Publications 2020

314 publications

Clonal competition within complex evolutionary hierarchies shapes AML over time
Sandén C, Lilljebjörn H, Orsmark Pietras C, ..., Ågerstam H, Fioretos T
Nat Commun 11 (1) - [2020-12-00; online 2020-02-05]
Clinical Genomics Lund [Service]
Distinct pre-initiation steps in human mitochondrial translation
Khawaja A, Itoh Y, Remes C, ..., Amunts A, Rorbach J
Nat Commun 11 (1) 1-10 [2020-12-00; online 2020-06-10]
Cryo-EM [Service]
Primary cell wall inspired micro containers as a step towards a synthetic plant cell
Paulraj T, Wennmalm S, Wieland DCF, ..., Cárdenas M, Svagan AJ
Nat Commun 11 (1) - [2020-12-00; online 2020-02-19]
Advanced Light Microscopy (ALM) [Collaborative]
Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish
Banote RK, Chebli J, Şatır TM, ..., Abramsson A, Zetterberg H
Sci Rep 10 (1) - [2020-12-00; online 2020-06-23]
Genome Engineering Zebrafish [Collaborative]
A complex DICER1 syndrome phenotype associated with a germline pathogenic variant affecting the RNase IIIa domain of DICER1.
Pontén E, Frisk S, Taylan F, ..., Lagerstedt-Robinson K, Nordgren A
pii: jmedgenet-2020-107385
J. Med. Genet. - (-) - [2020-11-18; online 2020-11-18]
Clinical Genomics Stockholm [Service]
Cryo‐EM structure of native human uromodulin, a zona pellucida module polymer
Stsiapanava A, Xu C, Brunati M, ..., Wu B, Jovine L
EMBO J - (-) e106807 [2020-11-16; online 2020-11-16]
Cryo-EM [Collaborative]
Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer.
Mehmeti-Ajradini M, Bergenfelz C, Larsson AM, ..., Bexell D, Leandersson K
pii: 3/11/e202000893
Life Sci. Alliance 3 (11) - [2020-11-00; online 2020-09-21]
Mass Cytometry [Service]
Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9
Winkelmann I, Matsuoka R, Meier PF, ..., Beckstein O, Drew D
EMBO J - (-) - [2020-10-29; online 2020-10-29]
Cryo-EM [Service]
Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Flygaard RK, Mühleip A, Tobiasson V, Amunts A
pii: 10.1038/s41467-020-18993-6
Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]
Cryo-EM [Service]
Optotracing for selective fluorescence-based detection, visualization and quantification of live S. aureus in real-time.
Butina K, Tomac A, Choong FX, ..., Löffler S, Richter-Dahlfors A
pii: 10.1038/s41522-020-00150-y
NPJ Biofilms Microbiomes 6 (1) 35 [2020-10-09; online 2020-10-09]
Advanced Light Microscopy (ALM) [Service]
SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden.
Rudberg AS, Havervall S, Månberg A, ..., Hober S, Thålin C
pii: 10.1038/s41467-020-18848-0
Nat Commun 11 (1) 5064 [2020-10-08; online 2020-10-08]
Autoimmunity Profiling [Collaborative]
A latent lineage potential in resident neural stem cells enables spinal cord repair.
Llorens-Bobadilla E, Chell JM, Le Merre P, ..., Carlén M, Frisén J
pii: 370/6512/eabb8795
Science 370 (6512) - [2020-10-02; online 2020-10-03]
Advanced Light Microscopy (ALM) [Service]
Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.
Hong MG, Dodig-Crnković T, Chen X, ..., Magnusson PK, Schwenk JM
pii: 3/10/e202000817
Life Sci. Alliance 3 (10) - [2020-10-00; online 2020-07-31]
Autoimmunity Profiling [Service]
An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.
Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM
pii: 10.1038/s41467-020-18174-5 PDB: 6ZXN
Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]
Protein Science Facility (PSF) [Service]
Structural basis of mitochondrial translation
Aibara S, Singh V, Modelska A, Amunts A
Elife 9 (-) 1-17 [2020-08-19; online 2020-08-19]
Cryo-EM [Service]
Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis
Zhang Y, Cedervall J, Hamidi A, ..., Dimberg A, Olsson AK
Cancer Res 80 (16) 3345-3358 [2020-08-15; online 2020-06-25]
PLA and Single Cell Proteomics [Service]
Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy.
