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David Andrew Eccles

David Andrew Eccles
Gringene Bioinformatics · Bioinformatics

PhD (Genetics), BBmedSc (Genetics), BSc (Maths)

About

160
Publications
67,533
Reads
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9,787
Citations
Introduction
I currently work as a freelance bioinformatics research analyst in Wellington, New Zealand. My clients include the Genomics Research Centre of Queensland University of Technology (Brisbane, Australia), and the Malaghan Institute of Medical Research (Wellington, New Zealand). My long-term research aim is to study the differences in small-scale gene patterns between humans and other species, and I welcome any projects that will supplement this research.
Additional affiliations
August 2013 - July 2015
Malaghan Institute
Position
  • Bioinformatician
April 2012 - present
Gringene Bioinformatics
Position
  • Bioinformatics Research Analyst
Description
  • Working with other researchers to make their research easier, cheaper, faster, and more accurate. Most projects have involved processing whole-genome data, including the confirmation of analyses previously carried out by other researchers.
April 2012 - September 2013
Griffith University
Position
  • Bioinformatics Research Analyst
Description
  • I have carried out bioinformatics work (as Gringene Bioinformatics) for researchers at this research institute
Education
August 2005 - December 2011
Victoria University of Wellington
Field of study
  • Human Genetics
March 2004 - December 2004
Victoria University of Wellington
Field of study
  • Human Genetics
March 2000 - December 2003
Victoria University of Wellington
Field of study
  • Human Genetics

