US 5994515A
· Hoxie
· 1999
[cited by applicant]
US 6790611B2
· Lassen et al.
· 2004
[cited by applicant]
US 7745592B2
· Massie et al.
· 2010
[cited by applicant]
US 8383345B2
· Shendure et al.
· 2013
[cited by applicant]
US 8476225B2
· Casarez et al.
· 2013
[cited by applicant]
US 9139642B2
· Williamson et al.
· 2015
[cited by applicant]
US 9259433B2
· Huang et al.
· 2016
[cited by applicant]
US 20090214510A1
· Nabel et al.
· 2009
[cited by applicant]
EP 2423316A1
· 2012
[cited by applicant]
WO WO9845259A2
· 1998
[cited by applicant]
WO WO2006138118A2
· 2006
[cited by applicant]
WO WO2008147427A2
· 2008
[cited by applicant]
WO WO2009027057A1
· 2009
[cited by applicant]
WO WO2009151313A1
· 2009
[cited by applicant]
WO WO2012006596A2
· 2012
[cited by applicant]
WO WO2013006795A2
· 2013
[cited by applicant]
WO WO2013072917A2
· 2013
[cited by applicant]
WO WO2013147584A1
· 2013
[cited by applicant]
WO WO2014062892A1
· 2014
[cited by applicant]
WO WO2014201416
· 2014
[cited by applicant]
WO WO2015011483A1
· 2015
[cited by applicant]
WO WO2017143155A2
· 2017
[cited by applicant]
Behera, et al., “Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility,” Nat. Comm., vol. 9, No. 1, 2018, 15 pages.
[cited by applicant]
Dingens, et al., “Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody,” Cell Host Microbe., vol. 21, No. 6, 2017, pp. 777-787.
[cited by applicant]
Doud, et al., “Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin,” Viruses, vol. 8, No. 6, 2016, 17 pages.
[cited by applicant]
Doud, et al., “Complete mapping of viral escape from neutralizing antibodies,” PLOS Pathogens, vol. 13, No. 3, 2017, 20 pages.
[cited by applicant]
Haddox, et al., “Mapping mutational effects along the evolutionary landscape of HIV envelope,” Elife, 7. pii:, 2018, e34420, 29 pages.
[cited by applicant]
Invitation to Pay Fees Dated Oct. 7, 2019 in International Application No. PCT/US2019/039952, 5 pages.
[cited by applicant]
Search Report and Written Opinion Dated Dec. 6, 2019 for International Application No. PCT/US19/39952, 28 pages.
[cited by applicant]
Thyagarajan, et al., “The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin,” eLife, 2014, 26 pages.
[cited by applicant]
“Illumina Adapter Sequences,” retrieved Jun. 1, 2021, at <<https://support-docs.illumina.com/SHARE/AdapterSeq/illumina-adapter-sequences.pdf>>, Illumina, 2018, 45 pages.
[cited by applicant]
Anderson, et al., “Identification of epitopes on respiratory syncytial virus proteins by competitive binding immunoassay,” Journal of Clinical Microbiology, vol. 23, No. 3, 1986, pp. 475-480.
[cited by applicant]
Baron, et al., “Tetracycline-controlled transcription in eukaryotes: novel transactivators with graded transactivation potential,” Nucleic Acids Research, vol. 25, No. 14, 1997, pp. 2723-2729.
[cited by applicant]
Bersuker, et al., “Protein misfolding specifies recruitment to cytoplasmic inclusion bodies,” Journal of Cell Biology, vol. 213, No. 2, 2016, pp. 229-241.
[cited by applicant]
Blau & Rossi, “Tet B or not tet B: advances in tetracycline-inducible gene expression,” PNAS USA, vol. 96, No. 3, 1999, pp. 797-799.
[cited by applicant]
Bloom, “An experimentally determined evolutionary model dramatically improves phylogenetic fit,” Molecular Biology and Evolution, vol. 31, No. 8, 2014, pp. 1956-1978.
[cited by applicant]
Bloom, “Software for the analysis and visualization of deep mutational scanning data,” BMC Bioinformatics, vol. 16, No. 168, 2015, 13 pages.
[cited by applicant]
Bonger, et al., “General method for regulating protein stability with light,” ACS Chemical Biology, vol. 9, No. 1, 2014, pp. 111-115.
[cited by applicant]
Bossart, et al., “A neutralizing human monoclonal antibody protects african green monkeys from hendra virus challenge,” Science Translational Medicine, vol. 3, No. 105, 2011, 17 pages.
[cited by applicant]
Boyoglu-Barnum, et al., “Prophylaxis with a respiratory syncytial virus (RSV) anti-G protein monoclonal antibody shifts the adaptive immune response to RSV rA2-line19F infection from Th2 to Th1 in BALB/c mice,” Journal …
[cited by applicant]
Brown, et al., “lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells,” Cell, vol. 49, No. 5, 1987, pp. 603-612.
[cited by applicant]
Buchen-Osmond, “The Universal Virus Database ICTVdB,” Computing in Science & Engineering, vol. 5, 2003, pp. 16-25.
[cited by applicant]
Burcin, et al., “Adenovirus-mediated regulable target gene expression in vivo,” PNAS USA, vol. 96, No. 2, 1999, pp. 355-360.
[cited by applicant]
Burton, et al., “Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody,” Science, vol. 266, No. 5187, 1994, pp. 1024-1027.
[cited by applicant]
Chin, et al., “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data,” Nature Methods, vol. 10, No. 6, 2013, pp. 563-569.
[cited by applicant]
Coleman, et al., “Efficient large-scale production and concentration of HIV-1-based lentiviral vectors for use in vivo,” Physiological Genomics, vol. 12, No. 3, 2003, pp. 221-228.
[cited by applicant]
Corti, et al., “Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus,” PNAS USA, vol. 112, No. 33, 2015, pp. 10473-10478.
[cited by applicant]
Cronin, et al., “Altering the tropism of lentiviral vectors through pseudotyping,” Current Gene Therapy, vol. 5, No. 4, 2005, pp. 387-398.
[cited by applicant]
Dalba, et al., “Replication-competent vectors and empty virus-like particles: new retroviral vector designs for cancer gene therapy or vaccines,” Molecular Therapy, vol. 15, No. 3, 2007, pp. 457-466.
[cited by applicant]
De Wit, et al., “Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques,” PNAS USA, vol. 110, No. 41, 2013, pp. 16593-16603.
[cited by applicant]
DeBuysscher, et al., “Comparison of the pathogenicity of Nipah virus isolates from Bangladesh and Malaysia in the Syrian hamster,” PLoS Neglected Tropical Diseases, vol. 7, No. 1, 2013, 11 pages.
[cited by applicant]
DePristo, et al., “A framework for variation discovery and genotyping using next-generation DNA sequencing data,” Nature Genetics, vol. 43, No. 5, 2011, pp. 491-498.
[cited by applicant]
Diskin, et al., “Restricting HIV-1 pathways for escape using rationally designed anti-HIV-1 antibodies,” Journal of Experimental Medicine, vol. 210, No. 6, 2013, pp. 1235-1249.
[cited by applicant]
Doud, et al., “Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 Influenza hemagglutinin,” BioRxiv, 2018, 39 pages.
[cited by applicant]
Drugbank, “AMD-070,” retrieved on Jun. 1, 2021 at <<https://go.drugbank.com/drugs/DB05501>>, Drugbank Accession No. DB05501, 2007, 5 pages.
[cited by applicant]
Drugbank, “PRO-542,” retrieved on Jun. 1, 2021 at <<https://go.drugbank.com/drugs/DB05793>>, Drugbank Accession No. DB05793, 2007, 4 pages.
