Personal information

bioinformatics, computational genomics, type-2 diabetes, epigenetics, genomics, statistical genetics, population genetics, pipeline development, sequence analysis
New Zealand

Biography

My current role is as a Senior Bioinformatician at Oxford Nanopore Technologies in the Singapore Applications Team. I have extensive experience in computational genomics and bioinformatics, specialising in human health genomics. I completed a postdoc at Queensland University of Technology (Brisbane, Australia) working on the development of methods to deal with ever expanding genomic data sets and their access and interpretation back to the people that matter (i.e. clients, clinicians, researchers, public, etc). In my previous role I implemented deep learning techniques in several key genomic areas, including clinical variant calling/identification and base-calling of DNA sequence data. I also led the development of machine learning/AI technology on portable Nvidia modules for field/remote deployment and use, namely using Nanopore technology for affordable, accessible and portable sequencing. I was part of the Genomics Aoteoroa Bioinformatics Leadership Team for 3 years, where I was responsible for overseeing bioinformatics support for health projects across New Zealand. I have also been heavily involved in the Data Carpentries as an instructor and facilitator.

Activities

Employment (4)

Oxford Nanopore Technologies Plc: Oxford, Oxfordshire, GB

2022-03-21 to present | Senior Bioinformatician (Applications)
Employment
Source: Self-asserted source
Miles C Benton

Genomics Aotearoa: Dunedin, NZ

2019-05-30 to 2022-03-16 | Bioinformatics Leadership Team (Bioinformatics Capability)
Employment
Source: Self-asserted source
Miles C Benton

Institute of Environmental Science and Research Ltd: Porirua, Wellington, NZ

2018-07-02 to 2022-03-16 | Senior Scientist Bioinformatics and Data Science (Human Genomics)
Employment
Source: Self-asserted source
Miles C Benton

Queensland University of Technology Faculty of Health: Kelvin Grove, QLD, AU

2014-02-10 to 2018-06-30 | Post-Doctoral Research Fellow (Computational Genomics) (Institute of Health and Biomedical Innovation)
Employment
Source: Self-asserted source
Miles C Benton

Education and qualifications (3)

Griffith University - Gold Coast Campus: Southport, QLD, AU

2010-05-04 to 2014-05-05 | PhD (Genomics Research Centre, Health Sciences)
Education
Source: Self-asserted source
Miles C Benton

Victoria University of Wellington: Wellington, NZ

2007-07-15 to 2009-12-18 | Masters of Biomedical Science (Human Genetics) (School of Biological Sciences)
Education
Source: Self-asserted source
Miles C Benton

Victoria University of Wellington: Wellington, NZ

2004-03-02 to 2007-06-19 | Bachelor of Biomedical Science (Genetics, Molecular Pathology) (School of Biological Sciences)
Education
Source: Self-asserted source
Miles C Benton

Funding (1)

Validation of Blood Cell Lineage Specific DNA methylation markers

2016-05 to 2018-05 | Grant
Wellington Medical Research Foundation (Wellington, Wellington, NZ)
GRANT_NUMBER:

2015/255

Source: Self-asserted source
Miles C Benton

Works (50 of 59)

Items per page:
Page 1 of 2

EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics

Institute of Environmental Science and Research
2024 | Other
Contributors: Jürgen Hench; Claus Hultschig; Jon Brugger; Luigi Mariani; Raphael Guzman; Jehuda Soleman; Severina Leu; Miles C Benton; Irenäus Maria Stec; Ivana Bratic Hench et al.
Source: check_circle
DataCite

EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics

Institute of Environmental Science and Research
2024 | Other
Contributors: Jürgen Hench; Claus Hultschig; Jon Brugger; Luigi Mariani; Raphael Guzman; Jehuda Soleman; Severina Leu; Miles C Benton; Irenäus Maria Stec; Ivana Bratic Hench et al.
Source: check_circle
DataCite

EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics

Institute of Environmental Science and Research
2024 | Other
Contributors: Jürgen Hench; Claus Hultschig; Jon Brugger; Luigi Mariani; Raphael Guzman; Jehuda Soleman; Severina Leu; Miles C Benton; Irenäus Maria Stec; Ivana Bratic Hench et al.
Source: check_circle
DataCite

Nanopore Sequencing Enables Allelic Phasing of FLG Loss-of-Function Variants, Intragenic Copy Number Variation, and Methylation Status in Atopic Dermatitis and Ichthyosis Vulgaris

Journal of Investigative Dermatology
2024-08 | Journal article
Contributors: Colin Wong; Cheng-Yong Tham; Lin Yang; Miles C. Benton; Vipin Narang; Simon Denil; Kaibo Duan; Yik Weng Yew; Bernett Lee; Paola Florez de Sessions et al.
Source: check_circle
Crossref

