Detection of Unnatural Bases Using Raw Nanopore Sequencing Data

Assessing the prevalence and sequence diversity of Hepatitis B Virus in Sierra Leone with MinION

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Dr. Luke Meredith is a post-doctoral research fellow based at the University of Cambridge, working with Prof. Ian Goodfellow. Obtaining a PhD in Molecular Virology in 2009, Dr. Meredith's post-doctoral work focused on virus binding and entry. In 2015, he joined the West African Ebola outbreak response and spent 7 months in Sierra Leone, initially as part of the Public Health England diagnostic response, then subsequently as part of the clinical research team evaluating diagnostic tests. He then spent a further 3 months running the Ebola Outbreak Sequencing Service, providing real-time sequencing support to the response, enabling the rapid characterisation of EVD cases during the latter stages of the epidemic. Following the epidemic, Dr. Meredith played a key role in the establishment of the University of Makeni Infectious Disease Research Laboratory, a legacy teaching and research laboratory which provides training to Sierra Leonean graduate students, as well as being the base for research and surveillance projects monitoring the diversity and prevalence of infectious disease in Sierra Leone and surrounding countries in West Africa.

Bacterial species level identification and strain level differentiation using repetitive extragenic palindromic based amplicon sequencing with Oxford Nanopore Technology

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Lukasz Krych completed his PhD in Food Microbiology in 2014 at the University of Copenhagen, where he is now a post-doctoral researcher. He utilises molecular genetics and classical microbiological techniques to investigate the association of the gut microbiome with health and disease. This involves the development of novel data analysis tools, multivariate data mining and protocol optimisation. Lukasz is also R&D director at GenXone, a Polish biotech company specialising in the development of diagnostic products based on the latest DNA testing technologies.

Carika Weldon

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Dr Carika Weldon is a lecturer in Biomedical Science at De Montfort University in Leicester. Prior to joining the faculty as the youngest lecturer in the university’s history, she obtained her BSc (Hons) Medical Biochemistry in 2011 and her PhD in Biochemistry in 2015 from the University of Leicester.

Dr Weldon’s doctoral work focused on alternative splicing of the apoptotic gene Bcl-X. By creating the new FOLDeR method, she discovered that G-quadruplexes shifts the XS/XL ratio to favour the pro-apoptotic XS isoform. By screening over 30 G-quadruplex ligands, her work identified a suitable drug that could be used for treating cancers, based on its ability to shift the ratio almost 40-fold. In her own lab now she looks at how the presence of G-quadruplexes in pre-mRNA can influence alternative splicing in other genes.  She is utilizing the versatile technique of nanopore technology to detect modified guanine with the hopes of gaining more insight into the exciting fields of splicing and G-quadruplexes.

Recent publications

Weldon, C. et al. Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X. Nucleic Acids Research (2017). doi:10.1093/nar/gkx1122

Weldon, C. et al. Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA. Nature Chemical Biology 13, 18–20 (2017).

Cas9 targeted enrichment for nanopore profiling of methylation at known cancer drivers

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Timothy Gilpatrick is a current MD/PhD student at Johns Hopkins University working in the lab of Winston Timp to leverage sequencing technologies for insight into epigenetic states and transcriptional regulation. He received his BSc in Biochemistry from the University of Delaware, where he worked on characterizing the role of lipoprotein-associated enzymes in atherosclerosis. Prior to starting his graduate studies, he worked as a research fellow at the National Institutes of Health, where his work centered on understanding how microRNAs regulate epigenetic silencing machinery in mouse ES cells. He hopes to marry his interests in medicine and genomics to work in the development and application of sequencing-based diagnostic techniques. When not in lab, Timothy enjoys city biking, yoga, and music production.

