Nykter M, Lushchak O, Navas P, Pamplona R, Sanz A. Essential physiological differences characterise short- and long-lived strains of Drosophila melanogaster. J Gerontol A Biol Sci Med Sci. 2018 Jun 26. doi: 10.1093/gerona/gly143. [NGS] IF: 4.902

Lietzen N, An Le T. T. Jaakkola M, Kallionpää H, Oikarinen S, Mykkänen J, Knip M, Veijola R, Ilonen J, Toppari J, Hyöty H, Lahesmaa R, Elo L. Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes. Diabetologia. 2018 Feb;61(2):381-388. doi: 10.1007/s00125-017-4460-7. PMID: 29119244 [qPCR] IF: 6.023

Vähämiko S, Laiho A, Lund R, Isolauri E, Salminen S, Laitinen K. The impact of probiotic supplementation during pregnancy on DNA methylation of obesity-related genes in mothers and their children. Eur J Nutr. 2018 Jan 3. doi: 10.1007/s00394-017-1601-1. PMID: 29299736 [NGS] IF: 4.423

Knuuttila M, Mehmood A, Huhtaniemi R, Yatkin E, Häkkinen MR, Oksala R, Laajala TD, Ryberg H, Handelsman DJ, Aittokallio T, Auriola S, Ohlsson C, Laiho A, Elo LL, Sipilä P, Mäkelä SI, Poutanen M. Antiandrogens Reduce Intratumoral Androgen Concentrations and Induce Androgen Receptor Expression in Castration-Resistant Prostate Cancer Xenografts. Am J Pathol. 2018 Jan;188(1):216-228. doi: 10.1016/j.ajpath.2017.08.036. Epub 2017 Nov 7. PMID: 29126837 [NGS] IF: 4.583

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. Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter. Allergy. 2018 Aug;73(8):1735-1740. doi: 10.1111/all.13473. PMID: 29729188. [NGS] IF: 6.048

Ubaid Ullah, Andrabi SBA, Tripathi SK, Dirasantha O, Kanduri K, Rautio S, Gross CC, Lehtimäki S, Bala K, Tuomisto J, Bhatia U, Chakroborty D, Elo LL, Lähdesmäki H, Wiendl H, Rasool O, Lahesmaa R. Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells. Cell Rep. 2018 Feb 20;22(8):2094-2106. doi: 10.1016/j.celrep.2018.01.070. [NGS] IF: 8.282

Dunkel J, Viitala M, Karikoski M, Rantakari P, Virtakoivu R, Elima K, Hollmén M, Jalkanen S, Salmi M.Enhanced Antibody Production in Clever-1/Stabilin-1-Deficient Mice. Front Immunol. 2018 Oct 8;9:2257. doi: 10.3389/fimmu.2018.02257. eCollection 2018.PMID: 30349531 [qPCR] IF: 5.511

Huhtaniemi R, Oksala R, Knuuttila M, Mehmood A, Aho E, Laajala TD, Nicorici D, Aittokallio T, Laiho A, Elo L, Ohlsson C, Kallio P, Mäkelä S, Mustonen MVJ, Sipilä P, Poutanen M.Adrenals Contribute to Growth of Castration-Resistant VCaP Prostate Cancer Xenografts. Am J Pathol. 2018 Dec;188(12):2890-2901. doi: 10.1016/j.ajpath.2018.07.029. Epub 2018 Sep 28. PMID: 30273606. [NGS] IF: 4.583

Knuuttila M, Mehmood A, Mäki-Jouppila J, Ryberg H, Taimen P, Knaapila J, Ettala O, Boström PJ, Ohlsson C, Venäläinen MS, Laiho A, Elo LL, Sipilä P, Mäkelä SI, Poutanen M. Intratumoral androgen levels are linked to TMPRSS2-ERG fusion in prostate cancer. Endocr Relat Cancer. 2018 Sep;25(9):807-819. doi: 10.1530/ERC-18-0148. Epub 2018 May 17. PMID: 29773553 [NGS] IF: 5.331

Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Natunen T, Haapasalo A, Herukka SK, Kuusisto J, Soininen H, Kivipelto M, Laakso M, Hiltunen M. Decreased plasma C-reactive protein levels in APOE ε4 allele carriers. Ann Clin Transl Neurol. 2018 Sep 17;5(10):1229-1240. doi: 10.1002/acn3.639. eCollection 2018 Oct. PMID: 30349858 IF: 4.649

Pemmari A, Leppänen T, Paukkeri EL, Eskelinen A, Moilanen T, Moilanen E. Gene expression in adverse reaction to metal debris around metal-on-metal arthroplasty: An RNA-Seq-based study. J Trace Elem Med Biol. 2018 Jul;48:149-156. doi: 10.1016/j.jtemb.2018.03.014. Epub 2018 Mar 20. PMID: 29773173 [NGS] IF: 3.755

Vesterinen EJ, Puisto AIE, Blomberg AS, Lilley TM. Table for five, please: Dietary partitioning in boreal bats. Ecol Evol. 2018 Oct 12;8(22):10914-10937. doi: 10.1002/ece3.4559. eCollection 2018 Nov. PMID: 30519417 [NGS] IF: 2.34

Sormunen JJ, Klemola T, Hänninen J, Mäkelä S, Vuorinen I, Penttinen R, Sääksjärvi IE, Vesterinen EJ. The importance of study duration and spatial scale in pathogen detection-evidence from a tick-infested island. Emerg Microbes Infect. 2018 Nov 28;7(1):189. doi: 10.1038/s41426-018-0188-9. PMID: 30482899 [qPCR] IF: 6.032

Laaksonen M, Klemola T, Feuth E, Sormunen JJ, Puisto A, Mäkelä S, Penttinen R, Ruohomäki K, Hänninen J, Sääksjärvi IE, Vuorinen I, Sprong H, Hytönen J, Vesterinen EJ. Tick-borne pathogens in Finland: comparison of Ixodes ricinus and I. persulcatus in sympatric and parapatric areas. Parasit Vectors. 2018 Oct 24;11(1):556. doi: 10.1186/s13071-018-3131-y. PMID: 30355331 [qPCR] IF: 3.163

Schmidt NM, Mosbacher JB, Vesterinen EJ, Roslin T, Michelsen A. Limited dietary overlap amongst resident Arctic herbivores in winter: complementary insights from complementary methods. Oecologia. 2018 Jul;187(3):689-699. doi: 10.1007/s00442-018-4147-x. Epub 2018 Apr 26. PMID: 29700632 [NGS] IF: 3.127

Heliste J, Jokilammi A, Paatero I, Chakroborty D, Stark C, Savunen T, Laaksonen M, Elenius K. Receptor tyrosine kinase profiling of ischemic heart identifies ROR1 as a potential therapeutic target. BMC Cardiovasc Disord. 2018 Oct 20;18(1):196. doi: 10.1186/s12872-018-0933-y. PMID: 30342492 [qPCR] IF: 1.812

Narvi E, Vaparanta K, Karrila A, Chakroborty D, Knuutila S, Pulliainen A, Sundvall M, Elenius K. Different responses of colorectal cancer cells to alternative sequences of cetuximab and oxaliplatin. Sci Rep. 2018 Nov 8;8(1):16579. doi: 10.1038/s41598-018-34938-y. PMID: 30410004 [NGS] IF: 4.122

Paatero I, Veikkolainen V, Mäenpää M, Schmelzer E, Belting HG, Pelliniemi LJ, Elenius K. ErbB4 tyrosine kinase inhibition impairs neuromuscular development in zebrafish embryos. Mol Biol Cell. 2018 Nov 21:mbcE18070460. doi: 10.1091/mbc.E18-07-0460. [Epub ahead of print] PMID: 30462579 [NGS] IF: 3.512

Joensuu K, Uusitalo-Kylmälä L, Hentunen TA, Heino TJ. Angiogenic potential of human mesenchymal stromal cell and circulating mononuclear cell cocultures is reflected in the expression profiles of proangiogenic factors leading to endothelial cell and pericyte differentiation. J Tissue Eng Regen Med. 2018 Mar;12(3):775-783. doi: 10.1002/term.2496. Epub 2017 Sep 25. PMID: 28593699 [qPCR] IF: 4.089

Pölönen RP, Penttinen K, Swan H, Aalto-Setälä K. Antiarrhythmic Effects of Carvedilol and Flecainide in Cardiomyocytes Derived from Catecholaminergic Polymorphic Ventricular Tachycardia Patients. Stem Cells Int. 2018 Apr 12;2018:9109503. doi: 10.1155/2018/9109503. eCollection 2018. PMID: 29760739 [Karyolite] IF: 3.989

Hakkila K, Valev D, Antal T, Tyystjärvi E, Tyystjärvi T. Group 2 Sigma Factors Are Central Regulators of Oxidative Stress Acclimation in Cyanobacteria. Plant Cell Physiol. 2018 Nov 8. doi: 10.1093/pcp/pcy221. PMID: 30407607 [Microarrays] IF: 4.059

Kaur S, Abu-Shahba AG, Paananen RO, Hongisto H, Hiidenmaa H, Skottman H, Seppänen-Kaijansinkko R, Mannerström B. Small non-coding RNA landscape of extracellular vesicles from human stem cells. Sci Rep. 2018 Oct 19;8(1):15503. doi: 10.1038/s41598-018-33899-6. PMID: 30341351 [Karyotyping] IF: 4.122

Budzyńska PM, Kyläniemi MK, Lassila O, Nera KP, Alinikula J. BLIMP-1 is insufficient to induce antibody secretion in the absence of IRF4 in DT40 cells. Scand J Immunol. 2018 Mar; 87(3). doi: 10.1111/sji.12646. PMID: 29430664 [Microarrays] IF: 2.314

Ojalill M, Parikainen M, Rappu P, Aalto E, Jokinen J, Virtanen N, Siljamäki E, Heino J. Integrin α2β1 decelerates proliferation, but promotes survival and invasion of prostate cancer cells. Oncotarget. 2018 Aug 21;9(65):32435-32447. doi: 10.18632/oncotarget.25945.PMID: 30197754 [NGS, qPCR] IF: 5.168

Piipponen M, Heino J, Kähäri VM1, Nissinen L5. Long non-coding RNA PICSAR decreases adhesion and promotes migration of squamous carcinoma cells by downregulating α2β1 and α5β1 integrin expression. Biol Open. 2018 Nov 14;7(11). doi: 10.1242/bio.037044. PMID: 30429154 [NGS, qPCR] IF: 2.217

Mohammad I, Starskaia I, Nagy T, Guo J, Yatkin E, Väänänen K, Watford WT, Chen Z. Estrogen receptor α contributes to T cell-mediated autoimmune inflammation by promoting T cell activation and proliferation. Sci Signal. 2018 Apr 17;11(526). doi: 10.1126/scisignal.aap9415. PMID: 29666308 [NGS, qPCR] IF: 6.378

Heinosalo T, Gabriel M, Kallio L, Adhikari P, Huhtinen K, Laajala TD, Kaikkonen E, Mehmood A, Suvitie P, Kujari H, Aittokallio T, Perheentupa A, Poutanen M. Secreted frizzled-related protein 2 (SFRP2) expression promotes lesion proliferation via canonical WNT signaling and indicates lesion borders in extraovarian endometriosis. Hum Reprod. 2018 May 1;33(5): 817-831. doi: 10.1093/humrep/dey026. [Microarrays, qPCR] IF: 4.990

Albalushi H, Kurek M, Karlsson L, Landreh L, Kjartansdóttir KR, Söder O, Hovatta O, Stukenborg JB. Laminin 521 Stabilizes the Pluripotency Expression Pattern of Human Embryonic Stem Cells Initially Derived on Feeder Cells.Stem Cells Int. 2018 Feb 18;2018:7127042. doi: 10.1155/2018/7127042. eCollection 2018. [Karyolite] IF: 3.989

Mohammad I, Nousiainen K, Bhosale SD1, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z.Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells. PLoS Biol. 2018 May 31;16(5):e2004194. doi: 10.1371/journal.pbio.2004194. eCollection 2018 May [NGS] IF: 9.163

Adam M, Heikelä H, Sobolewski C, Portius D, Mäki-Jouppila J, Mehmood A, Adhikari P, Esposito I, Elo LL, Zhang FP, Ruohonen ST, Strauss L, Foti M, Poutanen M. Hydroxysteroid (17β) dehydrogenase 13 deficiency triggers hepatic steatosis and inflammation in mice. FASEB J. 2018 Jun;32(6):3434-3447. doi: 10.1096/fj.201700914R. Epub 2018 Jan 31.[NGS] IF: 5.595

Aakko S, Straume AH, Birkeland EE, Chen P, Qiao X, ‘Lønning PE, Kallio MJ.MYC-Induced miR-203b-3p and miR-203a-3p Control Bcl-xL Expression and Paclitaxel Sensitivity in Tumor Cells. Transl Oncol. 2019 Jan;12(1):170-179. doi:10.1016/j.tranon.2018.10.001. [NGS] IF: 3.071

2017

Lilja J, Zacharchenko T, Georgiadou M, Jacquemet G, De Franceschi N, Peuhu E, Hamidi H, Pouwels J, Martens V, Nia FH, Beifuss M, Boeckers T, Kreienkamp HJ, Barsukov IL, Ivaska J. SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nat Cell Biol. 2017 Apr;19(4):292-305. doi: 10.1038/ncb3487. [qPCR] IF: 20.060

Jacquemet G, Baghirov H, Georgiadou M, Sihto H, Peuhu E, Cettour-Janet P, He T, Perälä M, Kronqvist P, Joensuu H, Ivaska J. L-type calcium channels regulate filopodia stability and cancer cell invasion downstream of integrin signalling. Nat Commun. 2016 Dec 2;7:13297. doi: 10.1038/ncomms13297. [qPCR] IF: 12.124

Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res. 2017 Nov 16;45(20):11800-11820. doi: 10.1093/nar/gkx860. [NGS] IF: 10.162

Peuhu E, Kaukonen R, Lerche M, Saari M, Guzmán C, Rantakari P, De Franceschi N, Wärri A, Georgiadou M, Jacquemet G, Mattila E, Virtakoivu R, Liu Y, Attieh Y, Silva KA, Betz T, Sundberg JP, Salmi M, Deugnier MA, Eliceiri KW, Ivaska J. SHARPIN regulates collagen architecture and ductal outgrowth in the developing mouse mammary gland. EMBO J. 2017 Jan 17;36(2):165-182. doi:10.15252/embj.201694387. [NGS, qPCR] IF: 9.792

Antfolk D, Sjöqvist M, Cheng F, Isoniemi K, Duran CL, Rivero-Muller A, Antila C, Niemi R, Landor S, Bouten CVC, Bayless KJ, Eriksson JE, Sahlgren CM. Selective regulation of Notch ligands during angiogenesis is mediated by vimentin. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4574-E4581. doi: 10.1073/pnas.1703057114. [qPCR] IF: 9.661

Da Ros M, Lehtiniemi T, Olotu O, Fischer D, Zhang FP, Vihinen H, Jokitalo E, Sironen A, Toppari J, Kotaja N. FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy. 2017 Feb;13(2):302-321. doi: 10.1080/15548627.2016.1261319. [NGS] IF: 8.593

Wang J, Okkeri J, Pavic K, Wang Z, Kauko O, Halonen T, Sarek G, Ojala PM, Rao Z, Xu W, Westermarck J. Oncoprotein CIP2A is stabilized via interaction with tumor suppressor PP2A/B56. EMBO Rep. 2017 Mar;18(3):437-450. doi:10.15252/embr.201642788. [sanger] IF: 8.568

Antila CJM, Rraklli V, Blomster HA, Dahlström KM, Salminen TA, Holmberg J, Sistonen L, Sahlgren C. Sumoylation of Notch1 represses its target gene expression during cell stress. Cell Death Differ. 2018 Jan 5. doi:10.1038/s41418-017-0002-6. [qPCR] IF: 8.339

Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell Rep. 2017 Aug 8;20(6):1448-1462. doi:10.1016/j.celrep.2017.07.036. [NGS] IF: 8.282

Tripathi SK, Chen Z, Larjo A, Kanduri K, Nousiainen K, Äijo T, Ricaño-Ponce I, Hrdlickova B, Tuomela S, Laajala E, Salo V, Kumar V, Wijmenga C, Lähdesmäki H, Lahesmaa R. Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation. Cell Rep. 2017 May 30;19(9):1888-1901. doi: 10.1016/j.celrep.2017.05.013. [microarrays, qPCR] IF: 8.282

Georgiadou M, Lilja J, Jacquemet G, Guzmán C, Rafaeva M, Alibert C, Yan Y, Sahgal P, Lerche M, Manneville JB, Mäkelä TP, Ivaska J. AMPK negatively regulates tensin-dependent integrin activity. J Cell Biol. 2017 Apr 3;216(4):1107-1121. doi: 10.1083/jcb.201609066. [qPCR] IF: 7.955

