Publications

2022

Reubsaet, L., Thiede, B. & Halvorsen, T. G. Next generation VAMS® - trypsin immobilization for instant proteolysis in bottom-up protein determination. Adv. Sample Prep. 100027 (pre-proof)

Taavitsainen-Wahlroos, E. et al. Chlamydia pneumoniae Interferes with Macrophage Differentiation and Cell Cycle Regulation to Promote Its Replication. Cell. Microbiol. e9854449

Jonassen, K. R. et al. Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions. ISME J. 16, 580–590

Kallas, P. et al. Protein-coated nanostructured surfaces affect the adhesion of Escherichia coli. Nanoscale 14, 7736–7746

Hynne, H. et al. Proteomic Profiling of Saliva and Tears in Radiated Head and Neck Cancer Patients as Compared to Primary Sjögren’s Syndrome Patients. Int. J. Mol. Sci. 23, 3714

Berg, H. E. et al. Micro-pillar array columns (µPAC): an efficient tool for comparing tissue and cultured cells of glioblastoma. J. Chromatogr. Open 100047 in press

Olsen, C. et al. On-line reduction of insulin disulfide bonds with photoinduced radical reactions, upstream to nano liquid chromatography-mass spectrometry. Sep. Sci. PLUS n/a (early view)

Burger, B., Vaudel, M. & Barsnes, H. Automated splitting into batches for observational biomedical studies with sequential processing. Biostatistics kxac014

Reikvam, H. et al. Proteomic approaches for untangling pharmacological targets in acute myeloid leukemia. Expert Rev. Proteomics 0, 1–4

Paunas, F. T. I. et al. Proteomic signature of tubulointerstitial tissue predicts prognosis in IgAN. BMC Nephrol. 23, 118

Brackhan, M. et al. Isotope-labeled amyloid-β does not transmit to the brain in a prion-like manner after peripheral administration. EMBO Rep. n/a, e54405

Sarowar, S. et al. The Styryl Benzoic Acid Derivative DC10 Potentiates Radiotherapy by Targeting the xCT-Glutathione Axis. Front. Oncol. 12, 786739

Høiem, T. S. et al. An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue. Proteomics, e2100223.

Nguyen, M. T. et al. Smart proteolysis samplers for pre‐lab bottom‐up protein analysis – Performance of on‐paper digestion compared to conventional digestion. Separation Science plus. https://doi.org/10.1002/sscp.202100062

2021

Van Den Bossche, T. et al. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome 9, 243

Wang, Q. et al. UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. Mol. Oncol. Accepted/unedited

Upīte, J. et al. A New Tool for the Analysis of the Effect of Intracerebrally Injected Anti-Amyloid-β Compounds. J. Alzheimers Dis. 84, 1677–1690

Namasivayam, V. et al. Binding mode analysis of ABCA7 for the prediction of novel Alzheimer’s disease therapeutics. Comput. Struct. Biotechnol. J. 19, 6490–6504

Dib, S., Pahnke, J. & Gosselet, F. Role of ABCA7 in Human Health and in Alzheimer’s Disease. Int. J. Mol. Sci. 22, 4603

Möhle, L. et al. Dimethyl fumarate does not mitigate cognitive decline and β-amyloidosis in female APPPS1 mice. Brain Res. 1768, 147579

Skottvoll, F. S. et al. Direct Electromembrane Extraction based Mass Spectrometry: A Tool for Studying Drug Metabolism Properties of Liver Organoids. Anal. Sens. Accepted/unedited

Möhle, L. et al. Development of deep learning models for microglia analyses in brain tissue using DeePathology^TM STUDIO. J. Neurosci. Methods 364, 109371

Namasivayam, V. et al. Scaffold fragmentation and substructure hopping reveal potential, robustness, and limits of computer-aided pattern analysis (C@PA). Comput. Struct. Biotechnol. J. 19, 3269–3283

Svendsen, H. A. et al. Novel human melanoma brain metastasis models in athymic nude fox1nu mice: Site-specific metastasis patterns reflecting their clinical origin. Cancer Med. 10, 8604–8613