[cited by applicant]
Egeler, et al., “Ligand-switchable substrates for a ubiquitin-proteasome system,” Journal of Biological Chemistry, vol. 286, No. 36, 2011, pp. 31328-31336.
[cited by applicant]
Faden, et al., “Phenotypes on demand via switchable target protein degradation in multicellular organisms,” Nature Communications, vol. 7, No. 12202, 2016, 15 pages.
[cited by applicant]
Falkowska, et al., “Broadly neutralizing HIV antibodies define a glycan-dependent epitope on the prefusion conformation of gp41 on cleaved envelope trimers,” Immunity, vol. 40, No. 5, 2014, pp. 657-668.
[cited by applicant]
Findlay, et al., “Saturation editing of genomic regions by multiplex homology-directed repair,” Nature, vol. 513, No. 7516, 2014, pp. 120-123.
[cited by applicant]
Firnberg & Ostermeier, “PFunkel: efficient, expansive, user-defined mutagenesis,” PLoS One, vol. 7, No. 12, 2012, 10 pages.
[cited by applicant]
Fogle, et al., “Fozivudine tidoxil as single-agent therapy decreases plasma and cell-associated viremia during acute feline immunodeficiency virus infection,” Journal of Veterinary Internal Medicine, vol. 25, No. 3, 201…
[cited by applicant]
Fowler, et al., “Measuring the activity of protein variants on a large scale using deep mutational scanning,” Nature Protocol, vol. 9, No. 9, 2014, pp. 2267-2284.
[cited by applicant]
Francica, et al., “Steric shielding of surface epitopes and impaired immune recognition induced by the ebola virus glycoprotein,” PLoS Pathogens, vol. 6, No. 9, 2010, 13 pages.
[cited by applicant]
Galimi, et al., “A role for bone marrow-derived cells in the vasculature of noninjured CNS,” Blood, vol. 105, No. 6, 2005, pp. 2400-2402.
[cited by applicant]
Geisbert, et al., “Development of a new vaccine for the prevention of Lassa fever,” PLoS Medicine, vol. 2, No. 6, 2005, 9 pages.
[cited by applicant]
Geisbert, et al., “Therapeutic treatment of Nipah virus infection in nonhuman primates with a neutralizing human monoclonal antibody,” Science Translational Medicine, vol. 6, No. 242, 2014, 16 pages.
[cited by applicant]
Gong, et al., “Stability-mediated epistasis constrains the evolution of an influenza protein,” Elife, vol. 2, 2013, 19 pages.
[cited by applicant]
Gossen, et al., “Transcriptional activation by tetracyclines in mammalian cells,” Science, vol. 268, No. 5218, 1995, pp. 1766-1769.
[cited by applicant]
Gunther, et al., “Imported lassa fever in Germany: molecular characterization of a new lassa virus strain,” Emerging Infectious Diseases, vol. 6, No. 5, 2000, pp. 466-476.
[cited by applicant]
Haddox, et al., “Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture,” PLoS Pathogens, vol. 12, 2016, 32 pages.
[cited by applicant]
Hanna, et al., “Antiviral activity, pharmacokinetics, and safety of BMS-488043, a novel oral small-molecule HIV-1 attachment inhibitor, in HIV-1-infected subjects,” Antimicrobial Agents and Chemotherapy, vol. 55, No. 2,…
[cited by applicant]
Hartenbach & Fussenegger, “Autoregulated, bidirectional and multicistronic gas-inducible mammalian as well as lentiviral expression vectors,” Journal of Biotechnology, vol. 120, No. 1, 2005, pp. 83-98.
[cited by applicant]
Hiatt, et al., “Parallel, tag-directed assembly of locally derived short sequence reads,” Nature Methods, vol. 7, No. 2, 2010, pp. 119-122.
[cited by applicant]
Hilton, et al., “phydms: software for phylogenetic analyses informed by deep mutational scanning,” PeerJ, vol. 5, 2017, 20 pages.
