Publications – University of Copenhagen

StemPhys > Research > Publications




  1. A. Samadi, H. Klingberg, L. Jauffred, A. Kjaer, P.M. Bendix, L.B. Oddershede.
    Platinum nanoparticles: a non-toxic, effective and thermally stable alternative plasmonic material for cancer therapy and bioengineering.
    Nanoscale, accepted (2018).

  2. T. Stangner, T. Dahlberg, P. Svenmarker, J. Zakrisson, K. Wiklund, L.B. Oddershede, M. Andersson.
    Cooke-Triplet tweezers: more compact, robust, and efficient optical tweezers.
    Optics Letters vol. 43, p. 1990-1993, doi: 10.1364/OL.43.001990 (2018).

  3. A. Bahadori, G. Moreno-Pescador, L.B. Oddershede, P.M. Bendix.
    Remotely controlled fusion of selected vesicles and living cells: a key issue review.
    Reports on Progress in Physics, 81 p. 032602, doi: 10.1088/issn.0034-4885 (2018).

  4. E. A. Ober & F. P. Lemaigre.
    Development of the liver: insights into organ and tissue morphogenesis.
    Journal of Hepatology, doi: 10.1016/j.jhep.2018.01.005 (2018).


  1. A. Grapin-Botton & P. Serup. 
    Parsing the Pancreas. 
    The New England Journal of Medicine, 376(9), 886-888, doi: 10.1056/NEJMcibr1616217 (2017).

  2. K. Norregaard, R. Metzler, C.M. Ritter, K. Berg-Sorensen, L.B. Oddershede.
    Manipulation and motion of organelles and single molecules in living cells.
    Chemical Reviews, 117 (5), pp 4342–4375, DOI: 10.1021/acs.chemrev.6b00638 (2017).

  3. W.B. Hamilton, J.M. Brickman.
    Surveillance for secure differentiation.  
    I: Cell stem cell, Vol. 20, Nr. 1, 05.01.2017, s. 3-5, DOI: 10.1016/j.stem.2016.12.011 (2017).

  4. K.G.V. Anderson, W.B. Hamilton, F.V. Roske, A. Azad, T.E. Knudsen, M.A. Canham, L.M. Forrester, J.M. Brickman.
    Insulin fine-tunes self-renewal pathways governing naive pluripotency and extra-embryonic endoderm.
    Nature Cell Biology, 19, DOI:10.1038/ncb3617 (2017).

  5. K.R. Rosholm, N. Leijnse, A. Mantsiuo, V. Tkach, S.L. Pedersen, V.F. Wirth, L.B. Oddershede, K.J. Jensen, N.S. Hatzakis, P.M. Bendix, A. Callan-Jones, D. Stamou.
    Membrane curvature regulates ligand-specific membrane sorting of GPCRs in living cells.
    Nature Chemical Biology, DOI:10.1038/nchembio.2372 (2017).

  6. H. List Larsen, L. Martín-Coll, A.V. Nielsen, C.V.E. Wright, A. Trusina, Y.H.Kim, A. Grapin-Botton.
    Stochastic priming and spatial cues orchestrate heterogeneous clonal contribution to mouse pancreas organogenesis.
    Nature Communications, 19, DOI:10.1038/s41467-017-00258-4 (2017).

  7. L.A. Lonowski, A.R. Yoshiki Narimatsu, C.E. Delay, Z. Yang, F. Niola, K. Duda, E.A. Ober, H. Clausen, H.H. Wandall, S.H. Hansen, E.P. Bennett, M. Frödin.
    Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis.
    Nature Protocols, 12(3), 581-603, DOI:10.1038/nprot.2016.165 (2017).

  8. S. Boye, M. Perera Pérez, J. Martin Gonzalez, S.M.C. Morgani; M.H. Jensen, K. Sneppen, J.M. Brickman; A. Trusina.
    Four simple rules that are sufficient to generate the mammalian blastocyst.
    I.PLOS Biology, Bind 15, Nr. 7, e2000737, s. 1-30 (2017).

  9. L. Jauffred, R. Munk-Vejborg, K.S. Korolev, S. Brown, L.B. Oddershede.
    Chirality in microbial biofilms is mediated by close interactions between the cell surface and the substratum.
    The ISME Journal, Nature Publishing Group, 11, 1688–1701, DOI:10.1038/ismej.2017.19 (2017).

