By Dr Fabio Zanini

Journal articles

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, http://dx.doi.org/10.1038/s41598-023-50717-w

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, http://dx.doi.org/10.1038/s41590-023-01654-3

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, http://dx.doi.org/10.1128/mbio.01318-23

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, http://dx.doi.org/10.1016/j.isci.2023.106097

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, http://dx.doi.org/10.1182/blood.2022018602

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, http://dx.doi.org/10.21105/joss.04899

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, http://dx.doi.org/10.1182/blood-2022-163158

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, http://dx.doi.org/10.1038/s41556-022-00955-3

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, http://dx.doi.org/10.1097/01.hs9.0000845876.01682.15

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, http://dx.doi.org/10.1093/nar/gkac436

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, http://dx.doi.org/10.1093/bioinformatics/btac166

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, http://dx.doi.org/10.1093/bioinformatics/btac166

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, http://dx.doi.org/10.1182/blood.2020009707

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, http://dx.doi.org/10.1371/journal.pntd.0009306

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, http://dx.doi.org/10.1016/j.exphem.2021.12.255

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', , http://dx.doi.org/10.1101/2021.04.27.441649

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', , http://dx.doi.org/10.1101/2021.05.19.444776

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

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', , http://dx.doi.org/10.1101/2020.10.26.353797

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

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

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, 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', Proceedings of the National Academy of Sciences of the United States of America, 115, pp. E12363 - E12369, http://dx.doi.org/10.1073/pnas.1813819115

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, http://dx.doi.org/10.1038/s41586-018-0590-4

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, http://dx.doi.org/10.1016/j.antiviral.2018.05.001

Zanini F; Pu SY; Bekerman E; Einav S; Quake SR, 2018, 'Single-cell transcriptional dynamics of flavivirus infection', eLife, 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, 79, pp. E104 - E107, http://dx.doi.org/10.1097/QAI.0000000000001829

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; 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, 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 Evolution, 3, http://dx.doi.org/10.1093/ve/vex003

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

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

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, http://dx.doi.org/10.1016/j.jsb.2014.10.010

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, 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, 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, 87, pp. 11821 - 11830, http://dx.doi.org/10.1128/JVI.01692-13

Zanini F; Neher RA, 2013, 'Quantifying selection against synonymous mutations in HIV-1 env evolution', Journal of Virology, 87, pp. 11843 - 11850, http://dx.doi.org/10.1128/JVI.01529-13

Zanini F; Neher RA, 2012, 'FFPopSim: An efficient forward simulation package for the evolution of large populations', Bioinformatics, 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, 8, pp. 1404 - 1419, http://dx.doi.org/10.1039/c1sm06242e

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