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Items: 1 to 50 of 102

1.

Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells.

Giurato G, Nassa G, Salvati A, Alexandrova E, Rizzo F, Nyman TA, Weisz A, Tarallo R.

Sci Data. 2018 Mar 6;5:180031. doi: 10.1038/sdata.2018.31.

2.

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains.

Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K.

Microb Biotechnol. 2018 May;11(3):510-526. doi: 10.1111/1751-7915.13254. Epub 2018 Feb 28.

3.

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R.

Sci Rep. 2018 Jan 11;8(1):498. doi: 10.1038/s41598-017-18985-5.

4.

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A.

Genome Biol. 2017 Oct 6;18(1):189. doi: 10.1186/s13059-017-1321-0.

5.

Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins.

Bulanova D, Ianevski A, Bugai A, Akimov Y, Kuivanen S, Paavilainen H, Kakkola L, Nandania J, Turunen L, Ohman T, Ala-Hongisto H, Pesonen HM, Kuisma MS, Honkimaa A, Walton EL, Oksenych V, Lorey MB, Guschin D, Shim J, Kim J, Than TT, Chang SY, Hukkanen V, Kulesskiy E, Marjomaki VS, Julkunen I, Nyman TA, Matikainen S, Saarela JS, Sane F, Hober D, Gabriel G, De Brabander JK, Martikainen M, Windisch MP, Min JY, Bruzzone R, Aittokallio T, Vähä-Koskela M, Vapalahti O, Pulk A, Velagapudi V, Kainov DE.

Viruses. 2017 Sep 25;9(10). pii: E271. doi: 10.3390/v9100271.

6.

Proprotein convertase Furin1 expression in the Drosophila fat body is essential for a normal antimicrobial peptide response and bacterial host defense.

Aittomäki S, Valanne S, Lehtinen T, Matikainen S, Nyman TA, Rämet M, Pesu M.

FASEB J. 2017 Nov;31(11):4770-4782. doi: 10.1096/fj.201700296R. Epub 2017 Jul 13.

PMID:
28705811
7.

Proteomics to study macrophage response to viral infection.

Nyman TA, Matikainen S.

J Proteomics. 2018 May 30;180:99-107. doi: 10.1016/j.jprot.2017.06.018. Epub 2017 Jun 21. Review.

PMID:
28647517
8.

PACSIN2 accelerates nephrin trafficking and is up-regulated in diabetic kidney disease.

Dumont V, Tolvanen TA, Kuusela S, Wang H, Nyman TA, Lindfors S, Tienari J, Nisen H, Suetsugu S, Plomann M, Kawachi H, Lehtonen S.

FASEB J. 2017 Sep;31(9):3978-3990. doi: 10.1096/fj.201601265R. Epub 2017 May 26.

9.

Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells.

Nyman TA, Lorey MB, Cypryk W, Matikainen S.

Expert Rev Proteomics. 2017 May;14(5):395-407. doi: 10.1080/14789450.2017.1319768. Epub 2017 Apr 24. Review.

PMID:
28406322
10.

Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation.

Deptula P, Chamlagain B, Edelmann M, Sangsuwan P, Nyman TA, Savijoki K, Piironen V, Varmanen P.

Front Microbiol. 2017 Mar 8;8:368. doi: 10.3389/fmicb.2017.00368. eCollection 2017.

11.

Global Characterization of Protein Secretion from Human Macrophages Following Non-canonical Caspase-4/5 Inflammasome Activation.

Lorey MB, Rossi K, Eklund KK, Nyman TA, Matikainen S.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S187-S199. doi: 10.1074/mcp.M116.064840. Epub 2017 Feb 14.

12.

Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion.

Wasik AA, Dumont V, Tienari J, Nyman TA, Fogarty CL, Forsblom C, Lehto M, Lehtonen E, Groop PH, Lehtonen S.

Exp Cell Res. 2017 Jan 15;350(2):336-348. doi: 10.1016/j.yexcr.2016.12.010. Epub 2016 Dec 20.

13.