  10. R. Rasmussen, M.H. Jensen, M. L. Heltberg.
    Chaotic Dynamics Mediate Brain State Transitions, Driven by Changes in Extracellular Ion Concentrations.
    Cell Systems, 5 (6), doi: 10.1016/j.cels.2017.11.011 (2017).

  11. M. B. K. Petersen, A. Azad, C. Ingvorsen, K. Hess, M. Hansson, A. Grapin-Botton, C. Honore. 
    Single-Cell Gene Expression Analysis of a Human ESC Model of Pancreatic Endocrine Development Reveals Different Paths to b-Cell Differentiation
    Stem Cell Reports, 9(4), 1246-1261, doi:10.1016/j.stemcr.2017.08.009 (2017).

  12. A. Samadi, P.M. Bendix, L.B. Oddershede.

    Optical manipulation of individual strongly absorbing platinmum nanoparticles.
    Nanoscale, Vol. 9, 18449. DOI:10.1039/c7nr07374g (2017).

  13. S. Dahl-Jensen & A. Grapin-Botton. 
    The physics of organoids: a biophysical approach to understanding organogenesis. 
    Development, 144, 946-951, doi:10.1242/dev.143693 (2017).
  14. A. Bahadori, L.B. Oddershede, P.M. Bendix.
    Hot-nanoparticle-mediated fusion of selected cells.
    Nano Research, vol. 10, p. 2034-2045, DOI:10.1007/s12274-016-1392-3 (2017).

  15. H. L. Larsen & A. Grapin-Botton. 
    The molecular and morphogenetic basis of pancreas organogenesis

    Seminars in Cell & Developmental Biology, 66, 51-68, doi: 10.1016/j.semcdb.2017.01.005 (2017).

  16. A.-K. V. West, L. Wullkopf, A. Christensen, N. Leijnse, J.M. Tarp, J. Mathiesen, J.T. Erler, L.B. Oddershede.
    Dynamics of cancerous tissue correlates with invasiveness.
    Scientific Reports, Nature Publishing Group, DOI: 10.1038/srep43800 (2017).

  17. O. Schlesinger, Y. Chemla, M. Heltberg, E. Ozer, R. Marshall, V. Noireaux, M. H. Jensen, L. Alfonta.
    Tuning of Recombinant Protein Expression in Escherichia coli by Manipulating Transcription, Translation Initiation Rates, and Incorporation of Noncanonical Amino Acids.
    ACS Systhetic Biology, 6 (6), DOI: 10.1021/acssynbio.7b00019 (2017).

  18. S. Wang, S. R. Miller, E.A. Ober, K.C. Sadler.
    Making it new again: Insight into liver development, regeneration, and disease from zebrafish research.
    Current topics in developmental Biology, 124, 161-195, DOI: 10.1016/bs.ctdb.2016.11.012 (2017).

  19. T. Holst-Hansen, E.Abad, A. Muntasell, M. López-Botet, M.H. Jensen, A. Trusina, J. Garcia-Ojalvo.
    Impact of Zygosity on Bimodal Phenotype Distributions.
    Biophysical Journal, 113 (1), doi: 10.1016/j.bpj.2017.05.010 (2017).

  20. J.M. Brickman & P. Serup.
    Properties of embryoid bodies.

    I: Developmental Biology, Vol. 6, Nr. 2, DOI: 10.1002/wdev.259 (2017).

  21. Y. Chemla, M. Friedman, M. Heltberg, A. Bakhrat, E. Nagar, R. Schwarz, M. H. Jensen, L. Alfonta. Expanding the genetic code of a phtoautotrophic organism. Biochemistry, 56 (16), DOI:  10.1021/acs.biochem.7b00131 (2017).

  22. R. Portero Migueles, L. Shaw, N.P. Rodrigues, G. May, K. Henseleit, K.G.V. Anderson, H. Goker, Hakan, C.M. Jones, M.F.T.R. de Bruijn, J.M. Brickman, T. Enver.
    Transcriptional Regulation of Hhex in Hematopoiesis and Hematopoietic Stem Cell Ontogeny.
    I: Developmental Biology, Bind 424, Nr. 2, s. 236-245 (2017).

  23. K. Norregaard, J.T. Jørgensen, M. Simón, F. Melander, L.K. Kristensen, P.M. Bendix, T.L. Andresen, L.B. Oddershede, A. Kjaer.
    F-FDG PET/CT-based early treatment response evaluation of nanoparticle-assisted photothermal cancer therapy.
    PLoS One, Vol 12 (5), DOI:10.1371/journal.pone.0177997 (2017).

