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Items: 1 to 50 of 207

1.

Coxsackievirus B Persistence Modifies the Proteome and the Secretome of Pancreatic Ductal Cells.

Lietzén N, Hirvonen K, Honkimaa A, Buchacher T, Laiho JE, Oikarinen S, Mazur MA, Flodström-Tullberg M, Dufour E, Sioofy-Khojine AB, Hyöty H, Lahesmaa R.

iScience. 2019 Sep 27;19:340-357. doi: 10.1016/j.isci.2019.07.040. Epub 2019 Jul 29.

2.

L1TD1 - a prognostic marker for colon cancer.

Chakroborty D, Emani MR, Klén R, Böckelman C, Hagström J, Haglund C, Ristimäki A, Lahesmaa R, Elo LL.

BMC Cancer. 2019 Jul 23;19(1):727. doi: 10.1186/s12885-019-5952-2.

3.

Early Detection of Peripheral Blood Cell Signature in Children Developing β-Cell Autoimmunity at a Young Age.

Kallionpää H, Somani J, Tuomela S, Ullah U, de Albuquerque R, Lönnberg T, Komsi E, Siljander H, Honkanen J, Härkönen T, Peet A, Tillmann V, Chandra V, Anagandula MK, Frisk G, Otonkoski T, Rasool O, Lund R, Lähdesmäki H, Knip M, Lahesmaa R.

Diabetes. 2019 Oct;68(10):2024-2034. doi: 10.2337/db19-0287. Epub 2019 Jul 16.

PMID:
31311800
4.

CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases.

Singh DD, Hawkins RD, Lahesmaa R, Tripathi SK.

Semin Cell Dev Biol. 2019 Dec;96:32-43. doi: 10.1016/j.semcdb.2019.05.007. Epub 2019 Jun 20. Review.

PMID:
31112800
5.

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation.

Khare SP, Shetty A, Biradar R, Patta I, Chen ZJ, Sathe AV, Reddy PC, Lahesmaa R, Galande S.

Front Immunol. 2019 Apr 2;10:667. doi: 10.3389/fimmu.2019.00667. eCollection 2019.

6.

An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data.

Cheng L, Ramchandran S, Vatanen T, Lietzén N, Lahesmaa R, Vehtari A, Lähdesmäki H.

Nat Commun. 2019 Apr 17;10(1):1798. doi: 10.1038/s41467-019-09785-8.

7.

Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization.

Tripathi SK, Välikangas T, Shetty A, Khan MM, Moulder R, Bhosale SD, Komsi E, Salo V, De Albuquerque RS, Rasool O, Galande S, Elo LL, Lahesmaa R.

iScience. 2019 Jan 25;11:334-355. doi: 10.1016/j.isci.2018.12.020. Epub 2018 Dec 26.

8.

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.

Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA.

Cell. 2019 Feb 7;176(4):882-896.e18. doi: 10.1016/j.cell.2018.11.044. Epub 2019 Jan 10.

9.

Immunological biomarkers for the development and progression of type 1 diabetes.

Mathieu C, Lahesmaa R, Bonifacio E, Achenbach P, Tree T.

Diabetologia. 2018 Nov;61(11):2252-2258. doi: 10.1007/s00125-018-4726-8. Epub 2018 Sep 12. Review.

PMID:
30209538
10.

Serum Proteomic Profiling to Identify Biomarkers of Premature Carotid Atherosclerosis.

Bhosale SD, Moulder R, Venäläinen MS, Koskinen JS, Pitkänen N, Juonala MT, Kähönen MAP, Lehtimäki TJ, Viikari JSA, Elo LL, Goodlett DR, Lahesmaa R, Raitakari OT.

Sci Rep. 2018 Jun 15;8(1):9209. doi: 10.1038/s41598-018-27265-9.

11.

snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions.

Nousiainen K, Kanduri K, Ricaño-Ponce I, Wijmenga C, Lahesmaa R, Kumar V, Lähdesmäki H.

