PubRank

Simon D W Frost

Author PubWeight™ 137.39‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 HyPhy: hypothesis testing using phylogenies. Bioinformatics 2004 17.33
2 Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005 10.21
3 Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 2005 8.62
4 Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 2010 6.14
5 Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 2006 5.94
6 GARD: a genetic algorithm for recombination detection. Bioinformatics 2006 4.88
7 Evaluation of respondent-driven sampling. Epidemiology 2012 4.75
8 An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol 2009 3.11
9 Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol 2008 3.04
10 A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol 2011 2.88
11 A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol 2004 2.65
12 Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population. J Infect Dis 2003 2.54
13 Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol 2006 2.48
14 Immune-driven recombination and loss of control after HIV superinfection. J Exp Med 2008 2.34
15 Phylodynamics of infectious disease epidemics. Genetics 2009 2.15
16 Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities. Addiction 2007 2.14
17 Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology 2006 2.07
18 A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol 2008 1.96
19 An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol 2007 1.82
20 A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 2009 1.81
21 Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol 2007 1.71
22 Evolutionary fingerprinting of genes. Mol Biol Evol 2009 1.64
23 Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission. J Infect Dis 2007 1.64
24 Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection. J Infect Dis 2007 1.59
25 Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol 2012 1.51
26 A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol 2004 1.42
27 Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinformatics 2008 1.40
28 Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit? Sex Transm Dis 2009 1.37
29 Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 2009 1.37
30 Individual and network factors associated with prevalent hepatitis C infection among rural Appalachian injection drug users. Am J Public Health 2012 1.35
31 Respondent driven sampling--where we are and where should we be going? Sex Transm Infect 2012 1.35
32 Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog 2007 1.31
33 Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity. AIDS 2002 1.28
34 Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Biol 2006 1.25
35 Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals. J Virol 2002 1.24
36 Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog 2011 1.21
37 Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol 2009 1.19
38 Evaluation of the role of location and distance in recruitment in respondent-driven sampling. Int J Health Geogr 2011 1.14
39 Beyond bushmeat: animal contact, injury, and zoonotic disease risk in Western Uganda. Ecohealth 2014 1.13
40 Capture-recapture methods and respondent-driven sampling: their potential and limitations. Sex Transm Infect 2011 1.13
41 Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions. AIDS 2002 1.12
42 Evolution of the interferon alpha gene family in eutherian mammals. Gene 2007 1.12
43 Epidemiological bridging by injection drug use drives an early HIV epidemic. Epidemics 2010 1.07
44 Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1. J Virol 2005 1.05
45 Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS One 2009 1.04
46 Detecting signatures of selection from DNA sequences using Datamonkey. Methods Mol Biol 2009 1.01
47 Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. PLoS One 2011 0.99
48 Hepatitis C virus and alanine aminotransferase kinetics following B-lymphocyte depletion with rituximab: evidence for a significant role of humoral immunity in the control of viremia in chronic HCV liver disease. Blood 2007 0.99
49 Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners. J Acquir Immune Defic Syndr 2006 0.97
50 Evolutionary model selection with a genetic algorithm: a case study using stem RNA. Mol Biol Evol 2006 0.97
51 Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populations. Virology 2008 0.94
52 Respondent driven sampling: determinants of recruitment and a method to improve point estimation. PLoS One 2013 0.93
53 Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection. J Virol 2004 0.93
54 Mixed adjuvant formulations reveal a new combination that elicit antibody response comparable to Freund's adjuvants. PLoS One 2012 0.93
55 Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virus-infected macaques: implications for challenge dose selection. J Virol 2011 0.92
56 Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California. Sex Transm Infect 2010 0.91
57 Sampling through time and phylodynamic inference with coalescent and birth-death models. J R Soc Interface 2014 0.88
58 Can non-lytic CD8+ T cells drive HIV-1 escape? PLoS Pathog 2013 0.87
59 Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Virus Genes 2007 0.86
60 Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels. J Acquir Immune Defic Syndr 2008 0.86
61 Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. J Virol 2007 0.85
62 Human immunodeficiency virus-1 RNA levels in cerebrospinal fluid exhibit a set point in clinically stable patients not receiving antiretroviral therapy. J Infect Dis 2003 0.85
63 Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China. AIDS Res Hum Retroviruses 2015 0.82
64 Association of antiretroviral resistance genotypes with response to therapy--comparison of three models. Antivir Ther 2002 0.80
65 Molecular and contextual markers of hepatitis C virus and drug abuse. Mol Diagn Ther 2009 0.80
66 Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. PLoS One 2013 0.75
67 Viral kinetics and hepatitis C. Hepatology 2003 0.75