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Mathias Uhlén

Dr. Mathias Uhlén, Senior Professor of Microbiology

Mathias Uhlén.

KTH School of Engineering Sciences in Chemistry, Biotechnology and Health
Department of Protein Science
Division of Systems Biology
KTH Royal Institute of Technology (CBH School)
106 91 Stockholm, Sweden
Email: mathiasu@kth.se
Direct phone: +46 70 513 2101

CV (docx 463 kB)

Biography

Dr Uhlen received his PhD in chemistry at the Royal Institute of Technology (KTH), Stockholm, Sweden in 1984. After a post-doc period at the EMBL in Heidelberg, Germany, he became professor at KTH in 1988. His research has resulted in more than 800 peer-reviewed publications leading to more than 120,000 academic citations with an h-index of 147 (Google Scholar). His focus in science has been technology- and data-driven research, involving protein science, antibody engineering, AI-based systems biology and precision medicine. A list of selected scientific achievements are shown below.

Dr Uhlen has been the Director of the Human Protein Atlas program since the launch in 2003 and was the Founding Director the Science for Life Laboratory (SciLIfeLab) between 2010 and 2015. He is member of the Royal Swedish Academy of Engineering Science (IVA), the Royal Swedish Academy of Science (KVA), the National Academy of Engineering (NAE) in USA and the European Molecular Biology Organization (EMBO). He was the President of the European Federation of Biotechnology (EFB) from 2015 to 2019 and he was the Vice-President of the Royal Institute of Technology (KTH) from 1999 to 2001. He is the co-initiator of the annual KTH Innovation Award established in 2020 and the Science and SciLifeLab Prize for Young Scientists established in 2013. He is Honorary Doctor at Chalmers University, Sweden (2011) and Rouen University, France (2020).

Career

1979 M.Sc. in Chemical Engineering, Royal Institute of Technology (KTH) , Sweden

1984 PhD Royal Institute of Technology, Sweden

1985 – 86 Post-doc, EMBL , Heidelberg, Germany

1988 Professor in Microbiology, KTH, Sweden

1999 – 2001 Vice-President of University, external relations, KTH, Sweden

2003 – Director of the Human Protein Atlas (HPA)  program

2010 – 2015 Founding Director, Science for Life Laboratory (SciLifeLab)

2012 – 2020 Professor (20%), Danish Technical University (DTU) , Denmark

2019 – 2025 Guest professor (25%) at Karolinska Institutet

2019 – 2024 Member of the Board of Directors for the Swedish Research Council

2024 – Senior professor (25%), KTH, Stockholm, Sweden

Recognition

Bibliometry

(Statistics according to Google Scholar, January 2026)

  • Number of publications in total: 800

  • Number of total citations: 125,000 citations

  • Number of citations last year (2025): 11,300

  • H-index: 147

See full publication lists on Google Scholar , Web of Science  or ORCID .

Relevant links

Entrepeneurial achievements (selected)

More than 70 international patent applications. Founders of 20 start-up companies and former member of several Board of Directors, including public companies such as Bure (Sweden), Biotage (Sweden), Alligator Bioscience (Sweden), Novozymes (Denmark), Nordiag (Norway) and Amersham (UK). Vice-President KTH (1999–2001) responsible for external relations.

Key scientific achievements

1. Next generation DNA sequencing

The concept of real time sequencing by synthesis is today used in all major “next generation sequencing” systems and it has led to hundreds of thousand publications in the last decade. This concept involves the detecting of the incorporation of nucleotides in real-time during synthesis by a DNA polymerase on a solid support. The concept of “sequencing by synthesis”, first described in 1993 (1), depends on several important underlying technologies, including attachment of DNA to solid supports (2,3), the use of engineered polymerases for synthesis of a complementary nucleotide and the detection of the incorporated nucleotide in real-time to generate sequencing (4). This platform was successfully used in the first massive parallel sequencing instrument (454) launched in 2005 (5) and this scientific break-through was later followed by alternative technology platforms, often based on fluorescent detection, as reviewed by Uhlen and Quake (6). The principle of “sequencing by synthesis with real-time detection” is today used in all major next generation DNA sequencing systems.

