List of works - Ronald G Collman

A Summary of the First HIV Microbiome Workshop 2015.

scientific article

A Summary of the Third Annual HIV Microbiome Workshop

article

A comprehensive analysis of the naturally occurring polymorphisms in HIV-1 Vpr: potential impact on CTL epitopes

scientific article published on 23 August 2008

A novel CCR5 mutation common in sooty mangabeys reveals SIVsmm infection of CCR5-null natural hosts and efficient alternative coreceptor use in vivo

scientific article

A summary of the second annual HIV Microbiome workshop.

scientific article published on 13 September 2017

Adaptive mutations in a human immunodeficiency virus type 1 envelope protein with a truncated V3 loop restore function by improving interactions with CD4.

scientific article

Administration of nucleoside-modified mRNA encoding broadly neutralizing antibody protects humanized mice from HIV-1 challenge

scientific article published on 02 March 2017

Advances in macrophage and dendritic cell biology in HIV-1 infection stress key understudied areas in infection, pathogenesis, and analysis of viral reservoirs.

scientific article published on 25 August 2006

Alcohol use and abuse among patients with multidrug-resistant tuberculosis in Botswana.

scientific article published on 07 September 2012

Allometry and Ecology of the Bilaterian Gut Microbiome

scientific article published on 27 March 2018

An infectious molecular clone of an unusual macrophage-tropic and highly cytopathic strain of human immunodeficiency virus type 1 ⬇️

scientific article published on December 1, 1992

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV

scientific article published on 20 December 2012

Application of 'Omics' and Systems Biology to Sarcoidosis Research

scientific article published on 20 October 2017

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

scientific article

Associating microbiome composition with environmental covariates using generalized UniFrac distances

scientific article

BCR-ABL1 alters SDF-1alpha-mediated adhesive responses through the beta2 integrin LFA-1 in leukemia cells

scientific article published on 13 March 2008

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

scientific article published on 08 October 2018

CD4 + T Cells Support Production of Simian Immunodeficiency Virus Env Antibodies That Enforce CD4-Dependent Entry and Shape Tropism In Vivo ⬇️

scientific article published on 03 July 2013

CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells

scientific article (publication date: October 2014)

CD4 receptor diversity in chimpanzees protects against SIV infection

scientific article published on 04 February 2019

CNS inflammation and macrophage/microglial biology associated with HIV-1 infection.

scientific article published on 19 September 2009

CXCR6-Mediated Simian Immunodeficiency Virus SIVagmSab Entry into Sabaeus African Green Monkey Lymphocytes Implicates Widespread Use of Non-CCR5 Pathways in Natural Host Infections.

scientific article published on 30 November 2016

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

scientific article published on 11 July 2018

Characterization and Implementation of a Diverse Simian Immunodeficiency Virus SIVsm Envelope Panel in the Assessment of Neutralizing Antibody Breadth Elicited in Rhesus Macaques by Multimodal Vaccines Expressing the SIVmac239 Envelope.

scientific article published on 27 May 2015

Chemokine receptor utilization and macrophage signaling by human immunodeficiency virus type 1 gp120: Implications for neuropathogenesis

article

Circulating human CD4 and CD8 T cells do not have large intracellular pools of CCR5

scientific article

Clinical outcomes among persons with pulmonary tuberculosis caused by Mycobacterium tuberculosis isolates with phenotypic heterogeneity in results of drug-susceptibility tests

scientific article

Co-receptor antagonists as HIV-1 entry inhibitors.

scientific article published on February 2004

Coevolutionary dynamics between tribe Cercopithecini tetherins and their lentiviruses.

scientific article

Composition and dynamics of the respiratory tract microbiome in intubated patients.

scientific article published on 11 February 2016

Constrained use of CCR5 on CD4+ lymphocytes by R5X4 HIV-1: efficiency of Env-CCR5 interactions and low CCR5 expression determine a range of restricted CCR5-mediated entry

scientific article

Contrasting Use of CCR5 Structural Determinants by R5 and R5X4 Variants within a Human Immunodeficiency Virus Type 1 Primary Isolate Quasispecies ⬇️

scientific article published on November 1, 2003

Decreased plasticity of coreceptor use by CD4-independent SIV Envs that emerge in vivo

scientific article

Depletion of CD4⁺ T cells abrogates post-peak decline of viremia in SIV-infected rhesus macaques

scientific article

Differences in the rate of nicotine metabolism among smokers with and without HIV

scientific article published on 01 May 2019

Differential regulation of host cellular genes by HIV-1 viral protein R (Vpr): cDNA microarray analysis using isogenic virus

scientific article

Disordered microbial communities in the upper respiratory tract of cigarette smokers

