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List of works by Stephen H. Hughes

2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one-based HIV-1 integrase inhibitors

scientific article published on 21 December 2007

4-amino-1-hydroxy-2-oxo-1,8-naphthyridine-containing compounds having high potency against raltegravir-resistant integrase mutants of HIV-1

scientific article

4′- C -Methyl-2′-Deoxyadenosine and 4′- C -Ethyl-2′-Deoxyadenosine Inhibit HIV-1 Replication ⬇️

scientific article published on February 22, 2011

6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 integrase inhibitors ⬇️

scientific article published on October 27, 2012

A 4'-C-ethynyl-2',3'-dideoxynucleoside analogue highlights the role of the 3'-OH in anti-HIV active 4'-C-ethynyl-2'-deoxy nucleosides

scientific article published on October 2004

A Homology Model of HIV-1 Integrase and Analysis of Mutations Designed to Test the Model ⬇️

scientific article published on March 27, 2013

A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants

scientific article

A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude

scientific article

A novel mechanism for inhibition of HIV-1 reverse transcriptase

scientific article published in December 2002

Activities, Crystal Structures, and Molecular Dynamics of Dihydro-1 H -isoindole Derivatives, Inhibitors of HIV-1 Integrase

scientific article

Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity

scientific article

Alternate polypurine tracts (PPTs) affect the rous sarcoma virus RNase H cleavage specificity and reveal a preferential cleavage following a GA dinucleotide sequence at the PPT-U3 junction

scientific article

Alternate polypurine tracts affect rous sarcoma virus integration in vivo

scientific article

Analysis of amino acids in the beta7-beta8 loop of human immunodeficiency virus type 1 reverse transcriptase for their role in virus replication

scientific article published on 10 November 2006

Analysis of the Zidovudine Resistance Mutations T215Y, M41L, and L210W in HIV-1 Reverse Transcriptase

scientific article

Apparent defects in processive DNA synthesis, strand transfer, and primer elongation of Met-184 mutants of HIV-1 reverse transcriptase derive solely from a dNTP utilization defect

scientific article published on 24 January 2008

Attentive navigation for viewpoint control in virtual environments

scientific article published in January 2005

Autosomal dominant and sporadic monocytopenia with susceptibility to mycobacteria, fungi, papillomaviruses, and myelodysplasia

scientific article

Avian bic, a gene isolated from a common retroviral site in avian leukosis virus-induced lymphomas that encodes a noncoding RNA, cooperates with c-myc in lymphomagenesis and erythroleukemogenesis

scientific article

Bicyclic 1-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxamide-containing HIV-1 integrase inhibitors having high antiviral potency against cells harboring raltegravir-resistant integrase mutants

scientific article published on 10 February 2014

Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration

article

Characterization of the polymerase and RNase H activities of human foamy virus reverse transcriptase

scientific article

Clonal expansion of CAR T cells harboring lentivector integration in the CBL gene following anti-CD22 CAR T-cell therapy

scientific article published on 01 August 2019

Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans

scientific article published on 10 July 2019

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

scientific article published on 8 February 2016

Combining mutations in HIV-1 reverse transcriptase with mutations in the HIV-1 polypurine tract affects RNase H cleavages involved in PPT utilization

scientific article published on 10 February 2006

Construction and characterization of a replication-competent retroviral shuttle vector plasmid

scientific article

Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design

scientific article

Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: a new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains

scientific article

Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.

scientific article

Crystallography and the design of anti-AIDS drugs: conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors

scientific article

D-(+)-iso-methanocarbathymidine: a high-affinity substrate for herpes simplex virus 1 thymidine kinase

scientific article published on July 2008

Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugs

scientific article published on September 2004

Development of tricyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors

scientific article

Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and LEDGF/p75 on the efficiency and specificity of viral DNA integration

scientific article

Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles

scientific article published on 24 March 2014

Drug resistant integrase mutants cause aberrant HIV integrations

scientific article published on 29 September 2016

Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage

scientific article published on December 2004

Effects of substitutions at the 4' and 2 positions on the bioactivity of 4'-ethynyl-2-fluoro-2'-deoxyadenosine

scientific article published on 07 October 2013

Effects of the Delta67 complex of mutations in human immunodeficiency virus type 1 reverse transcriptase on nucleoside analog excision

scientific article published on September 2004

Efficacies of Cabotegravir and Bictegravir against drug-resistant HIV-1 integrase mutants

scientific article

Enhancers are major targets for murine leukemia virus vector integration

scientific article

Examination of halogen substituent effects on HIV-1 integrase inhibitors derived from 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-ones and 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones

scientific article published on 28 March 2009

False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector

scientific article published on February 2014

Fixed conformation nucleoside analogs effectively inhibit excision-proficient HIV-1 reverse transcriptases

scientific article

Flexible use of nuclear import pathways by HIV-1.

