Spatial Proteomics

N-terminal proteoforms may engage in different protein complexes.

Bogaert A, Fijalkowska D, Staes A, ..., Calderwood MA, Gevaert K

Life Sci. Alliance 6 (8) - [2023-08-00; online 2023-06-14]

Human resident liver myeloid cells protect against metabolic stress in obesity.

Barreby E, Strunz B, Nock S, ..., Chen P, Aouadi M

Nat Metab 5 (7) 1188-1203 [2023-07-00; online 2023-07-06]

The emerging landscape of spatial profiling technologies.

Moffitt JR, Lundberg E, Heyn H

Nat. Rev. Genet. 23 (12) 741-759 [2022-12-00; online 2022-07-20]

Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases.

Nicoś M, Harbers L, Patrucco E, ..., Ambrogio C, Crosetto N

JTO Clin Res Rep 3 (12) 100435 [2022-12-00; online 2022-11-11]

FRET-FISH probes chromatin compaction at individual genomic loci in single cells.

Mota A, Berezicki S, Wernersson E, ..., Crosetto N, Bienko M

Nat Commun 13 (1) 6680 [2022-11-05; online 2022-11-05]

Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes.

Pillon NJ, Smith JAB, Alm PS, ..., Krook A, Zierath JR

Sci Adv 8 (36) eabo3192 [2022-09-09; online 2022-09-07]

Deep Visual Proteomics defines single-cell identity and heterogeneity.

Mund A, Coscia F, Kriston A, ..., Horvath P, Mann M

Nat. Biotechnol. 40 (8) 1231-1240 [2022-08-00; online 2022-05-19]

The immune cell atlas of human neuroblastoma.

Verhoeven BM, Mei S, Olsen TK, ..., Johnsen JI, Baryawno N

Cell Reports Medicine 3 (6) 100657 [2022-06-21; online 2022-06-09]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Spatial Proteomics [Service]

DOI Crossref

Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing

Kaimal JM, Tampere M, Le TH, ..., Östling P, Stadler C

- - (-) - [2022-03-29; online 2022-03-29]

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M

Sci Data 9 (1) 47 [2022-02-10; online 2022-02-10]

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

DOI Crossref

Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M

- - (-) - [2022-02-02; online 2022-02-02]

A multi-scale map of cell structure fusing protein images and interactions.

Qin Y, Huttlin EL, Winsnes CF, ..., Lundberg E, Ideker T

Nature - (-) - [2021-11-24; online 2021-11-24]

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.

Hickey JW, Neumann EK, Radtke AJ, ..., Kelleher NL, Saka SK

Nat. Methods - (-) - [2021-11-22; online 2021-11-22]

A roadmap for the Human Developmental Cell Atlas.

Haniffa M, Taylor D, Linnarsson S, ..., Webb S, Human Cell Atlas Developmental Biological Network

Nature 597 (7875) 196-205 [2021-09-00; online 2021-09-08]

In Situ Sequencing (ISS) [Collaborative] Spatial Proteomics

Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Lundberg E, Funke J, Uhlmann V, ..., Carpenter A, Coehlo LP

Cell Syst 12 (5) 384-387 [2021-05-19; online 2021-05-21]

Subcellular proteomics.

Christopher JA, Stadler C, Martin CE, ..., Emili A, Lilley KS

Nat Rev Methods Primers 1 (1) - [2021-04-29; online 2021-04-29]

Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics.

Gnann C, Cesnik AJ, Lundberg E

Trends Cancer 7 (4) 278-282 [2021-04-00; online 2021-01-10]

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.

Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E

Nature 590 (7847) 649-654 [2021-02-00; online 2021-02-24]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics [Collaborative]

Building a high-quality Human Cell Atlas.

Rozenblatt-Rosen O, Shin JW, Rood JE, ..., Regev A, Heyn H

Nat. Biotechnol. 39 (2) 149-153 [2021-02-00; online 2021-01-28]

A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface.

Bäckström A, Kugel L, Gnann C, ..., Lundberg E, Stadler C

J. Histochem. Cytochem. 68 (7) 473-489 [2020-07-00; online 2020-06-20]

Affinity Proteomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Spatial Proteomics [Collaborative]

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]

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]

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 2019-01-20]

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]

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]

Chemical Biology Consortium Sweden (CBCS) [Service] Spatial Proteomics [Service]

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

Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]

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 [2018-10-00; online 2018-10-01]

BioImage Informatics [Collaborative] Spatial Proteomics [Collaborative]

Myopathy With SQSTM1 and TIA1 Variants: Clinical and Pathological Features.

Niu Z, Pontifex CS, Berini S, ..., Pfeffer G, Milone M

Front Neurol 9 (-) 147 [2018-03-19; online 2018-03-19]

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 [2018-03-06; online 2018-03-08]

Integrated Microscopy Technologies Stockholm [Service] Spatial Proteomics [Collaborative]

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

Boström J, Sramkova Z, Salašová A, ..., Altun M, Andäng M

PLoS ONE 12 (12) e0188772 [2017-12-11; online 2017-12-11]

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS.