Pasumarthy KK, Doni Jayavelu N, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements. Stem Cell Reports. 2017 Sep 12;9(3):999-1015. doi:10.1016/j.stemcr.2017.07.018. [NGS] IF: 7.338

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 Reports. 2017 May 9;8(5):1442-1454. doi:10.1016/j.stemcr.2017.04.016. [NGS, qPCR] IF: 7.338

Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med. 2017 Aug 18;9(1):75. doi: 10.1186/s13073-017-0467-4. Review. [single cell omics] IF: 7.071

Lehtinen L, Vainio P, Wikman H, Huhtala H, Mueller V, Kallioniemi A, Pantel K2, Kronqvist P1, Kallioniemi O6,7, Carpèn O1,8, Iljin K9. PLA2G7 associates with hormone receptor negativity in clinical breast cancer samples and regulates epithelial-mesenchymal transition in cultured breast cancer cells. J Pathol Clin Res. 2017 Apr 4;3(2):123-138. doi: 10.1002/cjp2.69. [Microarrays, qPCR] IF: 6.894

Pruikkonen S, Kallio MJ. Excess of a Rassf1-targeting microRNA, miR-193a-3p, perturbs cell division fidelity. Br J Cancer. 2017 May 23;116(11):1451-1461. doi: 10.1038/bjc.2017.110. [qPCR] IF: 6.716

Peuhu E, Virtakoivu R, Mai A, Wärri A, Ivaska J. Epithelial vimentin plays a functional role in mammary gland development. Development. 2017 Nov 15;144(22):4103-4113. doi: 10.1242/dev.154229. [NGS] IF: 5.843

Farshchian M, Nissinen L, Siljamäki E, Riihilä P, Piipponen M, Kivisaari A, Kallajoki M, Grénman R, Peltonen J, Peltonen S, Quint KD, Bavinck JNB, Kähäri VM. Tumor cell-specific AIM2 regulates growth and invasion of cutaneous squamous cell carcinoma. Oncotarget. 2017 Jul 11;8(28):45825-45836. doi: 10.18632/oncotarget.17573. [NGS] IF: 5.168

Posada IMD, Lectez B, Sharma M, Oetken-Lindholm C, Yetukuri L, Zhou Y, Aittokallio T, Abankwa D. Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner. Oncotarget. 2017 Jul 4;8(27):44550-44566. doi: 10.18632/oncotarget.17819. PMID: 28562352 [NGS] IF: 5.168

Doroszko M, Chrusciel M, Stelmaszewska J, Slezak T, Rivero-Muller A, Padzik A, Anisimowicz S, Wolczynski S, Huhtaniemi I, Toppari J, Rahman NA. Luteinizing Hormone and GATA4 Action in the Adrenocortical Tumorigenesis of Gonadectomized Female Mice. Cell Physiol Biochem. 2017;43(3):1064-1076. doi: 10.1159/000481718. [Sanger] IF: 5.104

Stauffer J, Panda B, Eeva T, Rainio M, Ilmonen P. Telomere damage and redox status alterations in free-living passerines exposed to metals. Sci Total Environ. 2017 Jan 1;575:841-848. doi: 10.1016/j.scitotenv.2016.09.131. [qPCR] IF: 4.9

Ailanen L, Ruohonen ST, Vähätalo LH, Tuomainen K, Eerola K, Salomäki-Myftari H, Röyttä M, Laiho A, Ahotupa M, Gylling H, Savontaus E. The metabolic syndrome in mice overexpressing neuropeptide Y in noradrenergic neurons. J Endocrinol. 2017 Jul;234(1):57-72. doi: 10.1530/JOE-16-0223. [Microarrays] IF: 4.706

Kiamehr M, Viiri LE, Vihervaara T, Koistinen KM, Hilvo M, Ekroos K, Käkelä R, Aalto-Setälä K. Lipidomic profiling of patient-specific iPSC-derived hepatocyte-like cells. Dis Model Mech. 2017 Sep 1;10(9):1141-1153. doi:10.1242/dmm.030841. [karyolite] IF: 4.691

Vainio E, Jurvansuu J, Hyder R, M, Piri T, Tuomivirta T, Poimala A, Xu Ping, Mäkelä S, Nitisa D, Hantula J. The partitivirus HetPV13-an1 mediates severe growth debilitation and major alterations in the gene expression of a fungal forest pathogen. JVirol. 2017 Dec13; 01744-17. doi:10.1128/JVI.01744-17. PMID: 29237832 [NGS] IF: 4.663

Haapalainen AM, Karjalainen MK, Daddali R, Ohlmeier S, Anttonen J, Määttä TA, Salminen A, Mahlman M, Bergmann U, Mäkikallio K, Ojaniemi M, Hallman M, Rämet M. Expression of CPPED1 in human trophoblasts is associated with timing of term birth. J Cell Mol Med. 2017 Nov 29. doi: 10.1111/jcmm.13402. [ngs] IF: 4.499

Breitling S, Hui Z, Zabini D, Hu Y, Hoffmann J, Goldenberg NM, Tabuchi A, Buelow R, Dos Santos C, Kuebler WM. The mast cell-B cell axis in lung vascular remodeling and pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol. 2017 May 1;312(5):L710-L721. doi: 10.1152/ajplung.00311.2016. Epub 2017 Feb 24. PMID: 28235950 [Microarrays] IF: 4.281

Jokela H, Hakkarainen J, Kätkänaho L, Pakarinen P, Ruohonen ST, Tena-Sempere M, Zhang FP, Poutanen M. Deleting the mouse Hsd17b1 gene results in a hypomorphic Naglu allele and a phenotype mimicking a lysosomal storage disease. Sci Rep. 2017 Nov 27;7(1):16406. doi: 10.1038/s41598-017-16618-5. [NGS] IF: 4.259

Singh A, Gotherwal V, Junni P, Vijayan V, Tiwari M, Ganju P, Kumar A, Sharma P, Fatima T, Gupta A, Holla A, Kar HK, Khanna S, Thukral L, Malik G, Natarajan K, Gadgil CJ, Lahesmaa R, Natarajan VT, Rani R, Gokhale RS. Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo. Sci Rep. 2017 Aug 29;7(1):9860. doi: 10.1038/s41598-017-10253-w. [microarrays]

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. doi:10.1038/s41598-017-01624-4. [NGS, qPCR] IF: 4.259

Weldatsadik RG, Wang J, Puhakainen K, Jiao H, Jalava J, Räisänen K, Datta N, Skoog T, Vuopio J, Jokiranta TS, Kere J. Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus. Sci Rep. 2017 Mar 31;7:45771. doi:10.1038/srep45771. [ngs] IF: 4.259

Miragaia R*, Zhang X*, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Single-cell RNA-seq resolves self antigen expression during mTEC development. Sci Rep. 2018 Jan 12;8(685). doi:10.1038/s41598-017-19100-4. [single cell omics] IF: 4.259

Riihilä P, Nissinen L, Farshchian M, Kallajoki M, Kivisaari A, Meri S, Grénman R, Peltonen S, Peltonen J, Pihlajaniemi T, Heljasvaara R, Kähäri VM. Complement Component C3 and Complement Factor B Promote Growth of Cutaneous Squamous Cell Carcinoma. Am J Pathol. 2017 May;187(5):1186-1197. doi: 10.1016/j.ajpath.2017.01.006. [qPCR] IF: 4.057

Joensuu K, Uusitalo-Kylmälä L, Hentunen TA, Heino TJ. Angiogenic potential of human mesenchymal stromal cell and circulating mononuclear cell cocultures is reflected in the expression profiles of proangiogenic factors leading to endothelial cell and pericyte differentiation. J Tissue Eng Regen Med. 2017 Jun 7. doi: 10.1002/term.2496. [Epub ahead of print] PMID: 28593699 [qPCR] IF: 3.989

Götting M, Nikinmaa MJ. Transcriptomic Analysis of Young and Old Erythrocytes of Fish. Front Physiol. 2017 Dec 12; 8:1046. doi: 10.3389/fphys.2017.01046. [NGS, qPCR] IF: 3.746

Uusi-Rauva K, Blom T, von Schantz-Fant C, Blom T, Jalanko A, Kyttälä A. Induced Pluripotent Stem Cells Derived from a CLN5 Patient Manifest Phenotypic Characteristics of Neuronal Ceroid Lipofuscinoses. Int J Mol Sci. 2017 May 1;18(5). pii: E955. doi: 10.3390/ijms18050955. [Karyolite] IF: 3.226

Stauffer J, Bruneaux M, Panda B, Visse M, Vasemägi A, Ilmonen P. Telomere length and antioxidant defense associate with parasite-induced retarded growth in wild brown trout. Oecologia. 2017 Nov;185(3):365-374. doi:10.1007/s00442-017-3953-x. [qPCR] IF: 3.130

Nissinen L, Siljamäki E, Riihilä P, Piipponen M, Farshchian M, Kivisaari A, Kallajoki M, Raiko L, Peltonen J, Peltonen S, Kähäri VM. Expression of claudin-11 by tumor cells in cutaneous squamous cell carcinoma is dependent on the activity of p38δ. Exp Dermatol. 2017 Sep;26(9):771-777. doi: 10.1111/exd.13278. [NGS] IF: 2.532

Budzyński MA, Crul T, Himanen SV, Toth N, Otvos F, Sistonen L, Vigh L. Chaperone co-inducer BGP-15 inhibits histone deacetylases and enhances the heat shock response through increased chromatin accessibility. Cell Stress Chaperones. 2017 Sep;22(5):717-728. doi: 10.1007/s12192-017-0798-5. [qPCR] IF: 2.411

Huhtinen A, Hongisto V, Laiho A, Löyttyniemi E, Pijnenburg D, Scheinin M. Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells. BMC Syst Biol. 2017 Jun 28;11(1):65. doi: 10.1186/s12918-017-0439-8.PMID:28659168. IF: 2.303

Rintala A, Pietilä S, Munukka E, Eerola E, Pursiheimo JP, Laiho A, Pekkala S, Huovinen P. Gut Microbiota Analysis Results Are Highly Dependent on the 16S rRNA Gene Target Region, Whereas the Impact of DNA Extraction Is Minor. J Biomol Tech. 2017 Apr;28(1):19-30. doi: 10.7171/jbt.17-2801-003. [bioinfo] IF: 1.62

Jernström S, Hongisto V, Leivonen SK, Due EU, Tadele DS, Edgren H, Kallioniemi O, Perälä M, Mælandsmo GM, Sahlberg KK. Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. Breast Cancer (Dove Med Press). 2017 Mar 21;9:185-198. doi: 10.2147/BCTT.S115600. [microarrays] IF: 1.572

Mantziari A, Aakko J, Kumar H, Tölkkö S, du Toit E, Salminen S, Isolauri E, Rautava S. The Impact of Storage Conditions on the Stability of Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis Bb12 in Human Milk. Breastfeed Med. 2017 Nov;12(9):566-569. doi: 10.1089/bfm.2017.0051. Epub 2017 Jul 28. PMID: 28753043 [sanger] IF: 1.28

Boström P, Sainio A, Eigėlienė N, Jokilammi A, Elenius K, Koskivuo I, Järveläinen H. Human Metaplastic Breast Carcinoma and Decorin. Cancer Microenviron. 2017 Dec;10(1-3):39-48. doi: 10.1007/s12307-017-0195-8. [qPCR] IF: 0.825

Pakharukova N, Tuittila M, Paavilainen S, Zavialov A. Methylation, crystallization and SAD phasing of the Csu pilus CsuC-CsuE chaperone-adhesin subunit pre-assembly complex from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun. 2017 Aug 1;73(Pt 8):450-454. doi: 10.1107/S2053230X17009566. [sanger] IF: 0.799

Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM. HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma. Cancer Metab. 2017 Jul 4;5:5. doi: 10.1186/s40170-017-0167-y. [qPCR] IF:

Hugenholtz F, Ritari J, Nylund L, Davids M, Satokari R, de Vos WM. Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months. Int J Microbiol. 2017;2017:9547063. doi: 10.1155/2017/9547063. Epub 2017 Aug 24. PMID: 28912815 [NGS] IF:

He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K. High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene. 2017 Jan 5;596:137-146. doi: 10.1016/j.gene.2016.10.021. [NGS, qPCR]

Budzyńska PM, Kyläniemi MK, Kallonen T, Soikkeli AI, Nera KP, Lassila O, Alinikula J. Bach2 regulates AID-mediated immunoglobulin gene conversion and somatic hypermutation in DT40 B cells. Eur J Immunol. 2017 Jun;47(6):993-1001. doi: 10.1002/eji.201646895. Epub 2017 Apr 11. [NGS]

Kaunisto KM, Roslin T, Sääksjärvi IE, Vesterinen EJ. Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces. Ecology and Evolution. 2017 Oct 7 (20):8588-8598. doi: 10.1002/ece3.3404 [NGS]

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

Cordova ZM, Grönholm A, Kytölä V, Taverniti V, Hämäläinen S, Aittomäki S, Niininen W, Junttila I, Ylipää A, Nykter M, Pesu M. Myeloid cell expressed proprotein convertase FURIN attenuates inflammation. Oncotarget. 2016 Aug 23;7(34):54392-54404. doi: 10.18632/oncotarget.11106. IF: 5.008 [Microarrays]

Kemppainen E, George J, Garipler G, Tuomela T, Kiviranta E, Soga T, Dunn CD, Jacobs HT. Mitochondrial Dysfunction Plus High-Sugar Diet Provokes a Metabolic Crisis That Inhibits Growth. PLoS One. 2016 Jan 26;11(1):e0145836. doi: 10.1371/journal.pone.0145836. . IF: 3.057 [NGS]

Kemppainen K, Wentus N, Lassila T, Laiho A, Törnquist K. Sphingosylphosphorylcholine regulates the Hippo signaling pathway in a dual manner. Cell Signal. 2016 Dec;28(12):1894-1903. doi: 10.1016/j.cellsig.2016.09.004. IF: 4.191 [Bioinformatics, Microarrays, qPCR]

Lewis M1, Götting M1, Anttila K1, Kanerva M1, Prokkola JM1, Seppänen E2, Kolari I2, Nikinmaa M1. Different Relationship between hsp70 mRNA and hsp70 Levels in the Heat Shock Response of Two Salmonids with Dissimilar Temperature Preference. Front Physiol. 2016 Nov 7;7:511. eCollection 2016. IF: 4.031 [qPCR]

Piipponen M, Nissinen L, Farshchian M, Riihilä P, Kivisaari A, Kallajoki M, Peltonen J, Peltonen S, Kähäri VM. Long Noncoding RNA PICSAR Promotes Growth of Cutaneous Squamous Cell Carcinoma by Regulating ERK1/2 Activity. J Invest Dermatol. 2016 Aug;136(8):1701-10. doi: 10.1016/j.jid.2016.03.028. Epub 2016 Apr 2. IF: 6.915 [NGS, qPCR]

Hu X, Pokharel K, Peippo J, Ghanem N, Zhaboyev I, Kantanen J, Li MH. Identification and characterization of miRNAs in the ovaries of a highly prolific sheep breed. Anim Genet. 2016 Apr;47(2):234-9. doi: 10.1111/age.12385. [NGS]

Domsgen E, Lind K, Kong L, Hühn MH, Rasool O, van Kuppeveld F, Korsgren O, Lahesmaa R, Flodström-Tullberg M. An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets. Sci Rep. 2016 Dec 21;6:39378. doi:10.1038/srep39378. [NGS] IF: 5.228

Côme C, Cvrljevic A, Khan MM, Treise I, Adler T, Aguilar-Pimentel JA, Au-Yeung B, Sittig E, Laajala TD, Chen Y, Oeder S, Calzada-Wack J, Horsch M, Aittokallio T, Busch DH, Ollert MW, Neff F, Beckers J, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Chen Z, Lahesmaa R, Westermarck J. CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection. PLoS One. 2016 Apr 21;11(4):e0152996. doi: 10.1371/journal.pone.0152996. [Microarrays]

Haugas M, Tikker L, Achim K, Salminen M, Partanen J. Gata2 and Gata3 regulate the differentiation of serotonergic and glutamatergic neuron subtypes of the dorsal raphe. Development. 2016 Oct 27. pii: dev.136614. [Epub ahead of print] [Microarrays]

Hukelmann JL, Anderson KE, Sinclair LV, Grzes KM, Murillo AB, Hawkins PT, Stephens LR, Lamond AI, Cantrell DA. The cytotoxic T cell proteome and its shaping by the kinase mTOR. Nat Immunol. 2016 Jan;17(1):104-12. doi: 10.1038/ni.3314. [Microarrays]

Hulmi JJ, Hentilä J, DeRuisseau KC, Oliveira BM, Papaioannou KG, Autio R, Kujala UM, Ritvos O, Kainulainen H, Korkmaz A, Atalay M. Effects of muscular dystrophy, exercise and blocking activin receptor IIB ligands on the unfolded protein response and oxidative stress. Free Radic Biol Med. 2016 Oct;99:308-322. doi: 10.1016/j.freeradbiomed.2016.08.017. [Microarrays]

