Publications by Tuula Anneli Nyman

167 publications found

Publications 2024

1. Abusdal M, Normann KR, Nyman TA, Øystese KAB, Sundaram AYM, Dahlberg D, Lekva T, Bollerslev J, Berg JP, Olarescu NC (2024)
   PCSK1N as a tumor size marker and an ER stress response protein in corticotroph pituitary adenomas
   J Clin Endocrinol Metab (in press)
   DOI 10.1210/clinem/dgae643, PubMed 39288010
2. Górska AM, Santos-García I, Eiriz I, Brüning T, Nyman T, Pahnke J (2024)
   Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers
   J Neurosci Methods, 411, 110239
   DOI 10.1016/j.jneumeth.2024.110239, PubMed 39102902
3. Hilander T, Awadhpersad R, Monteuuis G, Broda KL, Pohjanpelto M, Pyman E, Singh SK, Nyman TA, Crevel I, Taylor RW, Saada A, Balboa D, Battersby BJ, Jackson CB, Carroll CJ (2024)
   Supernumerary proteins of the human mitochondrial ribosomal small subunit are integral for assembly and translation
   iScience, 27 (7), 110185
   DOI 10.1016/j.isci.2024.110185, PubMed 39015150
4. Kang Y, Hepojoki J, Maldonado RS, Mito T, Terzioglu M, Manninen T, Kant R, Singh S, Othman A, Verma R, Uusimaa J, Wartiovaara K, Kareinen L, Zamboni N, Nyman TA, Paetau A, Kipar A, Vapalahti O, Suomalainen A (2024)
   Ancestral allele of DNA polymerase gamma modifies antiviral tolerance
   Nature, 628 (8009), 844-853
   DOI 10.1038/s41586-024-07260-z, PubMed 38570685
5. Katare PB, Dalmao-Fernandez A, Mengeste AM, Navabakbar F, Hamarsland H, Ellefsen S, Berge RK, Bakke HG, Nyman TA, Kase ET, Rustan AC, Thoresen GH (2024)
   Krill oil supplementation in vivo promotes increased fuel metabolism and protein synthesis in cultured human skeletal muscle cells
   Front Nutr, 11, 1452768
   DOI 10.3389/fnut.2024.1452768, PubMed 39555189
6. Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V (2024)
   Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
   NPJ Syst Biol Appl, 10 (1), 73
   DOI 10.1038/s41540-024-00402-z, PubMed 38997321
7. Loivamaa I, Sillanpää A, Deptula P, Chamlagain B, Edelmann M, Auvinen P, Nyman TA, Savijoki K, Piironen V, Varmanen P (2024)
   Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis
   mSystems, 9 (10), e0061524
   DOI 10.1128/msystems.00615-24, PubMed 39345151
8. Stevanovic S, Dalmao-Fernandez A, Mohamed D, Nyman TA, Kostovski E, Iversen PO, Savikj M, Nikolic N, Rustan AC, Thoresen GH, Kase ET (2024)
   Time-dependent reduction in oxidative capacity among cultured myotubes from spinal cord injured individuals
   Acta Physiol (Oxf), 240 (7), e14156
   DOI 10.1111/apha.14156, PubMed 38711362