Cassava Virus Action Project

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Chiron basecaller

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Lachlan completed a Bachelor of Science at Australian National University, majoring in Mathematics. After several years out of science working in consulting, he went to the Wellcome Trust Sanger Institute, UK to complete a PhD in bioinformatics. Lachlan was a research fellow at the School of Public Health, Imperial College London, largely working on methodology for genome-wide association studies. He returned to Australia in 2012 to start a group at the Institute for Molecular Bioscience, University of Queensland where his group works on developing genomics and bioinformatics tools in infectious disease and cancer.

Clinical applications for real-time sequencing in leukaemia

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Dr. Cecilia Yeung is an Associate Member at the Fred Hutchinson Cancer Research Center where she serves as the medical director of the Molecular Oncology Laboratory. She is an Assistant Professor at the University of Washington, Department of Anatomic Pathology where she serves as the chair of the Clinical Competency Committee for the Molecular Genetics Pathology Fellowship, and the director for the Molecular Pathology Elective. She is the co-coordinator and speaker of the Molecular Pathology Lecture Series for residents and fellows. She is a member of the Board of Directors and the chair of the Teaching and Education Committee at the Association for Molecular Pathology.  Her clinical appointment at Seattle Cancer Care Alliance is where she focuses her pathology diagnostic skills in immunotherapy, transplant, and hematopathology. Her research interest focuses on developing novel molecular diagnostics for hematologic malignancies, and improving correlative data from clinical trials via implementation of better translational medicine diagnostic assays.

Dr. Olga Sala Torra is a staff scientist in the Radich laboratory at the Fred Hutchinson Cancer Research Center in Seattle, WA. Her main research interests are the application of gene expression and sequencing techniques to the detection of minimal residual disease in leukemias, and the development of low-cost diagnostic methods for hematologic malignancies that can be useful in low-income countries.

Recent publications

Sala Torra, O. et al. Next-Generation Sequencing in Adult B cell Acute Lymphoblastic Leukemia Patients. Biology of Blood and Marrow Transplantation 23, 691–696 (2017).

Torra, O. S., Beppu, L., Smith, J. L., Welden, L., Georgievski, J., Gupta, K. Radich, J. P. (2016, June 2). Paper or plastic? BCR-ABL1 quantitation and mutation detection from dried blood spots. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-12-689059

Clive Brown: Plenary from London Calling 2018

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Complex structural variants resolved by short-read and long-read whole genome sequencing in Mendelian disorders

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Alba Sanchis-Juan studied Biochemistry and Biomedicine at University of Valencia, Spain. She is a PhD student and works at the Department of Haematology, University of Cambridge. Her study has been focused on the use of next-generation sequencing for clinical research and diagnosis. Currently, she performs data analysis of whole genome sequence data of individuals with neurodevelopmental disorders.

Recent publications

Sanchis-Juan, A. et al. Complex structural variants resolved by short-read and long-read whole genome sequencing in Mendelian disorders. bioRxiv 281683 (2018). doi:10.1101/281683

Coral holobionte species identification onboard Tara with MinION sequencing of multiple barcodes.

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Quentin Carradec received his PhD in genetics and molecular biology from Pierre and Marie Curie University in Paris in 2014. He currently works on environmental genomics at Genoscope Institute, France in Patrick Wincker’s research group. His research focuses on the diversity and activity of marine planktonic species with the analysis of metagenomic and metatranscriptomic sequencing data in the framework of Tara expedition projects. He recently joined the Tara Pacific project to study resistance and adaptation of coral holobionte to environmental change.

De novo sequencing and assembly of plant genomes using nanopore long reads

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Jean-Marc Aury is a researcher at Genoscope since 2003. He was focused on eukaryotic genome analysis and was a main actor of several genome projects, like paramecium, grape, banana, cocoa and oak. He is now the team leader of a bioinformatic group which is focused on sequencing data production, genome assembly and gene prediction in eukaryotic genomes, with a broad interest in methodological development. Genoscope acts as the French National Sequencing Centre since 1998 and has an extensive experience in large sequencing projects (for example the Tara Oceans metagenomic project). Genoscope has participated in the MinION and PromethION Early Access Program.

