Dr David Eccles completed his postgraduate degree in biomedical science at Te Herenga Waka—Victoria University of Wellington in 2011. David is a Postdoctoral Research Fellow and Bioinformatics Research Analyst. He began working at the Institute in 2013 and collaborates with various scientists around the world.
Research interests
"My main interest is exploring the biological code (DNA) that instructs our bodies how to work and how to respond to our environment. I am particularly fascinated by looking for patterns in DNA (or the absence of patterns), and investigating how those patterns describe organisms and influence biological systems.
"The treasure and curse of bioinformatics is that almost every project opens up a new and unexpected area of research. I am excited by the discoveries we make, and have a constant battle with myself to clear my head of finished projects, and concentrate on new tasks and projects that await me.
"I work as the glue between biologists and computers, helping with project design, data analysis and result presentation. I support researchers by using computer programs and can even develop custom software solutions for their projects. This work is usually called bioinformatics. It can speed up an analysis to be up to 5-10 times faster and allows researchers to explore existing data in more depth than previously possible. When the scientists I work with are no longer shackled to slow data processing, they are free to spend that time getting creative and expanding their research."
Publications
2023
Urban L, Perlas A, Francino O, Martí-Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada-Flores M, Marques-Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C (2023). Real-time genomics for One Health. Mol Syst Biol. 19(8):e11686
2022
Munoz-Erazo L, Schmidt AJ, Shinko D, Eccles DA, Price KM (2022). Creation of High-Dimensional Reduction Analysis-Compatible Histocytometry Files from Images of Densely-Packed Cells and/or Variable Stain Intensity. Curr Protoc. 2(5):e441
Herst PM, Carson GM, Eccles DA, Berridge MV (2022). Bioenergetic and Metabolic Adaptation in Tumor Progression and Metastasis. Front Oncol. 12:857686. 2022
Burnard SM, Lea RA, Benton M, Eccles D, Kennedy DW, Lechner-Scott J, Scott RJ (2021). Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. Genes (Basel). 13(1):87
2021
Mayer JU, Hilligan KL, Chandler JS, Eccles DA, Old SI, Domingues RG, Yang J, Webb GR, Munoz-Erazo L, Hyde EJ, Wakelin KA, Tang SC, Chappell SC, von Daake S, Brombacher F, Mackay CR, Sher A, Tussiwand R, Connor LM, Gallego-Ortega D, Jankovic D, Le Gros G, Hepworth MR, Lamiable O, Ronchese F (2021). Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization. Nat Immunol. 2021 Nov 18
Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE (2021). Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol. 2021 Aug 23
2020
Shepherd AL, Smith AAT, Wakelin KA, Kuhn S, Yang J, Eccles DA, Ronchese F (2020). A semi-automated technique for adenoma quantification in the ApcMin mouse using FeatureCounter. Sci Rep. 10(1):3064
2019
Clark DW, Eccles D, et al (2019). Associations of autozygosity with a broad range of human phenotypes. Nat Commun. 10(1):4957
Boykin LM, Sseruwagi P, Alicai T, Ateka E, Mohammed IU, Stanton JL, Kayuki C, Mark D, Fute T, Erasto J, Bachwenkizi H, Muga B, Mumo N, Mwangi J, Abidrabo P, Okao-Okuja G, Omuut G, Akol J, Apio HB, Osingada F, Kehoe MA, Eccles D, Savill A, Lamb S, Kinene T, Rawle CB, Muralidhar A, Mayall K, Tairo F, Ndunguru J (2019). Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa. Genes (Basel). 21;10(9)
2018
Schalamun M, Nagar R, Kainer D, Beavan E, Rathjen J, Eccles D, Lanfear R, Schwessinger B (2018) Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Mol Ecol Resources 19(1):77-89
Eccles DA, Chandler J, Camberis M, Henrissat B, Koren S, Le Gros G, Ewbank JJ (2018) De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads. BMC Biol 16(1):6
2017
Chandler J, Camberis M, Bouchery T, Blaxter M, Le Gros G, Eccles DA. (2017) Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis. F1000Res.
Stuart S, Benton MC, Eccles DA, Sutherland HG, Haupt LM, Lea RA, Griffiths LR. (2017) Gene-centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility. Mol Genet Genomic Med.
Connor LM, Tang SC, Cognard E, Ochiai S, Hilligan KL, Old SI, Pellefigues C, White RF, Patel D, Smith AA, Eccles DA, Lamiable O, McConnell MJ, Ronchese F. (2017) Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles. J Exp Med.
2015
Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE (2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res.
Wang J, Moore NE, Deng YM, Eccles DA, Hall RJ. (2015) MinION nanopore sequencing of an influenza genome. Front Microbiol.
Benton MC, Johnstone A, Eccles D, Harmon B, Hayes MT, Lea RA, Griffiths L, Hoffman EP, Stubbs RS, Macartney-Coxson D.(2015) An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biol.
Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, Bajzikova M, Kovarova J, Peterka M, Yan B, Pesdar EA, Sobol M, Filimonenko A, Stuart S, Vondrusova M, Kluckova K, Sachaphibulkij K, Rohlena J, Hozak P, Truksa J, Eccles D, Haupt LM, Griffiths LR, Neuzil J, Berridge MV. (2015) Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab.
2013
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc.
Roxburgh RH, Marquis-Nicholson R, Ashton F, George AM, Lea RA, Eccles D, Mossman S, Bird T, van Gassen KL, Kamsteeg EJ, Love DR. (2013) The p.Ala510Val mutation in the SPG7 (paraplegin) gene is the most common mutation causing adult onset neurogenetic disease in patients of British ancestry. J Neurol.
2012
Benton M, Macartney-Coxson D, Eccles D, Griffiths L, Chambers G, Lea R. (2012) Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population. PLoS One.
Eccles DA, Macartney-Coxson D, Chambers GK, Lea RA.(2012) A unique demographic history exists for the MAO-A gene in Polynesians. J Hum Genet.
Myles S, Lea RA, Ohashi J, Chambers GK, Weiss JG, Hardouin E, Engelken J, Macartney-Coxson DP, Eccles DA, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M. (2011) Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Med Genet.