Publications 2023

1. Cypryk W, Czernek L, Horodecka K, Chrzanowski J, Stańczak M, Nurmi K, Bilicka M, Gadzinowski M, Walczak-Drzewiecka A, Stensland M, Eklund K, Fendler W, Nyman TA, Matikainen S (2023)
   Lipopolysaccharide Primes Human Macrophages for Noncanonical Inflammasome-Induced Extracellular Vesicle Secretion
   J Immunol, 210 (3), 322-334
   DOI 10.4049/jimmunol.2200444, PubMed 36525001
2. Frerker N, Karlsen TA, Stensland M, Nyman TA, Rayner S, Brinchmann JE (2023)
   Comparison between articular chondrocytes and mesenchymal stromal cells for the production of articular cartilage implants
   Front Bioeng Biotechnol, 11, 1116513
   DOI 10.3389/fbioe.2023.1116513, PubMed 36896010
3. Gorski K, Jackson CB, Nyman TA, Rezov V, Battersby BJ, Lehesjoki AE (2023)
   Progressive mitochondrial dysfunction in cerebellar synaptosomes of cystatin B-deficient mice
   Front Mol Neurosci, 16, 1175851
   DOI 10.3389/fnmol.2023.1175851, PubMed 37251643
4. Hammarén MM, Luukinen H, Sillanpää A, Remans K, Lapouge K, Custódio T, Löw C, Myllymäki H, Montonen T, Seeger M, Robertson J, Nyman TA, Savijoki K, Parikka M (2023)
   In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies
   mSystems, 8 (3), e0107322
   DOI 10.1128/msystems.01073-22, PubMed 37184670
5. Harrison SP, Siller R, Tanaka Y, Chollet ME, de la Morena-Barrio ME, Xiang Y, Patterson B, Andersen E, Bravo-Pérez C, Kempf H, Åsrud KS, Lunov O, Dejneka A, Mowinckel MC, Stavik B, Sandset PM, Melum E, Baumgarten S, Bonanini F, Kurek D, Mathapati S, Almaas R, Sharma K, Wilson SR, Skottvoll FS et al. (2023)
   Scalable production of tissue-like vascularized liver organoids from human PSCs
   Exp Mol Med, 55 (9), 2005-2024
   DOI 10.1038/s12276-023-01074-1, PubMed 37653039
6. Kangas P, Nyman TA, Metsähonkala L, Burns C, Tempest R, Williams T, Karttunen J, Jokinen TS (2023)
   Towards optimised extracellular vesicle proteomics from cerebrospinal fluid
   Sci Rep, 13 (1), 9564
   DOI 10.1038/s41598-023-36706-z, PubMed 37308520
7. Krapf SA, Lund J, Bakke HG, Nyman TA, Bartesaghi S, Peng XR, Rustan AC, Thoresen GH, Kase ET (2023)
   SENP2 knockdown in human adipocytes reduces glucose metabolism and lipid accumulation, while increases lipid oxidation
   Metabol Open, 18, 100234
   DOI 10.1016/j.metop.2023.100234, PubMed 37013149
8. Lunde NN, Osoble NMM, Fernandez AD, Antobreh AS, Jafari A, Singh S, Nyman TA, Rustan AC, Solberg R, Thoresen GH (2023)
   Interplay between Cultured Human Osteoblastic and Skeletal Muscle Cells: Effects of Conditioned Media on Glucose and Fatty Acid Metabolism
   Biomedicines, 11 (11)
   DOI 10.3390/biomedicines11112908, PubMed 38001909
9. Misceo D, Lirussi L, Strømme P, Sumathipala D, Guerin A, Wolf NI, Server A, Stensland M, Dalhus B, Tolun A, Kroes HY, Nyman TA, Nilsen HL, Frengen E (2023)
   A homozygous POLR1A variant causes leukodystrophy and affects protein homeostasis
   Brain, 146 (8), 3513-3527
   DOI 10.1093/brain/awad086, PubMed 36917474
10. Saidu NEB, Aarsund M, Sørensen E, Stensland M, Nyman TA, Ulvmoen A, Wu Y, Inngjerdingen M (2023)
    Identifying a core protein signature of small extracellular vesicles derived from B-cell precursor acute lymphoblastic leukaemia
    Scand J Immunol, 99 (3), e13341
    DOI 10.1111/sji.13341, PubMed 38441169
11. Ueland T, Äikäs LAO, Dahl TB, Gregersen I, Olsen MB, Michelsen A, Schanke Y, Holopainen M, Ruhanen H, Singh S, NOR-SOLIDARITY Consortium, Tveita AA, Finbråten AK, Heggelund L, Trøseid M, Dyrhol-Riise AM, Nyman TA, Holven KB, Öörni K, Aukrust P, Halvorsen B (2023)
    Low-density lipoprotein particles carrying proinflammatory proteins with altered aggregation pattern detected in COVID-19 patients 3 months after hospitalization
    J Infect, 86 (5), 489-492
    DOI 10.1016/j.jinf.2023.02.024, PubMed 36822413
12. Aas V, Øvstebø R, Brusletto BS, Aspelin T, Trøseid AS, Qureshi S, Eid DSO, Olstad OK, Nyman TA, Haug KBF (2023)
    Distinct microRNA and protein profiles of extracellular vesicles secreted from myotubes from morbidly obese donors with type 2 diabetes in response to electrical pulse stimulation
    Front Physiol, 14, 1143966
    DOI 10.3389/fphys.2023.1143966, PubMed 37064893

Publications 2022

1. Hautala K, Pursiainen J, Näreaho A, Nyman T, Varmanen P, Sukura A, Nielsen MK, Savijoki K (2022)
   Label-free quantitative proteomics and immunoblotting identifies immunoreactive and other excretory-secretory (E/S) proteins of Anoplocephala perfoliata
   Front Immunol, 13, 1045468
   DOI 10.3389/fimmu.2022.1045468, PubMed 36466892
2. Høyer H, Busk ØL, Esbensen QY, Røsby O, Hilmarsen HT, Russell MB, Nyman TA, Braathen GJ, Nilsen HL (2022)
   Clinical characteristics and proteome modifications in two Charcot-Marie-Tooth families with the AARS1 Arg326Trp mutation
   BMC Neurol, 22 (1), 299
   DOI 10.1186/s12883-022-02828-6, PubMed 35971119
3. Mengeste AM, Nikolić N, Dalmao Fernandez A, Feng YZ, Nyman TA, Kersten S, Haugen F, Kase ET, Aas V, Rustan AC, Thoresen GH (2022)
   Insight Into the Metabolic Adaptations of Electrically Pulse-Stimulated Human Myotubes Using Global Analysis of the Transcriptome and Proteome
   Front Physiol, 13, 928195
   DOI 10.3389/fphys.2022.928195, PubMed 35874526
4. Salvati A, Melone V, Sellitto A, Rizzo F, Tarallo R, Nyman TA, Giurato G, Nassa G, Weisz A (2022)
   Combinatorial targeting of a chromatin complex comprising Dot1L, menin and the tyrosine kinase BAZ1B reveals a new therapeutic vulnerability of endocrine therapy-resistant breast cancer
   Breast Cancer Res, 24 (1), 52
   DOI 10.1186/s13058-022-01547-7, PubMed 35850772
5. Aarsund M, Nyman TA, Stensland ME, Wu Y, Inngjerdingen M (2022)
   Isolation of a cytolytic subpopulation of extracellular vesicles derived from NK cells containing NKG7 and cytolytic proteins
   Front Immunol, 13, 977353
   DOI 10.3389/fimmu.2022.977353, PubMed 36189227

Publications 2021

1. Borowicz P, Sundvold V, Chan H, Abrahamsen G, Kjelstrup H, Nyman TA, Spurkland A (2021)
   Tyr¹⁹² Regulates Lymphocyte-Specific Tyrosine Kinase Activity in T Cells
   J Immunol, 207 (4), 1128-1137
   DOI 10.4049/jimmunol.2001105, PubMed 34321230
2. Holm S, Kared H, Michelsen AE, Kong XY, Dahl TB, Schultz NH, Nyman TA, Fladeby C, Seljeflot I, Ueland T, Stensland M, Mjaaland S, Goll GL, Nissen-Meyer LS, Aukrust P, Skagen K, Gregersen I, Skjelland M, Holme PA, Munthe LA, Halvorsen B (2021)
   Immune complexes, innate immunity, and NETosis in ChAdOx1 vaccine-induced thrombocytopenia
   Eur Heart J, 42 (39), 4064-4072
   DOI 10.1093/eurheartj/ehab506, PubMed 34405870
3. Kaivola J, Nyman TA, Matikainen S (2021)
   Inflammasomes and SARS-CoV-2 Infection
   Viruses, 13 (12)
   DOI 10.3390/v13122513, PubMed 34960782
4. Mirlashari MR, Vetlesen A, Nissen-Meyer LSH, Stensland ME, Singh SK, Nyman TA, Hetland G (2021)
   Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients
   Proteomics Clin Appl, 15 (6), e2100022
   DOI 10.1002/prca.202100022, PubMed 34510746
5. Quiles-Jiménez A, Gregersen I, Segers FM, Skarpengland T, Kroustallaki P, Yang K, Kong XY, Lauritzen KH, Olsen MB, Karlsen TR, Nyman TA, Sagen EL, Bjerkeli V, Suganthan R, Nygård S, Scheffler K, Prins J, Van der Veer E, Øgaard JD, Fløisand Y, Jørgensen HF, Holven KB, Biessen EA, Nilsen H, Dahl TB et al. (2021)
   DNA glycosylase Neil3 regulates vascular smooth muscle cell biology during atherosclerosis development
   Atherosclerosis, 324, 123-132
   DOI 10.1016/j.atherosclerosis.2021.02.023, PubMed 33714552
6. Reigada I, San-Martin-Galindo P, Gilbert-Girard S, Chiaro J, Cerullo V, Savijoki K, Nyman TA, Fallarero A, Miettinen I (2021)
   Surfaceome and Exoproteome Dynamics in Dual-Species Pseudomonas aeruginosa and Staphylococcus aureus Biofilms
   Front Microbiol, 12, 672975
   DOI 10.3389/fmicb.2021.672975, PubMed 34248881
7. Røberg-Larsen H, Lundanes E, Nyman TA, Berven FS, Wilson SR (2021)
   Liquid chromatography, a key tool for the advancement of single-cell omics analysis
   Anal Chim Acta, 1178, 338551
   DOI 10.1016/j.aca.2021.338551, PubMed 34482862
8. San-Martin-Galindo P, Rosqvist E, Tolvanen S, Miettinen I, Savijoki K, Nyman TA, Fallarero A, Peltonen J (2021)
   Modulation of virulence factors of Staphylococcus aureus by nanostructured surfaces
   Mater. Des., 208, 109879
   DOI 10.1016/j.matdes.2021.109879
9. Savijoki K, Myllymäki H, Luukinen H, Paulamäki L, Vanha-Aho LM, Svorjova A, Miettinen I, Fallarero A, Ihalainen TO, Yli-Kauhaluoma J, Nyman TA, Parikka M (2021)
   Surface-Shaving Proteomics of Mycobacterium marinum Identifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance, and Persistence
   mSystems, 6 (3), e0050021
   DOI 10.1128/mSystems.00500-21, PubMed 34156290
10. Skagen C, Nyman TA, Peng XR, O'Mahony G, Kase ET, Rustan AC, Thoresen GH (2021)
    Chronic treatment with terbutaline increases glucose and oleic acid oxidation and protein synthesis in cultured human myotubes
    Curr Res Pharmacol Drug Discov, 2, 100039
    DOI 10.1016/j.crphar.2021.100039, PubMed 34909668
11. Snapkov I, Chernigovskaya M, Sinitcyn P, Lê Quý K, Nyman TA, Greiff V (2021)
    Progress and challenges in mass spectrometry-based analysis of antibody repertoires
    Trends Biotechnol, 40 (4), 463-481
    DOI 10.1016/j.tibtech.2021.08.006, PubMed 34535228
12. Stamnaes J, Stray D, Stensland M, Sarna VK, Nyman TA, Lundin KEA, Sollid LM (2021)
    In Well-Treated Celiac Patients Low-Level Mucosal Inflammation Predicts Response to 14-day Gluten Challenge
    Adv Sci (Weinh), 8 (4), 2003526
    DOI 10.1002/advs.202003526, PubMed 33643806
13. Vestad B, Nyman TA, Hove-Skovsgaard M, Stensland M, Hoel H, Trøseid AS, Aspelin T, Aass HCD, Puhka M, Hov JR, Nielsen SD, Øvstebø R, Trøseid M (2021)
    Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk
    Sci Rep, 11 (1), 21936
    DOI 10.1038/s41598-021-01334-y, PubMed 34754007
14. Wanichawan P, Skogestad J, Lunde M, Støle TP, Stensland M, Nyman TA, Sjaastad I, Sejersted OM, Aronsen JM, Carlson CR (2021)
    Design of a Proteolytically Stable Sodium-Calcium Exchanger 1 Activator Peptide for In Vivo Studies
    Front Pharmacol, 12, 638646
    DOI 10.3389/fphar.2021.638646, PubMed 34163352

