By Associate Professor Fabio Zanini

Preprints

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

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

Zanini F, 2025, A universal tool for visualisation of networks and trees in Python, http://dx.doi.org/10.12688/f1000research.173131.1

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

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

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

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://dx.doi.org/10.48550/arxiv.2311.10260

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/10.48550/arxiv.2209.09145

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, 2022, 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

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

Putri GH; Anders S; Pyl PT; Pimanda JE; Zanini F, 2021, Analysing high-throughput sequencing data in Python with HTSeq 2.0, http://dx.doi.org/10.48550/arxiv.2112.00939

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

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

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

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

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

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

Sveiven SN; Knutsen C; Zanini F; Cornfield DN; Alvira CM, A Transcriptional Atlas of Endothelial Cell Zonation Along the Pulmonary Vascular Tree, http://dx.doi.org/10.1101/2025.05.17.654540

Bhuyan GS; Yan F; Nguyen MNT; Chung HM; Zou X; Gullapalli V; Vaughan L; Stonehouse O; Hampton HR; Shen S; Truong P; Dissanayake R; Ghodousi ES; Joshi S; Koch FC; Zanini F; Vafaee F; Huang Y; Thoms JAI; Faridani OR; Jolly CJ; Pimanda JE, Cell-state-specific mechanisms of 5-azacytidine response in myelodysplastic neoplasms, http://dx.doi.org/10.64898/2026.04.26.720516

Thoms JAI; Knezevic K; Harvey G; Huang Y; Seneviratne JA; Carter DR; Subramanian S; Skhinas J; Chacon D; Shah A; de Jong I; Beck D; Göttgens B; Larsson J; Wong JWH; Zanini F; Pimanda JE, Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells, http://dx.doi.org/10.1101/2020.10.26.353797

Domingo-Gonzalez R; Zanini F; Che X; Liu M; Jones RC; Swift MA; Quake SR; Cornfield DN; Alvira CM, 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

Zanini F; Brodin J; Albert J; Neher RA, Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing, http://dx.doi.org/10.1101/077313

Xu Y; Ahn J; Zanini F, Fast and lightweight cell atlas approximations across organs and organisms, http://dx.doi.org/10.1101/2024.01.03.573994

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, 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

Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Rojas OLA; Sanz AM; Sahoo MK; Robinson ML; Gelvez RM; Bueno N; Luciani F; Pinsky BA; Montoya JG; Cardenas MIE; Centeno LAV; Garrido EMR; Rosso F; Quake SR; Zanini F; Einav S, Global and cell type-specific immunological hallmarks of severe dengue progression, http://dx.doi.org/10.1101/2022.12.11.519930

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, Hepatitis C Virus Infects and Perturbs Liver Stem Cells, http://dx.doi.org/10.1101/2021.10.26.465357

Gatt C; Xie Y; Wahi K; Johansson EMV; Zanini F, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton, http://dx.doi.org/10.1101/2024.08.25.609620

Xie Y; Habibalahi A; Anwer AG; Wahi K; Gatt C; Johansson EMV; Holst J; Goldys E; Zanini F, Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq, http://dx.doi.org/10.1101/2024.01.27.577536

Zanini F; Che X; Suresh NE; Knutsen C; Klavina P; Xie Y; Domingo-Gonzalez R; Liu M; Jones RC; Quake SR; Alvira CM; Cornfield DN, Lung mesenchymal cell diversity rapidly increases at birth and is profoundly altered by hyperoxia, http://dx.doi.org/10.1101/2021.05.19.444776

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, Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer, http://dx.doi.org/10.1101/2024.02.21.581493

Chandrakanthan V; Rorimpandey P; Zanini F; Chacon D; Kang YC; Knezevic K; Huang Y; Qiao Q; Oliver RA; Unnikrishnan A; Carter DR; Lee B; Brownlee C; Power C; Mendez-Ferrer S; Enikolopov G; Walsh W; Göttgens B; Taoudi S; Beck D; Pimanda JE, 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

Zanini F; Berghuis BA; Jones RC; di Robilant BN; Nong RY; Norton J; Clarke MF; Quake SR, Northstar enables automatic classification of known and novel cell types from tumor samples, http://dx.doi.org/10.1101/820928

Zhang D; Knutsen C; Stroud DJ; Che X; Cornfield DN; Zanini F; Alvira CM, 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

Zanini F; Pu S-Y; Bekerman E; Einav S; Quake SR, Single-cell transcriptional dynamics of flavivirus infection, http://dx.doi.org/10.1101/203331

Gatt C; Kikuchi K; Liu C; Kaymak E; Hellemans S; Koja F; Bourguignon T; Zanini F, Social caste switching triggers emergence of novel cellular identities in Zootermopsis termites, http://dx.doi.org/10.64898/2026.04.12.718059

Yao Z; Zanini F; Kumar S; Karim M; Saul S; Bhalla N; Panpradist N; Muniz A; Narayanan A; Quake SR; Einav S, The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection, http://dx.doi.org/10.1101/2020.02.18.955393

Zanini F; Robinson ML; Croote D; Sahoo MK; Sanz AM; Ortiz-Lasso E; Albornoz LL; Suarez FR; Montoya JG; Pinsky BA; Quake SR; Einav S, Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection, http://dx.doi.org/10.1101/388181

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