Publications 2019

741 publications

Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.
Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S
pii: 10.1186/s13075-019-2066-9 pmc: PMC6915963
Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]
Plasma Profiling [Service]
Depression, GABA, and Age Correlate with Plasma Levels of Inflammatory Markers
Bhandage AK, Cunningham JL, Jin Z, ..., Ekselius L, Birnir B
Int J Mol Sci 20 (24) 6172 [2019-12-06; online 2019-12-06]
PLA and Single Cell Proteomics [Collaborative]
Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.
Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K
pii: 10.1038/s41598-019-54493-4
Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]
BioImage Informatics [Service]
DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.
Tsagiopoulou M, Papakonstantinou N, Moysiadis T, ..., Rosenquist R, Stamatopoulos K
pii: 10.1186/s13148-019-0783-1
Clin Epigenetics 11 (1) 177 [2019-12-02; online 2019-12-02]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC
Nirwan N, Itoh Y, Singh P, ..., Amunts A, Saikrishnan K
Nat Commun 10 (1) 1-9 [2019-12-00; online 2019-07-11]
Cryo-EM [Service]
A Mitochondrial LYR Protein Is Required for Complex I Assembly.
Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW
pii: pp.19.00822 pmc: PMC6878026
Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]
Proteogenomics [Collaborative]
Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells
Mehmeti M, Bergenfelz C, Källberg E, ..., André I, Leandersson K
Commun Biol 2 (1) - [2019-12-00; online 2019-05-09]
Targeted and Structural Proteomics [Service]
A bacterial assay for rapid screening of IAA catabolic enzymes
Brunoni F, Collani S, Šimura J, ..., Bellini C, Ljung K
Plant Methods 15 (1) - [2019-12-00; online 2019-11-04]
Swedish Metabolomics Centre (SMC) [Service]
A microfluidic platform towards automated multiplexed in situ sequencing
Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M
Sci Rep 9 (1) - [2019-12-00; online 2019-03-05]
In Situ Sequencing (ISS) [Technology development]
Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis
van der Post S, Jabbar KS, Birchenough G, ..., Johansson MEV, Hansson GC
Gut 68 (12) 2142-2151 [2019-12-00; online 2019-03-26]
Centre for Cellular Imaging [Service]
Cardiovascular organ damage in type 2 diabetes mellitus: the role of lipids and inflammation
Kozakova M, Morizzo C, Goncalves I, ..., Nilsson J, Palombo C
Cardiovasc Diabetol 18 (1) - [2019-12-00; online 2019-05-10]
Clinical Biomarkers [Service]
MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M
pii: S2589-0042(19)30399-2 pmc: PMC6889365
iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]
Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]
Synthesis of Indomorphan Pseudo-Natural Product Inhibitors of Glucose Transporters GLUT-1 and -3
Ceballos J, Schwalfenberg M, Karageorgis G, ..., Ziegler S, Waldmann H
Angew. Chem. Int. Ed. 58 (47) 17016-17025 [2019-11-18; online 2019-10-07]
Swedish Metabolomics Centre (SMC) [Service]
Counting the Number of Glutamate Molecules in Single Synaptic Vesicles
Wang Y, Fathali H, Mishra D, ..., Skibicka KP, Cans AS
J. Am. Chem. Soc. 141 (44) 17507-17511 [2019-11-06; online 2019-10-23]
Gothenburg Imaging Mass Spectrometry [Service]
Myc-dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF receptor-2
Testini C, Smith RO, Jin Y, ..., Hellström M, Claesson‐Welsh L
EMBO rep 20 (11) - [2019-11-05; online 2019-09-23]
Proteogenomics [Service]
The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function
Volk JK, Nyström EEL, van der Post S, ..., Hansson GC, Birchenough GMH
- 216 (11) 2602-2618 [2019-11-04; online 2019-08-16]
Centre for Cellular Imaging [Service]
Tuning drug release from polyoxazoline-drug conjugates
Harris JM, Bentley MD, Moreadith RW, ..., Dizman B, Nordstierna L
European Polymer Journal 120 (-) 109241 [2019-11-00; online 2019-11-00]
Swedish NMR Centre (SNC) [Service]
A revised solid-state NMR method to assess the crystallinity of cellulose
Sparrman T, Svenningsson L, Sahlin-Sjövold K, ..., Westman G, Bernin D
Cellulose 26 (17) 8993-9003 [2019-11-00; online 2019-09-03]
Swedish NMR Centre (SNC) [Collaborative]
Association of PTHrP levels in CSF with Alzheimer’s disease biomarkers
Kushnir MM, Michno W, Rockwood AL, ..., Strathmann FG, Hanrieder J
Clinical Mass Spectrometry 14 (-) 124-129 [2019-11-00; online 2019-11-00]
Gothenburg Imaging Mass Spectrometry [Service]
Identification of two abundant Aerococcus urinae cell wall-anchored proteins.