Recent publications

Istace, B. et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience 6, (2017).

Schmidt, M. H. et al. de novo assembly of a new Solanum pennellii accession using nanopore sequencing. The Plant Cell tpc.00521.2017 (2017). doi:10.1105/tpc.17.00521

Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nature Communications 9,(2018).

Madoui, M. A. et al. Genome assembly using nanopore-guided long and error-free DNA reads. BMC Genomics 16, (2015).

Detecting DNA modifications and structural variants from nanopore long-read sequencing data

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Detection of clinically relevant molecular alterations in CLL by nanopore sequencing

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Dr Adam Burns is a post-doctoral researcher in the Oxford Molecular Diagnostics Centre based in the Department of Oncology at the University of Oxford. His research focuses on developing next-generation sequencing-based tools for clinical diagnostic use. After obtaining his BSc from the University of Hull, Adam worked in industry for five years before joining Oxford University in 2009. There he developed screening assays for clinically relevant mutations, including KRAS, BRAF and JAK2, across a range of haematological malignancies. As part of his PhD from Oxford Brookes University in 2016, Adam developed targeted and whole genome sequencing approaches to help diagnose haematological malignancies. This work was subsequently adopted for routine diagnostic use in the Oxford University Hospitals NHS Foundation Trust and also informed the Genomics England 100,000 Genomes Project. Adam’s current research is centred on using nanopore sequencing, and other patient-near technologies, as an accurate, low-cost, easy-to-use screening platform to detect clinically relevant genetic changes in haematological malignancies for use in resource-poor regions of the world.

Recent publications

Burns, A. et al. Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups. Leukemia 32, 332–342 (2018)

Stamatopoulos B, et al. Targeted deep sequencing reveals clinically relevant subclonal IgHV rearrangements in chronic lymphocytic leukemia. Leukemia 31, 837–845 (2017)

Pellagatti, A. et al. Targeted resequencing analysis of 31 genes commonly mutated in myeloid disorders in serial samples from myelodysplastic syndrome patients showing disease progression. Leukemia 30, 247–250 (2016)

Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

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Christos Proukakis is a clinical academic neurologist, holding a senior lectureship at UCL Institute of Neurology and is an honorary consultant neurologist at the Royal Free NHS Trust. His work focuses on Parkinson’s disease, investigating the role of somatic mutations and the utility of new sequencing technologies.

Recent publications

Nacheva, E. et al. DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS ONE 12, (2017)

Kara, E. et al. Genetic and phenotypic characterization of complex hereditary spastic paraplegia. Brain 139: 1904-18, (2016)

Kiely, AP. et al. Distinct clinical and neuropathological features of G51D SNCA mutation cases compared with SNCA duplication and H50Q mutation. Mol Neurodegener,10:41, (2015)

Porcari, R. et al. The H50Q mutation induces a 10-fold decrease in the solubility of α-synuclein. Journal of Biological Chemistry 290, 2395–2404 (2015)

Beavan, M. et al. Evolution of prodromal clinical markers of parkinson disease in a GBA mutation-positive cohort. JAMA Neurology 72, 201–208 (2015).

Determining novel antimicrobial resistance mechanisms with Oxford Nanopore long-read sequencing data

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Dr. Hanson is currently an Assistant Professor in the Department of Epidemiology, Human Genetics and Environmental Sciences in the School of Public Health, and the Department of Internal Medicine, Division of Infectious Diseases. He also serves as the Associate Director of Microbial Genomics in the Center for Antimicrobial Resistance and Microbial Genomics (CARMiG) at the McGovern Medical School.

Dr. Hanson’s research interests are in infectious disease transmission and colonization, how microbial communities impact the development of disease, and how antimicrobial resistance develops and transmits through society. He uses a combination of existing and innovative laboratory techniques, as well as cutting-edge sequencing and bioinformatics within his lab’s research.

