Cell Profiling

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Publications

2021 (47)

2020 (592)

2019 (746)

2018 (664)

2017 (705)

2016 (673)

2015 (434)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

1989 (1)

All (5103)


Facilities

Journals

SciLifeLab National facility since 2013.

61 publications

Year 2020

DOI Crossref
A sample preparation protocol for high throughput immunofluorescence of suspension cells
Backstrom A, Kugel L, Gnann C, ..., Lundberg E, Stadler C
J. Histochem. Cytochem. 68 (7) 473-489 [2020-06-20; online 2020-01-20]
Bioinformatics Compute and Storage [Service] Cell Profiling [Technology development]

Year 2019

PubMed DOI Crossref
The human secretome
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Translational Plasma Profiling [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]
DOI Crossref
Spatial proteomics: a powerful discovery tool for cell biology
Lundberg E, Borner GHH
Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-18]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats
Corman A, Jung B, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O
Cell Chem Biol 26 (2) 235-243.e5 [2019-02-00; online 2019-02-00]
Cell Profiling [Service] Chemical Biology Consortium Sweden (CBCS) [Service]

Year 2018

PubMed DOI Crossref
A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.
Dusart P, Fagerberg L, Perisic L, ..., Odeberg J, Butler LM
pii: 10.1038/s41598-018-32859-4 pmc: PMC6168570
Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]
Bioinformatics Compute and Storage [Service] Cell Profiling [Service]
DOI Crossref
Deep learning is combined with massive-scale citizen science to improve large-scale image classification
Sullivan DP, Winsnes CF, Åkesson L, ..., Szantner A, Lundberg E
Nat Biotechnol 36 (9) 820-828 [2018-08-20; online 2018-08-20]
BioImage Informatics [Collaborative] Cell Profiling [Collaborative]
PubMed DOI Crossref
Myopathy With SQSTM1 and TIA1 Variants: Clinical and Pathological Features.
Niu Z, Pontifex CS, Berini S, ..., Pfeffer G, Milone M
pmc: PMC5868303
Front Neurol 9 (-) 147 [2018-03-19; online 2018-03-19]
Cell Profiling [Service]
DOI Crossref
CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium
Mönnich M, Borgeskov L, Breslin L, ..., Larsen LA, Pedersen LB
Cell Rep 22 (10) 2584-2592 [2018-03-00; online 2018-03-00]
Advanced Light Microscopy (ALM) [Service] Cell Profiling [Collaborative]

Year 2017

PubMed DOI Crossref
Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells
Boström J, Sramkova Z, Salašová A, ..., Altun M, Andäng M
GEO: GSE104736
PLoS ONE 12 (12) e0188772 [2017-12-11; online 2017-12-11]
Cell Profiling [Collaborative]
PubMed DOI Crossref
Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS
Ly T, Whigham A, Clarke R, ..., Wadsworth P, Lamond AI
PRIDE: PXD007787
Elife 6 (-) - [2017-10-20; online 2017-10-20]
Cell Profiling [Collaborative]
PubMed DOI Crossref
A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E
pii: science.aal3321
Science 356 (6340) - [2017-05-26; online 2017-05-11]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T
pii: 1621161114 pmc: PMC5338371
Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Cell Profiling [Collaborative]
PubMed DOI Crossref
Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.
Skogs M, Stadler C, Schutten R, ..., Uhlén M, Lundberg E
J. Proteome Res. 16 (1) 147-155 [2017-01-06; online 2016-10-12]
Cell Profiling [Technology development]

Year 2016

PubMed DOI Crossref
The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw S, Iskar M, Ori A, ..., Bork P, Pepperkok R
pii: jcb.201601090 pmc: PMC5119934
J. Cell Biol. 215 (4) 543-558 [2016-11-21; online 2016-11-08]
Cell Profiling [Collaborative]
PubMed DOI Crossref
A proposal for validation of antibodies.
Uhlen M, Bandrowski A, Carr S, ..., Snyder M, Yamamoto T
pii: nmeth.3995
Nat. Methods 13 (10) 823-827 [2016-10-00; online 2016-09-07]
Cell Profiling [Collaborative]
PubMed DOI Crossref
Systems Proteomics View of the Endogenous Human Claudin Protein Family.
Liu F, Koval M, Ranganathan S, ..., Kelleher NL, Baker MS
pmc: PMC4777318 mid: NIHMS760862
J. Proteome Res. 15 (2) 339-359 [2016-02-05; online 2015-12-19]
Cell Profiling [Service]

