List of works - Susanna L Lamers

Brain-specific HIV Nef identified in multiple patients with neurological disease

scientific article

Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants.

scientific article

Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population

scientific article published on 15 December 2017

Correction for Rife et al., Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephaliti

scientific article published on 12 September 2016

Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma

scientific article

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

scientific article published in November 2017

Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology.

scientific article published on February 2012

Emerging Patterns in HIV-1 gp120 Variable Domains in Anatomical Tissues in the Absence of a Plasma Viral Load

scientific article published on 10 April 2019

Eradication of HIV from Tissue Reservoirs: Challenges for the Cure

scientific article

Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis

scientific article published on 27 April 2016

Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology

scientific article

Factors related to HIV-associated neurocognitive impairment differ with age.

scientific article

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2.

scientific article published on 27 May 2015

Geographic HIV type 1 subtype distribution in Rakai district, Uganda

scientific article published on October 2009

Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins

scientific article published on 27 May 2015

HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads.

scientific article published on 27 July 2016

HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer.

scientific article published on 27 July 2016

HIV type 1 genetic variation in foreskin and blood from subjects in Rakai, Uganda

scientific article

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS.

scientific article published on 29 August 2016

HIV-1 Nef Protein Visits B-Cells via Macrophage Nanotubes: A Mechanism for AIDS-Related Lymphoma Pathogenesis? ⬇️

scientific article published on December 1, 2010

HIV-1 Nef in macrophage-mediated disease pathogenesis.

scientific article published on December 2012

HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013.

scientific article

HIV-1 nef protein structures associated with brain infection and dementia pathogenesis

scientific article (publication date: 9 February 2011)

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues ⬇️

scientific article published on November 3, 2010

HIV-1 subtype distribution and diversity over 18 years in Rakai, Uganda

scientific article published on 12 April 2020

HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy

scientific article

HIV-miR-H1 evolvability during HIV pathogenesis

scientific article

High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS.

scientific article published on 30 July 2009

Human immunodeficiency virus-1 evolutionary patterns associated with pathogenic processes in the brain

scientific article

Identification of dual-tropic HIV-1 using evolved neural networks

scientific article published on 26 September 2015

Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.

scientific article published on 8 November 2016

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks

scientific article published on 22 February 2019

Increased replication of non-syncytium-inducing HIV type 1 isolates in monocyte-derived macrophages is linked to advanced disease in infected children

scientific article published on March 2002

Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo

scientific article published on July 1993

Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies

scientific article published on 29 April 2020

Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains

scientific article published on 01 February 2020

Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS.

scientific article published on 20 August 2013

Low Rates of Transmitted Drug Resistance Among Newly Identified HIV-1 Seroconverters in Rural Rakai, Uganda

scientific article published on 31 October 2016

Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms

scientific article

Molecular surveillance of methicillin-resistant Staphylococcus aureus genomes in hospital unexpectedly reveals discordance between temporal and genetic clustering

scientific article published on 18 June 2020

On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition

scientific article published on 12 April 2016

Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection.

scientific article

Persistence of HIV transmission clusters among people who inject drugs

scientific article published on 07 August 2020

Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission

scientific article

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS.

scientific article published in September 2005

Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort

article

Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks

scientific article

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.

scientific article published on 5 July 2018

Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda

scientific article published on 02 March 2020

Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources

scientific article published on 28 June 2011

Spatial phylodynamics of HIV-1 epidemic emergence in east Africa.

scientific article

Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.

scientific article

The HIV nef protein within ARL is genetically and structurally distinct from those in the brain of patients with HAD.

scientific article published on 11 October 2010

The Spleen Is an HIV-1 Sanctuary During Combined Antiretroviral Therapy

scientific article published on 30 October 2017

The meningeal lymphatic system: a route for HIV brain migration?

scientific article published on 16 November 2015

The prevalence of HIV-1 DNA in AIDS-related lymphoma and Kaposi Sarcoma throughout the AIDS epidemic

article

Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

scientific article published on 3 June 2015

Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues

scientific article published on 23 April 2018

Urogenital Chlamydia trachomatis multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia.

scientific article published on 11 April 2018

List of works by Susanna L Lamers

Brain-specific HIV Nef identified in multiple patients with neurological disease

Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants.

Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population

Correction for Rife et al., Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephaliti

Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology.

Emerging Patterns in HIV-1 gp120 Variable Domains in Anatomical Tissues in the Absence of a Plasma Viral Load

Eradication of HIV from Tissue Reservoirs: Challenges for the Cure

Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis

Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology

Factors related to HIV-associated neurocognitive impairment differ with age.

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2.

Geographic HIV type 1 subtype distribution in Rakai district, Uganda

Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins

HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads.

HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer.

HIV type 1 genetic variation in foreskin and blood from subjects in Rakai, Uganda

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS.

HIV-1 Nef Protein Visits B-Cells via Macrophage Nanotubes: A Mechanism for AIDS-Related Lymphoma Pathogenesis? ⬇️

HIV-1 Nef in macrophage-mediated disease pathogenesis.

HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013.

HIV-1 nef protein structures associated with brain infection and dementia pathogenesis

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues ⬇️

HIV-1 subtype distribution and diversity over 18 years in Rakai, Uganda

HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy

HIV-miR-H1 evolvability during HIV pathogenesis

High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS.

Human immunodeficiency virus-1 evolutionary patterns associated with pathogenic processes in the brain

Identification of dual-tropic HIV-1 using evolved neural networks

Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks

Increased replication of non-syncytium-inducing HIV type 1 isolates in monocyte-derived macrophages is linked to advanced disease in infected children

Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo

Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies

Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains

Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS.

Low Rates of Transmitted Drug Resistance Among Newly Identified HIV-1 Seroconverters in Rural Rakai, Uganda

Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms

Molecular surveillance of methicillin-resistant Staphylococcus aureus genomes in hospital unexpectedly reveals discordance between temporal and genetic clustering

On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition

Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection.

Persistence of HIV transmission clusters among people who inject drugs

Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS.

Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort

Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.

Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda

Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources

Spatial phylodynamics of HIV-1 epidemic emergence in east Africa.

Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.

The HIV nef protein within ARL is genetically and structurally distinct from those in the brain of patients with HAD.

The Spleen Is an HIV-1 Sanctuary During Combined Antiretroviral Therapy

The meningeal lymphatic system: a route for HIV brain migration?

The prevalence of HIV-1 DNA in AIDS-related lymphoma and Kaposi Sarcoma throughout the AIDS epidemic

Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues

Urogenital Chlamydia trachomatis multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia.