Dr Fabio   Zanini
Senior Research Fellow

Dr Fabio Zanini

medicine-health
POW Clinical School Operating

fabilab logo

 

    Lab website: http://fabilab.org.

 

OPEN PHD POSITION: Single cell immunology and live cell imaging. Details here.

Selected Publications

Single cell biology

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).

Single cell virology of dengue and Zika virus

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).

Cell atlases

ZANINI F, Berghuis B, et al. Quake SR. northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors. biorXiv (2019).

HIV evolution

ZANINI F, Puller V, Brodin J, Albert J, Neher RA. In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus evolution (2017).

ZANINI F, Brodin J, et al. Albert J, Neher RA. Population genomics of intrapatient HIV-1 evolution. eLife (2015).

ZANINI F, Neher RA. Quantifying selection against synonymous mutations in HIV-1 env evolution. J. Virology (2013).

 

Bio

  • 2015: PhD in Bioinformatics from the University of Tuebingen in HIV evolution.
  • 2016-2019: Postdoc at Stanford University in single cell biology of viral disease and tissue composition.
  • Since October 2019: Group leader at UNSW, working on computational and single cell approaches to severe dengue, neonatal lung disease, and cancer.
Mobile
0415078943
Location
Lowy Cancer Research Centre 2nd floor