Senneby E, Sunnerhagen T, Hallström B, ..., Karlsson C, Rasmussen M
pii: S1438-4221(18)30350-3
Int. J. Med. Microbiol. 309 (7) 151325 [2019-11-00; online 2019-06-24]
Targeted and Structural Proteomics [Collaborative]
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Dobie R, Wilson-Kanamori JR, Henderson BEP, ..., Marioni JC, Henderson NC
Cell Rep 29 (7) 1832-1847.e8 [2019-11-00; online 2019-11-00]
Eukaryotic Single Cell Genomics (ESCG) [Service]
Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.
Papoutsoglou G, Lagani V, Schmidt A, ..., Tegnér J, Tsamardinos I
Cytometry A 95 (11) 1178-1190 [2019-11-00; online 2019-11-06]
Mass Cytometry [Service]
Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching
Gustavsson E, Isaksson L, Persson C, ..., Orekhov V, Westenhoff S
Biophysical Journal - (-) - [2019-11-00; online 2019-11-00]
Swedish NMR Centre (SNC) [Collaborative]
Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers.
Chatterjee S, Lee LY, Kawahara R, ..., Palmisano G, Thaysen-Andersen M
Proteomics 19 (21-22) e1900010 [2019-11-00; online 2019-10-16]
Glycoproteomics [Collaborative]
PIN-driven auxin transport emerged early in streptophyte evolution
Skokan R, Medvecká E, Viaene T, ..., Petrášek J, Friml J
NPLANTS 5 (11) 1114-1119 [2019-11-00; online 2019-11-11]
Swedish Metabolomics Centre (SMC) [Service]
Diagnostic pitfalls in vitamin B6-dependent epilepsy caused by mutations in the PLPBP gene.
Jensen KV, Frid M, Stödberg T, ..., Darin N, Grønborg S
pii: JMD212063 pmc: PMC6850975
JIMD Rep 50 (1) 1-8 [2019-11-00; online 2019-09-30]
Clinical Genomics Stockholm [Service]
Viral antigens elicit augmented immune responses in primary Sjögren’s syndrome
Björk A, Thorlacius GE, Mofors J, ..., Kvarnström M, Wahren-Herlenius M
- - (-) - [2019-10-30; online 2019-10-30]
Clinical Biomarkers [Service]
Detection of a High-Turnover Serotonin Circuit in the Mouse Brain Using Mass Spectrometry Imaging.
Sugiyama E, Guerrini MM, Honda K, ..., Suematsu M, Sugiura Y
pii: S2589-0042(19)30375-X pmc: PMC6818351
iScience 20 (-) 359-372 [2019-10-25; online 2019-09-27]
National Resource for Mass Spectrometry Imaging [Service]
The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell–specific adapter protein
Andersen TCB, Kristiansen PE, Huszenicza Z, ..., Andreotti AH, Spurkland A
J. Biol. Chem. 294 (42) 15480-15494 [2019-10-18; online 2019-09-04]
Swedish NMR Centre (SNC) [Collaborative]
DPI Selectively Inhibits Intracellular NADPH Oxidase Activity in Human Neutrophils.
Buck A, Sanchez Klose FP, Venkatakrishnan V, ..., Christenson K, Bylund J
pii: 3/10/488
Immunohorizons 3 (10) 488-497 [2019-10-18; online 2019-10-18]
Glycoproteomics [Service]
A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding
Fleming CL, Sandoz PA, Inghardt T, ..., Grøtli M, Andréasson J
Angew. Chem. Int. Ed. 58 (42) 15000-15004 [2019-10-14; online 2019-09-05]
Centre for Cellular Imaging [Service]
Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.
