Associate Professor Fabio Zanini

Back to

��

�� Lab website: .

��

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

Selected Publications

Cell atlases

Bioinformatics

Developmental biology

Cancer

Virology

��

Bio

2019-current: Group leader at ��¼�, 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 | 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, pp. A7583 - A7583,

Journal articles | 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,

Journal articles | 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,

Journal articles | 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,

Journal articles | 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,

Journal articles | 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, pp. A5438 - A5438,

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, 43, pp. 5857 - 5882,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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', ,

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,

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,

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,

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', ,

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', ,

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', ,

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,

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,

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', ,

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', ,

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,

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,

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', ,

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,

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,

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,

Journal articles | 2018

Zanini F; Pu SY; Bekerman E; Einav S; Quake SR, 2018, 'Single-cell transcriptional dynamics of flavivirus infection', Elife, 7,

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', ,

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,

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,

Journal articles | 2017

Zanini F; Pu S-Y; Bekerman E; Einav S; Quake S, 2017, 'Single-cell transcriptional dynamics of flavivirus infection', ,

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,

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', ,

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,

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', ,

Journal articles | 2016

Zanini F; Puller V; Brodin J; Albert J; Neher R, 2016, 'In-vivo mutation rates and fitness landscape of HIV-1', ,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,
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,
Preprints | 2025

Sveiven S; Knutsen C; Zanini F; Cornfield D; Alvira C, 2025, Single Cell RNA Sequencing Reveals Gene Expression Continuums Along the Spatial Hierarchy of the Pulmonary Circulation,

Preprints | 2025

Xu Y; Gatt C; Kaymak E; Kikuchi K; Bourguignon T; Zanini F, 2025, Exploration and generation of cell transcriptomes over deep evolutionary time,

Conference Papers | 2024

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,

Preprints | 2024

Gatt C; Xie Y; Wahi K; Johansson E; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton,

Preprints | 2024

Gatt C; Xie Y; Wahi K; Johansson EMV; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton,

Preprints | 2024

Gatt C; Xie Y; Wahi K; Johansson EMV; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton,

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,

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,

Preprints | 2024

Xu Y; Ahn J; Zanini F, 2024, Fast and lightweight cell atlas approximations across organs and organisms,

Preprints | 2023

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,

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, pp. A4657 - A4657, presented at American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,

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, pp. A1891 - A1891, presented at American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,

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, pp. A3769 - A3769, presented at American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,

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, pp. A6202 - A6202, presented at American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC,

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 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

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,

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,

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,

Preprints | 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,

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,

Preprints | 2021

Putri GH; Anders S; Pyl PT; Pimanda JE; Zanini F, 2021, Analysing high-throughput sequencing data in Python with HTSeq 2.0,

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,

Preprints | 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,

Preprints | 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,

Preprints | 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,

Preprints | 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,

Preprints | 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,

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,

Preprints | 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,

Preprints | 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,

Preprints | 2017

Zanini F; Pu S-Y; Bekerman E; Einav S; Quake S, 2017, Single-cell transcriptional dynamics of flavivirus infection,

Preprints | 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,

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,

Preprints | 2016

Zanini F; Brodin J; Albert J; Neher R, 2016, Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing,

Preprints | 2016

Zanini F; Puller V; Brodin J; Albert J; Neher R, 2016, In-vivo mutation rates and fitness landscape of HIV-1,

Preprints | 2016

Zanini F; Puller V; Brodin J; Albert J; Neher R, 2016, In-vivo mutation rates and fitness landscape of HIV-1,

Preprints | 2015

Zanini F; Brodin J; Thebo L; Lanz C; Bratt G; Albert J; Neher RA, 2015, Population genomics of intrapatient HIV-1 evolution,

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,

Preprints | 2013

Zanini F; Neher RA, 2013, Deleterious synonymous mutations hitchhike to high frequency in HIV-1 env evolution,

Preprints | 2012

Zanini F; Neher RA, 2012, FFPopSim: An efficient forward simulation package for the evolution of large populations,

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,

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,

Chan Zuckerberg Initiative grants for essential open source software ($270,000, year 2021)
��¼� 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:

My Teaching

Current teaching:

Single cell virology, guest lecture University of Sydney (April 2020)
Scientific programming in Python, ��¼� Medicine (March-May 2020)

���������¼�

Follow

Associate Professor Fabio Zanini

Follow me

��

������ Lab website: .

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

Selected Publications

Cell atlases

Bioinformatics

Developmental biology

Cancer

Virology

Bio

��¼�

�� Lab website: .