Publications

  • Journal articles | 2021
    Dr Fabio Zanini
    Thoms JAI; Truong P; Subramanian S; Knezevic K; Harvey G; Huang Y; Seneviratne JA; Carter DR; Joshi S; Skhinas J; Chacon D; Shah A; de Jong I; Beck D; Gottgens B; Larsson J; Wong JWH; Zanini F; Pimanda JE, 2021, 'Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells.', Blood, http://dx.doi.org/10.1182/blood.2020009707
    Journal articles | 2021
    Dr Fabio Zanini
    Yao Z; Zanini F; Kumar S; Karim M; Saul S; Bhalla N; Panpradist N; Muniz A; Narayanan A; Quake SR; Einav S, 2021, 'The transcriptional landscape of venezuelan equine encephalitis virus (TC-83) infection', PLoS Neglected Tropical Diseases, vol. 15, pp. e0009306, http://dx.doi.org/10.1371/journal.pntd.0009306
    Journal articles | 2021
    Dr Fabio Zanini
    Zanini F; Che X; Suresh N; Knutsen C; Klavina P; Xie Y; Domingo-Gonzalez R; Jones R; Quake S; Alvira C; Cornfield D, 2021, 'Progressive Increases in Mesenchymal Cell Diversity Modulate Lung Development and are Attenuated by Hyperoxia', , http://dx.doi.org/10.1101/2021.05.19.444776
    Journal articles | 2021
    Dr Fabio Zanini
    Zanini F; Che X; Knutsen C; Liu M; Suresh N; Domingo-Gonzalez R; Dou S; Jones R; Cornfield D; Quake S; Alvira C, 2021, 'Phenotypic diversity and sensitivity to injury of the pulmonary endothelium during a period of rapid postnatal growth', , http://dx.doi.org/10.1101/2021.04.27.441649
    Journal articles | 2020
    Dr Fabio Zanini
    Domingo-Gonzalez R; Zanini F; Che X; Liu M; Jones RC; Swift MA; Quake SR; Cornfield DN; Alvira CM, 2020, 'Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution', eLife, vol. 9, pp. 1 - 39, http://dx.doi.org/10.7554/eLife.56890
    Journal articles | 2020
    Dr Fabio Zanini
    Hong JP; Reynoso GV; Andhey PS; Swain A; Turner JS; Boon ACM; Krammer F; Ellebedy AH; Zanini F; Artyomov M; Hickman HD; Diamond MS, 2020, 'An Agonistic Anti-CD137 Antibody Disrupts Lymphoid Follicle Structure and T-Cell-Dependent Antibody Responses', Cell Reports Medicine, vol. 1, http://dx.doi.org/10.1016/j.xcrm.2020.100035
    Journal articles | 2020
    Dr Fabio Zanini
    Zanini F; Berghuis BA; Jones RC; Nicolis di Robilant B; Nong RY; Norton JA; Clarke MF; Quake SR, 2020, 'Northstar enables automatic classification of known and novel cell types from tumor samples', Scientific Reports, vol. 10, http://dx.doi.org/10.1038/s41598-020-71805-1
    Journal articles | 2020
    Dr Fabio Zanini
    Yao Z; Zanini F; Kumar S; Karim M; Saul S; Bhalla N; Panpradist N; Muniz A; Narayanan A; Quake S; Einav S, 2020, 'The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection', , http://dx.doi.org/10.1101/2020.02.18.955393
    Journal articles | 2020
    Dr Fabio Zanini
    Domingo-Gonzalez R; Zanini F; Che X; Liu M; Jones R; Swift M; Quake S; Cornfield D; Alvira C, 2020, 'Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution', , http://dx.doi.org/10.1101/2020.02.10.942359
    Journal articles | 2019
    Dr Fabio Zanini
    Durham ND; Agrawal A; Waltari E; Croote D; Zanini F; Fouch M; Davidson E; Smith O; Carabajal E; Pak JE; Doranz BJ; Robinson M; Sanz AM; Albornoz LL; Rosso F; Einav S; Quake SR; McCutcheon KM; Goo L, 2019, 'Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics', eLife, vol. 8, http://dx.doi.org/10.7554/eLife.52384
    Journal articles | 2019
    Dr Fabio Zanini
    Zanini F; Berghuis B; Jones R; Nicolis di Robilant B; Nong RY; Norton J; Clarke M; Quake S, 2019, 'Northstar enables automatic classification of known and novel cell types from tumor samples', , http://dx.doi.org/10.1101/820928
    Journal articles | 2018
    Dr Fabio Zanini
    Pu S-Y; Xiao F; Schor S; Bekerman E; Zanini F; Barouch-Bentov R; Nagamine CM; Einav S, 2018, 'Feasibility and biological rationale of repurposing sunitinib and erlotinib for dengue treatment.', Antiviral Res, vol. 155, pp. 67 - 75, http://dx.doi.org/10.1016/j.antiviral.2018.05.001
    Journal articles | 2018
    Dr Fabio Zanini
    Zanini F; Robinson ML; Croote D; Sahoo MK; Sanz AM; Ortiz-Lasso E; Albornoz LL; Rosso F; Montoya JG; Goo L; Pinsky BA; Quake SR; Einav S, 2018, 'Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue.', Proc Natl Acad Sci U S A, vol. 115, pp. E12363 - E12369, http://dx.doi.org/10.1073/pnas.1813819115
    Journal articles | 2018
    Dr Fabio Zanini
    Christensen-Quick A; Chaillon A; Yek C; Zanini F; Jordan P; Ignacio C; Caballero G; Gianella S; Smith D, 2018, 'Influenza vaccination can broadly activate the HIV reservoir during antiretroviral therapy', Journal of Acquired Immune Deficiency Syndromes, vol. 79, pp. E104 - E107, http://dx.doi.org/10.1097/QAI.0000000000001829
    Journal articles | 2018
    Dr Fabio Zanini
    Zanini F; Pu SY; Bekerman E; Einav S; Quake SR, 2018, 'Single-cell transcriptional dynamics of flavivirus infection', eLife, vol. 7, http://dx.doi.org/10.7554/eLife.32942
    Journal articles | 2018
    Dr Fabio Zanini
    Zanini F; Robinson M; Croote D; Sahoo MK; Sanz AM; Ortiz-Lasso E; Albornoz LL; Suarez FR; Montoya J; Pinsky B; Quake S; Einav S, 2018, 'Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection', , http://dx.doi.org/10.1101/388181
    Journal articles | 2017
    Dr Fabio Zanini
    Zanini F; Puller V; Brodin J; Albert J; Neher RA, 2017, 'In vivo mutation rates and the landscape of fitness costs of HIV-1.', Virus Evol, vol. 3, pp. vex003, http://dx.doi.org/10.1093/ve/vex003
