R. Swanstrom

发表

Analysis of retroviral protease cleavage sites reveals two types of cleavage sites and the structural requirements of the P1 amino acid.

C. Hutchison, L. Everitt, S. Pettit, 1991, The Journal of biological chemistry.

Characterization of unintegrated retroviral DNA with long terminal repeat-associated cell-derived inserts

R. Swanstrom, M. Dunn, J. Olsen, 1992, Journal of virology.

Architecture and Secondary Structure of an Entire HIV-1 RNA Genome

Kristen K. Dang, K. Weeks, Kristen K Dang, 2009, Nature.

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice

Xiaotao Lu, Alexandra Schäfer, Ralph S. Baric, 2020, Science Translational Medicine.

Interplay between Single Resistance-Associated Mutations in the HIV-1 Protease and Viral Infectivity, Protease Activity, and Inhibitor Sensitivity

R. Swanstrom, N. Parkin, Sook-Kyung Lee, 2011, Antimicrobial Agents and Chemotherapy.

Non-Nucleoside Phenotypic Hypersusceptibility Cut-Point Determination from ACTG 359

D. Katzenstein, R. Haubrich, R. Swanstrom, 2007, HIV clinical trials.

Context Surrounding Processing Sites Is Crucial in Determining Cleavage Rate of a Subset of Processing Sites in HIV-1 Gag and Gag-Pro-Pol Polyprotein Precursors by Viral Protease*

C. Schiffer, Ayşegül Özen, R. Swanstrom, 2012, The Journal of Biological Chemistry.

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

Cassandra B. Jabara, Corbin D. Jones, J. Roach, 2011, Proceedings of the National Academy of Sciences.

Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks.

R. Swanstrom, N. Hoffman, W. Resch, 2001, Virology.

Independent Evolution of Human Immunodeficiency Virus Type 1 env V1/V2 and V4/V5 Hypervariable Regions during Chronic Infection

R. Swanstrom, J. Nelson, K. Kitrinos, 2007, Journal of Virology.

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

B. Korber, B. Haynes, P. Sharp, 2008, Journal of Virology.

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

Hui Li, Tanmoy Bhattacharya, Xiping Wei, 2008, Proceedings of the National Academy of Sciences.

Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression.

Edward M Kennedy, B. Cullen, R. Swanstrom, 2019, Cell host & microbe.

Genetic characteristics of the V3 region associated with CXCR4 usage in HIV-1 subtype C isolates.

L. Ping, R. Swanstrom, L. Morris, 2006, Virology.

Characterization of Human Immunodeficiency Virus Type 1 in Saliva and Blood Plasma by V3-Specific Heteroduplex Tracking Assay and Genotype Analyses

R. Swanstrom, J. Nelson, L. Patton, 2001, Journal of Virology.

Macrophage Tropism of Human Immunodeficiency Virus Type 1 Isolates from Brain and Lymphoid Tissues Predicts Neurotropism Independent of Coreceptor Specificity

E. De Clercq, Steven Wolinsky, K. Kunstman, 2001, Journal of Virology.

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

Sara R. Selitsky, Dante S. Bortone, E. Wallen, 2018, The Journal of clinical investigation.

β-d-N4-hydroxycytidine Inhibits SARS-CoV-2 Through Lethal Mutagenesis But Is Also Mutagenic To Mammalian Cells

Shuntai Zhou, R. Baric, M. Heise, 2021, The Journal of infectious diseases.

A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia.

R. Swanstrom, I. Hoffman, Myron S. Cohen, 2010, The Journal of infectious diseases.

Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization

Jerome H. Kim, B. Korber, P. Hraber, 2016, PLoS pathogens.

The leader sequence of the subgenomic mRNA's of Rous sarcoma virus is approximately 390 nucleotides

H. Varmus, R. Swanstrom, J. Bishop, 1982, Journal of virology.

Evolution of the HIV-1 env Gene in the Rag2−/− γC−/− Humanized Mouse Model

R. Swanstrom, William L. Ince, L. Su, 2009, Journal of Virology.

Role of Low CD4 Levels in the Influence of Human Immunodeficiency Virus Type 1 Envelope V1 and V2 Regions on Entry and Spread in Macrophages

B. Chesebro, R. Swanstrom, D. Kabat, 2005, Journal of Virology.

HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands to Optimize Hydrogen Bonding in the Substrate Envelope.

Nese Kurt Yilmaz, Celia A. Schiffer, Akbar Ali, 2019, Journal of medicinal chemistry.

Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells

R. Swanstrom, J. Garcia, S. Anderson, 1993, Journal of virology.

Development and characterization of a new single cycle vaccine vector in the simian immunodeficiency virus model system.

R. Swanstrom, Y. Tang, 2008, Virology.

Dynamics of simian immunodeficiency virus populations in blood and cerebrospinal fluid over the full course of infection.

Philip R. Johnson, R. Swanstrom, M. Connell, 2007, The Journal of infectious diseases.

Selection of High-Level Resistance to Human Immunodeficiency Virus Type 1 Protease Inhibitors

Wolfgang Resch, R. Swanstrom, D. Irlbeck, 2003, Antimicrobial Agents and Chemotherapy.

Selection of HIV-1 for resistance to fifth-generation protease inhibitors reveals two independent pathways to high-level resistance

Shuntai Zhou, C. Schiffer, R. Swanstrom, 2019, bioRxiv.

A multiple-site-specific heteroduplex tracking assay as a tool for the study of viral population dynamics.

R. Swanstrom, N. Parkin, W. Resch, 2001, Proceedings of the National Academy of Sciences of the United States of America.

The activity of the protease of human immunodeficiency virus type 1 is initiated at the membrane of infected cells before the release of viral proteins and is required for release to occur with maximum efficiency

A. Kaplan, R. Swanstrom, M. Manchester, 1994, Journal of virology.

tRNATrp as primer for RNA-directed DNA polymerase: structural determinants of function.

H. Goodman, R. Swanstrom, J. Bishop, 1979, The Journal of biological chemistry.

Correction of the apical membrane chloride permeability defect in polarized cystic fibrosis airway epithelia following retroviral-mediated gene transfer.

R. Swanstrom, J. Olsen, J. Yankaskas, 1992, Human gene therapy.

pM to µM - Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.

Shuntai Zhou, C. Schiffer, D. Bolon, 2019, ACS chemical biology.

Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV ‑ 1 Protease in Conferring Drug Resistance

D. Bolon, R. Swanstrom, E. Nalivaika, 2019 .

Antigenicity and Immunogenicity of Transmitted/Founder, Consensus, and Chronic Envelope Glycoproteins of Human Immunodeficiency Virus Type 1

A. Lapedes, B. Korber, Haiyan Chen, 2013, Journal of Virology.

Strategy for Immunogen Design CCR 5 Utilization and Suggests a New Identifies Differences in Glycosylation and C Human Immunodeficiency Virus Type 1 Acute and Chronic Infections with Subtype Comparison of Viral Env Proteins from

Cassandra, E. L. Potter, Vermeulen, 2013 .

HIV-1 replication capacity: Setting the pace of disease

R. Swanstrom, C. Williamson, 2015, Proceedings of the National Academy of Sciences.

Durability of response to treatment among antiretroviral-experienced subjects: 48-week results from AIDS Clinical Trials Group Protocol 359.

D. Katzenstein, R. Haubrich, S. Lagakos, 2002, The Journal of infectious diseases.

Genotypic susceptibility scores and HIV type 1 RNA responses in treatment-experienced subjects with HIV type 1 infection.

D. Katzenstein, R. Haubrich, R. Swanstrom, 2008, AIDS research and human retroviruses.

HIV-1 CNS COMPARTMENTALIZATION AND CYTOKINE INTERPLAY IN NON-SUBTYPE B HIV-1 INFECTIONS IN NIGERIA AND MALAWI.

Shuntai Zhou, R. Swanstrom, K. Robertson, 2020, AIDS research and human retroviruses.

HIV-1 Central Nervous System Compartmentalization and Cytokine Interplay in Non-Subtype B HIV-1 Infections in Nigeria and Malawi

A. Ogunniyi, R. Swanstrom, K. Robertson, 2020 .

Quantitation of herpes simplex virus type 1 RNA in infected HeLa cells

R. Swanstrom, J. Stringer, E. Wagner, 1977, Journal of virology.

Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing

P. Bieniasz, R. Swanstrom, A. Emery, 2019, Journal of Virology.

Predicting Efavirenz Concentrations in the Brain Tissue of HIV‐Infected Individuals and Exploring their Relationship to Neurocognitive Impairment

R. Swanstrom, R. Price, P. Luciw, 2019, Clinical and translational science.

Retroviruses: strategies of replication.

R. Swanstrom, P. Vogt, 1990, Current topics in microbiology and immunology.

An anomalous Ty1 structure attributed to an error in reverse transcription

B. Errede, R. Swanstrom, M. Company, 1986, Molecular and cellular biology.

Suppression of Human Immunodeficiency Virus Type 1 (HIV-1) Viremia with Reverse Transcriptase and Integrase Inhibitors, CD4+ T-Cell Recovery, and Viral Rebound upon Interruption of Therapy in a New Model for HIV Treatment in the Humanized Rag2−/−γc−/− Mouse

R. Swanstrom, D. Margolis, William L. Ince, 2009, Journal of Virology.

Characterization of the Transmitted Virus in an Ongoing HIV-1 Epidemic Driven by Injecting Drug Use.

D. Frishman, Shuntai Zhou, D. Montefiori, 2018, AIDS research and human retroviruses.

The HIV-1 latent reservoir is largely sensitive to circulating T cells

A. Adimora, Shuntai Zhou, R. Swanstrom, 2019, eLife.

A fitness bottleneck in HIV-1 transmission

R. Swanstrom, S. Joseph, 2014, Science.

Specificity Neurotropism Independent of Coreceptor from Brain and Lymphoid Tissues Predicts Immunodeficiency Virus Type 1 Isolates Macrophage Tropism of Human

Kimberly, K. Kunstman, R. Swanstrom, 2001 .

Using HIV-1 sequence variability to explore virus biology.

R. Swanstrom, J. Nelson, N. Hoffman, 2001, Virus research.

Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells

R. Swanstrom, H. Akiyama, S. Gummuluru, 2017, Journal of Virology.

Evolving Character of Chronic Central Nervous System HIV Infection

D. Fuchs, H. Zetterberg, R. Swanstrom, 2014, Seminars in Neurology.

Short communication: HIV type 1 subtype C variants transmitted through the bottleneck of breastfeeding are sensitive to new generation broadly neutralizing antibodies directed against quaternary and CD4-binding site epitopes.

D. Montefiori, S. Meshnick, R. Swanstrom, 2013, AIDS research and human retroviruses.

The terminal redundancy of the retrovirus genome facilitates chain elongation by reverse transcriptase.

H. Varmus, R. Swanstrom, J. Bishop, 1981, The Journal of biological chemistry.

Female genital tract shedding of HIV-1 is rare in women with suppressed HIV-1 in plasma.

A. Adimora, K. Anastos, R. Swanstrom, 2020, AIDS.

Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication

P. Bieniasz, R. Swanstrom, Daniel Blanco-Melo, 2018, PLoS pathogens.

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.

R. Swanstrom, A. Emery, Liang-Yuan Chiu, 2022, Journal of molecular biology.

AnAnomalous TYlStructure Attributed toanError in Reverse Transcription

R. Swanstrom, 1986 .

Characterization of Macrophage-Tropic HIV-1 Infection of Central Nervous System Cells and the Influence of Inflammation

Krishna C. Kanchi, Shuntai Zhou, R. Swanstrom, 2022, Journal of virology.

Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.

M. Hudgens, Shuntai Zhou, R. Swanstrom, 2022, ACS infectious diseases.

Epitranscriptomic addition of m 6 A regulates HIV-1 RNA stability and alternative splicing

B. Cullen, R. Swanstrom, K. Tsai, 2021 .

Subtype-Speciﬁc Conformational Differences within the V3 Region of Subtype B and Subtype C Human Immunodeﬁciency Virus Type 1 Env Proteins (cid:1)

R. Swanstrom, N. Hoffman, Milloni B. Patel, 2007 .

Genetic analysis of the Rous sarcoma virus subgroup D env gene: mammal tropism correlates with temperature sensitivity of gp85

R. Swanstrom, J. Olsen, C. Bova-Hill, 1991, Journal of virology.

Efficiency of gene transfer for restoration of normal airway epithelial function in cystic fibrosis

J C Olsen, R. Swanstrom, J. Olsen, 1992, Nature genetics.

HIV Reservoirs in the Central Nervous System

R. Swanstrom, E. Dukhovlinova, L. Tompkins, 2016 .

Effects of Genital Tract Inflammation on Human Immunodeficiency Virus Type 1 V3 Populations in Blood and Semen

P. Vernazza, L. Ping, R. Swanstrom, 2000, Journal of Virology.

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

Feng Gao, Bette Korber, Tongye Shen, 2011, PLoS pathogens.

Effects of rapid antigen degradation and VEE glycoprotein specificity on immune responses induced by a VEE replicon vaccine.

R. Johnston, A. Whitmore, R. Swanstrom, 2008, Virology.

Vaccination of Macaques against Pathogenic Simian Immunodeficiency Virus with Venezuelan Equine Encephalitis Virus Replicon Particles

Philip R. Johnson, R. Johnston, D. Montefiori, 2000, Journal of Virology.

Reply to Troth et al

Shuntai Zhou, R. Schinazi, R. Swanstrom, 2021, Journal of Infectious Diseases.

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus

Alexandra Schäfer, Ralph S. Baric, Amy C. Sims, 2020, bioRxiv.

3'-Azido-3'-deoxythymidine inhibits the replication of avian leukosis virus

R. Swanstrom, J. Olsen, P. Furman, 1987, Journal of virology.

Independent Evolution of Human Immunodeﬁciency Virus Type 1 env V1/V2 and V4/V5 Hypervariable Regions during Chronic Infection (cid:1)

R. Swanstrom, J. Nelson, K. Kitrinos, 2007 .

Improving Viral Protease Inhibitors to Counter Drug Resistance.

C. Schiffer, R. Swanstrom, Nese Kurt Yilmaz, 2016, Trends in microbiology.

Improving Viral Protease Inhibitors to Counter Drug

C. Schiffer, R. Swanstrom, R. Yilmaz, 2016 .

Generation and Characterization of a Bivalent HIV-1 Subtype C gp120 Protein Boost for Proof-of-Concept HIV Vaccine Efficacy Trials in Southern Africa

E. Go, H. Desaire, H. Liao, 2016, PloS one.

HIV reservoirs: what, where and how to target them

R. Siliciano, M. Churchill, R. Swanstrom, 2015, Nature Reviews Microbiology.

Compartmentalization, Viral Evolution, and Viral Latency of HIV in the CNS

R. Swanstrom, E. Dukhovlinova, Kathryn T. Arrildt, 2015, Current HIV/AIDS Reports.

Subtype-Specific Conformational Differences within the V3 Region of Subtype B and Subtype C Human Immunodeficiency Virus Type 1 Env Proteins

R. Swanstrom, N. Hoffman, Milloni B. Patel, 2007, Journal of Virology.

Retrovirus envelope glycoproteins.

R. Swanstrom, E. Hunter, Eric Hunter, 1990, Current topics in microbiology and immunology.

The avian retrovirus env gene family: molecular analysis of host range and antigenic variants

R. Swanstrom, J. Olsen, C. Bova, 1988, Journal of virology.

env genes of avian retroviruses: nucleotide sequence and molecular recombinants define host range determinants.

R. Swanstrom, C. Bova, J. Manfredi, 1986, Virology.

Sequencing the Biology of Entry: The Retroviral env Gene

William D. Graham, Shuntai Zhou, R. Swanstrom, 2017, Current topics in microbiology and immunology.

Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

Hezhao Ji, Rami Kantor, Santiago Ávila-Ríos, 2020, Viruses.

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

P. Mieczkowski, Shuntai Zhou, Corbin D. Jones, 2015, Journal of Virology.

5 Replication of Retroviruses

H. Varmus, R. Swanstrom, 1982 .

Transduction of a cellular oncogene: the genesis of Rous sarcoma virus.

H. Varmus, R. Swanstrom, J. Bishop, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Synthesis, Assembly, and Processing of Viral Proteins

R. Swanstrom, J. Wills, 1997 .

Quantification of Entry Phenotypes of Macrophage-Tropic HIV-1 across a Wide Range of CD4 Densities

J. Hoxie, R. Swanstrom, Benhur Lee, 2013, Journal of Virology.

The association of the infecting DNA of herpes simplex virus with cellular components.

R. Swanstrom, J. Stringer, E. Wagner, 1976, Virology.

Restricted transcription of the herpes simplex virus genome occurring early after infection and in the presence of metabolic inhibitors.

R. Swanstrom, E. Wagner, K. Pivo, 1975, Virology.

Interaction of psoralen derivatives with the RNA genome of Rous sarcoma virus.

J. Hearst, R. Swanstrom, J. Bishop, 1981, Virology.

Measuring allelic heterogeneity in Plasmodium falciparum by a heteroduplex tracking assay.

S. Meshnick, C. Wongsrichanalai, R. Swanstrom, 2005, The American journal of tropical medicine and hygiene.

Vaccination of macaques with SIV immunogens delivered by Venezuelan equine encephalitis virus replicon particle vectors followed by a mucosal challenge with SIVsmE660.

Philip R. Johnson, R. Johnston, D. Montefiori, 2005, Vaccine.

Characterization and selection of HIV-1 subtype C isolates for use in vaccine development.

Maureen F. Maughan, R. Johnston, L. Ping, 2003, AIDS research and human retroviruses.

Alphavirus Replicon Particles as Candidate HIV Vaccines

Philip R. Johnson, David Montefiori, Maureen F. Maughan, 2002, IUBMB life.

Randomized study of saquinavir with ritonavir or nelfinavir together with delavirdine, adefovir, or both in human immunodeficiency virus-infected adults with virologic failure on indinavir: AIDS Clinical Trials Group Study 359.

D. Katzenstein, R. Haubrich, S. Lagakos, 2000, The Journal of infectious diseases.

Conditional human immunodeficiency virus type 1 protease mutants show no role for the viral protease early in virus replication

A. Kaplan, R. Swanstrom, M. Manchester, 1996, Journal of virology.

Epitranscriptomic Addition of m 5C to HIV-1 Transcripts Regulates Viral Gene Expression

B. Cullen, R. Swanstrom, K. Tsai, 2019, SSRN Electronic Journal.

No evidence for naturally occurring mutations resistant to HIV-1 reverse-transcriptase inhibitors among South African HIV-1 subtype C isolates

L. Ping, S. Karim, R. Swanstrom, 2000 .

Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

C. A. Lewis, R. Wolfenden, Shuntai Zhou, 2016, Proceedings of the National Academy of Sciences.

HIV-1 pathogenesis: the virus.

R. Swanstrom, J. Coffin, Ronald Swanstrom, 2012, Cold Spring Harbor perspectives in medicine.

Large scale screening of human sera for HCV RNA and GBV‐C RNA

R. Swanstrom, J. Eron, J. Keys, 2014, Journal of medical virology.

Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants

P. Vernazza, L. Ping, R. Swanstrom, 1999, Journal of Virology.

Characterization of an HIV-1 isolate displaying an apparent absence of virion-associated reverse transcriptase activity.

