Emma Lundberg

Emma Lundberg

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Emma Lundberg

Emma Lundberg

Publications by authors named "Emma Lundberg"

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Spatial proteomics: a powerful discovery tool for cell biology.

Nat Rev Mol Cell Biol 2019 May;20(5):285-302

Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany.

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http://www.nature.com/articles/s41580-018-0094-y
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http://dx.doi.org/10.1038/s41580-018-0094-yDOI Listing
May 2019

Deep learning is combined with massive-scale citizen science to improve large-scale image classification.

Nat Biotechnol 2018 10 20;36(9):820-828. Epub 2018 Aug 20.

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nbt.4225DOI Listing
October 2018

Experimental validation of predicted cancer genes using FRET.

Methods Appl Fluoresc 2018 Apr 25;6(3):035007. Epub 2018 Apr 25.

Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.

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http://dx.doi.org/10.1088/2050-6120/aab932DOI Listing
April 2018

Seeing More: A Future of Augmented Microscopy.

Cell 2018 04;173(3):546-548

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, 171 21, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.04.003DOI Listing
April 2018

GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles.

Cell Syst 2018 Feb 7;6(2):230-244.e1. Epub 2018 Feb 7.

School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840522PMC
February 2018

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

J Proteome Res 2017 12 9;16(12):4281-4287. Epub 2017 Oct 9.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.7b00375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872831PMC
December 2017

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.

J Proteome Res 2017 01 26;16(1):147-155. Epub 2016 Oct 26.

Science for Life Laboratory, Royal Institute of Technology , SE-114 28 Stockholm, Sweden.

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http://dx.doi.org/10.1021/acs.jproteome.6b00821DOI Listing
January 2017

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

J Proteome Res 2016 11 20;15(11):3951-3960. Epub 2016 Sep 20.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129622PMC
November 2016

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

J Cell Biol 2016 Nov 8;215(4):543-558. Epub 2016 Nov 8.

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany

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http://dx.doi.org/10.1083/jcb.201601090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119934PMC
November 2016

A proposal for validation of antibodies.

Nat Methods 2016 10 5;13(10):823-7. Epub 2016 Sep 5.

Biofluid Biomarker Center, Niigata University, Niigata, Japan.

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http://dx.doi.org/10.1038/nmeth.3995DOI Listing
October 2016

Gene-specific correlation of RNA and protein levels in human cells and tissues.

Mol Syst Biol 2016 Oct 20;12(10):883. Epub 2016 Oct 20.

Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081484PMC
http://dx.doi.org/10.15252/msb.20167144DOI Listing
October 2016

Towards a functional definition of the mitochondrial human proteome.

EuPA Open Proteom 2016 Mar 7;10:24-27. Epub 2016 Jan 7.

Santa Lucia IRCCS Foundation, I-00143 Rome, Italy.

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http://dx.doi.org/10.1016/j.euprot.2016.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988588PMC
March 2016

Introducing the Affinity Binder Knockdown Initiative⿿A public⿿private partnership for validation of affinity reagents.

EuPA Open Proteom 2016 Mar 7;10:56-58. Epub 2016 Jan 7.

Royal Institute of Technology (KTH), Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1016/j.euprot.2016.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988587PMC
March 2016

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

J Proteome Res 2016 Feb 12;15(2):339-59. Epub 2016 Jan 12.

Department of Chemistry, Department of Molecular Biosciences, and Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777318PMC
February 2016

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

J Proteome Res 2015 Sep 30;14(9):3452-60. Epub 2015 Jul 30.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755311PMC
September 2015

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

FASEB J 2014 Jul 19;28(7):2901-14. Epub 2014 Mar 19.

Science for Life Laboratory and Department of Proteomics, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden

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http://dx.doi.org/10.1096/fj.14-250555DOI Listing
July 2014

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

Mol Cell Proteomics 2014 Jun 10;13(6):1611-24. Epub 2014 Apr 10.

From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden; ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden;

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http://dx.doi.org/10.1074/mcp.M113.034140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047479PMC
June 2014

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

Genome Med 2012 18;4(11):86. Epub 2012 Nov 18.

KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.

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http://dx.doi.org/10.1186/gm387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580420PMC
May 2014

RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.

J Proteome Res 2014 Apr 12;13(4):2019-27. Epub 2014 Mar 12.

Science for Life Laboratory, KTH - Royal Institute of Technology , SE-171 21 Stockholm, Sweden.

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http://dx.doi.org/10.1021/pr401156gDOI Listing
April 2014

Antibody performance in western blot applications is context-dependent.

Biotechnol J 2014 Mar 29;9(3):435-45. Epub 2014 Jan 29.

Division of Proteomics, School of Biotechnology, Albanova University Center, KTH - Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1002/biot.201300341DOI Listing
March 2014

A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.

J Proteome Res 2014 Mar 17;13(3):1669-76. Epub 2014 Feb 17.

Science for Life Laboratory, KTH-Royal Institute of Technology , SE-171 21 Stockholm, Sweden.

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http://dx.doi.org/10.1021/pr4011525DOI Listing
March 2014

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

J Proteome Res 2014 Jan 23;13(1):15-20. Epub 2013 Dec 23.

SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1021/pr401144xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928647PMC
January 2014

Centrosome isolation and analysis by mass spectrometry-based proteomics.

Methods Enzymol 2013 ;525:371-93

Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

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http://dx.doi.org/10.1016/B978-0-12-397944-5.00018-3DOI Listing
September 2013

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

Mol Cell Proteomics 2013 Jun 22;12(6):1709-22. Epub 2013 Feb 22.

Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1074/mcp.M112.024919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675825PMC
June 2013

Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.

PLoS One 2012 30;7(11):e50514. Epub 2012 Nov 30.

Center for Bioimage Informatics and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050514PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511558PMC
May 2013

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

Nat Methods 2013 Apr 24;10(4):315-23. Epub 2013 Feb 24.

KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nmeth.2377DOI Listing
April 2013

RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.

J Proteome Res 2013 Jan 20;12(1):299-307. Epub 2012 Dec 20.

Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden.

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http://dx.doi.org/10.1021/pr3009308DOI Listing
January 2013

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

BMC Genomics 2012 Oct 30;13:574. Epub 2012 Oct 30.

KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495644PMC
October 2012

A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.

BMC Med 2012 Sep 12;10:103. Epub 2012 Sep 12.

Department of Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala University, Dag Hammarskjölds väg 20, Uppsala, 751 85 Sweden.

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http://dx.doi.org/10.1186/1741-7015-10-103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523031PMC
September 2012

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

J Proteomics 2012 Apr 15;75(7):2236-51. Epub 2012 Feb 15.

Science for Life Laboratory, Royal Institute of Technology, Stockholm, SE-171 65, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S187439191200070
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http://dx.doi.org/10.1016/j.jprot.2012.01.030DOI Listing
April 2012

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

Mol Cell Proteomics 2012 Mar 16;11(3):M111.013680. Epub 2011 Oct 16.

Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH United Kingdom.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M111.013680
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http://dx.doi.org/10.1074/mcp.M111.013680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316725PMC
March 2012

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

Mol Cell Proteomics 2012 Mar 29;11(3):M111.014407. Epub 2011 Oct 29.

Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.

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http://dx.doi.org/10.1074/mcp.M111.014407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316733PMC
March 2012

Antibody-based protein profiling of the human chromosome 21.

Mol Cell Proteomics 2012 Mar 31;11(3):M111.013458. Epub 2011 Oct 31.

Science for Life Laboratory, Royal Institute of Technology, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1074/mcp.M111.013458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316724PMC
March 2012

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

Protein Sci 2011 Nov 12;20(11):1824-35. Epub 2011 Oct 12.

Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, 10691 Stockholm, Sweden.

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http://dx.doi.org/10.1002/pro.716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267947PMC
November 2011

Mapping the subcellular protein distribution in three human cell lines.

J Proteome Res 2011 Aug 29;10(8):3766-77. Epub 2011 Jun 29.

School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, SE-106 91, Sweden.

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http://dx.doi.org/10.1021/pr200379aDOI Listing
August 2011

What determines specific cell functions?

