Publications 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Kaivola J, Nyman TA, Matikainen S (2021)
Inflammasomes and SARS-CoV-2 Infection
Viruses, 13 (12)
DOI 10.3390/v13122513, PubMed 34960782

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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