Back to
Dr Fabio Zanini

Dr Fabio Zanini

Senior Research Fellow
Medicine & Health
School of Clinical Medicine

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.
Mobile
0415078943
E-mail
fabio.zanini@unsw.edu.au
Location
Lowy Building (C25), Room 211
  • Journal articles | 2024
    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, http://dx.doi.org/10.1038/s44318-024-00271-6
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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, 8, pp. 4899 - 4899, http://dx.doi.org/10.21105/joss.04899
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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, 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 2022
    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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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, http://dx.doi.org/10.1371/journal.pntd.0009306
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 2020
    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
    Journal articles | 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
    Journal articles | 2019
    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
    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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 2018
    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
    Journal articles | 2018
    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 | 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
    Journal articles | 2017
    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
    Journal articles | 2017
    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 | 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
    Journal articles | 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
    Journal articles | 2016
    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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 2015
    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
    Journal articles | 2014
    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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 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
    Journal articles | 2013
    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
    Journal articles | 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
    Journal articles | 2012
    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
  • Working Papers | 2021
    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
  • Preprints | 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
    Preprints | 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
    Preprints | 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
    Preprints | 2024
    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
    Preprints | 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
    Preprints | 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
    Conference Papers | 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
    Conference Papers | 2023
    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
    Conference Papers | 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
    Conference Papers | 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
    Conference Papers | 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
    Preprints | 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
    Preprints | 2022
    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
    Preprints | 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
    Preprints | 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
    Preprints | 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
    Conference Papers | 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; 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
    Preprints | 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
    Preprints | 2016
    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, , http://dx.doi.org/10.48550/arxiv.1605.05367
    Preprints | 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/10.48550/arxiv.1603.06634
    Preprints | 2015
    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/10.48550/arxiv.1509.02483
    Conference Papers | 2014
    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
    Preprints | 2013
    Zanini F; Neher RA, 2013, Deleterious synonymous mutations hitchhike to high frequency in HIV-1 env evolution, , http://dx.doi.org/10.48550/arxiv.1303.0805
    Preprints | 2012
    Zanini F; Neher RA, 2012, FFPopSim: An efficient forward simulation package for the evolution of large populations, , http://dx.doi.org/10.48550/arxiv.1207.6916
    Preprints | 2011
    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.1109.3101
    Preprints |
    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)

My Research Supervision

SEE LAB WEBSITE: https://fabilab.org/pages/people.html

My Teaching

Current teaching:

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