Fabio Zanini

Associate Professor

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    Lab website: https://fabilab.org.

 

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)

PUBLICATIONS
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Preprints
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Mione M; Lorenzini F; Bontempi V; Calore A; Pecchini I; Pancher M; Silveira AB; Sidarovich V; Mattè A; Valentini C; Busarello E; Abdelfattah N; Stern M-H; Tebaldi T; Yun K; Zanini F, 2026, Role of myeloid cells and leukotriene signalling in Uveal Melanoma progression, http://dx.doi.org/10.21203/rs.3.rs-8735458/v1
2026
Sveiven SN; Knutsen C; Zanini F; Cornfield DN; Alvira CM, 2026, A Transcriptional Atlas of Endothelial Cell Zonation Along the Pulmonary Vascular Tree., http://dx.doi.org/10.1101/2025.05.17.654540
2026
Thoms JAI; Hampton HR; Boon PLS; Stonehouse O; Zou X; Chung HM; Koch FC; Yan F; Joshi S; Nguyen MNT; Hung D; Wright DC; Vafaee F; Polizzotto MN; Swarbrick A; Huang Y; Jolly CJ; Zanini F; Pimanda JE, 2026, Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy, http://dx.doi.org/10.64898/2026.03.13.711488
2026
Zhang D; Knutsen C; Stroud DJ; Che X; Cornfield DN; Zanini F; Alvira CM, 2025, Postnatal Abrogation of VEGFR2 Blocks Terminal Cap2 Differentiation by Preventing the Developmental Progression from a Capillary Intermediate Cell State., http://dx.doi.org/10.1101/2025.07.23.666389
2025
Xu Y; Gatt C; Kaymak E; Kikuchi K; Bourguignon T; Zanini F, 2025, Exploration and generation of cell transcriptomes over deep evolutionary time, http://dx.doi.org/10.1101/2025.02.19.639005
2025
Wahi K; Freidman N; Wang Q; Devadason M; Quek L-E; Pang A; Lloyd L; Larance M; Zanini F; Harvey K; O’Toole S; Guan YF; Holst J, 2024, Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer, http://dx.doi.org/10.1101/2024.02.21.581493
2024
Xie Y; Habibalahi A; Anwer A; Wahi K; Gatt C; Johansson E; Holst J; Goldys E; Zanini F, 2024, Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq, http://dx.doi.org/10.1101/2024.01.27.577536
2024
Gatt C; Xie Y; Wahi K; Johansson E; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton, http://dx.doi.org/10.1101/2024.08.25.609620
2024
Gatt C; Xie Y; Wahi K; Johansson EMV; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton, http://dx.doi.org/10.7554/elife.102991.1
2024
Xu Y; Ahn J; Zanini F, 2024, Fast and lightweight cell atlas approximations across organs and organisms, http://dx.doi.org/10.1101/2024.01.03.573994
2024
Gatt C; Xie Y; Wahi K; Johansson EMV; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton, http://dx.doi.org/10.7554/elife.102991
2024
Antonov M; Csárdi G; Horvát S; Müller K; Nepusz T; Noom D; Salmon M; Traag V; Welles BF; Zanini F, 2023, igraph enables fast and robust network analysis across programming languages, http://arxiv.org/abs/2311.10260v1
2023
Horvát S; Podkalicki J; Csárdi G; Nepusz T; Traag V; Zanini F; Noom D, 2022, IGraph/M: graph theory and network analysis for Mathematica, http://dx.doi.org/10.21105/joss.04899
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
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
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; 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
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
Putri GH; Anders S; Pyl PT; Pimanda JE; Zanini F, 2021, Analysing high-throughput sequencing data in Python with HTSeq 2.0, http://arxiv.org/abs/2112.00939v1
2021
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
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
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 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
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; 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
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
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
2017
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
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
2016
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; Thebo L; Lanz C; Bratt G; Albert J; Neher RA, 2015, Population genomics of intrapatient HIV-1 evolution, http://dx.doi.org/10.7554/eLife.11282
