Published in Bioinformatics on June 22, 2007
Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PLoS One (2011) 2.36
Phylogenetic insights into regional HIV transmission. AIDS (2012) 1.18
Two independent pathways for self-recognition in Proteus mirabilis are linked by type VI-dependent export. MBio (2013) 1.15
Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission. PLoS One (2010) 1.13
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PLoS One (2009) 1.09
Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461. PLoS One (2011) 1.08
Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford) (2012) 1.04
De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae. PLoS One (2014) 0.98
RCDB: Renal Cancer Gene Database. BMC Res Notes (2012) 0.95
Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma (2012) 0.94
Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet (2014) 0.92
Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PLoS One (2007) 0.92
4E10-resistant HIV-1 isolated from four subjects with rare membrane-proximal external region polymorphisms. PLoS One (2010) 0.91
OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol (2012) 0.90
PcarnBase: development of a transcriptomic database for the brain coral Platygyra carnosus. Mar Biotechnol (NY) (2012) 0.90
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res (2014) 0.88
Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol (2014) 0.88
The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases. BMC Bioinformatics (2007) 0.87
Lack of Effectiveness of Antiretroviral Therapy in Preventing HIV Infection in Serodiscordant Couples in Uganda: An Observational Study. PLoS One (2015) 0.87
Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters. J Infect Dis (2015) 0.87
The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell (2017) 0.86
Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes. Planta (2013) 0.84
LipocalinPred: a SVM-based method for prediction of lipocalins. BMC Bioinformatics (2009) 0.83
Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics (2014) 0.83
Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE). PLoS One (2012) 0.79
MULTBLAST: A web application for multiple BLAST searches. Bioinformation (2010) 0.79
Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures. Retrovirology (2017) 0.79
Profile of T cell recognition of HIV type 1 consensus group M Gag and Nef peptides in a clade A1- and D-infected Ugandan population. AIDS Res Hum Retroviruses (2011) 0.78
Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. J Gen Virol (2015) 0.78
VH1-44 gene usage defines a subset of canine B-cell lymphomas associated with better patient survival. Vet Immunol Immunopathol (2013) 0.78
A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics (2014) 0.78
HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. Planta (2013) 0.78
A component of the Sec61 ER protein transporting pore is required for plant susceptibility to powdery mildew. Front Plant Sci (2013) 0.78
HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data. AIDS Res Hum Retroviruses (2015) 0.77
Comment on "The origins of sexually transmitted HIV among men who have sex with men". Sci Transl Med (2010) 0.77
A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology. Extremophiles (2014) 0.76
Evolutionary, Comparative and Functional Analyses of the Brassinosteroid Receptor Gene, BRI1, in Wheat and Its Relation to Other Plant Genomes. PLoS One (2015) 0.76
blastjs: a BLAST+ wrapper for Node.js. BMC Res Notes (2016) 0.76
FARME DB: a functional antibiotic resistance element database. Database (Oxford) (2017) 0.75
viruSITE-integrated database for viral genomics. Database (Oxford) (2016) 0.75
YeastWeb: a workset-centric web resource for gene family analysis in yeast. BMC Genomics (2010) 0.75
The Wheat Mediator Subunit TaMED25 Interacts with the Transcription Factor TaEIL1 to Negatively Regulate Disease Resistance against Powdery Mildew. Plant Physiol (2016) 0.75
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. BMC Bioinformatics (2009) 0.75
A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.). Plant Methods (2015) 0.75
Are PECTIN ESTERASE INHIBITOR Genes Involved in Mediating Resistance to Rhynchosporium commune in Barley? PLoS One (2016) 0.75
Human cancer databases (review). Oncol Rep (2014) 0.75
Pharmacometabolomics Informs Viromics toward Precision Medicine. Front Pharmacol (2016) 0.75
A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland. Sci Rep (2016) 0.75
The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair. BMC Plant Biol (2012) 0.75
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. PLoS One (2015) 0.75
Exploring new alleles for frost tolerance in winter rye. Theor Appl Genet (2017) 0.75
Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes. Front Microbiol (2017) 0.75
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med (2006) 10.34
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med (2009) 7.01
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol (2006) 6.30
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med (2009) 6.22
Towards an HIV cure: a global scientific strategy. Nat Rev Immunol (2012) 5.52