scientific article

Foamy Retrovirus Integrase Contains a Pol Dimerization Domain Required for Protease Activation ⬇️

scientific article published on December 1, 2010

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation ⬇️

scientific article published on February 28, 2013

HIV-1 Integrase Inhibitors That Are Broadly Effective against Drug-Resistant Mutants.

scientific article

HIV-1 Integrase Inhibitors that are active against Drug-Resistant Integrase Mutants

scientific article published on 29 June 2020

HIV-1 Reverse Transcriptase Structure with RNase H Inhibitor Dihydroxy Benzoyl Naphthyl Hydrazone Bound at a Novel Site

scientific article

HIV-1 and HIV-2 Reverse Transcriptases: Different Mechanisms of Resistance to Nucleoside Reverse Transcriptase Inhibitors ⬇️

scientific article published on March 21, 2012

HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision

scholarly article

HRP2 determines the efficiency and specificity of HIV-1 integration in LEDGF/p75 knockout cells but does not contribute to the antiviral activity of a potent LEDGF/p75-binding site integrase inhibitor

scientific article

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations

scientific article

Human Immunodeficiency Virus Type 1 Capsid Mutation N74D Alters Cyclophilin A Dependence and Impairs Macrophage Infection ⬇️

scientific article published on February 1, 2012

Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses

scientific article published on 4 April 2007

Identification of a 3-aminoimidazo[1,2-a]pyridine inhibitor of HIV-1 reverse transcriptase

scientific article

Identification of glycosylation sites in the SU component of the Avian Sarcoma/Leukosis virus Envelope Glycoprotein (Subgroup A) by mass spectrometry

scientific article published on August 2004

Improved Baculovirus Vectors for Transduction and Gene Expression in Human Pancreatic Islet Cells

article

In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).

scientific article

In vitro analysis of the effects of mutations in the G-tract of the human immunodeficiency virus type 1 polypurine tract on RNase H cleavage specificity

scientific article published on 21 November 2006

In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques

scientific article published on December 2004

In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT.

scientific article published on 12 July 2007

Insertional activation of <i>STAT3</i> and <i>LCK</i> by HIV-1 proviruses in T cell lymphomas

scientific article published on 13 October 2021

Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

scientific article published on 07 April 2021

Integration of rous sarcoma virus DNA: a CA dinucleotide is not required for integration of the U3 end of viral DNA.

scientific article published on 03 September 2008

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

scientific article

Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration

scientific article

MK-0536 Inhibits HIV-1 Integrases Resistant to Raltegravir ⬇️

scientific article published on August 29, 2011

Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate with In Vitro Activity ⬇️

scientific article published on October 28, 2011

Multiple Origins of Virus Persistence during Natural Control of HIV Infection

scientific article published on 20 July 2016

Mutagenesis of Human Immunodeficiency Virus Reverse Transcriptase p51 Subunit Defines Residues Contributing to Vinylogous Urea Inhibition of Ribonuclease H Activity ⬇️

scientific article published on November 21, 2011

Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity.

scientific article

Mutation of the catalytic domain of the foamy virus reverse transcriptase leads to loss of processivity and infectivity

scientific article

Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis

scientific article published in April 2004

Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replication

scientific article

Mutations in HIV-1 reverse transcriptase cause misfolding and miscleavage by the viral protease ⬇️

scientific article published on July 11, 2013

Mutations in human immunodeficiency virus type 1 reverse transcriptase that make it sensitive to degradation by the viral protease in virions are selected against in patients

scientific article published on 18 June 2015

Mutations in the 5′ End of the Human Immunodeficiency Virus Type 1 Polypurine Tract Affect RNase H Cleavage Specificity and Virus Titer ⬇️

scientific article published on October 1, 2003

Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo.

