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Publications by Emma Käller Lundberg

Peer reviewed

Articles

[2]
S. Sariyar et al., "High-parametric protein maps reveal the spatial organization in early-developing human lung," Nature Communications, vol. 15, no. 1, pp. 9381, 2024.
[3]
M. R. King et al., "Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient," Cell, vol. 187, no. 8, pp. 24-1889, 2024.
[4]
A. Cesnik et al., "Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes," Annual Review of Biomedical Data Science, vol. 7, no. 1, pp. 369-389, 2024.
[6]
D. R. Dou et al., "Xist ribonucleoproteins promote female sex-biased autoimmunity," Cell, vol. 187, no. 3, pp. 16-733, 2024.
[8]
G. T. Johnson et al., "Building the next generation of virtual cells to understand cellular biology," Biophysical Journal, vol. 122, no. 18, pp. 3560-3569, 2023.
[9]
E. M. Quardokus et al., "Organ Mapping Antibody Panels : a community resource for standardized multiplexed tissue imaging," Nature Methods, vol. 20, no. 8, pp. 1174-1178, 2023.
[11]
G. Kustatscher et al., "An open invitation to the Understudied Proteins Initiative," Nature Biotechnology, vol. 40, no. 6, pp. 815-817, 2022.
[12]
T. Le et al., "Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition," Nature Methods, vol. 19, no. 10, pp. 1221-1229, 2022.
[13]
N. Bagheri et al., "Commentary The new era of quantitative cell imaging-challenges and opportunities," Molecular Cell, vol. 82, no. 2, pp. 241-247, 2022.
[14]
B. Andrews et al., "Imaging cell biology," Nature Cell Biology, vol. 24, no. 8, pp. 1180-1185, 2022.
[15]
K. E. Burnum-Johnson et al., "New Views of Old Proteins : Clarifying the Enigmatic Proteome," Molecular & Cellular Proteomics, vol. 21, no. 7, 2022.
[17]
R. D. Melani et al., "The Blood Proteoform Atlas : A reference map of proteoforms in human hematopoietic cells," Science, vol. 375, no. 6579, pp. 411-+, 2022.
[18]
J. R. Moffitt, E. Lundberg and H. Heyn, "The emerging landscape of spatial profiling technologies," Nature reviews genetics, vol. 23, no. 12, pp. 741-759, 2022.
[19]
G. Kustatscher et al., "Understudied proteins : opportunities and challenges for functional proteomics," Nature Methods, vol. 19, no. 7, pp. 774-779, 2022.
[20]
Y. Qin et al., "A multi-scale map of cell structure fusing protein images and interactions," Nature, vol. 600, no. 7889, pp. 536-+, 2021.
[21]
O. Rozenblatt-Rosen et al., "Building a high-quality Human Cell Atlas," Nature Biotechnology, vol. 39, no. 2, pp. 149-153, 2021.
[22]
E. Gómez-de-Mariscal et al., "DeepImageJ : A user-friendly environment to run deep learning models in ImageJ," Nature Methods, vol. 18, no. 10, pp. 1192-1195, 2021.
[24]
H. Pinkard et al., "Pycro-Manager : open-source software for customized and reproducible microscope control," Nature Methods, vol. 18, no. 3, pp. 226-+, 2021.
[25]
D. Mahdessian et al., "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics," Nature, vol. 590, no. 7847, 2021.
[26]
[27]
A. Bäckström et al., "A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface," Journal of Histochemistry and Cytochemistry, vol. 68, no. 7, pp. 473-489, 2020.
[28]
W. Ouyang et al., "Analysis of the Human Protein Atlas Image Classification competition (vol 16, pg 1254, 2019)," Nature Methods, vol. 17, no. 1, pp. 115-115, 2020.
[29]
W. Ouyang et al., "Analysis of the Human Protein Atlas Image Classification competition (vol 54, pg 2112, 2019)," Nature Methods, vol. 17, no. 2, pp. 241-241, 2020.
[30]
[32]
W. Ouyang et al., "ImJoy : an open-source computational platform for the deep learning era," Nature Methods, vol. 16, no. 12, pp. 1199-1200, 2019.
[33]
E. Lundberg and G. H. H. Borner, "Spatial proteomics : a powerful discovery tool for cell biology," Nature reviews. Molecular cell biology, vol. 20, no. 5, pp. 285-302, 2019.
[34]
M. Uhlén et al., "The human secretome," Science Signaling, vol. 12, no. 609, 2019.
[36]
D. P. Sullivan et al., "Deep learning is combined with massive-scale citizen science to improve large-scale image classification," Nature Biotechnology, vol. 36, no. 9, pp. 820-+, 2018.
[37]
D. Guala et al., "Experimental validation of predicted cancer genes using FRET," METHODS AND APPLICATIONS IN FLUORESCENCE, vol. 6, no. 3, 2018.
[39]
R. Aebersold et al., "How many human proteoforms are there?," Nature Chemical Biology, vol. 14, no. 3, pp. 206-214, 2018.