Mikus M, Zandian A, Sjöberg R, ..., van Hage M, Ohlin M
pii: S0091-6749(20)31108-8
J. Allergy Clin. Immunol. - (-) - [2020-08-10; online 2020-08-10]
Autoimmunity Profiling [Collaborative]
Systems-level immunomonitoring from acute to recovery phase of severe COVID-19
Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P
Cell Reports Medicine - (-) 100078 [2020-08-00; online 2020-08-00]
Mass Cytometry [Collaborative]
SLC12A2 mutations cause NKCC1 deficiency with encephalopathy and impaired secretory epithelia.
Stödberg T, Magnusson M, Lesko N, ..., Stranneheim H, Wedell A
pii: NG2020013649 pmc: PMC7357422
Neurol Genet 6 (4) e478 [2020-08-00; online 2020-07-02]
Clinical Genomics Stockholm [Service]
Immunocyte single cell analysis of vaccine‐induced narcolepsy
Lind A, Salami F, Landtblom A, ..., Adolfsson J, Elding Larsson H
Eur. J. Immunol. - (-) - [2020-07-30; online 2020-07-30]
Mass Cytometry [Service]
Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics.
Engvall M, Cahill N, Jonsson BI, ..., Hallböök H, Cavelier L
pii: 10.1186/s12920-020-00739-4 pmc: PMC7388219
BMC Med Genomics 13 (1) 106 [2020-07-29; online 2020-07-29]
Clinical Genomics Uppsala [Technology development]
Loqusdb: added value of an observations database of local genomic variation.
Magnusson M, Eisfeldt J, Nilsson D, ..., Wedell A, Stranneheim H
pii: 10.1186/s12859-020-03609-z pmc: PMC7329469
BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]
Clinical Genomics Stockholm [Service]
Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA.
Baronti L, Guzzetti I, Ebrahimi P, ..., Chen AA, Petzold K
pii: 10.1038/s41586-020-2336-3
Nature 583 (7814) 139-144 [2020-07-00; online 2020-05-27]
Protein Science Facility (PSF) [Service]
Human Immune System Variation during 1 Year
Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P
Cell Rep 32 (3) 107923 [2020-07-00; online 2020-07-00]
Mass Cytometry [Collaborative]
Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.
Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J
pii: 10.1038/s41591-020-0969-2
Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]
Clinical Genomics Stockholm [Service]
Lysine-specific demethylase 1A (LSD1) restricts ex vivo propagation of human HSCs and is a target of UM171
Subramaniam A, Žemaitis K, Safaee Talkhoncheh M, ..., Zubarev RA, Larsson J
- - (-) - [2020-06-24; online 2020-06-24]
Chemical Proteomics [Collaborative]
A sample preparation protocol for high throughput immunofluorescence of suspension cells
Backstrom A, Kugel L, Gnann C, ..., Lundberg E, Stadler C
JHC - (-) - [2020-06-20; online 2020-01-20]
Cell Profiling [Technology development]
Chanjo: Clincal grade sequence coverage analysis
Andeer R, Magnusson M, Wedell A, Stranneheim H
F1000Res 9 (-) 615 [2020-06-16; online 2020-06-16]
Clinical Genomics Stockholm [Technology development]
GPSeq reveals the radial organization of chromatin in the cell nucleus
Girelli G, Custodio J, Kallas T, ..., Crosetto N, Bienko M
Nat Biotechnol - (-) - [2020-05-25; online 2020-05-25]
Advanced Light Microscopy (ALM) [Service]
A chemical screen identifies a link between lipid metabolism and mRNA translation
Corman A, Kanellis DC, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O
- - (-) - [2020-05-11; online 2020-05-11]
Chemical Biology Consortium Sweden (CBCS) [Service]
A molecular mechanism explaining albuminuria in kidney disease
Butt L, Unnersjö-Jess D, Höhne M, ..., Schermer B, Benzing T
Nat Metab 2 (5) 461-474 [2020-05-00; online 2020-05-11]
Advanced Light Microscopy (ALM) [Collaborative]
Fungi and Oomycetes in the Irrigation Water of Forest Nurseries
Marčiulynas A, Marčiulynienė D, Lynikienė J, ..., Vaičiukynė M, Menkis A
Forests 11 (4) 459 [2020-04-18; online 2020-04-18]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
Genetic Associations Between Childhood Psychopathology and Adult Depression and Associated Traits in 42 998 Individuals: A Meta-Analysis.
Akingbuwa WA, Hammerschlag AR, Jami ES, ..., Middeldorp CM, and the Bipolar Disorder and Major Depressive Disorder Working Groups of the Psychiatric Genomics Consortium
pii: 2763801 pmc: PMC7160753
JAMA Psychiatry - (-) - [2020-04-15; online 2020-04-15]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.