scientific article

Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo

scientific article

Mutations in the U5 sequences adjacent to the primer binding site do not affect tRNA cleavage by rous sarcoma virus RNase H but do cause aberrant integrations in vivo

scientific article

Mutations in the thumb allow human immunodeficiency virus type 1 reverse transcriptase to be cleaved by protease in virions

scientific article published on 16 September 2009

Mutations of a residue within the polyproline-rich region of Env alter the replication rate and level of cytopathic effects in chimeric avian retroviral vectors

scientific article

Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication

scientific article

Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA

scientific article published on April 2004

Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro.

scientific article published in March 2002

Nucleoside analog resistance caused by insertions in the fingers of human immunodeficiency virus type 1 reverse transcriptase involves ATP-mediated excision.

scientific article

On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data

scientific article

PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1

scientific article

Protein delivery using engineered virus-like particles ⬇️

scientific article published on September 26, 2011

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

scientific article

Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors

scientific article published on 24 June 2008

Reprogramming human T cell function and specificity with non-viral genome targeting

Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap

scientific article

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

scientific article published on 04 July 2016

Reverse Transcription of Retroviruses and LTR Retrotransposons.

scientific article published in April 2015

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 V

article

Roles of viral and cellular proteins in the expression of alternatively spliced HTLV-1 pX mRNAs

scientific article published on December 2003

Rous sarcoma virus (RSV) integration in vivo: a CA dinucleotide is not required in U3, and RSV linear DNA does not autointegrate

scientific article

Selectivity for strand-transfer over 3'-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme-DNA interactions in the active site

scientific article published on July 2016

Structural Basis for the Role of the K65R Mutation in HIV-1 Reverse Transcriptase Polymerization, Excision Antagonism, and Tenofovir Resistance

scientific article

Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572)

scientific article

Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures

scientific article published on 17 August 2021

Structural basis of HIV-1 resistance to AZT by excision

scientific article

Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition

scientific article

Structure of HIV-1 Reverse Transcriptase with the Inhibitor β-Thujaplicinol Bound at the RNase H Active Site

scientific article

Structure-Based Non-Nucleoside Inhibitor Design: Developing Inhibitors that Are Effective Against Resistant Mutants

scientific article published on 02 August 2020

Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir

scientific article published on 25 April 2004

Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.

scientific article

Synthesis of conformationally locked carbocyclic nucleoside phosphonates to probe the active site of HIV-1 RT.

scientific article published on January 2008

Synthesis, biological activity, and crystal structure of potent nonnucleoside inhibitors of HIV-1 reverse transcriptase that retain activity against mutant forms of the enzyme

scientific article

Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases

scientific article

The Integrator complex controls the termination of transcription at diverse classes of gene targets

scientific article

The M184V mutation reduces the selective excision of zidovudine 5'-monophosphate (AZTMP) by the reverse transcriptase of human immunodeficiency virus type 1

scientific article

The effects of RNase H inhibitors and nevirapine on the susceptibility of HIV-1 to AZT and 3TC ⬇️

scientific article published on September 9, 2011

The effects of alternate polypurine tracts (PPTs) and mutations of sequences adjacent to the PPT on viral replication and cleavage specificity of the Rous sarcoma virus reverse transcriptase

scientific article published on 18 June 2008

The history of N-methanocarbathymidine: the investigation of a conformational concept leads to the discovery of a potent and selective nucleoside antiviral agent

scientific article

The level of reverse transcriptase (RT) in human immunodeficiency virus type 1 particles affects susceptibility to nonnucleoside RT inhibitors but not to lamivudine

scientific article

The nucleoside analogs 4'C-methyl thymidine and 4'C-ethyl thymidine block DNA synthesis by wild-type HIV-1 RT and excision proficient NRTI resistant RT variants

scientific article

The nucleoside analogue D-carba T blocks HIV-1 reverse transcription

scientific article published on September 2009

Transduction of rhesus macaque hematopoietic stem and progenitor cells with avian sarcoma and leukosis virus vectors

scientific article

Trapping HIV-1 reverse transcriptase before and after translocation on DNA.

scientific article published on 28 January 2003

Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations ⬇️

scientific article published on August 19, 2013

Two Coselected Distal Mutations in HIV-1 Reverse Transcriptase (RT) Alter Susceptibility to Nonnucleoside RT Inhibitors and Nucleoside Analogs.

scientific article published on 15 May 2019

Varicella-zoster virus necrotising retinitis, retinal vasculitis and panuveitis following uncomplicated chickenpox in an immunocompetent child

scientific article

What Integration Sites Tell Us about HIV Persistence

scientific article published on May 2016

Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance?

scientific article

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