Papers

* = equal contribution

Updated list on Google Scholar.

2023

• L Ghita, Z Yao, Y Xie, V Duran et al. F Zanini*, S Einav* Global and cell type-specific immunological hallmarks of severe dengue progression (bioRxiv)
• F Zanini et al. Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during postnatal growth (iScience)

2022

• GH Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 (Bioinformatics)
• AS Schnegg-Kaufmann, JAI Thoms et al., F Zanini*, JE Pimanda* Contribution of mutant HSC clones to immature and mature cells in MDS and CMML, and variations with AZA therapy (Blood)
• SM Zandavi, FC Koch, A Vijayan, F Zanini, FV Mora, DG Ortega, F Vafaee Disentangling single-cell omics representation with a power spectral density-based feature extraction (NAR)
• Vashe Chandrakanthan et al. (including F Zanini) Mesoderm-derived PDGFRA+ cells regulate the emergence of hematopoietic stem cells in the dorsal aorta (NCB)

2021

• F Zanini et al. Progressive Increases in Mesenchymal Cell Diversity Modulate Lung Development and are Attenuated by Hyperoxia (bioRxiv)
• J Thoms et al. F Zanini*, JE Pimanda* Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells (Blood)
• Z Yao*, F Zanini*, et al. The transcriptional landscale of Venezuelan equine encephalitis virus infection (PLOS Neglected Tropical Diseases)

2020

• F Zanini*, BA Berghuis* et al. northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors (Scientific Reports)
• R Domingo-Gonzales*, F Zanini*, et al. Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution (eLife)
• Tabula Muris Consortium (including F Zanini). A single-cell transcriptomic atlas characterizes ageing tissues in the mouse (Nature)

Older papers (before Fabilab):

2019

• ND Durham, A Agrawal, E Waltari, D Croote, F Zanini et al. Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics (eLife)

2018

• Zanini F*, Robinson ML* et al. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue (PNAS)
• Zanini F*, Pu SY* et al. Single-cell transcriptional dynamics of flavivirus infection (eLife)
• A Christensen-Quick, A Chaillon, C Yek, F Zanini et al. Influenza Vaccination Can Broadly Activate the HIV Reservoir During Antiretroviral Therapy (JAIDS)
• Tabula Muris Consortium (including F Zanini). Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris: The Tabula Muris Consortium (Nature)
• SY Pu, F Xiao, S Schor, E Bekerman, F Zanini et al. Feasibility and biological rationale of repurposing sunitinib and erlotinib for dengue treatment (Antiviral research)

2017

• F Zanini, J Brodin, J Albert, RA Neher. Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing (Virus research)
• F Zanini, V Puller, J Brodin, J Albert, RA Neher. In vivo mutation rates and the landscape of fitness costs of HIV-1 (Virus Evolution)

2016

• J Brodin, F Zanini, L Thebo, C Lanz, G Bratt, RA Neher, J Albert. Establishment and stability of the latent HIV-1 DNA reservoir (eLife)

2015

• F Zanini, J Brodin, L Thebo, C Lanz, G Bratt, J Albert, RA Neher. Population genomics of intrapatient HIV-1 evolution (eLife)