Genital HIV-1 RNA predicts risk of heterosexual HIV-1 transmission. Sci Transl Med (2011) 5.21
Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis (2008) 4.86
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med (2009) 4.79
Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science (2007) 4.60
Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol (2003) 4.56
Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature (2010) 4.35
Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature (2012) 3.83
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog (2010) 3.68
HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J Clin Invest (2005) 3.62
Tetherin-driven adaptation of Vpu and Nef function and the evolution of pandemic and nonpandemic HIV-1 strains. Cell Host Microbe (2009) 3.58
Decay of the HIV reservoir in patients receiving antiretroviral therapy for extended periods: implications for eradication of virus. J Infect Dis (2007) 3.50
Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat Immunol (2005) 3.23
Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. J Virol (2005) 2.82
Pervasive genomic recombination of HIV-1 in vivo. Genetics (2004) 2.79
Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature (2009) 2.78
Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J Virol (2008) 2.72
Virus population homogenization following acute human immunodeficiency virus type 1 infection. J Virol (2002) 2.71
Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nat Med (2011) 2.71
Wide variation in the multiplicity of HIV-1 infection among injection drug users. J Virol (2010) 2.67
Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences. J Virol (2003) 2.53
Selection on the human immunodeficiency virus type 1 proteome following primary infection. J Virol (2006) 2.48
Estimating the impact of plasma HIV-1 RNA reductions on heterosexual HIV-1 transmission risk. PLoS One (2010) 2.48
Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. J Virol (2003) 2.46
Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PLoS One (2011) 2.36
Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog (2009) 2.36
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32
Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy. J Virol (2003) 2.31
HIV-1 group M conserved elements vaccine. PLoS Pathog (2007) 2.28
Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. J Virol (2007) 2.26
Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. J Virol (2005) 2.25
Consensus and ancestral state HIV vaccines. Science (2003) 2.24
Dual HIV-1 infection associated with rapid disease progression. Lancet (2004) 2.17
HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. J Virol (2008) 2.14
Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope. Nat Immunol (2006) 2.11
Lung eQTLs to help reveal the molecular underpinnings of asthma. PLoS Genet (2012) 2.09
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS One (2008) 2.06
A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. J Virol (2006) 2.05
Coping with viral diversity in HIV vaccine design. PLoS Comput Biol (2007) 2.01
Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J Virol Methods (2006) 1.99
Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. J Immunol (2006) 1.98
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques (2010) 1.88
Equal plasma viral loads predict a similar rate of CD4+ T cell decline in human immunodeficiency virus (HIV) type 1- and HIV-2-infected individuals from Senegal, West Africa. J Infect Dis (2002) 1.87
Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. J Virol (2006) 1.82
Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res (2003) 1.79
Origin and biology of simian immunodeficiency virus in wild-living western gorillas. J Virol (2008) 1.76
Plasma viral loads during early HIV-1 infection are similar in subtype C- and non-subtype C-infected African seroconverters. J Infect Dis (2013) 1.74
Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med (2011) 1.73
HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. J Infect Dis (2008) 1.70
Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. J Virol (2003) 1.62
HIV-specific probabilistic models of protein evolution. PLoS One (2007) 1.61
Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS (2004) 1.51
Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS. J Virol (2002) 1.50
CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PLoS One (2012) 1.48
Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins. J Virol (2007) 1.46
The malagarasi river does not form an absolute barrier to chimpanzee movement in Western Tanzania. PLoS One (2013) 1.44
Novel genes for airway wall thickness identified with combined genome-wide association and expression analyses. Am J Respir Crit Care Med (2015) 1.44
Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol (2011) 1.41
Virus-specific CD8+ T-cell responses better define HIV disease progression than HLA genotype. J Virol (2010) 1.39
Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology (2008) 1.38
Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. J Virol (2007) 1.37
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
Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure. PLoS One (2011) 1.35