Tuula Anneli Nyman
Position: Group leader
Phone: +47 230 73019
Email:
 

Author network for Tuula Anneli Nyman by COREMINE medical


Publications 2017

Deptula P, Chamlagain B, Edelmann M, Sangsuwan P, Nyman TA, Savijoki K, Piironen V, Varmanen P (2017)
Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation
Front Microbiol, 8, 368
PubMed 28337185

Lorey MB, Rossi K, Eklund KK, Nyman TA, Matikainen S (2017)
Global characterization of protein secretion from human macrophages following non-canonical caspase-4/5 inflammasome activation
Mol Cell Proteomics (in press)
PubMed 28196878

Publications 2016

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 (2016)
Influenza virus NS1 protein binds cellular DNA to block transcription of antiviral genes
Biochim Biophys Acta, 1859 (11), 1440-1448
PubMed 27664935

Bæk KT, Bowman L, Millership C, Dupont Søgaard M, Kaever V, Siljamäki P, Savijoki K, Varmanen P, Nyman TA, Gründling A, Frees D (2016)
The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone
MBio, 7 (4)
PubMed 27507828

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 (2016)
HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression
EMBO J, 35 (13), 1385-99
PubMed 27234299

Cypryk W, Lorey M, Puustinen A, Nyman TA, Matikainen S (2016)
Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection
J Proteome Res, 16 (1), 217-227
PubMed 27723984

Fu Y, Gaelings L, Söderholm S, Belanov S, Nandania J, Nyman TA, Matikainen S, Anders S, Velagapudi V, Kainov DE (2016)
JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses
Antiviral Res, 133, 23-31
PubMed 27451344

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 (2016)
Regulation of kynurenine biosynthesis during influenza virus infection
FEBS J, 284 (2), 222-236
PubMed 27860276

Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE (2016)
Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction
Viruses, 8 (10)
PubMed 27690086

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 (2016)
Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages
Mol Cell Proteomics, 15 (10), 3203-3219
PubMed 27486199

Varghese FS, Thaa B, Amrun SN, Simarmata D, Rausalu K, Nyman TA, Merits A, McInerney GM, Ng LF, Ahola T (2016)
The Antiviral Alkaloid Berberine Reduces Chikungunya Virus-Induced Mitogen-Activated Protein Kinase Signaling
J Virol, 90 (21), 9743-9757
PubMed 27535052

Välimäki E, Cypryk W, Virkanen J, Nurmi K, Turunen PM, Eklund KK, Åkerman KE, Nyman TA, Matikainen S (2016)
Calpain Activity Is Essential for ATP-Driven Unconventional Vesicle-Mediated Protein Secretion and Inflammasome Activation in Human Macrophages
J Immunol, 197 (8), 3315-3325
PubMed 27638862

Wasik AA, Dumont V, Tienari J, Nyman TA, Fogarty CL, Forsblom C, Lehto M, Lehtonen E, Groop PH, Lehtonen S (2016)
Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion
Exp Cell Res, 350 (2), 336-348
PubMed 28011197

Publications 2015

Anastasina M, Schepens B, Söderholm S, Nyman TA, Matikainen S, Saksela K, Saelens X, Kainov DE (2015)
The C terminus of NS1 protein of influenza A/WSN/1933(H1N1) virus modulates antiviral responses in infected human macrophages and mice
J Gen Virol, 96 (8), 2086-91
PubMed 25934792

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 (2015)
Activating stimuli induce platelet microRNA modulation and proteome reorganisation
Thromb Haemost, 114 (1), 96-108
PubMed 25903651

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 (2015)
Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice
Genetics, 200 (1), 221-35
PubMed 25808953

Savijoki K, Skogman M, Fallarero A, Nyman TA, Sukura A, Vuorela P, Varmanen P (2015)
Penicillin G increases the synthesis of a suicidal marker (CidC) and virulence (HlgBC) proteins in Staphylococcus aureus biofilm cells
Int J Med Microbiol, 306 (1), 69-74
PubMed 26725755

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 (2015)
Identification of cytoplasmic proteins interacting with unliganded estrogen receptor α and β in human breast cancer cells
Proteomics, 15 (11), 1801-7
PubMed 25604459

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 (2015)
Immuno-modulating properties of saliphenylhalamide, SNS-032, obatoclax, and gemcitabine
Antiviral Res, 126, 69-80
PubMed 26738783

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 et al. (2015)
Biological properties of extracellular vesicles and their physiological functions
J Extracell Vesicles, 4, 27066
PubMed 25979354

Öhman T, Söderholm S, Paidikondala M, Lietzén N, Matikainen S, Nyman TA (2015)
Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells
Proteomics, 15 (12), 2087-97
PubMed 25764225

Publications 2014

Cypryk W, Ohman T, Eskelinen EL, Matikainen S, Nyman TA (2014)
Quantitative proteomics of extracellular vesicles released from human monocyte-derived macrophages upon β-glucan stimulation
J Proteome Res, 13 (5), 2468-77
PubMed 24670152

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 (2014)
Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro
Antimicrob Agents Chemother, 58 (7), 3689-96
PubMed 24752266

Elo LL, Karjalainen R, Ohman T, Hintsanen P, Nyman TA, Heckman CA, Aittokallio T (2014)
Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia
Proteomics, 14 (21-22), 2443-53
PubMed 25211154

Espino E, Koskenniemi K, Mato-Rodriguez L, Nyman TA, Reunanen J, Koponen J, Öhman T, Siljamäki P, Alatossava T, Varmanen P, Savijoki K (2014)
Uncovering surface-exposed antigens of Lactobacillus rhamnosus by cell shaving proteomics and two-dimensional immunoblotting
J Proteome Res, 14 (2), 1010-24
PubMed 25531588

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 et al. (2014)
Mutation update and genotype-phenotype correlations of novel and previously described mutations in TPM2 and TPM3 causing congenital myopathies
Hum Mutat, 35 (7), 779-90
PubMed 24692096

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 (2014)
Post-transcriptional regulation of human breast cancer cell proteome by unliganded estrogen receptor β via microRNAs
Mol Cell Proteomics, 13 (4), 1076-90
PubMed 24525454

Salomäki T, Karonen T, Siljamäki P, Savijoki K, Nyman TA, Varmanen P, Iivanainen A (2014)
A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation
J Appl Microbiol, 118 (1), 1-10
PubMed 25308550

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 (2014)
Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains
J Proteome Res (in press)
PubMed 25014494

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 (2014)
Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins
Proteomics, 14 (16), 1890-4
PubMed 24909406

Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA (2014)
Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence
J Proteome Res, 13 (7), 3249-61
PubMed 24840314

Söderholm S, Hintsanen P, Ohman T, Aittokallio T, Nyman TA (2014)
PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
Proteome Sci, 12, 36
PubMed 25028575

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 (2014)
Ezrin is down-regulated in diabetic kidney glomeruli and regulates actin reorganization and glucose uptake via GLUT1 in cultured podocytes
Am J Pathol, 184 (6), 1727-39
PubMed 24726496

Weber-Boyvat M, Kentala H, Lilja J, Vihervaara T, Hanninen R, Zhou Y, Peränen J, Nyman TA, Ivaska J, Olkkonen VM (2014)
OSBP-related protein 3 (ORP3) coupling with VAMP-associated protein A regulates R-Ras activity
Exp Cell Res, 331 (2), 278-91
PubMed 25447204

Öhman T, Söderholm S, Hintsanen P, Välimäki E, Lietzén N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA (2014)
Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway
Mol Cell Proteomics, 13 (10), 2604-17
PubMed 24997996

Öhman T, Teirilä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S (2014)
Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages
J Immunol, 192 (12), 5952-62
PubMed 24808366

Aatonen MT, Ohman T, Nyman TA, Laitinen S, Grönholm M, Siljander PR (2014)
Isolation and characterization of platelet-derived extracellular vesicles
J Extracell Vesicles, 3
PubMed 25147646

Publications 2013

Kankkunen P, Välimäki E, Rintahaka J, Palomäki J, Nyman T, Alenius H, Wolff H, Matikainen S (2013)
Trichothecene mycotoxins activate NLRP3 inflammasome through a P2X7 receptor and Src tyrosine kinase dependent pathway
Hum Immunol, 75 (2), 134-40
PubMed 24269698

Makarov A, Ylivinkka I, Nyman TA, Hyytiäinen M, Keski-Oja J (2013)
Ephrin-As, Eph receptors and integrin α3 interact and colocalise at membrane protrusions of U251MG glioblastoma cells
Cell Biol Int, 37 (10), 1080-8
PubMed 23686814

Richter U, Lahtinen T, Marttinen P, Myöhänen M, Greco D, Cannino G, Jacobs HT, Lietzén N, Nyman TA, Battersby BJ (2013)
A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation
Curr Biol, 23 (6), 535-41
PubMed 23453957

Turunen JJ, Verma B, Nyman TA, Frilander MJ (2013)
HnRNPH1/H2, U1 snRNP, and U11 snRNP cooperate to regulate the stability of the U11-48K pre-mRNA
RNA, 19 (3), 380-9
PubMed 23335637

Välimäki E, Miettinen JJ, Lietzén N, Matikainen S, Nyman TA (2013)
Monosodium urate activates Src/Pyk2/PI3 kinase and cathepsin dependent unconventional protein secretion from human primary macrophages
Mol Cell Proteomics, 12 (3), 749-63
PubMed 23292187

Ylivinkka I, Hu Y, Chen P, Rantanen V, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M (2013)
Netrin-1-induced activation of Notch signaling mediates glioblastoma cell invasion
J Cell Sci, 126 (Pt 11), 2459-69
PubMed 23549787

Publications 2012

Bien J, Näreaho A, Varmanen P, Gozdzik K, Moskwa B, Cabaj W, Nyman TA, Savijoki K (2012)
Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting
Proteome Sci, 10 (1), 10
PubMed 22325190

Cirillo F, Nassa G, Tarallo R, Stellato C, De Filippo MR, Ambrosino C, Baumann M, Nyman TA, Weisz A (2012)
Molecular mechanisms of selective estrogen receptor modulator activity in human breast cancer cells: identification of novel nuclear cofactors of antiestrogen-ERα complexes by interaction proteomics
J Proteome Res, 12 (1), 421-31
PubMed 23170835

Hu Y, Ylivinkka I, Chen P, Li L, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M (2012)
Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling
Neoplasia, 14 (3), 219-27
PubMed 22496621

Miettinen JJ, Matikainen S, Nyman TA (2012)
Global secretome characterization of herpes simplex virus 1-infected human primary macrophages
J Virol, 86 (23), 12770-8
PubMed 22973042

Rostila A, Puustinen A, Toljamo T, Vuopala K, Lindström I, Nyman TA, Oksa P, Vehmas T, Anttila SL (2012)
Peroxiredoxins and tropomyosins as plasma biomarkers for lung cancer and asbestos exposure
Lung Cancer, 77 (2), 450-9
PubMed 22537621

Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T, Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I (2012)
Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins
Biol Psychiatry, 73 (6), 583-90
PubMed 23036959

Publications 2011

Frees D, Andersen JH, Hemmingsen L, Koskenniemi K, Bæk KT, Muhammed MK, Gudeta DD, Nyman TA, Sukura A, Varmanen P, Savijoki K (2011)
New insights into Staphylococcus aureus stress tolerance and virulence regulation from an analysis of the role of the ClpP protease in the strains Newman, COL, and SA564
J Proteome Res, 11 (1), 95-108
PubMed 22112206

Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P (2011)
Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG
J Proteomics, 75 (4), 1357-74
PubMed 22119544

Laulajainen M, Muranen T, Nyman TA, Carpén O, Grönholm M (2011)
Multistep phosphorylation by oncogenic kinases enhances the degradation of the NF2 tumor suppressor merlin
Neoplasia, 13 (7), 643-52
PubMed 21750658

Lietzén N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, Matikainen S, Nyman TA (2011)
Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages
PLoS Pathog, 7 (5), e1001340
PubMed 21589892

Laakso K, Koskenniemi K, Koponen J, Kankainen M, Surakka A, Salusjärvi T, Auvinen P, Savijoki K, Nyman TA, Kalkkinen N, Tynkkynen S, Varmanen P (2011)
Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
Microb Biotechnol, 4 (6), 746-66
PubMed 21883975

Rintahaka J, Lietzén N, Öhman T, Nyman TA, Matikainen S (2011)
Recognition of cytoplasmic RNA results in cathepsin-dependent inflammasome activation and apoptosis in human macrophages
J Immunol, 186 (5), 3085-92
PubMed 21257972

Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA (2011)
Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705
J Proteome Res, 10 (8), 3460-73
PubMed 21615180

Publications 2010

Ambrosino C, Tarallo R, Bamundo A, Cuomo D, Franci G, Nassa G, Paris O, Ravo M, Giovane A, Zambrano N, Lepikhova T, Jänne OA, Baumann M, Nyman TA, Cicatiello L, Weisz A (2010)
Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei
Mol Cell Proteomics, 9 (6), 1352-67
PubMed 20308691

Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusjärvi T, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P (2010)
Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG
Mol Cell Proteomics, 10 (2), M110.002741
PubMed 21078892

Lehtimäki S, Tillander S, Puustinen A, Matikainen S, Nyman T, Fyhrquist N, Savinko T, Majuri ML, Wolff H, Alenius H, Lauerma A (2010)
Absence of CCR4 exacerbates skin inflammation in an oxazolone-induced contact hypersensitivity model
J Invest Dermatol, 130 (12), 2743-51
PubMed 20631725

Lehto M, Airaksinen L, Puustinen A, Tillander S, Hannula S, Nyman T, Toskala E, Alenius H, Lauerma A (2010)
Thaumatin-like protein and baker's respiratory allergy
Ann Allergy Asthma Immunol, 104 (2), 139-46
PubMed 20306817

Lietzén N, Natri L, Nevalainen OS, Salmi J, Nyman TA (2010)
Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon
J Proteome Res, 9 (12), 6795-800
PubMed 20973569

Moulder R, Lönnberg T, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R (2010)
Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation
Mol Cell Proteomics, 9 (9), 1937-53
PubMed 20467038

Nassa G, Tarallo R, Ambrosino C, Bamundo A, Ferraro L, Paris O, Ravo M, Guzzi PH, Cannataro M, Baumann M, Nyman TA, Nola E, Weisz A (2010)
A large set of estrogen receptor β-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei
Proteomics, 11 (1), 159-65
PubMed 21182203

Nassa G, Tarallo R, Guzzi PH, Ferraro L, Cirillo F, Ravo M, Nola E, Baumann M, Nyman TA, Cannataro M, Ambrosino C, Weisz A (2010)
Comparative analysis of nuclear estrogen receptor alpha and beta interactomes in breast cancer cells
Mol Biosyst, 7 (3), 667-76
PubMed 21173974

Ohman T, Lietzén N, Välimäki E, Melchjorsen J, Matikainen S, Nyman TA (2010)
Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes
J Proteome Res, 9 (3), 1549-64
PubMed 20070120

Piippo M, Lietzén N, Nevalainen OS, Salmi J, Nyman TA (2010)
Pripper: prediction of caspase cleavage sites from whole proteomes
BMC Bioinformatics, 11, 320
PubMed 20546630

