By Associate Professor Fabio Zanini

Conference Papers

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

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

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

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

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

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

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

Grimaldo M; Roosen-Runge F; Jalarvo N; Zamponi M; Zanini F; Hennig M; Zhang F; Schreiber F; Seydel T, 2015, 'High-resolution neutron spectroscopy on protein solution samples', in EPJ Web of Conferences, EDP Sciences, pp. 02005, http://dx.doi.org/10.1051/epjconf/20158302005

Conference Abstracts

Forst ML; Knutsen C; Barnes EA; Che X; Zanini F; Alvira CM; Cornfield DN, 2026, 'Single-cell Transcriptomics Reveal Novel Dlk1+and Steap4+Positive Mural Cell Subtypes in Mouse and Human Lung Tissue', in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, OXFORD UNIV PRESS, Vol. 212, http://dx.doi.org/10.1093/ajrccm/aamag162.5366

Working Papers

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

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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