scientific article

Divergent CD4+ T memory stem cell dynamics in pathogenic and nonpathogenic simian immunodeficiency virus infections

scientific article

Dualtropic CXCR6/CCR5 Simian Immunodeficiency Virus (SIV) Infection of Sooty Mangabey Primary Lymphocytes: Distinct Coreceptor Use in Natural versus Pathogenic Hosts of SIV

scientific article

Effect of Highly Active Antiretroviral Therapy on Viral Burden in the Lungs of HIV‐Infected Subjects

article

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

scientific article published on 04 April 2016

Entry coreceptor use and fusion inhibitor T20 sensitivity of dual-tropic R5X4 HIV-1 in primary macrophage infection.

scientific article published on March 2008

Erratum: Longer hospital stay is associated with high rates of tuberculosis-related morbidity and mortality within 12 months after discharge in a referral hospital in Sub-Saharan Africa

scientific article published on 10 May 2015

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates.

scientific article published on 11 April 2018

Examining the relationship between alcohol use and high-risk sex practices in a population of women with high HIV incidence despite high levels of HIV-related knowledge.

scientific article published on 15 January 2014

Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV

scientific article (publication date: 6 March 2014)

HIV and cells of macrophage/dendritic lineage and other non-T cell reservoirs: new answers yield new questions

scientific article

HIV-1 entry and entry inhibitors as therapeutic agents

scientific article

HIV-1 envelope-receptor interactions required for macrophage infection and implications for current HIV-1 cure strategies

scientific article

HIV-1 gp120 and chemokines activate ion channels in primary macrophages through CCR5 and CXCR4 stimulation

scientific article

HIV-1 gp120 chemokine receptor-mediated signaling in human macrophages

scientific article (publication date: 2003)

HIV-1 gp120-induced TNF-{alpha} production by primary human macrophages is mediated by phosphatidylinositol-3 (PI-3) kinase and mitogen-activated protein (MAP) kinase pathways.

scientific article

Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization.

scientific article published on 10 June 2009

Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens.

scientific article published on 11 May 2015

Human immunodeficiency virus type 1 tropism for human macrophages

scientific article

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing

scientific article

Induction of Heme Oxygenase-1 Deficiency and Associated Glutamate-Mediated Neurotoxicity Is a Highly Conserved HIV Phenotype of Chronic Macrophage Infection That Is Resistant to Antiretroviral Therapy

scientific article

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.

scientific article

Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus

scientific article published in November 2011

Longer hospital stay is associated with higher rates of tuberculosis-related morbidity and mortality within 12 months after discharge in a referral hospital in Sub-Saharan Africa

scientific article

Loss of CXCR6 coreceptor usage characterizes pathogenic lentiviruses.

scientific article published on 16 April 2018

Low levels of SIV infection in sooty mangabey central memory CD⁴⁺ T cells are associated with limited CCR5 expression

scientific article published on 26 June 2011

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

scientific article

Macrophage activation through CCR5- and CXCR4-mediated gp120-elicited signaling pathways

scientific article (publication date: November 2003)

Marginal Effects of Systemic CCR5 Blockade with Maraviroc on Oral Simian Immunodeficiency Virus Transmission to Infant Macaques

article

Measurement of antiretroviral drugs in the lungs of HIV-infected patients

scientific article

Membrane-based, sedimentation-assisted plasma separator for point-of-care applications

scientific article published on 25 October 2013

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples.

scientific article

Miniaturized devices for point of care molecular detection of HIV.

scientific article

Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes

scientific article

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit

scientific article published on 18 December 2018

Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents.

scientific article published on 29 May 2019

Monocyte migration and LFA-1-mediated attachment to brain microvascular endothelia is regulated by SDF-1 alpha through Lyn kinase

scientific article

Mutagenesis of the putative alpha-helical domain of the Vpr protein of human immunodeficiency virus type 1: effect on stability and virion incorporation

scientific article

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions

scientific article published on 01 August 2018

Optimizing methods and dodging pitfalls in microbiome research

scientific article (publication date: 5 May 2017)

Persistent high mortality in advanced HIV/TB despite appropriate antiretroviral and antitubercular therapy: an emerging challenge

scientific article

Placebo-controlled randomized clinical trial testing the efficacy and safety of varenicline for smokers with HIV

scientific article published on 07 May 2019

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

scientific article published on 29 March 2015

Preferential use of CXCR4 by R5X4 human immunodeficiency virus type 1 isolates for infection of primary lymphocytes ⬇️

scientific article

R5X4 HIV-1 coreceptor use in primary target cells: implications for coreceptor entry blocking strategies

scientific article

Rate of Nicotine Metabolism and Tobacco Use among Persons with HIV: Implications for Treatment and Research

article

Rationale and design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Sarcoidosis protocol

journal article published in 2015

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness

scientific article published on 01 May 2019

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness

scientific article published on 01 August 2019

Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales

scientific article published on 18 August 2021

Retinoblastoma protein induction by HIV viremia or CCR5 in monocytes exposed to HIV-1 mediates protection from activation-induced apoptosis: ex vivo and in vitro study.