Sanchez A, Kuras M, Murillo JR, ..., Betancourt LH, Marko-Varga G
pii: 10.1007/s10565-019-09494-4
Cell Biol. Toxicol. - (-) - [2019-10-10; online 2019-10-10]
Targeted and Structural Proteomics [Service]
SynQuant: an automatic tool to quantify synapses from microscopy images
Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G
- - (-) - [2019-10-09; online 2019-10-09]
BioImage Informatics [Collaborative]
Apolipoprotein E impairs amyloid‐β fibril elongation and maturation
Islam T, Gharibyan AL, Golchin SA, ..., Olofsson L, Olofsson A
FEBS J - (-) - [2019-10-09; online 2019-10-09]
Cryo-EM [Service]
Proteomic Analysis of Longitudinal Changes in Blood Pressure
Lin YT, Fall T, Hammar U, ..., Engström G, Sundström J
J Clin Med 8 (10) 1585 [2019-10-02; online 2019-10-02]
Clinical Biomarkers [Service]
Fam83F induces p53 stabilisation and promotes its activity.
Salama M, Benitez-Riquelme D, Elabd S, ..., Davidson G, Blattner C
pii: 10.1038/s41418-019-0281-1 pmc: PMC6748130
Cell Death Differ. 26 (10) 2125-2138 [2019-10-00; online 2019-01-28]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
A clonal expression biomarker associates with lung cancer mortality.
Biswas D, Birkbak NJ, Rosenthal R, ..., Swanton C, TRACERx Consortium
pii: 10.1038/s41591-019-0595-z
Nat. Med. 25 (10) 1540-1548 [2019-10-00; online 2019-10-07]
Clinical Genomics Uppsala [Collaborative]
Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging.
Shariatgorji M, Nilsson A, Fridjonsdottir E, ..., Odell LR, Andrén PE
pii: 10.1038/s41592-019-0551-3
Nat. Methods 16 (10) 1021-1028 [2019-10-00; online 2019-09-23]
National Resource for Mass Spectrometry Imaging [Technology development]
Implantable Organic Electronic Ion Pump Enables ABA Hormone Delivery for Control of Stomata in an Intact Tobacco Plant
Bernacka‐Wojcik I, Huerta M, Tybrandt K, ..., Berggren M, Stavrinidou E
Small 15 (43) 1902189 [2019-10-00; online 2019-09-12]
Swedish Metabolomics Centre (SMC) [Service]
Isolation and characterization of microvesicles from mesenchymal stem cells
Mohammadi MR, Riazifar M, Pone EJ, ..., Lotvall J, Zhao W
Methods - (-) - [2019-10-00; online 2019-10-00]
Centre for Cellular Imaging [Service]
Cell generation dynamics underlying naive T-cell homeostasis in adult humans.
Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J
pii: PBIOLOGY-D-19-01355
PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]
Real time MRI to elucidate the functionality of coating films intended for modified release
Bernin D, Marucci M, Boissier C, ..., Olsson U, Abrahmsén-Alami S
Journal of Controlled Release 311-312 (-) 117-124 [2019-10-00; online 2019-10-00]
Swedish NMR Centre (SNC) [Collaborative]
The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity.
Papoutsoglou P, Tsubakihara Y, Caja L, ..., Heldin CH, Moustakas A
pii: S2211-1247(19)31062-9
Cell Rep 28 (12) 3182-3198.e11 [2019-09-17; online 2019-09-19]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
Nestin Regulates Neurogenesis in Mice Through Notch Signaling From Astrocytes to Neural Stem Cells
Wilhelmsson U, Lebkuechner I, Leke R, ..., Pekna M, Pekny M
- 29 (10) 4050-4066 [2019-09-13; online 2019-01-03]
Centre for Cellular Imaging [Service]
Chemical screening pipeline for identification of specific plant autophagy modulators
Dauphinee AN, Cardoso C, Dalman K, ..., Bozhkov P, Minina EA
Plant Physiol. 181 (3) pp.00647.2019 [2019-09-05; online 2019-09-05]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
Protein prenylation restrains innate immunity by inhibiting Rac1 effector interactions.
Akula MK, Ibrahim MX, Ivarsson EG, ..., Sayin VI, Bergo MO
pii: 10.1038/s41467-019-11606-x pmc: PMC6726657
Nat Commun 10 (1) 3975 [2019-09-04; online 2019-09-04]
Glycoproteomics [Service]
Vimentin Phosphorylation Is Required for Normal Cell Division of Immature Astrocytes
Pablo , Marasek , Pozo-Rodrigálvarez , ..., Pekna , Pekny
Cells 8 (9) 1016 [2019-09-01; online 2019-09-01]
Centre for Cellular Imaging [Service]
Dimerization of 9,10-anthraquinone-2,7-Disulfonic acid (AQDS)
Wiberg C, Carney TJ, Brushett F, Ahlberg E, Wang E
Electrochimica Acta 317 (-) 478-485 [2019-09-00; online 2019-09-00]
Swedish NMR Centre (SNC) [Service]
FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis
Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK
Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]
Clinical Genomics Lund [Service]
Multiplexed analysis of the secretin-like GPCR-RAMP interactome.
