Rapid (epi-) genomic classification of brain tumors using nanopore sequencing
Linear assembly of a human Y centromere using MinION nanopore long read sequences
Complex tomato genomes: Easy with nanopores
Analysis tools for nanopore data
Rapid resistome mapping using nanopore sequencing
Clive Brown Plenary Talk
Chief Technology Officer at Oxford Nanopore. On the Executive team, he is responsible for all of the Company’s product-development activities. Clive leads the specification and design of the Company’s nanopore-based sensing platform, including strand DNA/RNA sequencing and protein-sensing applications with a strong focus on scientific excellence and successful adoption by the scientific community. Clive joined Oxford Nanopore from the Wellcome Trust Sanger Institute (Cambridge, UK) where he played a key role in the adoption and exploitation of 'next generation' DNA sequencing platforms. This involved helping to set up the world’s largest single installation of Illumina (formerly Solexa) Genome Analyzers in a production sequencing environment, initially used to pioneer the 1000 genomes project. From early 2003 he was Director of Computational Biology and IT at Solexa Ltd, where he was central to the development and commercialisation of the Genome Analyzer (GA). Solexa was sold to Illumina for $650m in early 2007 after the successful placement and adoption of 12 instruments. The Solexa technology, now commercialised by Illumina, is the market-leading DNA sequencing technology driving the renaissance in DNA-based discovery. He has a strong background in computer science and genetics/molecular biology and manages interdisciplinary teams including mechanical engineering, electronics, physics, surface chemistry, electrophysiology, software engineering and applications (of the technology). Clive applies modern agile management techniques to the entire product-development lifecycle. Clive has also held various management and consulting positions at GlaxoWellcome, Oxford Glycosciences and other EU- and US-based organisations. He has worked at the interface between computing and science, ranging from genetics to proteomics. He holds degrees in Genetics and Computational Biology from the University of York.
Stopping Outbreaks becoming Epidemics
Nick Loman speaks at the Oxford Nanopore conference, London Calling, on his work using the portable Nanopore Technology to perform genomic surveillance of outbreaks such as Ebola and Zika.
Crop innovation using nanopore sequencing
KeyGene develops and provides cutting edge and proprietary breeding technologies for accelerated crop improvement with long term partners in both vegetable and field crops. Modern plant breeding and whole genome sequence information go hand in hand and, as such, KeyGene has generated high quality de novo genome assemblies of many crops, plant pathogens and pests using PacBio and Illumina platforms. Since Oxford Nanopore sequencing allows direct sequencing of DNA fragments of tens of kilobases or even megabases in size, we explore the technology for its potential to resolve complex genomic regions and to facilitate the accurate assembly of (partial) heterozygous and polyploid genomes. Last year, we have reported the assembly of the ~54 megabase eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species causing severe diseases in a wide range of crops. Given these promising results, we have recently started to sequence and assemble the genome of a melon variety (~450 Mb) on the MinION Mk1 B. KeyGene also participates in the PromethION Early Access Programme (PEAP) to produce sequence data on an industrial scale and the VolTRAX Introduction Programme (V.I.P.) for automated sample preparation. Progress and challenges in these projects will be presented and discussed during the break out session.
Raymond Hulzink is a scientific researcher at KeyGene, a plant biotechnology company in the Netherlands. In the last eight years, he gained much experience in the field of Nextn Generation Sequencing with expertise on a wide range of platforms (Illumina, Pacific Biosciences, Oxford Nanopore Technologies etc.). In the department of Technology Development, he is involved in the development of novel sequencing applications and molecular marker methods. In 2014, he joined the Oxford Nanopore MinION™’s early access programme. Recently, he joined the PromethION early access and VolTRAX introduction programs to evaluate the applicability of these systems for molecular plant breeding.
Next to his job at KeyGene, Raymond is member of the Scientific Advisory Board at ProteoNic BV, a biotechnology company offering products and services for improving recombinant protein production. Raymond earned his PhD in Molecular Plant Physiology at the Radboud University of Nijmegen on the regulation of gene expression. After his PhD, Raymond was postdoctoral researcher in the plant department of the NIOO-KNAW and studied the evolution of disease resistance in plants following a functional and comparative genomics approach. Furthermore, he worked as a post-doc at KeyGene where he was involved in map-based cloning of plant disease resistance genes.
Lightweight sequencing of massive genomes
In Leiden, the birth place of the Dutch flower bulb industry, we aim to sequence the 35 Gbp tulip genome. With the current large data volumes and very long reads, nanopore technology has become an interesting option for sequencing such massive, repeat-rich genomes. In my talk, I will outline some of the bioinformatics challenges, and how we intend to address these. As a proof of principle of these ideas, we have recently sequenced and assembled the 900 Mbp genome of the European eel.
Christiaan Henkel is a molecular biologist turned bioinformatician. For the past eight years, he has studied the genomes of a wide variety of organisms, ranging from bacteria to snakes (and including quite a few fish species). Currently, he is working on eel and tulip genomics at Leiden University and University of Applied Sciences Leiden, in collaboration with genomics companies BaseClear and ZF-screens.