Devon O'Rourke

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Devon O'Rourke is a PhD candidate at the University of New Hampshire and co-advised by Dr. Matt MacManes and Dr. Jeffrey Foster. He uses nanopore in his day job investigating functional genomics of disease resistance in North American bats. He uses nanopore just for fun, conducting metagenomic experiments within high school and college classes with the goal of doing cool science anytime, anywhere, by anyone, on any budget.

Evaluating the extensively drug-resistant Klebsiella pneumoniae resistome via MinION direct RNA sequencing

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Miranda Pitt completed her undergraduate studies at The University of Queensland, Australia. Courses selected in her Bachelor of Biomedical Science degree predominantly focused on infectious disease, immunology and genetics. In 2013, she commenced an Honours degree at the University of Queensland Diamantina Institute, where she investigated differential gene expression in an ankylosing spondylitis mouse model and received an Honours Class I. She is currently a PhD student at the Institute for Molecular Bioscience at The University of Queensland. Her research delves into understanding the mode of action of last resort antibiotics against multidrug-resistant gram-negative bacteria and the genetic basis underpinning resistance.

Recent publications

Pitt, ME. et al. Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae. Microb Genom (ahead of print) (2018) doi: 10.1099/mgen.0.000158.

Evaluation of nanopore sequencing for bacterial biothreat pathogens

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Amy Gargis is a microbiologist at the U.S. Centers for Disease Control and Prevention (CDC), Atlanta. Dr. Gargis earned her M.S. and Ph.D. in Microbiology from The University of Alabama. After receiving her Ph.D. in 2010, she joined the Division of Laboratory Systems at the CDC, where she focused on efforts to improve the quality of genetic testing in the clinical and public health laboratory setting. Dr. Gargis was co-lead in organizing two national workgroups of experts to review and establish consensus guidelines for scientific principles, clinical laboratory practices, regulatory requirements, and professional standards for next-generation sequencing. In 2014, Dr. Gargis joined the BioDefense Research and Development Laboratory within the Division of Preparedness and Emerging Infections at the CDC. In this position, she works to develop and optimize rapid assays to characterize biological threat agents, with an emphasis on detection of antibiotic resistance.

Recent publications

Gargis, A. S., Kalman, L. & Lubin, I. M. Assuring the quality of next-generation sequencing in clinical microbiology and public health laboratories. Journal of Clinical Microbiology 54, (2016)

Gargis, A. S. et al. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nature Biotechnology 33, 689–693 (2015)

Gargis, a S. et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnology 30, 1033–1036 (2012)

Genome assembly in Drosophila using nanopore

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Danny Miller received both an MD and PhD from the University of Kansas and completed his PhD work in the laboratory of Scott Hawley at the Stowers Institute for Medical Research. He has always been interested in sequencing more species of Drosophila and understanding structural variation within the melanogaster species group and jumped at the chance to sequence and assemble multiple Drosophila genomes using nanopore technology. He will begin a combined residency in Pediatrics and Medical Genetics at the University of Washington and Seattle Children’s Hospital in June 2018.

Recent publications

Miller, D. E., Staber, C., Zeitlinger, J., & Hawley, R. S. (2018). High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing. BioRxiv, 8601, 267393. https://doi.org/10.1101/267393

Solares, E. A., Chakraborty, M., Miller, D. E., Kalsow, S., Hall, K. E., Perera, A. G. Hawley, R. S. (2018). Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing. BioRxiv, 267401. https://doi.org/10.1101/267401

Haplotyping of key cardiac disease genes using long-read sequencing

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Alex is a PhD candidate in Euan Ashley's lab at Stanford University, studying hypertrophic cardiomyopathy. Her thesis research involves sequencing and haplotyping clinically relevant genes in cardiac disease and using that information to design allele-specific, precision therapeutics.