Year 2015

PubMed DOI Crossref
The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.
Gustafsson Sheppard N, Jarl L, Mahadessian D, ..., Jain M, Nilsson R
pii: srep15029 pmc: PMC4602236
Sci Rep 5 (-) 15029 [2015-10-13; online 2015-10-13]
Cell Profiling
PubMed DOI Crossref
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.
Omenn GS, Lane L, Lundberg EK, ..., Nesvizhskii AI, Deutsch EW
pmc: PMC4755311 mid: NIHMS755250
J. Proteome Res. 14 (9) 3452-3460 [2015-09-04; online 2015-07-15]
Cell Profiling
PubMed DOI Crossref
Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.
Horvatovich P, Lundberg EK, Chen YJ, ..., Paik YK, Hancock WS
J. Proteome Res. 14 (9) 3415-3431 [2015-09-04; online 2015-06-16]
Cell Profiling
PubMed DOI Crossref
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.
O'Hurley G, Busch C, Fagerberg L, ..., Uhlén M, Pontén F
pii: PONE-D-15-13741 pmc: PMC4523174
PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development] Translational Plasma Profiling
PubMed DOI Crossref
Proteomics. Tissue-based map of the human proteome.
Uhlén M, Fagerberg L, Hallström BM, ..., Nielsen J, Pontén F
pii: 347/6220/1260419
Science 347 (6220) 1260419 [2015-01-23; online 2015-01-24]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Year 2014

PubMed DOI Crossref
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Kampf C, Mardinoglu A, Fagerberg L, ..., Nielsen J, Uhlen M
pii: fj.14-250555
FASEB J. 28 (7) 2901-2914 [2014-07-00; online 2014-03-22]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling
PubMed DOI Crossref
Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.
Edfors F, Boström T, Forsström B, ..., Mann M, Uhlen M
pii: M113.034140 pmc: PMC4047479
Mol. Cell Proteomics 13 (6) 1611-1624 [2014-06-00; online 2014-04-12]
Cell Profiling
PubMed DOI Crossref
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
Stadler C, Fagerberg L, Sivertsson Å, ..., Lundberg E, Uhlén M
J. Proteome Res. 13 (4) 2019-2027 [2014-04-04; online 2014-03-04]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.
Alm T, von Feilitzen K, Lundberg E, Sivertsson Å, Uhlén M
J. Proteome Res. 13 (3) 1669-1676 [2014-03-07; online 2014-02-19]
Cell Profiling
PubMed DOI Crossref
Molecular- and organelle-based predictive paradigm underlying recovery by left ventricular assist device support.
Liem DA, Nsair A, Setty SP, ..., Ping P, Deng MC
pii: CIRCHEARTFAILURE.113.000250 pmc: PMC4397259 mid: NIHMS557965
Circ Heart Fail 7 (2) 359-366 [2014-03-01; online 2014-03-20]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Antibody performance in western blot applications is context-dependent.
Algenäs C, Agaton C, Fagerberg L, ..., Ottosson Takanen J, Hober S
Biotechnol J 9 (3) 435-445 [2014-03-00; online 2014-01-10]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Fagerberg L, Hallström BM, Oksvold P, ..., Ponten F, Uhlén M
pii: M113.035600 pmc: PMC3916642
Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]
Autoimmunity Profiling [Technology development] Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling Translational Plasma Profiling [Technology development]
PubMed DOI Crossref
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.
Lane L, Bairoch A, Beavis RC, ..., Lundberg E, Omenn GS
pmc: PMC3928647 mid: NIHMS551794
J. Proteome Res. 13 (1) 15-20 [2014-01-03; online 2013-12-25]
Cell Profiling

Year 2013

PubMed DOI Crossref
Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).
Fagerberg L, Oksvold P, Skogs M, ..., von Feilitzen K, Uhlén M
J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling
PubMed DOI Crossref
Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.
Geiger T, Velic A, Macek B, ..., Cox J, Mann M
pii: M112.024919 pmc: PMC3675825
Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.
Rexhepaj E, Agnarsdóttir M, Bergman J, ..., Lundberg E, Ponten F
pii: PONE-D-12-33946 pmc: PMC3656869
PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.
Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E
pii: 1216436110 pmc: PMC3637701
Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]
Cell Profiling
PubMed DOI Crossref
Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.
Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E
pii: nmeth.2377
Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]
Cell Profiling
PubMed DOI Crossref
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.
Liu S, Im H, Bairoch A, ..., Beavis RC, Hancock WS
pmc: PMC4142220 mid: NIHMS431316
J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]
Cell Profiling
PubMed DOI Crossref
RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.
Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E
J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]
Cell Profiling