R. Swanstrom, R. Buckheit, 1991, AIDS research and human retroviruses.

Evolutionary pathways to NS5A inhibitor resistance in genotype 1 hepatitis C virus

C. Burch, Shuntai Zhou, F. Hu, 2018, Antiviral Research.

Hepatitis C Virus (HCV) NS3 Sequence Diversity and Antiviral Resistance-Associated Variant Frequency in HCV/HIV Coinfection

Cassandra B. Jabara, M. Hudgens, F. Hu, 2014, Antimicrobial Agents and Chemotherapy.

Expression and processing of the AIDS virus reverse transcriptase in Escherichia coli.

C. Hutchison, M. Edgell, W. Farmerie, 1987, Science.

Viral Protease Inhibitors

C. Schiffer, R. Swanstrom, Sook-Kyung Lee, 2009, Handbook of experimental pharmacology.

The p2 domain of human immunodeficiency virus type 1 Gag regulates sequential proteolytic processing and is required to produce fully infectious virions

A. Kaplan, S. Pettit, R. Swanstrom, 1994, Journal of virology.

Selection of multiple human immunodeficiency virus type 1 variants that encode viral proteases with decreased sensitivity to an inhibitor of the viral protease.

L. Everitt, A. Kaplan, D. Norbeck, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Identification of temperature-sensitive mutants of the human immunodeficiency virus type 1 protease through saturation mutagenesis. Amino acid side chain requirements for temperature sensitivity.

C. Hutchison, L. Everitt, D. Loeb, 1994, The Journal of biological chemistry.

HIV-1 Populations in Semen Arise through Multiple Mechanisms

Cassandra B. Jabara, Corbin D. Jones, P. Borrow, 2010, PLoS pathogens.

HIV-1 populations in blood and breast milk are similar.

L. Ping, R. Swanstrom, F. Martinson, 2004, Virology.

HIV-1 Replication in the Central Nervous System Occurs in Two Distinct Cell Types

R. Swanstrom, R. Price, S Spudich, 2011, PLoS pathogens.

Compartmentalized Human Immunodeficiency Virus Type 1 Originates from Long-Lived Cells in Some Subjects with HIV-1–Associated Dementia

R. Swanstrom, R. Price, P. Harrington, 2009, PLoS pathogens.

Compartmentalized Human Immunodeficiency Virus Type 1 Present in Cerebrospinal Fluid Is Produced by Short-Lived Cells

D. Haas, R. Swanstrom, K. Ritola, 2005, Journal of Virology.

Weighted phenotypic susceptibility scores are predictive of the HIV-1 RNA response in protease inhibitor-experienced HIV-1-infected subjects.

D. Katzenstein, R. Haubrich, R. Swanstrom, 2004, The Journal of infectious diseases.

Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing

B. Cullen, R. Swanstrom, K. Tsai, 2021, bioRxiv.

The triple threat of HIV-1 protease inhibitors.

R. Wolfenden, R. Swanstrom, Sook-Kyung Lee, 2015, Current topics in microbiology and immunology.

Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates

A. Kaplan, S. Pettit, R. Swanstrom, 2005, Retrovirology.

A genetic approach for identifying critical residues in the fingers and palm subdomains of HIV-1 reverse transcriptase.

G J Pielak, C. Hutchison, J. Wrobel, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Complete mutagenesis of the HIV-1 protease

Marianne Manchester, C. Hutchison, L. Everitt, 1989, Nature.

Compensatory evolution in RNA secondary structures increases substitution rate variation among sites.

Kristen K. Dang, Jennifer L. Knies, Kristen K Dang, 2008, Molecular biology and evolution.

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses

R. Swanstrom, A. Kashuba, S. Joseph, 2015, Nature Reviews Microbiology.

Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo

R. Swanstrom, D. Glueck, D. Shugars, 1993, Journal of virology.

Mutational analysis of human immunodeficiency virus type 1 protease suggests functional homology with aspartic proteinases

C. Hutchison, M. Edgell, W. Farmerie, 1989, Journal of virology.

HIV-1 target cells in the CNS

R. Swanstrom, S. Joseph, Kathryn T. Arrildt, 2014, Journal of NeuroVirology.

Regulation of synthesis of herpes simplex type 1 virus mRNA during productive infection.

R. Swanstrom, E. Wagner, 1974, Virology.

Complete mutagenesis of protein coding domains.

C. Hutchison, D. Loeb, R. Swanstrom, 1991, Methods in enzymology.

Genetic analysis of the Rous sarcoma virus subgroup D env gene: mammal tropism correlates with temperature sensitivity of gp85

R. Swanstrom, C. Bova-Hill, Carol Bova-Hill, 1991, Journal of virology.

Cleavage of HIV-1 gag polyprotein synthesized in vitro: sequential cleavage by the viral protease.

C. Hutchison, D. Loeb, R. Swanstrom, 1989, AIDS research and human retroviruses.

A new pathway in the generation of defective retrovirus DNA

R. Swanstrom, J. Olsen, Ronald Swanstrom, 1985, Journal of virology.

Nucleotide sequence of the 5' noncoding region and part of the gag gene of Rous sarcoma virus

H. Varmus, R. Swanstrom, J. Bishop, 1982, Journal of virology.

Exclusive and Persistent Use of the Entry Coreceptor CXCR4 by Human Immunodeficiency Virus Type 1 from a Subject Homozygous for CCR5 Δ32

S. O’Brien, J. Mascola, T. O'Brien, 1998, Journal of Virology.

The Choreography of HIV-1 Proteolytic Processing and Virion Assembly*

R. Swanstrom, Sook-Kyung Lee, Marc Potempa, 2012, The Journal of Biological Chemistry.

Nucleotide sequence of cloned unintegrated avian sarcoma virus DNA: viral DNA contains direct and inverted repeats similar to those in transposable elements.

H. Varmus, R. Swanstrom, J. Bishop, 1981, Proceedings of the National Academy of Sciences of the United States of America.

Rearrangements in unintegrated retroviral DNA are complex and are the result of multiple genetic determinants

R. Swanstrom, J. Olsen, D. Grandgenett, 1990, Journal of virology.

The nucleotide sequence of an untranslated but conserved domain at the 3' end of the avian sarcoma virus genome

J. M. Bishop, H. M. Goodman, A. P. Czernilofsky, 1980, Nucleic Acids Res..

Human immunodeficiency virus type 1 Gag proteins are processed in two cellular compartments.

A. Kaplan, R. Swanstrom, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Variation in the molecular size of the DNA from closely related strains of type I herpes simplex virus.

R. Swanstrom, E. Wagner, M. Rice, 1976, Biochimica et biophysica acta.

Transcription of the Herpes Simplex Virus Genome in Human Cells

R. Swanstrom, E. Wagner, M. Stafford, 1972, Journal of virology.

Nuclease mechanism of the avian retrovirus pp32 endonuclease

R. Swanstrom, J. Olsen, D. Grandgenett, 1986, Journal of virology.

Proteolytic Processing of the P2/Nucleocapsid Cleavage Site Is Critical for Human Immunodeficiency Virus Type 1 RNA Dimer Maturation

S. Pettit, R. Swanstrom, J. Mak, 2001, Journal of Virology.

Structure of a replication intermediate in the synthesis of Rous sarcoma virus DNA in vivo

H. Varmus, R. Swanstrom, J. Bishop, 1982, Journal of virology.

lnteractiqn of Psoralen Derivatives with the RNA Genome of Rous Sarcoma Virus

J. Hearst, R. Swanstrom, J. Bishop, 2003 .

Structure and immunogenicity of alternative forms of the simian immunodeficiency virus gag protein expressed using Venezuelan equine encephalitis virus replicon particles.

R. Johnston, A. Whitmore, R. Swanstrom, 2007, Virology.

The HIV-1 gag precursor is processed via two pathways: implications for cytotoxicity.

A. Kaplan, R. Swanstrom, 1991, Biomedica biochimica acta.

DNA intermediates in the replication of retroviruses are structurally (and perhaps functionally) related to transposable elements.

H. Varmus, S. Hughes, G. Payne, 1981, Cold Spring Harbor symposia on quantitative biology.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

Shuntai Zhou, D. Peaper, R. Swanstrom, 2023, Cell reports. Medicine.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

Shuntai Zhou, R. Swanstrom, C. Castaldi, 2023, Cell Reports Medicine.

HIV-1: To Splice or Not to Splice, That Is the Question

R. Swanstrom, A. Emery, 2021, Viruses.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

Shuntai Zhou, D. Peaper, R. Swanstrom, 2023, Cell reports. Medicine.

Stephan Oroszlan and the Proteolytic Processing of Retroviral Proteins: Following A Pro

W. Sundquist, R. Swanstrom, 2021, Viruses.

Impact of Clade, Geography, and Age of the Epidemic on HIV-1 Neutralization by Antibodies

Jerome H. Kim, A. Lapedes, B. Korber, 2014, Journal of Virology.

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

Feng Gao, Hui Li, Guido Ferrari, 2012, The Journal of clinical investigation.

Major Coexisting Human Immunodeficiency Virus Type 1 env Gene Subpopulations in the Peripheral Blood Are Produced by Cells with Similar Turnover Rates and Show Little Evidence of Genetic Compartmentalization

C. Burch, R. Swanstrom, R. Price, 2009, Journal of Virology.

HIV pathogenesis: dynamics and genetics of viral populations and infected cells.

R. Swanstrom, J. Coffin, 2013, Cold Spring Harbor perspectives in medicine.

Acute HIV Infection: Implications for HIV Spread, Disease Progression, and Vaccine Development

R. Swanstrom, Jeffrey A. Anderson, M. Cohen, 2005 .

Correlation between env V1/V2 Region Diversification and Neutralizing Antibodies during Primary Infection by Simian Immunodeficiency Virus sm in Rhesus Macaques

Philip R. Johnson, R. Johnston, D. Montefiori, 2004, Journal of Virology.

Human immunodeficiency virus type-1 protease inhibitors: therapeutic successes and failures, suppression and resistance.

R. Swanstrom, R Swanstrom, J Erona, 2000, Pharmacology & therapeutics.

Pre-Clinical Development of a Recombinant, Replication-Competent Adenovirus Serotype 4 Vector Vaccine Expressing HIV-1 Envelope 1086 Clade C

H. Liao, B. Haynes, D. Montefiori, 2013, PloS one.

Turnover of env Variable Region 1 and 2 Genotypes in Subjects with Late-Stage Human Immunodeficiency Virus Type 1 Infection

R. Swanstrom, J. Nelson, N. Hoffman, 2003, Journal of Virology.

Variability in the Human Immunodeficiency Virus Type 1 gp120 Env Protein Linked to Phenotype-Associated Changes in the V3 Loop

Noah G. Hoffman, R. Swanstrom, N. Hoffman, 2002, Journal of Virology.

Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children

Cassandra B. Jabara, R. Swanstrom, R. Heyderman, 2012, PLoS pathogens.

Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba.

Anne-Mieke Vandamme, Philippe Lemey, Sonia Resik, 2007, AIDS research and human retroviruses.

Phenotypic Correlates of HIV-1 Macrophage Tropism

William D. Graham, D. Montefiori, L. Ping, 2015, Journal of Virology.

The HIV-1 Env Protein: A Coat of Many Colors

R. Swanstrom, S. Joseph, Kathryn T. Arrildt, 2012, Current HIV/AIDS Reports.

The molecular epidemiology of HIV-1 envelope diversity during HIV-1 subtype C vertical transmission in Malawian mother–infant pairs

Kristen K. Dang, C. Burch, S. Meshnick, 2008, AIDS.

Multiple V1/V2 env Variants Are Frequently Present during Primary Infection with Human Immunodeficiency Virus Type 1

R. Swanstrom, J. Nelson, N. Hoffman, 2004, Journal of Virology.

Virologic risk factors for vertical transmission of HIV type 1 in Puerto Rico.

R. Swanstrom, C. Cadilla, G. Hillyer, 2002, AIDS research and human retroviruses.

V3 loop of the human immunodeficiency virus type 1 Env protein: interpreting sequence variability

B. Margolin, R. Swanstrom, L. Milich, 1993, Journal of virology.

Effect of a Protease Inhibitor-Induced Genetic Bottleneck on Human Immunodeficiency Virus Type 1 env Gene Populations

R. Swanstrom, J. Nelson, K. Kitrinos, 2005, Journal of Virology.

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

R. Swanstrom, H. Chu, B. Korber, 2009, Journal of Virology.

The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation

Shuntai Zhou, S. Karim, R. Swanstrom, 2019, Science Translational Medicine.

Ongoing HIV Transmission and the HIV Care Continuum in North Carolina

L. Ping, R. Swanstrom, W. Miller, 2015, PloS one.

Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design

E. L. Potter, Cassandra B. Jabara, H. Chu, 2013, Journal of Virology.

Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape

Lynn Morris, Penny L Moore, Michael S Seaman, 2012, Nature Medicine.

CAPRISA 004 tenofovir microbicide trial: no impact of tenofovir gel on the HIV transmission bottleneck.

S. Karim, R. Swanstrom, C. Williamson, 2012, The Journal of infectious diseases.

A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays.

G. Shaw, N. Parrish, L. Ping, 2010, Virology.

Using Primer-ID Deep Sequencing to Detect Recent Human Immunodeficiency Virus Type 1 Infection

Ann M. Dennis, Shuntai Zhou, R. Swanstrom, 2018, The Journal of infectious diseases.

Treatment as Prevention: Characterization of Partner Infections in the HIV Prevention Trials Network 052 Trial

T. Quinn, L. Ping, R. Swanstrom, 2017, Journal of acquired immune deficiency syndromes.

HIV-1 Transmission during Early Antiretroviral Therapy: Evaluation of Two HIV-1 Transmission Events in the HPTN 052 Prevention Study

Lei Wang, Allen G. Rodrigo, Susan H. Eshleman, 2013, PloS one.

Clonal Sequences Recovered from Plasma from Patients with Residual HIV-1 Viremia and on Intensified Antiretroviral Therapy Are Identical to Replicating Viral RNAs Recovered from Circulating Resting CD4+ T Cells

John M. Coffin, William Ince, R. Swanstrom, 2011, Journal of Virology.

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

H. Chu, B. Korber, B. Haynes, 2009, Journal of Virology.

Covariation of amino acid positions in HIV-1 protease.

Celia A Schiffer, C. Schiffer, R. Swanstrom, 2003, Virology.

Postnatally-transmitted HIV-1 Envelope variants have similar neutralization-sensitivity and function to that of nontransmitted breast milk variants

G. Learn, B. Haynes, D. Montefiori, 2013, Retrovirology.

HIV-1 Sequence Diversity as a Window Into HIV-1 Biology

R. Swanstrom, G. Schnell, Milloni B. Patel, 2008 .

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis

Sergei L. Kosakovsky Pond, Shuntai Zhou, R. Swanstrom, 2020, Journal of Virology.

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without STI-associated Urethritis

Sergei L. Kosakovsky Pond, Shuntai Zhou, R. Swanstrom, 2020, bioRxiv.

The evolution of HIV‐1 entry phenotypes as a guide to changing target cells

R. Swanstrom, S. Joseph, 2018, Journal of leukocyte biology.

Characterizing HIV-1 Splicing by Using Next-Generation Sequencing

Shuntai Zhou, R. Swanstrom, Elizabeth Pollom, 2017, Journal of Virology.

Diversity and Tropism of HIV-1 Rebound Virus Populations in Plasma Level After Treatment Discontinuation.

Shuntai Zhou, R. Swanstrom, I. Frank, 2016, The Journal of infectious diseases.

Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions

Shuntai Zhou, R. Swanstrom, B. Hauser, 2016, Journal of Virology.

The Genetic Bottleneck in Vertical Transmission of Subtype C HIV-1 Is Not Driven by Selection of Especially Neutralization-Resistant Virus from the Maternal Viral Population

D. Montefiori, S. Meshnick, R. Swanstrom, 2011, Journal of Virology.

Cross-Sectional Detection of Acute HIV Infection: Timing of Transmission, Inflammation and Antiretroviral Therapy

Guido Ferrari, Hui Li, David Margolis, 2011, PloS one.

Compartmentalization and Clonal Amplification of HIV-1 Variants in the Cerebrospinal Fluid during Primary Infection

R. Swanstrom, R. Price, S Spudich, 2009, Journal of Virology.

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes

R. Swanstrom, William L. Ince, G. Schnell, 2008, Nucleic acids research.

Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates

Tobias Sing, Andrew J. Low, M. Jensen, 2007, AIDS.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

Shuntai Zhou, D. Peaper, R. Swanstrom, 2023, Cell reports. Medicine.

Blocking Formation of the Stable HIV Reservoir: A New Perspective for HIV-1 Cure

R. Swanstrom, N. Goonetilleke, S. Joseph, 2019, Front. Immunol..

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

Mark Howison, Shuntai Zhou, R. Paredes, 2020, Viruses.

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain.

Cassandra B. Jabara, Shuntai Zhou, R. Swanstrom, 2015, AIDS research and human retroviruses.

Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy

James I Mullins, M. Jensen, J. Mullins, 2004, AIDS.

Fact and Fiction about 1%: Next Generation Sequencing and the Detection of Minor Drug Resistant Variants in HIV-1 Populations with and without Unique Molecular Identifiers

Shuntai Zhou, R. Swanstrom, 2020, Viruses.

Near Real-Time Identification of Recent HIV Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by MPID-NGS in North Carolina.

Ann M. Dennis, Shuntai Zhou, Corbin D. Jones, 2020, The Journal of infectious diseases.

Combined noncanonical NF-κB agonism and targeted BET bromodomain inhibition reverse HIV latency ex vivo

B. Strahl, A. Sanchez, R. Prinjha, 2022, The Journal of clinical investigation.

A sensitive assay using a native protein substrate for screening HIV-1 maturation inhibitors targeting the protease cleavage site between the matrix and capsid.

C. Schiffer, W. Janzen, R. Swanstrom, 2013, Biochemistry.

R5 Macrophage-Tropic HIV-1 in the Male Genital Tract

Shuntai Zhou, L. Ping, R. Swanstrom, 2015, Journal of Virology.

Constrained mutational sampling of amino acids in HIV-1 protease evolution

C. Schiffer, D. Bolon, T. Whitfield, 2018, bioRxiv.

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

Kristen K. Dang, E. L. Potter, K. Weeks, 2013, PLoS pathogens.

HIV-1 RNA Detected in the CNS after Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells.

R. Swanstrom, R. Price, N. Archin, 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Increased Human Immunodeficiency Virus Type 1 (HIV-1) env Compartmentalization in the Presence of HIV-1-Associated Dementia

R. Swanstrom, C. Hall, K. Robertson, 2005, Journal of Virology.

Curing HIV: Seeking to Target and Clear Persistent Infection

R. Swanstrom, D. Margolis, G. Ferrari, 2020, Cell.

Nonsuppressible viremia during HIV-1 therapy meets molecular virology

R. Swanstrom, A. Emery, S. Joseph, 2023, The Journal of clinical investigation.

Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course

Cassandra B. Jabara, C. Burch, R. Ellis, 2009, AIDS.

Rebound HIV-1 in cerebrospinal fluid after antiviral therapy interruption is mainly clonally amplified R5 T cell-tropic virus

Shuntai Zhou, R. Swanstrom, R. Price, 2023, Nature Microbiology.

HIV-1 target cells in the CNS

R. Swanstrom, S. Joseph, Kathryn T. Arrildt, 2015, Journal of NeuroVirology.

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

Matthew D. Edwards, P. Bieniasz, D. Kuritzkes, 2020, Nature.

Humoral, mucosal, and cellular immunity in response to a human immunodeficiency virus type 1 immunogen expressed by a Venezuelan equine encephalitis virus vaccine vector

R. Johnston, J. Frelinger, M. Betts, 1997, Journal of virology.

Genetic variability of the human immunodeficiency virus: statistical and biological issues.

B. Margolin, R. Swanstrom, F. Seillier-Moiseiwitsch, 1994, Annual review of genetics.

Epitranscriptomic Regulation of HIV-1 Gene Expression by m 5C and the Novel m 5C Reader MBD2

B. Cullen, R. Swanstrom, K. Tsai, 2019, SSRN Electronic Journal.

HIV type 1 protease inhibitors fail to inhibit HTLV-I Gag processing in infected cells.

S. Pettit, R. Swanstrom, D. Derse, 1998, AIDS research and human retroviruses.

Determinants of the human immunodeficiency virus type 1 p15NC-RNA interaction that affect enhanced cleavage by the viral protease

M. Rayner, S. Pettit, R. Swanstrom, 1997, Journal of virology.

The regulation of sequential processing of HIV-1 Gag by the viral protease.

S. Pettit, R. Swanstrom, S. Erickson-Viitanen, 1998, Advances in experimental medicine and biology.

Compartmentalized Replication of R5 T Cell-Tropic HIV-1 in the Central Nervous System Early in the Course of Infection

R. Swanstrom, R. Price, S Spudich, 2015, PLoS pathogens.

Replacement of the P1 Amino Acid of Human Immunodeficiency Virus Type 1 Gag Processing Sites Can Inhibit or Enhance the Rate of Cleavage by the Viral Protease

Celia A. Schiffer, C. Schiffer, S. Pettit, 2002, Journal of Virology.

Nelfinavir-Resistant, Amprenavir-Hypersusceptible Strains of Human Immunodeficiency Virus Type 1 Carrying an N88S Mutation in Protease Have Reduced Infectivity, Reduced Replication Capacity, and Reduced Fitness and Process the Gag Polyprotein Precursor Aberrantly

R. Swanstrom, N. Parkin, A. Gamarnik, 2002, Journal of Virology.

Human immunodeficiency virus type 1 virions composed of unprocessed Gag and Gag-Pol precursors are capable of reverse transcribing viral genomic RNA

A. Kaplan, D. Norbeck, D. Kempf, 1994, Antimicrobial Agents and Chemotherapy.

Characterization of HIV-1 protease mutants: random, directed, selected.

R. Swanstrom, 1994, Current opinion in biotechnology.

Partial inhibition of the human immunodeficiency virus type 1 protease results in aberrant virus assembly and the formation of noninfectious particles

A. Kaplan, D. Norbeck, D. Kempf, 1993, Journal of virology.

Analysis of temperature-sensitive mutants of the HIV-1 protease.

C. Hutchison, L. Everitt, D. Loeb, 1991, Advances in experimental medicine and biology.

A Strongly Transdominant Mutation in the Human Immunodeficiency Virus Type 1 gag Gene Defines an Achilles Heel in the Virus Life Cycle

R. Swanstrom, Sook-Kyung Lee, Janera Harris, 2009, Journal of Virology.

Evolution of Human Immunodeficiency Virus Type 1 Protease Genotypes and Phenotypes In Vivo under Selective Pressure of the Protease Inhibitor Ritonavir

R. Swanstrom, N. Parkin, Janera Harris, 2005, Journal of Virology.

Patterns of Changes in Human Immunodeficiency Virus Type 1 V3 Sequence Populations Late in Infection

R. Swanstrom, J. Nelson, F. Baribaud, 2000, Journal of Virology.

Accuracy of the TRUGENE HIV-1 Genotyping Kit

V. Johnson, D. Kuritzkes, R. Grant, 2003, Journal of Clinical Microbiology.

Highlights of the Global HIV-1 CSF Escape Consortium Meeting, 9 June 2016, Bethesda, MD, USA

A. Winston, R. Swanstrom, R. Price, 2016, Journal of virus eradication.

The nature of resistance to human immunodeficiency virus type-1 protease inhibitors

R. Swanstrom, W. Shao, T. Smith, 2000 .

Venezuelan equine encephalitis virus vectors expressing HIV-1 proteins: vector design strategies for improved vaccine efficacy.

R. Johnston, J. Frelinger, M. Betts, 1999, Vaccine.

The HIV type 1 protease inhibitor saquinavir can select for multiple mutations that confer increasing resistance.

R. Swanstrom, D. Irlbeck, R. Coombs, 1999, AIDS research and human retroviruses.

HIV-1 Protease Uses Bi-Specific S2/S2’ Subsites To Optimize Cleavage of Two Classes of Target Sites

C. Schiffer, C. Carter, R. Swanstrom, 2018, bioRxiv.

A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro.

C. Schiffer, R. Swanstrom, E. Nalivaika, 2015, Journal of molecular biology.

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1–Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing

R. Shafer, Shuntai Zhou, S. Holmes, 2017, The Journal of infectious diseases.

Quantification of the Latent HIV-1 Reservoir Using Ultra Deep Sequencing and Primer ID in a Viral Outgrowth Assay

M. Hudgens, Shuntai Zhou, R. Swanstrom, 2017, Journal of acquired immune deficiency syndromes.

Integrating the HIV-1 assembly/maturation pathway

R. Swanstrom, Marc Potempa, 2013, Proceedings of the National Academy of Sciences of the United States of America.

Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability

B. Cullen, R. Swanstrom, K. Tsai, 2020, bioRxiv.

Article Commentary: Targeting Chronic Central Nervous System HIV Infection

R. Swanstrom, R. Price, 2012, Antiviral therapy.

Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein.

B. Margolin, R. Swanstrom, L. Milich, 1997, Virology.

Evolutionary variants of the human immunodeficiency virus type 1 V3 region characterized by using a heteroduplex tracking assay

R. Swanstrom, J. Nelson, S. Fiscus, 1997, Journal of virology.

HIV-1 is Transported into the Central Nervous System by Trafficking Infected Cells

R. Swanstrom, R. Price, J. Eron, 2023, Pathogens & immunity.

Human Immunodeficiency Virus Type 1 RNA Detected in the Central Nervous System (CNS) After Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells

R. Swanstrom, N. Archin, K. Robertson, 2019 .

Affinofile Assay for Identifying Macrophage-Tropic HIV-1.