[40]
D. P. Sullivan and E. Lundberg, "Seeing More : A Future of Augmented Microscopy," Cell, vol. 173, no. 3, pp. 546-548, 2018.
[42]
J. Carreras-Puigvert et al., "A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family," Nature Communications, vol. 8, no. 1, 2017.
[43]
M. Uhlén et al., "A pathology atlas of the human cancer transcriptome," Science, vol. 357, no. 6352, pp. 660-+, 2017.
[44]
P. J. Thul et al., "A subcellular map of the human proteome," Science, vol. 356, no. 6340, 2017.
[45]
M. Skogs et al., "Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins," Journal of Proteome Research, vol. 16, no. 1, pp. 147-155, 2017.
[47]
G. S. Omenn et al., "Progress on the HUPO Draft Human Proteome : 2017 Metrics of the Human Proteome Project," Journal of Proteome Research, vol. 16, no. 12, pp. 4281-4287, 2017.
[49]
T. Alkasalias et al., "RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo," Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 8, pp. E1413-E1421, 2017.
[50]
A. Regev et al., "The Human Cell Atlas," eLIFE, vol. 6, 2017.
[51]
H. Clevers et al., "What Is Your Conceptual Definition of "Cell Type'' in the Context of a Mature Organism?," CELL SYSTEMS, vol. 4, no. 3, pp. 255-259, 2017.
[52]
F. Danielsson et al., "An image-based view of the microtubule proteome," Molecular Biology of the Cell, vol. 27, 2016.
[54]
M. Wiking et al., "Drafting the intermediate filament proteome," Molecular Biology of the Cell, vol. 27, 2016.
[55]
M. Wiking, M. Uhlén and E. Lundberg, "Drafting the mitochondrial proteome," Molecular Biology of the Cell, vol. 27, 2016.
[56]
F. Edfors et al., "Gene-specific correlation of RNA and protein levels in human cells and tissues," Molecular Systems Biology, vol. 12, no. 10, 2016.
[57]
T. Alm, E. Lundberg and M. Uhlén, "Introducing the Affinity Binder Knockdown Initiative-A public-private partnership for validation of affinity reagents," EuPA Open Proteomics, vol. 10, pp. 56-58, 2016.
[58]
A. Åkesson et al., "Large-scale spatial mapping of the nuclear human proteome.," Molecular Biology of the Cell, vol. 27, 2016.
[60]
C. F. Winsnes et al., "Multi-label prediction of subcellular localization in confocal images using deep neural networks," Molecular Biology of the Cell, vol. 27, no. 25, 2016.
[61]
[62]
D. Mahdessian et al., "Profiling the human cytoplasmic proteome.," Molecular Biology of the Cell, vol. 27, 2016.
[64]
[65]
P. Thul, R. Pepperkok and E. Lundberg, "Spatial Proteomic Profiling of the Golgi Apparatus by Indirect Immunofluorescent Microscopy.," Molecular Biology of the Cell, vol. 27, 2016.
[66]
D. Mahdessian et al., "Spatiotemporal variations of the human proteome associated to cell cycle progression," Molecular Biology of the Cell, vol. 27, 2016.
[67]
F. Liu et al., "Systems Proteomics View of the Endogenous Human Claudin Protein Family," Journal of Proteome Research, vol. 15, no. 2, pp. 339-359, 2016.
[68]
T. L. Alm, E. Lundberg and M. Uhlén, "The Affinity Binder Knockdown Initiative.," Molecular Biology of the Cell, vol. 27, 2016.
[69]
S. Scharaw et al., "The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR," Journal of Cell Biology, vol. 215, no. 4, pp. 543-558, 2016.
[70]
M. Fasano et al., "Towards a functional definition of the mitochondrial human proteome," EuPA Open Proteomics, vol. 10, pp. 24-27, 2016.
[71]
D. P. Sullivan, E. Lundberg and M. Uhlén, "Understanding cellular shape modulation and motility : the Actin associated human proteome," Molecular Biology of the Cell, vol. 27, 2016.
[72]
I. Amit et al., "Voices of biotech," Nature Biotechnology, vol. 34, no. 3, pp. 270-275, 2016.
[74]
[75]
M. Uhlén et al., "Tissue-based map of the human proteome," Science, vol. 347, no. 6220, pp. 1260419, 2015.
[76]
T. Alm et al., "A Chromosome-Centric Analysis of Antibodies Directed toward the Human Proteome Using Antibodypedia," Journal of Proteome Research, vol. 13, no. 3, pp. 1669-1676, 2014.
[77]
C. Älgenäs et al., "Antibody performance in western blot applications is context- dependent," Biotechnology Journal, vol. 9, no. 3, pp. 435-445, 2014.
[78]
F. Edfors et al., "Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins," Molecular & Cellular Proteomics, vol. 13, no. 6, pp. 1611-1624, 2014.
[79]
L. Lane et al., "Metrics for the Human Proteome Project 2013-2014 and Strategies for Finding Missing Proteins," Journal of Proteome Research, vol. 13, no. 1, pp. 15-20, 2014.