Maddirevula, S. et al. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant. Hum. Genet. doi:10.1007/s00439-021-02391-z

Hildrestrand, G. A. et al. NEIL1 and NEIL2 DNA glycosylases modulate anxiety and learning in a cooperative manner in mice. Commun. Biol. 4, 1–14

Grønningsæter, I. S. et al. Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells; Characterization of Patient Heterogeneity. J. Pers. Med. 11, 779

Waløen, K. et al. Cysteine Modification by Ebselen Reduces the Stability and Cellular Levels of 14-3-3 Proteins. Mol. Pharmacol. 100, 155–169

Bjarkum, A. A. et al. Human blood serum proteome changes after 6 hours of sleep deprivation at night. Sleep Sci. Pract. 5, 14

Pahnke, J. et al. Strategies to gain novel Alzheimer’s disease diagnostics and therapeutics using modulators of ABCA transporters. Free Neuropathol. 2, 33–33

Borovkova, M. et al. Screening of Alzheimer’s disease with multiwavelength Stokes polarimetry in a mouse model. IEEE Trans. Med. Imaging 1–1

Aasebø, E. et al. Patient Heterogeneity in Acute Myeloid Leukemia: Leukemic Cell Communication by Release of Soluble Mediators and Its Effects on Mesenchymal Stem Cells. Diseases 9, 74

Farag, Y. M. et al. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. J. Proteome Res. doi:10.1021/acs.jproteome.1c00678

Aasebø, E. et al. Proteomic Characterization of Spontaneous Stress-Induced In Vitro Apoptosis of Human Acute Myeloid Leukemia Cells; Focus on Patient Heterogeneity and Endoplasmic Reticulum Stress. Hemato 2, 607–627

Johannsen, C. et al. Comparison of LFQ and IPTL for Protein Identification and Relative Quantification. Mol. Basel Switz. 26, 5330

Myrbråten, I. S. et al. SmdA is a novel cell morphology determinant in Staphylococcus aureus. bioRxiv doi:10.1101/2021.11.23.469651.

Andersen, E. et al. Molecular Characterization of Two Homozygous Factor VII Variants Associated with Intracranial Bleeding. Thromb. Haemost. 121, 1588–1598

Vestad, B. et al. Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk. Sci. Rep. 11, 21936

Skåne, A., et al. Comparative proteomic profiling reveals specific adaption of Vibrio anguillarum to oxidative stress, iron deprivation and humoral components of innate immunity. J. Proteomics 104412. doi:10.1016/j.jprot.2021.104412.

Mendel, M. et al. Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell 184, 3125-3142.e25

Sumabe, B. K. et al. Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis. Biomolecules 11, 843

Lirussi, L. et al. RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 11, 76

Pinto, S. M. et al. Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation. Front. Immunol. 12, 679458

Mirlashari, M. R. et al. Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients. Proteomics Clin. Appl. e2100022  doi:10.1002/prca.202100022

Snapkov, I. et al. Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol. doi:10.1016/j.tibtech.2021.08.006

Abudu, Y. P. et al. SAMM50 acts with p62 in piecemeal basal- and OXPHOS-induced mitophagy of SAM and MICOS components. J. Cell Biol. 220

Rye, T. K. et al. Electromembrane extraction of peptides using deep eutectic solvents as liquid membrane. Anal. Chim. Acta 1175, 338717

McKitterick, N. et al. On-line duplex molecularly imprinted solid-phase extraction for analysis of low-abundant biomarkers in human serum by liquid chromatography-tandem mass spectrometry. J. Chromatogr. A 1655, 462490

Wanichawan, P. et al. Design of a Proteolytically Stable Sodium-Calcium Exchanger 1 Activator Peptide for In Vivo Studies. Front. Pharmacol. 12, 1328

Reigada, I. et al. Surfaceome and Exoproteome Dynamics in Dual-Species Pseudomonas aeruginosa and Staphylococcus aureus Biofilms. Front. Microbiol. 12, 1571

