Nick Owens
Senior Lecturer in Data Science and Artificial Intelligence
N.D.L.Owens@exeter.ac.uk
RILD Building
University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
Overview
Nick Owens is a Senior Lecturer in Data Science and Artificial Intelligence in the Department of Clinical and Biomedical Sciences at the University of Exeter.
Nick received both an MEng in Computer Science and a PhD in biologically inspired algorithms/machine learning from the University of York. Nick moved to apply his background to biology for his first post-doctoral work at the Francis Crick Institute (formerly MRC National Institute for Medical Research) on gene regulation in early Xenopus development, he used computational methods to understand transcriptional dynamics at the zygotic genome activation. Following this, he undertook further computational biology post-doctoral work on gene regulation at Institut Pasteur, Paris. There he worked on how co-operative binding of transcription factors and chromatin states control cell fate and self-renewal in mouse embryonic stem cells.
In 2019, Nick moved to the University of Exeter to establish his group studying gene regulatory defects in disease.
Qualifications
- MEng, Computer Systems and Software Engineering, University of York
- PhD, University of York
Research
Research interests
Nick is interested in how transcription factors bind cooperatively to regulate gene expression and how this depends on local chromatin features such as nucleosome positioning. Nick applies computational tools to understand how the sequence specifies transcription factor logic and local chromatin organisation. He uses these methods to gain mechanistic into sequence variants implicated in diabetes.
Publications
Journal articles
Wakeling M, Owens NDL, Hopkinson JR, Johnson MB, Houghton JAL, Dastamani A, Flaxman CS, Wyatt RC, Hewat TI, Hopkins JJ, et al (In Press). A novel disease mechanism leading to the expression of a disallowed gene in the pancreatic beta-cell identified by non-coding, regulatory mutations controlling HK1. Nature Genetics Abstract.
De Franco E, Owens N, Hattersley A, Flanagan S, Wakeling M, Johnson M, Wright C (In Press). Primate-specific ZNF808 is essential for pancreatic development in humans. Nature Genetics
Laver TW, Wakeling MN, Caswell RC, Bunce B, Yau D, Männistö JME, Houghton JAL, Hopkins JJ, Weedon MN, Saraff V, et al (2024). Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements. Eur J Hum Genet Abstract. Author URL.
Sempou E, Kostiuk V, Zhu J, Cecilia Guerra M, Tyan L, Hwang W, Camacho-Aguilar E, Caplan MJ, Zenisek D, Warmflash A, et al (2023). Author Correction: Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR. Nat Commun, 14(1). Author URL.
Davies J, Franklin A, Walker E, Owens N, Bray N, Bamford RA, Commin G, Chioza B, Burrage J, Dempster E, et al (2022). 1. DEVELOPMENTAL TRAJECTORIES OF DNA METHYLATION IN NEURAL CELL POPULATIONS IN HUMAN CORTEX AND LINKS TO NEURODEVELOPMENTAL DISORDERS. European Neuropsychopharmacology, 63
Owens NDL, Flanagan SE (2022). Disrupted β-cell-specific gene silencing causes congenital hyperinsulinism. NATURE GENETICS, 54(11), 1597-1598. Author URL.
Sempou E, Kostiuk V, Zhu J, Cecilia Guerra M, Tyan L, Hwang W, Camacho-Aguilar E, Caplan MJ, Zenisek D, Warmflash A, et al (2022). Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR. Nat Commun, 13(1). Abstract. Author URL.
Bernard LD, Dubois A, Heurtier V, Fischer V, Gonzalez I, Chervova A, Tachtsidi A, Gil N, Owens N, Bates LE, et al (2022). OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency. NUCLEIC ACIDS RESEARCH, 50(13), 7367-7379. Author URL.
Festuccia N, Owens N, Chervova A, Dubois A, Navarro P (2021). The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency. Development, 148(17). Abstract.
Coux RX, Owens NDL, Navarro P (2020). Chromatin accessibility and transcription factor binding through the perspective of mitosis. Transcription, 11(5), 236-240. Abstract.
Raveux A, Stedman A, Coqueran S, Vandormael-Pournin S, Owens N, Romagnolo B, Cohen-Tannoudji M (2020). Compensation between Wnt-driven tumorigenesis and cellular responses to ribosome biogenesis inhibition in the murine intestinal epithelium. Cell Death Differ, 27(10), 2872-2887. Abstract. Author URL.
Owens NDL, De Domenico E, Gilchrist MJ (2019). An RNA-seq protocol for differential expression analysis. Cold Spring Harbor Protocols, 2019(6), 498-506. Abstract.
Owens N, Papadopoulou T, Festuccia N, Tachtsidi A, Gonzalez I, Dubois A, Vandormael-Pournin S, Nora EP, Bruneau BG, Cohen-Tannoudji M, et al (2019). CTCF confers local nucleosome resiliency after DNA replication and during mitosis. Elife, 8 Abstract. Author URL.
Gentsch GE, Spruce T, Owens NDL, Smith JC (2019). Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals. Nat Commun, 10(1). Abstract. Author URL.
Gentsch GE, Spruce T, Owens NDL, Monteiro RS, Smith JC (2019). The Innate Immune Response of Frog Embryos to Antisense Morpholino Oligomers Depends on Developmental Stage, GC Content and Dose. Dev Cell, 49(4), 506-507. Author URL.