Järvi S, Isojärvi J, Kangasjärvi S, Salojärvi J, Mamedov F, Suorsa M, Aro EM. Photosystem II Repair and Plant Immunity: Lessons Learned from Arabidopsis Mutant Lacking the THYLAKOID LUMEN PROTEIN 18.3. Front Plant Sci. 2016 Mar 31;7:405. doi: 10.3389/fpls.2016.00405. [Microarrays]

Kangas SM, Ohlmeier S, Sormunen R, Jouhilahti EM, Peltonen S, Peltonen J, Heape AM. An approach to comprehensive genome and proteome expression analyses in Schwann cells and neurons during peripheral nerve myelin formation. J Neurochem. 2016 Sep;138(6):830-44. doi: 10.1111/jnc.13722. [Microarrays, Bioinformatics]

Kankare M, Parker DJ, Merisalo M, Salminen TS, Hoikkala A. Transcriptional Differences between Diapausing and Non-Diapausing D. montana Females Reared under the Same Photoperiod and Temperature. PLoS One. 2016 Aug 29;11(8):e0161852. doi: 10.1371/journal.pone.0161852. [NGS]

Kaukonen R, Mai A, Georgiadou M, Saari M, De Franceschi N, Betz T, Sihto H, Ventelä S, Elo L, Jokitalo E, Westermarck J, Kellokumpu-Lehtinen PL, Joensuu H, Grenman R, Ivaska J. Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription. Nat Commun. 2016 Aug 4;7:12237. doi: 10.1038/ncomms12237. [NGS, qPCR]

Kemiläinen H, Adam M, Mäki-Jouppila J, Damdimopoulou P, Damdimopoulos AE, Kere J, Hovatta O, Laajala TD, Aittokallio T, Adamski J, Ryberg H, Ohlsson C, Strauss L, Poutanen M. The Hydroxysteroid (17β) Dehydrogenase Family Gene HSD17B12 Is Involved in the Prostaglandin Synthesis Pathway, the Ovarian Function, and Regulation of Fertility. Endocrinology. 2016 Oct;157(10):3719-3730 [Microarrays, Bioinformatics]

Koskinen S, Hakkila K, Gunnelius L, Kurkela J, Wada H, Tyystjärvi T. In vivo recruitment analysis and a mutant strain without any group 2 σ factor reveal roles of different σ factors in cyanobacteria. Mol Microbiol. 2016 Jan;99(1):43-54. doi: 10.1111/mmi.13214. [Microarrays]

Lövgren J, Pursiheimo JP, Pyykkö M, Salmi J, Lamminmäki U. Next generation sequencing of all variable loops of synthetic single framework scFv-Application in anti-HDL antibody selections. N Biotechnol. 2016 Dec 25;33(6):790-796. doi: 10.1016/j.nbt.2016.07.009. [NGS]

Mustila H, Paananen P, Battchikova N, Santana-Sánchez A, Muth-Pawlak D, Hagemann M, Aro EM, Allahverdiyeva Y. The Flavodiiron Protein Flv3 Functions as a Homo-Oligomer During Stress Acclimation and is Distinct from the Flv1/Flv3 Hetero-Oligomer Specific to the O2 Photoreduction Pathway. Plant Cell Physiol. 2016 Mar 2. pii: pcw047. [Epub ahead of print] [Microarrays]

Palani S, Elima K, Ekholm E, Jalkanen S, Salmi M. Monocyte Stabilin-1 Suppresses the Activation of Th1 Lymphocytes. J Immunol. 2016 Jan 1;196(1):115-23. doi: 10.4049/jimmunol.1500257. Epub 2015 Nov 25. [NGS, Microarrays, Bioinformatics, qPCR] IF: 4.922

Parker DJ, Ritchie MG, Kankare M. Preparing for Winter: The Transcriptomic Response Associated with Different Day Lengths in Drosophila montana. G3 (Bethesda). 2016 May 3;6(5):1373-81. doi: 10.1534/g3.116.027870. [NGS]

Routila J, Mäkelä JA, Luukkaa H, Leivo I, Irjala H, Westermarck J, Mäkitie A, Ventelä S. Potential role for inhibition of protein phosphatase 2A tumor suppressor in salivary gland malignancies. Genes Chromosomes Cancer. 2016 Jan;55(1):69-81. doi: 10.1002/gcc.22312. [Microarrays, Bioinformatics]

Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Straume AH, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, Kallio MJ. Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells’ sensitivity to paclitaxel. Oncotarget. 2016 Mar 15;7(11):12267-85. doi: 10.18632/oncotarget.7860. [qPCR]

Tuomela S, Rautio S, Ahlfors H, Öling V, Salo V, Ullah U, Chen Z, Hämälistö S, Tripathi SK, Äijö T, Rasool O, Soueidan H, Wessels L, Stockinger B, Lähdesmäki H, Lahesmaa R. Comparative analysis of human and mouse transcriptomes of Th17 cell priming. Oncotarget. 2016 Mar 22;7(12):13416-28. doi: 10.18632/oncotarget.7963. [NGS]

Vuorinen AL, Kalpio M, Linderborg KM, Hoppula KB, Karhu ST, Yang B, Kallio HP. Triacylglycerol biosynthesis in developing Ribes nigrum and Ribes rubrum seeds from gene expression to oil composition. Food Chem. 2016 Apr 1;196:976-87. doi: 10.1016/j.foodchem.2015.10.010. [qPCR] IF:3.391

Walter J, Lynch F, Battchikova N, Aro EM, Gollan PJ. Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120. J Exp Bot. 2016 Jun;67(13):3997-4008. doi: 10.1093/jxb/erw112. [NGS]

Vehmas AP, Adam M, Laajala TD, Kastenmüller G, Prehn C, Rozman J, Ohlsson C, Fuchs H, Hrabě de Angelis M, Gailus-Durner V, Elo LL, Aittokallio T, Adamski J, Corthals G, Poutanen M, Strauss L. Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse. J Proteomics. 2016 Feb 5;133:66-75. doi: 10.1016/j.jprot.2015.12.009. [Microarrays]

West G, Gullmets J, Virtanen L, Li SP, Keinänen A, Shimi T, Mauermann M, Heliö T, Kaartinen M, Ollila L, Kuusisto J, Eriksson JE, Goldman RD, Herrmann H, Taimen P. Deleterious assembly of the lamin A/C mutant p.S143P causes ER stress in familial dilated cardiomyopathy. J Cell Sci. 2016 Jul 15;129(14):2732-43. doi: 10.1242/jcs.184150. [Microarrays]

Wu S, Johansson J, Hovatta O, Rising A. Efficient passage of human pluripotent stem cells on spider silk matrices under xeno-free conditions. Cell Mol Life Sci. 2016 Apr;73(7):1479-88. doi: 10.1007/s00018-015-2053-5. [Karyotyping]

Österblad M, Karah N, Halkilahti J, Sarkkinen H, Uhlin BE, Jalava J. Rare Detection of the Acinetobacter Class D Carbapenemase blaOXA-23 Gene in Proteus mirabilis. Antimicrob Agents Chemother. 2016 Apr 22;60(5):3243-5. doi: 10.1128/AAC.03119-15. [NGS]

Sormunen JJ, Penttinen R, Klemola T, Hänninen J, Vuorinen I, Laaksonen M, Sääksjärvi IE, Ruohomäki K, Vesterinen EJ. Tick-borne bacterial pathogens in southwestern Finland. Parasit Vectors. 2016 Mar 22;9:168. doi: 10.1186/s13071-016-1449-x. [qPCR]

Da Ros M, Lehtiniemi T, Olotu O, Fischer D, Zhang FP, Vihinen H, Jokitalo E, Sironen A, Toppari J, Kotaja N. FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy. 2016 Dec 8:0. [NGS]

Peuhu E, Kaukonen R, Lerche M, Saari M, Guzmán C, Rantakari P, De Franceschi N, Wärri A, Georgiadou M, Jacquemet G, Mattila E, Virtakoivu R, Liu Y, Attieh Y, Silva KA, Betz T, Sundberg JP, Salmi M, Deugnier MA, Eliceiri KW, Ivaska J. SHARPIN regulates collagen architecture and ductal outgrowth in the developing mouse mammary gland. EMBO J. 2016 Dec 14. pii: e201694387. [NGS, qPCR]

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]

• Kramná L, Kolářová K, Oikarinen S, Pursiheimo JP, Ilonen J, Simell O, Knip M, Veijola R, Hyöty H, Cinek O. Gut virome sequencing in children with early islet autoimmunity. Diabetes Care. 2015 May;38(5):930-3. IF: 8.42 [NGS]

• Vahdat S, Mousavi SA, Omrani G, Gholampour M, Sotoodehnejadnematalahi F, Ghazizadeh Z, Gharechahi J, Baharvand H, Salekdeh GH, Aghdami N. Cellular and molecular characterization of human cardiac stem cells reveals key features essential for their function and safety. Stem Cells Dev. 2015 Jun 15;24(12):1390-404. IF: 3.727 [microarrays]

• Siller R, Greenhough S, Naumovska E, Sullivan GJ. Small-molecule-driven hepatocyte differentiation of human pluripotent stem cells. Stem Cell Reports. 2015 May 12;4(5):939-52. IF: 5.365 [karyolite]

• Riihilä P, Nissinen L, Farshchian M, Kivisaari A, Ala-aho R, Kallajoki M, Grénman R, Meri S, Peltonen S, Peltonen J, Kähäri VM. Complement factor I promotes progression of cutaneous squamous cell carcinoma. J Invest Dermatol. 2015 Feb;135(2):579-88. IF: 7.216 [NGS]

• Palani S, Elima K, Ekholm E, Jalkanen S, Salmi M. Monocyte Stabilin-1 Suppresses the Activation of Th1 Lymphocytes. J Immunol. 2015 Nov 25. pii: 1500257. IF: 4.922 [microarrays, NGS, qPCR]

• Kainulainen H, Papaioannou KG, Silvennoinen M, Autio R, Saarela J, Oliveira BM, Nyqvist M, Pasternack A, ‘t Hoen PA, Kujala UM, Ritvos O, Hulmi JJ. Myostatin/activin blocking combined with exercise reconditions skeletal muscle expression profile of mdx mice. Mol Cell Endocrinol. 2015 Jan 5;399:131-42. IF: 4.405 [microarrays]

• Laukkanen MO, Cammarota F, Esposito T, Salvatore M, Castellone MD. Extracellular superoxide dismutase regulates the expression of small gtpase regulatory proteins GEFs, GAPs, and GDI. PLoS One. 2015 Mar 9;10(3):e0121441. IF: 3.234 [microarrays]

• Elovaara H, Huusko T, Maksimow M, Elima K, Yegutkin GG, Skurnik M, Dobrindt U, Siitonen A, McPherson MJ, Salmi M, Jalkanen S. Primary Amine Oxidase of Escherichia coli Is a Metabolic Enzyme that Can Use a Human Leukocyte Molecule as a Substrate. PLoS One. 2015 Nov 10;10(11):e0142367. IF: 3.234 [microarrays]

• Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grénman S, Lehtonen R, Carpén O, Hautaniemi S. Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy. Cancer Res. 2015 Aug 1;75(15):2987-98. IF: 9.329 [qPCR]
• Nurminen V, Neme A, Ryynänen J, Heikkinen S, Seuter S, Carlberg C.The transcriptional regulator BCL6 participates in the secondary gene regulatory response to vitamin D. Biochim Biophys Acta. 2015 Mar;1849(3):300-8. IF: 6.332 [microarrays]

• Renkonen J, Toppila-Salmi S, Joenväärä S, Mattila P, Parviainen V, Hagström J, Haglund, Lehtonen M, Renkonen R. Expression of Toll-like receptors in nasal epithelium in allergic rhinitis. APMIS. 2015 Aug;123(8):716-25. IF: 2.042 [microarrays]

• Rauhala L, Hämäläinen L, Dunlop TW, Pehkonen P, Bart G, Kokkonen M, Tammi M, Tammi R, Pasonen-Seppänen S. The organic osmolyte betaine induces keratin 2 expression in rat epidermal keratinocytes – A genome-wide study in UVB irradiated organotypic 3D cultures. Toxicol In Vitro. 2015 Dec 25;30(1 Pt B):462-75. IF: 2.903 [microarray]

• Konert G1, Rahikainen M1, Trotta A1, Durian G1, Salojärvi J2, Khorobrykh S1, Tyystjärvi E1, Kangasjärvi S1. Subunits B’γ and B’ζ of protein phosphatase 2A regulate photo-oxidative stress responses and growth in Arabidopsis thaliana. Plant Cell Environ. 2015 Dec;38(12):2641-51. IF: 6.96 [microarray]

• Leder EH, McCairns RJ, Leinonen T, Cano JM, Viitaniemi HM, Nikinmaa M, Primmer CR, Merilä J. The evolution and adaptive potential of transcriptional variation in sticklebacks–signatures of selection and widespread heritability. Mol Biol Evol. 2015 Mar;32(3):674-89. IF: 9.105 [microarray]

• Mäki-Jouppila JH, Pruikkonen S, Tambe MB, Aure MR, Halonen T, Salmela AL, Laine L, Børresen-Dale AL, Kallio MJ.MicroRNA let-7b regulates genomic balance by targeting Aurora B kinase. Mol Oncol. 2015 Jun;9(6):1056-70. IF: 5.331 [qPCR]

• Routila J, Mäkelä JA, Luukkaa H, Leivo I, Irjala H, Westermarck J, Mäkitie A, Ventelä S,. Potential role for inhibition of protein phosphatase 2A tumor suppressor in salivary gland malignancies. Genes Chromosomes Cancer. 2015 Sep 23. IF: 4.041 [microarrays] [qPCR]

• Kainulainen H, Papaioannou KG, Silvennoinen M, Autio R, Saarela J, Oliveira BM, Nyqvist M, Pasternack A, ‘t Hoen PA, Kujala UM, Ritvos O, Hulmi JJ. Myostatin/activin blocking combined with exercise reconditions skeletal muscle expression profile of mdx mice. Mol Cell Endocrinol. 2015 Jan 5;399:131-42. [microarrays]

• Björk JK, Åkerfelt M, Joutsen J, Puustinen MC, Cheng F, Sistonen L, Nees M. Heat-shock factor 2 is a suppressor of prostate cancer invasion. Oncogene. 2015 Jun 29. IF: 8.459 [microarrays] [qPCR]

• Hyder CL, Kemppainen K, Isoniemi KO, Imanishi SY, Goto H, Inagaki M, Fazeli E, Eriksson JE, Törnquist K. Sphingolipids inhibit vimentin-dependent cell migration. J Cell Sci. 2015 Jun 1;128(11):2057-69. IF 5.4 [qPCR]

• Asghar MN, Silvander JS, Helenius TO, Lähdeniemi IA, Alam C, Fortelius LE, Holmsten RO, Toivola DM. The amount of keratins matters for stress protection of the colonic epithelium. PLoS One. 2015 May 22;10(5):e0127436. IF 3.53  [microarrays]

• Högel H, Miikkulainen P, Bino L, Jaakkola PM. Hypoxia inducible prolyl hydroxylase PHD3 maintains carcinoma cell growth by decreasing the stability of p27. Mol Cancer. 2015 Jul 30;14:143. doi: 10.1186/s12943-015-0410-5. IF 4.26 [qPCR]

• Anssi L. Vuorinena, , , Niko Markkinena, Marika Kalpioa, Kaisa M. Linderborga, Baoru Yanga, b, Heikki P. Kallio. Effect of growth environment on the gene expression and lipids related to triacylglycerol biosynthesis in sea buckthorn (Hippophaë rhamnoides) berries. Food Research International Volume 77, Part 3, November 2015, Pages 608–619 [qPCR] IF 2.818

• Trehan A, Rotgers E, Coffey ET, Huhtaniemi I, Rivero-Müller A. CANDLES, an assay for monitoring GPCR induced cAMP generation in cell cultures. Cell Commun Signal. 2014 Nov 4;12:70. doi: 10.1186/s12964-014-0070-x. IF: 3.38 [Sanger]

• Rivero-Müller A, Potorac I, Pintiaux A, Daly AF, Thiry A, Rydlewski C, Nisolle M, Parent AS, Huhtaniemi I, Beckers A4 A novel inactivating mutation of the LH/chorionic gonadotrophin receptor with impaired membrane trafficking leading to Leydig cell hypoplasia type 1. Eur J Endocrinol. 2015 Jun;172(6):K27-36. IF: 4.069 [Sanger]

