List of works - Chris Bailey-Kellogg

A Chimeric Antigen Receptor That Binds to a Conserved Site on MICA

scientific article published on 09 October 2020

A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers

scientific article

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

scientific article published on 16 December 2011

A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs

scientific article published on 28 October 2011

A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers

scientific article published on 27 April 2011

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

scientific article

A random graph approach to NMR sequential assignment.

scientific article

A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry

scientific article

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions.

scientific article published in February 2011

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

scientific article published on 30 May 2016

Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins

scientific article

Algorithms for optimizing cross-overs in DNA shuffling

scientific article

Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination

scientific article

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

scientific article

Analysis of self-associating proteins by singular value decomposition of solution scattering data

scientific article

Analysis of sequence-reactivity space for protein-protein interactions

scientific article published in February 2005

Antibody Fab-Fc properties outperform titer in predictive models of SIV vaccine-induced protection

scientific article published on 02 May 2019

Antibody humanization by structure-based computational protein design.

scientific article

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

scientific article published on 15 May 2019

Ballast: a ball-based algorithm for structural motifs

scientific article published on February 2013

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

scientific article published on 5 March 2013

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

scientific article

Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition

scientific article published on 11 August 2020

Characterizing the space of interatomic distance distribution functions consistent with solution scattering data

scientific article

Combinatorial resurfacing of Dengue envelope protein domain III antigens selectively ablates epitopes associated with serotype-specific or infection-enhancing antibody responses

scientific article published on 23 June 2020

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity

scientific article published on 06 October 2021

Computationally driven antibody engineering enables simultaneous humanization and thermostabilization.

scientific article published on 21 June 2016

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

scientific article

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

scientific article

Computationally-driven identification of antibody epitopes.

scientific article published on 4 December 2017

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination

scientific article published on 31 August 2020

Contact replacement for NMR resonance assignment

scientific article

DAR-901 vaccine for the prevention of infection with Mycobacterium tuberculosis among BCG-immunized adolescents in Tanzania: A randomized controlled, double-blind phase 2b trial

scientific article published on 28 September 2020

Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo.

scientific article published on May 2015

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

scientific article

Design and engineering of deimmunized biotherapeutics.

scientific article published on 17 June 2016

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

scientific article published on 15 September 2015

DisruPPI: structure-based computational redesign algorithm for protein binding disruption.

scientific article

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

scientific article published on 18 December 2013

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

scientific article published on 9 November 2016

EpiSweep: Computationally Driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity While Maintaining Function

scientific article

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

scientific article published on 01 October 2016

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

scientific article published on 8 March 2018

Functional evolution within a protein superfamily

scientific article published in May 2006

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

scientific article published on 21 February 2014

Globally deimmunized lysostaphin evades human immune surveillance and enables highly efficacious repeat dosing

scientific article published on 02 September 2020

Graphical models of protein-protein interaction specificity from correlated mutations and interaction data

scientific article

Graphical models of residue coupling in protein families.

scientific article published in April 2008

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Hypergraph model of multi-residue interactions in proteins: sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination

scientific article

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

scientific article published on November 2014

Immune camouflage: relevance to vaccines and human immunology

scientific article published on January 2014

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations

article

Improved multiple sequence alignments using coupled pattern mining

scientific article

Induction of cross-reactive HIV-1 specific antibody responses by engineered V1V2 immunogens with reduced conformational plasticity

scientific article published on 17 March 2020

Inferential backbone assignment for sparse data

scientific article

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

scientific article

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

scientific article published on 22 April 2020

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

scientific article published on 01 January 2014

Learning sequence determinants of protein:protein interaction specificity with sparse graphical models

scientific article published on 14 May 2015

MMFPh: a maximal motif finder for phosphoproteomics datasets

scientific article

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

scientific article

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

scientific article

Mixture of Experts for Predicting Antibody-Antigen Binding Affinity from Antigen Sequence

Model-based assignment and inference of protein backbone Nuclear Magnetic Resonances.

scientific article

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

scientific article published on 02 February 2017

NMR structural inference of symmetric homo-oligomers

scientific article published on 30 June 2011

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

scientific article published on 8 April 2013

Optimization algorithms for functional deimmunization of therapeutic proteins

scientific article

Optimization of combinatorial mutagenesis.

