Lundberg E

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Family name Lundberg
Given name Emma
Initials E
ORCID

ORCID 0000-0001-7034-0850
Affiliations Department of Protein Science, Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden.

50 publications

PubMed DOI Crossref
Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics.
Schaffer LV, Hu M, Qian G, ..., Lundberg E, Ideker T
Nature 646 (8086) E16 [2025-10-00; online 2025-10-03]
PubMed DOI Crossref
Multimodal cell maps as a foundation for structural and functional genomics.
Schaffer LV, Hu M, Qian G, ..., Lundberg E, Ideker T
Nature 642 (8066) 222-231 [2025-06-00; online 2025-04-09]
PubMed DOI Crossref
Cell shapes decode molecular phenotypes in image-based spatial proteomics.
Le T, Leineweber WD, Viana MP, ..., Rafelski SM, Lundberg E
bioRxiv - (-) - [2025-05-16; online 2025-05-16]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Streamlining Multiplexed Tissue Image Analysis with PIPΣX: An Integrated Automated Pipeline for Image Processing and EXploration for Diverse Tissue Types.
Mardamshina M, Navarro FB, Casals AM, ..., Wählby C, Lundberg E
bioRxiv - (-) - [2025-05-09; online 2025-05-09]
DOI Crossref
Multiplexed Deep Visual Proteomics Unveils Spatial Heterogeneity and Rare Endocrine States in Human Adult Pancreatic Islets
Mardamshina M, Dorka N, Thielert M, ..., Mann M, Lundberg E
- - (-) - [2025-04-27; online 2025-04-27]
DOI Crossref
A Morpho-Proteomic Atlas of Mitosis at Sub-Minute Resolution
Migh E, Miczán V, Post F, ..., Mann M, Horvath P
- - (-) - [2025-04-10; online 2025-04-10]
PubMed DOI Crossref
Enabling global image data sharing in the life sciences.
Bajcsy P, Bhattiprolu S, Börner K, ..., Taylor A, Keppler A
Nat. Methods 22 (4) 672-676 [2025-04-00; online 2025-03-28]
PubMed DOI Crossref
Flexible and robust cell type annotation for highly multiplexed tissue images.
Sun H, Yu S, Casals AM, ..., Lundberg E, Murphy RF
bioRxiv - (-) - [2024-12-17; online 2024-12-17]
PubMed DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung.
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]
DOI Crossref
Dissecting autonomous enzymatic variability in single cells
Gnann C, Sigaeva A, Le T, ..., Axelsson U, Lundberg E
- - (-) - [2024-10-04; online 2024-10-04]
PubMed DOI Crossref
Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.
Lee H, Langseth CM, Salas SM, ..., Grillo M, Nilsson M
Development 151 (16) - [2024-08-15; online 2024-08-29]
PubMed DOI Crossref
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.
Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M
Nat. Methods 21 (7) 1245-1256 [2024-07-00; online 2024-06-06]
Magda Bienko SciLifeLab Fellow
DOI Crossref
Spatial Dynamics of the Developing Human Heart
Lázár E, Mauron R, Andrusivová Ž, ..., Adameyko I, Lundeberg J
- - (-) - [2024-03-14; online 2024-03-14]
DOI Crossref
A high-resolution spatial map of cilia-associated proteins based on characterization of the human fallopian tube-specific proteome
Lindskog C, Norradin FH, Digre A, ..., Hansen J, Uhlén M
- - (-) - [2024-02-09; online 2024-02-09]
DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
- - (-) - [2024-01-25; online 2024-01-25]
PubMed DOI Crossref
Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.
Jain Y, Godwin LL, Joshi S, ..., Lundberg E, Börner K
Nat Commun 14 (1) 4656 [2023-08-03; online 2023-08-03]
PubMed DOI Crossref
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.
Quardokus EM, Saunders DC, McDonough E, ..., Börner K, Radtke AJ
Nat. Methods 20 (8) 1174-1178 [2023-08-00; online 2023-07-19]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat. Cell Biol. 25 (2) 351-365 [2023-02-00; online 2023-01-16]
DOI Crossref
ISG15-modification of the Arp2/3 complex restricts pathogen spread
Zhang Y, Ripley B, Ouyang W, ..., Guerra S, Radoshevich L
- - (-) - [2022-12-27; online 2022-12-27]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
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]
DOI Crossref
Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers
King MR, Lin AZ, Ruff KM, ..., Lundberg E, Pappu RV
- - (-) - [2022-11-05; online 2022-11-05]
DDLS Fellow Wei Ouyang
DOI Crossref
Spatiotemporal dynamics of DNA repair proteins between the Golgi and nucleus maintain genomic stability
Galea G, Kuodyte K, Khan MM, ..., Lundberg E, Pepperkok R
- - (-) - [2022-10-17; online 2022-10-17]
PubMed DOI Crossref
Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.
Le T, Winsnes CF, Axelsson U, ..., Ouyang W, Lundberg E
Nat. Methods 19 (10) 1221-1229 [2022-10-00; online 2022-09-29]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
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]
PubMed DOI Crossref
Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E
