Global Proteomics and Proteogenomics

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SciLifeLab Infrastructure Unit Since 2017. Previously called "Proteogenomics".

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2017

Ended: Current

Year 2024

PubMed DOI Crossref
Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.
Emanuelsson EB, Arif M, Reitzner SM, ..., Sundberg CJ, Chapman MA
iScience 27 (1) 108638 [2024-01-19; online 2023-12-05]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Nuclear Hsp104 safeguards the dormant translation machinery during quiescence.
Kohler V, Kohler A, Berglund LL, ..., Andréasson C, Büttner S
Nat Commun 15 (1) 315 [2024-01-05; online 2024-01-05]
Global Proteomics and Proteogenomics [Service]

Year 2023

PubMed DOI Crossref
The heat shock protein LarA activates the Lon protease in response to proteotoxic stress.
Omnus DJ, Fink MJ, Kallazhi A, ..., Landreh M, Jonas K
Nat Commun 14 (1) 7636 [2023-11-22; online 2023-11-22]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Regulation of the general stress response sigma factor σT by Lon-mediated proteolysis.
Akar R, Fink MJ, Omnus DJ, Jonas K
J. Bacteriol. 205 (11) e0022823 [2023-11-06; online 2023-11-06]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors.
Chiaro J, Antignani G, Feola S, ..., Lehtiö J, Cerullo V
Nat Commun 14 (1) 7056 [2023-11-03; online 2023-11-03]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress.
Brunner A, Li Q, Fisicaro S, ..., Orre LM, Sangfelt O
Mol. Cell 83 (20) 3720-3739.e8 [2023-10-19; online 2023-08-16]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Endothelial VEGFR2-PLCγ signaling regulates vascular permeability and antitumor immunity through eNOS/Src.
Sjöberg E, Melssen M, Richards M, ..., Dimberg A, Claesson-Welsh L
J. Clin. Invest. 133 (20) - [2023-10-16; online 2023-10-16]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Precision cancer medicine: Concepts, current practice, and future developments.
Edsjö A, Holmquist L, Geoerger B, ..., Siu LL, Stenzinger A
J. Intern. Med. 294 (4) 455-481 [2023-10-00; online 2023-08-28]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Comprehensive proteomics and meta-analysis of COVID-19 host response.
Babačić H, Christ W, Araújo JE, ..., Klingström J, Pernemalm M
Nat Commun 14 (1) 5921 [2023-09-22; online 2023-09-22]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Non-classical HLA-E restricted CMV 15-mer peptides are recognized by adaptive NK cells and induce memory responses.
Martín Almazán N, Sala BM, Sandalova T, ..., Achour A, Sarhan D
Front Immunol 14 (-) 1230718 [2023-09-21; online 2023-09-21]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Verticillium longisporum phospholipase VlsPLA2 is a virulence factor that targets host nuclei and modulates plant immunity.
Rafiei V, Vélëz H, Piombo E, Dubey M, Tzelepis G
Mol. Plant Pathol. 24 (9) 1078-1092 [2023-09-00; online 2023-05-12]
Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Public and patient involvement: a survey on knowledge, experience and opinions among researchers within a precision oncology European project.
Mosconi P, Colombo C, Paletta P, ..., Brunelli C, CEE_DART Consortium
BMC Cancer 23 (1) 814 [2023-08-30; online 2023-08-30]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Deciphering the Role of p60AmotL2 in Epithelial Extrusion and Cell Detachment.
Cui W, Subramani A, Fonseca P, ..., Lundqvist A, Holmgren L
Cells 12 (17) - [2023-08-28; online 2023-08-28]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Insights into cellular behavior and micromolecular communication in urothelial micrografts.
Juul N, Willacy O, Mamand DR, ..., Chamorro CI, Fossum M
Sci Rep 13 (1) 13589 [2023-08-21; online 2023-08-21]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Complementarity-determining region clustering may cause CAR-T cell dysfunction.
Sarén T, Saronio G, Marti Torrell P, ..., Yu D, Essand M
Nat Commun 14 (1) 4732 [2023-08-10; online 2023-08-10]
Bioinformatics Support for Computational Resources [Service] Drug Discovery and Development (DDD) [Collaborative] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells.
Boussardon C, Carrie C, Keech O
J. Exp. Bot. 74 (14) 4110-4124 [2023-08-03; online 2023-04-08]
Global Proteomics and Proteogenomics [Service] Integrated Microscopy Technologies Umeå [Service]
PubMed DOI Crossref
Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma.
Panizza E, Regalado BD, Wang F, ..., Cerione RA, Antonyak MA
Life Sci. Alliance 6 (6) - [2023-06-00; online 2023-04-10]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
Majumdar S, Emmerich A, Krakovka S, ..., Svärd SG, Sanyal S
Nucleic Acids Res. 51 (7) 3436-3451 [2023-04-24; online 2023-03-14]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Interleukin-6 trans-signaling induced laminin switch contributes to reduced trans-endothelial migration of granulocytic cells.
Zegeye MM, Matic L, Lengquist M, ..., Ljungberg LU, Kumawat AK
Atherosclerosis 371 (-) 41-53 [2023-04-00; online 2023-03-22]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children.
Stratmann S, Vesterlund M, Umer HM, ..., Lehtiö J, Holmfeldt L
Leukemia 37 (3) 550-559 [2023-03-00; online 2022-12-26]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative]

