Our Publications
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#37: Convergent evolution and targeting of diverse E2 epitopes by human broadly neutralizing antibodies are associated with HCV clearance
Ogega CO, Skinner NE, Schoenle MV, Wilcox XE, Frumento N, Wright DA, Paul HT, Sinnis-Bourozikas A, Clark KE, Figueroa A, Bjorkman PJ, Ray SC, Flyak AI, Bailey JR.
Immunity. 2024 Mar 15:S1074-7613(24)00097-9.
Featured by Cornell Chronicle! You can read the article here
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#36: Neutralizing antibodies evolve to exploit vulnerable sites in the HCV envelope glycoprotein E2 and mediate spontaneous clearance of infection
Frumento N, Sinnis-Bourozikas A, Paul HT, Stavrakis G, Zahid MN, Wang S, Ray SC, Flyak AI, Shaw GM, Cox AL, Bailey JR.
Immunity. 2024 Jan 9;57(1):40-51.e5.
Featured in TWiV podcast: Episode 1079: Rock of phages! You can listen to the the episode here
Publications before Cornell
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#35: Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals
Bozhanova NG, Flyak AI, Ruiz SE, Salas J, Rho S, Bombardi RG, Myers L, Soto C, Bailey JR, Crowe JE, Bjorkman PJ, Meiler J.
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#34: Repeated exposure to heterologous hepatitis C viruses associates with enhanced neutralizing antibody breadth and potency
Frumento N, Figueroa A, Wang T, Zahid MN, Wang S, Massaccesi G, Stavrakis G, Crowe JE Jr, Flyak AI, Ji H, Ray SC, Shaw G, Cox AL, Bailey JR.
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#33: Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization
Weber T, Potthoff J, Bizu S, Labuhn M, Dold L, Schoofs T, Horning M, Ercanoglu MS, Kreer C, Gieselmann L, Vanshylla K, Langhans B, Janicki H, Ströh LJ, Knops E, Nierhoff D, Spengler U, Kaiser R, Bjorkman PJ, Krey T, Bankwitz D, Pfeifer N, Pietschmann T, Flyak AI, Klein F.
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#32: B cell overexpression of FCRL5 and PD-1 is associated with low antibody titers in HCV infectiontem
Ogega CO, Skinner NE, Flyak AI, Clark KE, Board NL, Bjorkman PJ, Crowe JE Jr, Cox AL, Ray SC, Bailey JR.
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#31: Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations
Muecksch F, Weisblum Y, Barnes CO, Schmidt F, Schaefer-Babajew D, Wang Z, C Lorenzi JC, Flyak AI, DeLaitsch AT, Huey-Tubman KE, Hou S, Schiffer CA, Gaebler C, Da Silva J, Poston D, Finkin S, Cho A, Cipolla M, Oliveira TY, Millard KG, Ramos V, Gazumyan A, Rutkowska M, Caskey M, Nussenzweig MC, Bjorkman PJ, Hatziioannou T, Bieniasz PD.
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#30: Mechanisms of HCV resistance to broadly neutralizing antibodies
Frumento N, Flyak AI, Bailey JR.
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#29: Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies
Murin CD, Gilchuk P, Ilinykh PA, Huang K, Kuzmina N, Shen X, Bruhn JF, Bryan AL, Davidson E, Doranz BJ, Williamson LE, Copps J, Alkutkar T, Flyak AI, Bukreyev A, Crowe JE Jr, Ward AB.
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#28: New SARS-CoV-2 B cell receptor signatures in at-risk populationsList Item
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#27: Nur77 controls tolerance induction, terminal differentiation, and effector functions in semi-invariant natural killer T cells
Kumar A, Hill TM, Gordy LE, Suryadevara N, Wu L, Flyak AI, Bezbradica JS, Van Kaer L, Joyce S.
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#26: An ultralong CDRH2 in HCV neutralizing antibody demonstrates structural plasticity of antibodies against E2 glycoprotein
Flyak AI, Ruiz SE, Salas J, Rho S, Bailey JR, Bjorkman PJ.
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#25: Plasma deconvolution identifies broadly neutralizing antibodies associated with hepatitis C virus clearance
Kinchen VJ, Massaccesi G, Flyak AI, Mankowski MC, Colbert MD, Osburn WO, Ray SC, Cox AL, Crowe JE Jr, Bailey JR.
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#24: Broadly Neutralizing Antibodies Targeting New Sites of Vulnerability in Hepatitis C Virus E1E2
Colbert MD, Flyak AI, Ogega CO, Kinchen VJ, Massaccesi G, Hernandez M, Davidson E, Doranz BJ, Cox AL, Crowe JE Jr, Bailey JR.
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#23: Cross-reactive neutralizing human survivor monoclonal antibody BDBV223 targets the ebolavirus stalk
King LB, West BR, Moyer CL, Gilchuk P, Flyak A, Ilinykh PA, Bombardi R, Hui S, Huang K, Bukreyev A, Crowe JE Jr, Saphire EO.
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#22: Early Human B Cell Response to Ebola Virus in Four U.S. Survivors of Infection
Williamson LE, Flyak AI, Kose N, Bombardi R, Branchizio A, Reddy S, Davidson E, Doranz BJ, Fusco ML, Saphire EO, Halfmann PJ, Kawaoka Y, Piper AE, Glass PJ, Crowe JE Jr.
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#21: Broadly Neutralizing Antibody Mediated Clearance of Human Hepatitis C Virus Infection
Kinchen VJ, Zahid MN, Flyak AI, Soliman MG, Learn GH, Wang S, Davidson E, Doranz BJ, Ray SC, Cox AL, Crowe JE Jr, Bjorkman PJ, Shaw GM, Bailey JR.
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#20: HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design
Flyak AI, Ruiz S, Colbert MD, Luong T, Crowe JE Jr, Bailey JR, Bjorkman PJ.
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#19: Asymmetric antiviral effects of ebolavirus antibodies targeting glycoprotein stem and glycan cap
Ilinykh PA, Santos RI, Gunn BM, Kuzmina NA, Shen X, Huang K, Gilchuk P, Flyak AI, Younan P, Alter G, Crowe JE Jr, Bukreyev A.
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#18: Antibody-Dependent Enhancement of Ebola Virus Infection by Human Antibodies Isolated from Survivors
Kuzmina NA, Younan P, Gilchuk P, Santos RI, Flyak AI, Ilinykh PA, Huang K, Lubaki NM, Ramanathan P, Crowe JE Jr, Bukreyev A.
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#17: Multifunctional Pan-ebolavirus Antibody Recognizes a Site of Broad Vulnerability on the Ebolavirus Glycoprotein
Gilchuk P, Kuzmina N, Ilinykh PA, Huang K, Gunn BM, Bryan A, Davidson E, Doranz BJ, Turner HL, Fusco ML, Bramble MS, Hoff NA, Binshtein E, Kose N, Flyak AI, Flinko R, Orlandi C, Carnahan R, Parrish EH, Sevy AM, Bombardi RG, Singh PK, Mukadi P, Muyembe-Tamfum JJ, Ohi MD, Saphire EO, Lewis GK, Alter G, Ward AB, Rimoin AW, Bukreyev A, Crowe JE Jr.
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#16: Efficacy of Human Monoclonal Antibody Monotherapy Against Bundibugyo Virus Infection in Nonhuman Primates
Gilchuk P, Mire CE, Geisbert JB, Agans KN, Deer DJ, Cross RW, Slaughter JC, Flyak AI, Mani J, Pauly MH, Velasco J, Whaley KJ, Zeitlin L, Geisbert TW, Crowe JE Jr.
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#15: Broadly neutralizing antibodies from human survivors target a conserved site in the Ebola virus glycoprotein HR2-MPER region
Flyak AI, Kuzmina N, Murin CD, Bryan C, Davidson E, Gilchuk P, Gulka CP, Ilinykh PA, Shen X, Huang K, Ramanathan P, Turner H, Fusco ML, Lampley R, Kose N, King H, Sapparapu G, Doranz BJ, Ksiazek TG, Wright DW, Saphire EO, Ward AB, Bukreyev A, Crowe JE Jr.
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#14: The Marburgvirus-Neutralizing Human Monoclonal Antibody MR191 Targets a Conserved Site to Block Virus Receptor Binding
King LB, Fusco ML, Flyak AI, Ilinykh PA, Huang K, Gunn B, Kirchdoerfer RN, Hastie KM, Sangha AK, Meiler J, Alter G, Bukreyev A, Crowe JE Jr, Saphire EO.
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#13: Synergistic anti-HCV broadly neutralizing human monoclonal antibodies with independent mechanisms
Mankowski MC, Kinchen VJ, Wasilewski LN, Flyak AI, Ray SC, Crowe JE Jr, Bailey JR.
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#12: Broadly neutralizing antibodies with few somatic mutations and hepatitis C virus clearance
Bailey JR, Flyak AI, Cohen VJ, Li H, Wasilewski LN, Snider AE, Wang S, Learn GH, Kose N, Loerinc L, Lampley R, Cox AL, Pfaff JM, Doranz BJ, Shaw GM, Ray SC, Crowe JE Jr.
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#11: Therapeutic treatment of Marburg and Ravn virus infection in nonhuman primates with a human monoclonal antibody
Mire CE, Geisbert JB, Borisevich V, Fenton KA, Agans KN, Flyak AI, Deer DJ, Steinkellner H, Bohorov O, Bohorova N, Goodman C, Hiatt A, Kim DH, Pauly MH, Velasco J, Whaley KJ, Crowe JE Jr, Zeitlin L, Geisbert TW.
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#10: A "Trojan horse" bispecific-antibody strategy for broad protection against ebolaviruses
Wec AZ, Nyakatura EK, Herbert AS, Howell KA, Holtsberg FW, Bakken RR, Mittler E, Christin JR, Shulenin S, Jangra RK, Bharrhan S, Kuehne AI, Bornholdt ZA, Flyak AI, Saphire EO, Crowe JE Jr, Aman MJ, Dye JM, Lai JR, Chandran K.
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#9: Structures of Ebola virus GP and sGP in complex with therapeutic antibodies
Pallesen J, Murin CD, de Val N, Cottrell CA, Hastie KM, Turner HL, Fusco ML, Flyak AI, Zeitlin L, Crowe JE Jr, Andersen KG, Saphire EO, Ward AB.
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#8: Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies
Bornholdt ZA, Ndungo E, Fusco ML, Bale S, Flyak AI, Crowe JE Jr, Chandran K, Saphire EO.
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#7: Chimeric Filoviruses for Identification and Characterization of Monoclonal Antibodies
Ilinykh PA, Shen X, Flyak AI, Kuzmina N, Ksiazek TG, Crowe JE Jr, Bukreyev A.
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#6: Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection
Flyak AI, Shen X, Murin CD, Turner HL, David JA, Fusco ML, Lampley R, Kose N, Ilinykh PA, Kuzmina N, Branchizio A, King H, Brown L, Bryan C, Davidson E, Doranz BJ, Slaughter JC, Sapparapu G, Klages C, Ksiazek TG, Saphire EO, Ward AB, Bukreyev A, Crowe JE Jr.
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#5: Isolation and Characterization of Broad and Ultrapotent Human Monoclonal Antibodies with Therapeutic Activity against Chikungunya Virus
Smith SA, Silva LA, Fox JM, Flyak AI, Kose N, Sapparapu G, Khomandiak S, Ashbrook AW, Kahle KM, Fong RH, Swayne S, Doranz BJ, McGee CE, Heise MT, Pal P, Brien JD, Austin SK, Diamond MS, Dermody TS, Crowe JE Jr.
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#4: Structural basis for Marburg virus neutralization by a cross-reactive human antibody
Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE Jr, Saphire EO.
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#3: Mechanism of human antibody-mediated neutralization of Marburg virus
Flyak AI, Ilinykh PA, Murin CD, Garron T, Shen X, Fusco ML, Hashiguchi T, Bornholdt ZA, Slaughter JC, Sapparapu G, Klages C, Ksiazek TG, Ward AB, Saphire EO, Bukreyev A, Crowe JE Jr.
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#2: IL-15 regulates homeostasis and terminal maturation of NKT cells
Gordy LE, Bezbradica JS, Flyak AI, Spencer CT, Dunkle A, Sun J, Stanic AK, Boothby MR, He YW, Zhao Z, Van Kaer L, Joyce S.
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#1: In silico analysis of the structure of variable domains of mouse single-chain antibodies specific to the human recombinant interferon beta1b
Flyak AI, Pavlova MV, Gilchuk PV.