Recent publications

Dainis, A.M. Cardiovascular precision medicine in the genomics era. JACC: Basic to Translational Science, 3, 313-326 (2018)

High Coverage, Ultra-long Read Sequencing

How MinION sequencing is helping us solve real-life environmental biotechnology issues

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Human genome sequencing on PromethION

Human genome sequencing on PromethION to investigate tandem repeats in dementia

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Arne De Roeck is a PhD student in the Neurodegenerative Brain Diseases Group at the Center for Molecular Neurology (CMN), VIB – University of Antwerp, led by Prof. dr. Christine Van Broeckhoven. CMN has several decades of expertise in genetics of dementia and has been part of the Oxford Nanopore Technologies adventure from the beginning. In 2018, CMN sequenced several human whole genomes on PromethION, achieving some of the first and highest yield sequencing runs in the field.

Improving MinION read accuracy to enable the high-throughput analysis of single cell transcriptomes.

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Chris Vollmers graduated with a M.S. in Biomedical Sciences from the University of Wuerzburg in Germany before pursuing a Ph.D. through a shared program between the University of Heidelberg in Germany and the Salk Institute for Biological Studies in La Jolla, California. He then joined the lab of Stephen Quake at Stanford University as a postdoctoral fellow and worked on developing genomic tools to analyze B cells on population and single cell levels. He now continues this work in his own lab in the Biomolecular Engineering Department at UCSC since 2014.

Recent publications

Byrne, A. et al. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nature Communications 8, (2017)

Insights into vancomycin-resistant enterococci outbreaks through short- and long-read sequencing

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Interactive exploration of base calls in nanopore data

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Matthew Links is an Assistant Professor in the Department of Animal and Poultry Science and an associate member of the Computer Science Department at the University of Saskatchewan. His interests in the microbiome have involved numerous contexts: enhanced oil recovery, the rhizosphere, infectious diseases as well as plant and animal health. In these settings Dr. Links’ work has demonstrated that cpn60 is a robust DNA barcode that can be used in microbial profiling studies and provides significant advantages over other genes commonly used for microbial profiling. Recent work has resulted in a novel enrichment technique for microbial profiling (Capture-Seq) that eliminates the need for universal PCR and dramatically reduces the amount of shotgun sequencing data required to gain quantitative information about microbiota from any ecological niche. Matthew’s current work with nanopore sequencing is focused on allowing researchers to interrogate the signal data directly. A key goal of his work is to enable visualization of signal event data in a way that allows a researcher to assess whether a base call was in error, whether the sample was actually from a mixed sample, or represents a heterozygote.

Recent publications

Albert, A. Y. K. et al. A study of the vaginal microbiome in healthy Canadian women utilizing cpn60-based molecular profiling reveals distinct Gardnerella subgroup community state types. PLoS ONE 10, (2015).

Links, M. G. et al. Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytologist 202, 542–553 (2014).

Links, M. G., Chaban, B., Hemmingsen, S. M., Muirhead, K. & Hill, J. E. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences. Microbiome 1, 23 (2013).

Links, M. G., Dumonceaux, T. J., Hemmingsen, S. M. & Hill, J. E. The Chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE 7, (2012).

Jennifer Gardy

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Dr. Jennifer Gardy is a Senior Scientist at the British Columbia Centre for Disease Control, and holds the Canada Research Chair in Public Health Genomics at the University of British Columbia. Her team pioneered the genomic epidemiology approach to infectious disease outbreak investigation. Her work continues to focus on how genomics can impact communicable disease prevention and control, particularly in the areas of tuberculosis, as well as vaccine-preventable childhood diseases. Jennifer is a member of the National Academies of Science, Engineering, and Medicine’s Forum on Microbial Threats, and a scientific advisor to uBiome and Animalbiome. When not tracking microbes, Jennifer works in science communication - she is a regular science documentary presenter on Canadian national television, and wrote a children’s book about microbes called “It’s Catching: the Infectious World of Germs and Microbes”.