  24. M. L. Heltberg, S. Kristhna, M.H. Jensen.
    Time Correlations in Mode Hopping of Coupled Oscillators.
    Journal of Statistical Physics, 167 (3-4), doi: 10.1007/s10955-017-1750-x (2017).

Published proceedings and book contributions:


  1. J. Tranekjaer Joergensen, K. Norregaard, P. Tian, P.M. Bendix, A. Kjaer, L.B. Oddershede.
    Single Particle and PET-based platform for identifying optimal plasmonic nano-heaters for photothermal cancer therapy.
    Scientific Reports, vol. 6 p. 30076-(1-10) (2016).
  3. Y.F. Barooji, A. Rorvig-Lund, S. Semsey, S.N.S. Reihani, P.M. Bendix.
    Dynamics of membrane nanotubes coated with I-BAR.
    Scientific Reports, vol. 6 p. 30054--(1-12) (2016).
  5. A. Bahadori, A.R. Lund, S. Semsey, L.B. Oddershede, P.M. Bendix.
    Controlled cellular fusion using optically trapped plasmonic nano-heaters.
    Proceedings of SPIE, vol. 9922 p. 1-10 (2016).
  7. C.M. Ritter, J.M. Brickman, L.B. Oddershede.
    Optical quantification of forces at play during stem cell differentiation.
    Proceedings of SPIE, vol. 9764 p. 97640J-(1-9) (2016).
  8. S.B. Dahl-Jensen, M. Figueiredo-Larsen, A. Grapin-Botton & K. Sneppen.
    Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas,
    Phys. Biol. 13 016007, DOI: 10.1088/1478-3975/13/1/016007 (2016).

  9. A. Bahadori, L.B. Oddershede, P.M. Bendix.
    Hot-nanoparticle-mediated fusion of selected cells.
    Nano Research.
    DOI: 10.1007/s12274-016-1392-3 (2016)

  10. M.J.Obersriebnig, E.M.H.Pallesen, K.Sneppen, A. Trusina, G. Thon.
    Nucleation and spreading of a heterochromatic domain in fission yeast.
    Nature Communications, Vol. 7, 11518 (2016).
    Doi: 10.1038/ncomms11518

  11. Raphaël B. Di Roberto, B. Chang, A. Trusina.
    Evolution of a G. protein-coupled receptor response by mutations in regulatory network interactions.
    Peisajovich, Sergio G. Nature Communications, Vol 7, 12344, 04.08.2016.
    Doi: 10.1038/ncomms12344. (2016)

  12. R.S. Illingworth, J.J. Hölzenspies, F.V. Roske, W.A. Bickmore, J.M. Brickman.
    Polycomb enables primitive endoderm lineage priming in embryonic stem cells.
    Elife, October 10, 5. pii: e14926. (2016)
    DOI: 10.7554/eLife.14926

  13. S. Vedel, H. Nunns, A. Košmrlj, S. Semsey, A. Trusina.
    Asymmetric Damage Segregation Consitutes an Emergent Population-Level Stress Response.
    Cell Systems. (13.07.2016).
    DOI: 10.1016/j.cels.2016.06.008

  14. M.L. Heltberg, R. Kellogg, S. Krishna, S. Tay, M.H. Jensen.
    Noise-induced NP-kB Mode Hopping Enables Temporal Gene Multiplexing.
    Cell Systems, 532-539, (21.12. 2016)
    DOI: 10.1016/j.cels.2016.11.014

  15. J.Martin Gonzalez, S.M. Morgani, R.A. Bone, K. Bonderup, S. Abelchian, C. Brakebusch, J.M. Brickman.
    Embryonic Stem Cell Culture Conditions Support Distinct States Associated with Different Developmental Stages and Potency.
    Stem Cell Reports, 7 (2): 177:91. (09.08.2016)
    DOI: 10.1016/j.stemcr.2016.07.009

  16. C. Berclaz, A. Schmidt-Christensen, D. Szlag, J. Extermann, L.Hansen, A. Bouwens, M. Viliger, J. Goulley, F. Schuit, A. Grapin-Botton, T. Lasser, D. Holmberg.
    Longitudinal three-dimensional visualization of autoimmune diabetes by functional optical coherence imaging.
    Diabetologia, 59 (3): 550-9, (03.2016)
    DOI: 10.1007/s00125-015-3819-x