Publications 2020

1. Eieland AK, Normann KR, Sundaram AYM, Nyman TA, Øystese KAB, Lekva T, Berg JP, Bollerslev J, Olarescu NC (2020)
   Distinct Pattern of Endoplasmic Reticulum Protein Processing and Extracellular Matrix Proteins in Functioning and Silent Corticotroph Pituitary Adenomas
   Cancers (Basel), 12 (10)
   DOI 10.3390/cancers12102980, PubMed 33066652
2. Gigantino V, Salvati A, Giurato G, Palumbo D, Strianese O, Rizzo F, Tarallo R, Nyman TA, Weisz A, Nassa G (2020)
   Identification of Antiestrogen-Bound Estrogen Receptor α Interactomes in Hormone-Responsive Human Breast Cancer Cell Nuclei
   Proteomics, 20 (19-20), e2000135
   DOI 10.1002/pmic.202000135, PubMed 32865868
3. Gorski K, Spoljaric A, Nyman TA, Kaila K, Battersby BJ, Lehesjoki AE (2020)
   Quantitative Changes in the Mitochondrial Proteome of Cerebellar Synaptosomes From Preclinical Cystatin B-Deficient Mice
   Front Mol Neurosci, 13, 570640
   DOI 10.3389/fnmol.2020.570640, PubMed 33281550
4. Krapf SA, Lund J, Lundkvist M, Dale MG, Nyman TA, Thoresen GH, Kase ET (2020)
   Pancreatic cancer cells show lower oleic acid oxidation and their conditioned medium inhibits oleic acid oxidation in human myotubes
   Pancreatology, 20 (4), 676-682
   DOI 10.1016/j.pan.2020.04.014, PubMed 32360002
5. Louwe MC, Olsen MB, Kaasbøll OJ, Yang K, Fosshaug LE, Alfsnes K, Øgaard JDS, Rashidi A, Skulberg VM, Yang M, de Miranda Fonseca D, Sharma A, Aronsen JM, Schrumpf E, Ahmed MS, Dahl CP, Nyman TA, Ueland T, Melum E, Halvorsen BE, Bjørås M, Attramadal H, Sjaastad I, Aukrust P, Yndestad A (2020)
   Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction
   JACC Basic Transl Sci, 5 (12), 1210-1224
   DOI 10.1016/j.jacbts.2020.09.013, PubMed 33426377
6. Mathiesen SB, Lunde M, Stensland M, Martinsen M, Nyman TA, Christensen G, Carlson CR (2020)
   The Cardiac Syndecan-2 Interactome
   Front Cell Dev Biol, 8, 792
   DOI 10.3389/fcell.2020.00792, PubMed 32984315
7. Matikainen S, Nyman TA, Cypryk W (2020)
   Function and Regulation of Noncanonical Caspase-4/5/11 Inflammasome
   J Immunol, 204 (12), 3063-3069
   DOI 10.4049/jimmunol.2000373, PubMed 32513874
8. Matikainen S, Nyman TA, Cypryk W (2020)
   Inflammasomes: Exosomal miRNAs loaded for action
   J Cell Biol, 219 (10)
   DOI 10.1083/jcb.202008130, PubMed 32970793
9. Savijoki K, Miettinen I, Nyman TA, Kortesoja M, Hanski L, Varmanen P, Fallarero A (2020)
   Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of Staphylococcus aureus
   Microorganisms, 8 (1)
   DOI 10.3390/microorganisms8010106, PubMed 31940921
10. Szibor M, Schreckenberg R, Gizatullina Z, Dufour E, Wiesnet M, Dhandapani PK, Debska-Vielhaber G, Heidler J, Wittig I, Nyman TA, Gärtner U, Hall AR, Pell V, Viscomi C, Krieg T, Murphy MP, Braun T, Gellerich FN, Schlüter KD, Jacobs HT (2020)
    Respiratory chain signalling is essential for adaptive remodelling following cardiac ischaemia
    J Cell Mol Med, 24 (6), 3534-3548
    DOI 10.1111/jcmm.15043, PubMed 32040259

Publications 2019

1. Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A (2019)
   Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer
   Mol Cell Proteomics, 19 (2), 245-260
   DOI 10.1074/mcp.RA119.001817, PubMed 31792072
2. Hiltunen AK, Savijoki K, Nyman TA, Miettinen I, Ihalainen P, Peltonen J, Fallarero A (2019)
   Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
   Microorganisms, 7 (12)
   DOI 10.3390/microorganisms7120584, PubMed 31756969
3. Lunde NN, Gregersen I, Ueland T, Shetelig C, Holm S, Kong XY, Michelsen AE, Otterdal K, Yndestad A, Broch K, Gullestad L, Nyman TA, Bendz B, Eritsland J, Hoffmann P, Skagen K, Gonçalves I, Nilsson J, Grenegård M, Poreba M, Drag M, Seljeflot I, Sporsheim B, Espevik T, Skjelland M et al. (2019)
   Legumain is upregulated in acute cardiovascular events and associated with improved outcome - potentially related to anti-inflammatory effects on macrophages
   Atherosclerosis, 296, 74-82
   DOI 10.1016/j.atherosclerosis.2019.12.008, PubMed 31870625
4. Mathiesen SB, Lunde M, Aronsen JM, Romaine A, Kaupang A, Martinsen M, de Souza GA, Nyman TA, Sjaastad I, Christensen G, Carlson CR (2019)
   The cardiac syndecan-4 interactome reveals a role for syndecan-4 in nuclear translocation of muscle LIM protein (MLP)
   J Biol Chem, 294 (22), 8717-8731
   DOI 10.1074/jbc.RA118.006423, PubMed 30967474
5. Nassa G, Giurato G, Salvati A, Gigantino V, Pecoraro G, Lamberti J, Rizzo F, Nyman TA, Tarallo R, Weisz A (2019)
   The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei
   Sci Data, 6 (1), 173
   DOI 10.1038/s41597-019-0179-2, PubMed 31527615
6. Nassa G, Salvati A, Tarallo R, Gigantino V, Alexandrova E, Memoli D, Sellitto A, Rizzo F, Malanga D, Mirante T, Morelli E, Nees M, Åkerfelt M, Kangaspeska S, Nyman TA, Milanesi L, Giurato G, Weisz A (2019)
   Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells
   Sci Adv, 5 (2), eaav5590
   DOI 10.1126/sciadv.aav5590, PubMed 30775443
7. Richter U, Ng KY, Suomi F, Marttinen P, Turunen T, Jackson C, Suomalainen A, Vihinen H, Jokitalo E, Nyman TA, Isokallio MA, Stewart JB, Mancini C, Brusco A, Seneca S, Lombès A, Taylor RW, Battersby BJ (2019)
   Mitochondrial stress response triggered by defects in protein synthesis quality control
   Life Sci Alliance, 2 (1)
   DOI 10.26508/lsa.201800219, PubMed 30683687
8. Savijoki K, Nyman TA, Kainulainen V, Miettinen I, Siljamäki P, Fallarero A, Sandholm J, Satokari R, Varmanen P (2019)
   Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG
   Front Microbiol, 10, 1272
   DOI 10.3389/fmicb.2019.01272, PubMed 31231350
9. Yang K, Lauritzen KH, Olsen MB, Dahl TB, Ranheim T, Ahmed MS, Attramadal H, Aukrust P, Halvorsen B, Nyman TA, Sandanger Ø, Yndestad A (2019)
   Low Cellular NAD⁺ Compromises Lipopolysaccharide-Induced Inflammatory Responses via Inhibiting TLR4 Signal Transduction in Human Monocytes
   J Immunol, 203 (6), 1598-1608
   DOI 10.4049/jimmunol.1801382, PubMed 31427442