Recent publications

Crisan, A., McKee, G., Munzner, T. & Gardy, J. L. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory. PeerJ 2018, (2018)

Gardy, J. L. & Loman, N. J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nature reviews. Genetics 19, 9–20 (2018)

Guthrie, J. L. et al. Molecular Epidemiology of Tuberculosis in British Columbia, Canada - A 10-Year Retrospective Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America (2017). doi:10.1093/cid/cix906

Gardy, J. L. (2017) ‘Mycobacterium chimaera: unraveling a mystery through genomics’, The Lancet Infectious Diseases, pp. 1004–1005. doi: 10.1016/S1473-3099(17)30356-0

Didelot, X. et al. (2017) ‘Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks’, Molecular Biology and Evolution, 34(4), pp. 997–1007. doi: 10.1093/molbev/msw275

Know your onion - the impact of long reads on large genomes

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Richard Finkers graduated in plant breeding working on the identification of loci contributing to resistance to Botrytis cinerea in the tomato. He now leads a research group which focuses on genomics approaches and big data strategies to improve breeding research. The genomics approach mainly seeks to understand the structure and genetic diversity in large and complex crops, for example the development of methodologies to phase sequence reads in the onion (16Gb diploid outbreeding crop) and the four expected phases in the potato (autotetraploid outbreeding crop). Research in big data focuses on strategies to make heterogeneous types of research data FAIR (findable, accessible, interoperable and re-usable) and as input for novel strategies to develop the crops needed for the future.

Where genomics approaches are bridged with phenomics

Recent publications

Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3, 160018 (2016)

Aflitos, S. et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal 80, 136–148 (2014)

Motazedi, E., Finkers, R., Maliepaard, C. & de Ridder, D. Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study. Briefings in Bioinformatics bbw126 (2017). doi:10.1093/bib/bbw126

LOGAN: Lossless graph-based analysis of NGS datasets

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Making infection control in hospitals smarter using nanopore sequencing

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Dr. Nagarajan is Associate Director and Senior Group Leader in the Genome Institute of Singapore, and Adjunct Associate Professor in the Department of Computer Science at the National University of Singapore. His research focuses on developing cutting edge genome analytical tools and using them to study the role of microbial communities in human health. His team conducts research at the interface of genetics, computer science and microbiology, in particular using a systems biology approach to understand host-microbiome-pathogen interactions in various disease conditions. Dr. Nagarajan received a B.A. in Computer Science and Mathematics from Ohio Wesleyan University in 2000, and a Ph.D. in Computer Science from Cornell University in 2006, advised by Prof. Uri Keich. He did his postdoctoral work in the Center for Bioinformatics and Computational Biology at the University of Maryland working on problems in genome assembly and metagenomics with Prof. Mihai Pop.

Mapping multi-contact chromatin interactions on the MinION

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Dr. de Ridder is Principle Investigator / Associate professor in Bioinformatics. His lab specializes in creating novel computational strategies and algorithms that transform, normalize, integrate and mine large volumes of data. Much of his research floats on machine learning approaches. His recent work has focussed on computational approaches to map chromatin interactions using long-read sequencing platforms.

Recent publications

Allahyar, A. et al. Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies. bioRxiv 206094 (2017). doi:10.1101/206094

Matt Loose

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Dr Matt Loose is based at the School of Life Sciences, University of Nottingham. A developmental biologist and bioinformatician, he also heads up DeepSeq, the University of Nottingham next-generation sequencing service. The DeepSeq lab is equipped with MinION, GridION and now PromethION. DeepSeq actively encouraged Nottingham Academics to apply to join the Nanopore Community and, in return, supported participants with both library prep and bioinformatics, and led to the development of tools including MinoTour and also working on Read Until. Matt was initially interested in the generation of long-reads to sequence novel genomes alongside real-time analysis of MinION data. To that end, he recently co-led with Prof Nick Loman the sequencing and assembly of the first reference human genome on the MinION. DeepSeq also have a small urn in their possession, although perhaps not for much longer.