Ly T, Whigham A, Clarke R, ..., Wadsworth P, Lamond AI

Elife 6 (-) - [2017-10-20; online 2017-10-20]

A subcellular map of the human proteome.

Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E

Science 356 (6340) - [2017-05-26; online 2017-05-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Spatial Proteomics [Collaborative]

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

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] Spatial Proteomics [Collaborative]

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]

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

Scharaw S, Iskar M, Ori A, ..., Bork P, Pepperkok R

J. Cell Biol. 215 (4) 543-558 [2016-11-21; online 2016-11-08]

A proposal for validation of antibodies.

Uhlen M, Bandrowski A, Carr S, ..., Snyder M, Yamamoto T

Nat. Methods 13 (10) 823-827 [2016-10-00; online 2016-09-05]

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Liu F, Koval M, Ranganathan S, ..., Kelleher NL, Baker MS

J. Proteome Res. 15 (2) 339-359 [2016-02-05; online 2016-01-12]

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Gustafsson Sheppard N, Jarl L, Mahadessian D, ..., Jain M, Nilsson R

Sci Rep 5 (-) 15029 [2015-10-13; online 2015-10-13]

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 2015-07-23]

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

J. Proteome Res. 14 (9) 3452-3460 [2015-09-04; online 2015-07-15]

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

PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]

Affinity Proteomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Proteomics. Tissue-based map of the human proteome.

Uhlén M, Fagerberg L, Hallström BM, ..., Nielsen J, Pontén F

Science 347 (6220) 1260419 [2015-01-23; online 2015-01-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

The human liver-specific proteome defined by transcriptomics and antibody-based profiling.

Kampf C, Mardinoglu A, Fagerberg L, ..., Nielsen J, Uhlen M

FASEB J. 28 (7) 2901-2914 [2014-07-00; online 2014-03-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.

Edfors F, Boström T, Forsström B, ..., Mann M, Uhlen M

Mol. Cell Proteomics 13 (6) 1611-1624 [2014-06-00; online 2014-04-12]

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]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

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]

Molecular- and organelle-based predictive paradigm underlying recovery by left ventricular assist device support.

Liem DA, Nsair A, Setty SP, ..., Ping P, Deng MC

Circ Heart Fail 7 (2) 359-366 [2014-03-01; online 2014-03-20]

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]

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

Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.

Lane L, Bairoch A, Beavis RC, ..., Lundberg E, Omenn GS

J. Proteome Res. 13 (1) 15-20 [2014-01-03; online 2013-12-25]

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]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.

Geiger T, Velic A, Macek B, ..., Cox J, Mann M

Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]

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

PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]

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

Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E

Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]

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]

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

J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]

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

PLoS ONE 7 (11) e50514 [2012-11-30; online 2012-11-30]

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

PLoS ONE 7 (11) e50292 [2012-11-28; online 2012-11-28]

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.

Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J

Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.

Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P

BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

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]

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

BMC Med 10 (-) 103 [2012-09-12; online 2012-09-12]

Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy.

Stadler C, Hjelmare M, Neumann B, ..., Uhlén M, Lundberg E

J Proteomics 75 (7) 2236-2251 [2012-04-03; online 2012-03-01]

Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.

Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.013680 [2012-03-00; online 2011-10-18]

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

Mol. Cell Proteomics 11 (3) M111.014035 [2012-03-00; online 2012-02-06]

Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.

Larance M, Kirkwood KJ, Xirodimas DP, ..., Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.014407 [2012-03-00; online 2011-10-29]

Antibody-based protein profiling of the human chromosome 21.

Uhlén M, Oksvold P, Älgenäs C, ..., Kondo T, Sivertsson Å

Mol. Cell Proteomics 11 (3) M111.013458 [2012-03-00; online 2011-11-02]

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

Mol. Cell Proteomics 11 (3) O111.009613 [2012-03-00; online 2011-10-04]

Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.

Hjelm B, Forsström B, Igel U, ..., Johansson C, Uhlén M

Protein Sci. 20 (11) 1824-1835 [2011-11-00; online 2011-09-08]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] Spatial Proteomics

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]

SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.

Magnusson K, de Wit M, Brennan DJ, ..., Jirström K, Pontén F

Am. J. Surg. Pathol. 35 (7) 937-948 [2011-07-00; online 2011-06-17]

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.

Jakobsen L, Vanselow K, Skogs M, ..., Hyman AA, Andersen JS

EMBO J. 30 (8) 1520-1535 [2011-04-20; online 2011-03-15]

Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M

Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics

Towards a knowledge-based Human Protein Atlas.

Uhlen M, Oksvold P, Fagerberg L, ..., Björling L, Ponten F

Nat. Biotechnol. 28 (12) 1248-1250 [2010-12-00; online 2010-12-09]

Creation of an antibody-based subcellular protein atlas.

Lundberg E, Uhlén M

Proteomics 10 (22) 3984-3996 [2010-11-00; online 2010-07-22]

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

Cancer Sci. 101 (7) 1624-1631 [2010-07-00; online 2010-03-19]

A single fixation protocol for proteome-wide immunofluorescence localization studies.

Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E

J Proteomics 73 (6) 1067-1078 [2010-04-18; online 2009-11-10]