Akanksha Jain

Research Interests

I am interested in understanding the developmental dynamics that shape the human brain, and how these processes are dysregulated in disease. My research combines stem-cell derived brain organoids, long-term lightsheet imaging, spatial transcriptomics, and single-cell genomics to uncover how morphogenetic patterns emerge from molecular and mechanical programs.

Employment

• Assistant Professor (Neural Morphogenomics Lab), Department of Molecular Life Sciences, University of Zurich (From January 2026)
• Oberassistant, Department of Molecular Life Sciences, University of Zurich (Sep–Dec 2025)
• Oberassistant, Department of Biosystems Science and Engineering, ETH Zurich (Mar–Aug 2025)
• Postdoctoral Researcher, ETH Zurich, Department of Biosystems Science and Engineering (2019–2025)

Education

• Ph.D., Molecular Cell Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden (2013–2019)
• M.Sc., Biology, Tata Institute of Fundamental Research, Mumbai (2010–2013)
• B.Sc. (Hons), Botany, Hindu College, University of Delhi (2007–2010)

Selected Publications

• Jain A*, Gut G* et al. Morphodynamics of human early brain organoid development. Nature (2025). *Equal contribution.
• Sanchis-Calleja F.*, Azbukina N.*, Jain A, et al. Systematic screening of morphogen patterning in human neural organoids with multiplexed single-cell transcriptomics. Nature Methods (in press, 2025).
• Jain A. Marangoni flows underlie symmetry breaking in early mouse gastruloids. Nature Physics (2025).
• Kasuba K.*, Flaschner G.*, Jain A*, Krieg M.*, et al. Five challenges towards exploring the mechanobiology of complex cellular systems. Nature Nanotechnology (under revision, 2025).
• Ahn S., Jain A, et al. Fibronectin-templated multi-component fibrillar extracellular matrices to modulate tissue-specific cell dynamics. Biomaterials (2024).
• Fleck J*, Jansen S*, Jain A, et al. Inferring and perturbing cell fate regulomes in human brain organoids. Nature (2022).
• Jain A, Ulman V, Mukherjee A, et al. Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation. Nature Communications (2020).
• Jain A*, Dutta P*, Jana S*, et al. Kinesin-2 transports Orco into the olfactory cilium of Drosophila melanogaster. PLoS Genetics (2021).

Teaching

• EMBO Lightsheet Microscopy Course — Lecturer, Dresden (Aug 2025)
• EMBO Lightsheet Microscopy Course — Lecturer & TA, Brno (2022)
• Single-cell Technologies Master’s Course, ETH Zurich — Teaching Assistant (2020–2024)
• EMBO Lightsheet Microscopy Course, MPI-CBG Dresden — Teaching Assistant (2018)

Honors & Awards

• Travel Grant — Latsis Symposium on Smart Microscopy, EPFL (2024)
• Nikon International Small World in Motion — Honorable Mention (2023)
• NCCR Representative, Locarno Film Festival (2021)
• Best Poster Award — EMBL-IBEC Winter Conference, Barcelona (2020)
• Travel Grant — EMBO Bridging Cell and Tissue Mechanics, Santiago (2019)
• DIGS-BB PhD Fellowship, Dresden International Graduate School (2015–2017)
• Junior Research Fellowship, Department of Atomic Energy and TIFR (2010–2013)
• Best Poster & Best Talk — M2T2 Conference, India (2013)

Invited Talks

• France-BioImaging Advanced Training on Light-Sheet Microscopy, Bordeaux (Nov 2024)
• Microphysiological Systems: from Organoids to Organs-on-Chip, Cargèse (Sept 2024)
• MBL Lightsheet Microscopy Conference, Woods Hole (May 2024)
• Beyond Imaging: Visualization, Analysis and Inference, Monash University (Apr 2023)
• EMBO Lightsheet Course, CEITEC Brno (Aug 2022)
• Mechanics of Epithelia Symposium, Cambridge University (Mar 2021)

Technical Expertise

• Stem-cell and human brain organoid culture
• Lightsheet microscopy (SPIM), confocal, spinning disk, and two-photon imaging
• Single-cell & spatial transcriptomics (Visium, MERFISH, 10x Genomics)
• Multiplexed immunohistochemistry and 4i imaging
• CRISPR/Cas genome editing
• Computational analysis (R, Python, MATLAB, Bash)