By Dr 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 C71. NEW INSIGHTS IN BRONCHOPULMONARY DYSPLASIA, American Thoracic Society, pp. A5765 - A5765, 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.a5765

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

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

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

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

Xu Y; Ahn J; Zanini F, 2024, Fast and lightweight cell atlas approximations across organs and organisms, http://dx.doi.org/10.1101/2024.01.03.573994

Gatt C; Xie Y; Wahi K; Johansson E; Zanini F, 2024, Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton, http://dx.doi.org/10.1101/2024.08.25.609620

Xie Y; Habibalahi A; Anwer A; Wahi K; Gatt C; Johansson E; Holst J; Goldys E; Zanini F, 2024, Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq, http://dx.doi.org/10.1101/2024.01.27.577536

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, 2024, Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer, http://dx.doi.org/10.1101/2024.02.21.581493

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://arxiv.org/abs/2311.10260v1

Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Agudelo Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez 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, 2022, Global and cell type-specific immunological hallmarks of severe dengue progression, http://dx.doi.org/10.1101/2022.12.11.519930

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/10.21105/joss.04899

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://arxiv.org/abs/2112.00939v1

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, 2021, Hepatitis C Virus Infects and Perturbs Liver Stem Cells, http://dx.doi.org/10.1101/2021.10.26.465357

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, 2019, 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

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; 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

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

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, 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

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