Key selected references:

  1. Nyrén, Pettersson and Uhlen (1993) Anal. Biochem. 208: 171-175

  2. Ståhl et al (1988) Nucleic Acids Res. 16, 3025-3038

  3. Uhlen (1991) Nature. 340 (6236): 733–734

  4. Ronaghi, Uhlen and Nyren (1998) Science 281: 363- 365

  5. Margulies et al (2005) Nature 437 (7057): 376-380

  6. Uhlen and Quake (2023) Trends Biotechnol. 41 (12): 1565-1572

2. The Human Protein Atlas

The Human Protein Atlas program started in 2003 with the aim to contribute to the holistic understanding of all the proteins encoded from our DNA. The objective of the program has been to map all the human proteins in cells, tissues, organs and blood using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and AI-based systems biology. During the first 20 years, the open access resource has launched several million web pages with 10 million high-resolution microscope images, to allow individual researchers both in industry and academia to explore the proteome space across the human body. The portal is one of the most visited medical databases in the world with most visitors from Europe, North America and Asia. The program, chaired by Uhlen, is built on several scientific achievements as outlined below:
Generation and use of antibodies targeting human cDNA-encoded proteins.A new concept was developed to generate antibodies to the gene products of cDNA expressed from the human genome. A pilot project was published in 2003, in which the genes encoded from human chromosome 21 was analysed (1).

The Human Protein Atlas. The Human Protein Atlas (www.proteinatlas.org) was launched in 2005 with the aim to contribute to the holistic understanding of all the human proteome. The objective of the program (2) was to map all the human proteins in cells, tissues, organs and blood using integration of various omics technologies. The open access resource has launched new versions annually and it contains several million web pages with more than 10 million high-resolution microscope images.

The Tissue Atlas. This resource, launched in 2014, focuses on the expression profiles in human tissues of genes both on the mRNA and protein level (3). The protein expression data from 45 normal human tissue types is derived from antibody-based protein profiling using conventional and multiplex immunohistochemistry. All underlying images of immunohistochemistry-stained normal tissues are available together with knowledge-based annotation of protein expression levels. The Tissue Atlas paper published in Science in 2015 is one of the most cited scientific publications in life science in the last decade.

The Subcellular Atlas.This resource, launched in 2017, provides insights into the expression and spatiotemporal distribution of proteins in human cells (4). The subcellular localization of the protein, based on “in-house” generated data, has been classified into one or more of 49 different organelles and subcellular structures.

The Pathology Atlas. This resource, launched in 2017, contains information based on mRNA expression data from 21 cancer types as well as protein data from 20 cancers analysed by IHC and 11 cancer types analysed using MS (5). This data is displayed together with millions of in-house generated immunohistochemically stained tissue sections images.

The Blood (Immune Cell) Atlas.This resource, launched in 2019, contains single cell information on genome-wide RNA expression profiles of human protein-coding genes covering various B- and T-cells, monocytes, granulocytes and dendritic cells (6). The transcriptomics analysis covers 18 cell types isolated with cell sorting and includes classification based on specificity, distribution and expression cluster across all immune cells

The Human Secretome. A comprehensive analysis of proteins predicted to be secreted in human cells was done, providing information about the final localization in the human body, including the proteins actively secreted to peripheral blood (7).

The Brain Atlas.This resource, launched in 2020, provides comprehensive spatial profiling of the brain, including overview of protein expression in the mammalian brain based on integration of data from human, pig and mouse (8). Transcriptomics data combined with affinity-based protein in situ localization down to single cell detail is available in this brain-centric sub atlas of the Human Protein Atlas.

The Single Cell Atlas.The Single Cell resource of the open access Human Protein Atlas, launched in 2021 (9), presents comprehensive data on gene expression across various human tissues and cell types. The resource provides insights into mRNA and protein expression patterns.

The Pan-Disease Blood Atlas.Several analytical platforms have been used to analyse the blood protein profiles in healthy individuals as well as patients with various diseases. The concept has been used to generate an open access Human Disease Blood Atlas with the objective to serve as a resource for researchers interesting in precision and translational medicine (10).