2015
Zanini F; Neher RA, 2013, Deleterious synonymous mutations hitchhike to high frequency in HIV-1 env evolution, http://dx.doi.org/10.1128/JVI.01529-13
2013
Zanini F; Neher RA, 2012, FFPopSim: An efficient forward simulation package for the evolution of large populations, http://arxiv.org/abs/1207.6916v1
2012
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/10.1039/C1SM06242E
2011
Journal articles
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Zanini F, 2025, 'A universal tool for visualisation of networks and trees in Python', F1000research, 14, http://dx.doi.org/10.12688/f1000research.173131.1
2025
Pimanda J; Hampton H; Boon P; Jolly C; Joshi S; Nguyen M; Koch F; Vafaee F; Polizzotto M; Swarbrick A; Thoms J; Zanini F, 2025, '3237 – LONGITUDINAL SINGLE-CELL PROFILING OF MDS STEM/PROGENITOR CELLS REVEALS FEATURES OF AZACITIDINE RESPONSE AND RESISTANCE', Experimental Hematology, 151, pp. 105231 - 105231, http://dx.doi.org/10.1016/j.exphem.2025.105231
2025
Hemberg M; Marini F; Ghazanfar S; Al Ajami A; Abassi N; Anchang B; Benayoun BA; Cao Y; Chen K; Cuesta-Astroz Y; DeBruine Z; Dendrou CA; De Vlaminck I; Imkeller K; Korsunsky I; Lederer AR; Li JJ; Meysman P; Miller CL; Mullan KA; Ohler U; Panwar P; Patikas N; Schuck J; Siu JHY; Triche TJ; Tsankov A; van der Laan SW; Yajima M; Yang J; Zanini F; Jelic I, 2025, 'Insights, opportunities, and challenges provided by large cell atlases', Genome Biology, 26, http://dx.doi.org/10.1186/s13059-025-03771-8
2025
Karim M; Mishra M; Lo CW; Saul S; Cagirici HB; Gourdelier M; Ghita L; Ojha A; Tran DHN; Agrawal A; McGraw C; East MP; Gammeltoft KA; Sahoo MK; Mooney NA; Johnson GL; Das S; Leyssen P; Neyts J; Chiu W; Cohen CA; Bukh J; Gottwein J; Dye JM; Neff N; Jackson PK; Pinsky BA; Laitinen T; Pantsar T; Poso A; Zanini F; De Jonghe S; Asquith CRM; Einav S, 2025, 'PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2', Nature Communications, 16, http://dx.doi.org/10.1038/s41467-025-61759-1
2025
Xie Y; Habibalahi A; Anwer AG; Wahi K; Bailey J; Lin F; Gatt C; Johansson EMV; Chtanova T; Holst J; Goldys E; Zanini F, 2025, 'Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq', Genome Research, 35, pp. 1809 - 1820, http://dx.doi.org/10.1101/gr.280014.124
2025
Cira NJ; Paull ML; Sinha S; Zanini F; Ma EY; Riedel-Kruse IH, 2025, 'Structure, motion, and multiscale search of traveling networks', Nature Communications, 16, http://dx.doi.org/10.1038/s41467-024-54342-7
2025
Zhang D; Che X; Knutsen C; Kum A; Cornfield DN; Zanini F; Alvira CM, 2025, 'Abrogation of VEGFR2 Signaling in Capillary-2 Endothelial Cells During Postnatal Development Impairs Cap2 Differentiation and Induces Lung Fibrosis', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 211, http://dx.doi.org/10.1164/ajrccm.2025.211.Abstracts.A5438
2025
Che X; Barnes EA; Zhang D; Knutsen C; Kum A; Zanini F; Alvira CM; Cornfield DN, 2025, 'The Developmental Program in Neonatal Pulmonary Pericytes Facilitates Alveolarization and Is Uniquely Susceptible to Hyperoxia-induced Lung Injury', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 211, http://dx.doi.org/10.1164/ajrccm.2025.211.Abstracts.A7583
2025
Wahi K; Freidman N; Wang Q; Devadason M; Quek LE; Pang A; Lloyd L; Larance M; Zanini F; Harvey K; O’Toole S; Guan YF; Holst J, 2024, 'Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer', EMBO Journal, 43, pp. 5857 - 5882, http://dx.doi.org/10.1038/s44318-024-00271-6
2024
Zanini F; Che X; Suresh NE; Knutsen C; Klavina P; Xie Y; Domingo-Gonzalez R; Liu M; Kum A; Jones RC; Quake SR; Alvira CM; Cornfield DN, 2024, 'Hyperoxia prevents the dynamic neonatal increases in lung mesenchymal cell diversity', Scientific Reports, 14, http://dx.doi.org/10.1038/s41598-023-50717-w
2024
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, 8, pp. 4899 - 4899, http://dx.doi.org/10.21105/joss.04899
2023
Meyers NL; Ashuach T; Lyons DE; Khalid MM; Simoneau CR; Erickson AL; Bouhaddou M; Nguyen TT; Renuka Kumar G; Taha TY; Natarajan V; Baron JL; Neff N; Zanini F; Mahmoudi T; Quake SR; Krogan NJ; Cooper S; McDevitt TC; Yosef N; Ott M, 2023, 'Hepatitis C virus infects and perturbs liver stem cells', Mbio, 14, http://dx.doi.org/10.1128/mbio.01318-23
2023
Schnegg-Kaufmann AS; Thoms JAI; Bhuyan GS; Hampton HR; Vaughan L; Rutherford K; Kakadia PM; Lee HM; Johansson Beves 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, http://dx.doi.org/10.1016/j.isci.2023.106097
2023
Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Rebellón-Sánchez DE; Agudelo-Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez-Ramirez 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, 2023, 'Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach', Nature Immunology, 24, pp. 2150 - 2163, http://dx.doi.org/10.1038/s41590-023-01654-3
2023
Thoms JAI; Schnegg-Kaufmann A; Bhuyan GS; Hampton HR; Vaughan L; Rutherford K; Kakadia PM; Lee HM; Johansson E; Failes TW; Arndt GM; Koval J; Davidson S; Lindeman R; Warburton P; Rodriguez-Meira A; Mead AJ; Unnikrishnan A; Hertzberg M; Polizzotto MN; Papaemmanuil E; Bohlander SK; Faridani O; Jolly CJ; Zanini F; Pimanda JE, 2022, 'Clinical Response to Azacytidine (AZA) Is Associated with Increased Contribution from Mutated Blood Progenitors: Insights from Single Cell Genotyping of Matched Stem/Progenitor and Mature Blood Cells from MDS/CMML Patients Pre- and Post-AZA Treatment', Blood, 140, pp. 9751 - 9752, http://dx.doi.org/10.1182/blood-2022-163158
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
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
Putri GH; Anders S; Pyl PT; Pimanda JE; Zanini F, 2022, 'Analysing high-throughput sequencing data in Python with HTSeq 2.0.', Bioinformatics, 38, pp. 2943 - 2945, http://dx.doi.org/10.1093/bioinformatics/btac166
2022
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; Power C, 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
Putri GH; Anders S; Pyl PT; Pimanda JE; Zanini F, 2022, 'Analysing high-throughput sequencing data in Python with HTSeq 2.0', Bioinformatics, 38, pp. 2943 - 2945, http://dx.doi.org/10.1093/bioinformatics/btac166
2022
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, http://dx.doi.org/10.1371/journal.pntd.0009306
2021
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
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
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
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
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; Pu SY; Bekerman E; Einav S; Quake SR, 2018, 'Single-cell transcriptional dynamics of flavivirus infection', Elife, 7, http://dx.doi.org/10.7554/eLife.32942
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
Schaum N; Karkanias J; Neff NF; May AP; Quake SR; Wyss-Coray T; Darmanis S; Batson J; Botvinnik O; Chen MB; Chen S; Green F; Jones RC; Maynard A; Penland L; Pisco AO; Sit RV; Stanley GM; Webber JT; Zanini F; Baghel AS; Bakerman I; Bansal I; Berdnik D; Bilen B; Brownfield D; Cain C; Cho M; Cirolia G; Conley SD; Demers A; Demir K; de Morree A; Divita T; du Bois H; Dulgeroff LBT; Ebadi H; Espinoza FH; Fish M; Gan Q; George BM; Gillich A; Genetiano G; Gu X; Gulati GS; Hang Y; Hosseinzadeh S; Huang A; Iram T; Isobe T; Ives F; Kao KS; Karnam G; Kershner AM; Kiss BM; Kong W; Kumar ME; Lam JY; Lee DP; Lee SE; Li G; Li Q; Liu L; Lo A; Lu WJ; Manjunath A; May KL; May OL; McKay M; Metzger RJ; Mignardi M; Min D; Nabhan AN; Ng KM; Noh J; Patkar R; Peng WC; Puccinelli R; Rulifson EJ; Sikandar SS; Sinha R; Szade K; Tan W; Tato C; Tellez K; Travaglini KJ; Tropini C; Waldburger L; van Weele LJ; Wosczyna MN; Xiang J; Xue S; Youngyunpipatkul J; Zardeneta ME; Zhang F; Zhou L; Castro P; Croote D; DeRisi JL; Kuo CS, 2018, 'Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris', Nature, 562, pp. 367 - 372, http://dx.doi.org/10.1038/s41586-018-0590-4
2018
Pu SY; 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 Research, 155, pp. 67 - 75, http://dx.doi.org/10.1016/j.antiviral.2018.05.001
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', Proceedings of the National Academy of Sciences of the United States of America, 115, pp. E12363 - E12369, http://dx.doi.org/10.1073/pnas.1813819115
2018