• Manzini S, Viiri LE, Marttila S, Aalto-Setälä K. A Comparative View on Easy to Deploy non-Integrating Methods for Patient-Specific iPSC Production. Stem Cell Rev. 2015 Dec;11(6):900-8. doi: 10.1007/s12015-015-9619-3. IF: 2.768 [Karyotyping]
• Penttinen K, Swan H, Vanninen S, Paavola J, Lahtinen AM, Kontula K, Aalto-Setälä K . Antiarrhythmic Effects of Dantrolene in Patients with Catecholaminergic Polymorphic Ventricular Tachycardia and Replication of the Responses Using iPSC Models. PLoS One. 2015 May 8;10(5):e0125366. doi: 10.1371/journal.pone.0125366. eCollection 2015. IF: 3.234 [Karyotyping]

• Penttinen K, Siirtola H, Àvalos-Salguero J, Vainio T, Juhola M, Aalto-Setälä K. Novel Analysis Software for Detecting and Classifying Ca2+ Transient Abnormalities in Stem Cell-Derived Cardiomyocytes. PLoS One. 2015 Aug 26;10(8):e0135806. IF: 3.234 [Karyotyping]

• Vehmas AP, Adam M, Laajala TD, Kastenmüller G, Prehn C, Rozman J, Ohlsson C, Fuchs H, Hrabě de Angelis M, Gailus-Durner V, Elo LL, Aittokallio T, Adamski J, Corthals G, Poutanen M, Strauss L. Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse. J Proteomics. 2015 Dec 9;133:66-75. IF: 3.888 [microarrays]

• Aakula A, Leivonen SK, Hintsanen P, Aittokallio T, Ceder Y, Børresen-Dale AL, Perälä M, Östling P, Kallioniemi O. MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth. Mol Oncol. 2015 Aug;9(7):1287-300.  IF: 5.331 [microarrays]

• Undeutsch H, Löf C, Pakarinen P, Poutanen M, Kero J. Thyrocyte-specific Dicer1 deficiency alters thyroid follicular organization and prevents goiter development. Endocrinology. 2015 Apr;156(4):1590-601. IF: 4.503 [NGS]

• Sanmark H, Huovinen T, Matikka T, Pettersson T, Lahti M, Lamminmäki U. Fast conversion of scFv to Fab antibodies using type IIs restriction enzymes. J Immunol Methods. 2015 Nov;426:134-9. IF: 1.82 [sanger]

• Liton MF, Peltola MT, Vehniäinen M, Kuusela E, Pettersson T, Lamminmäki U, Pettersson K, Brockmann EC. Phage display aided improvement of a unique prostate-specific antigen (PSA) antibody unreactive with Lys(145)-Lys(146) internally cleaved forms. J Immunol Methods. 2015 Jul;422:72-9. IF: 1.82 [sanger]
• Pekkala S, Munukka E, Kong L, Pöllänen E, Autio R, Roos C, Wiklund P, Fischer-Posovszky P, Wabitsch M, Alen M, Huovinen P, Cheng S. Toll-like receptor 5 in obesity: the role of gut microbiota and adipose tissue inflammation. Obesity (Silver Spring). 2015 Mar;23(3):581-90. IF: 3.724 [microarray]

• Malinen M, Toropainen S, Jääskeläinen T, Sahu B, Jänne OA, Palvimo JJ. Androgen receptor- and PIAS1-regulated gene programs in molecular apocrine breast cancer cells. Mol Cell Endocrinol. 2015 Oct 15;414:91-8. IF: 4.405 [Microarrays]

• Rotgers E, Nurmio M, Pietilä E, Cisneros-Montalvo S, Toppari J. E2F1 controls germ cell apoptosis during the first wave of spermatogenesis. Andrology. 2015 Sep;3(5):1000-14. IF: 2.298 [Microarrays]

• Xu E, Vaahtera L, Hõrak H, Hincha DK, Heyer AG, Brosché M. Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana. Plant Cell Environ. 2015 Jul;38(7):1418-33. IF: 6.96 [NGS]

• Xu E, Vaahtera L, Brosché M. Roles of
• Defense Hormones in the Regulation of Ozone-Induced Changes in Gene Expression and Cell Death. Mol Plant. 2015 Dec 7;8(12):1776-94. IF: 6.337 [NGS]

• Moreno-Baylach MJ, Puttonen KA, Tenorio-Laranga J, Venäläinen JI, Storvik M, Forsberg MM, García-Horsman JA. Prolyl endopeptidase is involved in cellular signalling in human neuroblastoma SH-SY5Y cells. Neurosignals. 2011;19(2):97-109. IF: 2.0 [microarrays]

• Aakko J, Endo A, Mangani C, Maleta K, Ashorn P, Isolauri E, Salminen S. Distinctive Intestinal Lactobacillus Communities in 6-Month-Old Infants From Rural Malawi and Southwestern Finland. J Pediatr Gastroenterol Nutr. 2015 Dec;61(6):641-8. IF: 2.625 [sanger]

• Elovaara H. Microarray studies on the effect of silencing tynA in Escherichia coli K-12. Genomics Data Volume 7, March 2016, Pages 159–161. IF: 0.111 [microarrays]

• Heinonen MT, Laine AP, Söderhäll C, Gruzieva O, Rautio S, Melén E, Pershagen G, Lähdesmäki HJ, Knip M, Ilonen J, Henttinen TA, Kere J, Lahesmaa R; Finnish Pediatric Diabetes Registry. GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy. J Immunol. 2015 Jun 15;194(12):5885-94. IF: 4.922 [qPCR]

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]

• Tikkanen M, Gollan PJ, Mekala NR, Isojärvi J, Aro EM. Light-harvesting mutants show differential gene expression upon shift to high light as a consequence of photosynthetic redox and reactive oxygen species metabolism. Philos Trans R Soc Lond B Biol Sci. 2014 Mar 3;369(1640):20130229. [microarrays]
• Virtanen SS, Kukkonen-Macchi A, Vainio M, Elima K, Härkönen PL, Jalkanen S, Yegutkin GG. Adenosine inhibits tumor cell invasion via receptor-independent mechanisms. Mol Cancer Res. 2014 Dec;12(12):1863-74. [qPCR]
• Mauro Scaravilli, Paola Asero, Teuvo LJ Tammela, Tapio Visakorpi, Outi R Saramäki. Mapping of the chromosomal amplification 1p21-22 in bladder cancer. BMC Res Notes. 2014; 7: 547. [microarrays]
• Mark Screen, Per Harald Jonson, Olayinka Raheem, Johanna Palmio, Reijo Laaksonen, Terho Lehtimäki, Mario Sirito, Ralf Krahe, Peter Hackman, Bjarne Udd. Abnormal Splicing of NEDD4 in Myotonic Dystrophy Type 2: Possible Link to Statin Adverse Reactions. Am J Pathol. 2014 August; 184(8): 2322–2332. [microarrays]
• Tuomas Huovinen, Markku Syrjänpää, Hanna Sanmark, Titta Seppä, Sultana Akter, Liton Md Ferdhos Khan, Urpo Lamminmäki. The selection performance of an antibody library displayed on filamentous phage coat proteins p9, p3 and truncated p3. BMC Res Notes. 2014; 7: 661. [sequencing]
• Karikoski M, Marttila-Ichihara F, Elima K, Rantakari P, Hollmén M, Kelkka T, Gerke H, Huovinen V, Irjala H, Holmdahl R, Salmi M, Jalkanen S. Clever-1/stabilin-1 controls cancer growth and metastasis. Clin Cancer Res. 2014 Dec 15;20(24):6452-64. [qPCR]
• Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Res. 2014 Feb;42(3):1474-96. IF: 8.808 [microarrays]
• Pavet V, Shlyakhtina Y, He T, Ceschin DG, Kohonen P, Perälä M, Kallioniemi O, Gronemeyer H. Plasminogen activator urokinase expression reveals TRAIL responsiveness and supports fractional survival of cancer cells. Cell Death Dis. 2014 Jan 30;5:e1043. IF 8.371. [microarrays, QPCR]
• Liisa Gunnelius, Kaisa Hakkila, Juha Kurkela, Hajime Wada, Esa Tyystjärvi and Taina Tyystjärvi. The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. Nucleic Acids Res. 2014 Jan 29. IF 8.278. [microarrays]
• Vuorinen AL, Kalpio M, Linderborg KM, Kortesniemi M, Lehto K, Niemi J, Yang B, Kallio HP. Coordinate changes in gene expression and triacylglycerol composition in the developing seeds of oilseed rape (Brassica napus) and turnip rape (Brassica rapa). Food Chem. 2014 Feb 15;145:664-73. IF 3.34. [QPCR]
• Gunnelius L, Kurkela J, Hakkila K, Koskinen S, Parikainen M, Tyystjärvi T. The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis sp. PCC 6803. PLoS One. 2014 Nov 11;9(11):e112599. IF 3.53. [microarrays]
• Heinonen MT, Kanduri K, Lähdesmäki HJ, Lahesmaa R, Henttinen TA. Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation. Immunol Cell Biol. 2014 Oct 7. IF 4.21. [microarrays, QPCR]
• Kallionpää H, Laajala E, Oling V, Härkönen T, Tillmann V, Dorshakova NV, Ilonen J, Lähdesmäki H, Knip M, Lahesmaa R; DIABIMMUNE Study Group. Standard of hygiene and immune adaptation in newborn infants. Clin Immunol. 2014 Nov;155(1):136-47. IF: 3.992. [microarrays]
• Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics. 2014 Jun 15;30(12):i113-20. IF 5.47. [microarrays]
• Kelkka T, Kienhöfer D, Hoffmann M, Linja M, Wing K, Sareila O, Hultqvist M, Laajala E, Chen Z, Vasconcelos J, Neves E, Guedes M, Marques L, Krönke G, Helminen M, Kainulainen L, Olofsson P, Jalkanen S, Lahesmaa R, Souto-Carneiro MM, Holmdahl R. Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature. Antioxid Redox Signal. 2014 Dec 1;21(16):2231-45. IF 8.20. [microarrays]
• Hämäläinen S, Nurminen N, Ahlfors H, Oikarinen S, Sioofy-Khojine AB, Frisk G, Oberste MS, Lahesmaa R, Pesu M, Hyöty H. Coxsackievirus B1 reveals strain specific differences in plasmacytoid dendritic cell mediated immunogenicity. J Med Virol. 2014 Aug;86(8):1412-20. IF: 2.217. [microarrays]
• Munukka E, Pekkala S, Wiklund P, Rasool O, Borra R, Kong L, Ojanen X, Cheng SM, Roos C, Tuomela S, Alen M, Lahesmaa R, Cheng S. Gut-adipose tissue axis in hepatic fat accumulation in humans. J Hepatol. 2014 Jul;61(1):132-8. IF 10.4. [microarrays]
• Kallionpää H, Elo LL, Laajala E, Mykkänen J, Ricaño-Ponce I, Vaarma M, Laajala TD, Hyöty H, Ilonen J, Veijola R, Simell T, Wijmenga C, Knip M, Lähdesmäki H, Simell O, Lahesmaa R. Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility. Diabetes. 2014 Jul;63(7):2402-14. IF 7.9. [microarrays]
• Roncagalli R, Hauri S, Fiore F, Liang Y, Chen Z, Sansoni A, Kanduri K, Joly R, Malzac A, Lähdesmäki H, Lahesmaa R, Yamasaki S, Saito T, Malissen M, Aebersold R, Gstaiger M, Malissen B. Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub. Nat Immunol. 2014 Apr;15(4):384-92. IF 24.97. [microarrays]   
• Sutinen P, Malinen M, Heikkinen S, Palvimo JJ. SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner. Nucleic Acids Res. 2014 Jul;42(13):8310-9. IF 8.81. [microarrays]      
• Toropainen S, Malinen M, Kaikkonen S, Rytinki M, Jääskeläinen T, Sahu B, Jänne OA, Palvimo JJ. SUMO ligase PIAS1 functions as a target gene selective androgen receptor coregulator on prostate cancer cell chromatin. Nucleic Acids Res. 2014 Dec 30. IF 8.808. [microarrays]     
• Paakinaho V, Kaikkonen S, Levonen AL, Palvimo JJ. Electrophilic lipid mediator 15-deoxy-Δ12,14-prostaglandin j2 modifies glucocorticoid signaling via receptor SUMOylation. Mol Cell Biol. 2014 Sep;34(17):3202-13. IF: 5.036. [microarrays]   
• Paakinaho V, Kaikkonen S, Makkonen H, Benes V, Palvimo JJ. SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor. Nucleic Acids Res. 2014 Feb;42(3):1575-92. IF 8.81. [microarrays] 
• Vähätalo LH, Ruohonen ST, Mäkelä S, Kovalainen M, Huotari A, Mäkelä KA, Määttä JA, Miinalainen I, Gilsbach R, Hein L, Ailanen L, Mattila M, Eerola K, Röyttä M,  Ruohonen S, Herzig K, Savontaus E. Neuropeptide Y in the noradrenergic neurones induces obesity and inhibits sympathetic tone in mice. Acta Physiol (Oxf). 2014 Dec 6. IF 4.251. [NGS] 
• Xu E, Vaahtera L, Hõrak H, Hincha DK, Heyer AG, Brosché M. Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana. Plant Cell Environ.  2014 Dec 12. IF 5.906. [NGS]     
• Riihilä PM, Nissinen LM, Ala-aho R, Kallajoki M, Grénman R, Meri S, Peltonen S, Peltonen J, Kähäri VM. Complement factor H: a biomarker for progression of cutaneous squamous cell carcinoma. J Invest Dermatol.  2014 Feb;134(2):498-506. (IF 6.372) [microarray, bioinformatics]
• Morrison VL, James MJ, Grzes K, Cook P, Glass DG, Savinko T, Lek HS, Gawden-Bone C, Watts C, Millington OR, MacDonald AS, Fagerholm SC. Loss of beta2-integrin-mediated cytoskeletal linkage reprogrammes dendritic cells to a mature migratory phenotype.  Nat Commun. 2014 Oct 28;5:5359. IF 10.742. [NGS]     
• Riihilä P, Nissinen L, Farshchian M, Kivisaari A, Ala-Aho R, Kallajoki M, Grénman R, Meri S, Peltonen S, Peltonen J, Kähäri VM. Complement Factor I Promotes Progression of Cutaneous Squamous Cell Carcinoma. J Invest Dermatol. 2014 Sep 3. IF: 6.372. [NGS]    
• Leder EH, McCairns RJ, Leinonen T, Cano JM, Viitaniemi HM, Nikinmaa M, Primmer CR, Merilä J. The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks-Signatures of Selection and Widespread Heritability. Mol Biol Evol. 2014 Nov 25. IF 14.31. [microarrays]    
• Knuuttila M, Yatkin E, Kallio J, Savolainen S, Laajala TD, Aittokallio T, Oksala R, Häkkinen M, Keski-Rahkonen P, Auriola S, Poutanen M, Mäkelä S. Castration induces up-regulation of intratumoral androgen biosynthesis and androgen receptor expression in an orthotopic VCaP human prostate cancer xenograft model. Am J Pathol. 2014 Aug;184(8):2163-73. IF: 4.602. [microarrays]       
• Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H. Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery. BMC Biol. 2014 Dec 9;12(1):103. IF 7.43. [sanger sequencing]   
• Winsel S, Mäki-Jouppila J, Tambe M, Aure MR, Pruikkonen S, Salmela AL, Halonen T, Leivonen SK, Kallio L, Børresen-Dale AL, Kallio MJ. Excess of miRNA-378a-5p perturbs mitotic fidelity and correlates with breast cancer tumourigenesis in vivo. Br J Cancer. 2014 Nov 25;111(11):2142-51. IF: 4.817. [microarrays]
• Xu E, Brosché M. Salicylic acid signaling inhibits apoplastic reactive oxygen species signaling. BMC Plant Biol. 2014 Jun 4;14:155. doi: 10.1186/1471-2229-14-155. IF 4. [microarrays]      
• Arjonen A, Kaukonen R, Mattila E, Rouhi P, Högnäs G, Sihto H, Miller BW, Morton JP, Bucher E, Taimen P, Virtakoivu R, Cao Y, Sansom OJ, Joensuu H, Ivaska J. Mutant p53-associated myosin-X upregulation promotes breast cancer invasion and metastasis. J Clin Invest. 2014 Mar 3;124(3):1069-82. IF 13.765. [QPCR]
• Jada B, Soitamo AJ, Siddiqui SA, Murukesan G, Aro EM, Salakoski T, Lehto K. Multiple different defense mechanisms are activated in the young transgenic tobacco plants which express the full length genome of the Tobacco mosaic virus, and are resistant against this virus. PLoS One. 2014 Sep 22;9(9):e107778. IF: 3.534. [microarrays]
• Kanerva M, Vehmas A, Nikinmaa M, Vuori KA. Spatial Variation in Transcript and Protein Abundance of Atlantic Salmon during Feeding Migration in the Baltic Sea. Environ Sci Technol. 2014 Nov 17. IF: 5.481. [microarrays]
• Salomäki H, Heinäniemi M, Vähätalo LH, Ailanen L, Eerola K, Ruohonen ST, Pesonen U, Koulu M. Prenatal metformin exposure in a maternal high fat diet mouse model alters the transcriptome and modifies the metabolic responses of the offspring. PLoS One. 2014 Dec 26;9(12):e115778. IF 3.53. [microarrays]
• Rytinki M, Kaikkonen S, Sutinen P, Paakinaho V, Rahkama V, Palvimo JJ. Dynamic SUMOylation is linked to the activity cycles of androgen receptor in the cell nucleus. Mol Cell Biol. 2012 Oct;32(20):4195-205. IF: 5.036. [microarrays]
• Nurminen V, Neme A, Ryynänen J, Heikkinen S, Seuter S, Carlberg C. The transcriptional regulator BCL6 participates in the secondary gene regulatory response to vitamin D. Biochim Biophys Acta. 2014 Dec 5. pii: S1874-9399(14)00295-8. IF: 5.440. [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.

