Dr Fabio Zanini


Fields of Research (FoR)

Bioinformatics Software, Virology, Cancer Therapy (excl. Chemotherapy and Radiation Therapy), Cancer Cell Biology


fabilab logo


    Lab website:


OPEN POSITIONS IN THE LAB: Please check out lab website above!

Selected Publications

Cell atlases

TABULA MURIS CONSORTIUM. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature (2020).

ZANINI F, Berghuis B, et al. Quake SR. northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors. Scientific Reports (2020).

TABULA MURIS CONSORTIUM. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature (2018)


Putri G et al., ZANINI F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics (2022)

Developmental biology

ZANINI F et al. Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during postnatal growth. iScience (2023)

Domingo-Gonzales R*, ZANINI F*, et al. Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution. eLife (2020).


Schnegg-Kaufmann A et al., ZANINI F+, PIMANDA J+. Contribution of mutant HSC clones to immature and mature cells in MDS and CMML, and variations with AZA therapy. Blood (2022).

Thoms J et al., ZANINI F+, PIMANDA J+. Disruption of a GATA2-TAL1-ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells. Blood (2021).


XIE Y*, GHITA L* et al. ZANINI F+, EINAV S+. Global and cell type-specific immunological hallmarks of severe dengue progression. bioRxiv (2023)

ZANINI F, Robinson ML, et al. Quake SR, Einav S. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. PNAS (2018).

ZANINI F, Pu S, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. eLife (2018).



  • 2019-current: Group leader at UNSW, working on computational and single cell approaches to severe dengue, neonatal lung disease, cancer, and marine biology.
  • 2016-2019: Postdoc at Stanford University in single cell biology of viral disease and tissue composition.
  • 2015: PhD in Bioinformatics from the Max Planck Institute for Developmental Biology and the University of Tuebingen.

My Grants

  • Chan Zuckerberg Initiative grants for essential open source software ($270,000, year 2021)
  • UNSW Cellular Genomics Future seed grant (years 2021-2022)
  • NIH R01 (years 2021-2024)
  • NIH R01 (years 2022-2025)
  • NIH R01 (years 2022-2025, 2nd grant)
  • ARC Discovery Grant (years 2023-2025)
  • NHMRC Ideas Grant (years 2023-2025)

My Research Supervision

Supervision keywords

Areas of supervision

Single cell omics, software engineering, data science, bioinformatics, bioengineering, molecular biology, marine biology.

Currently supervising

My Teaching

Current teaching:

  • Single cell virology, guest lecture University of Sydney (April 2020)
  • Scientific programming in Python, UNSW Medicine (March-May 2020)
View less