Publications 2018

1. Cypryk W, Nyman TA, Matikainen S (2018)
   From Inflammasome to Exosome-Does Extracellular Vesicle Secretion Constitute an Inflammasome-Dependent Immune Response?
   Front Immunol, 9, 2188
   DOI 10.3389/fimmu.2018.02188, PubMed 30319640
2. Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K (2018)
   Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains
   Microb Biotechnol, 11 (3), 510-526
   DOI 10.1111/1751-7915.13254, PubMed 29488359
3. Giurato G, Nassa G, Salvati A, Alexandrova E, Rizzo F, Nyman TA, Weisz A, Tarallo R (2018)
   Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells
   Sci Data, 5, 180031
   DOI 10.1038/sdata.2018.31, PubMed 29509190
4. 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 (2018)
   Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications
   Sci Rep, 8 (1), 498
   DOI 10.1038/s41598-017-18985-5, PubMed 29323256
5. Sikorski K, Mehta A, Inngjerdingen M, Thakor F, Kling S, Kalina T, Nyman TA, Stensland ME, Zhou W, de Souza GA, Holden L, Stuchly J, Templin M, Lund-Johansen F (2018)
   A high-throughput pipeline for validation of antibodies
   Nat Methods, 15 (11), 909-912
   DOI 10.1038/s41592-018-0179-8, PubMed 30377371

Publications 2017

1. Aittomäki S, Valanne S, Lehtinen T, Matikainen S, Nyman TA, Rämet M, Pesu M (2017)
   Proprotein convertase Furin1 expression in the Drosophila fat body is essential for a normal antimicrobial peptide response and bacterial host defense
   FASEB J, 31 (11), 4770-4782
   DOI 10.1096/fj.201700296R, PubMed 28705811
2. 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 et al. (2017)
   Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins
   Viruses, 9 (10)
   DOI 10.3390/v9100271, PubMed 28946654
3. 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
   DOI 10.3389/fmicb.2017.00368, PubMed 28337185
4. Dumont V, Tolvanen TA, Kuusela S, Wang H, Nyman TA, Lindfors S, Tienari J, Nisen H, Suetsugu S, Plomann M, Kawachi H, Lehtonen S (2017)
   PACSIN2 accelerates nephrin trafficking and is up-regulated in diabetic kidney disease
   FASEB J, 31 (9), 3978-3990
   DOI 10.1096/fj.201601265R, PubMed 28550045
5. 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, 16 (4 suppl 1), S187-S199
   DOI 10.1074/mcp.M116.064840, PubMed 28196878
6. Nyman TA, Lorey MB, Cypryk W, Matikainen S (2017)
   Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells
   Expert Rev Proteomics, 14 (5), 395-407
   DOI 10.1080/14789450.2017.1319768, PubMed 28406322
7. Nyman TA, Matikainen S (2017)
   Proteomics to study macrophage response to viral infection
   J Proteomics, 180, 99-107
   DOI 10.1016/j.jprot.2017.06.018, PubMed 28647517
8. 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 (2017)
   The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading
   Genome Biol, 18 (1), 189
   DOI 10.1186/s13059-017-1321-0, PubMed 29017520

Publications 2016

1. 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
   DOI 10.1016/j.bbagrm.2016.09.005, PubMed 27664935
2. 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)
   DOI 10.1128/mBio.01228-16, PubMed 27507828
3. 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
   DOI 10.15252/embj.201593458, PubMed 27234299
4. 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
   DOI 10.1021/acs.jproteome.6b00596, PubMed 27723984
5. 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
   DOI 10.1016/j.antiviral.2016.07.008, PubMed 27451344
6. 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
   DOI 10.1111/febs.13966, PubMed 27860276
7. 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)
   DOI 10.3390/v8100269, PubMed 27690086
8. 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
   DOI 10.1074/mcp.M116.057984, PubMed 27486199
9. Varghese FS, Thaa B, Amrun SN, Simarmata D, Rausalu K, Nyman TA, Merits A, McInerney GM, Ng LFP, Ahola T (2016)
   The Antiviral Alkaloid Berberine Reduces Chikungunya Virus-Induced Mitogen-Activated Protein Kinase Signaling
   J Virol, 90 (21), 9743-9757
   DOI 10.1128/JVI.01382-16, PubMed 27535052
10. 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
    DOI 10.4049/jimmunol.1501840, PubMed 27638862
11. 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
    DOI 10.1016/j.yexcr.2016.12.010, PubMed 28011197

Publications 2015

1. 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), 2086-2091
   DOI 10.1099/vir.0.000171, PubMed 25934792
2. 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
   DOI 10.1160/TH14-09-0726, PubMed 25903651
3. 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
   DOI 10.1534/genetics.115.175596, PubMed 25808953
4. 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
   DOI 10.1016/j.ijmm.2015.11.006, PubMed 26725755
5. 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
   DOI 10.1002/pmic.201400404, PubMed 25604459
6. 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
   DOI 10.1016/j.antiviral.2015.12.011, PubMed 26738783
7. 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
   DOI 10.3402/jev.v4.27066, PubMed 25979354
8. 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
   DOI 10.1002/pmic.201400586, PubMed 25764225

Publications 2014

1. 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
   DOI 10.1021/pr4012552, PubMed 24670152
2. 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
   DOI 10.1128/AAC.02798-13, PubMed 24752266
3. 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
   DOI 10.1002/pmic.201300460, PubMed 25211154
4. 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
   DOI 10.1021/pr501041a, PubMed 25531588
5. 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
   DOI 10.1002/humu.22554, PubMed 24692096
6. 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
   DOI 10.1074/mcp.M113.030403, PubMed 24525454
7. 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
   DOI 10.1111/jam.12664, PubMed 25308550
8. 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, 13 (8), 3748-3762
   DOI 10.1021/pr500322d, PubMed 25014494
9. 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
   DOI 10.1002/pmic.201300275, PubMed 24909406
10. 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
    DOI 10.1021/pr500075j, PubMed 24840314
11. Söderholm S, Hintsanen P, Öhman 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
    DOI 10.1186/1477-5956-12-36, PubMed 25028575
12. 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
    DOI 10.1016/j.ajpath.2014.03.002, PubMed 24726496
13. 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
    DOI 10.1016/j.yexcr.2014.10.019, PubMed 25447204
14. 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
    DOI 10.1074/mcp.M114.038968, PubMed 24997996
15. 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
    DOI 10.4049/jimmunol.1303213, PubMed 24808366
16. 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
    DOI 10.3402/jev.v3.24692, PubMed 25147646

Publications 2013

1. 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
   DOI 10.1016/j.humimm.2013.11.010, PubMed 24269698
2. 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
   DOI 10.1002/cbin.10134, PubMed 23686814
3. 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
   DOI 10.1016/j.cub.2013.02.019, PubMed 23453957
4. 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
   DOI 10.1261/rna.036715.112, PubMed 23335637
5. 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
   DOI 10.1074/mcp.M112.024661, PubMed 23292187
6. 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
   DOI 10.1242/jcs.120022, PubMed 23549787

Publications 2012

1. 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
   DOI 10.1186/1477-5956-10-10, PubMed 22325190
2. 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
   DOI 10.1021/pr300753u, PubMed 23170835
3. 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
   DOI 10.1593/neo.111396, PubMed 22496621
4. 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
   DOI 10.1128/JVI.01545-12, PubMed 22973042
5. 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
   DOI 10.1016/j.lungcan.2012.03.024, PubMed 22537621
6. 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
   DOI 10.1016/j.biopsych.2012.08.012, PubMed 23036959

Publications 2011

1. 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
   DOI 10.1021/pr200956s, PubMed 22112206
2. 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
   DOI 10.1016/j.jprot.2011.11.009, PubMed 22119544
3. 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
   DOI 10.1593/neo.11356, PubMed 21750658
4. 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
   DOI 10.1371/journal.ppat.1001340, PubMed 21589892
5. 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
   DOI 10.1111/j.1751-7915.2011.00275.x, PubMed 21883975
6. 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
   DOI 10.4049/jimmunol.1002051, PubMed 21257972
7. 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
   DOI 10.1021/pr2000896, PubMed 21615180