Zanini F; Brodin J; Albert J; Neher RA, 2017, 'Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing', Virus Research, 239, pp. 106 - 114, http://dx.doi.org/10.1016/j.virusres.2016.12.009
2017
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 Evolution, 3, http://dx.doi.org/10.1093/ve/vex003
2017
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, 5, http://dx.doi.org/10.7554/eLife.18889
2016
Zanini F; Brodin J; Thebo L; Lanz C; Bratt G; Albert J; Neher RA, 2015, 'Population genomics of intrapatient HIV-1 evolution', Elife, 4, http://dx.doi.org/10.7554/eLife.11282
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
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
Hartmann MD; Boichenko I; Coles M; Zanini F; Lupas AN; Hernandez Alvarez B, 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
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
Magalska A; Schellhaus AK; Moreno-Andrés 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
Zanini F; Neher RA, 2013, 'Quantifying selection against synonymous mutations in HIV-1 env evolution', Journal of Virology, 87, pp. 11843 - 11850, http://dx.doi.org/10.1128/JVI.01529-13
2013
Zanini F; Neher RA, 2013, 'Quantifying selection against synonymous mutations in HIV-1 env evolution', Journal of Virology, 87, pp. 11821 - 11830, http://dx.doi.org/10.1128/JVI.01692-13
2013
Zanini F; Neher RA, 2012, 'FFPopSim: An efficient forward simulation package for the evolution of large populations', Bioinformatics, 28, pp. 3332 - 3333, http://dx.doi.org/10.1093/bioinformatics/bts633
2012
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
Conference Papers
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Dinh DT; Barnes EA; Fornes D; Knutsen C; Che X; Zanini F; Alvira CM; Cornfield DN, 2024, 'Neonatal Hyperoxia Causes Pulmonary Hypertension and Increases Pulmonary Vascular Smooth Muscle Cell Calponin-1 Expression', in B94. BEST OF PEDIATRICS, American Thoracic Society, pp. A4693 - A4693, presented at American Thoracic Society 2024 International Conference, May 17-22, 2024 - San Diego, CA, http://dx.doi.org/10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a4693
2024
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, pp. A1891 - A1891, 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
Saito T; Knutsen C; Liu M; Che X; Zhang D; Zanini F; Alvira C, 2023, 'Galanin-positive Macrophages Are Intimately Associated With the Pulmonary Vasculature During Late Embryogenesis', in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC, DC, Washington, presented at International Conference of the American-Thoracic-Society (ATS), DC, Washington, 19 May 2023 - 24 May 2023
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 AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC, DC, Washington, presented at International Conference of the American-Thoracic-Society (ATS), DC, Washington, 19 May 2023 - 24 May 2023
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, pp. A4657 - A4657, 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
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, pp. A3769 - A3769, 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
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; Gottgens B; Larsson J; Wong J; Zanini F; Pimanda J, 2021, 'DISRUPTION OF A GATA2, TAL1, ERG REGULATORY CIRCUIT PROMOTES ERYTHROID TRANSITION IN HEALTHY AND LEUKEMIC STEM CELLS', in EXPERIMENTAL HEMATOLOGY, ELSEVIER SCIENCE INC, pp. S59 - S59, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000985360500079&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2021
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
Working Papers
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Vafaee F; Gallego-Ortega D; Zanini F; Zandavi SM; Koch F; Valdes Mora F, 2021, Disentangling single-cell omics representation with a power spectral density-based feature extraction, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2021.10.25.465657
2021

GRANTS
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  • 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)
Organisational units
lensChief Investigators