Evaluating the suitability of current mitochondrial DNA interpretation guidelines for multigenerational whole mitochondrial genome comparisons

Journal of Forensic Sciences
2022-09 | Journal article
Contributors: Jasmine R. Connell; Miles C. Benton; Rodney A. Lea; Heidi G. Sutherland; Larisa M. Haupt; Kirsty M. Wright; Lyn R. Griffiths
Source: check_circle
Crossref

Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population

Scientific Reports
2022-04-26 | Journal article
Contributors: J. R. Connell; M. C. Benton; R. A. Lea; H. G. Sutherland; J. Chaseling; L. M. Haupt; K. M. Wright; L. R. Griffiths
Source: check_circle
Crossref

Nanopore sequencing on Nvidia Jetson SoM boards

Zenodo
2021-09-22 | Other
Contributors: Miles C Benton
Source: check_circle
DataCite

sirselim/GPU-musings: First Citable Build

Zenodo
2021-06-21 | Other
Contributors: Miles C Benton
Source: check_circle
DataCite

sirselim/GPU-musings: First Citable Build

Zenodo
2021-06-21 | Other
Contributors: Miles C Benton
Source: check_circle
DataCite

DNA methylation in blood—Potential to provide new insights into cell biology

PLOS ONE
2020-11-04 | Journal article
Contributors: Donia Macartney-Coxson; Osman El-Maarri; Alanna M. Cameron; Jane Clapham; Miles C. Benton
Source: check_circle
Crossref

sirselim/bootNet: First release to coincide with MS manuscript publication

Zenodo
2020-07-30 | Other
Contributors: Miles C Benton; Ray Blick; Nicolemwhite85; Sean Burnard
Source: check_circle
DataCite

sirselim/bootNet: First release to coincide with MS manuscript publication

Zenodo
2020-07-30 | Other
Contributors: Miles C Benton; Ray Blick; Nicolemwhite85; Sean Burnard
Source: check_circle
DataCite

Investigating the influence of mtDNA and nuclear encoded mitochondrial variants on high intensity interval training outcomes

Scientific Reports
2020-07-06 | Journal article
Contributors: N. R. Harvey; S. Voisin; R. A. Lea; X. Yan; M. C. Benton; I. D. Papadimitriou; M. Jacques; L. M. Haupt; K. J. Ashton; N. Eynon et al.
Source: check_circle
Crossref

Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort

Translational Psychiatry
2020-04-22 | Journal article
Contributors: Amy J. Osborne; John F. Pearson; Alexandra J. Noble; Neil J. Gemmell; L. John Horwood; Joseph M. Boden; Miles C. Benton; Donia P. Macartney-Coxson; Martin A. Kennedy
Source: check_circle
Crossref

MicroRNA Profiling in Adipose Before and After Weight Loss Highlights the Role of miR‐223‐3p and the NLRP3 Inflammasome

Obesity
2020-03 | Journal article
Contributors: Donia Macartney‐Coxson; Kirsty Danielson; Jane Clapham; Miles C. Benton; Alice Johnstone; Angela Jones; Odette Shaw; Ronald D. Hagan; Eric P. Hoffman; Mark Hayes et al.
Source: check_circle
Crossref

Identification of novel mitochondrial and mitochondrial related genetic loci associated with exercise response in the Gene SMART study

2020-02-20 | Preprint
Contributors: NR Harvey; S Voisin; RA Lea; X Yan; MC Benton; ID Papadimitriou; M Jacques; LM Haupt; KJ Ashton; N Eynon et al.
Source: check_circle
Crossref

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Figshare
2019 | Other
Contributors: Donia Macartney-Coxson; Miles C Benton; Ray Blick; Richard S. Stubbs; Ronald D. Hagan; Michael A. Langston
Source: check_circle
DataCite

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Figshare
2019 | Other
Contributors: Donia Macartney-Coxson; Miles C Benton; Ray Blick; Richard S. Stubbs; Ronald D. Hagan; Michael A. Langston
Source: check_circle
DataCite

miRNA Signatures of Insulin Resistance in Obesity

Figshare
2019 | Other
Contributors: Angela Jones; Kirsty M. Danielson; Miles C Benton; Olivia Ziegler; Ravi Shah; Richard S. Stubbs; Saumya Das; Donia Macartney-Coxson
Source: check_circle
DataCite

miRNA Signatures of Insulin Resistance in Obesity

Figshare
2019 | Other
Contributors: Angela Jones; Kirsty M. Danielson; Miles C Benton; Olivia Ziegler; Ravi Shah; Richard S. Stubbs; Saumya Das; Donia Macartney-Coxson
Source: check_circle
DataCite

Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort

2019-11-04 | Other
Contributors: Amy J. Osborne; John F. Pearson; Alexandra J. Noble; Neil J. Gemmell; L. John Horwood; Joseph M. Boden; Miles Benton; Donia P. Macartney-Coxson; Martin A. Kennedy
Source: check_circle
Crossref

DNA methylation in blood - potential to provide new insights in immune cell biology

2019-08-21 | Other
Contributors: Donia Macartney-Coxson; Alanna Cameron; Jane Clapham; Miles C Benton
Source: check_circle
Crossref

sirselim/immunecell_methylation_paper_data: First release of data for immune cell epigenetics (methylation) manuscript

Zenodo
2019-08-13 | Dataset
Contributors: Miles C Benton
Source: check_circle
DataCite

sirselim/immunecell_methylation_paper_data: First release of data for immune cell epigenetics (methylation) manuscript

Zenodo
2019-08-13 | Dataset
Contributors: Miles C Benton
Source: check_circle
DataCite

Cell-type specific analysis of heterogeneous methylation signal using a Bayesian model-based approach

2019-06-26 | Other
Contributors: Daniel W Kennedy; Nicole M White; Miles C Benton; Rodney A Lea; Kerrie Mengersen
Source: check_circle
Crossref

Genome-wide DNA methylation changes in CD19+ B cells from relapsing-remitting multiple sclerosis patients

Scientific Reports
2018-11-27 | Journal article
Contributors: Vicki E. Maltby; Rodney A. Lea; Moira C. Graves; Katherine A. Sanders; Miles C. Benton; Lotti Tajouri; Rodney J. Scott; Jeannette Lechner-Scott
Source: check_circle
Crossref

Current Understanding of DNA Methylation and Age-related Disease

OBM Genetics
2018-04 | Journal article
Contributors: Eunise M. Aquino; Genomics Research Centre; Institute of Health and Biomedical Innovation; School of Biomedical Sciences; Queensland University of Technology; Brisbane; Australia; Miles C. Benton; Larisa M. Haupt; Heidi G. Sutherland et al.
Source: Self-asserted source
Miles C Benton via Crossref Metadata Search

EXOME SEQUENCING DIAGNOSES X-LINKED MOESIN-ASSOCIATED IMMUNODEFICIENCY IN A PRIMARY IMMUNODEFICIENCY CASE

Frontiers in Immunology
2018-02 | Journal article
Source: Self-asserted source
Miles C Benton

Expression QTL analysis of glaucoma endophenotypes in the Norfolk Island isolate provides evidence that immune-related genes are associated with optic disc size.

Journal of human genetics
2018-01 | Journal article
Contributors: Fang Kho P; Lea RA; Benton MC; Eccles D; Haupt LM; Hewitt AW; Sherwin JC; Mackey DA; Griffiths LR
Source: Self-asserted source
Miles C Benton via Europe PubMed Central

Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes

Frontiers in Genetics
2018-01-16 | Journal article
Source: Self-asserted source
Miles C Benton

Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm.

PloS one
2017 | Journal article
Contributors: White N; Benton M; Kennedy D; Fox A; Griffiths L; Lea R; Mengersen K
Source: Self-asserted source
Miles C Benton via Europe PubMed Central

Differential methylation at MHC in CD4+ T cells is associated with multiple sclerosis independently of HLA-DRB1.

Clinical epigenetics
2017 | Journal article
Source: Self-asserted source
Miles C Benton via Europe PubMed Central

Genome-wide linkage and association analysis of primary open-angle glaucoma endophenotypes in the Norfolk Island isolate.

Molecular vision
2017 | Journal article
Source: Self-asserted source
Miles C Benton via Europe PubMed Central

miRNA Signatures of Insulin Resistance in Obesity

Obesity
2017-08 | Journal article
Contributors: Angela Jones; Kirsty M. Danielson; Miles C. Benton; Olivia Ziegler; Ravi Shah; Richard S. Stubbs; Saumya Das; Donia Macartney-Coxson
Source: Self-asserted source
Miles C Benton via Crossref Metadata Search

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Clinical Epigenetics
2017-05-03 | Journal article
Contributors: Donia Macartney-Coxson; Miles C. Benton; Ray Blick; Richard S. Stubbs; Ronald D. Hagan; Michael A. Langston
Source: Self-asserted source
Miles C Benton via Crossref Metadata Search

Methylome-wide association study of whole blood DNA in the Norfolk Island isolate identifies robust loci associated with age

Aging
2017-02 | Journal article
Contributors: Miles C. Benton; Heidi G. Sutherland; Donia Macartney-Coxson; Larisa M. Haupt; Rodney A. Lea; Lyn R. Griffiths
Source: Self-asserted source
Miles C Benton via Crossref Metadata Search

Gene-centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility

Molecular Genetics & Genomic Medicine
2017-01 | Journal article
Source: Self-asserted source
Miles C Benton

Next-generation sequencing reveals broad down-regulation of microRNAs in secondary progressive multiple sclerosis CD4+ T cells.