Gentsch GE, Owens NDL, Smith JC (2019). The Spatiotemporal Control of Zygotic Genome Activation. iScience, 16, 485-498. Abstract. Author URL.
Heurtier V, Owens N, Gonzalez I, Mueller F, Proux C, Mornico D, Clerc P, Dubois A, Navarro P (2019). The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells. Nat Commun, 10(1). Abstract. Author URL.
Festuccia N, Owens N, Papadopoulou T, Gonzalez I, Tachtsidi A, Vandoermel-Pournin S, Gallego E, Gutierrez N, Dubois A, Cohen-Tannoudji M, et al (2019). Transcription factor activity and nucleosome organization in mitosis. Genome Res, 29(2), 250-260. Abstract. Author URL.
Festuccia N, Owens N, Navarro P (2018). Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Lett, 592(6), 852-877. Abstract. Author URL.
Gentsch GE, Spruce T, Monteiro RS, Owens NDL, Martin SR, Smith JC (2018). Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus. Dev Cell, 44(5), 597-610.e10. Abstract. Author URL.
Forouzmand E, Owens NDL, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KWY (2017). Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Developmental Biology, 426(2), 401-408. Abstract.
Festuccia N, Gonzalez I, Owens N, Navarro P (2017). Mitotic bookmarking in development and stem cells. Development, 144(20), 3633-3645. Abstract. Author URL.
Robson A, Owens NDL, Baserga SJ, Khokha MK, Griffin JN (2016). Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Dev Biol, 16(1). Abstract. Author URL.
Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK (2016). Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Reports, 14(3), 632-647. Abstract.
De Domenico E, Owens NDL, Grant IM, Gomes-Faria R, Gilchrist MJ (2015). Molecular asymmetry in the 8-cell stage Xenopus tropicalis embryo described by single blastomere transcript sequencing. Developmental Biology, 408(2), 252-268. Abstract.
DiMeglio P, Duarte JH, Ahlfors H, Owens NDL, Li Y, Villanova F, Tosi I, Hirota K, Nestle FO, Mrowietz U, et al (2014). Activation of the aryl hydrocarbon receptor dampens the severity of inflammatory skin conditions. Immunity, 40(6), 989-1001. Abstract.
Collart C, Owens NDL, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ, et al (2014). High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development (Cambridge), 141(9), 1927-1939. Abstract.
Bewick AJ, Chain FJJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens NDL, Seifertova E, Krylov V, Macha J, Tlapakova T, et al (2013). A large pseudoautosomal region on the Sex chromosomes of the frog Silurana tropicalis. Genome Biology and Evolution, 5(6), 1087-1098. Abstract.
Seifertova E, Zimmerman LB, Gilchrist MJ, Macha J, Kubickova S, Cernohorska H, Zarsky V, Owens NDL, Sesay AK, Tlapakova T, et al (2013). Efficient high-throughput sequencing of a laser microdissected chromosome arm. BMC Genomics, 14(1). Abstract.
Gentsch GE, Owens NDL, Martin SR, Piccinelli P, Faial T, Trotter MWB, Gilchrist MJ, Smith JC (2013). InVivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency. Cell Reports, 4(6), 1185-1196. Abstract.
Owens NDL, Greensted A, Timmis J, Tyrrell A (2013). The Receptor Density Algorithm. THEORETICAL COMPUTER SCIENCE, 481, 51-73. Author URL.
Hilder JA, Owens NDL, Neal MJ, Hickey PJ, Cairns SN, Kilgour DPA, Timmis J, Tyrrell AM (2012). Chemical Detection Using the Receptor Density Algorithm. IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART C-APPLICATIONS AND REVIEWS, 42(6), 1730-1741. Author URL.
Owens NDL, Timmis J, Greensted A, Tyrrell A (2010). Elucidation of T cell signalling models. J Theor Biol, 262(3), 452-470. Abstract. Author URL.
Owens N, Stepney S (2010). Investigations of Game of Life Cellular Automata Rules on Penrose Tilings: Lifetime, Ash, and Oscillator Statistics. JOURNAL OF CELLULAR AUTOMATA, 5(3), 207-225. Author URL.
Conferences
Gentsch G, Spruce T, Owens N, Smith J (2017). Genome activation in <i>Xenopus tropicalis</i>. Author URL.
Di Meglio P, Duarte JH, Ahlfors H, Owens NDL, Li Y, Villanova F, Tosi I, Hirota K, Nestle FO, Mrowietz U, et al (2014). Environmental factors transmitted by the aryl hydrocarbon receptor influence the severity of psoriatic inflammation. Author URL.
Hilder JA, Owens NDL, Hickey PJ, Cairns SN, Kilgour DPA, Timmis J, Tyrrell A (2011). Parameter optimisation in the receptor density algorithm. Abstract.
Owens NDL, Greensted A, Timmis J, Tyrrell A (2009). T Cell Receptor Signalling Inspired Kernel Density Estimation and Anomaly Detection. Author URL.
Timmis J, Andrews P, Owens N, Clark E (2008). Immune systems and computation: an interdisciplinary adventure. Author URL.
Owens NDL, Timmis J, Greensted A, Tyrrell A (2008). Modelling the tunability of early T cell signalling events. Author URL.
Tyrrell AM, Timmis J, Greensted AJ, Owens ND (2007). Evolvable hardware, a fundamental technology for homeostasis. Author URL.
Owens ND, Timmis J, Greensted AJ, Tyrell AM (2007). On immune inspired homeostasis for electronic systems. Author URL.