Year 2022

PubMed DOI Crossref
Altered expression of the IGF2‑H19 locus and mitochondrial respiratory complexes in adrenocortical carcinoma.
Scicluna P, Caramuta S, Kjellin H, ..., Lui WO, Larsson C
Int. J. Oncol. 61 (5) - [2022-11-00; online 2022-09-28]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Herbst SA, Vesterlund M, Helmboldt AJ, ..., Lehtiö J, Dietrich S
Nat Commun 13 (1) 6226 [2022-10-20; online 2022-10-20]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
The Expression of the Immunoproteasome Subunit PSMB9 Is Related to Distinct Molecular Subtypes of Uterine Leiomyosarcoma.
Maia Falcão R, Kokaraki G, De Wispelaere W, ..., Carlson JW, Petta TB
Cancers (Basel) 14 (20) - [2022-10-13; online 2022-10-13]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Manganese-driven CoQ deficiency.
Diessl J, Berndtsson J, Broeskamp F, ..., Ott M, Büttner S
Nat Commun 13 (1) 6061 [2022-10-13; online 2022-10-13]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse.
Diaz Lozano IM, Sork H, Stone VM, ..., Gabrielsson S, Flodström-Tullberg M
Front Endocrinol (Lausanne) 13 (-) 971313 [2022-09-28; online 2022-09-28]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.
Arslan T, Pan Y, Mermelekas G, ..., Orre LM, Lehtiö J
Nat Protoc 17 (8) 1832-1867 [2022-08-00; online 2022-06-22]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome.
Silwal-Pandit L, Stålberg SM, Johansson HJ, ..., Lehtiö J, Kure EH
Cancer Res Commun 2 (6) 434-446 [2022-06-00; online 2022-06-14]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Itoh Y, Khawaja A, Laptev I, ..., Rorbach J, Amunts A
Nature 606 (7914) 603-608 [2022-06-00; online 2022-06-08]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis.
Rykaczewska U, Zhao Q, Saliba-Gustafsson P, ..., Hedin U, Matic L
Arterioscler. Thromb. Vasc. Biol. 42 (5) 659-676 [2022-05-00; online 2022-03-24]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Author Correction: The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.
Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J
Nat Cancer 3 (5) 649 [2022-05-00; online 2022-04-23]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Gastrointestinal mucus in dog: Physiological characteristics, composition, and structural properties.
Dubbelboer IR, Barmpatsalou V, Rodler A, ..., Häggström J, Bergström CAS
Eur J Pharm Biopharm 173 (-) 92-102 [2022-04-00; online 2022-02-25]
Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines.
Feola S, Chiaro J, Martins B, ..., Lehtiö J, Cerullo V
Elife 11 (-) - [2022-03-22; online 2022-03-22]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.
Umer HM, Audain E, Zhu Y, ..., Branca RM, Perez-Riverol Y
Bioinformatics 38 (5) 1470-1472 [2022-02-07; online 2021-12-15]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.
Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J
Nat Cancer 3 (2) 251-261 [2022-02-00; online 2022-02-24]
Global Proteomics and Proteogenomics [Technology development]