Clinical epigenetics
2016-08-27 | Journal article
Source: Self-asserted source
Miles C Benton

A Phenomic Scan of the Norfolk Island Genetic Isolate Identifies a Major Pleiotropic Effect Locus Associated with Metabolic and Renal Disorder Markers

PLoS Genetics
2015 | Journal article
EID:

2-s2.0-84946595091

Contributors: Benton, M.C.; Lea, R.A.; Macartney-Coxson, D.; Hanna, M.; Eccles, D.A.; Carless, M.A.; Chambers, G.K.; Bellis, C.; Goring, H.H.; Curran, J.E. et al.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

Erratum to: 'Mutiny on the Bounty': The genetic history of Norfolk Island reveals extreme gender-biased admixture [Invest Genet. 2015; 6:11.]

Investigative Genetics
2015 | Journal article
EID:

2-s2.0-84959150692

Contributors: Benton, M.C.; Stuart, S.; Bellis, C.; Macartney-Coxson, D.; Eccles, D.; Curran, J.E.; Chambers, G.; Blangero, J.; Lea, R.A.; Griffiths, L.R.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

Genome-wide DNA methylation profiling of CD8+ T cells shows a distinct epigenetic signature to CD4+ T cells in multiple sclerosis patients

Clinical Epigenetics
2015 | Journal article
EID:

2-s2.0-84946232632

Contributors: Maltby, V.E.; Graves, M.C.; Lea, R.A.; Benton, M.C.; Sanders, K.A.; Tajouri, L.; Scott, R.J.; Lechner-Scott, J.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

Protocol for assessing maternal, environmental and epigenetic risk factors for dental caries in children

BMC Oral Health
2015 | Journal article
EID:

2-s2.0-84958887142

Contributors: Fernando, S.; Speicher, D.J.; Bakr, M.M.; Benton, M.C.; Lea, R.A.; Scuffham, P.A.; Mihala, G.; Johnson, N.W.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

Serum bilirubin concentration is modified by UGT1A1 Haplotypes and influences risk of Type-2 diabetes in the Norfolk Island genetic isolate

BMC Genetics
2015 | Journal article
EID:

2-s2.0-84949236307

Contributors: Benton, M.C.; Lea, R.A.; Macartney-Coxson, D.; Bellis, C.; Carless, M.A.; Curran, J.E.; Hanna, M.; Eccles, D.; Chambers, G.K.; Blangero, J. et al.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

‘Mutiny on the Bounty’: the genetic history of Norfolk Island reveals extreme gender-biased admixture

Investigative Genetics
2015-09 | Journal article
Source: Self-asserted source
Miles C Benton
grade
Preferred source (of 2)‎

Common polygenic variation contributes to risk of migraine in the Norfolk Island population.

Human genetics
2015-07 | Journal article
Source: Self-asserted source
Miles C Benton
grade
Preferred source (of 2)‎

Directional dominance on stature and cognition in diverse human populations

Nature
2015-07 | Journal article
Source: Self-asserted source
Miles C Benton
grade
Preferred source (of 2)‎

mRNA and microRNA analysis reveals modulation of biochemical pathways related to addiction in the ventral tegmental area of methamphetamine self-administering rats

BMC Neuroscience
2015-07 | Journal article
Source: Self-asserted source
Miles C Benton
grade
Preferred source (of 2)‎

An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss

Genome Biology
2015-01 | Journal article
Source: Self-asserted source
Miles C Benton
grade
Preferred source (of 2)‎

Characteristic DNA methylation profiles in peripheral blood monocytes are associated with inflammatory phenotypes of asthma

Epigenetics
2014 | Journal article
EID:

2-s2.0-84908157912

Contributors: Gunawardhana, L.P.; Gibson, P.G.; Simpson, J.L.; Benton, M.C.; Lea, R.A.; Baines, K.J.
Source: Self-asserted source
Miles C Benton via Scopus - Elsevier

E-MTAB-3052 - Methylation profiling by array of human paired adipose tissue (subcutaneous and omentum) before and after gastric-bypass and weight loss

2014 | Dataset
OTHER-ID:

E-MTAB-3052

Source: check_circle
EMBL-EBI
Items per page:
Page 1 of 2

Peer review (3 reviews for 2 publications/grants)

Review activity for Clinical epigenetics (1)
Review activity for Nature biotechnology. (2)