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)
Bioinformatics
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).
Cancer
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).
Virology
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).
Bio
- 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.
Current teaching:
- Single cell virology, guest lecture University of Sydney (April 2020)
- Scientific programming in Python, UNSW Medicine (March-May 2020)
Knutsen C; Che X; Liu M; Zanini F; Cornfield DN; Alvira CM,
2023,
'Long-Standing Alterations in Pulmonary Vascular Cell Phenotype and Cell-Cell Communication Upon Recovery From Acute Hyperoxia Defined at Single-Cell Resolution', in
A54. PEDIATRIC PULMONARY VASCULAR DISEASE,
American Thoracic Society, presented at
American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,
http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1891 2023
Liu M; Knutsen C; Che X; Cornfield DN; Zanini F; Alvira CM,
2023,
'Developmental Expression of Paternally Expressed Gene-3 Promotes Angiogenic Function in General Capillary Endothelial Cells From the Early Alveolar Lung', in
B58. DON'T FORGET ABOUT THE BLOOD VESSELS! PULMONARY VASCULAR FUNCTION IN ACUTE LUNG INJURY,
American Thoracic Society, presented at
American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,
http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a3769 2023
Dinh DT; Barnes EA; Ito R; Knutsen C; Che X; Zanini F; Alvira CM; Cornfield DN,
2023,
'Neonatal Hyperoxia Causes Vascular Smooth Muscle Specific Transcriptomic Changes and Pulmonary Hypertension', in
C26. UNRAVELING THE GORDIAN KNOT: MULTI-DIMENSIONAL -OMICs AND SIGNALING MOTIFS IN PULMONARY VASCULAR DISEASE,
American Thoracic Society, presented at
American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,
http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a4657 2023
Zhang D; Che X; Knutsen C; Liu M; Suresh NE; Saito T; Cornfield D; Zanini F; Alvira CM,
2023,
'Alterations of Aerocyte Capillary Phenotype During Postnatal Development and in Response to Injury', in
C71. NEW INSIGHTS IN BRONCHOPULMONARY DYSPLASIA,
American Thoracic Society, presented at
American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,
http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a5765 2023
Saito T; Knutsen C; Liu M; Che X; Zhang D; Zanini F; Alvira CM,
2023,
'Galanin-positive Macrophages Are Intimately Associated With the Pulmonary Vasculature During Late Embryogenesis', in
D13. INNATE AND ADAPTIVE IMMUNE MECHANISMS REGULATING LUNG DISEASE,
American Thoracic Society, presented at
American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,
http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6202 2023
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,
FRANCE, Autrans, presented at
11th International Conference on Quasielastic Neutron Scattering / 6th International Workshop on Inelastic Neutron Spectrometers (QENS/WINS),
FRANCE, Autrans,
11 May 2014 - 16 May 2014,
http://dx.doi.org/10.1051/epjconf/20158302005 2014
Schnegg-Kaufmann AS; Thoms JAI; Bhuyan GS; Hampton HR; Vaughan L; Rutherford K; Kakadia PM; Lee HM; Johansson EMV; Failes TW; Arndt GM; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead AJ; Unnikrishnan A; Davidson S; Polizzotto MN; Hertzberg M; Papaemmanuil E; Bohlander SK; Faridani OR; Jolly CJ; Zanini F; Pimanda JE,
2023,
'Contribution of mutant HSC clones to immature and mature cells in MDS and CMML, and variations with AZA therapy',
Blood,
141,
pp. 1316 - 1321,
http://dx.doi.org/10.1182/blood.2022018602 2023
Zanini F; Che X; Knutsen C; Liu M; Suresh NE; Domingo-Gonzalez R; Dou SH; Zhang D; Pryhuber GS; Jones RC; Quake SR; Cornfield DN; Alvira CM,
2023,
'Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during postnatal growth',