Year 2021

PubMed DOI Crossref
Chitinase 3 like 1 is a regulator of smooth muscle cell physiology and atherosclerotic lesion stability.
Tsantilas P, Lao S, Wu Z, ..., Maegdefessel L, Leeper NJ
Cardiovasc. Res. 117 (14) 2767-2780 [2021-12-17; online 2021-01-21]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Physiological properties, composition and structural profiling of porcine gastrointestinal mucus.
Barmpatsalou V, Dubbelboer IR, Rodler A, ..., Pedersen BL, Bergström CAS
Eur J Pharm Biopharm 169 (-) 156-167 [2021-12-00; online 2021-10-20]
Global Proteomics and Proteogenomics [Service] Integrated Microscopy Technologies Umeå [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.
Sáinz-Jaspeado M, Smith RO, Plunde O, ..., Bäck M, Claesson-Welsh L
Circulation 144 (20) 1629-1645 [2021-11-16; online 2021-10-12]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.
Lehtiö J, Arslan T, Siavelis I, ..., Staaf J, Orre LM
Nat Cancer 2 (11) 1224-1242 [2021-11-00; online 2021-11-22]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification.
Feola S, Haapala M, Peltonen K, ..., Sikanen TM, Cerullo V
ACS Nano 15 (10) 15992-16010 [2021-10-26; online 2021-10-04]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle.
Omnus DJ, Fink MJ, Szwedo K, Jonas K
Elife 10 (-) - [2021-10-25; online 2021-10-25]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Fine Tuning of Phosphorothioate Inclusion in 2'-O-Methyl Oligonucleotides Contributes to Specific Cell Targeting for Splice-Switching Modulation.
Aoki Y, Rocha CSJ, Lehto T, ..., Behlke MA, Andaloussi SE
Front Physiol 12 (-) 689179 [2021-10-13; online 2021-10-13]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound.
Giovannucci TA, Salomons FA, Haraldsson M, ..., Johnsen JI, Dantuma NP
Cell Death Dis 12 (10) 914 [2021-10-06; online 2021-10-06]
CRISPR Functional Genomics [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma.
Cao X, Sandberg A, Araújo JE, ..., Eriksson LE, Pernemalm M
J. Proteome Res. 20 (9) 4610-4620 [2021-09-03; online 2021-07-28]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
The Amot/integrin protein complex transmits mechanical forces required for vascular expansion.
Zhang Y, Zhang Y, Kameishi S, ..., Cavallo F, Holmgren L
Cell Rep 36 (8) 109616 [2021-08-24; online 2021-08-26]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J
Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]
Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.
Guo M, Goudarzi KM, Abedi S, ..., Nistér M, Hägerstrand D
Oncogene 40 (32) 5066-5080 [2021-08-00; online 2021-05-21]
Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy.
Peltonen K, Feola S, Umer HM, ..., Lehtiö J, Cerullo V
Cancers (Basel) 13 (14) - [2021-07-07; online 2021-07-07]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Thermal proteome profiling identifies PIP4K2A and ZADH2 as off-targets of Polo-like kinase 1 inhibitor volasertib.
Goroshchuk O, Kolosenko I, Kunold E, ..., Jafari R, Palm-Apergi C
FASEB J. 35 (7) e21741 [2021-07-00; online 2021-06-19]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.
Veerman RE, Teeuwen L, Czarnewski P, ..., Gabrielsson S, Eldh M
J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Proteomic Profiling of Tissue Exosomes Indicates Continuous Release of Malignant Exosomes in Urinary Bladder Cancer Patients, Even with Pathologically Undetectable Tumour.
Eldh M, Mints M, Hiltbrunner S, ..., Sherif A, Gabrielsson S
Cancers (Basel) 13 (13) - [2021-06-29; online 2021-06-29]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
SOCS3 Expression by Thymic Stromal Cells Is Required for Normal T Cell Development.
Gao Y, Liu R, He C, ..., Carow B, Rottenberg ME
Front Immunol 12 (-) 642173 [2021-03-18; online 2021-03-18]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Extracellular Vesicles for the Treatment of Radiation-Induced Normal Tissue Toxicity in the Lung.
Montay-Gruel P, Zhu Y, Petit B, ..., Vozenin MC, Limoli CL
Front Oncol 10 (-) 602763 [2021-03-02; online 2021-03-02]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Mechanism of membrane-tethered mitochondrial protein synthesis.
Itoh Y, Andréll J, Choi A, ..., Battersby BJ, Amunts A
Science 371 (6531) 846-849 [2021-02-19; online 2021-02-20]
Global Proteomics and Proteogenomics [Service]