Sane P, Tuomisto F, Wiedmer SK, Nyman T, Vattulainen I, Holopainen JM (2010)
Temperature-induced structural transition in-situ in porcine lens--changes observed in void size distribution
Biochim Biophys Acta, 1798 (5), 958-65
PubMed 20122897

Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A (2010)
Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS
Proteomics, 11 (1), 172-9
PubMed 21182205

Weber-Boyvat M, Aro N, Chernov KG, Nyman T, Jäntti J (2010)
Sec1p and Mso1p C-terminal tails cooperate with the SNAREs and Sec4p in polarized exocytosis
Mol Biol Cell, 22 (2), 230-44
PubMed 21119007

Publications 2009

Korolainen MA, Nyman TA, Aittokallio T, Pirttilä T (2009)
An update on clinical proteomics in Alzheimer's research
J Neurochem, 112 (6), 1386-414
PubMed 20050976

Ohman T, Rintahaka J, Kalkkinen N, Matikainen S, Nyman TA (2009)
Actin and RIG-I/MAVS signaling components translocate to mitochondria upon influenza A virus infection of human primary macrophages
J Immunol, 182 (9), 5682-92
PubMed 19380815

Salmi J, Nyman TA, Nevalainen OS, Aittokallio T (2009)
Filtering strategies for improving protein identification in high-throughput MS/MS studies
Proteomics, 9 (4), 848-60
PubMed 19160393

Tuomela S, Rautajoki KJ, Moulder R, Nyman TA, Lahesmaa R (2009)
Identification of novel Stat6 regulated proteins in IL-4-treated mouse lymphocytes
Proteomics, 9 (4), 1087-98
PubMed 19180534

Publications 2008

Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R (2008)
Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation
Mol Cell Proteomics, 8 (1), 32-44
PubMed 18701445

Korolainen MA, Corthals GL, Kouvonen P, Kurkinen KM, Nyman TA (2008)
3rd Annual FinnProt Meeting: from cells to systems
Expert Rev Proteomics, 5 (3), 389-91
PubMed 18532906

Publications 2007

Korolainen MA, Nyman TA, Nyyssönen P, Hartikainen ES, Pirttilä T (2007)
Multiplexed proteomic analysis of oxidation and concentrations of cerebrospinal fluid proteins in Alzheimer disease
Clin Chem, 53 (4), 657-65
PubMed 17289803

Rakkola R, Matikainen S, Nyman TA (2007)
Proteome analysis of human macrophages reveals the upregulation of manganese-containing superoxide dismutase after toll-like receptor activation
Proteomics, 7 (3), 378-84
PubMed 17211829

Publications 2006

Rautajoki KJ, Marttila EM, Nyman TA, Lahesmaa R (2006)
Interleukin-4 inhibits caspase-3 by regulating several proteins in the Fas pathway during initial stages of human T helper 2 cell differentiation
Mol Cell Proteomics, 6 (2), 238-51
PubMed 17114647

Takatalo MS, Kouvonen P, Corthals G, Nyman TA, Rönnholm RH (2006)
Identification of new Golgi complex specific proteins by direct organelle proteomic analysis
Proteomics, 6 (12), 3502-8
PubMed 16691549

Publications 2005

Aittokallio T, Salmi J, Nyman TA, Nevalainen OS (2005)
Geometrical distortions in two-dimensional gels: applicable correction methods
J Chromatogr B Analyt Technol Biomed Life Sci, 815 (1-2), 25-37
PubMed 15652796

Björkblom B, Ostman N, Hongisto V, Komarovski V, Filén JJ, Nyman TA, Kallunki T, Courtney MJ, Coffey ET (2005)
Constitutively active cytoplasmic c-Jun N-terminal kinase 1 is a dominant regulator of dendritic architecture: role of microtubule-associated protein 2 as an effector
J Neurosci, 25 (27), 6350-61
PubMed 16000625

Filén JJ, Nyman TA, Korhonen J, Goodlett DR, Lahesmaa R (2005)
Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12
Proteomics, 5 (18), 4719-32
PubMed 16247730

