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Depletion of T Cell Epitopes in Lysostaphin Mitigates Anti-Drug Antibody Response and Enhances Antibacterial Efficacy In Vivo.

Zhao H, Verma D, Li W, Choi Y, Ndong C, Fiering SN, Bailey-Kellogg C, Griswold KE.

Chem Biol. 2015 May 21;22(5):629-639. doi: 10.1016/j.chembiol.2015.04.017.


Learning Sequence Determinants of Protein:Protein Interaction Specificity with Sparse Graphical Models.

Kamisetty H, Ghosh B, Langmead CJ, Bailey-Kellogg C.

J Comput Biol. 2015 May 14. [Epub ahead of print]


Machine learning methods enable predictive modeling of antibody feature:function relationships in RV144 vaccinees.

Choi I, Chung AW, Suscovich TJ, Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, O'Connell RJ, Francis D, Robb ML, Michael NL, Kim JH, Alter G, Ackerman ME, Bailey-Kellogg C.

PLoS Comput Biol. 2015 Apr 13;11(4):e1004185. doi: 10.1371/journal.pcbi.1004185. eCollection 2015 Apr.


Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads.

Salvat RS, Choi Y, Bishop A, Bailey-Kellogg C, Griswold KE.

Biotechnol Bioeng. 2015 Feb 5. doi: 10.1002/bit.25554. [Epub ahead of print]


Structure-based design of combinatorial mutagenesis libraries.

Verma D, Grigoryan G, Bailey-Kellogg C.

Protein Sci. 2015 May;24(5):895-908. doi: 10.1002/pro.2642. Epub 2015 Mar 2.


Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate.

Salvat RS, Parker AS, Choi Y, Bailey-Kellogg C, Griswold KE.

PLoS Comput Biol. 2015 Jan 8;11(1):e1003988. doi: 10.1371/journal.pcbi.1003988. eCollection 2015 Jan.


Immune camouflage: relevance to vaccines and human immunology.

De Groot AS, Moise L, Liu R, Gutierrez AH, Tassone R, Bailey-Kellogg C, Martin W.

Hum Vaccin Immunother. 2014;10(12):3570-5. doi: 10.4161/hv.36134.


Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models.

Kamisetty H, Ghosh B, Langmead CJ, Bailey-Kellogg C.

Res Comput Mol Biol. 2014;8394:129-143.


Smarter vaccine design will circumvent regulatory T cell-mediated evasion in chronic HIV and HCV infection.

Moise L, Terry F, Gutierrez AH, Tassone R, Losikoff P, Gregory SH, Bailey-Kellogg C, Martin WD, De Groot AS.

Front Microbiol. 2014 Oct 6;5:502. doi: 10.3389/fmicb.2014.00502. eCollection 2014.


Identification of antibody glycosylation structures that predict monoclonal antibody Fc-effector function.

Chung AW, Crispin M, Pritchard L, Robinson H, Gorny MK, Yu X, Bailey-Kellogg C, Ackerman ME, Scanlan C, Zolla-Pazner S, Alter G.

AIDS. 2014 Nov 13;28(17):2523-30. doi: 10.1097/QAD.0000000000000444.


HCV epitope, homologous to multiple human protein sequences, induces a regulatory T cell response in infected patients.

Losikoff PT, Mishra S, Terry F, Gutierrez A, Ardito MT, Fast L, Nevola M, Martin WD, Bailey-Kellogg C, De Groot AS, Gregory SH.

J Hepatol. 2015 Jan;62(1):48-55. doi: 10.1016/j.jhep.2014.08.026. Epub 2014 Aug 23.


Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage.

He L, De Groot AS, Gutierrez AH, Martin WD, Moise L, Bailey-Kellogg C.

BMC Bioinformatics. 2014;15 Suppl 4:S1. doi: 10.1186/1471-2105-15-S4-S1. Epub 2014 Mar 19.


Stoichiometries and affinities of interacting proteins from concentration series of solution scattering data: decomposition by least squares and quadratic optimization.

Chandola H, Williamson TE, Craig BA, Friedman AM, Bailey-Kellogg C.

J Appl Crystallogr. 2014 May 10;47(Pt 3):899-914. eCollection 2014 Jun 1.


CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production.

Bailey-Kellogg C, Gutiérrez AH, Moise L, Terry F, Martin WD, De Groot AS.

Biotechnol Bioeng. 2014 Nov;111(11):2170-82. doi: 10.1002/bit.25286. Epub 2014 Jul 14.


Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate.

Salvat RS, Parker AS, Guilliams A, Choi Y, Bailey-Kellogg C, Griswold KE.

Cell Mol Life Sci. 2014 Dec;71(24):4869-80. doi: 10.1007/s00018-014-1652-x. Epub 2014 Jun 1.


A high throughput MHC II binding assay for quantitative analysis of peptide epitopes.

Salvat R, Moise L, Bailey-Kellogg C, Griswold KE.

J Vis Exp. 2014 Mar 25;(85). doi: 10.3791/51308.


Polyfunctional Fc-effector profiles mediated by IgG subclass selection distinguish RV144 and VAX003 vaccines.

Chung AW, Ghebremichael M, Robinson H, Brown E, Choi I, Lane S, Dugast AS, Schoen MK, Rolland M, Suscovich TJ, Mahan AE, Liao L, Streeck H, Andrews C, Rerks-Ngarm S, Nitayaphan S, de Souza MS, Kaewkungwal J, Pitisuttithum P, Francis D, Michael NL, Kim JH, Bailey-Kellogg C, Ackerman ME, Alter G.

Sci Transl Med. 2014 Mar 19;6(228):228ra38. doi: 10.1126/scitranslmed.3007736.


Gene and protein sequence optimization for high-level production of fully active and aglycosylated lysostaphin in Pichia pastoris.

Zhao H, Blazanovic K, Choi Y, Bailey-Kellogg C, Griswold KE.

Appl Environ Microbiol. 2014 May;80(9):2746-53. doi: 10.1128/AEM.03914-13. Epub 2014 Feb 21.


Improved multiple sequence alignments using coupled pattern mining.

Hossain KS, Patnaik D, Laxman S, Jain P, Bailey-Kellogg C, Ramakrishnan N.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1098-112. doi: 10.1109/TCBB.2013.36.


Divergent antibody subclass and specificity profiles but not protective HLA-B alleles are associated with variable antibody effector function among HIV-1 controllers.

Lai JI, Licht AF, Dugast AS, Suscovich T, Choi I, Bailey-Kellogg C, Alter G, Ackerman ME.

J Virol. 2014 Mar;88(5):2799-809. doi: 10.1128/JVI.03130-13. Epub 2013 Dec 18.

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