Published in Phys Rev E Stat Nonlin Soft Matter Phys on December 04, 2013
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1. Mol Biol Evol (2015) 1.05
The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing. PLoS Comput Biol (2014) 1.02
Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. PLoS Comput Biol (2015) 0.82
Exploring the miRNA regulatory network using evolutionary correlations. PLoS Comput Biol (2014) 0.78
Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nat Commun (2016) 0.77
Scaling laws describe memories of host-pathogen riposte in the HIV population. Proc Natl Acad Sci U S A (2015) 0.77
In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evol (2017) 0.75
Inferring Microscopic Kinetic Rates from Stationary State Distributions. J Chem Theory Comput (2014) 0.75
Statistical Mechanics and Thermodynamics of Viral Evolution. PLoS One (2015) 0.75
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol (2017) 0.75
Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design. J Virol (2014) 0.75
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science (1996) 21.81
Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften (1971) 13.09
Diversity considerations in HIV-1 vaccine selection. Science (2002) 9.60
HIV and SIV CTL escape: implications for vaccine design. Nat Rev Immunol (2004) 5.18
Toward an AIDS vaccine. Science (2008) 4.83
Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol (2007) 4.64
Evidence for positive epistasis in HIV-1. Science (2004) 4.12
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog (2012) 3.35
The application of statistical physics to evolutionary biology. Proc Natl Acad Sci U S A (2005) 2.69
Design and pre-clinical evaluation of a universal HIV-1 vaccine. PLoS One (2007) 2.61
Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci U S A (2011) 2.37
Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog (2009) 2.36
HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One (2009) 2.16
Structural biology of HIV. J Mol Biol (1999) 2.03
Quasispecies theory in the context of population genetics. BMC Evol Biol (2005) 2.02
Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc Natl Acad Sci U S A (1999) 2.00
Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity (2013) 2.00
Quantifying influenza vaccine efficacy and antigenic distance. Vaccine (2006) 1.97
Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol (2006) 1.58
Dynamics of immune escape during HIV/SIV infection. PLoS Comput Biol (2008) 1.54
Sequence space localization in the immune system response to vaccination and disease. Phys Rev Lett (2003) 1.39
Error thresholds for molecular quasispecies as phase transitions: From simple landscapes to spin-glass models. Phys Rev A (1992) 1.37
Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet (2012) 1.17
Quasispecies theory for finite populations. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 1.03
Exact solution of the Eigen model with general fitness functions and degradation rates. Proc Natl Acad Sci U S A (2006) 0.94
A finite population model of molecular evolution: theory and computation. J Comput Biol (2012) 0.83
Population dynamics in a spin-glass model of chemical evolution. J Mol Evol (1989) 0.83
Physical theory of the competition that allows HIV to escape from the immune system. Phys Rev Lett (2006) 0.82
Surface ordering and finite-size effects in liquid-crystal films. Phys Rev B Condens Matter (1991) 0.78
Error catastrophe and phase transition in the empirical fitness landscape of HIV. Phys Rev E Stat Nonlin Soft Matter Phys (2015) 0.79
Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics. J Chem Phys (2015) 0.76