Year 2012

PubMed DOI Crossref
Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.
Li J, Newberg JY, Uhlén M, Lundberg E, Murphy RF
pii: PONE-D-12-11801 pmc: PMC3511558
PLoS ONE 7 (11) e50514 [2012-11-30; online 2012-11-30]
Cell Profiling
PubMed DOI Crossref
Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines.
Li J, Shariff A, Wiking M, ..., Rohde GK, Murphy RF
pii: PONE-D-12-11800 pmc: PMC3508979
PLoS ONE 7 (11) e50292 [2012-11-28; online 2012-11-28]
Cell Profiling
PubMed DOI Crossref
Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.
Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J
pii: gm387 pmc: PMC3580420
Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P
pii: 1471-2164-13-574 pmc: PMC3495644
BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.
Bock T, Moest H, Omasits U, ..., Frei K, Wollscheid B
J. Proteome Res. 11 (10) 4885-4893 [2012-10-05; online 2012-08-23]
Cell Profiling
PubMed DOI Crossref
A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.
Kampf C, Bergman J, Oksvold P, ..., Uhlén M, Ponten F
pii: 1741-7015-10-103 pmc: PMC3523031
BMC Med 10 (-) 103 [2012-09-12; online 2012-09-12]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy.
Stadler C, Hjelmare M, Neumann B, ..., Uhlén M, Lundberg E
pii: S1874-3919(12)00070-X
J Proteomics 75 (7) 2236-2251 [2012-04-03; online 2012-03-01]
Cell Profiling
PubMed DOI Crossref
Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.
Dengjel J, Høyer-Hansen M, Nielsen MO, ..., Jäättelä M, Andersen JS
pii: M111.014035 pmc: PMC3316729
Mol. Cell Proteomics 11 (3) M111.014035 [2012-03-00; online 2012-02-09]
Cell Profiling
PubMed DOI Crossref
Antibody-based protein profiling of the human chromosome 21.
Uhlén M, Oksvold P, Älgenäs C, ..., Kondo T, Sivertsson Å
pii: M111.013458 pmc: PMC3316724
Mol. Cell Proteomics 11 (3) M111.013458 [2012-03-00; online 2011-11-02]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.
Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M
pii: O111.009613 pmc: PMC3316735
Mol. Cell Proteomics 11 (3) O111.009613 [2012-03-00; online 2011-10-04]
Cell Profiling
PubMed DOI Crossref
Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.
Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI
pii: M111.013680 pmc: PMC3316725
Mol. Cell Proteomics 11 (3) M111.013680 [2012-03-00; online 2011-10-18]
Cell Profiling
PubMed DOI Crossref
Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.
Larance M, Kirkwood KJ, Xirodimas DP, ..., Uhlen M, Lamond AI
pii: M111.014407 pmc: PMC3316733
Mol. Cell Proteomics 11 (3) M111.014407 [2012-03-00; online 2011-11-01]
Cell Profiling

Year 2011

PubMed DOI Crossref
Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.
Hjelm B, Forsström B, Igel U, ..., Johansson C, Uhlén M
pmc: PMC3267947
Protein Sci. 20 (11) 1824-1835 [2011-11-00; online 2011-09-08]
Autoimmunity Profiling [Technology development] Cell Profiling Translational Plasma Profiling [Technology development]
PubMed DOI Crossref
Mapping the subcellular protein distribution in three human cell lines.
Fagerberg L, Stadler C, Skogs M, ..., Uhlén M, Lundberg E
J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-17]
Cell Profiling
PubMed DOI Crossref
SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.
Magnusson K, de Wit M, Brennan DJ, ..., Jirström K, Pontén F
pii: 00000478-201107000-00001
Am. J. Surg. Pathol. 35 (7) 937-948 [2011-07-00; online 2011-06-17]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.
Jakobsen L, Vanselow K, Skogs M, ..., Hyman AA, Andersen JS
pii: emboj201163 pmc: PMC3102290
EMBO J. 30 (8) 1520-1535 [2011-04-20; online 2011-03-15]
Cell Profiling

Year 2010

PubMed DOI Crossref
Defining the transcriptome and proteome in three functionally different human cell lines.
Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M
pii: msb2010106 pmc: PMC3018165 BioProject: PRJNA79633 SRA: SRP002338
Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Analysis of transcript and protein overlap in a human osteosarcoma cell line.
Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J
pii: 1471-2164-11-684 pmc: PMC3014981 BioProject: PRJNA79747 SRA: SRP003405
BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]
Cell Profiling NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Towards a knowledge-based Human Protein Atlas.
Uhlen M, Oksvold P, Fagerberg L, ..., Björling L, Ponten F
pii: nbt1210-1248
Nat. Biotechnol. 28 (12) 1248-1250 [2010-12-00; online 2010-12-09]
Autoimmunity Profiling [Technology development] Cell Profiling
PubMed DOI Crossref
Creation of an antibody-based subcellular protein atlas.
Lundberg E, Uhlén M
Proteomics 10 (22) 3984-3996 [2010-11-00; online 2010-07-22]
Cell Profiling
PubMed DOI Crossref
Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration.
Borsics T, Lundberg E, Geerts D, ..., Wester K, Bachmann AS
pii: CAS1570
Cancer Sci. 101 (7) 1624-1631 [2010-07-00; online 2010-04-24]
Cell Profiling
PubMed DOI Crossref
A single fixation protocol for proteome-wide immunofluorescence localization studies.
Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E
pii: S1874-3919(09)00310-8
J Proteomics 73 (6) 1067-1078 [2010-04-18; online 2009-11-10]
Cell Profiling
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