By Associate Professor Fabio Zanini

Journal articles

Karim M; Mishra M; Lo CW; Saul S; Cagirici HB; Gourdelier M; Ghita L; Ojha A; Tran DHN; Agrawal A; McGraw C; East MP; Gammeltoft KA; Sahoo MK; Mooney NA; Johnson GL; Das S; Leyssen P; Neyts J; Chiu W; Cohen CA; Bukh J; Gottwein J; Dye JM; Neff N; Jackson PK; Pinsky BA; Laitinen T; Pantsar T; Poso A; Zanini F; De Jonghe S; Asquith CRM; Einav S, 2025, 'PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2', Nature Communications, 16, http://dx.doi.org/10.1038/s41467-025-61759-1

Cira NJ; Paull ML; Sinha S; Zanini F; Ma EY; Riedel-Kruse IH, 2025, 'Structure, motion, and multiscale search of traveling networks', Nature Communications, 16, http://dx.doi.org/10.1038/s41467-024-54342-7

Xie Y; Habibalahi A; Anwer AG; Wahi K; Bailey J; Lin F; Gatt C; Johansson EMV; Chtanova T; Holst J; Goldys E; Zanini F, 2025, 'Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.', Genome Res, http://dx.doi.org/10.1101/gr.280014.124

Zhang D; Che X; Knutsen C; Kum A; Cornfield DN; Zanini F; Alvira CM, 2025, 'Abrogation of VEGFR2 Signaling in Capillary-2 Endothelial Cells During Postnatal Development Impairs Cap2 Differentiation and Induces Lung Fibrosis', American Journal of Respiratory and Critical Care Medicine, 211, pp. A5438 - A5438, http://dx.doi.org/10.1164/ajrccm.2025.211.abstracts.a5438

Che X; Barnes EA; Zhang D; Knutsen C; kum A; Zanini F; Alvira CM; Cornfield DN, 2025, 'The Developmental Program in Neonatal Pulmonary Pericytes Facilitates Alveolarization and Is Uniquely Susceptible to Hyperoxia-induced Lung Injury', American Journal of Respiratory and Critical Care Medicine, 211, pp. A7583 - A7583, http://dx.doi.org/10.1164/ajrccm.2025.211.abstracts.a7583

Wahi K; Freidman N; Wang Q; Devadason M; Quek LE; Pang A; Lloyd L; Larance M; Zanini F; Harvey K; O’Toole S; Guan YF; Holst J, 2024, 'Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer', EMBO Journal, 43, pp. 5857 - 5882, http://dx.doi.org/10.1038/s44318-024-00271-6

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; 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

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; 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; 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

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; 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

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

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

Saito T; Knutsen C; Liu M; Che X; Zhang D; Zanini F; Alvira CM, 2023, 'Galanin-positive Macrophages Are Intimately Associated With the Pulmonary Vasculature During Late Embryogenesis', in D13. INNATE AND ADAPTIVE IMMUNE MECHANISMS REGULATING LUNG DISEASE, American Thoracic Society, pp. A6202 - A6202, 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.a6202

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

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