  17. J. Tranekjaer Joergensen, K. Norregaard, P. Tian, P.M. Bendix, A. Kjaer, L.B. Oddershede.
    Single Particle and Pet-based platform for identifying optimal plasmonic nano-heaters forphotothermal cancer thearapy.
    Scientific Reports, Vol. 6 p. 30076-(1-10). (2016).
    DOI: 10.1038/srep30076

  18. Anne Grapin-Botton
    Three-dimensional pancreas organogenesis models.
    Diabetes Obes Metab, Issue Supplement 1:33-40. Review. (18.09.2016)
    DOI: 10.1111/dom.12720

  19. C.Berclaz, D. Szlag, D. Nguyen, J. Extermann, A. Bouwens, P.J. Marchand, J. Nilsson, A. Schmidt-Christensen, D. Holmberg, A. Grapin.Botton, T. Lasser.
    Label-free fast 3D coherent imaging reveals pancreatic islet micro-vascularization and dynamic blood flow.
    Biomed Opt Express. 7 (11): 4569-4580. (17.10.2016)
    DOI: 10.1364/BOE.7.004569

  20. A. E. Moelgaard, I. Zettler, J.H. Dammeyer, S. Lehman, M.H.Jensen. J. Mathiesen.
    Measure of Node Similarity in Multilayer Networks.
    PloS One, e0146096, 14.06.2016.
    DOI: 10.1371/journal.pone.0157436

  21. P. Tian, K. Lindorff-Larsen, W. Boomsma, M. H. Jensen, J. Mathiesen.
    A Montecarlo study of the early steps of functional amyloid formation.
    PloS One, e0146096. (08.01.2016).
    DOI: 10.1371/journal.pone.0146096

  22. M. Rothová, J. J. Hölzenspies, A. Livigni, S.N. Villegas, J. M. Brickman.
    Differentiation of Mouse Embryonic Stem Cells into Ventral Foregut Precursors.
    Curr. Protoc. Stem. Cell Biol. , 3; 36: 1G. 3.1.-12. Review. PMID. (03.02.2016)
    DOI: 10.1002/9780470151808.sc01g03s36

Published proceedings and book contributions:


