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

scientific article

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants is …
instance of (P31):
scholarly articleQ13442814

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P818arXiv ID1508.00463
P356DOI10.3390/V7102881
P932PMC publication ID4632389
P698PubMed publication ID26506369
P5875ResearchGate publication ID280695579

P50authorBarton HaynesQ4865631
Edward F KreiderQ56808336
David C. MontefioriQ63302725
M Anthony MoodyQ73297881
George M. ShawQ78514357
Kshitij WaghQ87965060
Hua-Xin LiaoQ88608388
Munir AlamQ89520930
Alan LapedesQ102311895
Elena E GiorgiQ122828494
Gerald H LearnQ54541884
Beatrice H. HahnQ55293537
Tanmoy BhattacharyaQ55414889
Mattia BonsignoriQ56808332
Bette KorberQ30505218
Peter T. HraberQ37366689
S GnanakaranQ41047925
P2093author name stringFeng Gao
Yingying Li
P2860cites workNeutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infectionQ24538985
Sequence logos: a new way to display consensus sequencesQ24598387
Increasing the potency and breadth of an HIV antibody by using structure-based rational designQ24631510
Structural definition of a conserved neutralization epitope on HIV-1 gp120Q24655948
Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine DesignQ26801759
Antibody responses to envelope glycoproteins in HIV-1 infectionQ26991572
HIV-1 neutralizing antibodies: understanding nature's pathwaysQ27000480
Multiple alignment using hidden Markov modelsQ52361706
Progress in HIV-1 vaccine developmentQ56600657
Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C VirusQ27478199
Viral Sequence Evolution in Acute Hepatitis C Virus InfectionQ27484985
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virusQ27644501
Developmental pathway for potent V1V2-directed HIV-neutralizing antibodiesQ27644515
Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01Q27663293
Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 BindingQ27670829
Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep SequencingQ27671696
Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2Q27675879
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120Q27678306
Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domainsQ27684503
Progress in HIV-1 vaccine development.Q27693849
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0Q27860476
WebLogo: A Sequence Logo GeneratorQ27860646
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodQ27861000
Not so different after all: a comparison of methods for detecting amino acid sites under selectionQ28306719
Elucidation of hepatitis C virus transmission and early diversification by single genome sequencingQ28482493
Loss and recovery of genetic diversity in adapting populations of HIVQ28539052
Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogeniesQ28602877
APE: Analyses of Phylogenetics and Evolution in R languageQ29546513
Antibody neutralization and escape by HIV-1Q29547345
Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine targetQ29547347
A new method for calculating evolutionary substitution ratesQ29615058
Broad neutralization coverage of HIV by multiple highly potent antibodiesQ29615361
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biologyQ29617583
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope geneQ29617599
Rapid evolution of the neutralizing antibody response to HIV type 1 infectionQ29618603
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionQ29619510
Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1Q29619511
Prognosis in HIV-1 infection predicted by the quantity of virus in plasmaQ29619980
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infectionQ30469621
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencingQ36540055
Emergence of stable polymorphisms driven by evolutionary games between mutantsQ36752893
Vaccines: correlates of vaccine-induced immunityQ37193062
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infectionQ37273158
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infectionQ37273195
The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility.Q37667754
The role of antibodies in HIV vaccinesQ37700725
Variable and conserved neutralization antigens of human immunodeficiency virusQ38891686
Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity MaturationQ38988188
DNA/amphiphilic block copolymer nanospheres promote low-dose DNA vaccinationQ39509643
Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.Q40016358
Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infectionQ40341996
Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestorsQ41818598
Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodiesQ42170932
Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infectionQ45771143
Retrieval and on-the-fly alignment of sequence fragments from the HIV database.Q48679004
Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residuesQ30644992
Adaptation to different human populations by HIV-1 revealed by codon-based analysesQ33247450
HIV-specific probabilistic models of protein evolutionQ33286820
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysisQ33592278
Protection of Macaques against pathogenic simian/human immunodeficiency virus 89.6PD by passive transfer of neutralizing antibodies.Q33647300
Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencingQ33680395
Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infectionQ33702217
Estimating time since infection in early homogeneous HIV-1 samples using a poisson modelQ33727328
Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virusQ33955998
Cooperation of B cell lineages in induction of HIV-1-broadly neutralizing antibodiesQ34114798
B-cell-lineage immunogen design in vaccine development with HIV-1 as a case studyQ34273373
Detecting individual sites subject to episodic diversifying selectionQ34341393
Envelope variants circulating as initial neutralization breadth developed in two HIV-infected subjects stimulate multiclade neutralizing antibodies in rabbits.Q34594513
Emergence of broadly neutralizing antibodies and viral coevolution in two subjects during the early stages of infection with human immunodeficiency virus type 1Q34594701
Amphiphilic block copolymers enhance the cellular uptake of DNA molecules through a facilitated plasma membrane transportQ34609270
Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks.Q34806845
A multiple-alignment based primer design algorithm for genetically highly variable DNA targetsQ34960846
Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individualsQ34962766
Sequential immunization with a subtype B HIV-1 envelope quasispecies partially mimics the in vivo development of neutralizing antibodiesQ34982715
Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypesQ35034268
HIV-1-specific antibody responses during acute and chronic HIV-1 infectionQ35096836
Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan AfricaQ35115540
Structure and immune recognition of trimeric pre-fusion HIV-1 Env.Q35142291
Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infectionQ35274776
The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutationsQ35377813
Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestorsQ35382871
Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escapeQ36000736
Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant VirusesQ36053810
Motif-optimized subtype A HIV envelope-based DNA vaccines rapidly elicit neutralizing antibodies when delivered sequentiallyQ36249053
Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escapeQ36388754
Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivoQ36414891
Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 InfectionQ36444787
Vertical T cell immunodominance and epitope entropy determine HIV-1 escapeQ36497283
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue10
P304page(s)5443-5475
P577publication date2015-10-21
P1433published inVirusesQ7935305
P1476titleLongitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants
P478volume7

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cites work (P2860)
Q36337888Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.
Q52595348Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak.
Q39108751Antibody-virus co-evolution in HIV infection: paths for HIV vaccine development
Q47108789Antigenic Variation and Immune Escape in the MTBC.
Q57796335Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth
Q52578356HIV Resistance Prediction to Reverse Transcriptase Inhibitors: Focus on Open Data.
Q34527469HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1.
Q47549195Immunogenicity in rabbits of SOSIP trimers from clades A, B and C, given individually, sequentially or in combinations
Q27644415Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody
Q47218587Multi-Envelope HIV-1 Vaccine Development: Two Targeted Immune Pathways, One Desired Protective Outcome.
Q39108740Polyvalent vaccine approaches to combat HIV-1 diversity
Q59351843Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals
Q30490942Stabilized HIV-1 envelope glycoprotein trimers for vaccine use.
Q57091049Stabilizing HIV-1 envelope glycoprotein trimers to induce neutralizing antibodies
Q40290521Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Q64090748The evolution of a super-swarm of foot-and-mouth disease virus in cattle

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