iScience,
26,
pp. 106097 - 106097,
http://dx.doi.org/10.1016/j.isci.2023.106097 2023
Horvát S; Podkalicki J; Csárdi G; Nepusz T; Traag V; Zanini F; Noom D, 2023, 'IGraph/M: graph theory and network analysis for
Mathematica',
Journal of Open Source Software, vol. 8, pp. 4899 - 4899,
http://dx.doi.org/10.21105/joss.048992023
Chandrakanthan V; Rorimpandey P; Zanini F; Chacon D; Olivier J; Joshi S; Kang YC; Knezevic K; Huang Y; Qiao Q; Oliver RA; Unnikrishnan A; Carter DR; Lee B; Brownlee C; Power C; Brink R; Mendez-Ferrer S; Enikolopov G; Walsh W; Göttgens B; Taoudi S; Beck D; Pimanda JE,
2022,
'Mesoderm-derived PDGFRA+ cells regulate the emergence of hematopoietic stem cells in the dorsal aorta',
Nature Cell Biology,
24,
pp. 1211 - 1225,
http://dx.doi.org/10.1038/s41556-022-00955-3 2022
Zandavi SM; Koch FC; Vijayan A; Zanini F; Mora FV; Ortega DG; Vafaee F,
2022,
'Disentangling single-cell omics representation with a power spectral density-based feature extraction',
Nucleic Acids Research,
50,
pp. 5482 - 5492,
http://dx.doi.org/10.1093/nar/gkac436 2022
Schnegg-Kaufmann A; Thoms J; Bhuyan GS; Henry H; Vaughan L; Rutherford K; Kakadia P; Johansson E; Failes T; Greg A; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead A; Unnikrishnan A; Bohlander S; Pappaemmanuil E; Faridani O; Jolly C; Zanini F; Pimanda J,
2022,
'P748: SINGLE CELL GENOTYPING OF MATCHED BONE MARROW AND PERIPHERAL BLOOD CELLS IN TREATMENT NAIVE AND AZA-TREATED MDS AND CMML',
HemaSphere,
6,
pp. 643 - 644,
http://dx.doi.org/10.1097/01.hs9.0000845876.01682.15 2022
Thoms J; Truong P; Subramanian S; Knezevic K; Harvey G; Huang Y; Seneviratne J; Carter D; Joshi S; Skhinas J; Chacon D; Shah A; de Jong I; Beck D; Göttgens B; Larsson J; Wong J; Zanini F; Pimanda J,
2021,
'3034 – DISRUPTION OF A GATA2, TAL1, ERG REGULATORY CIRCUIT PROMOTES ERYTHROID TRANSITION IN HEALTHY AND LEUKEMIC STEM CELLS',
Experimental Hematology,
100,
pp. S59 - S59,
http://dx.doi.org/10.1016/j.exphem.2021.12.255 2021
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; Göttgens 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,
138,
pp. 1441 - 1455,
http://dx.doi.org/10.1182/blood.2020009707 2021
Chandrakanthan V; Rorimpandey P; Zanini F; Chacon D; Kang YC; Knezevic K; Huang Y; Qiao Q; Oliver R; Unnikrishnan A; Carter D; Lee B; Brownlee C; Power C; Mendez-Ferrer S; Enikolopov G; Walsh W; Göttgens B; Taoudi S; Beck D; Pimanda J,
2021,
'Mesoderm-Derived PDGFRA+Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta',
,
http://dx.doi.org/10.1101/2021.08.08.455592 2021
Zanini F; Che X; Suresh N; Knutsen C; Klavina P; Xie Y; Domingo-Gonzalez R; Liu M; Jones R; Quake S; Alvira C; Cornfield D,
2021,
'Lung mesenchymal cell diversity rapidly increases at birth and is profoundly altered by hyperoxia',
,
http://dx.doi.org/10.1101/2021.05.19.444776 2021
Zanini F; Che X; Knutsen C; Liu M; Suresh N; Domingo-Gonzalez R; Dou S; Zhang D; Pryhuber G; Jones R; Quake S; Cornfield D; Alvira C,
2021,
'Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during a period of rapid postnatal growth',
,
http://dx.doi.org/10.1101/2021.04.27.441649 2021
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,
15,
pp. e0009306,
http://dx.doi.org/10.1371/journal.pntd.0009306 2021
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,
10,
http://dx.doi.org/10.1038/s41598-020-71805-1 2020
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 2020
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,
9,
pp. 1 - 39,
http://dx.doi.org/10.7554/eLife.56890 2020
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 2020
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,
1,
http://dx.doi.org/10.1016/j.xcrm.2020.100035 2020