• Gardberg M, Kaipio K, Lehtinen L, Mikkonen P, Heuser VD, Talvinen K, Iljin K, Kampf C, Uhlen M, Grénman R, Koivisto M, Carpén O. FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion. PLoS One. 2013 Sep 26;8(9):e74923. doi: 10.1371/journal.pone.0074923. [microarrays]
• He T, Haapa-Paananen S, Kaminskyy VO, Kohonen P, Fey V, Zhivotovsky B, Kallioniemi O, Perälä M. Inhibition of the mitochondrial pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase by doxorubicin and brequinar sensitizes cancer cells to TRAIL-induced apoptosis. Oncogene. 2013 Sep 9. IF 7.357. [QPCR]
• Narvi E, Jaakkola K, Winsel S, Oetken-Lindholm C, Halonen P, Kallio L, Kallio MJ. Altered TUBB3 expression contributes to the epothilone response of mitotic cells. Br J Cancer. 2013 Jan 15;108(1):82-90. IF 5.08. [QPCR]
• Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä JP, Vasemägi A, Primmer CR. Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar). BMC Genomics. 2013 Jul 3;14(1):439. IF 4.4. [bioanalyzer]
• Keuschnigg J, Karinen S, Auvinen K, Irjala H, Mpindi JP, Kallioniemi O, Hautaniemi S, Jalkanen S, Salmi M. Plasticity of blood- and lymphatic endothelial cells and marker identification. PLoS One. 2013 Sep 10;8(9):e74293. IF 3.7. [microarrays]
• Sareila O, Jaakkola N, Olofsson P, Kelkka T, Holmdahl R. Identification of a region in p47phox/NCF1 crucial for phagocytic NADPH oxidase (NOX2) activation. J Leukoc Biol. 2013 Mar;93(3):427-35. IF 4.57. [Sanger sequencing]
• Laine A, Sihto H, Come C, Rosenfeldt MT, Zwolinska A, Niemelä M, Khanna A, Chan EK, Kähäri VM, Kellokumpu-Lehtinen PL, Sansom OJ, Evan GI, Junttila MR, Ryan KM, Marine JC, Joensuu H, Westermarck J. Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1. Cancer Discov. 2013 Feb;3(2):182-97. IF 10.143 [QPCR]
• Sahlberg KK, Hongisto V, Edgren H, Mäkelä R, Hellström K, Due EU, Moen Vollan HK, Sahlberg N, Wolf M, Børresen-Dale AL, Perälä M, Kallioniemi O. The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells. Mol Oncol. 2013 Jun;7(3):392-401. [QPCR]
• Hongisto V, Jernström S, Fey V, Mpindi JP, Kleivi Sahlberg K, Kallioniemi O, Perälä M. High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells. PLoS One. 2013 Oct 23;8(10):e77232. IF 5 [microarrays, QPCR]
• D’Angelo G, Uemura T, Chuang CC, Polishchuk E, Santoro M, Ohvo-Rekilä H, Sato T, Di Tullio G, Varriale A, D’Auria S, Daniele T, Capuani F, Johannes L, Mattjus P, Monti M, Pucci P, Williams RL, Burke JE, Platt FM, Harada A, De Matteis MA. Vesicular and non-vesicular transport feed distinct glycosylation pathways in the Golgi. Nature. 2013 Sep 5;501(7465):116-20. IF 38.6
• Kjellberg MA, Mattjus P. Glycolipid transfer protein expression is affected by glycosphingolipid synthesis. PLoS One. 2013 Jul 24;8(7):e70283. IF 3.8 [QPCR]
• Kalhori V, Kemppainen K, Asghar MY, Bergelin N, Jaakkola P, Törnquist K. Sphingosine-1-Phosphate as a Regulator of Hypoxia-Induced Factor-1α in Thyroid Follicular Carcinoma Cells. PLoS One. 2013 Jun 18;8(6):e66189. IF 3.73 [QPCR]
• Lehtinen L, Ketola K, Mäkelä R, Mpindi JP, Viitala M, Kallioniemi O, Iljin K. High-throughput RNAi screening for novel modulators of vimentin expression identifies MTHFD2 as a regulator of breast cancer cell migration and invasion. Oncotarget. 2013 Jan;4(1):48-63.IF 6.636 [QPCR]
• Turpeinen H, Oksanen A, Kivinen V, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen VP, Nykter M, Pesu M. Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a). J Biol Chem. 2013 Dec 20;288(51):36610-23. [microarrays]
• Paakinaho V, Kaikkonen S, Makkonen H, Benes V, Palvimo JJ. SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor. Nucleic Acids Res. 2013 Nov 4. [Epub ahead of print] IF 8.278. [microarrays]
• Keuschnigg J, Karinen S, Auvinen K, Irjala H, Mpindi JP, Kallioniemi O, Hautaniemi S, Jalkanen S, Salmi M. Plasticity of blood- and lymphatic endothelial cells and marker identification. PLoS One. 2013 Sep 10;8(9):e74293. [microarrays]
• Seuter S, Heikkinen S, Carlberg C. Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression. Nucleic Acids Res. 2013 Jan 1;41(1):110-24.
• Rytkönen KT, Akbarzadeh A, Miandare HK, Kamei H, Duan C, Leder EH, Williams TA, Nikinmaa M (2013) Subfunctionalization of cyprinid hypoxia-inducible factors for roles in development and oxygen-sensing. Evolution. In press, DOI: 10.1111/j.1558-5646.2012.01820.x
• Sinclair LV, Rolf J, Emslie E, Shi YB, Taylor PM, Cantrell DA. Control of amino-acid transport by antigen receptors coordinates the metabolic reprogramming essential for T cell differentiation. Nat Immunol. 2013 May;14(5):500-8. doi: 10.1038/ni.2556.
• Suikkanen S, Kremp A, Hautala H, Krock B. Paralytic shellfish toxins or spirolides? The role of environmental and genetic factors in toxin production of the Alexandrium ostenfeldii complex. Harmful Algae (2013), 26:52-59.
• Sukumaran P, Löf C, Pulli I, Kemppainen K, Viitanen T, Törnquist K. Significance of the transient receptor potential canonical 2 (TRPC2) channel in the regulation of rat thyroid FRTL-5 cell proliferation, migration, adhesion and invasion. Mol Cell Endocrinol. 2013 Jul 15;374(1-2):10-21. doi: 10.1016/j.mce.2013.03.026.
• Kalhori V, Kemppainen K, Asghar MY, Bergelin N, Jaakkola P, Törnquist K. Sphingosine-1-Phosphate as a Regulator of Hypoxia-Induced Factor-1α in Thyroid Follicular Carcinoma Cells. PLoS One. 2013 Jun 18;8(6):e66189.
• Salomäki H, Vähätalo LH, Laurila K, Jäppinen NT, Penttinen AM, Ailanen L, Ilyasizadeh J, Pesonen U, Koulu M. Prenatal metformin exposure in mice programs the metabolic phenotype of the offspring during a high fat diet at adulthood. PLoS One. 2013;8(2):e56594. doi: 10.1371/journal.pone.0056594. Epub 2013 Feb 15.
• Tuomela S, Autio R, Buerki-Thurnherr T, Arslan O, Kunzmann A, Andersson-Willman B, Wick P, Mathur S, Scheynius A, Krug HF, Fadeel B, Lahesmaa R. Gene Expression Profiling of Immune-Competent Human Cells Exposed to Engineered Zinc Oxide or Titanium Dioxide Nanoparticles.  PLoS One. 2013 Jul 22;8(7):e68415.
• Kong L, Tuomela S, Hahne L, Ahlfors H, Yli-Harja O, Fadeel B, Lahesmaa R, Autio R. NanoMiner – Integrative Human Transcriptomics Data Resource for Nanoparticle Research. PLoS One. 2013 Jul 12;8(7):e68414.
• Jada B, Soitamo A, and Lehto K. Organ-specific alterations in tobacco transcriptome caused by the PVX-derived P25 silencing suppressor transgene. BMC Plant Biology 2013, 13:8.
• Laine A, Sihto H, Come C, Rosenfeldt MT, Zwolinska A, Niemelä M, Khanna A, Chan EK, Kähäri V-M, Kellokumpu-Lehtinen P-L, Sansom OJ, Evan GI, Junttila MR, Ryan KM, Marine J-C, Joensuu H, and Westermarck J. Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1. Cancer Discovery 2013;3(2): 182-197.
• Kujala UM, Mäkinen VP, Heinonen I, Soininen P, Kangas AJ, Leskinen TH, Rahkila P, Würtz P, Kovanen V, Cheng S, Sipilä S, Hirvensalo M, Telama R, Tammelin T, Savolainen MJ, Pouta A, O’Reilly PF, Mäntyselkä P, Viikari J, Kähönen M, Lehtimäki T, Elliott P, Vanhala MJ, Raitakari OT, Järvelin MR, Kaprio J, Kainulainen H, Ala-Korpela M. Long-term leisure-time physical activity and serum metabolome. Circulation. 2013 Jan 22;127(3):340-8.
• Hakkila K, Antal T, Gunnelius L, Kurkela J, Matthijs HC, Tyystjärvi E, Tyystjärvi T. Group 2 sigma factor mutant ΔsigCDE of the cyanobacterium Synechocystis sp. PCC 6803 reveals functionality of both carotenoids and flavodiiron proteins in photoprotection of photosystem II. Plant Cell Physiol. 2013 Nov;54(11):1780-90. IF 4.98 . [microarrays]
• Riihilä P, Nissinen L, Ala-Aho R, Kallajoki M, Grénman R, Meri S, Peltonen S, Peltonen J, Kähäri VM. Complement Factor H – a Biomarker for Progression of Cutaneous Squamous cell Carcinoma. J Invest Dermatol. 2013 Aug 12. doi: 10.1038/jid.2013.346
• Leivonen SK, Lazaridis K, Decock J, Chantry A, Edwards DR, Kähäri VM. TGF-β-elicited induction of tissue inhibitor of metalloproteinases (TIMP)-3 expression in fibroblasts involves complex interplay between Smad3, p38α, and ERK1/2. PLoS One. 2013;8(2):e57474. doi: 10.1371/journal.pone.0057474.

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.

• Yu XD, Fooks LJ, Moslehi-Mohebi E, Tischenko VM, Askarieh G, Knight SD, Macintyre S, Zavialov AV. Large is fast, small is tight: determinants of speed and affinity in subunit capture by a periplasmic chaperone. J Mol Biol. 2012 Apr 6;417(4):294-308. IF 4.5.
• Di Yu X, Dubnovitsky A, Pudney AF, Macintyre S, Knight SD, Zavialov AV. Allosteric mechanism controls traffic in the chaperone/usher pathway. Structure. 2012 Nov 7;20(11):1861-71. IF 6.4.
• Roy SP, Rahman MM, Yu XD, Tuittila M, Knight SD, Zavialov AV. Crystal structure of enterotoxigenic Escherichia coli colonization factor CS6 reveals a novel type of functional assembly. Mol Microbiol. 2012 Dec;86(5):1100-15. IF 5.
• Navarro MN, Sinclair LV, Feijoo-Carnero C, Clarke R, Matthews SA, Cantrell DA. Protein kinase D2 has a restricted but critical role in T cell antigen receptor signaling in mature T cells. Biochem J. 2012 Mar 15;442(3):649-59. (Services used: microarrays)
• Pehkonen P, Welter-Stahl L, Diwo J, Ryynanen J, Wienecke-Baldacchino A, Heikkinen S, Treuter E, Steffensen KR, Carlberg C. Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages. BMC Genomics. 2012 Jan 31;13(1):50.
• Niemelä M, Kauko O, Sihto H, Mpindi JP, Nicorici D, Pernilä P, Kallioniemi OP, Joensuu H, Hautaniemi S, Westermarck J. CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes. Oncogene. 2012 Sep 27;31(39):4266-78. (Services used: microarrays, qPCR)
• Hulmi JJ, Silvennoinen M, Lehti M, Kivelä R, Kainulainen H. Altered REDD1, myostatin, and Akt/mTOR/FoxO/MAPK signaling in streptozotocin-induced diabetic muscle atrophy. Am J Physiol Endocrinol Metab. 2012 Feb;302(3):E307-15.
• Koskinen A, Lukkarinen H, Moritz N, Aho H, Kääpä P, Soukka H. Fetal hyperglycemia alters lung structural development in neonatal rat. Pediatr Pulmonol. 2012 Mar;47(3):275-82.
• Mykkänen OT, Kalesnykas G, Adriaens M, Evelo CT, Törrönen R, Kaarniranta K. Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice. Mol Vis. 2012;18:2338-51. (Services used: microarrays, qPCR)
• Kolehmainen M, Mykkänen O, Kirjavainen PV, Leppänen T, Moilanen E, Adriaens M, Laaksonen DE, Hallikainen M, Puupponen-Pimiä R, Pulkkinen L, Mykkänen H, Gylling H, Poutanen K, Törrönen R. Bilberries reduce low-grade inflammation in individuals with features of metabolic syndrome. Mol Nutr Food Res. 2012 Oct;56(10):1501-10. (Services used: microarrays)
• Haapa-Paananen S, Kiviluoto S, Waltari M, Puputti M, Mpindi JP, Kohonen P, Tynninen O, Haapasalo H, Joensuu H, Perälä M, Kallioniemi O. HES6 gene is selectively overexpressed in glioma and represents an important transcriptional regulator of glioma proliferation. Oncogene. 2012 Mar 8;31(10):1299-310.
• Toriseva M, Ala-aho R, Peltonen S, Peltonen J, Grénman R, Kähäri VM. Keratinocyte growth factor induces gene expression signature associated with suppression of malignant phenotype of cutaneous squamous carcinoma cells. PLoS One. 2012;7(3):e33041. (Services used: microarrays, bioinformatics, qPCR)
• Toriseva M, Laato M, Carpén O, Ruohonen ST, Savontaus E, Inada M, Krane SM, Kähäri VM. MMP-13 regulates growth of wound granulation tissue and modulates gene expression signatures involved in inflammation, proteolysis, and cell viability. PLoS One. 2012;7(8):e42596. (Services used: microarrays, bioinformatics, qPCR)
• Lee Y, Sooranna SR, Terzidou V, Christian M, Brosens J, Huhtinen K, Poutanen M, Barton G, Johnson MR, Bennett PR. Interactions between inflammatory signals and the progesterone receptor in regulating gene expression in pregnant human uterine myocytes. J Cell Mol Med. 2012 Oct;16(10):2487-503. (Services used: microarrays)
• Morales LO, Brosché M, Vainonen J, Jenkins GI, Wargent JJ, Sipari N, Strid A, Lindfors AV, Tegelberg R, Aphalo PJ. Multiple Roles for UV RESISTANCE LOCUS 8 in Regulating Gene Expression and Metabolite Accumulation in Arabidopsis under Solar UV Radiation. Plant Physiol. 2012 Dec 18. (Services used: microarrays)
• Ahtiainen M, Alen M, Pöllänen E, Pulkkinen S, Ronkainen PH, Kujala UM, Kaprio J, Sipilä S, Kovanen V. Hormone therapy is associated with better body composition and adipokine/glucose profiles: a study with monozygotic co-twin control design. Menopause. 2012 Dec;19(12):1329-35. (Services used: microarrays)
• Sareila O, Jaakkola N, Olofsson P, Kelkka T, Holmdahl R. Identification of a region in p47phox/NCF1 crucial for phagocytic NADPH oxidase (NOX2) activation. J Leukoc Biol. 2012 Dec 27. [Epub ahead of print] (Services used: Sanger sequencing)
• Aijö T, Edelman SM, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H. An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. BMC Genomics. 2012 Oct 30;13:572. (Services used: microarrays)
• Ylipaasto P, Smura T, Gopalacharyulu P, Paananen A, Seppänen-Laakso T, Kaijalainen S, Ahlfors H, Korsgren O, Lakey JR, Lahesmaa R, Piemonti L, Oresic M, Galama J, Roivainen M. Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction. Diabetologia. 2012 Dec;55(12):3273-83. (Services used: microarrays, bioinformatics, qPCR)
• Soitamo AJ, Jada B, Lehto K. Expression of geminiviral AC2 RNA silencing suppressor changes sugar and jasmonate responsive gene expression in transgenic tobacco plants. BMC Plant Biol. 2012 Nov 7;12:204. (Services used: microarrays)
• Löf C, Sukumaran P, Viitanen T, Vainio M, Kemppainen K, Pulli I, Näsman J, Kukkonen JP, Törnquist K. Communication Between the Calcium and cAMP Pathways Regulate the Expression of the TSH Receptor: TRPC2 in the Center of Action. Mol Endocrinol. 2012 Dec;26(12):2046-57. (Services used: qPCR)
• Sukumaran P, Löf C, Kemppainen K, Kankaanpää P, Pulli I, Näsman J, Viitanen T, Törnquist K. Canonical Transient Receptor Potential Channel 2 (TRPC2) as a Major Regulator of Calcium Homeostasis in Rat Thyroid FRTL-5 Cells: IMPORTANCE OF PROTEIN KINASE C δ (PKCδ) AND STROMAL INTERACTION MOLECULE 2 (STIM2). J Biol Chem. 2012 Dec 28;287(53):44345-60. (Services used: Sanger sequencing, qPCR)
• Tahvanainen J, Kyläniemi MK, Kanduri K, Gupta B, Lähteenmäki H, Kallonen T, Rajavuori A, Rasool O, Koskinen PJ, Rao KV, Lähdesmäki H, Lahesmaa R. Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation. J Biol Chem. 2012 Dec 3. [Epub ahead of print] (Services used: microarrays)
• Nikula T, Mykkänen J, Simell O, Lahesmaa R. Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res. 2012 Nov 5. pii: S1931-5244(12)00364-7. (Services used: microarrays)
• Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Gupta B, Äijö T, Oikari L, Stockinger B, Lähdesmäki H, Lahesmaa R. Identification of early gene expression changes during human Th17 cell differentiation. Blood. 2012 Jun 7;119(23):e151-60. (Services used: microarrays)
• Lönnberg T, Yetukuri L, Seppänen-Laakso T, Lahesmaa R*, Orešič M*. T-cell activation induces selective changes of cellular lipidome. Front Biosci E5 : 558-573, 2013. *Equal contribution
• Rytkönen KT, Renshaw GM, Vainio PP, Ashton KJ, Williams-Pritchard G, Leder EH, Nikinmaa M. Transcriptional responses to hypoxia are enhanced by recurrent hypoxia (hypoxic preconditioning) in the epaulette shark. Physiol Genomics. 2012 Nov 16;44(22):1090-7. (Services used: qPCR)
• Nylund C, Rappu P, Pakula E, Heino A, Laato L, Elo LL, Vihinen P, Pyrhönen S, Owen GR, Larjava H, Kallajoki M, Heino J. Melanoma-associated cancer-testis antigen 16 (CT16) regulates the expression of apoptotic and antiapoptotic genes and promotes cell survival. PLoS One. 2012;7(9):e45382 (Services used: microarrays)
• Raiko L, Siljamäki E, Mahoney MG, Putaala H, Suominen E, Peltonen J, Peltonen S. Hailey-Hailey disease and tight junctions: Claudins 1 and 4 are regulated by ATP2C1 gene encoding Ca(2+) /Mn(2+) ATPase SPCA1 in cultured keratinocytes. Exp Dermatol. 2012 Aug;21(8):586-91. (Services used: qPCR)
• Finlay DK, Rosenzweig E, Sinclair LV, Feijoo-Carnero C, Hukelmann JL, Rolf J, Panteleyev AA, Okkenhaug K, Cantrell DA. PDK1 regulation of mTOR and hypoxia-inducible factor 1 integrate metabolism and migration of CD8+ T cells. J Exp Med. 2012 Dec 17;209(13):2441-53. (Services used: microarrays)
• Lehtinen L, Vainio P, Wikman H, Reemts J, Hilvo M, Issa R, Pollari S, Brandt B, Oresic M, Pantel K, Kallioniemi O, Iljin K. 15-hydroxyprostaglandin dehydrogenase associates with poor prognosis in breast cancer, induces epithelial-mesenchymal transition and promotes cell migration in cultured breast cancer cells. J Pathol. 2012 Mar;226(4):674-86. (Services used: microarrays, qPCR)
• Ketola K, Hilvo M, Hyötyläinen T, Vuoristo A, Ruskeepää AL, Orešič M, Kallioniemi O, Iljin K. Salinomycin inhibits prostate cancer growth and migration via induction of oxidative stress. Br J Cancer. 2012 Jan 3;106(1):99-106. (Services used: microarrays)
• Lepistö A, Rintamäki E. Coordination of plastid and light signaling pathways upon development of Arabidopsis leaves under various photoperiods. Mol Plant. 2012 Jul;5(4):799-816.
• Näreoja K, Näsman J. Characterization of α(2B)-adrenoceptor ligand binding in the presence of muscarinic toxin α and delineation of structural features of receptor binding selectivity. Eur J Pharmacol. 2012 May 15;683(1-3):63-70 (Services used: Sanger sequencing)
• Näreoja K, Louhivuori LM, Akerman KE, Meriluoto J, Näsman J. Glycosylphosphatidylinositol (GPI)-anchoring of mamba toxins enables cell-restricted receptor silencing. Biochem Biophys Res Commun. 2012 Jan 6;417(1):93-7. (Services used: Sanger sequencing)
• Mathiasen DP, Egebjerg C, Andersen SH, Rafn B, Puustinen P, Khanna A, Daugaard M, Valo E, Tuomela S, Bøttzauw T, Nielsen CF, Willumsen BM, Hautaniemi S, Lahesmaa R, Westermarck J, Jäättelä M, and Kallunki T. Identification of a c-Jun N-terminal kinase-2-dependent signal amplification cascade that regulates c-Myc levels in ras transformation. Oncogene, 31, 390-401, 2012

