Multi-locus amplicon sequencing approach to study microbial diversity at
Watch the video
Direct nanopore sequencing of canonical and modified bases in 16S ribosomal RNA
Watch the video
Enrichment and sensitivity methods
Watch the video
Identification of human leukocyte antigen splice variants by MinION cDNA sequencing
Watch the video
Assembly of large eukaryotic genomes using Oxford Nanopore
Watch the video
VolTRAX
Watch the video
Oxford Nanopore Technologies
Complex tomato genomes: Easy with nanopores
Watch the video
RWTH Aachen University
PathoTRACK project: Identification of microbial pathogens through NGS approaches
Watch the video
Real-time assembly of MinION sequencing data
Watch the video
Oxford Nanopore Technologies
Lightweight sequencing of massive genomes
Watch the video
Institute of Biology, Leiden
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.
Identifying and Quantifying Transcript Isoforms in Single-Cell Nanopore RNAse
Watch the video
Clive Brown Plenary Talk
Watch the video
Oxford Nanopore Technologies
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.
Nanopore Applications
Watch the video
Oxford Nanopore Technologies
Assembling genomes with complex genome repeats
Watch the video
Malaghan Institute of Medical Research
GeT experience of long read sequencing using the available technologies
Watch the video
Rapid resistome mapping using nanopore sequencing
Watch the video
Novo Nordisk Foundation Center for Biosustainability
SelectION: Identification of predefined genomic regions in large nanopore DNA s
Watch the video
Universität Schleswig-Holstein
CpG methylation detection of human mtDNA by nanopore sequencing
Watch the video
University of Bari
MinION microbiome profiling: going from on-the-go to go-to?
Watch the video
University of Aberystwyth
Our current perspective of our microbial world is heavily influenced by high throughput DNA sequencing and its limitations. Our interest in MinION sequencing has focused on developing approaches for sequencing in extreme environments to bypass some of the bottlenecks associated with sequencing in microbial ecology. In this talk I will introduce our work in extreme environments as varied as the terrestrial subsurface and Arctic glaciers. Our DeepSeq 1 and 2 experiments were conducted in the Earth’s subsurface and demonstrate the rapid generation of microbiome profiles using lightweight, offline, battery powered metagenomics workflows. Meanwhile, MinION sequencing is becoming integral to our Arctic fieldwork programme, revealing glacier microbial biofilm community structures and metagenomes while deployed in field camps and stations. As the MinION platform, workflows and tools are maturing the prospect of characterising Earth’s microbiomes at source is starting to be realised.
Arwyn Edwards is a microbial ecologist at Aberystwyth University. He is currently a Senior Lecturer in Biology at the Institute of Biological, Environmental & Rural Sciences and Director of the Interdisciplinary Centre for Environmental Microbiology. His research group is focused upon the evolution, structure, function and stability of microbial communities in extreme environments in response to environmental changes at both societally-relevant and “deep” geo/evolutionary timescales. Arwyn particularly enjoys taking Nanopore sequencing to strange new places.
Analysis tools for nanopore data
Watch the video
Ontario Institute for Cancer Research
Transcriptomic analysis via direct RNA sequencing and contextual splice variation
Watch the video
Developing rapid sample-to-result diagnostic workflows on the MinION
Watch the video
Linear assembly of a human Y centromere using MinION nanopore long read sequences
Watch the video
University of California, Santa Cruz
Direct RNA sequencing: What’s new?
Watch the video
Applications of raw nanopore signal processing: From modified bases to streaming basecalling and beyond
Watch the video
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
Simultaneous detection of DNA and RNA virus species involved in bovine respiratory
Watch the video
Detection of base analogues with the MinION
Watch the video
Universty of Oxford
Elucidating the brain expression profile of the neuropsychiatric disease gene CACNA1C
Watch the video
University of Oxford
Recent progress at UCSC: long reads, DNA, and RNA sequencing
Watch the video
UC Santa Cruz
Stopping Outbreaks becoming Epidemics
Watch the video
University of Birmingham
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.
Genomic epidemiology of Zika virus in the Americas
Watch the video
Rapid (epi-) genomic classification of brain tumors using nanopore sequencing
Watch the video
Direct RNA versus cDNA sequencing of C. elegans transcripts
Watch the video
Is the pot labelled correctly? Testing dairy products and probiotics using nan
Watch the video
Genotypic
Crop innovation using nanopore sequencing
Watch the video
Keygene N.V.
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.
Hybrid Nanopore and Illumina assembly: working towards the perfect bacterial genome
Watch the video
University of Melbourne
Telomere to telomere: complete (small) chromosomes using MinION
Watch the video
University of York
A portable system for rapid bacterial composition analysis using the MinION and a laptop computer
Watch the video
In-house training of the nanonet local basecaller: opportunities and challenges
Watch the video
Multiplex HLA-typing by nanopore sequencing
Watch the video
SciLifeLab
Tracking adaptive structural variation during host-pathogen conflict
Watch the video
Cas9-Assisted Targeting of Chromosome segments (CATCH) for targeted nanopore sequen
Watch the video
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Watch the video
Measuring DNA methylation with the MinION
Watch the video
Johns Hopkins University
Same-day tuberculosis diagnostic and surveillance information direct from sputum
Watch the video