Nature 608 (7924) E32 [2022-08-00; online 2022-08-06]
Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow
PubMed DOI Crossref
Understudied proteins: opportunities and challenges for functional proteomics.
Kustatscher G, Collins T, Gingras AC, ..., Ralser M, Rappsilber J
Nat. Methods 19 (7) 774-779 [2022-07-00; online 2022-05-10]
PubMed DOI Crossref
An open invitation to the Understudied Proteins Initiative.
Kustatscher G, Collins T, Gingras AC, ..., Ralser M, Rappsilber J
Nat. Biotechnol. 40 (6) 815-817 [2022-06-00; online 2022-05-10]
PubMed DOI Crossref
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 19 (3) 284-295 [2022-03-00; online 2021-11-22]
DOI Crossref
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M
- - (-) - [2022-02-02; online 2022-02-02]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.
Melani RD, Gerbasi VR, Anderson LC, ..., Levitsky J, Kelleher NL
Science (New York, N.Y.) 375 (6579) 411-418 [2022-01-28; online 2022-01-27]
DOI Crossref
Developmental origins of cell heterogeneity in the human lung
Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C
- - (-) - [2022-01-12; online 2022-01-12]
PubMed DOI Crossref
A multi-scale map of cell structure fusing protein images and interactions.
Qin Y, Huttlin EL, Winsnes CF, ..., Lundberg E, Ideker T
Nature 600 (7889) 536-542 [2021-12-00; online 2021-11-24]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ.
Gómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, ..., Muñoz-Barrutia A, Sage D
Nat. Methods 18 (10) 1192-1195 [2021-10-00; online 2021-09-30]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Pycro-Manager: open-source software for customized and reproducible microscope control.
Pinkard H, Stuurman N, Ivanov IE, ..., Mehta SB, Waller L
Nat. Methods 18 (3) 226-228 [2021-03-00; online 2021-03-07]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
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]
Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow
PubMed DOI Crossref
Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle.
Danielsson F, Mahdessian D, Axelsson U, ..., Thul PJ, Lundberg E
Proteomics 20 (23) e1900361 [2020-12-00; online 2020-08-26]
PubMed DOI Crossref
A high-stringency blueprint of the human proteome.
Adhikari S, Nice EC, Deutsch EW, ..., Aebersold R, Baker MS
Nat Commun 11 (1) 5301 [2020-10-16; online 2020-10-16]
PubMed DOI Crossref
Author Correction: Analysis of the Human Protein Atlas Image Classification competition.
Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E
Nat. Methods 17 (9) 948 [2020-09-00; online 2020-08-08]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder.
Stenström L, Mahdessian D, Gnann C, ..., Thul PJ, Lundberg E
Mol Syst Biol 16 (8) e9469 [2020-08-00; online 2020-08-04]
DDLS Fellow Wei Ouyang
DOI Crossref
Mapping cell structure across scales by fusing protein images and interactions
Qin Y, Winsnes CF, Huttlin EL, ..., Lundberg E, Ideker T
- - (-) - [2020-06-22; online 2020-06-22]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.
Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E
Nat. Methods 17 (2) 241 [2020-02-00; online 2020-01-24]
DDLS Fellow Wei Ouyang
DOI Crossref
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder
Stenström L, Mahdessian D, Gnann C, ..., Thul PJ, Lundberg E
- - (-) - [2020-01-30; online 2020-01-30]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.
Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E
Nat. Methods 17 (1) 115 [2020-01-00; online 2019-12-12]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Analysis of the Human Protein Atlas Image Classification competition.
Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E
Nat. Methods 16 (12) 1254-1261 [2019-12-00; online 2019-11-28]
DDLS Fellow Wei Ouyang
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]
Adil Mardinoglu DDLS Fellow Fredrik Edfors SciLifeLab Fellow
DOI Crossref
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
Gómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, ..., Muñoz-Barrutia A, Sage D
- - (-) - [2019-10-16; online 2019-10-16]
DDLS Fellow Wei Ouyang
PubMed 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 2019-01-20]
PubMed DOI Crossref
A pathology atlas of the human cancer transcriptome.
Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F
Science (New York, N.Y.) 357 (6352) eaan2507 [2017-08-18; online 2017-08-19]
Adil Mardinoglu Affiliated researcher DDLS Fellow Fredrik Edfors Muhammad Arif SciLifeLab Fellow
PubMed DOI Crossref
A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E
Science (New York, N.Y.) 356 (6340) eaal3321 [2017-05-26; online 2017-05-11]
Adil Mardinoglu Affiliated researcher SciLifeLab Fellow
PubMed DOI Crossref
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]
SciLifeLab Data Centre
Publications 9.5.1