[cited by applicant]
Hoffmann, et al., “A Dna transfection system for generation of influenza A virus from eight plasmids,” PNAS USA, vol. 97, No. 11, 2000, pp. 6108-6113.
[cited by applicant]
Hopf, et al., “Mutation effects predicted from sequence co-variation,” Nature Biotechnology, vol. 35, No. 2, 2017, pp. 128-135.
[cited by applicant]
Hu & Davidson, “The inducible lac operator-repressor system is functional in mammalian cells,” Cell, vol. 48, No. 4, 1987, pp. 555-566.
[cited by applicant]
Hussain & Lenard, “Characterization of PDR4, a
[cited by applicant]
Inokoshi, et al., “Cerulenin-resistant mutants of
[cited by applicant]
Iwamoto, “A general chemical method to regulate protein stability in the mammalian central nervous system,” Chemistry & Biology, vol. 17, No. 9, 2010, pp. 981-988.
[cited by applicant]
Jacobson, “Safety, pharmacokinetics, and antiretroviral activity of multiple doses of ibalizumab (formerly TNX-355), an anti-CD4 monoclonal antibody, in human immunodeficiency virus type 1-infected adults,” Antimicrobia…
[cited by applicant]
Jahrling, et al., “Endemic Lassa fever in Liberia. IV. Selection of optimally effective plasma for treatment by passive immunization,” Transactions of The Royal Society of Tropical Medicine and Hygiene, vol. 79, No. 3, …
[cited by applicant]
Jain & Varadarajan, “A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library,” Analytical Biochemistry, vol. 449, 2014, pp. 90-98.
[cited by applicant]
Jones, et al., “Live attenuated recombinant vaccine protects nonhuman primates against Ebola and Marburg viruses,” Nature Medicine, vol. 11, No. 786, 2005, pp. 786-790.
[cited by applicant]
Julien, et al., “Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans,” PLoS Pathogens, vol. 9, No. 5, 2013, 15 pages.
[cited by applicant]
Karin, et al., “Primary structure and transcription of an amplified genetic locus: the CUP1 locus of yeast,” PNAS USA, vol. 81, No. 2, 1984, pp. 337-341.
[cited by applicant]
Kepler, “Unconventional Interrogation Yields HIV's Escape Plan,” Cell Host & Microbe, vol. 21, No. 6, 2017, pp. 659-660.
[cited by applicant]
Khetawat & Broder, “A functional henipavirus envelope glycoprotein pseudotyped lentivirus assay system,” Virology Journal, vol. 7, 2010, 14 pages.
[cited by applicant]
Kitzman, et al., “Massively parallel single-amino-acid mutagenesis,” Nature Methods, vol. 12, No. 3, 2015, pp. 203-206.
[cited by applicant]
Kutner, et al., “Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors,” Nature Protocols, vol. 4, No. 4, 2009, pp. 495-505.
[cited by applicant]
Laird Smith, et al., “Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples,” Virus Evolution, vol. 2, No. 2, 2016, 8 pages.
[cited by applicant]
Larsen, et al., “The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms,” BMC Genomics, vol. 15, No. 720, 2014, 15 pages.
[cited by applicant]
Laursen & Wilson, “Broadly neutralizing antibodies against influenza viruses,” Antiviral Research, vol. 98, No. 3, 2013, pp. 476-483.
[cited by applicant]
Lee & Saphire, “Ebolavirus glycoprotein structure and mechanism of entry,” Future Virology, vol. 4, No. 6, 2009, pp. 621-635.
[cited by applicant]
Lee, et al., “Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants,” PNAS USA, vol. 115, No. 35, 2018, pp. E8276-E8285.
[cited by applicant]
Liu, et al., “Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector,” Scientific Reports, vol. 7, No. 1, 2017, 9 pages.