    Journal articles | 2017
    Dr Fabio Zanini
    Zanini F; Brodin J; Albert J; Neher RA, 2017, 'Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.', Virus Res, vol. 239, pp. 106 - 114, http://dx.doi.org/10.1016/j.virusres.2016.12.009
    Journal articles | 2017
    Dr Fabio Zanini
    Zanini F; Pu S-Y; Bekerman E; Einav S; Quake S, 2017, 'Single-cell transcriptional dynamics of flavivirus infection', , http://dx.doi.org/10.1101/203331
    Journal articles | 2016
    Dr Fabio Zanini
    Brodin J; Zanini F; Thebo L; Lanz C; Bratt G; Neher RA; Albert J, 2016, 'Establishment and stability of the latent HIV-1 DNA reservoir', eLife, vol. 5, http://dx.doi.org/10.7554/eLife.18889
    Journal articles | 2016
    Dr Fabio Zanini
    Zanini F; Brodin J; Albert J; Neher R, 2016, 'Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing', , http://dx.doi.org/10.1101/077313
    Journal articles | 2016
    Dr Fabio Zanini
    Brodin J; Zanini F; Thebo L; Lanz C; Bratt G; Neher R; Albert J, 2016, 'Establishment and stability of the latent HIV-1 DNA reservoir', , http://dx.doi.org/10.1101/053983
    Journal articles | 2016
    Dr Fabio Zanini
    Zanini F; Puller V; Brodin J; Albert J; Neher R, 2016, 'In-vivo mutation rates and fitness landscape of HIV-1', , http://dx.doi.org/10.1101/045039
    Journal articles | 2015
    Dr Fabio Zanini
    Zanini F; Brodin J; Thebo L; Lanz C; Bratt G; Albert J; Neher RA, 2015, 'Population genomics of intrapatient HIV-1 evolution.', Elife, vol. 4, http://dx.doi.org/10.7554/eLife.11282
    Journal articles | 2015
    Dr Fabio Zanini
    Grimaldo M; Roosen-Runge F; Hennig M; Zanini F; Zhang F; Zamponi M; Jalarvo N; Schreiber F; Seydel T, 2015, 'Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution', JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 6, pp. 2577 - 2582, http://dx.doi.org/10.1021/acs.jpclett.5b01073
    Journal articles | 2015
    Dr Fabio Zanini
    Grimaldo M; Roosen-Runge F; Hennig M; Zanini F; Zhang F; Jalarvo N; Zamponi M; Schreiber F; Seydel T, 2015, 'Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 17, pp. 4645 - 4655, http://dx.doi.org/10.1039/c4cp04944f
    Journal articles | 2014
    Dr Fabio Zanini
    Hartmann MD; Boichenko I; Coles M; Zanini F; Lupas AN; Alvarez BH, 2014, 'Thalidomide mimics uridine binding to an aromatic cage in cereblon', JOURNAL OF STRUCTURAL BIOLOGY, vol. 188, pp. 225 - 232, http://dx.doi.org/10.1016/j.jsb.2014.10.010
    Journal articles | 2014
    Dr Fabio Zanini
    Magalska A; Schellhaus AK; Moreno-Andres D; Zanini F; Schooley A; Sachdev R; Schwarz H; Madlung J; Antonin W, 2014, 'RuvB-like ATPases Function in Chromatin Decondensation at the End of Mitosis', DEVELOPMENTAL CELL, vol. 31, pp. 305 - 318, http://dx.doi.org/10.1016/j.devcel.2014.09.001
    Journal articles | 2014
    Dr Fabio Zanini
    Soraruf D; Roosen-Runge F; Grimaldo M; Zanini F; Schweins R; Seydel T; Zhang F; Roth R; Oettel M; Schreiber F, 2014, 'Protein cluster formation in aqueous solution in the presence of multivalent metal ions - a light scattering study', SOFT MATTER, vol. 10, pp. 894 - 902, http://dx.doi.org/10.1039/c3sm52447g
    Journal articles | 2013
    Dr Fabio Zanini
    Zanini F; Neher RA, 2013, 'Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution', JOURNAL OF VIROLOGY, vol. 87, pp. 11843 - 11850, http://dx.doi.org/10.1128/JVI.01529-13
    Journal articles | 2013
    Dr Fabio Zanini
    Zanini F; Neher RA, 2013, 'Quantifying selection against synonymous mutations in HIV-1 env evolution', Journal of Virology, vol. 87, pp. 11821 - 11830, http://dx.doi.org/10.1128/JVI.01692-13
    Journal articles | 2012
    Dr Fabio Zanini
    Zanini F; Neher RA, 2012, 'FFPopSim: an efficient forward simulation package for the evolution of large populations', BIOINFORMATICS, vol. 28, pp. 3332 - 3333, http://dx.doi.org/10.1093/bioinformatics/bts633
    Journal articles | 2012
    Dr Fabio Zanini
    Heinen M; Zanini F; Roosen-Runge F; Fedunova D; Zhang F; Hennig M; Seydel T; Schweins R; Sztucki M; Antalik M; Schreiber F; Naegele G, 2012, 'Viscosity and diffusion: crowding and salt effects in protein solutions', SOFT MATTER, vol. 8, pp. 1404 - 1419, http://dx.doi.org/10.1039/c1sm06242e
    Journal articles |
    Dr Fabio Zanini
    Thoms JAI; Knezevic K; Harvey G; Huang Y; Seneviratne JA; Carter DR; Subramanian S; Skhinas J; Chacon D; Shah A; de Jong I; Beck D; Göttgens B; Larsson J; Wong JWH; Zanini F; Pimanda JE, 'Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells', , http://dx.doi.org/10.1101/2020.10.26.353797
  • Conference Papers | 2014
    Dr Fabio Zanini
    Grimaldo M; Roosen-Runge F; Jalarvo N; Zamponi M; Zanini F; Hennig M; Zhang F; Schreiber F; Seydel T, 2014, 'High-resolution neutron spectroscopy on protein solution samples', in Frick B; Koza MM; Boehm M; Mutka H (eds.), QENS/WINS 2014 - 11TH INTERNATIONAL CONFERENCE ON QUASIELASTIC NEUTRON SCATTERING AND 6TH INTERNATIONAL WORKSHOP ON INELASTIC NEUTRON SPECTROMETERS, E D P SCIENCES, Autrans, FRANCE, presented at 11th International Conference on Quasielastic Neutron Scattering / 6th International Workshop on Inelastic Neutron Spectrometers (QENS/WINS), Autrans, FRANCE, 11 May 2014 - 16 May 2014, http://dx.doi.org/10.1051/epjconf/20158302005

Awards

  • Chan Zuckerberg Initiative grants for essential open source software ($270,000, year 2021)
  • UNSW Cellular Genomics Future seed grant (years 2021-2022)

Grants

Media