Stefan Semrau
Associate professor
- Name
- Dr. S. Semrau
- Telephone
- +31 71 527 5475
- semrau@physics.leidenuniv.nl
- ORCID iD
- 0000-0002-4245-2246
We study cell-fate decision-making using embryonic stem cells as a model system. Stem cells integrate a large number of cues to direct their development into a great variety of cell types. Using single-cell transcriptomics and single-molecule microscopy in combination with machine learning and mathematical modeling we seek to unravel the dynamics of the decision making process and understand the interplay of internal factors (epigenetics, cell cycle, stochastic gene expression) and external factors (signaling molecules, cell-cell contacts, mechanical cues). We believe that the basic principles discovered through our research will be of great value for applications in regenerative medicine and the eradication of cancer stem cells.
Associate professor
- Science
- Leiden Instituut Onderzoek Natuurkunde
- LION - Biological & Soft Matter
- Jong M.A. de, Adegeest E., Bérenger-Currias N.M.L.P., Mircea M, Merks R.M.H. & Semrau S. (2023), A combination of convergent extension and differential adhesion explains the shapes of elongating gastruloids. bioRxiv. [working paper].
- Cao X., Mircea M., Yakala G.K., Hil F.E. van den, Brescia M., Mei H., Mummery C.L., Semrau S. & Orlova V.V. (2023), ETV2 upregulation marks the specification of early cardiomyocytes and endothelial cells during co-differentiation, Stem Cells 41(2): 140-152.
- Mircea M., Hochane M., Fan X., Chuva de Sousa Lopes S.M., Garlaschelli D. & Semrau S. (2022), Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations, Genome Biology 23(1): 18.
- Semrau S. (2022), Why isn't each cell its own cell type?, Frontiers in Cell and Developmental Biology 10: 971721.
- Kessler M.D., Damask A., O'Keeffe S., Banerjee N., Li D., Watanabe K., Marketta A., VanMeter M., Horowitz J., Tang J., Kosmicki J.A., Rajagopal V.M., Zou Y., Houvras Y., Ghosh A., Gilles C., Mbatchou J., White R.R., Verweij N., Bovijn J., Parikshak N.N., LeBlanc M.G., Jones M., Glass D.J., LottaL.A., Cantor M.N., Atwal G.S., Locke A.E., Ferreira M.A.R., Deering R., Paulding C., Schuldiner A.R., Thurston G., Ferrando A.A., Salerno W., Reid J.G., Overton J.D., Marchini J., Kang H.M., Baras A., Abecasis G.R., Jorgenson E. & Semrau S. (2022), Common and rare variant associations with clonal haematopoiesis phenotypes, Nature 612: 301-309.
- Bérenger-Currias N.M.L.P., Mircea M., Adegeest E., Berg P.R. van den, Feliksik M., Hochane M., Idema T., Tans S.J. & Semrau S. (2022), A gastruloid model of the interaction between embryonic and extra-embryonic cell types, Journal of Tissue Engineering and Regenerative Medicine 13: 1-18.
- Mircea M. & Semrau S. (2021), How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification, Biochemical Society Transactions 49(6): 2509-2525.
- Giacomelli E., Meraviglia V., Campostrini G., Cochrane A., Cao X., Helden R.W.J. van, Krotenberg G.A., Mircea M., Kostidis S., Davis R.P., Meer B.J. van, Jost C.R., Koster A.J., Mei H., Míguez D.G., Mulder A.A., Ledesma-Terrón. M., Pompilio G., Sala L., Salvatori D.C.F., Slieker R.C., Sommariva E., Vries A.A.F. de, Giera M., Semrau S., Tertoolen L.G.J., Orlova V.V., Bellin M. & Mummery C.L. (2020), Human-iPSC-derived cardiac stromal cells enhance maturation in 3D cardiac microtissues and reveal non-cardiomyocyte contributions to heart disease, Cell Stem Cell 26(6): 862-879.
- Hochane M., Berg P.R. van den, Fan X., Bérenger-Currias N.M.L.P., Adegeest E.E., Bialecka M., Nieveen M., Menschaart M., Chuva de Sousa Lopes S.M. & Semrau S. (2019), Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development, PLoS Biology 17(2): e3000152.
- Song Y.L., Berg P.R. van den, Markoulaki S., Soldner F., Dall'Agnese A., Henninger J.E., Drotar J., Rosenau N., Cohen M.A., Young R.A., Semrau S., Stelzer Y. & Jaenisch R. (2019), Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs, Molecular Cell 75(5): 905-920.
- Messemaker T.C., Leeuwen S.M. van, Berg P.R. van den, Jong A.E.J. 't, Palstra R., Hoeben R.C., Semrau S. & Mikkers H.M.M. (2018), Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot, Scientific Reports 8: 386.
- Semrau S., Goldman J.E., Soumillon M., Mikkelsen T.S., Jaenisch R. & Oudenaarden A. van (2017), Dynamics of lineage commitment revealed by single-cell transcriptions of differentiating embryonic stem cells, Nature Communications 8: 1096.
- Slavov N., Semrau S., Airoldi E., Budnik B. & Oudenaarden A. van (2015), Differential Stoichiometry among Core Ribosomal Proteins, Cell reports 13(5): 865-873.
- Gomes Fernandes M., Dries R., Roost M.S., Semrau S., De Melo Bernardo A., Davis Richard P., Ramakrishnan R., Szuhai K., Maas E., Umans L., Abon Escalona V., Salvatori D., Deforce D., Van Criekinge W., Huylebroeck D., Mummery C., Zwijsen A. & De Sousa Lopes S.M. (2015), BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells, Stem Cell Reports 6(1): 85-94.
- Semrau S. & Oudenaarden A. van (2015), Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools, Annual review of cell and developmental biology 31(1): 317-345.
- Semrau Stefan, Holtzer Laurent, Gonzalez-Gaitan Marcos & Schmidt Thomas (2011), Quantification of Biological Interactions with Particle Image Cross-Correlation Spectroscopy (PICCS), Biophysical Journal 100(7): 1810-1818.
- Semrau S. (29 October 2009), Membrane heterogeneity : from lipid domains to curvature effects (Dissertatie. Leiden Institute of Physics (LION), Faculty of Science, Leiden University) Casimir PhD Series no. 2009-11. Supervisor(s) and Co-supervisor(s): Schmidt T., Storm C.
- Semrau S., Idema T., Holtzer L., Schmidt T. & Storm C. (2008), Accurate determination of elastic parameters for multicomponent membranes, Physical Review Letters 100(8): 088101.
- Semrau S. & Schmidt T. (2007), Particle image correlation spectroscopy (PICS): retrieving nanometer-scale correlations from high-density single-molecule position data, Biophysical Journal 92(2): 613-621.