Year 2020

PubMed DOI Crossref
Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses.
Tampere M, Pettke A, Salata C, ..., Jafari R, Puumalainen MR
Viruses 12 (12) 1423 [2020-12-10; online 2020-12-10]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy.
van Westering TLE, Johansson HJ, Hanson B, ..., Aoki Y, Roberts TC
Mol. Cell Proteomics 19 (12) 2047-2068 [2020-12-00; online 2020-09-29]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Flygaard RK, Mühleip A, Tobiasson V, Amunts A
Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Clarithromycin Exerts an Antibiofilm Effect against Salmonella enterica Serovar Typhimurium rdar Biofilm Formation and Transforms the Physiology towards an Apparent Oxygen-Depleted Energy and Carbon Metabolism.
Zafar M, Jahan H, Shafeeq S, ..., Römling U, Choudhary MI
Infect. Immun. 88 (11) - [2020-10-19; online 2020-10-19]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
Nat Commun 11 (1) 5187 [2020-10-14; online 2020-10-14]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity.
Lytrivi M, Ghaddar K, Lopes M, ..., Eizirik DL, Cnop M
BMC Genomics 21 (1) 590 [2020-08-26; online 2020-08-26]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
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] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
A 3D Cell Culture Model Identifies Wnt/β-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.
Oliva-Vilarnau N, Vorrink SU, Ingelman-Sundberg M, Lauschke VM
Adv Sci (Weinh) 7 (15) 2000248 [2020-08-00; online 2020-06-23]
Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells.
Kumar-Singh A, Shrinet J, Parniewska MM, ..., Dobra K, Hjerpe A
Biomolecules 10 (7) - [2020-07-11; online 2020-07-11]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
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
Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Collaborative] Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.
Tobiasson V, Amunts A
Elife 9 (-) 1-15 [2020-06-18; online 2020-06-18]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.
Zhu Y, Orre LM, Zhou Tran Y, ..., Anders S, Lehtiö J
Mol. Cell Proteomics 19 (6) 1047-1057 [2020-06-00; online 2020-03-23]
Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Lung developmental arrest caused by PDGF-A deletion: consequences for the adult mouse lung.
Gouveia L, Kraut S, Hadzic S, ..., Betsholtz C, Andrae J
Am J Physiol Lung Cell Mol Physiol 318 (4) L831-L843 [2020-04-01; online 2020-03-18]
Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics.
Herr P, Boström J, Rullman E, ..., Maddalo G, Altun M
Mol. Cell Proteomics 19 (4) 608-623 [2020-04-00; online 2020-02-12]
Global Proteomics and Proteogenomics [Collaborative]
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 6 (3) 314-320 [2020-03-00; online 2020-03-09]
Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]
PubMed DOI Crossref
PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.
Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L
Circ. Res. 126 (5) 571-585 [2020-02-28; online 2020-01-02]
Global Proteomics and Proteogenomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative]

