References

Ailor E, Betenbaugh MJ. 1999. Modifying secretion and post-translational processing in insect cells. Current Opinion in Biotechnology10 :142–145.
Ayres MD, Howard SC, Kuzio J, Lopez-Ferber M, Possee RD. 1994. The Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis Virus. Virology 202 :586–605.
Beperet I, Irons SL, Simón O, King LA, Williams T, Possee RD, López-Ferber M, Caballero P. 2014. Superinfection Exclusion in Alphabaculovirus Infections Is Concomitant with Actin Reorganization.J Virol 88 :3548–3556.
Bernal V, Carinhas N, Yokomizo AY, Carrondo MJT, Alves PM. 2009. Cell density effect in the baculovirus-insect cells system: A quantitative analysis of energetic metabolism. Biotechnology and Bioengineering 104 :162–180.
Bernal V, Monteiro F, Carinhas N, Ambrósio R, Alves PM. 2010. An integrated analysis of enzyme activities, cofactor pools and metabolic fluxes in baculovirus-infected Spodoptera frugiperda Sf9 cells.Journal of Biotechnology 150 :332–342.
Carinhas N, Bernal V, Monteiro F, Carrondo MJT, Oliveira R, Alves PM. 2010. Improving baculovirus production at high cell density through manipulation of energy metabolism. Metabolic Engineering12 :39–52.
Carinhas N, Robitaille AM, Moes S, Carrondo MJT, Jenoe P, Oliveira R, Alves PM. 2011. Quantitative Proteomics of Spodoptera frugiperda Cells during Growth and Baculovirus Infection. PLOS ONE6 :e26444.
Cecchini S, Virag T, Kotin RM. 2011. Reproducible High Yields of Recombinant Adeno-Associated Virus Produced Using Invertebrate Cells in 0.02- to 200-Liter Cultures. Hum Gene Ther22 :1021–1030.
Chen W, Yang X, Tetreau G, Song X, Coutu C, Hegedus D, Blissard G, Fei Z, Wang P. 2019. A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni. Molecular Ecology Resources 19 :485–496.
Chen Y-R, Zhong S, Fei Z, Gao S, Zhang S, Li Z, Wang P, Blissard GW. 2014. Transcriptome Responses of the Host Trichoplusia ni to Infection by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus.Journal of Virology 88 :13781–13797.
Correia R, Fernandes B, Alves PM, Carrondo MJT, Roldão A. 2020. Improving Influenza HA-Vlps Production in Insect High Five Cells via Adaptive Laboratory Evolution. Vaccines 8 :589.
Correia R, Fernandes B, Castro R, Nagaoka H, Takashima E, Tsuboi T, Fukushima A, Viebig NK, Depraetere H, Alves PM, Roldão A. 2022. Asexual Blood-Stage Malaria Vaccine Candidate PfRipr5: Enhanced Production in Insect Cells. Frontiers in Bioengineering and Biotechnology10 . https://www.frontiersin.org/articles/10.3389/fbioe.2022.908509.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 :15–21.
Doverskog M, Jacobsson U, Chapman BE, Kuchel PW, Häggström L. 2000. Determination of NADH-dependent glutamate synthase (GOGAT) in Spodoptera frugiperda (Sf9) insect cells by a selective 1H/15N NMR in vitro assay.Journal of Biotechnology 79 :87–97.
Fernandes B, Castro R, Bhoelan F, Bemelman D, Gomes RA, Costa J, Gomes-Alves P, Stegmann T, Amacker M, Alves PM, Fleury S, Roldão A. 2022a. Insect Cells for High-Yield Production of SARS-CoV-2 Spike Protein: Building a Virosome-Based COVID-19 Vaccine Candidate.Pharmaceutics 14 :854.
Fernandes B, Sousa M, Castro R, Schäfer A, Hauser J, Schulze K, Amacker M, Tamborrini M, Pluschke G, Alves PM, Fleury S, Roldão A. 2022b. Scalable Process for High-Yield Production of PfCyRPA Using Insect Cells for Inclusion in a Malaria Virosome-Based Vaccine Candidate.Frontiers in Bioengineering and Biotechnology 10 . https://www.frontiersin.org/articles/10.3389/fbioe.2022.879078.
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R. 2015. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.Genome Biol 16 :278.