R. Swanstrom, Benhur Lee, S. Joseph, 2014, Bio-protocol.

Mutational sensitivity patterns define critical residues in the palm subdomain of the reverse transcriptase of human immunodeficiency virus type 1.

C. Hutchison, A. Kaplan, R. Swanstrom, 1995, Nucleic acids research.

Sequence requirements of the HIV-1 protease flap region determined by saturation mutagenesis and kinetic analysis of flap mutants.

C. Hutchison, L. Everitt, D. Loeb, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Vaccination of Macaques against Pathogenic Simian Immunodeficiency Virus with Venezuelan Equine Encephalitis Virus Replicon Particles

Philip R. Johnson, R. Johnston, D. Montefiori, 2000, Journal of Virology.

The specificity of the HIV-1 protease

S. Pettit, R. Swanstrom, Ronald Swanstrom, 1993 .

Multivariable analysis to determine if HIV-1 Tat dicysteine motif is associated with neurodevelopmental delay in HIV-infected children in Malawi

E. Cromwell, R. Swanstrom, A. Van Rie, 2015, Behavioral and Brain Functions.

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations.

C. Schiffer, T. Whitfield, R. Swanstrom, 2017, Journal of chemical theory and computation.

HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues.

C. Schiffer, R. Swanstrom, E. Nalivaika, 2023, European journal of medicinal chemistry.

Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-Tetrahydrofuran in a Pseudo-Symmetric Dipeptide Isostere.

C. Schiffer, R. Swanstrom, E. Nalivaika, 2020, Journal of medicinal chemistry.

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

S. L. Upton, E. L. Potter, Shamit S. Prabhu, 2019, Nature Communications.

Use of Next Generation Sequencing in a State-Wide Strategy of HIV-1 Surveillance: Impact of the SARS-CoV-2 Pandemic on HIV-1 Diagnosis and Transmission.

Ann M. Dennis, Shuntai Zhou, R. Swanstrom, 2023, The Journal of infectious diseases.

Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates

A. Kaplan, S. Pettit, R. Swanstrom, 2005, Retrovirology.

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

E. L. Potter, Shamit S. Prabhu, H. Ke, 2019, Nature Communications.

Immunological correlates of the HIV-1 replication-competent reservoir size.

A. Perelson, L. McKinnon, R. Swanstrom, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Target Cell Availability, Rather than Breast Milk Factors, Dictates Mother-to-Infant Transmission of SIV in Sooty Mangabeys and Rhesus Macaques

R. Swanstrom, C. A. Derdeyn, D. Carnathan, 2014, PLoS pathogens.

Becker Digital

R. Swanstrom, A. Emery, B. Tolbert, 2023 .

Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity

C. Schiffer, R. Swanstrom, Gavin J. Henderson, 2006, Journal of Virology.

Analysis of HIV type 1 reverse transcriptase: comparing sequences of viral isolates with mutational data.

C. Hutchison, J. Wrobel, R. Swanstrom, 2000, AIDS research and human retroviruses.

Detecting Linked Genomic Mutations

Michael Z. Man, R. Swanstrom, F. Seillier-Moiseiwitsch, 1999 .

Two Genetic Differences between Closely Related Zika Virus Strains Determine Pathogenic Outcome in Mice

Shuntai Zhou, R. Swanstrom, Nathaniel J. Moorman, 2020, Journal of Virology.

Retrovirus-mediated gene transfer to cystic fibrosis airway epithelial cells: effect of selectable marker sequences on long-term expression.

R. Swanstrom, J. Olsen, R. Boucher, 1993, Nucleic acids research.

HIV-1 pathogenesis: the virus.

R. Swanstrom, J. Coffin, 2012, Cold Spring Harbor perspectives in medicine.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

Shuntai Zhou, R. Swanstrom, C. Castaldi, 2022, medRxiv : the preprint server for health sciences.

Antigenicity and Immunogenicity of Transmitted/Founder, Consensus, and Chronic Envelope Glycoproteins of Human Immunodeficiency Virus Type 1

A. Lapedes, B. Korber, Haiyan Chen, 2013, Journal of Virology.

The evolution of HIV‐1 entry phenotypes as a guide to changing target cells

R. Swanstrom, S. Joseph, 2018, Journal of Leukocyte Biology.

Human Immunodeficiency Virus (Retroviridae)

R. Swanstrom, A. Emery, Blaide M D Woodburn, 2021, Encyclopedia of Virology.

R5 Macrophage-Tropic HIV-1 in the Male Genital Tract

Shuntai Zhou, R. Swanstrom, I. Hoffman, 2015, Journal of Virology.

HIV : from biology to prevention and treatment : a subject collection from Cold Spring Harbor perspectives in medicine

F. Bushman, G. Nabel, R. Swanstrom, 2012 .

Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells

R. Swanstrom, H. Akiyama, S. Gummuluru, 2017, Journal of Virology.

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

A. Perelson, B. Korber, P. Hraber, 2012, Journal of Clinical Investigation.

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain.

Cassandra B. Jabara, Shuntai Zhou, R. Swanstrom, 2015, AIDS research and human retroviruses.

Multivariable analysis to determine if HIV-1 Tat dicysteine motif is associated with neurodevelopmental delay in HIV-infected children in Malawi

E. Cromwell, R. Swanstrom, A. Van Rie, 2015, Behavioral and Brain Functions.

Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells

R. Swanstrom, S. Anderson, García, 1993, Journal of virology.

Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome.

Shuntai Zhou, R. Baric, R. Swanstrom, 2021, Bio-protocol.

N4-Hydroxycytidine/Molnupiravir Inhibits RNA-Virus Induced Encephalitis by Producing Mutated Viruses with Reduced Fitness

Shuntai Zhou, R. Baric, R. Schinazi, 2023, bioRxiv.

Characterization and selection of HIV-1 subtype C isolates for use in vaccine development.

Maureen F. Maughan, R. Johnston, S. Karim, 2003, AIDS research and human retroviruses.

Improving Viral Protease Inhibitors to Counter Drug Resistance.

C. Schiffer, R. Swanstrom, Nese Kurt Yilmaz, 2016, Trends in Microbiology.

Structure and immunogenicity of alternative forms of the simian immunodeficiency virus gag protein expressed using Venezuelan equine encephalitis virus replicon particles.

R. Johnston, A. Whitmore, R. Swanstrom, 2007, Virology.