[cited by applicant]
Louie, et al., “Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies,” PNAS USA, vol. 115, No. 4, 2018, pp. E564-E573.
[cited by applicant]
Luke, et al., “Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes,” Journal of General Virology, vol. 89, 2008, pp. 1036-1042.
[cited by applicant]
Marzi, et al., “Ebola Vaccine. VSV-EBOV rapidly protects macaques against infection with the 2014/15 Ebola virus outbreak strain,” Science, vol. 349, 2015, pp. 739-742.
[cited by applicant]
Matheson, et al., “Antibody-free magnetic cell sorting of genetically modified primary human CD4+ T cells by one-step streptavidin affinity purification,” PloS One, vol. 9, No. 10, 2014, 8 pages.
[cited by applicant]
Matreyek, et al., “A platform for functional assessment of large variant libraries in mammalian cells,” Nucleic Acids Research, vol. 45, No. 11, 2017, 12 pages.
[cited by applicant]
Matsuzawa, et al., “Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway,” PNAS USA, vol. 102, No. 42, 2005, pp. 14982-14987.
[cited by applicant]
McKnight, et al., “Inhibition of human immunodeficiency virus fusion by a monoclonal antibody to a coreceptor (CXCR4) is both cell type and virus strain dependent,” Journal of Virology, vol. 71, No. 2, 1997, pp. 1692-26…
[cited by applicant]
Mire, et al., “Human-monoclonal-antibody therapy protects nonhuman primates against advanced Lassa fever,” Nature Medicine, vol. 23, No. 10, 2017, pp. 1146-1149.
[cited by applicant]
Mitta, et al., “Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression,” Nucleic Acids Research, vol. 32, …
[cited by applicant]
Miyoshi, et al., “Development of a self-inactivating lentivirus vector,” Journal of Virology, vol. 72, No. 10, 1998, pp. 8150-8157.
[cited by applicant]
Moncla, et al., “Influenza Evolution: New Insights into an Old Foe,” Trends in Microbiology, vol. 25, No. 6, 2017, pp. 432-434.
[cited by applicant]
Mullick, et al., “The cumate gene-switch: a system for regulated expression in mammalian cells,” BMC Biotechnology, vol. 6, No. 43, 2006, 18 pages.
[cited by applicant]
Munster, et al., “Protective efficacy of a novel simian adenovirus vaccine against lethal MERS-CoV challenge in a transgenic human DPP4 mouse model,” NPJ Vaccines, vol. 2, No. 28, 2017, 4 pages.
[cited by applicant]
Murin, et al., “Structures of protective antibodies reveal sites of vulnerability on Ebola virus,” PNAS USA, vol. 111, No. 48, 2014, pp. 17182-17187.
[cited by applicant]
Nakata, et al., “Potent Anti-R5 Human Immunodeficiency Virus Type 1 Effects of a CCR5 Antagonist, AK602/ONO4128/GW873140, in a Novel Human Peripheral Blood Mononuclear Cell Nonobese Diabetic-SCID, Interleukin-2 Receptor…
[cited by applicant]
Pascal, et al., “Pre- and postexposure efficacy of fully human antibodies against Spike protein in a novel humanized mouse model of MERS-CoV infection,” PNAS USA, vol. 112, No. 28, 2015, pp. 8738-8743.
[cited by applicant]
Pelegrin, et al., “Antiviral Monoclonal Antibodies: Can They Be More Than Simple Neutralizing Agents?,” Trends in Microbiology, vol. 23, No. 10, 2015, pp. 653-665.
[cited by applicant]
Pert, et al., “Octapeptides deduced from the neuropeptide receptor-like pattern of antigen T4 in brain potently inhibit human immunodeficiency virus receptor binding and T-cell infectivity,” PNAS USA, vol. 83, No. 23, 1…
[cited by applicant]
Poelwijk, et al., “Learning the pattern of epistasis linking genotype and phenotype in a protein,” Nature Communications, vol. 10, No. 4213, 2019, 11 pages.
