Emma Lundberg, Associate Professor
KTH Royal Institute of Technology

Research Interests

Our research is focused on spatial proteomics and cell biology. At the interface between bioimaging and proteomics are fundamental aspects of human cell biology systematically assessed at a single cell level using an antibody-based approach. The aim is to understand how human proteins are distributed in time and space, how variations and deviations in localization can contribute to cell type specificity as well as disease.

Compartmentalization of biological processes is a fundamental principle of eukaryotic cells that enables multiple processes to occur in parallel. The compartments are specialized for a particular cellular function and contain the molecules needed to fulfill it. Defects in compartment organization or protein mislocalization underlie the cause of many forms of human disease. Despite a great deal of research, basic questions about the spatial organization of many proteins and biological processes remain unanswered. Using computational image analysis we are also investigating variations of protein spatiotemporal expression patterns at the single cell level, in relation to the cell cycle or other deterministic factors.

A part of our work is the creation of the Cell Atlas, part of the Human Protein Atlas project, where the subcellular localization of all human proteins is being determined.

Through various measures we try to engage a wider community in our work. For example through a Citizen Science project called “Project Discovery” for classification of protein patterns in microscope images, integrated into the massively multiplayer online Sci-Fi game Eve Online with over 300.000 participants, and through the Kaggle Challenge “Human Protein Atlas Image Classification Challenge”.

Emma Lundberg is also Director of the Cell Profiling facility at SciLifeLab, enabling researchers to make use of the knowledge and resources of the Human Protein Atlas applied to their research projects.

Group members

Charlotte Stadler, Head of Cell Profiling national facility
Peter Thul, Lab manager Cell Atlas
Martin Hjelmare, Technology project manager
Ulrika Axelsson, Research engineer
Anna Bäckström, Research engineer
Anthony Cesnik, Postdoc (Stanford)
Jenny Fall, Lab technician
Christian Gnann, Research engineer
Diana Mahdessian, PhD-student
Anna Martinez Casals, Research engineer
Rutger Schutten, Research engineer
Wei Ouyang, Postdoc
Hao Xu, Researcher
Casper Winsnes, PhD-student
Lovisa Åkesson, PhD-student

Key publications

• Lundberg E and Borner G. Spatial Proteomics: A powerful discovery tool for cell biology. Nat Rev Mol Cell Biol. 2019 Jan 18.
• Sullivan D, Winsnes C, Åkesson L, Hjelmare M, Wiking M, Schutten R, Campbell L, Rhodes S, Leifsson H, Nordgren A, Smith K , Revaz B, players of EVE Online Project Discovery, Finnbogasson B, Szantner A, Lundberg E. Deep learning is combined with massive-scale citizen science to improve large-scale image classification. Nat Biotechnol. 2018 Oct;36(9):820-828
• Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E. A subcellular map of the human proteome. Science (2017)
• Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F.Tissue based map of the human proteome. Science (2015).
• Stadler, Rexhepaj, Singan, Murphy, Pepperkok, Uhlén, Simpson, Lundberg. Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.Nat Methods (2013).

External homepage

http://www.proteinatlas.org/cell

Contact

emma.lundberg@scilifelab.se