Thoms J; Knezevic K; Harvey G; Huang Y; Seneviratne J; Carter D; Subramanian S; Skhinas J; Chacon D; Shah A; de Jong I; Beck D; Göttgens B; Larsson J; Wong J; Zanini F; Pimanda J,
2020,
'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 2020
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 2019
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,
8,
http://dx.doi.org/10.7554/eLife.52384 2019
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 2018
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,
155,
pp. 67 - 75,
http://dx.doi.org/10.1016/j.antiviral.2018.05.001 2018
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,
79,
pp. E104 - E107,
http://dx.doi.org/10.1097/QAI.0000000000001829 2018
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,
115,
pp. E12363 - E12369,
http://dx.doi.org/10.1073/pnas.1813819115 2018
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,
3,
pp. vex003,
http://dx.doi.org/10.1093/ve/vex003 2017
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 2016
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 2016
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,
6,
pp. 2577 - 2582,
http://dx.doi.org/10.1021/acs.jpclett.5b01073 2015
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,
17,
pp. 4645 - 4655,
http://dx.doi.org/10.1039/c4cp04944f 2015
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,
10,
pp. 894 - 902,
http://dx.doi.org/10.1039/c3sm52447g 2014
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,
188,
pp. 225 - 232,
http://dx.doi.org/10.1016/j.jsb.2014.10.010 2014
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,
31,
pp. 305 - 318,
http://dx.doi.org/10.1016/j.devcel.2014.09.001 2014
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,
8,
pp. 1404 - 1419,
http://dx.doi.org/10.1039/c1sm06242e 2012
Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Agudelo Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez RM; Bueno N; Luciani F; Pinsky BA; Montoya JG; Estupiñan Cardenas MI; Villar Centeno LA; Rojas Garrido EM; Rosso F; Quake SR; Zanini F; Einav S,
2022,
Global and cell type-specific immunological hallmarks of severe dengue progression,
,
http://dx.doi.org/10.1101/2022.12.11.519930 2022
Schnegg-Kaufmann A; Thoms J; Bhuyan GS; Hampton H; Vaughan L; Rutherford K; Kakadia P; Johansson E; Failes T; Arndt G; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead A; Unnikrishnan A; Bohlander S; Papaemmanuil E; Faridani O; Jolly C; Zanini F; Pimanda J,
2022,
Single cell genotyping of matched bone marrow and peripheral blood cells in treatment naive and AZA-treated MDS and CMML,
,
http://dx.doi.org/10.1101/2022.01.20.476890 2022
Meyers NL; Ashuach T; Lyons DE; Simoneau CR; Erickson AL; Bouhaddou M; Nguyen TT; Khalid MM; Taha TY; Natarajan V; Baron JL; Neff N; Zanini F; Mahmoud T; Quake SR; Krogan NJ; Cooper S; McDevitt TC; Yosef N; Ott M,
2021,
Hepatitis C Virus Infects and Perturbs Liver Stem Cells,
,
http://dx.doi.org/10.1101/2021.10.26.465357 2021
Durham ND; Agrawal A; Waltari E; Croote D; Zanini F; Davidson E; Fouch M; 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,
Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics,
,
http://dx.doi.org/10.1101/790642 2019
Heinen M; Zanini F; Roosen-Runge F; Fedunová D; Zhang F; Hennig M; Seydel T; Schweins R; Sztucki M; Antalík M; Schreiber F; Nägele G, 2011, Viscosity and Diffusion: Crowding and Salt Effects in Protein Solutions,
http://dx.doi.org/10.48550/arxiv.1109.31012011
Zanini F; Che X; Knutsen C; Liu M; Suresh NE; Domingo-Gonzalez R; Dou SH; Pryhuber GS; Jones RC; Quake SR; Cornfield DN; Alvira CM,
Developmental Diversity and Unique Sensitivity to Injury of Lung Endothelial Subtypes During a Period of Rapid Postnatal Growth,
,
http://dx.doi.org/10.2139/ssrn.4160133
- 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)
