Publications by authors named "Luke C Swenson"

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"Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1.
David J H F Knapp, Rachel A McGovern, Art F Y Poon, Xiaoyin Zhong, Dennison Chan, Luke C Swenson

PLoS One· November 2015

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Risk of breast cancer with CXCR4-using HIV defined by V3 loop sequencing.
James J Goedert, Luke C Swenson, Laura A Napolitano, Mojgan Haddad, Kathryn Anastos

J Acquir Immune Defic Syndr· January 2015

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Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.
Richard H Liang, Theresa Mo, Winnie Dong, Guinevere Q Lee, Luke C Swenson

Nucleic Acids Res· July 2014

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HIV drug resistance detected during low-level viraemia is associated with subsequent virologic failure.
Luke C Swenson, Jeong Eun Min, Conan K Woods, Eric Cai, Jonathan Z Li

AIDS· May 2014

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Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration.
Luke C Swenson, Bryan Cobb, Anna Maria Geretti, P Richard Harrigan, Mario Poljak

J Clin Microbiol· February 2014

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Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure.
Luke C Swenson, Celia K S Chui, Chanson J Brumme, Dennison Chan, Conan K Woods

Antimicrob Agents Chemother· December 2013

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Reply to "Issues on results of the external quality assessment for proviral DNA testing of HIV-1 Tropism in the Maraviroc Switch collaborative study".
Elise Tu, Luke C Swenson, Sally Land, Sarah Pett, Sean Emery

J Clin Microbiol· December 2013

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Results of external quality assessment for proviral DNA testing of HIV tropism in the Maraviroc Switch collaborative study.
Elise Tu, Luke C Swenson, Sally Land, Sarah Pett, Sean Emery

J Clin Microbiol· July 2013

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Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing.
Luke C Swenson, Winnie W Y Dong, Theresa Mo, James Demarest, Doug Chapman

Clin Infect Dis· June 2013

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Development of a novel codon-specific polymerase chain reaction for the detection of CXCR4-utilizing HIV type 1 subtype B.
Sherry McLaughlin, Luke C Swenson, Shengbo Hu, Paul Hughes, P Richard Harrigan

AIDS Res Hum Retroviruses· May 2013

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Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing.
Guinevere Q Lee, Luke C Swenson, Art F Y Poon, Jeffrey N Martin, Hiroyu Hatano

PLoS One· April 2013

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Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.
Art F Y Poon, Luke C Swenson, Evelien M Bunnik, Diana Edo-Matas, Hanneke Schuitemaker

PLoS Comput Biol· April 2013

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Technical and regulatory shortcomings of the TaqMan version 1 HIV viral load assay.
Chanson J Brumme, Luke C Swenson, Brian Wynhoven, Benita Yip, Stuart Skinner

PLoS One· February 2013

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Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing.
David J H F Knapp, Rachel A McGovern, Winnie Dong, Art F Y Poon, Luke C Swenson

J Clin Microbiol· February 2013

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Next-generation sequencing to assess HIV tropism.
Luke C Swenson, Martin Däumer, Roger Paredes

Curr Opin HIV AIDS· September 2012

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Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.
Luke C Swenson, Theresa Mo, Winnie W Y Dong, Xiaoyin Zhong, Conan K Woods

Clin Infect Dis· October 2011

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Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.
Alexander Thielen, Thomas Lengauer, Luke C Swenson, Winnie W Y Dong, Rachel A McGovern

Antivir Ther· September 2011

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Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing.
Evelien M Bunnik, Luke C Swenson, Diana Edo-Matas, Wei Huang, Winnie Dong

PLoS Pathog· June 2011

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"Dynamic range" of inferred phenotypic HIV drug resistance values in clinical practice.
Luke C Swenson, Graham Pollock, Brian Wynhoven, Theresa Mo, Winnie Dong

PLoS One· February 2011

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Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients.
Luke C Swenson, Theresa Mo, Winnie W Y Dong, Xiaoyin Zhong, Conan K Woods

J Infect Dis· January 2011

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Genotypic inference of HIV-1 tropism using population-based sequencing of V3.
Rachel A McGovern, P Richard Harrigan, Luke C Swenson

J Vis Exp· December 2010

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Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.
Luke C Swenson, Andrew Moores, Andrew J Low, Alexander Thielen, Winnie Dong

J Acquir Immune Defic Syndr· August 2010

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Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.
Art F Y Poon, Luke C Swenson, Winnie W Y Dong, Wenjie Deng, Sergei L Kosakovsky Pond

Mol Biol Evol· April 2010

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HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins.
Zabrina L Brumme, Mina John, Jonathan M Carlson, Chanson J Brumme, Dennison Chan, Luke C Swenson

PLoS One· August 2009

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HIV coreceptor phenotyping in the clinical setting.
Andrew J Low, Luke C Swenson, P Richard Harrigan

AIDS Rev· November 2008

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