Korolainen MA, Auriola S, Nyman TA, Alafuzoff I, Pirttilä T (2005)
Proteomic analysis of glial fibrillary acidic protein in Alzheimer's disease and aging brain
Neurobiol Dis, 20 (3), 858-70
PubMed 15979880

Korolainen MA, Goldsteins G, Nyman TA, Alafuzoff I, Koistinaho J, Pirttilä T (2005)
Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain
Neurobiol Aging, 27 (1), 42-53
PubMed 16298240

Moulder R, Filén JJ, Salmi J, Katajamaa M, Nevalainen OS, Oresic M, Aittokallio T, Lahesmaa R, Nyman TA (2005)
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments
Proteomics, 5 (11), 2748-60
PubMed 15952233

Rakkola R, Matikainen S, Nyman TA (2005)
Proteome characterization of human NK-92 cells identifies novel IFN-alpha and IL-15 target genes
J Proteome Res, 4 (1), 75-82
PubMed 15707360

Rosengren AT, Nyman TA, Lahesmaa R (2005)
Proteome profiling of interleukin-12 treated human T helper cells
Proteomics, 5 (12), 3137-41
PubMed 16038020

Rosengren AT, Nyman TA, Syyrakki S, Matikainen S, Lahesmaa R (2005)
Proteomic and transcriptomic characterization of interferon-alpha-induced human primary T helper cells
Proteomics, 5 (2), 371-9
PubMed 15700245

Salmi J, Moulder R, Filén JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio T (2005)
Quality classification of tandem mass spectrometry data
Bioinformatics, 22 (4), 400-6
PubMed 16352652

Publications 2004

Rautajoki K, Nyman TA, Lahesmaa R (2004)
Proteome characterization of human T helper 1 and 2 cells
Proteomics, 4 (1), 84-92
PubMed 14730674

Publications 2003

Rosengren AT, Salmi JM, Aittokallio T, Westerholm J, Lahesmaa R, Nyman TA, Nevalainen OS (2003)
Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
Proteomics, 3 (10), 1936-46
PubMed 14625856

Publications 2002

Salmi J, Aittokallio T, Westerholm J, Griese M, Rosengren A, Nyman TA, Lahesmaa R, Nevalainen O (2002)
Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels
Proteomics, 2 (11), 1504-15
PubMed 12442250

Publications 2001

Nyman TA (2001)
The role of mass spectrometry in proteome studies
Biomol Eng, 18 (5), 221-7
PubMed 11911089

Nyman TA, Rosengren A, Syyrakki S, Pellinen TP, Rautajoki K, Lahesmaa R (2001)
A proteome database of human primary T helper cells
Electrophoresis, 22 (20), 4375-82
PubMed 11824605

Tarkka MT, Nyman TA, Kalkkinen N, Raudaskoski M (2001)
Scots pine expresses short-root-specific peroxidases during development
Eur J Biochem, 268 (1), 86-92
PubMed 11121106

Publications 2000

Nyman TA, Matikainen S, Sareneva T, Julkunen I, Kalkkinen N (2000)
Proteome analysis reveals ubiquitin-conjugating enzymes to be a new family of interferon-alpha-regulated genes
Eur J Biochem, 267 (13), 4011-9
PubMed 10866800

Publications 1998

Nyman TA, Kalkkinen N, Tölö H, Helin J (1998)
Structural characterisation of N-linked and O-linked oligosaccharides derived from interferon-alpha2b and interferon-alpha14c produced by Sendai-virus-induced human peripheral blood leukocytes
Eur J Biochem, 253 (2), 485-93
PubMed 9654101

Nyman TA, Tölö H, Parkkinen J, Kalkkinen N (1998)
Identification of nine interferon-alpha subtypes produced by Sendai virus-induced human peripheral blood leucocytes
Biochem J, 329 ( Pt 2), 295-302
PubMed 9425112