P. Hraber

发表

Evolving cellular automata to perform computations: mechanisms and impediments

Melanie Mitchell, J. Crutchfield, P. Hraber, 1994 .

Revisiting the Edge of Chaos: Evolving Cellular Automata to Perform Computations

James P. Crutchfield, Melanie Mitchell, Peter T. Hraber, 1993, Complex Syst..

S. Forrest, P. Hraber, Tim Jones, 1997 .

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

A. Perelson, G. Learn, B. Korber, 2009, The Journal of experimental medicine.

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

Chaim A. Schramm, K. Roskin, T. Kepler, 2013, Nature.

P. Hraber, E. Schultes, T. LaBean, 1996, RNA.

Estimating the Contributions of Selection and Self-Organization in RNA Secondary Structure

P. Hraber, E. Schultes, T. LaBean, 1999, Journal of Molecular Evolution.

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

T. Kepler, B. Korber, P. Hraber, 2017, Science Translational Medicine.

A parameterization of RNA sequence space

P. Hraber, E. Schultes, T. LaBean, 1999 .

Community assembly in a model ecosystem

P. Hraber, B. Milne, 1997 .

Formulation of stabilizer-free, nontoxic PLGA and elastin-PLGA nanoparticle delivery systems.

Steven B. Bradfute, P. Hraber, Jennifer S. Martinez, 2021, International journal of pharmaceutics.

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

Alan S. Perelson, Tanmoy Bhattacharya, Guido Ferrari, 2009, The Journal of experimental medicine.

Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

Fortunato Ferrara, Leslie Naranjo, P. Hraber, 2018, Front. Immunol..

Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State

P. Hraber, W. Fischer, B. McMahon, 2018, bioRxiv.

Structural transition and antibody binding of Ebola GP and Zika E proteins from pre-fusion to fusion-initiation states

P. Hraber, W. Fischer, B. McMahon, 2018, bioRxiv.

Detection of Critical Densities Associated with Pinon‐Juniper Woodland Ecotones

Timothy H. Keitt, Alan R. Johnson, Bruce T. Milne, 1996 .

Los Alamos Hepatitis C Virus Sequence and Human Immunology Databases: An Expanding Resource for Antiviral Research

P. Hraber, C. Kuiken, K. Yusim, 2007, Antiviral chemistry & chemotherapy.

Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization

Jerome H. Kim, B. Korber, P. Hraber, 2016, PLoS pathogens.

Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments

B. Korber, P. Hraber, J. Mascola, 2017, Journal of Virology.

Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth

Bette Korber, Gwo-Yu Chuang, Peter D. Kwong, 2018, Cell reports.

Resources to Discover and Use Short Linear Motifs in Viral Proteins

P. Hraber, B. McMahon, N. Generous, 2019, Trends in Biotechnology.

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

Chaim A. Schramm, T. Kepler, B. Korber, 2020, Science.

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

Chaim A. Schramm, T. Kepler, B. Korber, 2020, Science.

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

A. Lapedes, G. Learn, B. Korber, 2015, Viruses.

Polyvalent vaccine approaches to combat HIV‐1 diversity

B. Korber, P. Hraber, B. Hahn, 2017, Immunological reviews.

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

Ethan Romero-Severson, Bette Korber, Hui Li, 2018, Nature Communications.

Title Revisiting the Edge of Chaos : Evolving Cellular Automata to Perform Computations Permalink

P. Hraber, Mitchell, PerformComputationsMelanie, 2008 .

Envelope Vaccination Shapes Viral Envelope Evolution following Simian Immunodeficiency Virus Infection in Rhesus Monkeys

B. Korber, P. Hraber, J. Mascola, 2009, Journal of Virology.

Comparative analysis of expressed sequences in Phytophthora sojae.

B. Sobral, P. Hraber, M. Gijzen, 2000, Plant physiology.

Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences.

B. Sobral, P. Hraber, F. Govers, 1999, Fungal genetics and biology : FG & B.

Nucleoside-modified mRNA vaccines induce potent T follicular helper and germinal center B cell responses

D. Weissman, B. Korber, P. Hraber, 2018, The Journal of experimental medicine.

Correction: Corrigendum: Zika viral dynamics and shedding in rhesus and cynomolgus macaques

A. Perelson, P. Hraber, S. Higgs, 2017, Nature Medicine.

Epitope-Speciﬁc CD8 (cid:1) T Lymphocytes Cross-Recognize Mutant Simian Immunodeﬁciency Virus (SIV) Sequences but Fail To Contain Very Early Evolution and Eventual Fixation of Epitope Escape Mutations during SIV Infection (cid:1) †

P. Hraber, W. Fischer, Cliff Han, 2011 .

Extensive HLA class I allele promiscuity among viral CTL epitopes

Nebojsa Jojic, John Sidney, Alessandro Sette, 2007, European journal of immunology.