[80]
D. A. Liem et al., "Molecular- and Organelle-Based Predictive Paradigm Underlying Recovery by Left Ventricular Assist Device Support," Circulation Heart Failure, vol. 7, no. 2, pp. 359-366, 2014.
[81]
C. Stadler et al., "RNA- and Antibody-Based Profiling of the Human Proteome with Focus on Chromosome 19," Journal of Proteome Research, vol. 13, no. 4, pp. 2019-2027, 2014.
[82]
C. Kampf et al., "The human liver-specific proteome defined by transcriptomics and antibody-based profiling," The FASEB Journal, vol. 28, no. 7, pp. 2901-2914, 2014.
[83]
[85]
L. Fagerberg et al., "Contribution of antibody-based protein profiling to the human chromosome-centric proteome project (C-HPP)," Journal of Proteome Research, vol. 12, no. 6, pp. 2439-2448, 2013.
[87]
F. Danielsson et al., "Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 17, pp. 6853-6858, 2013.
[88]
F. Danielsson et al., "RNA Deep Sequencing as a Tool for Selection of Cell Lines for Systematic Subcellular Localization of All Human Proteins," Journal of Proteome Research, vol. 12, no. 1, pp. 231-239, 2013.
[91]
M. Uhlén et al., "Antibody-based Protein Profiling of the Human Chromosome 21," Molecular & Cellular Proteomics, vol. 11, no. 3, 2012.
[93]
M. Larance et al., "Characterization of MRFAP1 Turnover and Interactions Downstream of the NEDD8 Pathway," Molecular & Cellular Proteomics, vol. 11, no. 3, 2012.
[94]
B. Werne Solnestam et al., "Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs," BMC Genomics, vol. 13, no. 1, pp. 574, 2012.
[98]
[100]
[101]
B. Hjelm et al., "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies," Protein Science, vol. 20, no. 11, pp. 1824-1835, 2011.
[102]
L. Fagerberg et al., "Mapping the subcellular protein distribution in three human cell lines," Journal of Proteome Research, vol. 10, no. 8, pp. 3766-3777, 2011.
[104]
K. Magnusson et al., "SATB2 in Combination With Cytokeratin 20 Identifies Over 95% of all Colorectal Carcinomas," American Journal of Surgical Pathology, vol. 35, no. 7, pp. 937-948, 2011.
[105]
C. Stadler et al., "A single fixation protocol for proteome-wide immunofluorescence localization studies," Journal of Proteomics, vol. 73, no. 6, pp. 1067-1078, 2010.
[106]
D. Klevebring et al., "Analysis of transcript and protein overlap in a human osteosarcoma cell line," BMC Genomics, vol. 11, no. 1, pp. 684, 2010.
[107]
E. Lundberg and M. Uhlén, "Creation of an antibody-based subcellular protein atlas," Proteomics, vol. 10, no. 22, pp. 3984-3996, 2010.
[108]
E. Lundberg et al., "Defining the transcriptome and proteome in three functionally different human cell lines," Molecular Systems Biology, vol. 6, pp. 450, 2010.
[110]
J. Li et al., "Selection of affibody molecules to the ligand-binding site of the insulin-like growth factor-1 receptor," Biotechnology and applied biochemistry, vol. 55, pp. 99-109, 2010.
[112]
M. Uhlén et al., "Towards a knowledge-based Human Protein Atlas," Nature Biotechnology, vol. 28, no. 12, pp. 1248-1250, 2010.
[113]
F. Ponten et al., "A global view of protein expression in human cells, tissues, and organs," Molecular Systems Biology, vol. 5, 2009.
[115]
E. Lundberg, H. Brismar and T. Gräslund, "Selection and characterization of Affibody (R) ligands to the transcription factor c-Jun," Biotechnology and applied biochemistry, vol. 52, pp. 17-27, 2009.
[116]
S. Stromberg et al., "Selective Expression of Syntaxin-7 Protein in Benign Melanocytes and Malignant Melanoma," Journal of Proteome Research, vol. 8, no. 4, pp. 1639-1646, 2009.
[117]
L. Berglund et al., "A genecentric human protein atlas for expression profiles based on antibodies," Molecular & Cellular Proteomics, vol. 7, no. 10, pp. 2019-2027, 2008.
[118]
E. Vernet et al., "Affinity-based entrapment of the HER2 receptor in the endoplasmic reticulum using an affibody molecule," Journal of immunological methods, vol. 338, pp. 1-6, 2008.
[119]
[120]
L. Barbe et al., "Toward a confocal subcellular atlas of the human proteome," Molecular and cellular proteomics, vol. 7, no. 3, pp. 499-508, 2008.
[121]
E. Lundberg et al., "A novel method for reproducible fluorescent labeling of small amounts of antibodies on solid phase," JIM - Journal of Immunological Methods, vol. 322, no. 1-2, pp. 40-49, 2007.
[122]