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

• Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Närvä E, Ng S, Sourour M, Hämäläinen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T. Copy number variation and selection during reprogramming to pluripotency. Nature. 2011 Mar 3;471(7336):58-62.
• Tkachenko IV, Jääskeläinen T, Jääskeläinen J, Palvimo JJ, Voutilainen R. Interleukins 1α and 1β as regulators of steroidogenesis in human NCI-H295R adrenocortical cells. Steroids. 2011 Sep-Oct;76(10-11):1103-15.
• Björkman M, Ostling P, Härmä V, Virtanen J, Mpindi JP, Rantala J, Mirtti T, Vesterinen T, Lundin M, Sankila A, Rannikko A, Kaivanto E, Kohonen P, Kallioniemi O, Nees M. Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Oncogene. 2011 Nov 28. doi: 10.1038/onc.2011.512.
• Tommila M, Stark C, Jokilammi A, Peltonen V, Penttinen R, Ekholm E. Hemoglobin expression in rat experimental granulation tissue. J Mol Cell Biol. 2011 Jun;3(3):190-6.
• Farshchian M, Kivisaari A, Ala-Aho R, Riihilä P, Kallajoki M, Grénman R, Peltonen J, Pihlajaniemi T, Heljasvaara R, Kähäri VM. Serpin peptidase inhibitor clade A member 1 (SerpinA1) is a novel biomarker for progression of cutaneous squamous cell carcinoma. Am J Pathol. 2011 Sep;179(3):1110-9.
• Vainio P, Lehtinen L, Mirtti T, Hilvo M, Seppänen-Laakso T, Virtanen J, Sankila A, Nordling S, Lundin J, Rannikko A, Orešič M, Kallioniemi O, Iljin K. Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins. Oncotarget. 2011 Dec 22.
• Vainio P, Wolf M, Edgren H, He T, Kohonen P, Mpindi JP, Smit F, Verhaegh G, Schalken J, Perälä M, Iljin K, Kallioniemi O. Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer. Prostate. 2011 Sep 14. doi: 10.1002/pros.21487.
• Vainio P, Gupta S, Ketola K, Mirtti T, Mpindi JP, Kohonen P, Fey V, Perälä M, Smit F, Verhaegh G, Schalken J, Alanen KA, Kallioniemi O, Iljin K. Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer. Am J Pathol. 2011 Feb;178(2):525-36.
• Macintyre AN, Finlay D, Preston G, Sinclair LV, Waugh CM, Tamas P, Feijoo C, Okkenhaug K, Cantrell DA. Protein kinase B controls transcriptional programs that direct cytotoxic T cell fate but is dispensable for T cell metabolism. Immunity. 2011 Feb 25;34(2):224-36.
• Gorowiec MR, Catalano RD, Norman JE, Denison FC, Jabbour HN. Prokineticin 1 induces inflammatory response in human myometrium: a potential role in initiating term and preterm parturition. Am J Pathol. 2011 Dec;179(6):2709-19.
• Trotta, A., Wrzaczek, M., Scharte, J., Tikkanen, M., Konert, G., Rahikainen, M., Holmström, M., Hiltunen, HM., Rips, S., Sipari, N., Mulo, P., Weis, E., von Schaewen, A., Aro, EM. and Kangasjarvi, S. Regulatory subunit B of protein phosphatase 2A prevents unnecessary defense reactions under low light in Arabidopsis thaliana. Plant Physiology 2011 156:1464-1480
• Rintala E, Jouhten P, Toivari M, Wiebe MG, Maaheimo H, Penttilä M, Ruohonen L. Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. OMICS. 2011 Jul-Aug;15(7-8):461-76. doi: 10.1089/omi.2010.0082.
• Kallonen T, Gröndahl-Yli-Hannuksela K, Elomaa A, Lutyńska A, Fry NK, Mertsola J, He Q. Differences in the genomic content of Bordetella pertussis isolates before and after introduction of pertussis vaccines in four European countries. Infect Genet Evol. 2011 Dec;11(8):2034-42.
• Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C. Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy. Nucleic Acids Res. 2011 Nov;39(21):9181-93.
• Koponen T, Cerrada-Gimenez M, Pirinen E, Hohtola E, Paananen J, Vuohelainen S, Tusa M, Pirnes-Karhu S, Heikkinen S, Virkamäki A, Uimari A, Alhonen L, Laakso M. The activation of hepatic and muscle polyamine catabolism improves glucose homeostasis. Amino Acids. 2011 Aug 4.
• Soitamo AJ, Jada B, Lehto K. HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers. BMC Plant Biol. 2011 Apr 20;11:68.
• Sipilä P, Krutskikh A, Pujianto DA, Poutanen M, Huhtaniemi I. Regional expression of androgen receptor coregulators and androgen action in the mouse epididymis. J Androl. 2011 Nov;32(6):711-7.
• Navarro MN, Goebel J, Feijoo-Carnero C, Morrice N, Cantrell DA. Phosphoproteomic analysis reveals an intrinsic pathway for the regulation of histone deacetylase 7 that controls the function of cytotoxic T lymphocytes. Nat Immunol. 2011 Apr;12(4):352-61.
• Vuoriluoto K, Haugen H, Kiviluoto S, Mpindi JP, Nevo J, Gjerdrum C, Tiron C, Lorens JB, Ivaska J. Vimentin regulates EMT induction by Slug and oncogenic H-Ras and migration by governing Axl expression in breast cancer. Oncogene. 2011 Mar 24;30(12):1436-48.
• Westerlund N, Zdrojewska J, Padzik A, Komulainen E, Björkblom B, Rannikko E, Tararuk T, Garcia-Frigola C, Sandholm J, Nguyen L, Kallunki T, Courtney MJ, Coffey ET. Phosphorylation of SCG10/stathmin-2 determines multipolar stage exit and neuronal migration rate. Nat Neurosci. 2011 Mar;14(3):305-13.
• Hoffmann J, Yin J, Kukucka M, Yin N, Saarikko I, Sterner-Kock A, Fujii H, Leong-Poi H, Kuppe H, Schermuly RT, Kuebler WM. Mast cells promote lung vascular remodelling in pulmonary hypertension. Eur Respir J. 2011 Jun;37(6):1400-10.
• Sysi-Aho M, Ermolov A, Gopalacharyulu PV, Tripathi A, Seppänen-Laakso T, Maukonen J, Mattila I, Ruohonen ST, Vähätalo L, Yetukuri L, Härkönen T, Lindfors E, Nikkilä J, Ilonen J, Simell O, Saarela M, Knip M, Kaski S, Savontaus E, Orešič M. Metabolic regulation in progression to autoimmune diabetes. PLoS Comput Biol. 2011 Oct;7(10):e1002257.
• Heinonen J, Taipaleenmäki H, Roering P, Takatalo M, Harkness L, Sandholm J, Uusitalo-Järvinen H, Kassem M, Kiviranta I, Laitala-Leinonen T, Säämänen AM. Snorc is a novel cartilage specific small membrane proteoglycan expressed in differentiating and articular chondrocytes. Osteoarthritis Cartilage. 2011 Aug;19(8):1026-35.
• Pan PW, Parkkila AK, Autio S, Hilvo M, Sormunen R, Pastorekova S, Pastorek J, Haapasalo H, Parkkila S. Brain phenotype of carbonic anhydrase IX-deficient mice. Transgenic Res. 2011 May 6.
• Pan PW, Käyrä K, Leinonen J, Nissinen M, Parkkila S, Rajaniemi H. Gene expression profiling in the submandibular gland, stomach, and duodenum of CAVI-deficient mice. Transgenic Res. 2011 Jun;20(3):675-98.
• Ylihärsilä M, Valta T, Karp M, Hattara L, Harju E, Hölsä J, Saviranta P, Waris M, Soukka T. Oligonucleotide array-in-well platform for detection and genotyping human adenoviruses by utilizing upconverting phosphor label technology. Anal Chem. 2011 Feb 15;83(4):1456-61.
• Hussein S, Batada N, Vuoristo S, Autio R, Närvä E, Ng  S, Hämäläinen  R,  Olsson C,  Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Alitalo K, Lahesmaa R, Nagy A #, Otonkoski T# Increased mutation load is associated with reprogramming of human somatic cells .#.Equal contribution. Nature, (2011) 471:58-62
• Fathi A, Hatami M, Hajihosseini V, Fattahi F, Kiani S, Baharvand H, Salekdeh GH. Comprehensive gene expression analysis of human embryonic stem cells during differentiation into neural cells. PLoS One. 2011;6(7):e22856.
• Damdimopoulou P, Nurmi T, Salminen A, Damdimopoulos AE, Kotka M, van der Saag P, Strauss L, Poutanen M, Pongratz I, Mäkelä S. A single dose of enterolactone activates estrogen signaling and regulates expression of circadian clock genes in mice. J Nutr. 2011 Sep;141(9):1583-9.
• Bäckström E, Hogmalm A, Lappalainen U, Bry K. Developmental stage is a major determinant of lung injury in a murine model of bronchopulmonary dysplasia. Pediatr Res. 2011 Apr;69(4):312-8.
• Mitina GV, Tokarev YS, Movila AA, Yli-Mattila T. Polymorphism of Beauveria bassiana (Deuteromycota: Hyphomycetes) strains isolated from Ixodes ricinus (Acari: Ixodidae) in Moldova. Ticks and Tick Borne Diseases 2011 2:50-54.
• Yli-Mattila T, Ward T, O’Donnell K, Proctor RH, Burkin A, Kononenko G, Gavrilova O, Aoki T, McCormick SP, Gagkaeva T. F. sibiricum sp. nov; a novel type A trichothecene-producing
  Fusarium from northern Asia closely related to F. sporotrichioides and F. langsethiae. International Journal of Food Microbiology 2011 147:58-68.
• Rondinelli S, Näreoja K, Näsman J. Molecular conversion of muscarinic acetylcholine receptor M(5) to muscarinic toxin 7 (MT7)-binding protein. Toxins (Basel). 2011 Nov;3(11):1393-404. (Services used: Sanger sequencing)

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.

