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Items: 1 to 50 of 85

1.

High-resolution definition of humoral immune response correlates of effective immunity against HIV.

Alter G, Dowell KG, Brown EP, Suscovich TJ, Mikhailova A, Mahan AE, Walker BD, Nimmerjahn F, Bailey-Kellogg C, Ackerman ME.

Mol Syst Biol. 2018 Mar 26;14(3):e7881. doi: 10.15252/msb.20177881.

2.

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site.

Cheng HD, Grimm SK, Gilman MS, Gwom LC, Sok D, Sundling C, Donofrio G, Hedestam GBK, Bonsignori M, Haynes BF, Lahey TP, Maro I, von Reyn CF, Gorny MK, Zolla-Pazner S, Walker BD, Alter G, Burton DR, Robb ML, Krebs SJ, Seaman MS, Bailey-Kellogg C, Ackerman ME.

JCI Insight. 2018 Mar 8;3(5). pii: 97018. doi: 10.1172/jci.insight.97018. [Epub ahead of print]

3.

Computationally-driven identification of antibody epitopes.

Hua CK, Gacerez AT, Sentman CL, Ackerman ME, Choi Y, Bailey-Kellogg C.

Elife. 2017 Dec 4;6. pii: e29023. doi: 10.7554/eLife.29023.

4.

Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity.

Salvat RS, Verma D, Parker AS, Kirsch JR, Brooks SA, Bailey-Kellogg C, Griswold KE.

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):E5085-E5093. doi: 10.1073/pnas.1621233114. Epub 2017 Jun 12.

5.

Pentavalent HIV-1 vaccine protects against simian-human immunodeficiency virus challenge.

Bradley T, Pollara J, Santra S, Vandergrift N, Pittala S, Bailey-Kellogg C, Shen X, Parks R, Goodman D, Eaton A, Balachandran H, Mach LV, Saunders KO, Weiner JA, Scearce R, Sutherland LL, Phogat S, Tartaglia J, Reed SG, Hu SL, Theis JF, Pinter A, Montefiori DC, Kepler TB, Peachman KK, Rao M, Michael NL, Suscovich TJ, Alter G, Ackerman ME, Moody MA, Liao HX, Tomaras G, Ferrari G, Korber BT, Haynes BF.

Nat Commun. 2017 Jun 8;8:15711. doi: 10.1038/ncomms15711.

6.

Multiplexed Fc array for evaluation of antigen-specific antibody effector profiles.

Brown EP, Dowell KG, Boesch AW, Normandin E, Mahan AE, Chu T, Barouch DH, Bailey-Kellogg C, Alter G, Ackerman ME.

J Immunol Methods. 2017 Apr;443:33-44. doi: 10.1016/j.jim.2017.01.010. Epub 2017 Feb 3.

7.
8.

Diversity of Antiviral IgG Effector Activities Observed in HIV-Infected and Vaccinated Subjects.

Huang Y, Ferrari G, Alter G, Forthal DN, Kappes JC, Lewis GK, Love JC, Borate B, Harris L, Greene K, Gao H, Phan TB, Landucci G, Goods BA, Dowell KG, Cheng HD, Bailey-Kellogg C, Montefiori DC, Ackerman ME.

J Immunol. 2016 Dec 15;197(12):4603-4612. Epub 2016 Nov 9.

9.

Corrigendum: Adjuvant-dependent innate and adaptive immune signatures of risk of SIVmac251 acquisition.

Vaccari M, Gordon SN, Fourati S, Schifanella L, Liyanage NP, Cameron M, Keele BF, Shen X, Tomaras GD, Billings E, Rao M, Chung AW, Dowell KG, Bailey-Kellogg C, Brown EP, Ackerman ME, Vargas-Inchaustegui DA, Whitney S, Doster MN, Binello N, Pegu P, Montefiori DC, Foulds K, Quinn DS, Donaldson M, Liang F, Loré K, Roederer M, Koup RA, McDermott A, Ma ZM, Miller CJ, Phan TB, Forthal DN, Blackburn M, Caccuri F, Bissa M, Ferrari G, Kalyanaraman V, Ferrari MG, Thompson D, Robert-Guroff M, Ratto-Kim S, Kim JH, Michael NL, Phogat S, Barnett SW, Tartaglia J, Venzon D, Stablein DM, Alter G, Sekaly RP, Franchini G.