Year 2019

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
Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
A Mitochondrial LYR Protein Is Required for Complex I Assembly.
Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW
Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]
Global Proteomics and 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 (-) 2708 [2019-11-26; online 2019-11-26]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Global Proteomics and Proteogenomics [Technology development] Spatial Proteomics [Collaborative]
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
iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative]
PubMed 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] Global Proteomics and Proteogenomics [Service]
PubMed 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) e47845 [2019-11-05; online 2019-09-23]
Global Proteomics and Proteogenomics [Service]
PubMed 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 (-) 1067 [2019-10-18; online 2019-10-18]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Service]
PubMed 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]
Global Proteomics and 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]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]
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
Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]
Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] Bioinformatics Support for Computational Resources [Service] Global Proteomics and 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
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and 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. 25 (10) 3115-3127 [2019-05-15; online 2019-01-24]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Structural Proteomics [Service]
PubMed DOI Crossref
Breast cancer quantitative proteome and proteogenomic landscape.
Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Service]
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) 1519 [2019-04-03; online 2019-04-03]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Lund [Service] Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization.
Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J
Mol. Cell 73 (1) 166-182.e7 [2019-01-03; online 2019-01-05]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Technology development]

Year 2018

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]
Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Global Proteomics and Proteogenomics [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative]
PubMed 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]
Global Proteomics and 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
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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) 846 [2018-08-28; online 2018-08-28]
Global Proteomics and 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
JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]
Affinity Proteomics Stockholm [Collaborative] Bioinformatics Support for Computational Resources [Service] Global Proteomics and 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
Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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. 470 (-) 84-95 [2018-07-15; online 2017-10-03]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]
PubMed 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 [2018-07-00; online 2018-05-21]
Global Proteomics and Proteogenomics [Collaborative]
PubMed 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) 47 [2018-05-07; online 2018-05-07]
Global Proteomics and Proteogenomics [Collaborative]
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) 903 [2018-03-02; online 2018-03-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development]
PubMed 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. U.S.A. 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]
Global Proteomics and 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
Mol Plant 11 (2) 342-345 [2018-02-05; online 2017-11-26]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [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. 430 (3) 348-362 [2018-02-02; online 2017-11-26]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and 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
Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]
Global Proteomics and Proteogenomics [Collaborative]
PubMed DOI Crossref
Normalization of mass spectrometry data (NOMAD).
Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O
Adv Biol Regul 67 (-) 128-133 [2018-01-00; online 2017-11-20]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]
PubMed 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 [2018-01-00; online 2018-01-22]
Global Proteomics and Proteogenomics [Service]

Year 2017

PubMed 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 [2017-12-00; online 2017-12-27]
Global Proteomics and 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
Sci Rep 7 (1) 15453 [2017-11-13; online 2017-11-13]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Collaborative]
PubMed 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 [2017-10-00; online 2017-06-21]
Global Proteomics and 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
Oncotarget 8 (44) 77061-77074 [2017-09-29; online 2017-08-18]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and 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
BMC Cancer 17 (1) 650 [2017-09-15; online 2017-09-15]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and 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
Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed 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] Global Proteomics and 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
Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and 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 Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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) 61 [2017-04-01; online 2017-04-01]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and 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
Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.
Teixeira PF, Kmiec B, Branca RM, ..., Lehtiö J, Glaser E
Nat. Chem. Biol. 13 (1) 15-17 [2017-01-00; online 2016-10-31]
Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and 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
Sci Rep 6 (-) 35712 [2016-10-25; online 2016-10-25]
Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and 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] Global Proteomics and 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] Global Proteomics and Proteogenomics [Collaborative]
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Publications 9.5.0