Proteogenomics

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Publications

2020 (86)

2019 (735)

2018 (657)

2017 (692)

2016 (658)

2015 (424)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (4493)


Facilities

Journals

48 publications

Year 2020

PubMed DOI Crossref
Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly
Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A
NPLANTS - (-) - [2020-03-09; online 2020-03-09]
Cryo-EM [Service] Proteogenomics [Service]
PubMed DOI Crossref
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
Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]
Proteogenomics [Collaborative]

Year 2019

PubMed DOI Crossref
A Mitochondrial LYR Protein Is Required for Complex I Assembly.
Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW
pmc
Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]
Proteogenomics [Collaborative]
PubMed DOI Crossref
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia
Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K
Nat Commun 10 (1) - [2019-12-00; online 2019-04-03]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Proteogenomics [Technology development]
PubMed DOI Crossref
Breast cancer quantitative proteome and proteogenomic landscape
Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]
Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]
PubMed DOI Crossref
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.
Ross JM, Coppotelli G, Branca RM, ..., Sinclair DA, Olson L
pmc
Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]
Proteogenomics [Collaborative]
PubMed DOI Crossref
TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells
Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M
Front Immunol 10 (-) - [2019-11-26; online 2019-11-26]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cell Profiling [Collaborative] Proteogenomics [Technology development]
PubMed DOI Crossref
MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M
pmc
iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]
Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]
DOI Crossref
Structure of a mitochondrial ATP synthase with bound native cardiolipin
Mühleip A, McComas SE, Amunts A
Elife 8 (-) - [2019-11-18; online 2019-11-18]
Cryo-EM [Service] Proteogenomics [Service]
DOI Crossref
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]
DOI Crossref
Considerations and Implications in the Purification of Extracellular Vesicles – A Cautionary Tale
Lee YXF, Johansson H, Wood MJA, El Andaloussi S
Front. Neurosci. 13 (-) - [2019-10-18; online 2019-10-18]
Bioinformatics Compute and Storage [Service] Proteogenomics [Service]
DOI Crossref
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]
PubMed DOI Crossref
Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival
Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A
The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]
Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]
PubMed DOI Crossref
Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.
Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM
pmc
Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]
Autoimmunity Profiling [Technology development] Bioinformatics Compute and Storage [Service] Plasma Profiling [Technology development] Proteogenomics [Technology development]
PubMed DOI Crossref
The viral protein corona directs viral pathogenesis and amyloid aggregation.
Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S
pmc
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]
PubMed DOI Crossref
Ultrasensitive immunoprofiling of plasma extracellular vesicles identifies syndecan-1 as a potential tool for minimally invasive diagnosis of glioma.
Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M
Clin. Cancer Res. - (-) - [2019-01-24; online 2019-01-24]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development] Targeted and Structural Proteomics [Service]
PubMed DOI Crossref
SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization
Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J
Molecular Cell 73 (1) 166-182.e7 [2019-01-00; online 2019-01-00]
Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Year 2018

PubMed DOI Crossref
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J
Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]
DOI Crossref
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J
BMC Biol. 16 (1) - [2018-12-00; online 2018-05-07]
Proteogenomics [Collaborative]
PubMed DOI Crossref
Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin
Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A
Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]
Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S
BioProject SRA
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]
DOI Crossref
Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens
Srinivas V, Lebrette H, Lundin D, ..., Sjöberg BM, Högbom M
Nature 563 (7731) 416-420 [2018-11-00; online 2018-10-31]
Proteogenomics [Collaborative]
PubMed DOI Crossref
Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.
Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL
pmc
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment
Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R
Cell Death Dis 9 (9) - [2018-09-00; online 2018-08-28]
Proteogenomics [Collaborative]
PubMed DOI Crossref
Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.
Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U
pmc
JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]
Bioinformatics Compute and Storage [Service] Plasma Profiling [Collaborative] Proteogenomics [Collaborative]
DOI Crossref
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility
Wei B, Jolma A, Sahu B, ..., Taipale M, Taipale J
Nat Biotechnol 36 (6) 521-529 [2018-05-21; online 2018-05-21]
Proteogenomics [Collaborative]
DOI Crossref
MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling
Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M
Proc Natl Acad Sci USA 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]
Proteogenomics [Collaborative]
PubMed DOI Crossref
A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts
Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF
Molecular Plant 11 (2) 342-345 [2018-02-00; online 2018-02-00]
Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome
Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG
PLoS Pathog. 14 (1) e1006852 [2018-01-22; online 2018-01-22]
Proteogenomics [Service]
PubMed DOI Crossref
Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.
Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R
pmc
Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]
Proteogenomics [Collaborative]