Regulation of kynurenine biosynthesis during influenza virus infection.

Gaelings L, Söderholm S, Bugai A, Fu Y, Nandania J, Schepens B, Lorey MB, Tynell J, Vande Ginste L, Le Goffic R, Miller MS, Kuisma M, Marjomäki V, De Brabander J, Matikainen S, Nyman TA, Bamford DH, Saelens X, Julkunen I, Paavilainen H, Hukkanen V, Velagapudi V, Kainov DE.

FEBS J. 2017 Jan;284(2):222-236. doi: 10.1111/febs.13966. Epub 2016 Dec 14.

14.

Influenza virus NS1 protein binds cellular DNA to block transcription of antiviral genes.

Anastasina M, Le May N, Bugai A, Fu Y, Söderholm S, Gaelings L, Ohman T, Tynell J, Kyttänen S, Barboric M, Nyman TA, Matikainen S, Julkunen I, Butcher SJ, Egly JM, Kainov DE.

Biochim Biophys Acta. 2016 Nov;1859(11):1440-1448. doi: 10.1016/j.bbagrm.2016.09.005. Epub 2016 Sep 21.

PMID:
27664935
15.

Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection.

Cypryk W, Lorey M, Puustinen A, Nyman TA, Matikainen S.

J Proteome Res. 2017 Jan 6;16(1):217-227. doi: 10.1021/acs.jproteome.6b00596. Epub 2016 Nov 15.

PMID:
27723984
16.

Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction.

Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE.

Viruses. 2016 Sep 29;8(10). pii: E269. Review.

17.

Calpain Activity Is Essential for ATP-Driven Unconventional Vesicle-Mediated Protein Secretion and Inflammasome Activation in Human Macrophages.

Välimäki E, Cypryk W, Virkanen J, Nurmi K, Turunen PM, Eklund KK, Åkerman KE, Nyman TA, Matikainen S.

J Immunol. 2016 Oct 15;197(8):3315-3325. Epub 2016 Sep 16.

18.

The Antiviral Alkaloid Berberine Reduces Chikungunya Virus-Induced Mitogen-Activated Protein Kinase Signaling.

Varghese FS, Thaa B, Amrun SN, Simarmata D, Rausalu K, Nyman TA, Merits A, McInerney GM, Ng LF, Ahola T.

J Virol. 2016 Oct 14;90(21):9743-9757. Print 2016 Nov 1.

19.

The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone.

Bæk KT, Bowman L, Millership C, Dupont Søgaard M, Kaever V, Siljamäki P, Savijoki K, Varmanen P, Nyman TA, Gründling A, Frees D.

MBio. 2016 Aug 9;7(4). pii: e01228-16. doi: 10.1128/mBio.01228-16.

20.

Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages.

Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA.

Mol Cell Proteomics. 2016 Oct;15(10):3203-3219. Epub 2016 Aug 2.

21.

JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses.

Fu Y, Gaelings L, Söderholm S, Belanov S, Nandania J, Nyman TA, Matikainen S, Anders S, Velagapudi V, Kainov DE.

Antiviral Res. 2016 Sep;133:23-31. doi: 10.1016/j.antiviral.2016.07.008. Epub 2016 Jul 20.

PMID:
27451344
22.

HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression.

Christensen MH, Jensen SB, Miettinen JJ, Luecke S, Prabakaran T, Reinert LS, Mettenleiter T, Chen ZJ, Knipe DM, Sandri-Goldin RM, Enquist LW, Hartmann R, Mogensen TH, Rice SA, Nyman TA, Matikainen S, Paludan SR.

EMBO J. 2016 Jul 1;35(13):1385-99. doi: 10.15252/embj.201593458. Epub 2016 May 27.

23.

Immuno-modulating properties of saliphenylhalamide, SNS-032, obatoclax, and gemcitabine.

Söderholm S, Anastasina M, Islam MM, Tynell J, Poranen MM, Bamford DH, Stenman J, Julkunen I, Šaulienė I, De Brabander JK, Matikainen S, Nyman TA, Saelens X, Kainov D.