Publications 2010

1. 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
   DOI 10.1074/mcp.M900519-MCP200, PubMed 20308691
2. 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
   DOI 10.1074/mcp.M110.002741, PubMed 21078892
3. 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
   DOI 10.1038/jid.2010.208, PubMed 20631725
4. 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
   DOI 10.1016/j.anai.2009.11.062, PubMed 20306817
5. 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
   DOI 10.1021/pr100824w, PubMed 20973569
6. 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
   DOI 10.1074/mcp.M900483-MCP200, PubMed 20467038
7. 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
   DOI 10.1002/pmic.201000344, PubMed 21182203
8. 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
   DOI 10.1039/c0mb00145g, PubMed 21173974
9. 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
   DOI 10.1021/pr901040u, PubMed 20070120
10. Piippo M, Lietzén N, Nevalainen OS, Salmi J, Nyman TA (2010)
    Pripper: prediction of caspase cleavage sites from whole proteomes
    BMC Bioinformatics, 11, 320
    DOI 10.1186/1471-2105-11-320, PubMed 20546630
11. 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
    DOI 10.1016/j.bbamem.2010.01.011, PubMed 20122897
12. 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
    DOI 10.1002/pmic.201000217, PubMed 21182205
13. 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
    DOI 10.1091/mbc.E10-07-0592, PubMed 21119007

Publications 2009

1. Korolainen MA, Nyman TA, Aittokallio T, Pirttilä T (2009)
   An update on clinical proteomics in Alzheimer's research
   J Neurochem, 112 (6), 1386-414
   DOI 10.1111/j.1471-4159.2009.06558.x, PubMed 20050976
2. 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
   DOI 10.4049/jimmunol.0803093, PubMed 19380815
3. 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
   DOI 10.1002/pmic.200800517, PubMed 19160393
4. 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
   DOI 10.1002/pmic.200800161, PubMed 19180534

Publications 2008

1. 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
   DOI 10.1074/mcp.M800139-MCP200, PubMed 18701445
2. 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
   DOI 10.1586/14789450.5.3.389, PubMed 18532906

Publications 2007

1. 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
   DOI 10.1373/clinchem.2006.078014, PubMed 17289803
2. 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
   DOI 10.1002/pmic.200600582, PubMed 17211829

Publications 2006

1. 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
   DOI 10.1074/mcp.M600290-MCP200, PubMed 17114647
2. 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
   DOI 10.1002/pmic.200500516, PubMed 16691549

Publications 2005

1. 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
   DOI 10.1016/j.jchromb.2004.07.037, PubMed 15652796
2. 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
   DOI 10.1523/JNEUROSCI.1517-05.2005, PubMed 16000625
3. 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
   DOI 10.1002/pmic.200402016, PubMed 16247730
4. 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
   DOI 10.1016/j.nbd.2005.05.021, PubMed 15979880
5. 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
   DOI 10.1016/j.neurobiolaging.2004.11.010, PubMed 16298240
6. 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
   DOI 10.1002/pmic.200401187, PubMed 15952233
7. 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
   DOI 10.1021/pr049857b, PubMed 15707360
8. Rosengren AT, Nyman TA, Lahesmaa R (2005)
   Proteome profiling of interleukin-12 treated human T helper cells
   Proteomics, 5 (12), 3137-41
   DOI 10.1002/pmic.200401151, PubMed 16038020
9. 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
   DOI 10.1002/pmic.200400967, PubMed 15700245
10. 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
    DOI 10.1093/bioinformatics/bti829, PubMed 16352652

Publications 2004

1. Rautajoki K, Nyman TA, Lahesmaa R (2004)
   Proteome characterization of human T helper 1 and 2 cells
   Proteomics, 4 (1), 84-92
   DOI 10.1002/pmic.200300510, PubMed 14730674

Publications 2003

1. 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
   DOI 10.1002/pmic.200300544, PubMed 14625856

Publications 2002

1. 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
   DOI 10.1002/1615-9861(200211)2:11<1504::AID-PROT1504>3.0.CO;2-B, PubMed 12442250

Publications 2001

1. Nyman TA (2001)
   The role of mass spectrometry in proteome studies
   Biomol Eng, 18 (5), 221-7
   DOI 10.1016/s1389-0344(01)00097-1, PubMed 11911089
2. 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
   DOI 10.1002/1522-2683(200112)22:20<4375::AID-ELPS4375>3.0.CO;2-P, PubMed 11824605
3. 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
   DOI 10.1046/j.1432-1327.2001.01853.x, PubMed 11121106

Publications 2000

1. 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
   DOI 10.1046/j.1432-1327.2000.01433.x, PubMed 10866800

Publications 1998

1. 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
   DOI 10.1046/j.1432-1327.1998.2530485.x, PubMed 9654101
2. 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) (Pt 2), 295-302
   DOI 10.1042/bj3290295, PubMed 9425112