Lorenzen E, Dodig-Crnković T, Kotliar IB, ..., Schwenk JM, Sakmar TP
pii: aaw2778 pmc: PMC6750928
Sci Adv 5 (9) eaaw2778 [2019-09-00; online 2019-09-18]
Plasma Profiling [Collaborative]
Global extracellular vesicle proteomic signature defines U87-MG glioma cell hypoxic status with potential implications for non-invasive diagnostics.
Indira Chandran V, Welinder C, Gonçalves de Oliveira K, ..., Marko-Varga G, Belting M
pii: 10.1007/s11060-019-03262-4 pmc: PMC6764937
J. Neurooncol. 144 (3) 477-488 [2019-09-00; online 2019-08-14]
Targeted and Structural Proteomics [Service]
Yeast Volatomes Differentially Affect Larval Feeding in an Insect Herbivore
Ljunggren J, Borrero-Echeverry F, Chakraborty A, ..., Witzgall P, Bengtsson M
Appl Environ Microbiol 85 (21) - [2019-08-23; online 2019-10-16]
Swedish Metabolomics Centre (SMC) [Service]
Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.
Pin E, Sjöberg R, Andersson E, ..., Nilsson P, Månberg A
Methods Mol. Biol. 2044 (-) 303-318 [2019-08-23; online 2019-08-23]
Autoimmunity Profiling [Technology development]
Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats
Heinrich K, Leslie DJ, Morlock M, Bertilsson S, Jonas K
MBio 10 (4) - [2019-08-20; online 2019-08-20]
Proteogenomics [Service]
Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis.
Elowsson Rendin L, Löfdahl A, Åhrman E, ..., Malmström J, Westergren-Thorsson G
pii: ijms20164013 pmc: PMC6719040
Int J Mol Sci 20 (16) - [2019-08-17; online 2019-08-17]
Targeted and Structural Proteomics [Collaborative]
Nucleation of an Activating Conformational Change by a Cation−π Interaction
Rogne P, Andersson D, Grundström C, ..., Linusson A, Wolf-Watz M
Biochemistry 58 (32) 3408-3412 [2019-08-13; online 2019-07-24]
Swedish NMR Centre (SNC) [Service]
Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila.
Bonzom C, Hüttner S, Mirgorodskaya E, ..., Verhaert RMD, Olsson L
pii: 10.1186/s13568-019-0852-z pmc: PMC6691016
AMB Express 9 (1) 126 [2019-08-12; online 2019-08-12]
Glycoproteomics [Collaborative]
The Critical Role of Dysregulated RhoB Signaling Pathway in Radioresistance of Colorectal Cancer.
Liu N, Cui W, Jiang X, ..., Wang X, Sun XF
pii: S0360-3016(19)30653-4
Int. J. Radiat. Oncol. Biol. Phys. 104 (5) 1153-1164 [2019-08-01; online 2019-04-27]
Mass Cytometry [Service]
Systematic Development of Sandwich Immunoassays for the Plasma Secretome.
Häussler RS, Bendes A, Iglesias M, ..., Qundos U, Schwenk JM
Proteomics 19 (15) e1900008 [2019-08-00; online 2019-07-22]
Plasma Profiling [Technology development]
Clinical protein science in translational medicine targeting malignant melanoma.
Gil J, Betancourt LH, Pla I, ..., Malm J, Marko-Varga G
pii: 10.1007/s10565-019-09468-6 pmc: PMC6757020
Cell Biol. Toxicol. 35 (4) 293-332 [2019-08-00; online 2019-03-21]
Targeted and Structural Proteomics [Service]
Role of apolipoprotein C-III overproduction in diabetic dyslipidaemia.
Adiels M, Taskinen MR, Björnson E, ..., Packard C, Borén J
Diabetes Obes Metab 21 (8) 1861-1870 [2019-08-00; online 2019-05-08]
Glycoproteomics [Service]
Estrogen deprivation triggers an immunosuppressive phenotype in breast cancer cells
Hühn D, Martí-Rodrigo P, Mouron S, ..., Carreras-Puigvert J, Fernandez-Capetillo O
- - (-) - [2019-07-25; online 2019-07-25]
Chemical Biology Consortium Sweden (CBCS) [Service]
Annotations, Ontologies, and Whole Slide Images - Development of an Annotated Ontology-Driven Whole Slide Image Library of Normal and Abnormal Human Tissue.
