|HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins|
ZL Brumme, M John, JM Carlson, CJ Brumme, D Chan, MA Brockman, ...
PLoS One 4 (8), e6687, 2009
|Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients|
LC Swenson, T Mo, WWY Dong, X Zhong, CK Woods, MA Jensen, ...
Journal of Infectious Diseases 203 (2), 237-245, 2011
|Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc|
LC Swenson, T Mo, WWY Dong, X Zhong, CK Woods, A Thielen, ...
Clinical infectious diseases 53 (7), 732-742, 2011
|Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and “deep” sequencing to plasma RNA and proviral DNA|
LC Swenson, A Moores, AJ Low, A Thielen, W Dong, C Woods, ...
JAIDS Journal of Acquired Immune Deficiency Syndromes 54 (5), 506-510, 2010
|Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1|
AFY Poon, LC Swenson, WWY Dong, W Deng, SL Kosakovsky Pond, ...
Molecular biology and evolution 27 (4), 819-832, 2010
|Performance of HIV-1 Drug Resistance Testing at Low Level Viraemia and Its Ability to Predict Future Virologic Outcomes and Viral Evolution in Treatment-Naïve Individuals|
A Gonzalez-Serna, JE Min, C Woods, D Chan, V Lima, JSG Montaner, ...
Clinical Infectious Diseases 58 (8), 1165-1173, 2014
|Detection of inferred CCR5-and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing|
EM Bunnik, LC Swenson, D Edo-Matas, W Huang, W Dong, A Frantzell, ...
PLoS pathogens 7 (6), e1002106, 2011
|HIV drug resistance detected during low-level viraemia is associated with subsequent virologic failure|
LC Swenson, JE Min, CK Woods, E Cai, JZ Li, JSG Montaner, ...
AIDS 28 (8), 1125-1134, 2014
|Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration|
LC Swenson, B Cobb, AM Geretti, PR Harrigan, M Poljak, ...
Journal of clinical microbiology 52 (2), 517-523, 2014
|Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data|
AFY Poon, LC Swenson, EM Bunnik, D Edo-Matas, H Schuitemaker, ...
PLOS Computational Biology 8 (11), e1002753, 2012
|Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing|
LC Swenson, WWY Dong, T Mo, J Demarest, D Chapman, S Ellery, ...
Clinical infectious diseases 56 (11), 1659-1666, 2013
|Next-generation sequencing to assess HIV tropism|
LC Swenson, M Däumer, R Paredes
Current opinion in HIV and AIDS 7 (5), 478-485, 2012
|HIV coreceptor phenotyping in the clinical setting.|
AJ Low, LC Swenson, PR Harrigan
AIDS reviews 10 (3), 143-151, 2008
|Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing|
RH Liang, T Mo, W Dong, GQ Lee, LC Swenson, RM McCloskey, ...
Nucleic acids research 42 (12), e98-e98, 2014
|Genotypic inference of HIV-1 tropism using population-based sequencing of V3|
RA McGovern, PR Harrigan, LC Swenson
JoVE (Journal of Visualized Experiments), e2531, 2010
|Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure|
LC Swenson, CKS Chui, CJ Brumme, D Chan, CK Woods, T Mo, W Dong, ...
Antimicrobial agents and chemotherapy 57 (12), 6122-6130, 2013
|Quantification of HIV tropism by “deep” sequencing shows a broad distribution of prevalence of X4 variants in clinical samples that is associated with virological outcome|
L Swenson, W Dong, T Mo, C Woods, A Thielen, M Jensen, C Glascock, ...
16th Conference on retroviruses and opportunistic infections, 8-11, 2009
|Maraviroc, as a Switch Option, in HIV-1–infected Individuals With Stable, Well-controlled HIV Replication and R5-tropic Virus on Their First Nucleoside/Nucleotide Reverse …|
SL Pett, J Amin, A Horban, J Andrade-Villanueva, M Losso, N Porteiro, ...
Clinical Infectious Diseases 63 (1), 122-132, 2016
|Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 “deep” sequencing|
GQ Lee, LC Swenson, AFY Poon, JN Martin, H Hatano, SG Deeks, ...
PloS one 7 (9), e46181, 2012
|A single untimed plasma drug concentration measurement during low-level HIV viremia predicts virologic failure|
A Gonzalez-Serna, LC Swenson, B Watson, W Zhang, A Nohpal, ...
Clinical Microbiology and Infection 22 (12), 1004. e9-1004. e16, 2016