scientific article published on 13 June 2012

Role of HIV-1 Vpr in AIDS pathogenesis: relevance and implications of intravirion, intracellular and free Vpr.

scientific article

SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021

scientific article published on 08 February 2022

SIV Coreceptor Specificity in Natural and Non-Natural Host Infection: Implications for Cell Targeting and Differential Outcomes from Infection.

scientific article

Signaling mechanism of HIV-1 gp120 and virion-induced IL-1beta release in primary human macrophages.

scientific article published on May 2008

Statin modulation of monocyte phenotype and function: implications for HIV-1-associated neurocognitive disorders.

scientific article published on 28 March 2016

Substance P antagonist (CP-96,345) inhibits HIV-1 replication in human mononuclear phagocytes

scientific article published on 27 March 2001

Supraphysiologic control over HIV-1 replication mediated by CD8 T cells expressing a re-engineered CD4-based chimeric antigen receptor.

scientific article published on 12 October 2017

T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency

article

Target cell availability, rather than breast milk factors, dictates mother-to-infant transmission of SIV in sooty mangabeys and rhesus macaques

scientific article

The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction

scientific article

The lung microbiome in idiopathic pulmonary fibrosis. What does it mean and what should we do about it?

scientific article published in October 2014

The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report.

scientific article published on June 2013

Topographical continuity of bacterial populations in the healthy human respiratory tract

scientific article published on 16 June 2011

Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune control.

scientific article published in June 2008

Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant

scientific article published on 01 November 2019

Use of dual recombinant vaccinia virus vectors to assay viral glycoprotein-mediated fusion with transfection-resistant primary cell targets.

scientific article published on January 2004

Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients

scientific article

List of works by Ronald G Collman

A Summary of the First HIV Microbiome Workshop 2015.

A Summary of the Third Annual HIV Microbiome Workshop

A comprehensive analysis of the naturally occurring polymorphisms in HIV-1 Vpr: potential impact on CTL epitopes

A novel CCR5 mutation common in sooty mangabeys reveals SIVsmm infection of CCR5-null natural hosts and efficient alternative coreceptor use in vivo

A summary of the second annual HIV Microbiome workshop.

Adaptive mutations in a human immunodeficiency virus type 1 envelope protein with a truncated V3 loop restore function by improving interactions with CD4.

Administration of nucleoside-modified mRNA encoding broadly neutralizing antibody protects humanized mice from HIV-1 challenge

Advances in macrophage and dendritic cell biology in HIV-1 infection stress key understudied areas in infection, pathogenesis, and analysis of viral reservoirs.

Alcohol use and abuse among patients with multidrug-resistant tuberculosis in Botswana.

Allometry and Ecology of the Bilaterian Gut Microbiome

An infectious molecular clone of an unusual macrophage-tropic and highly cytopathic strain of human immunodeficiency virus type 1 ⬇️

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV

Application of 'Omics' and Systems Biology to Sarcoidosis Research

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

Associating microbiome composition with environmental covariates using generalized UniFrac distances

BCR-ABL1 alters SDF-1alpha-mediated adhesive responses through the beta2 integrin LFA-1 in leukemia cells

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

CD4 + T Cells Support Production of Simian Immunodeficiency Virus Env Antibodies That Enforce CD4-Dependent Entry and Shape Tropism In Vivo ⬇️

CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells

CD4 receptor diversity in chimpanzees protects against SIV infection

CNS inflammation and macrophage/microglial biology associated with HIV-1 infection.

CXCR6-Mediated Simian Immunodeficiency Virus SIVagmSab Entry into Sabaeus African Green Monkey Lymphocytes Implicates Widespread Use of Non-CCR5 Pathways in Natural Host Infections.

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

Characterization and Implementation of a Diverse Simian Immunodeficiency Virus SIVsm Envelope Panel in the Assessment of Neutralizing Antibody Breadth Elicited in Rhesus Macaques by Multimodal Vaccines Expressing the SIVmac239 Envelope.

Chemokine receptor utilization and macrophage signaling by human immunodeficiency virus type 1 gp120: Implications for neuropathogenesis

Circulating human CD4 and CD8 T cells do not have large intracellular pools of CCR5

Clinical outcomes among persons with pulmonary tuberculosis caused by Mycobacterium tuberculosis isolates with phenotypic heterogeneity in results of drug-susceptibility tests

Co-receptor antagonists as HIV-1 entry inhibitors.

Coevolutionary dynamics between tribe Cercopithecini tetherins and their lentiviruses.

Composition and dynamics of the respiratory tract microbiome in intubated patients.

Constrained use of CCR5 on CD4+ lymphocytes by R5X4 HIV-1: efficiency of Env-CCR5 interactions and low CCR5 expression determine a range of restricted CCR5-mediated entry

Contrasting Use of CCR5 Structural Determinants by R5 and R5X4 Variants within a Human Immunodeficiency Virus Type 1 Primary Isolate Quasispecies ⬇️

Decreased plasticity of coreceptor use by CD4-independent SIV Envs that emerge in vivo

Depletion of CD4⁺ T cells abrogates post-peak decline of viremia in SIV-infected rhesus macaques

Differences in the rate of nicotine metabolism among smokers with and without HIV

Differential regulation of host cellular genes by HIV-1 viral protein R (Vpr): cDNA microarray analysis using isogenic virus

Disordered microbial communities in the upper respiratory tract of cigarette smokers

Divergent CD4+ T memory stem cell dynamics in pathogenic and nonpathogenic simian immunodeficiency virus infections

Dualtropic CXCR6/CCR5 Simian Immunodeficiency Virus (SIV) Infection of Sooty Mangabey Primary Lymphocytes: Distinct Coreceptor Use in Natural versus Pathogenic Hosts of SIV

Effect of Highly Active Antiretroviral Therapy on Viral Burden in the Lungs of HIV‐Infected Subjects

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

Entry coreceptor use and fusion inhibitor T20 sensitivity of dual-tropic R5X4 HIV-1 in primary macrophage infection.

Erratum: Longer hospital stay is associated with high rates of tuberculosis-related morbidity and mortality within 12 months after discharge in a referral hospital in Sub-Saharan Africa

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates.

Examining the relationship between alcohol use and high-risk sex practices in a population of women with high HIV incidence despite high levels of HIV-related knowledge.

Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV

HIV and cells of macrophage/dendritic lineage and other non-T cell reservoirs: new answers yield new questions

HIV-1 entry and entry inhibitors as therapeutic agents

HIV-1 envelope-receptor interactions required for macrophage infection and implications for current HIV-1 cure strategies

HIV-1 gp120 and chemokines activate ion channels in primary macrophages through CCR5 and CXCR4 stimulation

HIV-1 gp120 chemokine receptor-mediated signaling in human macrophages

HIV-1 gp120-induced TNF-{alpha} production by primary human macrophages is mediated by phosphatidylinositol-3 (PI-3) kinase and mitogen-activated protein (MAP) kinase pathways.

Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization.

Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens.

Human immunodeficiency virus type 1 tropism for human macrophages

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing

Induction of Heme Oxygenase-1 Deficiency and Associated Glutamate-Mediated Neurotoxicity Is a Highly Conserved HIV Phenotype of Chronic Macrophage Infection That Is Resistant to Antiretroviral Therapy

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.

Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus

Longer hospital stay is associated with higher rates of tuberculosis-related morbidity and mortality within 12 months after discharge in a referral hospital in Sub-Saharan Africa

Loss of CXCR6 coreceptor usage characterizes pathogenic lentiviruses.

Low levels of SIV infection in sooty mangabey central memory CD⁴⁺ T cells are associated with limited CCR5 expression

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

Macrophage activation through CCR5- and CXCR4-mediated gp120-elicited signaling pathways

Marginal Effects of Systemic CCR5 Blockade with Maraviroc on Oral Simian Immunodeficiency Virus Transmission to Infant Macaques

Measurement of antiretroviral drugs in the lungs of HIV-infected patients

Membrane-based, sedimentation-assisted plasma separator for point-of-care applications

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples.

Miniaturized devices for point of care molecular detection of HIV.

Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit

Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents.

Monocyte migration and LFA-1-mediated attachment to brain microvascular endothelia is regulated by SDF-1 alpha through Lyn kinase

Mutagenesis of the putative alpha-helical domain of the Vpr protein of human immunodeficiency virus type 1: effect on stability and virion incorporation

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions

Optimizing methods and dodging pitfalls in microbiome research

Persistent high mortality in advanced HIV/TB despite appropriate antiretroviral and antitubercular therapy: an emerging challenge

Placebo-controlled randomized clinical trial testing the efficacy and safety of varenicline for smokers with HIV

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA