List of works by Tuula A. Nyman

3rd Annual FinnProt Meeting: from cells to systems

scientific article published in June 2008

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

scientific article

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments

scientific article

A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation.

scientific article published on 28 February 2013

A proteome database of human primary T helper cells.

scientific article

Absence of CCR4 exacerbates skin inflammation in an oxazolone-induced contact hypersensitivity model.

scientific article published on 15 July 2010

Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction

scientific article published on 09 December 2020

Actin and RIG-I/MAVS signaling components translocate to mitochondria upon influenza A virus infection of human primary macrophages.

scientific article published in May 2009

Activating stimuli induce platelet microRNA modulation and proteome reorganisation.

scientific article published on 23 April 2015

Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro.

scientific article

An update on clinical proteomics in Alzheimer's research

scientific article published on 24 December 2009

Ancestral allele of DNA polymerase gamma modifies antiviral tolerance

scientific article published in 2024

Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice

scientific article published on 25 July 2013

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

scientific article published on 25 September 2017

Biological properties of extracellular vesicles and their physiological functions.

scientific article published on 14 May 2015

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

scientific article published on 16 September 2016

Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12.

scientific article published in December 2005

Comparative Exoprotein Profiling of Different Staphylococcus epidermidis Strains Reveals Potential Link between Nonclassical Protein Export and Virulence

scientific article published on 02 June 2014

Comparative Proteome Cataloging of Lactobacillus rhamnosus Strains GG and Lc705

scientific article published on 17 June 2011

Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting

scientific article published on 11 February 2012

Comparative analysis of nuclear estrogen receptor alpha and beta interactomes in breast cancer cells.

scientific article published on 20 December 2010

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

scientific article published on 10 July 2014

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels

scientific article published in October 2003

Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon.

scientific article published on 11 November 2010

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

scientific journal article

Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes.

scientific article

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

scientific article

Determination of nine β-blockers in serum by micellar electrokinetic capillary chromatography

scientific article published on 01 July 1994

Distinct Pattern of Endoplasmic Reticulum Protein Processing and Extracellular Matrix Proteins in Functioning and Silent Corticotroph Pituitary Adenomas

scientific article published on 14 October 2020

Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG

scientific article published on 16 November 2011

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

scientific article published on 13 April 2014

Filtering strategies for improving protein identification in high-throughput MS/MS studies

scientific article published on February 2009

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

scientific article published on 8 March 2017

Function and Regulation of Noncanonical Caspase-4/5/11 Inflammasome

scientific article published on 01 June 2020

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

scientific article published on 18 July 2014

Geometrical distortions in two-dimensional gels: applicable correction methods.

scientific article

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

scientific article published on 14 February 2017

Global secretome characterization of herpes simplex virus 1-infected human primary macrophages.

scientific article published on 12 September 2012

Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of Staphylococcus aureus

scientific article published on 12 January 2020

Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium.

scientific article published on September 2011

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

scientific article published on 27 May 2016

Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels

scientific article published on 01 November 2002

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

scientific article published on 18 January 2013

Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei.

scientific article

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

scientific article

Identification of new Golgi complex specific proteins by direct organelle proteomic analysis.

scientific article

Identification of novel Stat6 regulated proteins in IL-4-treated mouse lymphocytes

scientific article published in February 2009

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

scientific article

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

scientific article

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

scientific article published on 21 September 2016

Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells

article

Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer

scientific article published on 02 December 2019

Interleukin-4 Inhibits Caspase-3 by Regulating Several Proteins in the Fas Pathway during Initial Stages of Human T Helper 2 Cell Differentiation

article

Isolation and characterization of platelet-derived extracellular vesicles

scientific article

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

scientific article published on 20 July 2016

Legumain is upregulated in acute cardiovascular events and associated with improved outcome - potentially related to anti-inflammatory effects on macrophages

scientific article published on 14 December 2019

Low Cellular NAD+ Compromises Lipopolysaccharide-Induced Inflammatory Responses via Inhibiting TLR4 Signal Transduction in Human Monocytes

scientific article published on 19 August 2019

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

scientific article published on 13 April 2017

Mitochondrial stress response triggered by defects in protein synthesis quality control

scientific article published on 25 January 2019

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

scientific article published on 30 November 2012

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins

scientific article

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

scientific article

Multiplexed proteomic analysis of oxidation and concentrations of cerebrospinal fluid proteins in Alzheimer disease

scientific article published on 8 February 2007

Multistep phosphorylation by oncogenic kinases enhances the degradation of the NF2 tumor suppressor merlin

scientific article published on July 2011

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

scientific article (publication date: July 2014)

Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling

scientific article published in March 2012

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

article

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

scientific article

Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain

scientific article

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

scientific article published on 3 December 2015

Peroxiredoxins and tropomyosins as plasma biomarkers for lung cancer and asbestos exposure

scientific article published on 24 April 2012

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

scientific article

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

scientific article published on 27 April 2015

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

scientific article

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

scientific article published on 2 August 2016

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

scientific article published on 13 February 2014

Pripper: prediction of caspase cleavage sites from whole proteomes

scientific article

Proteome analysis of human macrophages reveals the upregulation of manganese-containing superoxide dismutase after toll-like receptor activation

article

Proteome analysis reveals ubiquitin-conjugating enzymes to be a new family of interferon-alpha-regulated genes.

scientific article

Proteome characterization of human NK-92 cells identifies novel IFN-alpha and IL-15 target genes.

scientific article published on January 2005

Proteome characterization of human T helper 1 and 2 cells

scientific article published on 01 January 2004

Proteome profiling of interleukin-12 treated human T helper cells

scientific article published in August 2005

Proteomic analysis of glial fibrillary acidic protein in Alzheimer's disease and aging brain

scientific article published on 27 June 2005

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

scientific article

Proteomic and transcriptomic characterization of interferon-?-induced human primary T helper cells

scientific article published on 01 February 2005

Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG.

scientific article

Proteomics to study macrophage response to viral infection.

scientific article

Quality classification of tandem mass spectrometry data

scientific article

Quantitative Proteomics of Extracellular Vesicles Released from Human Monocyte-Derived Macrophages upon β-Glucan Stimulation

scientific article published on 16 April 2014

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

scientific article published on 25 March 2015

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

scientific article published on 6 March 2018

Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation

scientific article

Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation

scientific article

Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages

scientific article

Recognition of cytoplasmic RNA results in cathepsin-dependent inflammasome activation and apoptosis in human macrophages.

scientific article published on 21 January 2011

Regulation of kynurenine biosynthesis during influenza virus infection.

scientific article published on 18 November 2016

Respiratory chain signalling is essential for adaptive remodelling following cardiac ischaemia

scientific article published on 10 February 2020

Sec1p and Mso1p C-terminal tails cooperate with the SNAREs and Sec4p in polarized exocytosis

scientific article published on 30 November 2010

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

scientific article

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

scientific article published on 15 October 2014

Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials

scientific article published on 20 November 2019

Temperature-induced structural transition in-situ in porcine lens--changes observed in void size distribution

scientific article published in February 2010

Thaumatin-like protein and baker's respiratory allergy

scientific article published on 01 February 2010

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

scientific article published on 17 August 2016

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

scientific article published on May 2015

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

scientific article published on 9 August 2016

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

scientific article published on 6 October 2017

Trichothecene mycotoxins activate NLRP3 inflammasome through a P2X7 receptor and Src tyrosine kinase dependent pathway

scientific article published on 20 November 2013

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

scientific article published on 22 December 2014

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