scientific article

Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions

scientific article published in April 2011

Optimizing Bayes error for protein structure model selection by stability mutagenesis.

scientific article

Pareto Optimization of Combinatorial Mutagenesis Libraries

scientific article published on 23 July 2018

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

scientific article

Planning combinatorial disulfide cross-links for protein fold determination

scientific article

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

scientific article published on March 2014

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

scientific article published on 8 January 2016

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

scientific article published in December 2004

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

scientific article

Protein design by sampling an undirected graphical model of residue constraints

scientific article published on July 2009

Protein fragment swapping: a method for asymmetric, selective site-directed recombination

scientific article

Rapid determination of multiple linear kinase substrate motifs by mass spectrometry

scientific article

Reconsidering complete search algorithms for protein backbone NMR assignment

scientific article published on September 2005

Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules

scientific article

Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV

scientific article published on 03 September 2018

Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments

scientific article

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

scientific article published on 6 October 2014

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

scientific article

Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.

scientific article

Structure-based design of combinatorial mutagenesis libraries

scientific article published on 2 March 2015

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

scientific article published on 17 June 2015

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

scientific article published on 8 January 2013

Structure-guided deimmunization of therapeutic proteins

scientific article

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

scientific article published on 12 April 2013

Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen.

scientific article published in April 2018

List of works by Chris Bailey-Kellogg

A Chimeric Antigen Receptor That Binds to a Conserved Site on MICA

A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers

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

A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs

A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers

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

A random graph approach to NMR sequential assignment.

A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions.

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

Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins

Algorithms for optimizing cross-overs in DNA shuffling

Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

Analysis of self-associating proteins by singular value decomposition of solution scattering data

Analysis of sequence-reactivity space for protein-protein interactions

Antibody Fab-Fc properties outperform titer in predictive models of SIV vaccine-induced protection

Antibody humanization by structure-based computational protein design.

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

Ballast: a ball-based algorithm for structural motifs

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

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

Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition

Characterizing the space of interatomic distance distribution functions consistent with solution scattering data

Combinatorial resurfacing of Dengue envelope protein domain III antigens selectively ablates epitopes associated with serotype-specific or infection-enhancing antibody responses

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity

Computationally driven antibody engineering enables simultaneous humanization and thermostabilization.

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

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

Computationally-driven identification of antibody epitopes.

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination

Contact replacement for NMR resonance assignment

DAR-901 vaccine for the prevention of infection with Mycobacterium tuberculosis among BCG-immunized adolescents in Tanzania: A randomized controlled, double-blind phase 2b trial

Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo.

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

Design and engineering of deimmunized biotherapeutics.

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

DisruPPI: structure-based computational redesign algorithm for protein binding disruption.

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

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

EpiSweep: Computationally Driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity While Maintaining Function

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

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

Functional evolution within a protein superfamily

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

Globally deimmunized lysostaphin evades human immune surveillance and enables highly efficacious repeat dosing

Graphical models of protein-protein interaction specificity from correlated mutations and interaction data

Graphical models of residue coupling in protein families.

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

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

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

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

Hypergraph model of multi-residue interactions in proteins: sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination

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

Immune camouflage: relevance to vaccines and human immunology

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations

Improved multiple sequence alignments using coupled pattern mining

Induction of cross-reactive HIV-1 specific antibody responses by engineered V1V2 immunogens with reduced conformational plasticity

Inferential backbone assignment for sparse data

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

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

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

Learning sequence determinants of protein:protein interaction specificity with sparse graphical models

MMFPh: a maximal motif finder for phosphoproteomics datasets

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

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

Mixture of Experts for Predicting Antibody-Antigen Binding Affinity from Antigen Sequence

Model-based assignment and inference of protein backbone Nuclear Magnetic Resonances.

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

NMR structural inference of symmetric homo-oligomers

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

Optimization algorithms for functional deimmunization of therapeutic proteins

Optimization of combinatorial mutagenesis.

Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions

Optimizing Bayes error for protein structure model selection by stability mutagenesis.

Pareto Optimization of Combinatorial Mutagenesis Libraries

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

Planning combinatorial disulfide cross-links for protein fold determination

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