Nat Med. 2016 Oct 6;22(10):1192. doi: 10.1038/nm1016-1192a. No abstract available.

PMID:
27711066
10.

Computationally driven antibody engineering enables simultaneous humanization and thermostabilization.

Choi Y, Ndong C, Griswold KE, Bailey-Kellogg C.

Protein Eng Des Sel. 2016 Oct;29(10):419-426. doi: 10.1093/protein/gzw024. Epub 2016 Jun 21.

11.

Design and engineering of deimmunized biotherapeutics.

Griswold KE, Bailey-Kellogg C.

Curr Opin Struct Biol. 2016 Aug;39:79-88. doi: 10.1016/j.sbi.2016.06.003. Epub 2016 Jun 17. Review.

12.

Adjuvant-dependent innate and adaptive immune signatures of risk of SIVmac251 acquisition.

Vaccari M, Gordon SN, Fourati S, Schifanella L, Liyanage NP, Cameron M, Keele BF, Shen X, Tomaras GD, Billings E, Rao M, Chung AW, Dowell KG, Bailey-Kellogg C, Brown EP, Ackerman ME, Vargas-Inchaustegui DA, Whitney S, Doster MN, Binello N, Pegu P, Montefiori DC, Foulds K, Quinn DS, Donaldson M, Liang F, Loré K, Roederer M, Koup RA, McDermott A, Ma ZM, Miller CJ, Phan TB, Forthal DN, Blackburn M, Caccuri F, Bissa M, Ferrari G, Kalyanaraman V, Ferrari MG, Thompson D, Robert-Guroff M, Ratto-Kim S, Kim JH, Michael NL, Phogat S, Barnett SW, Tartaglia J, Venzon D, Stablein DM, Alter G, Sekaly RP, Franchini G.

Nat Med. 2016 Jul;22(7):762-70. doi: 10.1038/nm.4105. Epub 2016 May 30. Erratum in: Nat Med. 2016 Oct 6;22(10 ):1192.

PMID:
27239761
13.

Polyfunctional HIV-Specific Antibody Responses Are Associated with Spontaneous HIV Control.

Ackerman ME, Mikhailova A, Brown EP, Dowell KG, Walker BD, Bailey-Kellogg C, Suscovich TJ, Alter G.

PLoS Pathog. 2016 Jan 8;12(1):e1005315. doi: 10.1371/journal.ppat.1005315. eCollection 2016 Jan.

14.

Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell.

He L, De Groot AS, Bailey-Kellogg C.

Vaccine. 2015 Nov 27;33(48):6922-9. doi: 10.1016/j.vaccine.2015.08.099. Epub 2015 Oct 1.

PMID:
26428457
15.

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method.

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

BMC Bioinformatics. 2015 Sep 15;16:290. doi: 10.1186/s12859-015-0724-8.

16.

Antibody humanization by structure-based computational protein design.

Choi Y, Hua C, Sentman CL, Ackerman ME, Bailey-Kellogg C.

MAbs. 2015;7(6):1045-57. doi: 10.1080/19420862.2015.1076600. Epub 2015 Aug 7.

17.

Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance.

Blazanovic K, Zhao H, Choi Y, Li W, Salvat RS, Osipovitch DC, Fields J, Moise L, Berwin BL, Fiering SN, Bailey-Kellogg C, Griswold KE.

Mol Ther Methods Clin Dev. 2015 Jun 17;2:15021. doi: 10.1038/mtm.2015.21. eCollection 2015.

18.

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):629-39. doi: 10.1016/j.chembiol.2015.04.017.

19.

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 Jun;22(6):474-86. doi: 10.1089/cmb.2014.0289. Epub 2015 May 14.

20.

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.

21.