Borowicz, P. et al. Tyr192 Regulates Lymphocyte-Specific Tyrosine Kinase Activity in T Cells. J. Immunol. 207, 1128–1137

Holm, S. et al. Immune complexes, innate immunity, and NETosis in ChAdOx1 vaccine-induced thrombocytopenia. Eur. Heart J. doi:10.1093/eurheartj/ehab506

Wollen, K. L. et al. ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA. J. Transl. Med. 19, 287

Savijoki, K. et al. Surface-Shaving Proteomics of Mycobacterium marinum Identifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance, and Persistence. mSystems 6, e005002

Lorentzen, S. B. et al. Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes. J. Proteome Res. 20, 4041–4052

Jensen, S. et al. Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation. FEMS Microbiol. Ecol. 97

Mehta, S. et al. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research 10, 103

Mehta, S. et al. Updates on metaQuantome Software for Quantitative Metaproteomics. J. Proteome Res. 20, 2130–2137

Skagen, C. et al. Chronic treatment with terbutaline increases glucose and oleic acid oxidation and protein synthesis in cultured human myotubes. Curr. Res. Pharmacol. Drug Discov. 2, 100039

Alves, C. R. R. et al. Cancer-induced muscle atrophy is determined by intrinsic muscle oxidative capacity. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 35, e21714

Halvorsen, T. G. et al. Matrix-Assisted Ionization and Tandem Mass Spectrometry Capabilities in Protein Biomarker Characterization—An Initial Study Using the Small Cell Lung Cancer Biomarker Progastrin Releasing Peptide as a Model Compound. J. Am. Soc. Mass Spectrom. 32, 611–614

Alswady-Hoff, M. et al. Long-Term Exposure to Nanosized TiO2 Triggers Stress Responses and Cell Death Pathways in Pulmonary Epithelial Cells. Int. J. Mol. Sci. 22, 5349

Hernandez-Valladares, M. et al. Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid. Cancers 13, 2143

Halvorsen, T. G. et al. Affinity capture in bottom-up protein analysis – Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal. Chim. Acta 338714. doi:10.1016/j.aca.2021.338714

Aasebø, E. et al. Proteomic Comparison of Bone Marrow Derived Osteoblasts and Mesenchymal Stem Cells. Int. J. Mol. Sci. 22, 5665

Koehler, C. J. & Thiede, B. An Approach for Triplex-IPTL. Methods Mol. Biol. Clifton NJ 2228, 133–144.

Małecki, J. M. et al. Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Res. 49, 3185–3203 

Pizzi, E. et al. Next-Generation Dried Blood Spot Samplers for Protein Analysis: Describing Trypsin-Modified Smart Sampling Paper. Separations 8, 66

Berzaghi, R. et al. Secretion rates and protein composition of extracellular vesicles released by cancer-associated fibroblasts after radiation. J. Radiat. Res. doi:10.1093/jrr/rrab018

Olinski, R. et al. Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies. Int. J. Mol. Sci. 22, 4212.

Røberg-Larsen, H. et al. Liquid chromatography, a key tool for the advancement of single-cell omics analysis. Anal. Chim. Acta 338551. doi:10.1016/j.aca.2021.338551.

Nthiga, T. M. et al. Regulation of Golgi turnover by CALCOCO1-mediated selective autophagy. J. Cell Biol. 220

Wirth, M. et al. Phosphorylation of the LIR domain of SCOC modulates ATG8 binding affinity and specificity. J. Mol. Biol. 166987–166987. doi:10.1016/j.jmb.2021.166987.

Ramberg, H. et al. Proteomic analyses Identify Major Vault Protein as a Prognostic Biomarker for Fatal Prostate Cancer. Carcinogenesis. doi:10.1093/carcin/bgab015.

Quiles-Jiménez, A. et al. DNA glycosylase Neil3 regulates vascular smooth muscle cell biology during atherosclerosis development. Atherosclerosis. doi:10.1016/j.atherosclerosis.2021.02.023.

