Idse Heemskerk, PhD

 portrait of Idse Heemskerk
Associate Professor of Cell and Developmental Biology, Medical School
Associate Professor of Biophysics
Associate Professor of Physics, College of Literature, Science, and the Arts
[email protected]
Available to mentor
Idse Heemskerk, PhD
portrait of Idse Heemskerk
Associate Professor
  • About
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  • Qualifications
  • Center Memberships
  • Research Overview
  • Recent Publications

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    • About

    The goal of the Heemskerk lab is to understand how human pluripotent stem cells generate and interpret the chemical and physical signals that allow them to self-organize into spatial structures consisting of multiple cell types in vitro, and, by extension to the embryo, in vivo. By combining quantitative live-cell measurements and engineering tools such as micropatterning with predictive mathematical models we can answer currently intractable questions in developmental and stem cell biology.

    Links
    • Heemskerk Lab
    • Google Scholar

    Qualifications
    • Postdoctoral Fellow
      Rice University, United States
      2015 - 2018
      Postdoctoral Research
    • Postdoctoral Fellow
      University of California, Santa Barbara, Kavli Institute for Theoretical Physics, Santa Barbara, United States
      2012 - 2015
      Postdoctoral Research
    • PhD in Theoretical Physics
      University of California, Santa Barbara, CA, United States
      2007 - 2012
    • MS in Theoretical Physics
      Universiteit van Amsterdam, Amsterdam, Netherlands
      2004 - 2007
    • BSc in Computer Science
      Universiteit van Amsterdam, Amsterdam, Netherlands
      2002 - 2007
    • BSc in Physics
      Universiteit van Amsterdam, Amsterdam, Netherlands
      2001 - 2005

    Center Memberships
    • Center Member
      Center for Computational Medicine and Bioinformatics
    • Center Member
      Biosciences Initiative
    • Center Member
      Center for Cell Plasticity and Organ Design

    Research Overview

    What are the mechanisms through which stem cells give rise to self-organized embryonic structures and organs? How is the information required to form these structures encoded in highly dynamic signals? What is the role of the physical forces and geometric constraints in reproducible tissue patterning and morphogenesis?

    Recent Publications

     See All Publications
    • Preprint
      Interpretable decoding of cell fate from a snapshot of combinatorial signaling
      Fijabi A-B, Teague S, Freeburne E, Khan HA, Johnson C, Brückner D, Heemskerk I. 2026 May 18; openRxiv, DOI:10.64898/2026.05.17.725652
    • Journal Article
      Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids
      Jo K, Liu ZY, Patel G, Yu Z, Yao LA, Teague S, Johnson C, Spence J, Heemskerk I. Development Cambridge England, 2026 Feb 1; 153 (3): DOI:10.1242/dev.205459
      PMID: 41521789
    • Journal Article
      Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids
      Jo K, Liu Z-Y, Patel G, Yu Z, Yao L, Teague S, Johnson C, Spence J, Heemskerk I. eLife, 2024 Jul 15; DOI:10.1101/2024.07.08.602611
    • Journal Article
      Extended culture of 2D gastruloids to model human mesoderm development
      Chen B, Khan H, Yu Z, Yao LA, Freeburne E, Jo K, Johnson C, Heemskerk I. Nature Methods, 2025 Jun 1; 22 (6): 1355 - 1365. DOI:10.1038/s41592-025-02669-4
      PMID: 40335707
    • Chapter
      Linking Single-Cell Dynamics to Cell Fate in Differentiating hPSCs.
      Teague S, Yu Z, Heemskerk I. Methods Mol Biol, 2025 May 22; DOI:10.1007/7651_2025_638
      PMID: PMC12498548
    • Journal Article
      Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling
      Stapornwongkul KS, Hahn E, Poliński P, Salamó Palau L, Arató K, Yao LA, Williamson K, Gritti N, Anlas K, Osuna Lopez M, Patil KR, Heemskerk I, Ebisuya M, Trivedi V. Cell Stem Cell, 2025 May 1; 32 (5): 744 - 758.e7. DOI:10.1016/j.stem.2025.03.011
      PMID: 40245870
    • Journal Article
      Time-integrated BMP signaling determines fate in a stem cell model for early human development
      Teague S, Primavera G, Chen B, Liu ZY, Yao LA, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. Nature Communications, 2024 Dec 1; 15 (1): DOI:10.1038/s41467-024-45719-9
      PMID: 38368368
    • Presentation
      Insights into human gastrulation 
from stem cell-based models
      Heemskerk I. 2024 Dec 17;

    Featured News & Stories
    Department News

    Congratulations to our Exceptional Team!

    We are excited to celebrate 7 faculty promotions in the University of Michigan Medical School Department of Cell & Developmental Biology! Congratulations to Ben, Jay, Idse, Dubek, Jillian, Swathi, and Sunny!
         image from article
    Department News

    New Publication by Bohan Chen (Heemskerk Lab)!

    Nature Methods published the article "Extended culture of 2D gastruloids to model human mesoderm development."
         black circle with sparkle looking dots moving
    Health Lab

    Improved model system allows researchers to study embryo development

    Research improves upon a popular experimental model revealing more of the inner workings of a critical period during the formation of an embryo.
    Department News

    New Publication from the Heemskerk Lab

    "Mapping morphogenesis and mechanics in embryo models," has been published in Nature Methods.