Recent publications

Jain, M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 36(4) 338-345 (2018) doi: 10.1038/nbt.4060

Loose, M. W. The potential impact of nanopore sequencing on human genetics. Human Molecular Genetics 26, R202–R207 (2017)

Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature Protocols 12, 1261–1266 (2017).

Faria, N. R. et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546, 406–410 (2017)

Votintseva, A. A. et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. Journal of Clinical Microbiology 55, 1285–1298 (2017)

Jain, M. et al. MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000Research 6, 760 (2017)

Loose, M., Malla, S. & Stout, M. Real-time selective sequencing using nanopore technology. Nature Methods 13, 751–754 (2016)

Ip, C. L. C. et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research (2015) doi:10.12688/f1000research.7201.1

Measuring the transcriptome of the C. elegans lifecycle using direct RNA sequencing

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Nathan Roach is a PhD candidate in the labs of James Taylor and John Kim at Johns Hopkins University in the Cellular Molecular and Developmental Biology department.

Metagenomic nanopore sequencing: RNA viruses from lab to field

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MinION in the marine environment: from identifying tetrodotoxin producers to tracing sharks and rays using eDNA

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Reindert Nijland is an Assistant Professor at the Marine Animal Ecology group at Wageningen University, Netherlands. Since obtaining his PhD in molecular microbiology at University of Groningen, Netherlands, he has studied the interaction of bacteria with a diversity of hosts. At the Dove Marine Laboratory, Newcastle University, UK, he worked on biofilms of marine Bacillus species isolated from seaweed. After returning to the Netherlands, he studied bacterial pathogens and their interactions with the human and bovine immune systems at UMC Utrecht. In 2014, he again switched host organism, and joined Wageningen University to study the interactions of bacterial pathogens with their plant hosts. Reindert has a strong passion for marine biology, especially crabs. He enjoys scuba diving, underwater photography and underwater filming. In 2017, he could no longer resist the attraction of the marine environment, and joined the Marine Animal Ecology group. His current focus is on the interaction between marine hosts and their microbes. He developed approaches to identify microbial toxin gene clusters in shellfish. He also works on the development of methods for rapid on-site identification of eukaryotes such as crabs, fish and marine mammals by analysing environmental DNA (eDNA) using nanopore sequencing with the MinION.

Multi-contact chromosome conformation capture using nanopore sequencing in nematodes

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Peter Meister completed his PhD in Molecular and Cellular Genetics at Institut Curie/University of Paris before completing a post-doc at the Friedrich Miescher Institute in Basel. Since 2011 he has been group leader of the Cell Fate and Nuclear Organization Laboratory at University of Bern.

Nanopore sequencing in clinical diagnostics

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Graham Taylor was Head of the Regional Genetics Laboratory in Leeds with a long-standing interest in translating genomic technology into diagnostics. In 2006 he led a UK Department of Health Funded project “New genetic diagnostic technologies for consanguineous families at risk of recessive genetic disease” and moved to Cancer Research UK as Director of Genomic Services, where he led an evaluation of next-generation sequencing technology.

In 2009, as Head of the Genomics Translation Unit in Leeds, his team developed methods for diagnostic amplicon sequencing in fixed tissue, copy number variation analysis and streamlined conventional genetic testing using next-generation sequencing. In 2012 he joined the Department of Pathology at Melbourne University as the Herman Professor of Genomic Medicine, Director of the Australian Node of the Human Variome Project and Director of the Victorian Clinical Genetics Laboratories, helping to accredit both laboratories for exome-based clinical diagnostics.

From February 2016 he took up the post of Scientific Director of Clinical Genomics with ViaPath at Guy’s & St. Thomas’s Teaching Hospitals in London. Current research interests are around applications of long sequencing read technology in genetic diagnosis.