Scaletti ER, Vallin KS, Bräutigam L, ..., Stenmark P, Jemth AS
pii: RA120.012636 PDB: 6QVO
J. Biol. Chem. - (-) - [2020-03-06; online 2020-03-06]
Protein Science Facility (PSF) [Service]
Structure of a minimal photosystem I from the green alga Dunaliella salina
Perez-Boerema A, Klaiman D, Caspy I, ..., Amunts A, Nelson N
NPLANTS 6 (3) 321-327 [2020-03-02; online 2020-03-02]
Cryo-EM [Service]
Stressful Beginnings with Long-Term Consequences
Consiglio CR, Brodin P
Cell 180 (5) 820-821 [2020-03-00; online 2020-03-00]
Mass Cytometry [Collaborative]
Patterns of African and Asian admixture in the Afrikaner population of South Africa.
Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM
pii: 10.1186/s12915-020-0746-1
BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.
Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N
Scand. J. Immunol. - (-) e12864 [2020-02-13; online 2020-02-13]
Autoimmunity Profiling [Service]
Capsid Structure of a Marine Algal Virus of the Order Picornavirales
Munke A, Kimura K, Tomaru Y, Okamoto K
J Virol 94 (9) - [2020-02-05; online 2020-04-16]
Cryo-EM [Service]
Exosomes influence the behavior of human mesenchymal stem cells on titanium surfaces.
Wang X, Shah FA, Vazirisani F, ..., Ekström K, Thomsen P
pii: S0142-9612(19)30670-2
Biomaterials 230 (-) 119571 [2020-02-00; online 2019-10-24]
Glycoproteomics [Service]
Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin.
Roemhild R, Linkevicius M, Andersson DI
pii: PBIOLOGY-D-19-02723
PLoS Biol. 18 (1) e3000612 [2020-01-27; online 2020-01-27]
Glycoproteomics [Service]
Evolution of a new function by fusion between phage DNA and a bacterial gene.
Warsi O, Knopp M, Surkov S, Hultqvist JJ, Andersson DI
pii: 5707441
Mol. Biol. Evol. - (-) - [2020-01-16; online 2020-01-16]
Glycoproteomics [Service]
Proteomic analysis of follicular fluid during human ovulation.
Zakerkish F, Brännström M, Carlsohn E, ..., van der Post S, Thoroddsen A
Acta Obstet Gynecol Scand - (-) - [2020-01-16; online 2020-01-16]
Glycoproteomics [Service]
Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.
Bonomi A, Veglia F, Baldassarre D, ..., Gigante B, on behalf of the IMPROVE study group
pii: 10.1038/s41435-019-0090-z
Genes Immun. - (-) - [2020-01-14; online 2020-01-14]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.
Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG
pii: 10.1038/s41467-019-13931-7 pmc: PMC6952425
Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]
Chemical Proteomics [Service]
Integrative discovery of treatments for high-risk neuroblastoma.
Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S
pii: 10.1038/s41467-019-13817-8 pmc: PMC6941971
Nat Commun 11 (1) 71 [2020-01-03; online 2020-01-03]
Genome Engineering Zebrafish [Service]
A dual-action peptide-containing hydrogel targets wound infection and inflammation
Puthia M, Butrym M, Petrlova J, ..., Kjellström S, Schmidtchen A
Sci. Transl. Med. 12 (524) eaax6601 [2020-01-01; online 2020-01-01]
Targeted and Structural Proteomics [Collaborative]
Identification of novel diagnostic and prognostic biomarkers for abdominal aortic aneurysm
Memon AA, Zarrouk M, Ågren-Witteschus S, ..., Gottsäter A, Sundquist K
Eur J Prev Cardiolog 27 (2) 132-142 [2020-01-00; online 2019-08-29]
Clinical Biomarkers [Service]
The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.
Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S
pii: RA119.001737
Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]
Proteogenomics [Collaborative]
Copper nanoparticles have negligible direct antibacterial impact
Bastos CAP, Faria N, Wills J, ..., Rees P, Powell JJ
NanoImpact 17 (-) 100192 [2020-01-00; online 2020-01-00]
Gothenburg Imaging Mass Spectrometry [Collaborative]
Regulation of α-synuclein by chaperones in mammalian cells
Burmann BM, Gerez JA, Matečko-Burmann I, ..., Riek R, Hiller S
Nature 577 (7788) 127-132 [2020-01-00; online 2019-12-04]
Swedish NMR Centre (SNC) [Service]
Probabilistic cell typing enables fine mapping of closely related cell types in situ
Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M
Nat Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]
In Situ Sequencing (ISS) [Technology development]
In-plate toxicometabolomics of single zebrafish embryos
Ribbenstedt A, Posselt M, Brunius C, Benskin JP
Mol Omics - (-) - [2020-00-00; online 2020-00-00]
Genome Engineering Zebrafish [Service]