Publications

Publications (160)
Presentation
Full-text available
Every year at the end of May, Oxford Nanopore puts on a mixture of a trade show and an academic conference that they call London Calling. This year they had a hybrid conference, with about 300 people attending in person, and over 1000 people watching online. This presentation summarises a few talks from the conference, and adds a bit of my personal...
Presentation
Full-text available
Taz 5 is a Fused Deposition Modeling printer (FDM), or alternatively a Fused Filament Modeling (FFM) printer. They are a little over seven years old, designed and constructed in an open hardware fashion, and I have periodically upgraded them with a few bits and pieces over the years. This presentation showcases some of the things Taz 5 and I have...
Article
The power of high‐dimensional reduction techniques using multiparameter images has been demonstrated across a variety of different publications. Recently, we published an end‐to‐end low‐cost GUI‐based protocol for performing histocytometric spatial analysis on images derived from the most common microscope image formats. However, this protocol is l...
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
Differential expression analysis of transcript count tables using DESeq2
Preprint
Differential expression analysis of transcript count tables using DESeq2
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with...
Preprint
This protocol demonstrates how to map strand-oriented long reads to a genome, and visualise them in a genome browser. The general idea is to use minimap2 to create stranded BAM files, which are split for forward/reverse orientation then converted into BigWig format for display in a genome browser. Input(s): stranded fastq files (see protocol Prepar...
Preprint
This protocol demonstrates how to map strand-oriented long reads to a genome, and visualise them in a genome browser. The general idea is to use minimap2 to create stranded BAM files, which are split for forward/reverse orientation then converted into BigWig format for display in a genome browser. Input(s): stranded fastq files (see protocol Prepar...
Article
Full-text available
The ability of cancer cells to adjust their metabolism in response to environmental changes is a well-recognized hallmark of cancer. Diverse cancer and non-cancer cells within tumors compete for metabolic resources. Metabolic demands change frequently during tumor initiation, progression and metastasis, challenging our quest to better understand tu...
Article
Full-text available
Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that...
Preprint
This protocol is for a semi-manual method for read demultiplexing, as used after my presentation Sequencing DNA with Linux Cores and Nanopores to work out the number of reads captured by different barcodes. Input: reads as a FASTQ file, barcode sequences as a FASTA file Output: reads split into single FASTQ files per target [barcode] Note: barcode...
Article
Full-text available
The signals driving the adaptation of type 2 dendritic cells (DC2s) to diverse peripheral environments remain mostly undefined. We show that differentiation of CD11blo migratory DC2s—a DC2 population unique to the dermis—required IL-13 signaling dependent on the transcription factors STAT6 and KLF4, whereas DC2s in lung and small intestine were STA...
Article
Full-text available
Regeneration, the restoration of body parts after injury, is quite widespread in the animal kingdom. Species from virtually all Phyla possess regenerative abilities. Human beings, however, are poor regenerators. Yet, the progress of knowledge and technology in the fields of bioengineering, stem cells, and regenerative biology have fostered major ad...
Preprint
This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads. Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demul...
Preprint
Full-text available
This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads. Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demul...
Article
Full-text available
Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and populati...
Presentation
Full-text available
In our bodies, non-dividing differentiated cells go through the process of aerobic respiration most of the time, with about 7% of the produced ATP energy molecules derived from cellular glycolysis, with glycolysis byproducts used to produce most of the remaining ATP via the electron transport chain in the mitochondria. But what happens when the ce...
Preprint
Full-text available
Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While the...
Preprint
Full-text available
Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While the...
Article
Full-text available
Securing research funding is a challenge faced by most scientists in academic institutions worldwide. Funding success rates for all career stages are low, but the burden falls most heavily on early career researchers (ECRs). These are young investigators in training and new principal investigators who have a shorter track record. ECRs are dependent...
Preprint
Full-text available
Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species ar...
Article
The MinION is a portable sequencer that allows real time sequencing and low capital cost investment. We assess accuracy and cost-effectivess of the MinION for genetic diagnostic testing of known SCN1A mutations in Dravet Syndrome (DS). DNA samples (n = 7) from DS patients previously shown to carry SCN1A mutations via Ion Torrent and Sanger sequenci...
Preprint
Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species ar...
Preprint
Full-text available
The signals driving the adaptation of type-2 dendritic cells (DC2s) to diverse peripheral environments are not well understood. We show that the development of CD11blow migratory DC2s, a DC2 population unique to the dermis, requires STAT6- and KLF4-dependent IL-13 signaling, whereas DC2s in lung and small intestine are STAT6-independent. Dermal IL-...
Presentation
Full-text available
DNA is not random. Part of the non-randomness of DNA can be found in the repetitive structure of the DNA sequence, something that can be hard to discover or visualise, especially for instances where the unit of repeat is longer that the read length of a sequencer. My software tool, REPAVER, creates visualisations of DNA sequences of arbitrary lengt...
Article
Full-text available
Tumor cells without mitochondrial (mt) DNA (ρ0 cells) are auxotrophic for uridine, and their growth is supported by pyruvate. While ATP synthesis in ρ0 cells relies on glycolysis, they fail to form tumors unless they acquire mitochondria from stromal cells. Mitochondrial acquisition restores respiration that is essential for de novo pyrimidine bios...
Preprint
Securing research funding is a challenge faced by most scientists in academic institutions worldwide. Funding success rates for all career stages are low, but the burden falls most heavily on early career researchers (ECRs) - young investigators in training and new principal investigators - who have a shorter track record and are dependent on fundi...
Data
This is a template for a rapid review process, guiding a reviewer through the steps detailed in my presentation. Feel free to use this as a quick last-minute check of your own manuscripts, or for helping to formulate thoughts around other reviews.
Presentation
Full-text available
In this presentation I explaining a bit about how I read a research paper, with particular emphasis on the claims made around genetics. I will be drawing on the following three papers for inspiration: * [Ten Simple Rules for Reading a Scientific Paper](https://doi.org/10.1371/journal.pcbi.1008032) * [Elucidation of Genome Polymorphisms in Emerging...
Data
Full-resolution location maps (insets are reduced-resolution Pavian plots) to illustrate the range of sites sampled and the relative diversity of taxa identified in 13 riverine metagenomes.
Data
Representative taxonomy shown as Pavian plots for each of 13 metagenomes from 11 rivers.
Data
L50: length of the shortest read in the set of the longest 50% of base-called data; N50: number of reads in the set of the longest 50% of base-called data; rRNA: number of reads that contain ribosomal RNA genes; Features: predicted proteins; CDS: identified proteins; Subsystems: number of reads assigned to all Subsystem Level 1 functional categorie...
Data
The notation “NA” in parentheses is included where negative read set files included too few reads to be analysed in MG-RAST. Where accessions are given in parentheses, those refer to the barcoded negative control data. All FASTQ files are available from ENA via accessions Nos. PRJEB34137 and ERP116996.
Data
Read length distribution plots for sample (A and B) and negative (C and D) sequencing libraries. The cumulative sequenced bases plots (A and C) allow read length percentiles to be identified; read N10, N50, and N90 are indicated on the plot by vertical lines and a pair of circles. The digital electrophoresis plots (B and D) show the distribution of...
Article
Full-text available
*Background* Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river...
Article
Full-text available
Colorectal cancer is a major contributor to death and disease worldwide. The ApcMin mouse is a widely used model of intestinal neoplasia, as it carries a mutation also found in human colorectal cancers. However, the method most commonly used to quantify tumour burden in these mice is manual adenoma counting, which is time consuming and poorly suite...
Poster
Full-text available
Reduced reproductive fitness due to maladaptive traits, like reduced fertility, hampers recovery efforts for critically endangered species. To identify putative structural variants on the Z-chromosome, we are developing a workflow to generate high resolution long-read sequence data for kākāpō (Strigops habroptilus) with known reproductive success...
Article
Full-text available
The implementation and popularity of next generation sequencing (NGS) has led to the development of various rapid whole mitochondrial genome sequencing techniques. We summarise an efficient and cost-effective NGS approach for mitochondrial genomic DNA in humans using the Ion Torrent platform, and further discuss our bioinformatics pipeline for stre...
Article
Full-text available
In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding...
Preprint
Full-text available
Colorectal cancer is a major contributor to death and disease worldwide. The ApcMin mouse is a widely used model of intestinal neoplasia, as it carries a mutation also found in human colorectal cancers. However, the method most commonly used to quantify tumour burden in these mice is manual adenoma counting, which is time consuming and poorly suite...
Article
Full-text available
In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell...
Preprint
Full-text available
In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell...
Preprint
Full-text available
This document aims to agree on a broad, international strategy for the implementation of open scholarship that meets the needs of different national and regional communities but works globally.Scholarly research can be idealised as an inspirational process for advancing our collective knowledge to the benefit of all humankind. However, current rese...
Article
Full-text available
Long‐read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential is critically reliant on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake...
Preprint
Newly released Rapid Low Input by PCR Barcoding Sequencing Kit (SQK-RLB001); minor adjustments indicated by (*).
Preprint
Full-text available
Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential relies crucially on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which potentiates all laboratories to undertake t...
Article
Full-text available
Background We investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood.AimTo identify causative functional genetic variants related to an undiagnosed primary immu...
Article
Full-text available
Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes ar...
Data
Graph shown the number of reads that were mapped for the transcripts in the BUSCO database.
Data
"Missing" Unique Single-Copy Orthologues mapped to the Nippostrongylus brasiliensis genome
Article
Full-text available
Neisseria meningitidis causes meningococcal disease but is frequently carried in the throats of healthy individuals; the factors that determine whether invasive disease develops are not completely understood. We carried out detailed studies of isolates, collected from patients and their household contacts, to identify differences between commensal...
Article
Full-text available
Primary open-angle glaucoma (POAG) is influenced by both genetic and environmental factors. Despite significant progress in identifying genetic variants associated with POAG, there remains a substantial amount of unexplained heritability. Study design features that may enhance knowledge of the genetic architecture include focusing on multiple quant...
Presentation
Full-text available
Our body is continually pestered by foreign invaders of many different shapes and sizes. We have a modular immune system that has different forms of defence in response to these different classes of foreign invaders. One of these defences is called Th2, which is typically brought into play when the body becomes infected by parasites and bacteria. I...
Article
Full-text available
Purpose Primary open-angle glaucoma (POAG) refers to a group of heterogeneous diseases involving optic nerve damage. Two well-established risk factors for POAG are elevated intraocular pressure (IOP) and a thinner central corneal thickness (CCT). These endophenotypes exhibit a high degree of heritability across populations. Large-scale genome-wide...
Preprint
Full-text available
Eukaryotic genome assembly remains a challenge in part because of the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematode...
Article
Full-text available
Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A f...