Lab Chip 2011 Jun 8;11(12):2039-41. Epub 2011 Mar 8.

Science for Life Laboratory and Albanova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden.

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http://dx.doi.org/10.1039/c1lc90018hDOI Listing
June 2011

Selection and characterisation of affibody molecules inhibiting the interaction between Ras and Raf in vitro.

N Biotechnol 2010 Dec 30;27(6):766-73. Epub 2010 Jul 30.

Division of Molecular Biotechnology, Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.nbt.2010.07.016DOI Listing
December 2010

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

BMC Genomics 2010 Dec 2;11:684. Epub 2010 Dec 2.

Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, SE-171 65 Solna, Sweden.

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http://dx.doi.org/10.1186/1471-2164-11-684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014981PMC
December 2010

Creation of an antibody-based subcellular protein atlas.

Proteomics 2010 Nov;10(22):3984-96

School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden.

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http://dx.doi.org/10.1002/pmic.201000125DOI Listing
November 2010

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

J Proteomics 2010 Apr 5;73(6):1067-78. Epub 2009 Nov 5.

School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jprot.2009.10.012DOI Listing
April 2010

Selection of affibody molecules to the ligand-binding site of the insulin-like growth factor-1 receptor.

Biotechnol Appl Biochem 2010 Feb 25;55(2):99-109. Epub 2010 Feb 25.

Department of Molecular Biotechnology, Royal Institute of Technology, 106 91 Stockholm, Sweden.

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http://doi.wiley.com/10.1042/BA20090226
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http://dx.doi.org/10.1042/BA20090226DOI Listing
February 2010

Affibody-mediated retention of the epidermal growth factor receptor in the secretory compartments leads to inhibition of phosphorylation in the kinase domain.

N Biotechnol 2009 Sep;25(6):417-23

Department of Molecular Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, 10691 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.nbt.2009.02.001DOI Listing
September 2009

Selection and characterization of Affibody ligands to the transcription factor c-Jun.

Biotechnol Appl Biochem 2009 Jan;52(Pt 1):17-27

School of Biotechnology, Albanova University Center, Kungliga Tekniska Högskolan, Stockholm, Sweden.

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http://dx.doi.org/10.1042/BA20070178DOI Listing
January 2009

Automated Analysis of Human Protein Atlas Immunofluorescence Images.

Proc IEEE Int Symp Biomed Imaging 2009 ;5193229:1023-1026

Center for Bioimage Informatics and Dept. of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1109/ISBI.2009.5193229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901900PMC
January 2009

The correlation between cellular size and protein expression levels--normalization for global protein profiling.

J Proteomics 2008 Oct 5;71(4):448-60. Epub 2008 Jul 5.

School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jprot.2008.06.014DOI Listing
October 2008

Affinity-based entrapment of the HER2 receptor in the endoplasmic reticulum using an affibody molecule.

J Immunol Methods 2008 Sep 29;338(1-2):1-6. Epub 2008 Jul 29.

Department of Molecular Biotechnology, Royal Institute of Technology, Albanova University Center, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S002217590800207
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http://dx.doi.org/10.1016/j.jim.2008.06.005DOI Listing
September 2008

Toward a confocal subcellular atlas of the human proteome.

Mol Cell Proteomics 2008 Mar 19;7(3):499-508. Epub 2007 Nov 19.

Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M700325-MCP2
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http://dx.doi.org/10.1074/mcp.M700325-MCP200DOI Listing
March 2008

A novel method for reproducible fluorescent labeling of small amounts of antibodies on solid phase.

J Immunol Methods 2007 Apr 28;322(1-2):40-9. Epub 2007 Feb 28.

Department of Biotechnology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S002217590700044
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http://dx.doi.org/10.1016/j.jim.2007.01.023DOI Listing
April 2007

Site-specifically conjugated anti-HER2 Affibody molecules as one-step reagents for target expression analyses on cells and xenograft samples.

J Immunol Methods 2007 Jan 21;319(1-2):53-63. Epub 2006 Nov 21.

Department of Biotechnology, Albanova University Center, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jim.2006.10.013DOI Listing
January 2007