Research Topics
| Yi LiuSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
Molecular clock-like evolution of human immunodeficiency virus type 1Yi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, United States
Virology 329:101-8. 2004..Natural selection alone did not appear to obscure the clock-like evolution of HIV-1...- Selection dramatically reduces effective population size in HIV-1 infectionYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, 98195, USA
BMC Evol Biol 8:133. 2008..Although it is well known that selection can reduce Ne, high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size... - Waiting times for the appearance of cytotoxic T-lymphocyte escape mutants in chronic HIV-1 infectionYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, WA, 98195 8070, USA
Virology 347:140-6. 2006..Stochastic evolutionary forces, therefore, in addition to viral fitness costs and ineffective or attenuated CTL responses, must be taken into account when assessing the selection of CTL escape mutations... - Conserved HIV-1 epitopes continuously elicit subdominant cytotoxic T-lymphocyte responsesYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
J Infect Dis 200:1825-33. 2009..However, some studies have shown preferential or similar targeting of variable versus conserved epitopes during primary infection... - Novel cytotoxic T-lymphocyte escape mutation by a three-amino-acid insertion in the human immunodeficiency virus type 1 p6Pol and p6Gag late domain associated with drug resistanceJianhong Cao
Fred Hutchinson Cancer Research Center, D3 100, 1100 Fairview Avenue North, Seattle, WA 98109, USA
J Virol 82:495-502. 2008..Moreover, this escape mutation represents a novel mechanism whereby HIV-1 can alter its sequence within both the Gag and Pol proteins with potential functional consequences for viral replication and budding... - Selection on the human immunodeficiency virus type 1 proteome following primary infectionYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
J Virol 80:9519-29. 2006..Hence, a majority of the amino acids undergoing selection in this subject appeared to result from fitness-balanced CTL selection, confirming CTLs as a dominant selective force in HIV-1 infection... - Preinfection human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes failed to prevent HIV type 1 infection from strains genetically unrelated to viruses in long-term exposed partnersYi Liu
Department of Microbiology, University of Washington, Seattle, WA 98109, USA
J Virol 83:10821-9. 2009.... - Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escapeYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
J Virol 81:12179-88. 2007.... - HIV-1 envelope subregion length variation during disease progressionMarcel E Curlin
Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
PLoS Pathog 6:e1001228. 2010..V1V2 shortening during early and late-stage infection may reflect ineffective host immunity. Transmission from donors with chronic illness may have caused the modest increase in V1V2 length observed during the course of the pandemic... - Evolution of intrahost HIV-1 genetic diversity during chronic infectionDaniel Shriner
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
Evolution 60:1165-76. 2006..The metapopulation model links previous studies of viral dynamics and population genetics... - Virus-specific CD8+ T-cell responses better define HIV disease progression than HLA genotypeWarren L Dinges
Vaccine and Infectious Disease Institute, Statistical Center for HIV Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
J Virol 84:4461-8. 2010..These data suggest that vaccine immunogens should contain only conserved regions of HIV-1... - Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B virusesYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
Virology 374:229-33. 2008.... - Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processesJoshua T Herbeck
Department of Microbiology, SC 42, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
J Virol 85:7523-34. 2011..Furthermore, the diversity of HIV strains coupled with complex and individual-specific patterns of CTL escape did not reveal shared sequence characteristics of acute infection that could be harnessed for vaccine design... - DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sitesWenjie Deng
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
Biotechniques 48:405-8. 2010..DIVEIN is available at http://indra.mullins.microbiol.washington.edu/DIVEIN... - Dynamics of viral evolution and CTL responses in HIV-1 infectionYi Liu
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
PLoS ONE 6:e15639. 2011..Focusing early and rapidly proliferating CTL on persistent epitopes may be essential for durable viral control in HIV-1 infection... - Minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivityGirish S Kesturu
Thomas E. Starzl Transplantation Institute, Department of Surgery, School of Medicine, University of Pittsburgh, PA 15261, USA
Virology 348:437-48. 2006..COT or CON sequences derived from autologous virus samplings may be useful for increasing the sensitivity of assessments of immune reactivity against HIV... - Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cellsJustin R Bailey
Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
J Virol 80:6441-57. 2006..The sequences have been deposited in GenBank. The accession numbers are DQ 391282 to DQ 391351 (for env) and DQ 391352 to DQ 392955 (for RT)... - Properties of anti-gp41 core structure antibodies, which compete with sera of HIV-1-infected patientsOsamu Usami
Division of Infectious and Respiratory Diseases, Internal Medicine, Graduate School of Medicine, Tohoku University, 1-1 Seiryo-cho, Aoba-ku, Sendai-si, Miyagi-ken, Sendai 980-8574, Japan
Microbes Infect 7:650-7. 2005..69 and 98.6) but also against oligomeric gp41 specific epitope (binding site of mAb T26)... - Procedure for preparing peptide-major histocompatibility complex tetramers for direct quantification of antigen-specific cytotoxic T lymphocytesXian hui He
Key Laboratory of Ministry of Education of China for Tissue Transplantation and Immunology, Jinan University, Guangzhou 510632, Guangdong Province, China
World J Gastroenterol 11:4180-7. 2005..To establish a simplified method for generating peptide-major histocompatibility complex (MHC) class I tetramers... - Size reversion of a truncated DNAbeta associated with Tobacco curly shoot virusYajuan Qian
Institute of Biotechnology, Zhejiang University, Hangzhou 310029, PR China
Virus Res 131:288-92. 2008..The significance of these findings is discussed with respect to the constraints imposed on begomovirus genome size... - The Neurospora crassa circadian clockChristian Heintzen
Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
Adv Genet 58:25-66. 2007..In summarizing our current understanding of the molecular basis of the Neurospora circadian system, this chapter aims to elucidate the basic building blocks of model eukaryotic clocks as we understand them today... - Cloning, expression, and functional characterization of zebrafish Mist1Xiaofang Guo
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, PR China
Biochem Biophys Res Commun 359:20-6. 2007..These results suggest that Mist1 functions in an evolutionary conserved way as a key transcriptional regulator specific for exocrine pancreas development in zebrafish... - Phenotypic and functional analysis of LCMV gp33-41-specific CD8 T cells elicited by multiple peptide immunization in mice revealed the up-regulation of PD-1 expression on antigen-specific CD8 T cellsYi Liu
Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
Cell Mol Immunol 4:431-7. 2007.... - Phase determination of circadian gene expression in Synechococcus elongatus PCC 7942Hongtao Min
Department of Biology, Texas A and M University, College Station, TX 77843 3258, USA
J Biol Rhythms 19:103-12. 2004..elongatus. To test this hypothesis, they fused the well-characterized DNA topology-dependent Escherichia coli fis promoter to luciferase and showed that it acts as a class 2 promoter in S. elongatus...