  1. A. Grapin-Botton, P.A. Seymour & G. Gradwohl.
    Pairing-up SOX to kick-start beta cell genesis.
    Diabetologia, Vol. 58, No. 5, 05.2015, p. 859-861,
    DOI: (2015)
  2. A. Kosmrlj, P. Cordsen, A. Kyrsting, D.E. Otzen, L.B. Oddershede and M.H. Jensen.
    A monomer-trimer model supports intermittent glucagon fibril growth. 
    Scientific Reports 5, 9005 (2015) 
    DOI: 10.1038/srep09005
  3. A. Rørvig-Lund, A. Bahadori, S. Semsey, P.M. Bendix, L.B. Oddershede.
    Vesicle Fusion Triggered by Optically Heated Gold Nanoparticles.
    Nano Letters, vol. 15 p. 4183-4188 (2015). 
    DOI: 10.1021/acs.nanolett.5b01366
  4. A.F. Laing, S. Lowell & J. Brickman.
    Gro/TLE enables embryonic stem cell differentiation by repressing pluripotent gene expression
    Developmental Biology, Vol. 397, No. 1, 01.01.2015, p. 56-66.
  5. C. Berclaz, C.  Pache, A. Bouwens, D. Szlag, A. Lopez, L. Joosten, S. Ekim, M. Brom, M. Gotthardt, A. Grapin-Botton & T. Lasser.
    Combined Optical Coherence and Fluorescence Microscopy to assess dynamics and specificity of pancreatic beta-cell tracers
    Scientific Reports, Vol. 5, 19.05.2015,
  6. C. Greggio, F. De Franceschi & A. Grapin-Botton.
    In Vitro-Produced Pancreas Organogenesis Models In Three Dimensions : Self-Organization From Few Stem Cells Or Progenitors.
    Stem Cells, Vol. 33, No. 1, 01.2015, p. 8-14.
  7. E.A. Ober & A. Grappin-Botton.
    At new heights - endodermal lineages in development and disease. Development (Cambridge, England), Vol. 142, No. 11, 01.06.2015, p. 1912-1917, DOI: 
  8. H. Klingberg, L.B. Oddershede, K. Loeschner, E.H. Larsen, S. Loft, P. Møller. Uptake of gold nanoparticles in primary human endothelial cells. Toxicology research, vol. 4 p.655-666 (2015) 
    DOI: 10.1039/c4tx00061g
  9. H. Klingberg, S. Loft, L.B. Oddershede, P. Møller.
    Influence of flow, shear stress and adhesion molecule targeting on gold nanoparticle uptake in human endothelial cells.
    Nanoscale, vol. 7 p. 11409-11419 (2015),
    DOI: 10.1039/C5NR01467K.
  10. J. Holzenspies, G. Dela Cruz & J. Brickman.
    Resolving Heterogeneity: Fluorescence-Activated Cell Sorting of Dynamic Cell Populations from Feeder-Free Mouse Embryonic Stem Cell Culture, Methods in molecular biology (Clifton, N.J.), 2015.
  11. K.M. Bendtsen, M.H. Jensen; S. Krishna & S. Semsey.
    The role of mRNA and protein stability in the function of coupled positive and negative feedback systems in eukaryotic cells, Scientific Reports, Vol. 5, 13910, 14.09.2015.
  12. L. Jauffred, S. Mohammad-Reza Taheri, R. Schmitt, H. Linke, L.B. Oddershede. Optical Trapping of Gold Nanoparticles in Air.
    Nano Letters, vol. 15 p. 4713-4719 (2015), 
    DOI: 10.1021/acs.nanolett.5b01366, also featured at  and on the Women in Nanoscience blog 
  13. L.A. Lemaire, J. Goulley,Y.H. Kim, S. Carat, P. Jacquemin, J. Rougemont, D.B. Constam & A. Grapin-Botton.
    Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis.
    Development (Cambridge, England), Vol. 142, No. 5, 01.03.2015, p. 858-70.
  14. L.B. Oddershede.
    Voices of chemical biology.
    Nature Chemical Biology, vol. 11 p.378-379, 446-447, 752-753 (2015).
    DOI: 10.1038/nchembio.1820
  15. N. Leijnse, L.B. Oddershede, P.M. Bendix.
    An updated look at actin within filopodia. Cytoskeleton, vol.72 p.71-79 (2015).
  16. N. Leijnse, L.B. Oddershede, P.M. Bendix.
    Dynamic buckling of actin within filopodia.
    Communicative and Integrative Biology, vol.8 p. e1022010-(1-3) (2015).
    DOI: 10.1080/19420889.2015.1022010,
  17. N. Leijnse, L.B. Oddershede, P.M. Bendix.
    Helical buckling of actin inside filopodia generates traction. PNAS, vol. 112 p. 136-141 (2015),,
  18. N. Mitarai, M.H. Jensen, S. Semsey.
    Coupled positive and negative feedbacks produce diverse gene expression patterns in colonies, mBio, Vol. 6, Nr. 2, e00059, 07.04.2015.
  19. P. Tian, W. Boomsma, Y. Wang, D.E. Otzen, M.H. Jensen and K. Lindorf-Larsen. Structure of a Functional Amyloid Protein Computed Using Sequence Variation, J. Am. Chem. Soc., 137, pp 22 - 25.
    DOI: 10.1021/ja5093634 (2015)
  20. R.K. Schmitt, L. Jauffred, S. Mohammad-Reza Taheri, H. Linke, L.B. Oddershede. Optical trapping of gold aerosols. Proceedings of SPIE, vol. 9548 p.95480F-1 (2015)
  21. T.C.T Michaels, P. Yde, J.C.W Willis, D. Otzen, C.M. Dobson, A.K. Buell, T.P.J. Knowles, The length distribution of frangible biofilaments, Journal of Chemical Physics, Vol. 143, Nr. 16, 28.10.2015,
  22. Y.A. Kim, H. Larsen, P. Rué, L.A. Lemaire, J. Ferrer & A. Grapin-Botton.
    Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas.
    P L o S Biology, Vol. 13, No. 3, 03.2015, p. e1002111.
  23. S.M. Morgani & J.M. Brickman (2015).
    LIF supports primitive endoderm expansion during pre-implantation development.
    Development 2015 142: 3488-3499.
    DOI: 10.1242/dev.125021
  24. K. Koltowska, AK Lagendijk, C Pichol-Thievend, JC Fischer, M Francois, EA Ober, A.S. Yap, BM. Hogan. (2015)
    Vegfc Regulates Bipotential Precursor Division and Prox1 Expression to Promote Lymphatic Identity in Zebrafish”.  
    DOI: 10.1016/j.celrep.2015.10.055