Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants (Q36246646)

13 August 2017

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

1 reference

13 August 2017

2

1 reference

13 August 2017

Edward F Kreider

9

0 references

S Gnanakaran

S Gnanakaran

6

0 references

Peter T. Hraber

Peter Hraber

1

0 references

Tanmoy Bhattacharya

Tanmoy Bhattacharya

5

0 references

Beatrice H. Hahn

Beatrice H Hahn

12

0 references

David C. Montefiori

13

David C Montefiori

1 reference

13 August 2017

19

Barton F Haynes

1 reference

13 August 2017

11

George M Shaw

1 reference

13 August 2017

8

Gerald H Learn

1 reference

13 August 2017

14

S Munir Alam

1 reference

13 August 2017

16

M Anthony Moody

1 reference

13 August 2017

17

Hua-Xin Liao

1 reference

13 August 2017

15

Mattia Bonsignori

1 reference

13 August 2017

3

Kshitij Wagh

1 reference

13 August 2017

7

Alan S Lapedes

1 reference

13 August 2017

4

Elena E Giorgi

1 reference

13 August 2017

Yingying Li

10

1 reference

PMCID

4632389

13 August 2017

Feng Gao

18

1 reference

13 August 2017

21 October 2015

1 reference

13 August 2017

1 reference

13 August 2017

7

1 reference

13 August 2017

5443-5475

1 reference

13 August 2017

10

1 reference

Creative Commons Attribution 4.0 International

13 August 2017

start time

21 October 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

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Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design

1 October 2017

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Antibody responses to envelope glycoproteins in HIV-1 infection

1 October 2017

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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

1 October 2017

1 reference

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Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa

1 October 2017

1 reference

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The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations

1 October 2017

1 reference

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Structure and immune recognition of trimeric pre-fusion HIV-1 Env.

1 October 2017

1 reference

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Envelope variants circulating as initial neutralization breadth developed in two HIV-infected subjects stimulate multiclade neutralizing antibodies in rabbits.

1 October 2017

1 reference

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Emergence of broadly neutralizing antibodies and viral coevolution in two subjects during the early stages of infection with human immunodeficiency virus type 1

1 October 2017

1 reference

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Progress in HIV-1 vaccine development.

1 October 2017

1 reference

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

1 October 2017

1 reference

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

1 October 2017

1 reference

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

1 October 2017

1 reference

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Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

1 October 2017

1 reference

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Loss and recovery of genetic diversity in adapting populations of HIV

1 October 2017

1 reference

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

1 October 2017

1 reference

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Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes

1 October 2017

1 reference

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

HIV-1 neutralizing antibodies: understanding nature's pathways

1 October 2017

1 reference

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Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues

1 October 2017

1 reference

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Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120

1 October 2017

1 reference

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivo

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Detecting individual sites subject to episodic diversifying selection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Motif-optimized subtype A HIV envelope-based DNA vaccines rapidly elicit neutralizing antibodies when delivered sequentially

1 October 2017

1 reference

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Emergence of stable polymorphisms driven by evolutionary games between mutants

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

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Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

1 October 2017

1 reference

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Increasing the potency and breadth of an HIV antibody by using structure-based rational design

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Broad neutralization coverage of HIV by multiple highly potent antibodies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Sequential immunization with a subtype B HIV-1 envelope quasispecies partially mimics the in vivo development of neutralizing antibodies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Amphiphilic block copolymers enhance the cellular uptake of DNA molecules through a facilitated plasma membrane transport

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

The role of antibodies in HIV vaccines

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

HIV-1-specific antibody responses during acute and chronic HIV-1 infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

DNA/amphiphilic block copolymer nanospheres promote low-dose DNA vaccination

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virus

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Vaccines: correlates of vaccine-induced immunity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Viral Sequence Evolution in Acute Hepatitis C Virus Infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

HIV-specific probabilistic models of protein evolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Structural definition of a conserved neutralization epitope on HIV-1 gp120

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Adaptation to different human populations by HIV-1 revealed by codon-based analyses

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Not so different after all: a comparison of methods for detecting amino acid sites under selection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

WebLogo: A Sequence Logo Generator

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

APE: Analyses of Phylogenetics and Evolution in R language

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Antibody neutralization and escape by HIV-1

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Rapid evolution of the neutralizing antibody response to HIV type 1 infection

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Protection of Macaques against pathogenic simian/human immunodeficiency virus 89.6PD by passive transfer of neutralizing antibodies.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Prognosis in HIV-1 infection predicted by the quantity of virus in plasma

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

A new method for calculating evolutionary substitution rates

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Variable and conserved neutralization antigens of human immunodeficiency virus

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Sequence logos: a new way to display consensus sequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Progress in HIV-1 vaccine development

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Retrieval and on-the-fly alignment of sequence fragments from the HIV database.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

Multiple alignment using hidden Markov models.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4632389

22 September 2018

Identifiers

DOI

10.3390/V7102881

1 reference

13 August 2017

1 reference

1 reference

13 August 2017

1 reference

PMCID

4632389