Folimonova SY. 2012. Superinfection Exclusion Is an Active Virus-Controlled Function That Requires a Specific Viral Protein.Journal of Virology 86 :5554–5561.
Galibert L, Jacob A, Savy A, Dickx Y, Bonnin D, Lecomte C, Rivollet L, Sanatine P, Boutin Fontaine M, Le Bec C, Merten O-W. 2021. Monobac System–A Single Baculovirus for the Production of rAAV.Microorganisms 9 :1799.
Gotoh T, Ando N, Kikuchi K-I. 2008. Re-Infection Profile of Baculoviruses to Sf-9 Insect Cells that Have Already Been Infected: Virus Binding and Recombinant Protein Production. Journal of Chemical Engineering of Japan 41 :804–808.
Hao Y, Hao S, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R. 2021. Integrated analysis of multimodal single-cell data. Cell 0 . https://www.cell.com/cell/abstract/S0092-8674(21)00583-3.
Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM. 2022. Single cell RNA-sequencing: A powerful yet still challenging technology to study cellular heterogeneity. BioEssays 44 :2200084.
Koczka K, Peters P, Ernst W, Himmelbauer H, Nika L, Grabherr R. 2018. Comparative transcriptome analysis of a Trichoplusia ni cell line reveals distinct host responses to intracellular and secreted protein products expressed by recombinant baculoviruses. Journal of Biotechnology 270 :61–69.
Mena JA, Ramírez OT, Palomares LA. 2003. Titration of Non-Occluded Baculovirus Using a Cell Viability Assay. BioTechniques34 :260–264.
Mena JA, Ramírez OT, Palomares LA. 2007. Population kinetics during simultaneous infection of insect cells with two different recombinant baculoviruses for the production of rotavirus-like particles. BMC Biotechnology 7 :39.
Merten O-W. 2016. AAV vector production: state of the art developments and remaining challenges. In: .
Monteiro F, Bernal V, Alves P. 2016. Metabolic drivers of IC-BEVS productivity: Tackling the production of enveloped viral particles.Vaccine Technology VI . https://dc.engconfintl.org/vaccine_vi/110.
Monteiro F, Bernal V, Alves PM. 2017. The role of host cell physiology in the productivity of the baculovirus-insect cell system: Fluxome analysis of Trichoplusia ni and Spodoptera frugiperda cell lines.Biotechnology and Bioengineering 114 :674–684.
Monteiro F, Carinhas N, Carrondo MJT, Bernal V, Alves PM. 2012. Toward system-level understanding of baculovirus–host cell interactions: from molecular fundamental studies to large-scale proteomics approaches.Front. Microbiol. 3 . https://www.frontiersin.org/articles/10.3389/fmicb.2012.00391/full.
Nayyar N, Kaur I, Malhotra P, Bhatnagar RK. 2017. Quantitative proteomics of Sf21 cells during Baculovirus infection reveals progressive host proteome changes and its regulation by viral miRNA.Sci Rep 7 :10902.
Pais DAM, Galrão PRS, Kryzhanska A, Barbau J, Isidro IA, Alves PM. 2020. Holographic Imaging of Insect Cell Cultures: Online Non-Invasive Monitoring of Adeno-Associated Virus Production and Cell Concentration.Processes 8 :487.
Pais DAM, Portela RMC, Carrondo MJT, Isidro IA, Alves PM. 2019. Enabling PAT in insect cell bioprocesses: In situ monitoring of recombinant adeno-associated virus production by fluorescence spectroscopy.Biotechnology and Bioengineering 116 :2803–2814.
Palomares LA, López S, Ramírez OT. 2002. Strategies for manipulating the relative concentration of recombinant rotavirus structural proteins during simultaneous production by insect cells. Biotechnology and Bioengineering 78 :635–644.
Penaud-Budloo M, François A, Clément N, Ayuso E. 2018. Pharmacology of Recombinant Adeno-associated Virus Production. Mol Ther Methods Clin Dev 8 :166–180.
Rohrmann GF. 2013. Baculovirus Molecular Biology 3rd ed. Bethesda (MD): National Center for Biotechnology Information (US). http://www.ncbi.nlm.nih.gov/books/NBK114593/.
Rohrmann GF. 2019. Baculovirus infection: The cell cycle and apoptosis.Baculovirus Molecular Biology [Internet]. 4th edition . National Center for Biotechnology Information (US). https://www.ncbi.nlm.nih.gov/books/NBK543456/.
Roldão A, Oliveira R, Carrondo MJT, Alves PM. 2009. Error assessment in recombinant baculovirus titration: Evaluation of different methods.Journal of Virological Methods 159 :69–80.
Russell AB, Trapnell C, Bloom JD. 2018. Extreme heterogeneity of influenza virus infection in single cells. Ed. Arup K Chakraborty.eLife 7 :e32303.
Silvano M, Correia R, Virgolini N, Clarke C, Alves PM, Isidro IA, Roldão A. 2022. Gene Expression Analysis of Adapted Insect Cells during Influenza VLP Production Using RNA-Sequencing. Viruses14 :2238.
Smith GE, Summers MD, Fraser MJ. 1983. Production of human beta interferon in insect cells infected with a baculovirus expression vector. Mol Cell Biol 3 :2156–2165.
Smith RH, Levy JR, Kotin RM. 2009. A simplified baculovirus-AAV expression vector system coupled with one-step affinity purification yields high-titer rAAV stocks from insect cells. Mol Ther17 :1888–1896.
Sokolenko S, George S, Wagner A, Tuladhar A, Andrich JMS, Aucoin MG. 2012. Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks.Biotechnology Advances 30 :766–781.
Srivastava A, Mallela KMG, Deorkar N, Brophy G. 2021. Manufacturing Challenges and Rational Formulation Development for AAV Viral Vectors.Journal of Pharmaceutical Sciences 110 :2609–2624.
Sun J, Vera JC, Drnevich J, Lin YT, Ke R, Brooke CB. 2020. Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection. PLoS Pathog16 :e1008671.
Tennant JR. 1964. EVALUATION OF THE TRYPAN BLUE TECHNIQUE FOR DETERMINATION OF CELL VIABILITY. Transplantation2 :685–694.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin J-R, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani A-C, Johannessen CM, Andreev AY, Allen EMV, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. 2016. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352 :189–196.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. 2014. Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions.Nat Biotechnol 32 :381–386.
Tzani I, Herrmann N, Carillo S, Spargo CA, Hagan R, Barron N, Bones J, Dillmore WS, Clarke C. 2021. Tracing production instability in a clonally derived CHO cell line using single-cell transcriptomics.Biotechnology and Bioengineering 118 :2016–2030.
Virag T, Cecchini S, Kotin RM. 2009. Producing Recombinant Adeno-Associated Virus in Foster Cells: Overcoming Production Limitations Using a Baculovirus–Insect Cell Expression Strategy.Hum Gene Ther 20 :807–817.
Virgolini N, Hagan R, Correia R, Silvano M, Fernandes S, Alves PM, Clarke C, Roldão A, Isidro IA. 2022. Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno-associated virus.Biotechnology Journal n/a :2200466.
Wei L, Cao L, Miao Y, Wu S, Xu S, Wang R, Du J, Liang A, Fu Y. 2017. Transcriptome analysis of Spodoptera frugiperda 9 (Sf9) cells infected with baculovirus, AcMNPV or AcMNPV-BmK IT. Biotechnol Lett39 :1129–1139.
Xiao H, Ye X, Xu H, Mei Y, Yang Y, Chen X, Yang Y, Liu T, Yu Y, Yang W, Lu Z, Li F. 2020. The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion.Molecular Ecology Resources 20 :1050–1068.
Xue J, Qiao N, Zhang W, Cheng R-L, Zhang X-Q, Bao Y-Y, Xu Y-P, Gu L-Z, Han J-DJ, Zhang C-X. 2012. Dynamic Interactions between Bombyx mori Nucleopolyhedrovirus and Its Host Cells Revealed by Transcriptome Analysis. Journal of Virology 86 :7345–7359.
Yu G, Wang L-G, Han Y, He Q-Y. 2012. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. OMICS16 :284–287.
Yu Q, Xiong Y, Liu J, Wang Q, Qiu Y, Wen D. 2016. Comparative proteomics analysis of apoptotic Spodoptera frugiperda cells during p35 knockout Autographa californica multiple nucleopolyhedrovirus infection.Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 18 :21–29.