• Sainio A, Jokela T, Tammi MI, Järveläinen H. Hyperglycemic conditions modulate connective tissue reorganization by human vascular smooth muscle cells through stimulation of hyaluronan synthesis. Glycobiology. 2010 Sep;20(9):1117-26.
• Moulder R, Lönnberg T, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R. Quantitative Proteomics Analysis of the Nuclear Fraction of Human CD4+ Cells in the Early Phases of IL-4 Induced Th2 Differentiation. Mol Cell Proteomics. 2010 May 13.
• Ahlfors H, Limaye A, Elo LL, Tuomela S, Burute M, Gottimukkala K, Notani D, Rasool O, Galande S, Lahesmaa R. SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood. 2010 Jun 3.
• Laura L. Elo, Henna Järvenpää, Soile Tuomela, Sunil Raghav, Helena Ahlfors, Kirsti Laurila, Bhawna Gupta, Riikka J. Lund, Johanna Tahvanainen, R. David Hawkins, Matej Orešič, Harri Lähdesmäki, Omid Rasool, Kanury V. Rao, Tero Aittokallio, Riitta Lahesmaa, Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming, Immunity 2010, 32(6):852-862.
• Elo LL, Mykkänen J, Nikula T, Järvenpää H, Simell S, Aittokallio T, Hyöty H, Ilonen J, Veijola R, Simell T, Knip M, Simell O, Lahesmaa R. Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun. 2010 Aug;35(1):70-6.
• Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity.Nat Biotechnol. 2010 Apr;28(4):371-7.
• Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J, Ahlfors H, Coffey E, Rao KV, Rasool O, Lahesmaa R. Activating transcription factor 3 is a positive regulator of human IFNG gene expression. J Immunol. 2010 May 1;184(9):4990-9.
• Gupta S, Iljin K, Sara H, Mpindi JP, Mirtti T, Vainio P, Rantala J, Alanen K, Nees M, Kallioniemi O. FZD4 as a mediator of ERG oncogene-induced WNT signaling and epithelial-to-mesenchymal transition in human prostate cancer cells. Cancer Res. 2010 Sep 1;70(17):6735-45. 
• Ketola K, Vainio P, Fey V, Kallioniemi O, Iljin K. Monensin is a potent inducer of oxidative stress and inhibitor of androgen signaling leading to apoptosis in prostate cancer cells. Mol Cancer Ther. 2010 Dec;9(12):3175-85.
• Pöllänen E, Fey V, Törmäkangas T, Ronkainen PH, Taaffe DR, Takala T, Koskinen S, Cheng S, Puolakka J, Kujala UM, Suominen H, Sipilä S, Kovanen V. Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle. Age (Dordr). 2010 Sep;32(3):347-63. 
• Leder EH, Cano JM, Leinonen T, O’Hara RB, Nikinmaa M, Primmer CR, Merilä J. Female-biased expression on the X chromosome as a key step in sex chromosome evolution in threespine sticklebacks. Mol Biol Evol. 2010 Jul;27(7):1495-503. Epub 2010 Feb 8.
• Elo TD, Valve EM, Seppänen JA, Vuorikoski HJ, Mäkelä SI, Poutanen M, Kujala PM, Härkönen PL. Stromal activation associated with development of prostate cancer in prostate-targeted fibroblast growth factor 8b transgenic mice. Neoplasia. 2010 Nov;12(11):915-27.
• Mattila P, Renkonen J, Toppila-Salmi S, Parviainen V, Joenväärä S, Alff-Tuomala S, Nicorici D, Renkonen R. Time-series nasal epithelial transcriptomics during natural pollen exposure in healthy subjects and allergic patients. Allergy. 2010 Feb;65(2):175-83.
• Renkonen J, Mattila P, Parviainen V, Joenväärä S, Toppila-Salmi S, Renkonen R. A network analysis of the single nucleotide polymorphisms in acute allergic diseases. Allergy. 2010 Jan;65(1):40-7.
• Leskinen T, Rinnankoski-Tuikka R, Rintala M, Seppänen-Laakso T, Pöllänen E, Alen M, Sipilä S, Kaprio J, Kovanen V, Rahkila P, Oresic M, Kainulainen H, Kujala UM. Differences in muscle and adipose tissue gene expression and cardio-metabolic risk factors in the members of physical activity discordant twin pairs. PLoS One. 2010 Sep 16;5(9). pii: e12609.
• Stokes A, Joutsa J, Ala-Aho R, Pitchers M, Pennington CJ, Martin C, Premachandra DJ, Okada Y, Peltonen J, Grénman R, James HA, Edwards DR, Kähäri VM. Expression profiles and clinical correlations of degradome components in the tumor microenvironment of head and neck squamous cell carcinoma. Clin Cancer Res. 2010 Apr 1;16(7):2022-35.
• Kallio H, Hilvo M, Rodriguez A, Lappalainen EH, Lappalainen AM, Parkkila S. Global transcriptional response to carbonic anhydrase IX deficiency in the mouse stomach. BMC Genomics. 2010 Jun 23;11:397.
• Lindroos B, Aho KL, Kuokkanen H, Räty S, Huhtala H, Lemponen R, Yli-Harja O, Suuronen R, Miettinen S. Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. Tissue Eng Part A. 2010 Jul;16(7):2281-94.
• Sundvall M, Veikkolainen V, Kurppa K, Salah Z, Tvorogov D, van Zoelen EJ, Aqeilan R, Elenius K. Cell death or survival promoted by alternative isoforms of ErbB4. Mol Biol Cell. 2010 Dec;21(23):4275-86.
• Laurén HB, Lopez-Picon FR, Brandt AM, Rios-Rojas CJ, Holopainen IE. Transcriptome analysis of the hippocampal CA1 pyramidal cell region after kainic acid-induced status epilepticus in juvenile rats. PLoS One. 2010 May 20;5(5):e10733.
• Ronkainen PH, Pöllänen E, Alén M, Pitkänen R, Puolakka J, Kujala UM, Kaprio J, Sipilä S, Kovanen V. Global gene expression profiles in skeletal muscle of monozygotic female twins discordant for hormone replacement therapy. Aging Cell. 2010 Dec;9(6):1098-110.
• Pöllänen E, Ronkainen PH, Horttanainen M, Takala T, Puolakka J, Suominen H, Sipilä S, Kovanen V. Effects of combined hormone replacement therapy or its effective agents on the IGF-1 pathway in skeletal muscle. Growth Horm IGF Res. 2010 Oct;20(5):372-9.
• Kivelä R, Silvennoinen M, Lehti M, Rinnankoski-Tuikka R, Purhonen T, Ketola T, Pullinen K, Vuento M, Mutanen N, Sartor MA, Reunanen H, Koch LG, Britton SL, Kainulainen H. Gene expression centroids that link with low intrinsic aerobic exercise capacity and complex disease risk. FASEB J. 2010 Nov;24(11):4565-74.
• Sainio A, Jokela T, Tammi MI, Järveläinen H. Hyperglycemic conditions modulate connective tissue reorganization by human vascular smooth muscle cells through stimulation of hyaluronan synthesis. Glycobiology. 2010 Sep;20(9):1117-26.

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.

• Leder EH, Meril J, Primmer CR. A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus). BMC Genomics. 2009 Sep 11;10:426
• Kyläniemi MK, Haveri A, Vuola JM, Puolakkainen M, Lahesmaa R. Gene expression signatures characterizing the development of lymphocyte response during experimental Chlamydia pneumoniae infection. Microb Pathog. 2009 May;46(5):235-42. Epub 2009 Feb 4.
• Huhtinen K, Suvitie P, Hiissa J, Junnila J, Huvila J, Kujari H, Setälä M, Härkki P, Jalkanen J, Fraser J, Mäkinen J, Auranen A, Poutanen M, Perheentupa A. Serum HE4 concentration differentiates malignant ovarian tumours from ovarian endometriotic cysts.  Br J Cancer. 2009 Apr 21;100(8):1315-9
• Strauss L, Kallio J, Desai N, Pakarinen P, Miettinen T, Gyllin H, Albrecht M, Mäkelä S, Mayerhofer A, Poutanen M. Increased exposure to estrogens disturbs maturation, steroidogenesis, and cholesterol homeostasis via estrogen receptor alpha in adult mouse Leydig cells. Endocrinology. 2009 Jun;150(6):2865-72
• Mobini R, Andersson BA, Erjefält J, Hahn-Zoric M, Langston MA, Perkins AD, Cardell LO, Benson M. A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation. BMC Syst Biol. 2009 Feb 12;3:19
• Benson M, Mobini R, Barrenäs F, HalldÈn C, Naluai AT, Säll T, Cardell LO. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. Allergy. 2009 Feb 13
• Iljin K, Ketola K, Vainio P, Halonen P, Kohonen P, Fey V, Grafström RC, Perälä M, Kallioniemi O. High-throughput cell-based screening of 4910 known drugs and drug-like small molecules identifies disulfiram as an inhibitor of prostate cancer cell growth. Clin Cancer Res. 2009 Oct 1;15(19):6070-8.
• Sandqvist A, Björk JK, Akerfelt M, Chitikova Z, Grichine A, Vourc’h C, Jolly C, Salminen TA, Nymalm Y, Sistonen L. Heterotrimerization of heat-shock factors 1 and 2 provides a transcriptional switch in response to distinct stimuli. Mol Biol Cell. 2009 Mar;20(5):1340-7.
• Rintala E, Toivari M, Pitkänen JP, Wiebe MG, Ruohonen L, Penttilä M. Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae. BMC Genomics. 2009 Oct 5;10:461.
• Leinonen PT, Hägg PM, Peltonen S, Jouhilahti EM, Melkko J, Korkiamäki T, Oikarinen A, Peltonen J. Reevaluation of the normal epidermal calcium gradient, and analysis of calcium levels and ATP receptors in Hailey-Hailey and Darier epidermis. J Invest Dermatol. 2009 Jun;129(6):1379-87.
• Leskinen T, Waller K, Mutikainen S, Aaltonen S, Ronkainen PH, Alén M, Sipilä S, Kovanen V, Perhonen M, Pietiläinen KH, Cheng S, Suominen H, Kainulainen H, Kaprio J, Kujala UM. Effects of 32-year leisure time physical activity discordance in twin pairs on health (TWINACTIVE study): aims, design and results for physical fitness. Twin Res Hum Genet. 2009 Feb;12(1):108-17.
• Joenväärä S, Mattila P, Renkonen J, Mäkitie A, Toppila-Salmi S, Lehtonen M, Salmi P, Lehti S, Mäkinen J, Sormunen R, Paavonen T, Renkonen R. Caveolar transport through nasal epithelium of birch pollen allergen Bet v 1 in allergic patients. J Allergy Clin Immunol. 2009 Jul;124(1):135-142.e1-21.
• Renkonen J, Mattila P, Lehti S, Mäkinen J, Sormunen R, Tervo T, Paavonen T, Renkonen R. Birch pollen allergen Bet v 1 binds to and is transported through conjunctival epithelium in allergic patients. Allergy. 2009 Jun;64(6):868-75.
• Suomela S, Elomaa O, Skoog T, Ala-aho R, Jeskanen L, Pärssinen J, Latonen L, Grénman R, Kere J, Kähäri VM, Saarialho-Kere U. CCHCR1 is up-regulated in skin cancer and associated with EGFR expression. PLoS One. 2009 Jun 24;4(6):e6030.
• Waltering KK, Helenius MA, Sahu B, Manni V, Linja MJ, Jänne OA, Visakorpi T. Increased expression of androgen receptor sensitizes prostate cancer cells to low levels of androgens. Cancer Res. 2009 Oct 15;69(20):8141-9.

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

• Björkman M, Iljin K, Halonen P, Sara H, Kaivanto E, Nees M, Kallioniemi OP. Defining the molecular action of HDAC inhibitors and synergism with androgen deprivation in ERG-positive prostate cancer. Int. J. Cancer. 2008; 123: 2774-2781
• Mikhailov A, Sokolovskaya A, Yegutkin GG, Amdahl H, West A, Yagita H, Lahesmaa R, Thompson LF, Jalkanen S, Blokhin D, Eriksson JE. CD73 participates in cellular multiresistance program and protects against TRAIL-induced apoptosis. J. Immunol. 2008 Jul;181(1):464-75
• Rauhala HE, Porkka KP, Saramäki OR, Tammela TL, Visakorpi T. Clusterin is epigenetically regulated in prostate cancer. Int. J. Cancer. 2008 Oct;123(7):1601-9
• MacKenzie S, Balasch JC, Novoa B, Ribas L, Roher N, Krasnov A, Figueras A. Comparative analysis of the acute response of the trout, O. mykiss, head kidney to in vivo challenge with virulent and attenuated infectious hematopoietic necrosis virus and LPS-induced inflammation. BMC Genomics. 2008 ;9():141-0
• Kangasjärvi S, Lepistö A, Hännikäinen K, Piippo M, Luomala EM, Aro EM, Rintamäki E. Diverse roles for chloroplast stromal and thylakoid-bound ascorbate peroxidases in plant stress responses. Biochem. J. 2008 Jun;412(2):275-85
• Pekkinen M, Ahlström ME, Riehle U, Huttunen MM, Lamberg-Allardt CJ. Effects of phosphodiesterase 7 inhibition by RNA interference on the gene expression and differentiation of human mesenchymal stem cell-derived osteoblasts. Bone. 2008 Jul;43(1):84-91
• Barrenäs F, Andersson B, Cardell LO, Langston M, Mobini R, Perkins A, Soini J, Ståhl A, Benson M. Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine. 2008 Jun;42(3):325-9
• Jorgensen SM, Afanasyev S, Krasnov A. Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality. BMC Genomics. 2008 ;9():179-0
• Kivi N, Greco D, Auvinen P, Auvinen E. Genes involved in cell adhesion, cell motility and mitogenic signaling are altered due to HPV 16 E5 protein expression. Oncogene. 2008 Apr;27(18):2532-41
• Fliniaux I, Mikkola ML, Lefebvre S, Thesleff I. Identification of dkk4 as a target of Eda-A1/Edar pathway reveals an unexpected role of ectodysplasin as inhibitor of Wnt signalling in ectodermal placodes. Dev. Biol. 2008 Aug;320(1):60-71
• Taipaleenmäki H, Suomi S, Hentunen T, Laitala-Leinonen T, Säämänen AM. Impact of stromal cell composition on BMP-induced chondrogenic differentiation of mouse bone marrow derived mesenchymal cells. Exp. Cell Res. 2008 Aug;314(13):2400-10
• Soitamo AJ, Piippo M, Allahverdiyeva Y, Battchikova N, Aro EM. Light has a specific role in modulating Arabidopsis gene expression at low temperature. BMC Plant Biol. 2008 ;8():13-0
• Talvinen K, Tuikkala J, Nevalainen O, Rantanen A, Hirsimäki P, Sundström J, Kronqvist P. Proliferation marker securin identifies favourable outcome in invasive ductal breast cancer. Br. J. Cancer. 2008 Jul;99(2):335-40
• Salusjärvi L, Kankainen M, Soliymani R, Pitkänen JP, Penttilä M, Ruohonen L. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb. Cell Fact. 2008 ;7():18-0
• Vahisalu T, Kollist H, Wang YF, Nishimura N, Chan WY, Valerio G, Lamminmäki A, Brosché M, Moldau H, Desikan R, Schroeder JI, Kangasjärvi J. SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature. 2008 Mar;452(7186):487-91
• Schiotz BL, Jorgensen SM, Rexroad C, Gjoen T, Krasnov A. Transcriptomic analysis of responses to infectious salmon anemia virus infection in macrophage-like cells. Virus Res. 2008 Sep;136(1-2):65-74
• Elo LL, Filén S, Lahesmaa R, Aittokallio T. Reproducibility-optimized test statistic for ranking genes in microarray studies. 2008 Jul-Sep; 0;5(3):423-31
• Alakulppi N, Seikku P, Jaatinen T, Holmberg C, Laine J. Feasibility of diagnosing subclinical renal allograft rejection in children by whole blood gene expression analysis. Transplantation. 2008 Nov 15;86(9):1222-8.