Lindman K, Rose JF, Lindvall M, Lundström C, Treanor D
pii: JPI-10-22 pmc: PMC6669998 AIDA Data Hub: https://doi.org/10.23698/aida/drco AIDA Data Hub: https://doi.org/10.23698/aida/drsk
J Pathol Inform 10 (-) 22 [2019-07-23; online 2019-07-23]
AIDA Data Hub [Collaborative]
Vitamin D and Phenylbutyrate Supplementation Does Not Modulate Gut Derived Immune Activation in HIV-1
Missailidis C, Sørensen N, Ashenafi S, ..., Brighenti S, Bergman P
Nutrients 11 (7) 1675 [2019-07-21; online 2019-07-21]
Swedish Metabolomics Centre (SMC) [Service]
Systems-level immunomonitoring using self-sampled capillary blood
Josyula VS, Lakshmikanth T, Mikes J, Chen Y, Brodin P
- - (-) - [2019-07-08; online 2019-07-08]
Mass Cytometry [Technology development]
Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.
Edfors F, Forsström B, Vunk H, ..., Schwenk JM, Uhlen M
J. Proteome Res. 18 (7) 2706-2718 [2019-07-05; online 2019-06-07]
Plasma Profiling [Technology development]
Androgen Receptor Burden and Poor Response to Abiraterone or Enzalutamide in TP53 Wild-Type Metastatic Castration-Resistant Prostate Cancer.
De Laere B, Rajan P, Grönberg H, ..., Lindberg J, CORE-ARV-CTC and ProBIO Investigators
pii: 2732501 pmc: PMC6499126
JAMA Oncol 5 (7) 1060-1062 [2019-07-01; online 2019-05-03]
Clinical Genomics Stockholm [Service]
Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis.
Naegeli A, Bratanis E, Karlsson C, ..., Malmström J, Collin M
pii: jem.20190293 pmc: PMC6605743
J. Exp. Med. 216 (7) 1615-1629 [2019-07-01; online 2019-05-15]
Targeted and Structural Proteomics [Collaborative]
Serum metabolite profiles of habitual diet: evaluation by 1H-nuclear magnetic resonance analysis
Lindqvist HM, Rådjursöga M, Malmodin D, Winkvist A, Ellegård L
Am J Clin Nutr 110 (1) 53-62 [2019-07-01; online 2019-05-25]
Swedish NMR Centre (SNC) [Collaborative]
BACH1 Stabilization by Antioxidants Stimulates Lung Cancer Metastasis
Wiel C, Le Gal K, Ibrahim MX, ..., Sayin VI, Bergo MO
Cell 178 (2) 330-345.e22 [2019-07-00; online 2019-07-00]
Centre for Cellular Imaging [Service]
TRAF6 function as a novel co-regulator of Wnt3a target genes in prostate cancer
Aripaka K, Gudey SK, Zang G, ..., von Hofsten J, Landström M
EBioMedicine 45 (-) 192-207 [2019-07-00; online 2019-07-00]
PLA and Single Cell Proteomics [Service]
The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis
Laraia L, Friese A, Corkery DP, ..., Wu YW, Waldmann H
Nat Chem Biol 15 (7) 710-720 [2019-07-00; online 2019-06-20]
Biochemical Imaging Centre Umeå [Service]
Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain
Bigalke JM, Aibara S, Roth R, ..., Amunts A, Sandmark J
Sci Adv 5 (7) eaau4202 [2019-07-00; online 2019-07-31]
Cryo-EM [Service]
The autoimmune targets in IPEX are dominated by gut epithelial proteins
Eriksson D, Bacchetta R, Gunnarsson HI, ..., Kämpe O, Landegren N
Journal of Allergy and Clinical Immunology 144 (1) 327-330.e8 [2019-07-00; online 2019-07-00]
Autoimmunity Profiling [Service]
Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.
Andersson A, Remnestål J, Nellgård B, ..., Nilsson P, Fredolini C
pii: S0009-8981(19)30348-1
Clin. Chim. Acta 494 (-) 79-93 [2019-07-00; online 2019-03-09]
Plasma Profiling [Technology development]
Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.
Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE
pii: PONE-D-19-00673
PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Peptide-Loaded Cubosomes Functioning as an Antimicrobial Unit against Escherichia coli
Boge L, Browning KL, Nordström R, ..., Ringstad L, Andersson M
ACS Appl. Mater. Interfaces 11 (24) 21314-21322 [2019-06-19; online 2019-05-23]
Centre for Cellular Imaging [Service]
A Call for Blood-In Human Immunology.
Brodin P, Duffy D, Quintana-Murci L
pii: S1074-7613(19)30232-8
Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species
Baskaran P, Ekblad A, Soucémarianadin LN, ..., Schleucher J, Lindahl BD
FEMS Microbiol. Ecol. 95 (6) - [2019-06-01; online 2019-04-25]
Swedish NMR Centre (SNC) [Service]
Recombinant dermatan sulfate is a potent activator of heparin cofactor II-dependent inhibition of thrombin
Tykesson E, Maccarana M, Thorsson H, ..., Ellervik U, Westergren-Thorsson G
- 29 (6) 446-451 [2019-06-01; online 2019-04-23]
Swedish NMR Centre (SNC) [Service]
Toxic Activation of an AAA+ Protease by the Antibacterial Drug Cyclomarin A
Maurer M, Linder D, Franke KB, ..., Bukau B, Mogk A
Cell Chem Biol - (-) - [2019-06-00; online 2019-06-00]
Cryo-EM [Service]
Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx
Awad W, Al-Eryani Y, Ekström S, Logan DT, von Wachenfeldt C
Structure 27 (6) 923-936.e6 [2019-06-00; online 2019-06-00]
Targeted and Structural Proteomics [Service]
Circulating mast cell progenitors correlate with reduced lung function in allergic asthma
Salomonsson M, Malinovschi A, Kalm‐Stephens P, ..., Alving K, Hallgren J
Clin Exp Allergy 49 (6) 874-882 [2019-06-00; online 2019-06-03]
Clinical Biomarkers [Service]
The effects of male social environment on sperm phenotype and genome integrity
Silva WTAF, Sáez‐Espinosa P, Torijo‐Boix S, ..., Gómez‐Torres MJ, Immler S
J Evol Biol 32 (6) 535-544 [2019-06-00; online 2019-03-25]
Genome Engineering Zebrafish [Service]
Assembly mechanisms of the bacterial cytoskeletal protein FilP
Javadi A, Söderholm N, Olofsson A, Flärdh K, Sandblad L
Life Sci. Alliance 2 (3) e201800290 [2019-06-00; online 2019-06-26]
Cryo-EM [Collaborative]
Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.
Bedri SK, Nilsson OB, Fink K, ..., Grönlund H, Glaser A
pii: PONE-D-18-30095 pmc: PMC6541274
PLoS ONE 14 (5) e0217208 [2019-05-29; online 2019-05-29]
Plasma Profiling [Collaborative]
The viral protein corona directs viral pathogenesis and amyloid aggregation.
Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S
pii: 10.1038/s41467-019-10192-2 pmc: PMC6536551
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]
Distinct glycosylation in membrane proteins within neonatal versus adult myocardial tissue.
Contessotto P, Ellis BW, Jin C, ..., Kilcoyne M, Pandit A
pii: S0945-053X(19)30045-9
Matrix Biol. - (-) - [2019-05-17; online 2019-05-17]
Glycoproteomics [Service]
Identification of a non-canonical chondroitin sulfate linkage region trisaccharide.
Persson A, Nilsson J, Vorontsov E, Noborn F, Larson G
pii: 5368387
Glycobiology 29 (5) 366-371 [2019-05-01; online 2019-03-03]
Glycoproteomics [Collaborative]
FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex.
Lindén M, Thomsen C, Grundevik P, ..., Ståhlberg A, Åman P
pii: embr.201845766 pmc: PMC6500973
EMBO Rep. 20 (5) - [2019-05-00; online 2019-04-08]
Glycoproteomics [Service]
Helicobacter suis infection alters glycosylation and decreases the pathogen growth inhibiting effect and binding avidity of gastric mucins.
Padra M, Adamczyk B, Flahou B, ..., Karlsson NG, Lindén SK
pii: 10.1038/s41385-019-0154-4
Mucosal Immunol 12 (3) 784-794 [2019-05-00; online 2019-03-07]
Glycoproteomics [Service]
Structural basis for adPEO-causing mutations in the mitochondrial TWINKLE helicase
Peter B, Farge G, Pardo-Hernandez C, Tångefjord S, Falkenberg M
Hum Mol Genet 28 (7) 1090-1099 [2019-04-01; online 2018-11-29]
Centre for Cellular Imaging [Service]
Increased vascular endothelial growth factor D is associated with atrial fibrillation and ischaemic stroke
Berntsson J, Smith JG, Johnson LSB, ..., Nilsson J, Engström G
Heart 105 (7) 553-558 [2019-04-00; online 2018-10-16]
Clinical Biomarkers [Service]
Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring
Alavioon G, Cabrera Garcia A, LeChatelier M, Maklakov AA, Immler S
Evolution Letters 3 (2) 198-206 [2019-04-00; online 2019-02-14]
Genome Engineering Zebrafish [Service]
Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2.