Bioinformatics. 2018 Dec 1;34(23):4112-4114. doi: 10.1093/bioinformatics/bty460.

12.

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Schmidt A, Marabita F, Kiani NA, Gross CC, Johansson HJ, Éliás S, Rautio S, Eriksson M, Fernandes SJ, Silberberg G, Ullah U, Bhatia U, Lähdesmäki H, Lehtiö J, Gomez-Cabrero D, Wiendl H, Lahesmaa R, Tegnér J.

BMC Biol. 2018 May 7;16(1):47. doi: 10.1186/s12915-018-0518-3.

13.

Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter.

Lund RJ, Osmala M, Malonzo M, Lukkarinen M, Leino A, Salmi J, Vuorikoski S, Turunen R, Vuorinen T, Akdis C, Lähdesmäki H, Lahesmaa R, Jartti T.

Allergy. 2018 Aug;73(8):1735-1740. doi: 10.1111/all.13473. Epub 2018 May 21.

14.

Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood.

Lietzén N, Cheng L, Moulder R, Siljander H, Laajala E, Härkönen T, Peet A, Vehtari A, Tillmann V, Knip M, Lähdesmäki H, Lahesmaa R.

Sci Rep. 2018 Apr 12;8(1):5883. doi: 10.1038/s41598-018-24019-5.

15.

Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells.

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.

Cell Rep. 2018 Feb 20;22(8):2094-2106. doi: 10.1016/j.celrep.2018.01.070.

16.

Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors.

Mukherjee SP, Bondarenko O, Kohonen P, Andón FT, Brzicová T, Gessner I, Mathur S, Bottini M, Calligari P, Stella L, Kisin E, Shvedova A, Autio R, Salminen-Mankonen H, Lahesmaa R, Fadeel B.

Sci Rep. 2018 Jan 18;8(1):1115. doi: 10.1038/s41598-018-19521-9.

17.

Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling.

Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R.

Mass Spectrom Rev. 2018 Sep;37(5):583-606. doi: 10.1002/mas.21550. Epub 2017 Nov 9. Review.

PMID:
29120501
18.

Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes.

Lietzen N, An LTT, Jaakkola MK, Kallionpää H, Oikarinen S, Mykkänen J, Knip M, Veijola R, Ilonen J, Toppari J, Hyöty H, Lahesmaa R, Elo LL.

Diabetologia. 2018 Feb;61(2):381-388. doi: 10.1007/s00125-017-4460-7. Epub 2017 Nov 8.

19.

Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo.

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.

Sci Rep. 2017 Aug 29;7(1):9860. doi: 10.1038/s41598-017-10253-w.

20.

Mass Spectrometry-Based Serum Proteomics for Biomarker Discovery and Validation.

Bhosale SD, Moulder R, Kouvonen P, Lahesmaa R, Goodlett DR.

Methods Mol Biol. 2017;1619:451-466. doi: 10.1007/978-1-4939-7057-5_31.

PMID:
28674903
21.

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation.

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.

Cell Rep. 2017 May 30;19(9):1888-1901. doi: 10.1016/j.celrep.2017.05.013.

22.

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.

Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R.

Stem Cell Reports. 2017 May 9;8(5):1442-1454. doi: 10.1016/j.stemcr.2017.04.016.

23.

DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer.

Lund RJ, Huhtinen K, Salmi J, Rantala J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O.

Sci Rep. 2017 May 4;7(1):1469. doi: 10.1038/s41598-017-01624-4.

24.

Hyper-phosphorylation of Sequestosome-1 Distinguishes Resistance to Cisplatin in Patient Derived High Grade Serous Ovarian Cancer Cells.

Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR.

Mol Cell Proteomics. 2017 Jul;16(7):1377-1392. doi: 10.1074/mcp.M116.058321. Epub 2017 Apr 28.

25.

AMIGO2 modulates T cell functions and its deficiency in mice ameliorates experimental autoimmune encephalomyelitis.

Li Z, Khan MM, Kuja-Panula J, Wang H, Chen Y, Guo D, Chen ZJ, Lahesmaa R, Rauvala H, Tian L.

Brain Behav Immun. 2017 May;62:110-123. doi: 10.1016/j.bbi.2017.01.009. Epub 2017 Feb 1.

PMID:
28119027
26.

An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets.

Domsgen E, Lind K, Kong L, Hühn MH, Rasool O, van Kuppeveld F, Korsgren O, Lahesmaa R, Flodström-Tullberg M.

Sci Rep. 2016 Dec 21;6:39378. doi: 10.1038/srep39378.

27.

The progress and potential of proteomic biomarkers for type 1 diabetes in children.

Moulder R, Bhosale SD, Lahesmaa R, Goodlett DR.

Expert Rev Proteomics. 2017 Jan;14(1):31-41. doi: 10.1080/14789450.2017.1265449. Epub 2016 Dec 20. Review.

PMID:
27997253
28.

Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells.

Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund R.

Stem Cell Res. 2016 Nov;17(3):498-503. doi: 10.1016/j.scr.2016.09.025. Epub 2016 Sep 24.

29.

Pulmonary sarcoidosis is associated with exosomal vitamin D-binding protein and inflammatory molecules.

Martinez-Bravo MJ, Wahlund CJ, Qazi KR, Moulder R, Lukic A, Rådmark O, Lahesmaa R, Grunewald J, Eklund A, Gabrielsson S.

J Allergy Clin Immunol. 2017 Apr;139(4):1186-1194. doi: 10.1016/j.jaci.2016.05.051. Epub 2016 Aug 23.

PMID:
27566455
30.

Early signs of disease in type 1 diabetes.

Moulder R, Lahesmaa R.

Pediatr Diabetes. 2016 Jul;17 Suppl 22:43-8. doi: 10.1111/pedi.12329. Review.

PMID:
27411436
31.

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.

Toivonen R, Kong L, Rasool O, Lund RJ, Lahesmaa R, Hänninen A.

J Immunol. 2016 Jun 1;196(11):4750-9. doi: 10.4049/jimmunol.1600235. Epub 2016 Apr 27.

32.

CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection.

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.

PLoS One. 2016 Apr 21;11(4):e0152996. doi: 10.1371/journal.pone.0152996. eCollection 2016.

33.

Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

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.

Oncotarget. 2016 Mar 22;7(12):13416-28. doi: 10.18632/oncotarget.7963.

34.

Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells.

Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ.

Sci Rep. 2016 Feb 25;6:22190. doi: 10.1038/srep22190.

35.

Identification of global regulators of T-helper cell lineage specification.

Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R.

Genome Med. 2015 Nov 20;7:122. doi: 10.1186/s13073-015-0237-0.

36.

Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data.

Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H.

BMC Syst Biol. 2015 Nov 17;9:81. doi: 10.1186/s12918-015-0223-6.

37.

A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.

Gustafsson M, Gawel DR, Alfredsson L, Baranzini S, Björkander J, Blomgran R, Hellberg S, Eklund D, Ernerudh J, Kockum I, Konstantinell A, Lahesmaa R, Lentini A, Liljenström HR, Mattson L, Matussek A, Mellergård J, Mendez M, Olsson T, Pujana MA, Rasool O, Serra-Musach J, Stenmarker M, Tripathi S, Viitala M, Wang H, Zhang H, Nestor CE, Benson M.

Sci Transl Med. 2015 Nov 11;7(313):313ra178. doi: 10.1126/scitranslmed.aad2722.

38.

New Insights and Biomarkers for Type 1 Diabetes: Review for Scandinavian Journal of Immunology.

Heinonen MT, Moulder R, Lahesmaa R.

Scand J Immunol. 2015 Sep;82(3):244-53. doi: 10.1111/sji.12338. Review.

39.

GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy.

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.

J Immunol. 2015 Jun 15;194(12):5885-94. doi: 10.4049/jimmunol.1500016. Epub 2015 May 11.

40.

The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency.

Emani MR, Närvä E, Stubb A, Chakroborty D, Viitala M, Rokka A, Rahkonen N, Moulder R, Denessiouk K, Trokovic R, Lund R, Elo LL, Lahesmaa R.

Stem Cell Reports. 2015 Mar 10;4(3):519-28. doi: 10.1016/j.stemcr.2015.01.014. Epub 2015 Feb 19.

41.

Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells.

Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H.

BioData Min. 2014 Dec 13;7(1):32. doi: 10.1186/s13040-014-0032-2. eCollection 2014.

42.

Serum proteomes distinguish children developing type 1 diabetes in a cohort with HLA-conferred susceptibility.

Moulder R, Bhosale SD, Erkkilä T, Laajala E, Salmi J, Nguyen EV, Kallionpää H, Mykkänen J, Vähä-Mäkilä M, Hyöty H, Veijola R, Ilonen J, Simell T, Toppari J, Knip M, Goodlett DR, Lähdesmäki H, Simell O, Lahesmaa R.

Diabetes. 2015 Jun;64(6):2265-78. doi: 10.2337/db14-0983. Epub 2015 Jan 23.

43.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity.

Hrdlickova B, Kumar V, Kanduri K, Zhernakova DV, Tripathi S, Karjalainen J, Lund RJ, Li Y, Ullah U, Modderman R, Abdulahad W, Lähdesmäki H, Franke L, Lahesmaa R, Wijmenga C, Withoff S.

Genome Med. 2014 Oct 28;6(10):88. doi: 10.1186/s13073-014-0088-0. eCollection 2014.

44.

Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation.

Heinonen MT, Kanduri K, Lähdesmäki HJ, Lahesmaa R, Henttinen TA.

Immunol Cell Biol. 2015 Feb;93(2):158-66. doi: 10.1038/icb.2014.86. Epub 2014 Oct 7.

45.

Standard of hygiene and immune adaptation in newborn infants.

Kallionpää H, Laajala E, Öling V, Härkönen T, Tillmann V, Dorshakova NV, Ilonen J, Lähdesmäki H, Knip M, Lahesmaa R; DIABIMMUNE Study Group.

Clin Immunol. 2014 Nov;155(1):136-47. doi: 10.1016/j.clim.2014.09.009. Epub 2014 Sep 22.

46.

Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels.

Kumar V, Gutierrez-Achury J, Kanduri K, Almeida R, Hrdlickova B, Zhernakova DV, Westra HJ, Karjalainen J, Ricaño-Ponce I, Li Y, Stachurska A, Tigchelaar EF, Abdulahad WH, Lähdesmäki H, Hofker MH, Zhernakova A, Franke L, Lahesmaa R, Wijmenga C, Withoff S.

Hum Mol Genet. 2015 Jan 15;24(2):397-409. doi: 10.1093/hmg/ddu453. Epub 2014 Sep 4.

PMID:
25190711
47.

Transcriptional and epigenetic regulation of T-helper lineage specification.

Tripathi SK, Lahesmaa R.

Immunol Rev. 2014 Sep;261(1):62-83. doi: 10.1111/imr.12204. Review.

48.

The regulation and role of c-FLIP in human Th cell differentiation.

Kyläniemi MK, Kaukonen R, Myllyviita J, Rasool O, Lahesmaa R.

PLoS One. 2014 Jul 14;9(7):e102022. doi: 10.1371/journal.pone.0102022. eCollection 2014.

49.

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.

Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H.

Bioinformatics. 2014 Jun 15;30(12):i113-20. doi: 10.1093/bioinformatics/btu274.

50.

Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature.

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.

Antioxid Redox Signal. 2014 Dec 1;21(16):2231-45. doi: 10.1089/ars.2013.5828. Epub 2014 Jul 29.

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