Conference papers

[123]
J. Y. Newberg et al., "Automated analysis of human protein atlas immunofluorescence images," in Proceedings - 2009 IEEE International Symposium on Biomedical Imaging : From Nano to Macro, ISBI 2009, 2009, pp. 1023-1026.

Chapters in books

[124]
L. Jakobsen et al., "Centrosome Isolation and Analysis by Mass Spectrometry-Based Proteomics," in CILIA, PART B, : Academic Press, 2013, pp. 371-393.

Non-peer reviewed

Articles

[125]
D. M. Pacia et al., "Early AI Lifecycle Co-Reasoning : Ethics Through Integrated and Diverse Team Science," American Journal of Bioethics, vol. 24, no. 9, pp. 86-88, 2024.
[126]
Y. Zhang et al., "ISG15 modification of the Arp2/3 complex restricts pathogen spread," Molecular Biology of the Cell, vol. 34, no. 2, pp. 818-818, 2023.
[127]
K. Kuodyte et al., "The Golgi complex serves as a platform for the DNA damage response pathways," Molecular Biology of the Cell, vol. 34, no. 2, pp. 63-63, 2023.
[128]
K. Kuodyte et al., "The Golgi complex serves as a platform for the DNA damage response pathways," Molecular Biology of the Cell, vol. 34, no. 2, pp. 209-209, 2023.
[129]
C. Gnann, A. J. Cesnik and E. Lundberg, "Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics," Trends in cancer, vol. 7, no. 4, pp. 278-282, 2021.
[130]
E. Lundberg, "Dissecting the spatiotemporal subcellular distribution of the human proteome," European Journal of Human Genetics, vol. 27, pp. 764-764, 2019.
[131]
P. Anikeeva, E. Lundberg and X. Zhuang, "Voices in methods development," Nature Methods, vol. 16, no. 10, pp. 945-951, 2019.
[132]
P. J. Thul et al., "An image-based subcellular map of the human proteome.," Molecular Biology of the Cell, vol. 28, 2017.
[133]
P. Thul et al., "An image-based subcellular map of the human proteome.," Molecular Biology of the Cell, vol. 28, 2017.
[134]
P. Thul et al., "Exploring the Proteome of Multilocalizing Proteins," Molecular Biology of the Cell, vol. 28, 2017.
[135]
D. Mahdessian et al., "Spatiotemporal characterization of the human proteome.," Molecular Biology of the Cell, vol. 28, 2017.
[136]
M. Uhlen et al., "A proposal for validation of antibodies," Nature Methods, vol. 13, no. 10, pp. 823-+, 2016.
[137]
M. Wiking et al., "Drafting the intermediate filament proteome.," Molecular Biology of the Cell, vol. 27, 2016.
[140]
M. Skogs and E. Lundberg, "Proteins that assemble into Rods & Rings - subcellular protein complexes with unknown functions.," Molecular Biology of the Cell, vol. 26, 2015.
[141]
P. Horvatovich et al., "Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project," Journal of Proteome Research, vol. 14, no. 9, pp. 3415-3431, 2015.
[142]
T. L. Alm, E. Lundberg and M. Uhlén, "The Affinity Binder Knockdown Initiative," Molecular Biology of the Cell, vol. 26, 2015.
[144]
M. Wiking et al., "The Subcellular Protein Atlas," Molecular Biology of the Cell, vol. 25, 2014.
[146]
E. Lundberg and H. A. Svahn, "What determines specific cell functions?," Lab on a Chip, vol. 11, no. 12, pp. 2039-2041, 2011.
[147]
L. Jakobsen et al., "Functional proteomics of the human centrosome," New Biotechnology, vol. 27, pp. S82-S82, 2010.

Other

[149]
P. Thul et al., "A subcellular map of the human proteome," (Manuscript).
[151]
M. Wiking and E. K. Lundberg, "An image-based map of the human mitochondrial proteome," (Manuscript).
[159]
Latest sync with DiVA:
2024-12-13 00:01:55