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List of works by Thomas B. Kepler

A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays

scientific article published on 12 December 2010

A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays

article

A linear two-state model with complex dynamics

article

A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields

scientific article published on 8 January 2013

A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza

scientific article

Advantage of rare HLA supertype in HIV disease progression

scientific article

Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains

scientific article

Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity

scientific article published on 31 August 2016

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding.

scientific article published on 29 October 2007

An autoreactive antibody from an SLE/HIV-1 individual broadly neutralizes HIV-1.

scientific article published on 10 March 2014

An information-theoretic method for the treatment of plural ancestry in phylogenetics.

scientific article published on 21 March 2008

Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors

scientific article

Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization

scientific article

Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved

scientific article

B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study

scientific article

Bayesian Spatio-Dynamic Modeling in Cell Motility Studies: Learning Nonlinear Taxic Fields Guiding the Immune Response

article

Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial.

scientific article

Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin

scientific article

Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler

scientific article

Classification of osteoarthritis biomarkers: a proposed approach.

scientific article

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

scientific article

Comparison of multiple vaccine vectors in a single heterologous prime-boost trial

scientific article published on 20 September 2008

Cooperation of B cell lineages in induction of HIV-1-broadly neutralizing antibodies

scientific article

Correction: Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies

scientific article published on 02 December 2019

Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations

scientific article published in January 1998

Differential reactivity of germ line allelic variants of a broadly neutralizing HIV-1 antibody to a gp41 fusion intermediate conformation

scientific article published on 14 September 2011

Diversification of Ig superfamily genes in an invertebrate

scientific article published in July 2004

Drug concentration heterogeneity facilitates the evolution of drug resistance.

scientific article

Enhanced evolvability in immunoglobulin V genes under somatic hypermutation

scientific article published in July 1999

Envelope deglycosylation enhances antigenicity of HIV-1 gp41 epitopes for both broad neutralizing antibodies and their unmutated ancestor antibodies

scientific article

First qualification study of serum biomarkers as indicators of total body burden of osteoarthritis

scientific article (publication date: 17 March 2010)

Flow: Statistics, visualization and informatics for flow cytometry

scientific article published on 17 June 2008

Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains

scientific article

Geometric phase shifts under adiabatic parameter changes in classical dissipative systems

scientific article published in Physical Review Letters

H3N2 influenza infection elicits more cross-reactive and less clonally expanded anti-hemagglutinin antibodies than influenza vaccination

scientific article (publication date: 2011)

HIV DNA-Adenovirus Multiclade Envelope Vaccine Induces Gp41 Antibody Immunodominance in Rhesus Macaques

scientific article published on 09 August 2017

HIV-1 Envelope Mimicry of Host Enzyme Kynureninase Does Not Disrupt Tryptophan Metabolism.

scientific article published on 14 November 2016

HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies

scientific article published on 30 July 2015

High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies

scientific article published on 21 February 2009

Human immunodeficiency virus type 1-specific cytotoxic T lymphocyte activity is inversely correlated with HIV type 1 viral load in HIV type 1-infected long-term survivors

scientific article published in September 1999

Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies

scientific article

Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

scientific article

Immunogenic Stimulus for Germline Precursors of Antibodies that Engage the Influenza Hemagglutinin Receptor-Binding Site.

scientific article

Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies

scientific article

Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution

scientific article published in February 2001

Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions

scientific article published in February 2001

Improving peptide-MHC class I binding prediction for unbalanced datasets

scientific article

Inference of the HIV-1 VRC01 Antibody Lineage Unmutated Common Ancestor Reveals Alternative Pathways to Overcome a Key Glycan Barrier

article

Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain

scientific article

Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated

scientific article

Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations ⬇️

scientific article published on 23 November 2017

Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages

scientific article published on April 2016

Invertebrate immune systems--not homogeneous, not simple, not well understood

scientific article

Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields

scientific article published on 02 October 2019

Isolation of a human anti-HIV gp41 membrane proximal region neutralizing antibody by antigen-specific single B cell sorting

scientific article

Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage

scientific article published on 28 February 2015

Large-scale analysis of human heavy chain V(D)J recombination patterns

scientific article published on 27 February 2008

Longitudinal analysis of T-cell receptor variable beta chain repertoire in patients with acute graft-versus-host disease after allogeneic stem cell transplantation.

scientific article

Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody

scientific article

Measurement of cell migration on surface-bound fibronectin gradients

scientific article published in September 2004

Metastasizing patent claims on BRCA1

scientific article

Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide.