Year 2017

DOI Crossref
An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus
Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K
PLoS Genet. 13 (12) e1007148 [2017-12-27; online 2017-12-27]
Proteogenomics [Service]
PubMed DOI Crossref
Mechanism of peptide binding and cleavage by the human mitochondrial peptidase neurolysin.
Teixeira PF, Masuyer G, Pinho CM, ..., Stenmark P, Glaser E
J. Mol. Biol. - (-) - [2017-11-25; online 2017-11-25]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Normalization of mass spectrometry data (NOMAD).
Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O
Adv Biol Regul - (-) - [2017-11-20; online 2017-11-20]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.
Egaña I, Kaito H, Nitzsche A, ..., Hellström M, German Mouse Clinic Consortium
pmc
Sci Rep 7 (1) 15453 [2017-11-13; online 2017-11-13]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Collaborative]
DOI Crossref
Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia
Moisseiev E, Anderson JD, Oltjen S, ..., Nolta JA, Park SS
Current Eye Research 42 (10) 1358-1367 [2017-10-03; online 2017-06-21]
Proteogenomics [Service]
PubMed DOI Crossref
Molecular profiles of oxyphilic and chief cell parathyroid adenoma.
Lu M, Kjellin H, Fotouhi O, ..., Lehtiö J, Larsson C
Mol. Cell. Endocrinol. - (-) - [2017-10-03; online 2017-10-03]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization.
Zhao M, Spiess M, Johansson HJ, ..., Lehtiö J, Strömblad S
pmc
Oncotarget 8 (44) 77061-77074 [2017-09-29; online 2017-08-18]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells.
Reithmeier A, Panizza E, Krumpel M, ..., Ek-Rylander B, Andersson G
pmc
BMC Cancer 17 (1) 650 [2017-09-15; online 2017-09-15]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.
Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S
pmc
Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]
Clinical Proteomics Mass spectrometry [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Proteogenomics [Service]
DOI Crossref
Tuning Metabolome Coverage in Reversed Phase LC–MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition
Lindahl A, Sääf S, Lehtiö J, Nordström A
Anal. Chem. 89 (14) 7356-7364 [2017-07-18; online 2017-06-28]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Technology development]
PubMed DOI Crossref
Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.
Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J
pmc
Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]
PubMed DOI Crossref
Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.
Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M
Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics
Lindahl A, Heuchel R, Forshed J, ..., Löhr M, Nordström A
Metabolomics 13 (5) - [2017-05-00; online 2017-04-01]
Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.
Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J
pmc
Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative] Proteogenomics [Technology development]
PubMed DOI Crossref
A multi-step peptidolytic cascade for amino acid recovery in chloroplasts
Teixeira PF, Kmiec B, Branca RMM, ..., Lehtiö J, Glaser E
Nat Chem Biol 13 (1) 15-17 [2017-01-00; online 2016-10-31]
Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Year 2016

PubMed DOI Crossref
Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.
Maleki S, Kjellqvist S, Paloschi V, ..., Eriksson P, Björck HM
pmc
Sci Rep 6 (-) 35712 [2016-10-25; online 2016-10-25]
Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative]
PubMed DOI Crossref
Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.
Perisic Matic L, Rykaczewska U, Razuvaev A, ..., Hamsten A, Hedin U
Arterioscler. Thromb. Vasc. Biol. 36 (9) 1947-1961 [2016-09-00; online 2016-07-28]
Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative]
PubMed DOI Crossref
Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling.
Anderson JD, Johansson HJ, Graham CS, ..., Lehtiö J, Nolta JA
Stem Cells 34 (3) 601-613 [2016-03-00; online 2016-02-19]
Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative]
Software 3.2.19