Oveland, E. et al. Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Sci. Rep. 11, 7174

Aasebø, E. et al. The Constitutive Extracellular Protein Release by Acute Myeloid Leukemia Cells—A Proteomic Study of Patient Heterogeneity and Its Modulation by Mesenchymal Stromal Cells. Cancers 13, 1509

Kavli, B. et al. RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork. Nucleic Acids Res. doi:10.1093/nar/gkab195.

Askarian, F. et al. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nat. Commun. 12, 1230

Skogvold, H. B. et al. Bridging the polar and hydrophobic metabolome in single-run untargeted liquid chromatography-mass spectrometry dried blood spot metabolomics for clinical purposes. medRxiv  doi:10.1101/2021.03.22.21254119.

Bossche, T. V. D. et al. Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. bioRxiv doi:10.1101/2021.03.05.433915.

Martinez-Val, A. et al. Spatial-proteomics reveal in-vivo phospho-signaling dynamics at subcellular resolution. bioRxiv doi:10.1101/2021.02.02.425898.

Bascuñana, P., Brackhan, M. & Pahnke, J. Machine Learning-Supported Analyses Improve Quantitative Histological Assessments of Amyloid-β Deposits and Activated Microglia. J. Alzheimers Dis. 79, 597–605.

Namasivayam, V. et al. C@PA: Computer-Aided Pattern Analysis to Predict Multitarget ABC Transporter Inhibitors. J. Med. Chem. (2021) doi:10.1021/acs.jmedchem.0c02199.

Mosleth, E. F. et al. ‘Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis’, Scientific reports, 11(1), p. 4087.

Roberg-Larsen, H., Wilson, S. R. and Lundanes, E. ‘Recent advances in on-line upfront devices for sensitive bioanalytical nano LC methods’, Trends in analytical chemistry: TRAC, 136, p. 116190.

Skottvoll, F. S. et al. ‘Electromembrane Extraction and Mass Spectrometry for Liver Organoid Drug Metabolism Studies’, Analytical chemistry, 93(7), pp. 3576–3585.

Stamnaes, J. et al. ‘In Well-Treated Celiac Patients Low-Level Mucosal Inflammation Predicts Response to 14-day Gluten Challenge’, Advancement of science, 8(4), p. 2003526.

Zawadzka, M. et al. ‘Searching for a UV-filter in the eyes of high-flying birds’, Scientific reports, 11(1), p. 273.

Burger, B., Vaudel, M. and Barsnes, H. ‘Importance of Block Randomization When Designing Proteomics Experiments’, Journal of proteome research, 20(1), pp. 122–128.

2020

Kogler, S. et al. “Organoid-in-a-column” coupled on-line with liquid chromatography-mass spectrometry. bioRxiv 2020.09.08.282756 (2020) doi:10.1101/2020.09.08.282756.

Harrison, S. P. et al. Scalable production of tissue-like vascularised liver organoids from human PSCs. bioRxiv 2020.12.02.406835 (2020) doi:10.1101/2020.12.02.406835.

Hernandez-Valladares, M. et al. Biological characteristics of aging in human acute myeloid leukemia cells: the possible importance of aldehyde dehydrogenase, the cytoskeleton and altered transcriptional regulation. Aging 12, 24734–24777

Louwe, M. C. et al. Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. JACC Basic Transl. Sci. 5, 1210–1224

Tadele, D. S. et al. A cell competition–based small molecule screen identifies a novel compound that induces dual c-Myc depletion and p53 activation. J. Biol. Chem. 296, 100179

Nymark, M. et al. Functional studies of CpSRP54 in diatoms show that the mechanism of thylakoid protein insertion differs from plants and green algae. Plant J. doi:10.1111/tpj.15149

Tsjokajev, A. et al. Mass spectrometry-based measurements of cyclic adenosine monophosphate in cells, simplified using reversed phase liquid chromatography with a polar characterized stationary phase. J. Chromatogr. B 1160, 122384 

Michalak, L. et al. Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. Nat. Commun. 11, 5773