scientific article published on March 2017

Mixtures of Gaussian Wells: Theory, Computation, and Application

scientific article

Modeling and optimization of populations subject to time-dependent mutation ⬇️

scientific article published on August 29, 1995

Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells

scientific journal article

Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection

scientific article published on 17 January 2006

Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies

scientific article published on 17 September 2019

Open Source Research — the Power of Us

scientific article (publication date: 2006)

P19-50. Simulation of an MPER peptide samples epitope conformations of two broadly neutralizing antibodies

scientific article

Paradoxical suppression of poly-specific broadly neutralizing antibodies in the presence of strain-specific neutralizing antibodies following HIV infection

scientific article published on 16 February 2011

Pathway level analysis of gene expression using singular value decomposition

scientific article

Patient socioeconomic status is an independent predictor of operative mortality

scientific article published in September 2010

Physiological Insights from Cellular and Network Models of the Stomatogastric Nervous System of Lobsters and Crabs

article published in 1993

Potent and broad HIV-neutralizing antibodies in memory B cells and plasma

scientific article published on January 2017

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody

scientific article

Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection

scientific article published in August 1998

Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling

scientific article

Quantification of total T-cell receptor diversity by flow cytometry and spectratyping

scientific article

Quantitative evaluation of alternative mechanisms of blood and testes disposition of di(2-ethylhexyl) phthalate and mono(2-ethylhexyl) phthalate in rats

scientific article published in June 1999

Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth

scientific article published on 19 November 2020

Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation

scientific article

Reduction of conductance-based neuron models

scientific article

Rejoinder

Rescue of cytotoxic function in the CD8alpha knockout mouse by removal of MHC class II.

scientific article published on June 2008

Review of 54 patients with complete DiGeorge anomaly enrolled in protocols for thymus transplantation: outcome of 44 consecutive transplants

scientific article

Secretion of MIP-1β and MIP-1α by CD8(+) T-lymphocytes correlates with HIV-1 inhibition independent of coreceptor usage

scientific article published on 27 October 2010

Selective and site-specific mobilization of dermal dendritic cells and Langerhans cells by Th1- and Th2-polarizing adjuvants

scientific article

Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies

scientific article

Similar CD19 Dysregulation in Two Autoantibody-Associated Autoimmune Diseases Suggests a Shared Mechanism of B-Cell Tolerance Loss

scientific article published on 29 December 2006

SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements

scientific article published on 9 February 2010

SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations

scientific article published on 15 December 2005

Somatic hypermutation in B cells: an optimal control treatment

scientific article published in September 1993

SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization

scientific article

Spatial Mixture Modelling for Unobserved Point Processes: Examples in Immunofluorescence Histology

scientific article

Spatiotemporal programming of a simple inflammatory process

scientific article published on April 2007

Spike initiation and propagation on axons with slow inward currents

scientific article published on 01 January 1993

Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.

scientific article published on March 2017

Statistical analysis of antigen receptor spectratype data

scientific article

Statistical inference of sequence-dependent mutation rates.

scientific article

Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site

scientific article

Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee

scientific article published on 20 June 2015

Surface plasmon resonance measurements of plasma antibody avidity during primary and secondary responses to anthrax protective antigen

scientific article

Terminal deoxynucleotidyl transferases from elasmobranchs reveal structural conservation within vertebrates

scientific article published on 25 October 2003

The 185/333 gene family is a rapidly diversifying host-defense gene cluster in the purple sea urchin Strongylocentrotus purpuratus

scientific article

The Multiscale Systems Immunology project: software for cell-based immunological simulation

scientific article published on 28 April 2008

The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.

scientific article

The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly

scientific article

Toxin-coupled MHC class I tetramers can specifically ablate autoreactive CD8+ T cells and delay diabetes in nonobese diabetic mice

scientific article

Two distinct broadly neutralizing antibody specificities of different clonal lineages in a single HIV-1-infected donor: implications for vaccine design

scientific article published in February 2012

Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious

scientific article

Vaccine Elicitation of High Mannose-Dependent Neutralizing Antibodies against the V3-Glycan Broadly Neutralizing Epitope in Nonhuman Primates

scientific article

Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2

scientific article

Viral receptor-binding site antibodies with diverse germline origins

scientific article published on 7 May 2015

Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop

scientific article published on May 2017

Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood

scientific article published in March 2001

beta cell-specific CD4+ T cell clonotypes in peripheral blood and the pancreatic islets are distinct

scientific article published on 16 November 2009

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