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 Jul;112(7):1306-18. doi: 10.1002/bit.25554. Epub 2015 Feb 23.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

PMID:
25157982
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

PMID:
24384701
37.

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.

38.

Bayesian reconstruction of P(r) directly from two-dimensional detector images via a Markov chain Monte Carlo method.

Paul S, Friedman AM, Bailey-Kellogg C, Craig BA.

J Appl Crystallogr. 2013 Apr 1;46(Pt 2):404-414. Epub 2013 Mar 5.

39.

The two-faced T cell epitope: examining the host-microbe interface with JanusMatrix.

Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, VerBerkmoes NC, Sztein MB, Losikoff PT, Martin WD, Rothman AL, De Groot AS.

Hum Vaccin Immunother. 2013 Jul;9(7):1577-86. doi: 10.4161/hv.24615. Epub 2013 Apr 12.

40.

Natural variation in Fc glycosylation of HIV-specific antibodies impacts antiviral activity.

Ackerman ME, Crispin M, Yu X, Baruah K, Boesch AW, Harvey DJ, Dugast AS, Heizen EL, Ercan A, Choi I, Streeck H, Nigrovic PA, Bailey-Kellogg C, Scanlan C, Alter G.

J Clin Invest. 2013 May;123(5):2183-92. doi: 10.1172/JCI65708. Epub 2013 Apr 8.

41.

Structure-guided deimmunization of therapeutic proteins.

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

J Comput Biol. 2013 Feb;20(2):152-65. doi: 10.1089/cmb.2012.0251.

42.

Ballast: a ball-based algorithm for structural motifs.

He L, Vandin F, Pandurangan G, Bailey-Kellogg C.

J Comput Biol. 2013 Feb;20(2):137-51. doi: 10.1089/cmb.2012.0246.

43.

Structure-based redesign of proteins for minimal T-cell epitope content.

Choi Y, Griswold KE, Bailey-Kellogg C.

J Comput Chem. 2013 Apr 5;34(10):879-91. doi: 10.1002/jcc.23213. Epub 2013 Jan 8.

44.

High-throughput, multiplexed IgG subclassing of antigen-specific antibodies from clinical samples.

Brown EP, Licht AF, Dugast AS, Choi I, Bailey-Kellogg C, Alter G, Ackerman ME.

J Immunol Methods. 2012 Dec 14;386(1-2):117-23. doi: 10.1016/j.jim.2012.09.007. Epub 2012 Sep 27.

45.

Design and analysis of immune-evading enzymes for ADEPT therapy.

Osipovitch DC, Parker AS, Makokha CD, Desrosiers J, Kett WC, Moise L, Bailey-Kellogg C, Griswold KE.

Protein Eng Des Sel. 2012 Oct;25(10):613-23. Epub 2012 Aug 16.

46.

Rapid determination of multiple linear kinase substrate motifs by mass spectrometry.

Kettenbach AN, Wang T, Faherty BK, Madden DR, Knapp S, Bailey-Kellogg C, Gerber SA.

Chem Biol. 2012 May 25;19(5):608-18. doi: 10.1016/j.chembiol.2012.04.011.

47.

Algorithms for optimizing cross-overs in DNA shuffling.

He L, Friedman AM, Bailey-Kellogg C.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S3. doi: 10.1186/1471-2105-13-S3-S3.

48.

MMFPh: a maximal motif finder for phosphoproteomics datasets.

Wang T, Kettenbach AN, Gerber SA, Bailey-Kellogg C.

Bioinformatics. 2012 Jun 15;28(12):1562-70. doi: 10.1093/bioinformatics/bts195. Epub 2012 Apr 23.

49.

Planning combinatorial disulfide cross-links for protein fold determination.

Xiong F, Friedman AM, Bailey-Kellogg C.

BMC Bioinformatics. 2011 Nov 24;12 Suppl 12:S5. doi: 10.1186/1471-2105-12-S12-S5.

50.

A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments.

He L, Friedman AM, Bailey-Kellogg C.

Proteins. 2012 Mar;80(3):790-806. doi: 10.1002/prot.23237. Epub 2011 Dec 16.

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