Envelope Vaccination Shapes Viral Envelope Evolution following Simian Immunodeﬁciency Virus Infection in Rhesus Monkeys (cid:1)

B. Korber, P. Hraber, J. Mascola, 2009 .

T-Cell Vaccination Reduces Simian Immunodeﬁciency Virus Levels in Semen (cid:1)

P. Hraber, J. Mascola, N. Letvin, 2009 .

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

Tanmoy Bhattacharya, Eric Hunter, Debrah I Boeras, 2011, Proceedings of the National Academy of Sciences.

Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

Alan S. Perelson, Hui Li, Tanmoy Bhattacharya, 2012, PLoS pathogens.

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

Feng Gao, Bette Korber, Tongye Shen, 2011, PLoS pathogens.

The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research

Jennifer W. Weller, Bruno W. S. Sobral, Peter T. Hraber, 2000, Nucleic Acids Res..

Genital Tract Sequestration of SIV following Acute Infection

B. Korber, P. Hraber, J. Mascola, 2011, PLoS pathogens.

Vaccine Advances against Venezuelan, Eastern, and Western Equine Encephalitis Viruses

Steven B. Bradfute, P. Hraber, W. Fischer, 2020, Vaccines.

On the species of origin: diagnosing the source of symbiotic transcripts

P. Hraber, J. Weller, 2001, Genome Biology.

Clade C HIV-1 Envelope Vaccination Regimens Differ in Their Ability To Elicit Antibodies with Moderate Neutralization Breadth against Genetically Diverse Tier 2 HIV-1 Envelope Variants

B. Pulendran, P. Hraber, S. Kasturi, 2019, Journal of Virology.

Impact of Clade, Geography, and Age of the Epidemic on HIV-1 Neutralization by Antibodies

Jerome H. Kim, A. Lapedes, B. Korber, 2014, Journal of Virology.

Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes

William J Bruno, Carla Kuiken, C. Kuiken, 2006, Virology Journal.

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

Feng Gao, Hui Li, Guido Ferrari, 2012, The Journal of clinical investigation.

HLA and HIV Infection Progression: Application of the Minimum Description Length Principle to Statistical Genetics

Thomas B. Kepler, Peter T. Hraber, Bette T. Korber, 2005, ISBMDA.

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

Chaim A. Schramm, Cinque S. Soto, T. Kepler, 2016, Cell.

Zika viral dynamics and shedding in rhesus and cynomolgus macaques

A. Perelson, P. Hraber, S. Higgs, 2016, Nature Medicine.

The Genome Sequence DataBase (GSDB): improving data quality and data access

G. Singh, Adam C. Siepel, R. Thompson, 1998, Nucleic Acids Res..

Autologous Neutralizing Antibodies to the Transmitted/Founder Viruses Emerge Late after Simian Immunodeficiency Virus SIVmac251 Infection of Rhesus Monkeys

B. Korber, P. Hraber, N. Letvin, 2010, Journal of Virology.

Advantage of rare HLA supertype in HIV disease progression

James Theiler, Bette Korber, Robert Funkhouser, 2003, Nature Medicine.

Epitope-Specific CD8+ T Lymphocytes Cross-Recognize Mutant Simian Immunodeficiency Virus (SIV) Sequences but Fail To Contain Very Early Evolution and Eventual Fixation of Epitope Escape Mutations during SIV Infection

Bette Korber, Tanmoy Bhattacharya, Will Fischer, 2011, Journal of Virology.

Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1

Alan S. Perelson, Hui Li, Gary J. Nabel, 2009, The Journal of experimental medicine.

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

Alan S. Perelson, Feng Gao, Hui Li, 2012, PLoS pathogens.

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Alan S. Perelson, Hui Li, Tanmoy Bhattacharya, 2010, PLoS pathogens.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

B. Korber, P. Hraber, W. Fischer, 2013, BMC Bioinformatics.

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

Alan S. Perelson, Timothy C. Wallstrom, Tanmoy Bhattacharya, 2010, PloS one.

HIV-1 subtype C superinfected individuals mount low autologous neutralizing antibody responses prior to intrasubtype superinfection

P. Hraber, Tianwei Yu, J. Mulenga, 2012, Retrovirology.

Timing and source of subtype-C HIV-1 superinfection in the newly infected partner of Zambian couples with disparate viruses

P. Hraber, J. Mulenga, S. Allen, 2012, Retrovirology.

Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index.

William J. Bruno, Carla Kuiken, C. Kuiken, 2008, The Journal of general virology.

The hepatitis C sequence database in Los Alamos

Karina Yusim, Peter T. Hraber, Carla Kuiken, 2007, Nucleic Acids Res..

Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses.

B. Korber, P. Hraber, H. Liao, 2015, Cell host & microbe.

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

James Theiler, Karina Yusim, S. Gnanakaran, 2019, Cell host & microbe.

Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection

B. Korber, P. Hraber, J. Mascola, 2014, AIDS.

Neutralizing IgG at the Portal of Infection Mediates Protection against Vaginal Simian/Human Immunodeficiency Virus Challenge

P. Hraber, H. Liao, B. Haynes, 2013, Journal of Virology.

A parameterization of RNA sequence space

Erik Schultes, Thomas H. LaBean, Peter T. Hraber, 1999, Complex..

No Molecule Is an Island: Molecular Evolution and the Study of Sequence Space

Thomas H. LaBean, Peter Hraber, Erik A. Schultes, 2009, Algorithmic Bioprocesses.

TLR7 agonists induce transient viremia and reduce the viral reservoir in SIV-infected rhesus macaques on antiretroviral therapy

Jeffrey M. Gerold, William A. Lee, P. Hraber, 2018, Science Translational Medicine.

Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection

C. Kuiken, P. Hraber, K. Yusim, 2007, Hepatology.

Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies

Feng Gao, Tongqing Zhou, Thomas B. Kepler, 2014, Cell.

Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies

Raphael Gottardo, Hongmei Gao, Bette T. Korber, 2013, Journal of Virology.

Amplification patterns of three genomic regions predict distant recurrence in breast carcinoma.

P. Hraber, T. Bocklage, I. Rabinowitz, 2007, The Journal of molecular diagnostics : JMD.

HIV-1 Envelope Glycoproteins from Diverse Clades Differentiate Antibody Responses and Durability among Vaccinees

Allan C. deCamp, B. Korber, P. Hraber, 2018, Journal of Virology.

Recombinant renewable polyclonal antibodies

F. Lund-Johansen, P. Hraber, A. Bradbury, 2015, mAbs.

TRIM5 modulates penile mucosal acquisition of simian immunodeficiency virus in rhesus monkeys

B. Korber, P. Hraber, J. Mascola, 2011 .

The Ecology of Echo

Terry Jones, Stephanie Forrest, Peter T. Hraber, 1997, Artificial Life.

The TRIM5 Gene Modulates Penile Mucosal Acquisition of Simian Immunodeficiency Virus in Rhesus Monkeys

B. Korber, P. Hraber, J. Mascola, 2011, Journal of Virology.

Analysis of change in pinon-juniper woodlands based on aerial photography, 1930's-1980's

Alan R. Johnson, P. Hraber, B. Milne, 1999 .

T-Cell Vaccination Reduces Simian Immunodeficiency Virus Levels in Semen

P. Hraber, J. Mascola, N. Letvin, 2009, Journal of Virology.

Amphiphilic block copolymer delivery of a DNA vaccine against Zika virus.

Steven B. Bradfute, P. Hraber, B. Pitard, 2018, Vaccine.

Association of HLA class I supertypes with HIV-1 disease progression in the Chicago MACS: evidence for frequency-dependent selection

T. Kepler, B. Korber, P. Hraber, 2002 .

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

B. Korber, P. Hraber, B. Haynes, 2018, Nature Communications.

Correction for Hraber et al., “Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments”

B. Korber, P. Hraber, J. Mascola, 2018, Journal of Virology.

Dynamics, computation, and the “edge of chaos”: a re-examination

James P. Crutchfield, Melanie Mitchell, Peter Hraber, 1993, adap-org/9306003.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Mohan Krishnamoorthy, Thomas Leitner, Peter T. Hraber, 2013, BMC Bioinformatics.

A single, continuous metric to define tiered serum neutralization potency against HIV

B. Korber, P. Hraber, D. Montefiori, 2018, eLife.

P09-21 LB. Deep sequencing of HIV-1 from acute infection: low initial diversity, and rapid but variable CTL escape

P. Hraber, W. Fischer, Tanmoy Bhattacharya, 2009, Retrovirology.

Extensive HLA class I binding promiscuity among EBV- and HIV- derived cytotoxic T lymphocyte epitopes

Karina Yusim, Sharon Adams, F. M. Marincola, 2004 .

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

G. Learn, P. Hraber, B. Haynes, 2019, Cell host & microbe.

Zika viral dynamics and shedding in rhesus and cynomolgus macaques

A. Perelson, P. Hraber, S. Higgs, 2016, Nature Medicine.

Treatment With a TLR7 Agonist Induces Transient Viremia in SIV-Infected ART- Suppressed Monkeys

P. Hraber, T. Cihlar, J. Whitney, 2015 .

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

A. Perelson, B. Korber, P. Hraber, 2012, Journal of Clinical Investigation.

Revisiting the Edge of Chaos: Evolving Cellular Automata to Perform Computations

Melanie Mitchell, J. Crutchfield, P. Hraber, 1993, Complex Syst..

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

A. Perelson, G. Learn, B. Korber, 2009, The Journal of experimental medicine.