Key selected references:

  1. Agaton et al (2003) Mol. Cell. Proteomics doi: 10.1074/mcp.M300022-MCP200

  2. Uhlen et al (2010) Nature Biotechnology doi: 10.1038/nbt1210-1248.

  3. Uhlen et al (2015) Science, doi:10.1126/science.1260419.

  4. Thul et al (2017) Science doi: 10.1126/science.aal3321

  5. Uhlen et al (2017) Science, doi:10.1126/science.aan2507

  6. Uhlen et al (2019) Science, doi: 10.1126/science.aax9198

  7. Uhlen et al (2019) Science Signaling, doi: 10.1126/scisignal.aaz0274

  8. Sjöstedt et al (2020) Science, doi:10.1126/science.aay5947

  9. Karlsson et al (2021) Science Advances, doi: 10.1126/sciadv.abh2169

  10. Alvez et al (2025) Science, doi: 10.1126/science.adx2678.

3. Affinity-based protein engineering

Afffinity-based systems was developed to use specific binding of proteins (affinity) in combination with protein engineering. This principle has led to many successful applications widely used in the life science community, including engineered protein A (1) and protein G (2) for purification of antibodies, affinity tags for purification of recombinant fusion proteins(5,6), clinically validated protein scaffold binders, such as Affibodies (8) and alkali-stable matrix for purification of antibodies, such as MabSelect SuRe. This latter platform has been used for the manufacturing of the majority of therapeutic antibodies on the market today. In the following, some key selected achievments are listed:
Cloning of the genes for protein A and protein G. Both protein A (1) and protein G (2) are important products for affinity purification of antibodies, extensively used in academia and industry.

The use of biotin-streptavidin systems for molecular biology applications. The use of magnetic beads with streptavidin for capture of biotinylated DNA was first described in 1988 (3) and this concept has since led to multiple applications in life science (4).

The concept of affinity tags for purification of proteins. This broad concept was first described in 1986 (5) and allowed the use of tags for affinity purification of recombinant proteins. This principle has led to many thousands of published applications in the life science community (6).

The concept of in vivo half time extension using an albumin-binding domain.A concept to extend the half-life of biopharmaceuticals in human patients was developed, exemplified by the generation of fusion proteins containing the albumin-binding domain from streptococcal protein G (7)

Affibody and the concept of scaffold binders. This novel concept first described in 1997 (15) depends on the use of phage display and selection of high affinity binders to mimic the feature of target-specific antibodies. The concept has since been used in hundreds of publications both for medical and biotech applications (8).

The concept of alkali-stable protein ligands.  An alkali-stable ligand, later commercialised as MabSelect SuRe,was developed aimed for industrial applications to achieve “cleaning-in-place” (9). This affinity system concept has been used for the manufacturing of the majority of commercially available therapeutic antibodies on the market

Epitope mapping of antibodies. Several new approaches to characterize the binding sites of antibodies have been developed using both epitope mapping by peptide display (10) and comprehensive 2-D microarrays of peptides (11).

International working group for antibody validation (IWGAV).This group with members from Europe, Asia and USA, chaired by Uhlen, formulated five principles for validation of antibodies to be used in research (12).

Key selected references:

  1. Uhlen et al (1984) J Biol Chem. PMID: 6319407

  2. Olsson et al (1988) EMBO J doi: 10.1002/j.1460-2075.1986.tb04398.x.

  3. Ståhl et al (1988) Nucleic Acids Res. doi: 10.1093/nar/16.7.3025.

  4. Uhlen (1991) Nature. doi: 10.1038/340733a0

  5. Löwenadler et al (1986) EMBO J. doi: 10.1002/j.1460-2075.1986.tb04509.x

  6. Dahlson Leitao et al (2025) J Biotech doi: 10.1016/j.jbiotec.2025.07.018

  7. Nygren et al (1998) J. Mol. Recogn. doi: 10.1002/jmr.300010204.

  8. Nord et al (1997) Nature Biotechn. doi:10.1038/nbt0897-772

  9. Gulich et al (2000) J. Biotech. doi: 10.1016/s0168-1656(00)00259-5.

  10. Sjöberg et al (2012) N Biotechn. doi: 10.1016/j.nbt.2011.11.009.

  11. Rockberg et al (2008) Nature Methods doi: 10.1038/nmeth.1272

  12. Uhlen et al (2016) Nature Methods doi: 10.1038/nmeth.3995

4. The national infrastructure SciLifeLab

Dr Uhlen was the Founding Director of the Science for Life Laboratory initiated with support from the Swedish government in 2010. This national infrastructure, originally in Stockholm and Uppsala, was launched to allow technology- and data-driven research in life science. The number of researchers has grown to more than thousand at the Stockholm site, with collaborations across all universities in Sweden Many thousands of projects are executed annually, spanning many research fields, such as genomics, proteomics, structural biology, planetary biology, data-driven life science, drug development and precision medicine. Many projects in data-drive life science are supported by the non-profit Knut and Alice Wallenberg Foundation.

Key references:

  1. Travis (2010) Science 328: 805