Marcišauskas S, Ulfenborg B, Kristjansdottir B, Waldemarson S, Sundfeldt K
pii: S1874-3919(19)30025-9
J Proteomics 196 (-) 57-68 [2019-03-30; online 2019-01-30]
Glycoproteomics [Service]
High Serum sCD40 and a Distinct Colonic T Cell Profile in Ulcerative Colitis Associated With Primary Sclerosing Cholangitis
Lampinen M, Vessby J, Fredricsson A, ..., Rorsman F, Carlson M
- 13 (3) 341-350 [2019-03-26; online 2018-10-20]
Clinical Biomarkers [Service]
Time-Resolved Study of Silicate Slag Formation During Combustion of Wheat Straw Pellets
Strandberg A, Skoglund N, Thyrel M, ..., Broström M, Backman R
Energy Fuels 33 (3) 2308-2318 [2019-03-21; online 2019-02-21]
Biochemical Imaging Centre Umeå [Service]
Characterization of Double Leached Waelz Oxide for Identification of Fluoride Mineral
Sar S, Sundqvist Ökvist L, Sparrman T, Engström F, Samuelsson C
Metals 9 (3) 361 [2019-03-20; online 2019-03-20]
Swedish NMR Centre (SNC) [Service]
Detecting selection signatures in three Iranian sheep breeds
Manzari Z, Mehrabani‐Yeganeh H, Nejati‐Javaremi A, Moradi MH, Gholizadeh M
Anim Genet - (-) - [2019-03-18; online 2019-03-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Individual and stable autoantibody repertoires in healthy individuals.
Neiman M, Hellström C, Just D, ..., Uhlén M, Nilsson P
Autoimmunity - (-) 1-11 [2019-03-05; online 2019-03-05]
Autoimmunity Profiling [Collaborative]
Immune-informed mucin hydrogels evade fibrotic foreign body response in vivo
Yan H, Seignez C, Hjorth M, ..., Phillipson M, Crouzier T
- - (-) - [2019-02-19; online 2019-02-19]
Cell Profiling [Service]
Zinc depletion does not necessarily induce ribosome hibernation in mycobacteria
Tobiasson V, Dow A, Prisic S, Amunts A
Proc Natl Acad Sci USA 116 (7) 2395-2397 [2019-02-12; online 2019-01-25]
Cryo-EM [Service]
Spatiotemporal dissection of the cell cycle regulated human proteome
Mahdessian D, Sullivan D, Danielsson F, ..., Lindskog C, Lundberg E
- - (-) - [2019-02-07; online 2019-02-07]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]
Auxin export from proximal fruits drives arrest in competent inflorescence meristems
Ware A, Walker CH, Šimura J, ..., Wilson Z, Bennett T
- - (-) - [2019-02-06; online 2019-02-06]
Swedish Metabolomics Centre (SMC) [Service]
Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding
Verteramo ML, Stenström O, Ignjatović MM, ..., Ryde U, Akke M
J. Am. Chem. Soc. 141 (5) 2012-2026 [2019-02-06; online 2019-01-08]
Swedish NMR Centre (SNC) [Service]
GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical.
Alocci D, Mariethoz J, Gastaldello A, ..., Packer NH, Lisacek F
J. Proteome Res. 18 (2) 664-677 [2019-02-01; online 2019-01-15]
Glycoproteomics [Collaborative]
Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper.
Siart B, de Oliveira FMS, Shen Q, ..., Kamali-Moghaddam M, Wallner B
pii: S0003-2697(18)30655-9
Anal. Biochem. 566 (-) 146-150 [2019-02-01; online 2018-11-22]
PLA and Single Cell Proteomics [Technology development]
Disentangling the genetics of lean mass.
