ALI KALANTARI
Developmental And Stem Cell Scientist
San Francisco,CA
Summary
Developmental and stem cell biologist studying gut morphogenesis and enteric nervous system development through mouse embryology, human pluripotent stem cell models, multiplexed single-cell transcriptomics, ligand-receptor analysis, and functional perturbation experiments.
Overview
7
7
years of professional experience
Work History
Graduate Student Researcher
University of California, San Francisco
San Francisco, CA
01.2021 - 01.2026
- Defined how the developing ENS is patterned within a regionally specialized gut by integrating multiplexed single-cell RNA-seq across embryonic mouse small intestine (E13.5-E18.5) with hPSC-derived enteric ganglioid perturbation models.
- Identified the PTN/MDK-PTPRZ1 signaling axis as a spatially structured mesenchymal cue that fine-tunes ENS progenitor proliferation, neurogenesis, and neurotransmitter specification.
- Established and applied hPSC-derived enteric neuron and ganglioid workflows, bulk RNA-seq, imaging-based phenotyping, and functional perturbation assays to test candidate pathways.
- Contributed to a 582-compound screen identifying regulators of nitrergic motor neuron differentiation and to validation studies culminating in a Nature publication.
- Investigated extracellular matrix remodeling during intestinal villus morphogenesis using mouse explant culture, pharmacologic perturbation, and scRNA-seq; contributed to work published in Cell.
Research Assistant
Stem Cell and Developmental Biology Research
San Francisco, CA
01.2019 - 01.2020
- Maintained human pluripotent stem cell cultures, assisted with directed differentiation experiments, and supported day-to-day laboratory operations.
Education
Ph.D. - Developmental and Stem Cell Biology
University of California, San Francisco
San Francisco, CA03-2026
Bachelor of Arts - Integrative Biology
University of California, Berkeley
Berkeley, CA 05.2001 -
Skills
Experimental design
Scientific writing
In-vitro assays
Ex-vivo assays
Cell culture
Microscopy
Bioinformatics
Classroom instruction
PUBLICATIONS
- Kalantari, A., Klein, O.D., Gartner, Z. J., and Fattahi, F. ENS lineage potential is spatially unrestricted but modulated by regional PTPRZ1 signaling. Manuscript in preparation.
- Huycke, T. R., Hakkinen, T. J., Miyazaki, H., Srivastava, V., Barruet, E., McGinnis, C. S., Kalantari, A., Cornwall-Scoones, J., Vaka, D., Zhu, Q., Jo, H., Oria, R., Weaver, V. M., DeGrado, W. F., Thomson, M., Garikipati, K., Boffelli, D., Klein, O. D., and Gartner, Z. J. Patterning and folding of intestinal villi by active mesenchymal dewetting. Cell 187(12):3072-3089.e20 (2024).
- Majd, H., Samuel, R. M., Cesiulis, A., Ramirez, J. T., Kalantari, A., Barber, K., Farahvashi, S., Ghazizadeh, Z., Majd, A., Chemel, A. K., Richter, M. N., Das, S., Bendrick, J. L., Keefe, M. G., Wang, J., Shiv, R. K., Bhat, S., Khoroshkin, M., Yu, J., Nowakowski, T. J., et al. Engrafted nitrergic neurons derived from hPSCs improve gut dysmotility in mice. Nature 645(8079):158-167 (2025).
- Samuel, R. M., Majd, H., Richter, M. N., Ghazizadeh, Z., Zekavat, S. M., Navickas, A., Ramirez, J. T., Asgharian, H., Simoneau, C. R., Bonser, L. R., Koh, K. D., Garcia-Knight, M., Tassetto, M., Sunshine, S., Farahvashi, S., Kalantari, A., Liu, W., Andino, R., Zhao, H., Natarajan, P., Erle, D. J., Ott, M., Goodarzi, H., and Fattahi, F. Androgen signaling regulates SARS-CoV-2 receptor levels and is associated with severe COVID-19 symptoms in men. Cell Stem Cell 27(6):876-889.e12 (2020).
PRESENTATIONS AND TEACHING
Poster: Mapping the contribution of intrinsic and extrinsic signals in enteric neurogenesis and maturation. American Neurogastroenterology and Motility Society (ANMS) Annual Meeting, 2025.
Teaching Assistant: DSCB 257, Developmental & Stem Cell Biology, UCSF (2021).
Guest instructor: DSCB 257, UCSF (2024, 2025). Lecture and discussion session: "Methodologies and Techniques in Developmental Biology."
HONORS AND AWARDS
Matilda Edlund Scholarship (UCSF); Franklin M. Henry departmental award (UC Berkeley); summa cum laude (UC Berkeley).
Timeline
Graduate Student Researcher
University of California, San Francisco
01.2021 - 01.2026
Research Assistant
Stem Cell and Developmental Biology Research
01.2019 - 01.2020
Bachelor of Arts - Integrative Biology
University of California, Berkeley
05.2001 -
Ph.D. - Developmental and Stem Cell Biology
University of California, San Francisco