List of works by David C. Nickle

A large lung gene expression study identifying fibulin-5 as a novel player in tissue repair in COPD.

scientific article published on 2 July 2014

A pro-inflammatory role for the Frizzled-8 receptor in chronic bronchitis

scientific article published on 21 January 2016

Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

scientific article published on 01 June 2019

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load

scientific article published on 17 December 2006

COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression

scientific article

Characterization of drug resistance in antiretroviral-treated patients infected with HIV-1 CRF02_AG and AGK subtypes in Mali and Burkina Faso.

scientific article published in January 2008

Cloning and characterization of PDK4 on 7q21.3 encoding a fourth pyruvate dehydrogenase kinase isoenzyme in human

scientific article

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al.

scientific article published on January 2008

Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection

scientific article published on August 2004

Consensus and Ancestral State HIV Vaccines

scientific article published in Science

Coping with viral diversity in HIV vaccine design

scientific article

Correction: Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.

scientific article published on 21 March 2008

Correction: Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma.

scientific article published on 12 December 2012

Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

scientific article

Curiously modern DNA for a "250 million-year-old" bacterium

scientific article

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites

scientific article

Deficiency of FHL2 attenuates airway inflammation in mice and genetic variation associates with human bronchial hyper-responsiveness.

scientific article published on 28 July 2015

Differential lung tissue gene expression in males and females: implications for the susceptibility to develop COPD

scientific article published on 18 July 2019

Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD.

scientific article

Diverse homologues of the archaeal repressor NrpR function similarly in nitrogen regulation

scientific article published on 24 April 2007

Dual HIV-1 infection associated with rapid disease progression

scientific article (publication date: 21 February 2004)

EVOLUTION OF INTRAHOST HIV-1 GENETIC DIVERSITY DURING CHRONIC INFECTION

article

Elbasvir-Grazoprevir to Treat Hepatitis C Virus Infection in Persons Receiving Opioid Agonist Therapy: A Randomized Trial.

scientific article

Emergence of resistance-associated variants after failed triple therapy with vaniprevir in treatment-experienced non-cirrhotic patients with hepatitis C-genotype 1 infection: a population and clonal analysis

scientific article published on 10 June 2013

Evidence for human immunodeficiency virus type 1 replication in vivo in CD14(+) monocytes and its potential role as a source of virus in patients on highly active antiretroviral therapy

scientific article published on January 2002

Evolution of intrahost HIV-1 genetic diversity during chronic infection.

scientific article published in June 2006

Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments

scientific article

Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections

scientific article published on 21 February 2007

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

scientific article published in Science

Gene expression network analysis provides potential targets against SARS-CoV-2

scientific article published on 14 December 2020

Genetic characterization of rebounding human immunodeficiency virus type 1 in plasma during multiple interruptions of highly active antiretroviral therapy

scientific article

Genetic regulation of gene expression in the lung identifies CST3 and CD22 as potential causal genes for airflow obstruction.

scientific article published on 2 September 2014

Genetic regulation of gene expression of MIF family members in lung tissue

scientific article published on 12 October 2020

Genetic variants associated with susceptibility to idiopathic pulmonary fibrosis in people of European ancestry: a genome-wide association study.

scientific article published on 20 October 2017

Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis

scientific article published on 01 March 2020

Genome-Wide Interaction Analysis of Air Pollution Exposure and Childhood Asthma with Functional Follow-up

scientific article published on 30 November 2016

Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets

scientific article published on 6 February 2017

Genome-wide association study on the FEV1/FVC ratio in never-smokers identifies HHIP and FAM13A.

scientific article published on 6 September 2016

Genome-wide genetic ancestry measurements to predict lung function in European populations

Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms

scientific article published on 16 November 2018

HCV evolutionary genetics of SVR versus virologic failure assessed from the vaniprevir phase III registration trials

scientific article published on 3 March 2016

HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report.

scientific article published on 10 July 2007

HIV-1 group M conserved elements vaccine

scientific article

HIV-1 over time: fitness loss or robustness gain?

article

HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk?

scientific article

HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study

scientific article

HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir

scientific article

HIV-specific probabilistic models of protein evolution

scientific article

HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load

scientific article published on 23 April 2008

Hedgehog signaling in the airway epithelium of patients with chronic obstructive pulmonary disease

scientific article published on 04 March 2019

Human Immunodeficiency Virus Type 1 Subtype B Ancestral Envelope Protein Is Functional and Elicits Neutralizing Antibodies in Rabbits Similar to Those Elicited by a Circulating Subtype B Envelope

scientific article (publication date: 15 August 2005)

Human Lung Tissue Transcriptome: Influence of Sex and Age.

scientific article

Human PON2 gene at 7q21.3: cloning, multiple mRNA forms, and missense polymorphisms in the coding sequence

scientific article

Human fist evolution: a critique

scientific article published on 01 June 2013

Human immunodeficiency virus type 1 bound to B cells: relationship to virus replicating in CD4+ T cells and circulating in plasma

scientific article

Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

scientific article

Identification of Susceptibility Genes of Adult Asthma in French Canadian Women

scientific article published on 04 May 2016

Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk

scientific article published in Nature Communications

Immunogen sequence: the fourth tier of AIDS vaccine design

scientific article

Importance and detection of virus reservoirs and compartments of HIV infection

scientific article

Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences

scientific article published on December 2003

Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences

scientific article (publication date: 28 March 2011)

Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity

article

Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection

scientific article published on March 2004

Integrative Genomics of Emphysema-Associated Genes Reveals Potential Disease Biomarkers

scientific article published in May 2017

Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes

scientific article published on 12 June 2017

Latrophilin receptors: novel bronchodilator targets in asthma ⬇️

scientific article published on 20 June 2016

Letermovir Resistance Analysis in a Clinical Trial of Cytomegalovirus Prophylaxis for Hematopoietic Stem Cell Transplant Recipients

scientific article published on 01 March 2020

Leveraging lung tissue transcriptome to uncover candidate causal genes in COPD genetic associations.

scientific article published on 14 March 2018

Long-term follow-up of patients receiving boceprevir for treatment of chronic hepatitis C.

scientific article published on 24 October 2014

Lung eQTLs to help reveal the molecular underpinnings of asthma

scientific article

Lung expression quantitative trait loci data set identifies important functional polymorphisms in the asthma-associated IL1RL1 region

scientific article

Lung tissue gene-expression signature for the ageing lung in COPD.

scientific article

Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV).

scientific article published in April 2008

Moderate-to-severe asthma in individuals of European ancestry: a genome-wide association study

scientific article published on 11 December 2018

Molecular clock-like evolution of human immunodeficiency virus type 1.

scientific article

Molecular mechanisms underlying variations in lung function: a systems genetics analysis

scientific article published on 21 September 2015

Multidrug-resistant, dual-tropic HIV-1 and rapid progression

scientific article published on 01 June 2005

Multiethnic Meta-analysis Identifies New Loci for Pulmonary Function

Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function

scientific article published in Nature Communications

Neutralization of Diverse Human Cytomegalovirus Strains Conferred by Antibodies Targeting Viral gH/gL/pUL128-131 Pentameric Complex.

scientific article published on 11 January 2017

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

scientific article published on 25 February 2019

New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries

scholarly article published 12 June 2018

Novel Genes for Airway Wall Thickness Identified with Combined Genome-Wide Association and Expression Analyses

article

P17-14. Fitness-informed HIV-1 Gag-p24 vaccine design

article

PTTG1IP and MAML3, novel genomewide association study genes for severity of hyperresponsiveness in adult asthma

scientific article published on 6 October 2016

Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy

scientific article

Pervasive genomic recombination of HIV-1 in vivo

scientific article

Phenotypic and functional translation of IL1RL1 locus polymorphisms in lung tissue and asthmatic airway epithelium

scientific article published on 23 April 2020

Phylogeography of a Wide-Ranging Desert Lizard, Gambelia wislizenii (Crotaphytidae)

scientific article published on 7 May 1999

Polymorphisms associated with expression of BPIFA1/BPIFB1 and lung disease severity in cystic fibrosis

scientific article published on 9 January 2015

Potential impact of recombination on sitewise approaches for detecting positive natural selection

scientific article published on 01 April 2003

Presenting plasma HIV RNA level and rate of CD4 T-cell decline.

scientific article published in February 2007

Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank

scientific article published on 08 June 2021

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information

scientific article

Protein-altering germline mutations implicate novel genes related to lung cancer development

scientific article published on 11 May 2020

Rare HLA drive additional HIV evolution compared to more frequent alleles

scientific article published on March 2009

Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins

scientific article

Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins

scientific article (publication date: 30 May 2007)

Refining susceptibility loci of chronic obstructive pulmonary disease with lung eqtls

scientific article

Responsiveness to Ipratropium Bromide in Male and Female Patients with Mild to Moderate Chronic Obstructive Pulmonary Disease.

scientific article

Screening for acute HIV infection: lessons learned

scientific article published on 20 December 2006

Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS.

scientific article published on November 2002

Selection on the human immunodeficiency virus type 1 proteome following primary infection

scientific article

Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation

scientific article

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes

scientific article published on January 2006

Sulfatase modifying factor 1 (SUMF1) is associated with Chronic Obstructive Pulmonary Disease

scientific article

Surfactant protein D is a causal risk factor for COPD: results of Mendelian randomisation.

scientific article published on 30 November 2017

Susceptibility genes for lung diseases in the major histocompatibility complex revealed by lung expression quantitative trait loci analysis.

scientific article published on 12 May 2016

Susceptibility loci for lung cancer are associated with mRNA levels of nearby genes in the lung.

scientific article

Targeting of a CD8 T Cell Env Epitope Presented by HLA-B*5802 Is Associated with Markers of HIV Disease Progression and Lack of Selection Pressure

article

The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD

scientific article published in Scientific Reports

Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics

scientific article published on 8 February 2018

ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets

scientific article

Virologic resistance analysis from a phase 2 study of MK-5172 combined with pegylated interferon/ribavirin in treatment-naive patients with hepatitis C virus genotype 1 infection

scientific article published on 28 September 2014

Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.

scientific article

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