Antiviral Res. 2016 Feb;126:69-80. doi: 10.1016/j.antiviral.2015.12.011. Epub 2015 Dec 29.

24.

Penicillin G increases the synthesis of a suicidal marker (CidC) and virulence (HlgBC) proteins in Staphylococcus aureus biofilm cells.

Savijoki K, Skogman M, Fallarero A, Nyman TA, Sukura A, Vuorela P, Varmanen P.

Int J Med Microbiol. 2016 Jan;306(1):69-74. doi: 10.1016/j.ijmm.2015.11.006. Epub 2015 Dec 3.

PMID:
26725755
25.

Biological properties of extracellular vesicles and their physiological functions.

Yáñez-Mó M, Siljander PR, Andreu Z, Zavec AB, Borràs FE, Buzas EI, Buzas K, Casal E, Cappello F, Carvalho J, Colás E, Cordeiro-da Silva A, Fais S, Falcon-Perez JM, Ghobrial IM, Giebel B, Gimona M, Graner M, Gursel I, Gursel M, Heegaard NH, Hendrix A, Kierulf P, Kokubun K, Kosanovic M, Kralj-Iglic V, Krämer-Albers EM, Laitinen S, Lässer C, Lener T, Ligeti E, Linē A, Lipps G, Llorente A, Lötvall J, Manček-Keber M, Marcilla A, Mittelbrunn M, Nazarenko I, Nolte-'t Hoen EN, Nyman TA, O'Driscoll L, Olivan M, Oliveira C, Pállinger É, Del Portillo HA, Reventós J, Rigau M, Rohde E, Sammar M, Sánchez-Madrid F, Santarém N, Schallmoser K, Ostenfeld MS, Stoorvogel W, Stukelj R, Van der Grein SG, Vasconcelos MH, Wauben MH, De Wever O.

J Extracell Vesicles. 2015 May 14;4:27066. doi: 10.3402/jev.v4.27066. eCollection 2015.

26.

The C terminus of NS1 protein of influenza A/WSN/1933(H1N1) virus modulates antiviral responses in infected human macrophages and mice.

Anastasina M, Schepens B, Söderholm S, Nyman TA, Matikainen S, Saksela K, Saelens X, Kainov DE.

J Gen Virol. 2015 Aug;96(8):2086-91. doi: 10.1099/vir.0.000171. Epub 2015 May 1.

PMID:
25934792
27.

Activating stimuli induce platelet microRNA modulation and proteome reorganisation.

Cimmino G, Tarallo R, Nassa G, De Filippo MR, Giurato G, Ravo M, Rizzo F, Conte S, Pellegrino G, Cirillo P, Calabro P, Öhman T, Nyman TA, Weisz A, Golino P.

Thromb Haemost. 2015 Jul;114(1):96-108. doi: 10.1160/TH14-09-0726. Epub 2015 Apr 23.

PMID:
25903651
28.

Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice.

Jokinen R, Lahtinen T, Marttinen P, Myöhänen M, Ruotsalainen P, Yeung N, Shvetsova A, Kastaniotis AJ, Hiltunen JK, Öhman T, Nyman TA, Weiler H, Battersby BJ.

Genetics. 2015 May;200(1):221-35. doi: 10.1534/genetics.115.175596. Epub 2015 Mar 25.

29.

Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells.

Öhman T, Söderholm S, Paidikondala M, Lietzén N, Matikainen S, Nyman TA.

Proteomics. 2015 Jun;15(12):2087-97. doi: 10.1002/pmic.201400586. Epub 2015 Apr 27.

PMID:
25764225
30.

Identification of cytoplasmic proteins interacting with unliganded estrogen receptor α and β in human breast cancer cells.

Stellato C, Nassa G, Tarallo R, Giurato G, Ravo M, Rizzo F, Marchese G, Alexandrova E, Cordella A, Baumann M, Nyman TA, Weisz A, Ambrosino C.

Proteomics. 2015 Jun;15(11):1801-7. doi: 10.1002/pmic.201400404. Epub 2015 Mar 18.

