[HTML][HTML] Reverse vaccinology: developing vaccines in the era of genomics

A Sette, R Rappuoli - Immunity, 2010 - cell.com
The sequence of microbial genomes made all potential antigens of each pathogen available
for vaccine development. This increased by orders of magnitude potential vaccine targets in …

[HTML][HTML] Evolutionary analysis of the dynamics of viral infectious disease

OG Pybus, A Rambaut - Nature Reviews Genetics, 2009 - nature.com
Many organisms that cause infectious diseases, particularly RNA viruses, mutate so rapidly
that their evolutionary and ecological behaviours are inextricably linked. Consequently …

Efficient control of population structure in model organism association mapping

HM Kang, NA Zaitlen, CM Wade, A Kirby… - Genetics, 2008 - academic.oup.com
Genomewide association mapping in model organisms such as inbred mouse strains is a
promising approach for the identification of risk factors related to human diseases. However …

Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies

MS Seaman, H Janes, N Hawkins, LE Grandpre… - Journal of …, 2010 - Am Soc Microbiol
The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation of
current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the …

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

N Goonetilleke, MKP Liu… - Journal of experimental …, 2009 - rupress.org
Identification of the transmitted/founder virus makes possible, for the first time, a genome-
wide analysis of host immune responses against the infecting HIV-1 proteome. A complete …

[HTML][HTML] HIV-1 neutralizing antibody signatures and application to epitope-targeted vaccine design

CA Bricault, K Yusim, MS Seaman, H Yoon, J Theiler… - Cell host & …, 2019 - cell.com
Eliciting HIV-1-specific broadly neutralizing antibodies (bNAbs) remains a challenge for
vaccine development, and the potential of passively delivered bNAbs for prophylaxis and …

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

M Bonsignori, EF Kreider, D Fera… - Science translational …, 2017 - science.org
A preventive HIV-1 vaccine should induce HIV-1–specific broadly neutralizing antibodies
(bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to …

No evidence for distinct types in the evolution of SARS-CoV-2

OA MacLean, RJ Orton, JB Singer… - Virus …, 2020 - academic.oup.com
A recent study by Tang et al. claimed that two major types of severe acute respiratory
syndrome-coronavirus-2 (CoV-2) had evolved in the ongoing CoV disease-2019 pandemic …

Adaptation of HIV-1 to human leukocyte antigen class I

Y Kawashima, K Pfafferott, J Frater, P Matthews… - Nature, 2009 - nature.com
The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic
provides a rare opportunity to witness host–pathogen co-evolution involving humans. A focal …

Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty

J Parker, A Rambaut, OG Pybus - Infection, Genetics and Evolution, 2008 - Elsevier
Many recent studies have sought to quantify the degree to which viral phenotypic characters
(such as epidemiological risk group, geographic location, cell tropism, drug resistance state …