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

• Skommer J, Wlodkowic D, Pelkonen J. CXCR4 expression during tumour cell death. Leuk Res. 2007 Aug;31(8):1155-6
• Griggs R, Vihola A, Hackman P, Talvinen K, Haravuori H, Faulkner G, Eymard B, Richard I, Selcen D, Engel A, Carpen O, Udd B. Zaspopathy in a large classic late-onset distal myopathy family. Brain. 2007 Jun;130(Pt 6):1477-84
• Assämäki R, Sarlomo-Rikala M, Lopez-Guerrero JA, Lasota J, Andersson LC, Llombart-Bosch A, Miettinen M, Knuutila S. Array comparative genomic hybridization analysis of chromosomal imbalances and their target genes in gastrointestinal stromal tumors. Genes Chromosomes Cancer. 2007 Jun;46(6):564-76
• Kumar D, Srikanth R, Ahlfors H, Lahesmaa R, Rao KV. Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol. Syst. Biol. 2007 ;3():150-0
• Junttila MR, Puustinen P, Niemelä M, Ahola R, Arnold H, Böttzauw T, Ala-aho R, Nielsen C, Ivaska J, Taya Y, Lu SL, Lin S, Chan EK, Wang XJ, Grènman R, Kast J, Kallunki T, Sears R, Kähäri VM, Westermarck J. CIP2A inhibits PP2A in human malignancies. Cell. 2007 Jul;130(1):51-62
• Zhang P, Kerkelä E, Skottman H, Levkov L, Kivinen K, Lahesmaa R, Hovatta O, Kere J. Distinct sets of developmentally regulated genes that are expressed by human oocytes and human embryonic stem cells. Fertil. Steril. 2007 Mar;87(3):677-90
• Huttunen MM, Pekkinen M, Ahlström ME, Lamberg-Allardt CJ. Effects of bioactive peptides isoleucine-proline-proline (IPP), valine-proline-proline (VPP) and leucine-lysine-proline (LKP) on gene expression of osteoblasts differentiated from human mesenchymal stem cells. Br. J. Nutr. 2007 Oct;98(4):780-8
• Lehti TM, Silvennoinen M, Kivelä R, Kainulainen H, Komulainen J. Effects of streptozotocin-induced diabetes and physical training on gene expression of titin-based stretch-sensing complexes in mouse striated muscle. Am. J. Physiol. Endocrinol. Metab. 2007 Feb;292(2):0-42
• Pirinen E, Kuulasmaa T, Pietilä M, Heikkinen S, Tusa M, Itkonen P, Boman S, Skommer J, Virkamäki A, Hohtola E, Kettunen M, Fatrai S, Kansanen E, Koota S, Niiranen K, Parkkinen J, Levonen AL, Ylä-Herttuala S, Hiltunen JK, Alhonen L, Smith U, Jänne J, Laakso M. Enhanced polyamine catabolism alters homeostatic control of white adipose tissue mass, energy expenditure, and glucose metabolism. Mol. Cell. Biol. 2007 Jul;27(13):4953-67
• Lehtonen A, Ahlfors H, Veckman V, Miettinen M, Lahesmaa R, Julkunen I. Gene expression profiling during differentiation of human monocytes to macrophages or dendritic cells. J. Leukoc. Biol. 2007 Sep;82(3):710-20
• Skommer J, Wlodkowic D, Pelkonen J. Gene-expression profiling during curcumin-induced apoptosis reveals downregulation of CXCR4. Exp. Hematol. 2007 Jan;35(1):84-95
• Lund RJ, Löytömäki M, Naumanen T, Dixon C, Chen Z, Ahlfors H, Tuomela S, Tahvanainen J, Scheinin J, Henttinen T, Rasool O, Lahesmaa R. Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation. J. Immunol. 2007 Mar;178(6):3648-60
• Hemmoranta H, Satomaa T, Blomqvist M, Heiskanen A, Aitio O, Saarinen J, Natunen J, Partanen J, Laine J, Jaatinen T. N-glycan structures and associated gene expression reflect the characteristic N-glycosylation pattern of human hematopoietic stem and progenitor cells. Exp. Hematol. 2007 Aug;35(8):1279-92
• Pöllänen E, Ronkainen PH, Suominen H, Takala T, Koskinen S, Puolakka J, Sipilä S, Kovanen V. Muscular transcriptome in postmenopausal women with or without hormone replacement. Rejuvenation Res. 2007 Dec;10(4):485-500
• Bruland T, Anderssen E, Doseth B, Bergum H, Beisvag V, Laegreid A. Optimization of cDNA microarrays procedures using criteria that do not rely on external standards. BMC Genomics. 2007 ;8():377-0
• Airas L, Nikula T, Huang YH, Lahesmaa R, Wiendl H. Postpartum-activation of multiple sclerosis is associated with down-regulation of tolerogenic HLA-G. J. Neuroimmunol. 2007 Jul;187(1-2):205-11
• Lintala M, Allahverdiyeva Y, Kidron H, Piippo M, Battchikova N, Suorsa M, Rintamäki E, Salminen TA, Aro EM, Mulo P. Structural and functional characterization of ferredoxin-NADP+-oxidoreductase using knock-out mutants of Arabidopsis. Plant J. 2007 Mar;49(6):1041-52
• Elo LL, Järvenpää H, Oresic M, Lahesmaa R, Aittokallio T. Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics. 2007 Aug;23(16):2096-103
• Misikangas M, Pajari AM, Päivärinta E, Oikarinen SI, Rajakangas J, Marttinen M, Tanayama H, Törrönen R, Mutanen M. Three Nordic berries inhibit intestinal tumorigenesis in multiple intestinal neoplasia/+ mice by modulating beta-catenin signaling in the tumor and transcription in the mucosa. J. Nutr. 2007 Oct;137(10):2285-90
• Hartiala P, Hytönen J, Pelkonen J, Kimppa K, West A, Penttinen MA, Suhonen J, Lahesmaa R, Viljanen MK. Transcriptional response of human dendritic cells to Borrelia garinii–defective CD38 and CCR7 expression detected. J. Leukoc. Biol. 2007 Jul;82(1):33-43
• Mannonen L, Nikula T, Haveri A, Reinikainen A, Vuola JM, Lahesmaa R, Puolakkainen M. Up-regulation of host cell genes during interferon-gamma-induced persistent Chlamydia pneumoniae infection in HL cells. J. Infect. Dis. 2007 Jan;195(2):212-9
• Gupta R, Ruosaari S, Kulathinal S, Hollmén J, Auvinen P. Microarray image segmentation using additional dye–an experimental study. Mol. Cell. Probes. 2007 Oct-Dec; 0 ;21(5-6):321-8
• Ojala P, Virtanen E, Chen Z. Large-scale differential display analysis of T helper cell differentiation. Electrophoresis. 2007 Mar;28(6):903-17

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.

• MacKenzie S, Montserrat N, Mas M, Acerete L, Tort L, Krasnov A, Goetz FW, Planas JV. Bacterial lipopolysaccharide induces apoptosis in the trout ovary. Reprod. Biol. Endocrinol. 2006 ;4():46-0
• PÈnisson-Besnier I, Talvinen K, Dumez C, Vihola A, Dubas F, Fardeau M, Hackman P, Carpen O, Udd B. Myotilinopathy in a family with late onset myopathy. Neuromuscul Disord. 2006 Jul;16(7):427-31
• Talvinen K, Tuikkala J, Grönroos J, Huhtinen H, Kronqvist P, Aittokallio T, Nevalainen O, Hiekkanen H, Nevalainen T, Sundström J. Biochemical and clinical approaches in evaluating the prognosis of colon cancer. Anticancer Res. 2006 Nov-Dec; 0 ;26(6C):4745-51
• Vauhkonen H, Vauhkonen M, Sajantila A, Sipponen P, Knuutila S. Characterizing genetically stable and unstable gastric cancers by microsatellites and array comparative genomic hybridization. Cancer Genet. Cytogenet. 2006 Oct;170(2):133-9
• Piippo M, Allahverdiyeva Y, Paakkarinen V, Suoranta UM, Battchikova N, Aro EM. Chloroplast-mediated regulation of nuclear genes in Arabidopsis thaliana in the absence of light stress. Physiol. Genomics. 2006 Mar;25(1):142-52
• Vuori KA, Koskinen H, Krasnov A, Koivumäki P, Afanasyev S, Vuorinen PJ, Nikinmaa M. Developmental disturbances in early life stage mortality (M74) of Baltic salmon fry as studied by changes in gene expression. BMC Genomics. 2006 ;7():56-0
• Sipilä P, Pujianto DA, Shariatmadari R, Nikkilä J, Lehtoranta M, Huhtaniemi IT, Poutanen M. Differential endocrine regulation of genes enriched in initial segment and distal caput of the mouse epididymis as revealed by genome-wide expression profiling. Biol. Reprod. 2006 Aug;75(2):240-51
• Kivelä R, Silvennoinen M, Touvra AM, Lehti TM, Kainulainen H, Vihko V. Effects of experimental type 1 diabetes and exercise training on angiogenic gene expression and capillarization in skeletal muscle. FASEB J. 2006 Jul;20(9):1570-2
• Lehti TM, Silvennoinen M, Kivelä R, Kainulainen H, Komulainen J. Effects of streptozotocin-induced diabetes and physical training on gene expression of extracellular matrix proteins in mouse skeletal muscle. Am. J. Physiol. Endocrinol. Metab. 2006 May;290(5):0-7
• Aghajanova L, Skottman H, Strömberg AM, Inzunza J, Lahesmaa R, Hovatta O. Expression of leukemia inhibitory factor and its receptors is increased during differentiation of human embryonic stem cells. Fertil. Steril. 2006 Oct;86(4 Suppl):1193-209
• Jukkola T, Lahti L, Naserke T, Wurst W, Partanen J. FGF regulated gene-expression and neuronal differentiation in the developing midbrain-hindbrain region. Dev. Biol. 2006 Sep;297(1):141-57
• Kaur S, Vauhkonen H, Böhling T, Mertens F, Mandahl N, Knuutila S. Gene copy number changes in dermatofibrosarcoma protuberans – a fine-resolution study using array comparative genomic hybridization. Cytogenet. Genome Res. 2006 ;115(3-4):283-8
• Saramäki OR, Porkka KP, Vessella RL, Visakorpi T. Genetic aberrations in prostate cancer by microarray analysis. Int. J. Cancer. 2006 Sep;119(6):1322-
• Jaatinen T, Hemmoranta H, Hautaniemi S, Niemi J, Nicorici D, Laine J, Yli-Harja O, Partanen J. Global gene expression profile of human cord blood-derived CD133+ cells. Stem Cells. 2006 Mar;24(3):631-41
• Jalkanen J, Shariatmadari R, Pujianto DA, Sipilä P, Huhtaniemi I, Poutanen M. Identification of novel epididymal genes by expression profiling and in silico gene discovery. Mol. Cell. Endocrinol. 2006 May;250(1-2):163-8
• Elo LL, Katajamaa M, Lund R, Oresic M, Lahesmaa R, Aittokallio T. Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays. OMICS. 2006 ;10(3):369-80
• Capon F, Reece A, Ravindrarajah R, Chung E. Linkage of monogenic infantile hypertrophic pyloric stenosis to chromosome 16p12-p13 and evidence for genetic heterogeneity. Am. J. Hum. Genet. 2006 Aug;79(2):378-82
• Kaur S, Larramendy ML, Gentile M, Svarvar C, Koivisto-Korander R, Vauhkonen H, Scheinin I, Leminen A, Bützow R, Böhling T & Knuutila S. New Insights into the Cellular Pathways Affected in Primary Uterine Leiomyosarcoma. Cancer Genomics & Proteomics. 2006 ;3(6):347-354
• Chang Y, Ostling P, Akerfelt M, Trouillet D, Rallu M, Gitton Y, El Fatimy R, Fardeau V, Le Crom S, Morange M, Sistonen L, Mezger V. Role of heat-shock factor 2 in cerebral cortex formation and as a regulator of p35 expression. Genes Dev. 2006 Apr;20(7):836-47
• Hahtola S, Tuomela S, Elo L, Häkkinen T, Karenko L, Nedoszytko B, Heikkilä H, Saarialho-Kere U, Roszkiewicz J, Aittokallio T, Lahesmaa R, Ranki A. Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma. Clin. Cancer Res. 2006 Aug;12(16):4812-21
• MacKenzie S, Iliev D, Liarte C, Koskinen H, Planas JV, Goetz FW, Mölsä H, Krasnov A, Tort L. Transcriptional analysis of LPS-stimulated activation of trout (Oncorhynchus mykiss) monocyte/macrophage cells in primary culture treated with cortisol. Mol. Immunol. 2006 Mar;43(9):1340-8
• Hemmoranta H, Hautaniemi S, Niemi J, Nicorici D, Laine J, Yli-Harja O, Partanen J, Jaatinen T. Transcriptional profiling reflects shared and unique characters for CD34+ and CD133+ cells. Stem Cells Dev. 2006 Dec;15(6):839-51
• Skottman H, Strömberg AM, Matilainen E, Inzunza J, Hovatta O, Lahesmaa R. Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage. Stem Cells. 2006 Jan;24(1):151-67

2005

• Nikula T, West A, Katajamaa M, Lönnberg T, Sara R, Aittokallio T, Nevalainen OS, Lahesmaa R. A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses.. J. Immunol. Methods. 2005 Aug;303(1-2):122-34
• Götherström C, West A, Liden J, Uzunel M, Lahesmaa R, Le Blanc K. Difference in gene expression between human fetal liver and adult bone marrow mesenchymal stem cells.. Haematologica. 2005 Aug;90(8):1017-26
• Lehtonen A, Veckman V, Nikula T, Lahesmaa R, Kinnunen L, Matikainen S, Julkunen I. Differential expression of IFN regulatory factor 4 gene in human monocyte-derived dendritic cells and macrophages.. J. Immunol.. 2005 Nov;175(10):6570-9
• Rysä J, Leskinen H, Ilves M, Ruskoaho H. Distinct upregulation of extracellular matrix genes in transition from hypertrophy to hypertensive heart failure.. Hypertension. 2005 May;45(5):927-33
• Inkinen K, Lahesmaa R, Brandt A, Katajamaa M, Halme L, Höckerstedt K, Lautenschlager I. DNA microarray-based gene expression profiles of cytomegalovirus infection and acute rejection in liver transplants.. Transplant. Proc.. 2005 Mar;37(2):1227-9
• Rauhala HE, Porkka KP, Tolonen TT, Martikainen PM, Tammela TL, Visakorpi T. Dual-specificity phosphatase 1 and serum/glucocorticoid-regulated kinase are downregulated in prostate cancer.. Int. J. Cancer. 2005 Dec;117(5):738-45
• Aho TL, Lund RJ, Ylikoski EK, Matikainen S, Lahesmaa R, Koskinen PJ. 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.. Immunology. 2005 Sep;116(1):82-8
• Krasnov A, Koskinen H, Pehkonen P, Rexroad CE, Afanasyev S, Mölsä H. Gene expression in the brain and kidney of rainbow trout in response to handling stress.. BMC Genomics. 2005 ;6(1):3-0
• Skottman H, Mikkola M, Lundin K, Olsson C, Strömberg AM, Tuuri T, Otonkoski T, Hovatta O, Lahesmaa R. Gene expression signatures of seven individual human embryonic stem cell lines.. Stem Cells. 2005 Oct;23(9):1343-56
• Ylipaasto P, Kutlu B, Rasilainen S, Rasschaert J, Salmela K, Teerijoki H, Korsgren O, Lahesmaa R, Hovi T, Eizirik DL, Otonkoski T, Roivainen M. Global profiling of coxsackievirus- and cytokine-induced gene expression in human pancreatic islets.. Diabetologia. 2005 Aug;48(8):1510-22
• Lund R, Ahlfors H, Kainonen E, Lahesmaa AM, Dixon C, Lahesmaa R. Identification of genes involved in the initiation of human Th1 or Th2 cell commitment.. Eur. J. Immunol.. 2005 Nov;35(11):3307-19
• Elo LL, Lahti L, Skottman H, Kyläniemi M, Lahesmaa R, Aittokallio T. Integrating probe-level expression changes across generations of Affymetrix arrays.. Nucleic Acids Res.. 2005 ;33(22):0-0
• Krasnov A, Koskinen H, Afanasyev S, Mölsä H. Transcribed Tc1-like transposons in salmonid fish.. BMC Genomics. 2005 ;6():107
• Krasnov A, Koskinen H, Rexroad C, Afanasyev S, Mölsä H, Oikari A. Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss).. Aquat. Toxicol.. 2005 Aug;74(1):70-81

2004

• Ahlfors R, Lång S, Overmyer K, Jaspers P, Brosché M, Tauriainen A, Kollist H, Tuominen H, Belles-Boix E, Piippo M, Inzé D, Palva ET, Kangasjärvi J. Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses.. Plant Cell. 2004 Jul;16(7):1925-37
• Lund RJ, Chen Z, Scheinin J, Lahesmaa R. Early target genes of IL-12 and STAT4 signaling in th cells.. J. Immunol.. 2004 Jun;172(11):6775-82
• Sillanpää N, Magureanu CG, Murumägi A, Reinikainen A, West A, Manninen A, Lahti M, Ranki A, Saksela K, Krohn K, Lahesmaa R, Peterson P. Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage.. Mol. Immunol.. 2004 Nov;41(12):1185-98
• Koskinen H, Pehkonen P, Vehniäinen E, Krasnov A, Rexroad C, Afanasyev S, Mölsa H, Oikari A. Response of rainbow trout transcriptome to model chemical contaminants.. Biochem. Biophys. Res. Commun.. 2004 Jul;320(3):745-53

2003

• Aittokallio T, Kurki M, Nevalainen O, Nikula T, West A, Lahesmaa R. Computational strategies for analyzing data in gene expression microarray experiments.. J. Bioinformatics and Computational Biology. 2003 Oct;1(3):541-86
• Lund R, Aittokallio T, Nevalainen O, Lahesmaa R. Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes.. J. Immunol.. 2003 Nov;171(10):5328-36
• Chen Z, Lund R, Aittokallio T, Kosonen M, Nevalainen O, Lahesmaa R. Identification of novel IL-4/Stat6-regulated genes in T lymphocytes.. J. Immunol.. 2003 Oct;171(7):3627-35
• Qiao S, Pennanen P, Nazarova N, Lou YR, Tuohimaa P. Inhibition of fatty acid synthase expression by 1alpha,25-dihydroxyvitamin D3 in prostate cancer cells.. J. Steroid Biochem. Mol. Biol.. 2003 May;85(1):1-8

2002

• Petrova TV, Mäkinen T, Mäkelä TP, Saarela J, Virtanen I, Ferrell RE, Finegold DN, Kerjaschki D, Ylä-Herttuala S, Alitalo K. Lymphatic endothelial reprogramming of vascular endothelial cells by the Prox-1 homeobox transcription factor.. EMBO J.. 2002 Sep;21(17):4593-9