Select Publications

Journal articles

Vafaee F, 2021, 'Disentangling single-cell omics representation with a power spectral density-based feature extraction', bioRxiv, http://dx.doi.org/10.1101/2021.10.25.465657

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, vol. 138, pp. 1441 - 1455, http://dx.doi.org/10.1182/blood.2020009707

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

Zanini F; Che X; Suresh N; Knutsen C; Klavina P; Xie Y; Domingo-Gonzalez R; Jones R; Quake S; Alvira C; Cornfield D, 2021, 'Progressive Increases in Mesenchymal Cell Diversity Modulate Lung Development and are Attenuated by Hyperoxia', , http://dx.doi.org/10.1101/2021.05.19.444776

Zanini F; Che X; Knutsen C; Liu M; Suresh N; Domingo-Gonzalez R; Dou S; Jones R; Cornfield D; Quake S; Alvira C, 2021, 'Phenotypic diversity and sensitivity to injury of the pulmonary endothelium during a period of rapid postnatal growth', , http://dx.doi.org/10.1101/2021.04.27.441649

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, vol. 15, pp. e0009306, http://dx.doi.org/10.1371/journal.pntd.0009306

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, vol. 10, http://dx.doi.org/10.1038/s41598-020-71805-1

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, vol. 1, http://dx.doi.org/10.1016/j.xcrm.2020.100035

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, vol. 9, pp. 1 - 39, http://dx.doi.org/10.7554/eLife.56890

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

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

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, vol. 8, http://dx.doi.org/10.7554/eLife.52384

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

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.', Proc Natl Acad Sci U S A, vol. 115, pp. E12363 - E12369, http://dx.doi.org/10.1073/pnas.1813819115

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

Zanini F; Pu SY; Bekerman E; Einav S; Quake SR, 2018, 'Single-cell transcriptional dynamics of flavivirus infection', eLife, vol. 7, http://dx.doi.org/10.7554/eLife.32942

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, vol. 79, pp. E104 - E107, http://dx.doi.org/10.1097/QAI.0000000000001829

Pu S-Y; 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 Res, vol. 155, pp. 67 - 75, http://dx.doi.org/10.1016/j.antiviral.2018.05.001

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

Zanini F; Brodin J; Albert J; Neher RA, 2017, 'Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.', Virus Res, vol. 239, pp. 106 - 114, http://dx.doi.org/10.1016/j.virusres.2016.12.009

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 Evol, vol. 3, pp. vex003, http://dx.doi.org/10.1093/ve/vex003

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, vol. 5, http://dx.doi.org/10.7554/eLife.18889

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

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

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

Zanini F; Brodin J; Thebo L; Lanz C; Bratt G; Albert J; Neher RA, 2015, 'Population genomics of intrapatient HIV-1 evolution.', Elife, vol. 4, http://dx.doi.org/10.7554/eLife.11282

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, vol. 6, pp. 2577 - 2582, http://dx.doi.org/10.1021/acs.jpclett.5b01073

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, vol. 17, pp. 4645 - 4655, http://dx.doi.org/10.1039/c4cp04944f

Hartmann MD; Boichenko I; Coles M; Zanini F; Lupas AN; Alvarez BH, 2014, 'Thalidomide mimics uridine binding to an aromatic cage in cereblon', JOURNAL OF STRUCTURAL BIOLOGY, vol. 188, pp. 225 - 232, http://dx.doi.org/10.1016/j.jsb.2014.10.010

Magalska A; Schellhaus AK; Moreno-Andres 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, vol. 31, pp. 305 - 318, http://dx.doi.org/10.1016/j.devcel.2014.09.001

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, vol. 10, pp. 894 - 902, http://dx.doi.org/10.1039/c3sm52447g

Zanini F; Neher RA, 2013, 'Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution', JOURNAL OF VIROLOGY, vol. 87, pp. 11843 - 11850, http://dx.doi.org/10.1128/JVI.01529-13

Zanini F; Neher RA, 2013, 'Quantifying selection against synonymous mutations in HIV-1 env evolution', Journal of Virology, vol. 87, pp. 11821 - 11830, http://dx.doi.org/10.1128/JVI.01692-13

Zanini F; Neher RA, 2012, 'FFPopSim: an efficient forward simulation package for the evolution of large populations', BIOINFORMATICS, vol. 28, pp. 3332 - 3333, http://dx.doi.org/10.1093/bioinformatics/bts633

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, vol. 8, pp. 1404 - 1419, http://dx.doi.org/10.1039/c1sm06242e

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

Conference Papers

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, Autrans, FRANCE, presented at 11th International Conference on Quasielastic Neutron Scattering / 6th International Workshop on Inelastic Neutron Spectrometers (QENS/WINS), Autrans, FRANCE, 11 May 2014 - 16 May 2014, http://dx.doi.org/10.1051/epjconf/20158302005

Preprints

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

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

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


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