List of works - David C. Samuels

A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes

scientific article

A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells

scientific article published on May 2011

Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism?

scientific article published on 01 October 2002

Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations

scientific article

Alternative applications for distinct RNA sequencing strategies

scientific article

An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors

scientific article

Analysis of enzyme kinetic data for mtDNA replication

scientific article

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

scientific article

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control

scientific article published on 4 November 2013

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity

scientific article

Correlated tissue expression of genes of cytoplasmic and mitochondrial nucleotide metabolisms in normal tissues is disrupted in transformed tissues

scientific article

Data from artificial models of mitochondrial DNA disorders are not always applicable to humans

scientific article published in May 2014

Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation

scientific article published in September 2006

Discrete stochastic simulation methods for chemically reacting systems

scientific article

Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication ⬇️

scientific article published on August 4, 2011

Epidermal nerve fiber density, oxidative stress, and mitochondrial haplogroups in HIV-infected Thais initiating therapy

scientific article published on July 2014

Epigenetics, epidemiology and mitochondrial DNA diseases ⬇️

scientific article published on January 28, 2012

Estimating relative mitochondrial DNA copy number using high throughput sequencing data.

scientific article

European Mitochondrial DNA Haplogroups are Associated with Cerebrospinal Fluid Biomarkers of Inflammation in HIV Infection

scientific article published on September 2016

Evaluating purifying selection in the mitochondrial DNA of various mammalian species

scientific article (publication date: 2013)

Evaluation of allele frequency estimation using pooled sequencing data simulation

scientific article published on 7 February 2013

Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region

scientific article

Finding the lost treasures in exome sequencing data

scientific article

Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs.

scientific article

Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy

scientific article

Genome measures used for quality control are dependent on gene function and ancestry

scientific article published on 8 October 2014

Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study

scientific article published on 26 April 2017

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential

scientific article published on 21 November 2014

Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk

scientific article

High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates

scientific article

High-throughput sequencing in mitochondrial DNA research

scientific article

Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans

scientific article published on July 2016

Illumina human exome genotyping array clustering and quality control

scientific article published on 16 October 2014

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

scientific article

Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta.

scientific article published on 12 November 2009

Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells?

scientific article

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data

scientific article

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

scientific article published on 6 March 2013

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data.

scientific article

Mitochondria single nucleotide variation across six blood cell types

scientific article published on 5 March 2016

Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection

scientific article

Mitochondrial DNA deletions are associated with non-B DNA conformations

scientific article

Mitochondrial DNA mutations in human colonic crypt stem cells

scientific article published on November 2003

Mitochondrial DNA rearrangements in health and disease--a comprehensive study

scientific article published on 18 October 2013

Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck

scientific article published on 5 January 2016

Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER.

scientific article published on 17 October 2012

Mitochondrial Genomics and CD4 T-Cell Count Recovery After Antiretroviral Therapy Initiation in AIDS Clinical Trials Group Study 384 ⬇️

scientific article published on December 1, 2011

Mitochondrial Haplogroups Affect Severity But Not Prevalence of Diabetic Retinopathy

scientific article published on February 2017

Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster.

scientific article published on 19 October 2016

Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations

scientific article published on 26 June 2011

Mitochondrial genomics and antiretroviral therapy-associated metabolic complications in HIV-infected Black South Africans: a pilot study

scientific article published on 15 March 2013

Mitochondrial haplogroups are associated with severity of diabetic retinopathy.

scientific article

Multi-perspective quality control of Illumina RNA sequencing data analysis.

scientific article

Multi-perspective quality control of Illumina exome sequencing data using QC3.

scientific article

Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis.

scientific article

No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7393 cases and 5122 controls

scientific article

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

scientific article published on 08 June 2020

Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells

scientific article

OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules

scientific article

OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans

scientific article

POLG mutations cause decreased mitochondrial DNA repopulation rates following induced depletion in human fibroblasts.

scientific article

Pathogenic mitochondrial DNA mutations are common in the general population

scientific article published on August 2008

Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection

scientific article published on 01 April 2019

Poor correlations in the levels of pathogenic mitochondrial DNA mutations in polar bodies versus oocytes and blastomeres in humans.

scientific article

Power and sample size calculations for high-throughput sequencing-based experiments.

scientific article published on 09 June 2017

Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array.

scientific article

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

scientific article published on 12 October 2015

Recurrent tissue-specific mtDNA mutations are common in humans

scientific article

Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study

scientific article

Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial

scientific article

Segregation of mtDNA throughout human embryofetal development: m.3243A>G as a model system

scientific article

Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors

scientific article

StrandScript: evaluation of Illumina genotyping array design and strand correction

scientific article published on 08 April 2017

Strategies for processing and quality control of Illumina genotyping arrays.

scientific article published on 20 February 2017

T Cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384 ⬇️

scientific article published on August 27, 2012

The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration.

scientific article published on 3 December 2010

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data.

scientific article published on 3 October 2017

The diversity present in 5140 human mitochondrial genomes

scientific article published on 7 May 2009

The effect of strand bias in Illumina short-read sequencing data

scientific article

The effect of unhealthy β-cells on insulin secretion in pancreatic islets.

scientific article

The length of cytochrome c oxidase-negative segments in muscle fibres in patients with mtDNA myopathy

scientific article published on 01 November 2002

The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo

scientific article published on 05 December 2008

The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation

scientific article

Three-stage quality control strategies for DNA re-sequencing data

scientific article

Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome

scientific article published on 29 September 2017

Unique mitochondrial DNA in highly inbred feral cattle

scientific article (publication date: July 2012)

Universal heteroplasmy of human mitochondrial DNA.

scientific article

Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission

scientific article

What causes mitochondrial DNA deletions in human cells?

scientific article published on March 2008

What is influencing the phenotype of the common homozygous polymerase-γ mutation p.Ala467Thr?

scientific article

List of works by David C. Samuels

A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes

A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells

Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism?

Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations

Alternative applications for distinct RNA sequencing strategies

An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors

Analysis of enzyme kinetic data for mtDNA replication

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity

Correlated tissue expression of genes of cytoplasmic and mitochondrial nucleotide metabolisms in normal tissues is disrupted in transformed tissues

Data from artificial models of mitochondrial DNA disorders are not always applicable to humans

Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation

Discrete stochastic simulation methods for chemically reacting systems

Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication ⬇️

Epidermal nerve fiber density, oxidative stress, and mitochondrial haplogroups in HIV-infected Thais initiating therapy

Epigenetics, epidemiology and mitochondrial DNA diseases ⬇️

Estimating relative mitochondrial DNA copy number using high throughput sequencing data.

European Mitochondrial DNA Haplogroups are Associated with Cerebrospinal Fluid Biomarkers of Inflammation in HIV Infection

Evaluating purifying selection in the mitochondrial DNA of various mammalian species

Evaluation of allele frequency estimation using pooled sequencing data simulation

Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region

Finding the lost treasures in exome sequencing data

Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs.

Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy

Genome measures used for quality control are dependent on gene function and ancestry

Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential

Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk

High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates

High-throughput sequencing in mitochondrial DNA research

Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans

Illumina human exome genotyping array clustering and quality control

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta.

Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells?

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data.

Mitochondria single nucleotide variation across six blood cell types

Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection

Mitochondrial DNA deletions are associated with non-B DNA conformations

Mitochondrial DNA mutations in human colonic crypt stem cells

Mitochondrial DNA rearrangements in health and disease--a comprehensive study

Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck

Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER.

Mitochondrial Genomics and CD4 T-Cell Count Recovery After Antiretroviral Therapy Initiation in AIDS Clinical Trials Group Study 384 ⬇️

Mitochondrial Haplogroups Affect Severity But Not Prevalence of Diabetic Retinopathy

Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster.

Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations

Mitochondrial genomics and antiretroviral therapy-associated metabolic complications in HIV-infected Black South Africans: a pilot study

Mitochondrial haplogroups are associated with severity of diabetic retinopathy.

Multi-perspective quality control of Illumina RNA sequencing data analysis.

Multi-perspective quality control of Illumina exome sequencing data using QC3.

Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis.

No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7393 cases and 5122 controls

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells

OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules

OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans

POLG mutations cause decreased mitochondrial DNA repopulation rates following induced depletion in human fibroblasts.

Pathogenic mitochondrial DNA mutations are common in the general population

Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection

Poor correlations in the levels of pathogenic mitochondrial DNA mutations in polar bodies versus oocytes and blastomeres in humans.

Power and sample size calculations for high-throughput sequencing-based experiments.

Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array.

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

Recurrent tissue-specific mtDNA mutations are common in humans

Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study

Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial

Segregation of mtDNA throughout human embryofetal development: m.3243A>G as a model system

Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors

StrandScript: evaluation of Illumina genotyping array design and strand correction

Strategies for processing and quality control of Illumina genotyping arrays.

T Cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384 ⬇️

The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration.

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data.

The diversity present in 5140 human mitochondrial genomes

The effect of strand bias in Illumina short-read sequencing data