PMID:
25604459
31.

Uncovering surface-exposed antigens of Lactobacillus rhamnosus by cell shaving proteomics and two-dimensional immunoblotting.

Espino E, Koskenniemi K, Mato-Rodriguez L, Nyman TA, Reunanen J, Koponen J, Öhman T, Siljamäki P, Alatossava T, Varmanen P, Savijoki K.

J Proteome Res. 2015 Feb 6;14(2):1010-24. doi: 10.1021/pr501041a. Epub 2014 Dec 22.

PMID:
25531588
32.

OSBP-related protein 3 (ORP3) coupling with VAMP-associated protein A regulates R-Ras activity.

Weber-Boyvat M, Kentala H, Lilja J, Vihervaara T, Hanninen R, Zhou Y, Peränen J, Nyman TA, Ivaska J, Olkkonen VM.

Exp Cell Res. 2015 Feb 15;331(2):278-91. doi: 10.1016/j.yexcr.2014.10.019. Epub 2014 Oct 29.

PMID:
25447204
33.

A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation.

Salomäki T, Karonen T, Siljamäki P, Savijoki K, Nyman TA, Varmanen P, Iivanainen A.

J Appl Microbiol. 2015 Jan;118(1):1-10. doi: 10.1111/jam.12664. Epub 2014 Nov 27.

34.

Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia.

Elo LL, Karjalainen R, Ohman T, Hintsanen P, Nyman TA, Heckman CA, Aittokallio T.

Proteomics. 2014 Nov;14(21-22):2443-53. doi: 10.1002/pmic.201300460. Epub 2014 Oct 15.

PMID:
25211154
35.

Isolation and characterization of platelet-derived extracellular vesicles.

Aatonen MT, Ohman T, Nyman TA, Laitinen S, Grönholm M, Siljander PR.

J Extracell Vesicles. 2014 Aug 6;3. doi: 10.3402/jev.v3.24692. eCollection 2014.

36.

PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data.

Söderholm S, Hintsanen P, Öhman T, Aittokallio T, Nyman TA.

Proteome Sci. 2014 Jun 26;12:36. doi: 10.1186/1477-5956-12-36. eCollection 2014.

37.

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains.

Savijoki K, Iivanainen A, Siljamäki P, Laine PK, Paulin L, Karonen T, Pyörälä S, Kankainen M, Nyman TA, Salomäki T, Koskinen P, Holm L, Simojoki H, Taponen S, Sukura A, Kalkkinen N, Auvinen P, Varmanen P.

J Proteome Res. 2014 Jul 18. [Epub ahead of print]

PMID:
25014494
38.

Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway.

Öhman T, Söderholm S, Hintsanen P, Välimäki E, Lietzén N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA.

Mol Cell Proteomics. 2014 Oct;13(10):2604-17. doi: 10.1074/mcp.M114.038968. Epub 2014 Jul 5.

39.

Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins.

Siljamäki P, Varmanen P, Kankainen M, Pyörälä S, Karonen T, Iivanainen A, Auvinen P, Paulin L, Laine PK, Taponen S, Simojoki H, Sukura A, Nyman TA, Savijoki K.

Proteomics. 2014 Aug;14(16):1890-4. doi: 10.1002/pmic.201300275. Epub 2014 Jul 10.

PMID:
24909406
40.

Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence.

Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA.

J Proteome Res. 2014 Jul 3;13(7):3249-61. doi: 10.1021/pr500075j. Epub 2014 Jun 2.

PMID:
24840314
41.

Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages.

Öhman T, Teirilä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S.

J Immunol. 2014 Jun 15;192(12):5952-62. doi: 10.4049/jimmunol.1303213. Epub 2014 May 7.

42.

Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro.

Denisova OV, Söderholm S, Virtanen S, Von Schantz C, Bychkov D, Vashchinkina E, Desloovere J, Tynell J, Ikonen N, Theisen LL, Nyman TA, Matikainen S, Kallioniemi O, Julkunen I, Muller CP, Saelens X, Verkhusha VV, Kainov DE.

Antimicrob Agents Chemother. 2014 Jul;58(7):3689-96. doi: 10.1128/AAC.02798-13. Epub 2014 Apr 21.

43.

Ezrin is down-regulated in diabetic kidney glomeruli and regulates actin reorganization and glucose uptake via GLUT1 in cultured podocytes.

Wasik AA, Koskelainen S, Hyvönen ME, Musante L, Lehtonen E, Koskenniemi K, Tienari J, Vaheri A, Kerjaschki D, Szalay C, Révész C, Varmanen P, Nyman TA, Hamar P, Holthöfer H, Lehtonen S.

Am J Pathol. 2014 Jun;184(6):1727-39. doi: 10.1016/j.ajpath.2014.03.002. Epub 2014 Apr 13.

PMID:
24726496
44.

Mutation update and genotype-phenotype correlations of novel and previously described mutations in TPM2 and TPM3 causing congenital myopathies.

Marttila M, Lehtokari VL, Marston S, Nyman TA, Barnerias C, Beggs AH, Bertini E, Ceyhan-Birsoy O, Cintas P, Gerard M, Gilbert-Dussardier B, Hogue JS, Longman C, Eymard B, Frydman M, Kang PB, Klinge L, Kolski H, Lochmüller H, Magy L, Manel V, Mayer M, Mercuri E, North KN, Peudenier-Robert S, Pihko H, Probst FJ, Reisin R, Stewart W, Taratuto AL, de Visser M, Wilichowski E, Winer J, Nowak K, Laing NG, Winder TL, Monnier N, Clarke NF, Pelin K, Grönholm M, Wallgren-Pettersson C.

Hum Mutat. 2014 Jul;35(7):779-90. doi: 10.1002/humu.22554. Epub 2014 May 1.

45.

Quantitative proteomics of extracellular vesicles released from human monocyte-derived macrophages upon β-glucan stimulation.

Cypryk W, Ohman T, Eskelinen EL, Matikainen S, Nyman TA.

J Proteome Res. 2014 May 2;13(5):2468-77. doi: 10.1021/pr4012552. Epub 2014 Apr 16.

PMID:
24670152
46.

Post-transcriptional regulation of human breast cancer cell proteome by unliganded estrogen receptor β via microRNAs.

Nassa G, Tarallo R, Giurato G, De Filippo MR, Ravo M, Rizzo F, Stellato C, Ambrosino C, Baumann M, Lietzèn N, Nyman TA, Weisz A.

Mol Cell Proteomics. 2014 Apr;13(4):1076-90. doi: 10.1074/mcp.M113.030403. Epub 2014 Feb 13.

47.

Ephrin-As, Eph receptors and integrin α3 interact and colocalise at membrane protrusions of U251MG glioblastoma cells.

Makarov A, Ylivinkka I, Nyman TA, Hyytiäinen M, Keski-Oja J.

Cell Biol Int. 2013 Oct;37(10):1080-8. doi: 10.1002/cbin.10134. Epub 2013 Jun 18.

PMID:
23686814
48.

Netrin-1-induced activation of Notch signaling mediates glioblastoma cell invasion.

Ylivinkka I, Hu Y, Chen P, Rantanen V, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M.

J Cell Sci. 2013 Jun 1;126(Pt 11):2459-69. doi: 10.1242/jcs.120022. Epub 2013 Apr 2.

49.

A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation.

Richter U, Lahtinen T, Marttinen P, Myöhänen M, Greco D, Cannino G, Jacobs HT, Lietzén N, Nyman TA, Battersby BJ.

Curr Biol. 2013 Mar 18;23(6):535-41. doi: 10.1016/j.cub.2013.02.019. Epub 2013 Feb 28.

50.

HnRNPH1/H2, U1 snRNP, and U11 snRNP cooperate to regulate the stability of the U11-48K pre-mRNA.

Turunen JJ, Verma B, Nyman TA, Frilander MJ.

RNA. 2013 Mar;19(3):380-9. doi: 10.1261/rna.036715.112. Epub 2013 Jan 18.

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