[cited by applicant]
Pond, et al., “HyPhy: hypothesis testing using phylogenies,” Bioinformatics, vol. 21, No. 5, 2005, pp. 676-679.
[cited by applicant]
Qiu, et al., “Reversion of advanced Ebola virus disease in nonhuman primates with Zmapp,” Nature, vol. 514, No. 7520, 2014, pp. 47-53.
[cited by applicant]
Qiu, et al., “Two-mAb cocktail protects macaques against the Makona variant of Ebola virus,” Science Translational Medicine, vol. 8, No. 329, 2016, 11 pages.
[cited by applicant]
Renicke, et al., “A LOV2 domain-based optogenetic tool to control protein degradation and cellular function,” Chemistry & Biology, vol. 20, No. 4, 2013, pp. 619-626.
[cited by applicant]
Roberts, et al., “The advantages of SMRT sequencing,” Genome Biology, vol. 14, No. 7, 2013, 4 pages.
[cited by applicant]
Robinson, et al., “Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits,” Nature Communications, vol. 7, No. 11544, 2016, 14 pages.
[cited by applicant]
Russell, et al., “Improving pandemic influenza risk assessment,” Elife, vol. 3, 2014, 12 pages.
[cited by applicant]
Sailer & Harms, “Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps,” Genetics, vol. 205, No. 3, 2017, pp. 1079-1088.
[cited by applicant]
Sailer & Harms, “High-order epistasis shapes evolutionary trajectories,” PLOS Computational Biology, vol. 13, No. 5, 2017, 16 pages.
[cited by applicant]
Scheid, et al., “HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption,” Nature, vol. 535, No. 7613, 2016, pp. 556-560.
[cited by applicant]
Schutze, et al., “A streamlined protocol for emulsion polymerase chain reaction and subsequent purification,” Analytical Biochemistry, vol. 410, No. 1, 2011, pp. 155-157.
[cited by applicant]
Sommerstein, et al., “Arenavirus Glycan Shield Promotes Neutralizing Antibody Evasion and Protracted Infection,” PLoS Pathogens, vol. 11, No. 11, 2015, 25 pages.
[cited by applicant]
Tran, et al., “Mapping of Ebolavirus Neutralization by Monoclonal Antibodies in the ZMapp Cocktail Using Cryo-Electron Tomography and Studies of Cellular Entry,” Journal of Virology, vol. 90, No. 17, 2016, pp. 7618-7627.
[cited by applicant]
Travers, et al., “A flexible and efficient template format for circular consensus sequencing and SNP detection,” Nucleic Acids Research, vol. 38, No. 15, 2010, pp. 8 pages.
[cited by applicant]
Verity, et al., “Broad neutralization and complement-mediated lysis of HIV-1 by PEHRG214, a novel caprine anti-HIV-1 polyclonal antibody,” AIDS, vol. 20, No. 4, 2006, pp. 505-515.
[cited by applicant]
Wang, et al., “A regulatory system for use in gene transfer,” PNAS USA, vol. 91, No. 71, 1994, pp. 8180-8184.
[cited by applicant]
Whitehead, et al., “Nicking Mutagenesis: comprehensive single-site saturation mutagenesis,” Protocol Exchange, 2016, 9 pages.
[cited by applicant]
Witting, et al., “Characterization of a third generation lentiviral vector pseudotyped with Nipah virus envelope proteins for endothelial cell transduction,” Gene Therapy, vol. 20, 2013, pp. 997-1005.
[cited by applicant]
Wrenbeck, et al., “Plasmid-based one-pot saturation mutagenesis,” Nature Methods, vol. 13, No. 11, 2016, pp. 928-930.
[cited by applicant]
Extended European Search Report Dated Jun. 10, 2022 for European Patent Application No. 19824586.2, 9 pages.
[cited by applicant]