Karasik D, Zillikens MC, Hsu YH, ..., Kiel DP, Ohlsson C
pii: 5307112
Am. J. Clin. Nutr. 109 (2) 276-287 [2019-02-01; online 2019-02-06]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Circulating proteins as predictors of cardiovascular mortality in end-stage renal disease
Feldreich T, Nowak C, Fall T, ..., Green D, Ärnlöv J
J Nephrol 32 (1) 111-119 [2019-02-00; online 2018-11-29]
Clinical Biomarkers [Service]
Titanium release in peri-implantitis
Pettersson M, Pettersson J, Johansson A, Molin Thorén M
J Oral Rehabil 46 (2) 179-188 [2019-02-00; online 2018-11-16]
Biochemical Imaging Centre Umeå [Service]
Low Molecular Mass Myocardial Hyaluronan in Human Hypertrophic Cardiomyopathy
Lorén C, Dahl C, Do L, ..., Mörner S, Hellman U
Cells 8 (2) 97 [2019-01-29; online 2019-01-29]
Swedish NMR Centre (SNC) [Service]
Photoactivated Colibactin Probes Induce Cellular DNA Damage
Moodie LWK, Hubert M, Zhou X, ..., Wanrooij S, Hedberg C
Angew. Chem. Int. Ed. 58 (5) 1417-1421 [2019-01-28; online 2018-12-27]
Biochemical Imaging Centre Umeå [Service]
Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting.
Chauhan G, Adams HHH, Satizabal CL, ..., Debette S, Stroke Genetics Network (SiGN), the International Stroke Genetics Consortium (ISGC), METASTROKE, Alzheimer's Disease Genetics Consortium (ADGC), and the Neurology Working Group of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
pii: WNL.0000000000006851 pmc: PMC6369905
Neurology - (-) - [2019-01-16; online 2019-01-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Rapid determination of quaternary protein structures in complex biological samples.
Hauri S, Khakzad H, Happonen L, ..., Malmström J, Malmström L
pii: 10.1038/s41467-018-07986-1 pmc: PMC6331586
Nat Commun 10 (1) 192 [2019-01-14; online 2019-01-14]
Targeted and Structural Proteomics [Technology development]
The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli.
Joffre E, Nicklasson M, Álvarez-Carretero S, ..., Zhu B, Sjöling Å
pii: 10.1038/s41598-018-36414-z pmc: PMC6331568
Sci Rep 9 (1) 108 [2019-01-14; online 2019-01-14]
Glycoproteomics [Service]
Plasma kidney injury molecule-1 (p-KIM-1) levels and deterioration of kidney function over 16 years
Schulz CA, Engström G, Nilsson J, ..., Melander O, Orho-Melander M
- - (-) - [2019-01-09; online 2019-01-09]
Clinical Biomarkers [Service]
Auxin Function in the Brown Alga Dictyota dichotoma
Bogaert KA, Blommaert L, Ljung K, Beeckman T, De Clerck O
Plant Physiol. 179 (1) 280-299 [2019-01-00; online 2018-11-12]
Swedish Metabolomics Centre (SMC) [Service]
Tissue-specific hormone profiles from woody poplar roots under bending stress
De Zio E, Trupiano D, Karady M, ..., Ljung K, Scippa GS
Physiol Plantarum 165 (1) 101-113 [2019-01-00; online 2018-10-15]
Swedish Metabolomics Centre (SMC) [Service]
Pelvis Segmentation Using Multi-pass U-Net and Iterative Shape Estimation
Wang C, Connolly B, de Oliveira Lopes PF, Frangi AF, Smedby Ö
AIDA Data Hub: https://doi.org/10.23698/aida/ctpel
- - (-) 49-57 [2019-00-00; online 2019-01-09]
AIDA Data Hub [Service]
Joint and unique multiblock analysis of biological data – multiomics malaria study
Surowiec I, Skotare T, Sjögren R, ..., Normark J, Trygg J
Faraday Discuss. 218 (-) 268-283 [2019-00-00; online 2019-00-00]
Swedish Metabolomics Centre (SMC) [Service]
A phototherapeutic fluorescent β-cyclodextrin branched polymer delivering nitric oxide
Malanga M, Seggio M, Kirejev V, ..., Ericson MB, Sortino S
Biomater. Sci. 7 (6) 2272-2276 [2019-00-00; online 2019-00-00]
Centre for Cellular Imaging [Service]
Mass spectrometry imaging as a novel approach to measure hippocampal zinc
Dowlatshahi Pour M, Ren L, Jennische E, ..., Ewing AG, Malmberg P
J. Anal. At. Spectrom. 34 (8) 1581-1587 [2019-00-00; online 2019-00-00]
Gothenburg Imaging Mass Spectrometry [Collaborative]