M A Jensen
Affiliation: University of Washington
- Molecular population genetics and evolution of a prion-like protein in Saccharomyces cerevisiaeM A Jensen
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genetics 159:527-35. 2001..We also conclude that the clinical strains of S. cerevisiae are not recently derived and that outcrossing between strains in S. cerevisiae may be relatively rare in nature...
- Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequencesMark A Jensen
Department of Microbiology, University of Washington, Seattle, Washington 98195 8070, USA
J Virol 77:13376-88. 2003..We found that X4 viruses were lost in two ways: by the dying off of an established X4 lineage or by mutation back to low-scoring V3 loops...
- Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infectionDaniel Shriner
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
Genetics 166:1155-64. 2004..We conclude that the genetic variation in these data sets can be explained by a predominance of random genetic drift of neutral mutations with brief episodes of natural selection that were frequently masked by recombination...
- A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequencesMark A Jensen
Department of Microbiology, University of Washington, Seattle, WA, USA
J Virol 80:4698-704. 2006..We present bioinformatic evidence that particular sites may influence coreceptor usage differently, depending on the subtype...
- 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...
- Dual HIV-1 infection associated with rapid disease progressionGeoffrey S Gottlieb
Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195 8070, USA
Lancet 363:619-22. 2004..4 and <3.1 years, respectively). Our findings should prompt larger studies to assess the effect of dual infection at the population level...
- Predicting HIV-1 coreceptor usage with sequence analysisMark A Jensen
Department of Microbiology, Box 358070, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
AIDS Rev 5:104-12. 2003..Further development of these methods, by extending analysis to regions outside the V3 loop and to clades beyond subtype B, will extend our understanding of HIV-1 pathogenesis and inform treatment strategies...
- Potential impact of recombination on sitewise approaches for detecting positive natural selectionDaniel Shriner
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
Genet Res 81:115-21. 2003....
- Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartmentsDavid C Nickle
Departmentof Microbiology, University of Washington School of Medicine, Seattle 98195, USA
J Virol 77:5540-6. 2003..We report that existing statistical methods work quite well at detecting viral compartments, and we learn from simulations that viral divergence from a calculated most recent common ancestor is a strong predictor of viral reservoirs...
- HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case reportGeoffrey S Gottlieb
Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA 98195, USA
Clin Infect Dis 45:501-9. 2007..The occurrence of human immunodeficiency virus type 1 (HIV-1) superinfection has implications for vaccine development and our understanding of HIV pathogenesis and transmission...
- Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteinsMorgane Rolland
Department of Microbiology SC 42, University of Washington, Seattle, WA 98195 8070, USA
J Virol 81:8507-14. 2007....
- Anti-S-nitrosocysteine antibodies are a predictive marker for demyelination in experimental autoimmune encephalomyelitis: implications for multiple sclerosisAnne I Boullerne
Department of Neurology, University of Chicago, Chicago, Illinois 60637, USA
J Neurosci 22:123-32. 2002..Anti-SNO-cysteine Abs are also elevated at times of MS attacks and in progressive disease, suggesting a possible role for these Abs, measurable in blood, as a biological marker for clinical activity...
- Evolutionary dynamics of HIV-1 and the control of AIDSJ I Mullins
Departments of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
Curr Top Microbiol Immunol 299:171-92. 2006..This suggests some optimism for those attempting to identify sets of antigens that can generate effective humoral and cellular immune responses against HIV...
- HIV-specific probabilistic models of protein evolutionDavid C Nickle
Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
PLoS ONE 2:e503. 2007..We argue that our model derivation procedure is immediately applicable to other organisms with extensive sequence data available, such as Hepatitis C and Influenza A viruses...
- A novel Fc gamma receptor ligand augments humoral responses by targeting antigen to Fc gamma receptorsMark A Jensen
Department of Neurology, University of Chicago, Chicago, IL 60637, USA
Eur J Immunol 37:1139-48. 2007..008). Immunization with HSA1R4 yields greater T cell reactivity to HSA1 ex vivo than immunization with HSA1Fc (p<0.004). Linking antigenic peptides to linear HCH2 polymers may facilitate vaccine development...
- Immunoglobulin-like transcript 3, an inhibitor of T cell activation, is reduced on blood monocytes during multiple sclerosis relapses and is induced by interferon beta-1bMark A Jensen
Department of Neurology, The University of Chicago, Chicago, IL 60637, USA
Mult Scler 16:30-8. 2010..These findings identify a putative novel mechanism for the therapeutic benefit bestowed by Interferon beta and a new target for therapeutic intervention in relapsing-remitting multiple sclerosis...
- Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulansMark A Jensen
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 1573, USA
Genetics 160:493-507. 2002..We find evidence for recombinational exchange at this locus, and both species appear to be fixed for an insertion of the transposable element HB in an intron of ankyrin...
- Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progressionRyan M Troyer
Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
J Virol 79:9006-18. 2005..These data provide in vivo evidence that increasing HIV-1 replication efficiency may be related to a concomitant increase in HIV-1 diversity, which in turn may be a determining factor in disease progression...
- Consensus and ancestral state HIV vaccinesDavid C Nickle
Science 299:1515-8; author reply 1515-8. 2003
- Genetic characterization of rebounding human immunodeficiency virus type 1 in plasma during multiple interruptions of highly active antiretroviral therapyMark Dybul
Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
J Virol 77:3229-37. 2003..In addition, the data suggest that there may be multiple compartments contributing to the rebound of plasma viremia and to viral diversity from cycle to cycle of intermittent therapy...
- Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapyZabrina L Brumme
BC Centre for Excellence in HIV AIDS, St Paul s Hospital, The Faculty of Medicine, University of British Columbia, 603 1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6
AIDS 18:F1-9. 2004..We wished to determine the impact of specific V3 genotypes associated with viral phenotype and co-receptor usage on response to initial triple antiretroviral therapy...
- Predicting disease outcomes in the clinicMark A Jensen
Nat Biotechnol 26:611-2; author reply 6112-3. 2008