Nanopore sequencing in veterinary virology: from clinical sample to whole genome

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Guillaume completed a PhD in 2017 on the detection and characterization of respiratory pathogens using high-throughput PCR and next-generation sequencing methods. In November 2017 he joined the Chair of Biosecurity at the Veterinary School in Toulouse as an engineer in charge of the Clinical Diagnostics lab and development of new molecular tools for the detection and characterization of viral genomes.

Nanopore sequencing of cancer genomes

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Dr. Wigard Kloosterman is Group Leader and Associate Professor at the Department of Genetics within the Center for Molecular Medicine at the University Medical Center Utrecht in The Netherlands. The Kloosterman group has strong expertise in cancer genomics, bioinformatics and nanopore sequencing technology. Dr Kloosterman received a PhD from Utrecht University.

Nanopore sequencing of full-length 16S rRNA gene in low-biomass samples: subclinical mastitis in water buffalo

Nanopore sequencing permits de novo assembly of repetitive microbial genomes

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Nanopore sequencing-based diagnostics of bacteremia in septic patients

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NanoSV

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Jose Espejo Valle-Inclan is a PhD student in the group of Wigard Kloosterman at the University Medical Center in Utrecht, Netherlands. His research centres on cancer genomics, particularly on ovarian cancer and focusing on the role and detection of structural variation. He holds a BSc in Biochemistry from the Autonomous University of Madrid, Spain and an MSc in Bioinformatics from the Wageningen University, Netherlands.

Native RNA sequencing of human polyadenylated transcripts

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Angela Brooks is an Assistant Professor of Biomolecular Engineering at UC Santa Cruz. Her research group focuses on identifying cancer genome alterations that disrupt gene regulation, particularly through RNA splicing. Angela has expertise in transcriptome sequencing analysis, cancer genomics, functional genomics, and bioinformatics. She received her Ph.D. from UC Berkeley and was a post-doctoral fellow at the Dana-Farber Cancer Institute and the Broad Institute.

On-site nanopore sequencing of Darwin's finch genomes in the Galapagos

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Phasing regulatory SNVs to their regulating transcript regions in cancers by using MinION

Pilon

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Bruce Walker is Vice President of Technology at Applied Invention, as well as Visiting Scientist at the Broad Institute of MIT & Harvard, where he previously worked for over 10 years as Director of IT and Director of Genome Assembly and Analysis. Bruce holds a B.Sc. in Physics from MIT, and has spent most of his career developing scalable, high-performance computing architectures and algorithms.

Point of care Mycobacterium tuberculosis whole genome sequencing in remote rural Madagascar

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Simon Grandjean Lapierre is a trained infectious diseases specialist and medical microbiology physician with previous clinical, laboratory and infection control experience in sub-Saharan African countries. He holds post-doctoral graduate degrees in global health and molecular diagnostics applied mycobacterial diseases. He currently works as a clinical lecturer in Centre Hospitalier de l'Université de Montréal in Canada, and coordinates the tuberculosis research program of Stony Brook University in Madagascar. His research activities focus on the implementation of new point of care and highly fieldable technologies for tuberculosis control.

Niaina Rakotosamimanana is a microbiologist and lab director of the Mycobacterial Unit of the Pasteur Institute of Madagascar in charge of the tuberculosis research program. This includes operational research that evaluates new TB diagnostic tools and drug resistance surveys in collaboration with the National Tuberculosis Control Program (NTCP) of the Malagasy Ministry of Public Health. He is in the steering committee of the international network for data analysis that aims to coordinate NGS data handling and NGS capacity building inside the Pasteur Institute international network that is present in 33 countries worldwide.

PromethION sequencing of complex plant genomes

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PromethION: an alpha machine in production

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Andreas Hauser is a Staff Scientist, for the Laboratory for Functional Genome Analysis, at Gene Center Munich, LMU. He is also an entrepreneur.

Recent publications

Remmert, M., Biegert, A., Hauser, A. & Söding, J. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 9, 173–175 (2012).

Greif, P. A. et al. Somatic mutations in acute promyelocytic leukemia (APL) identified by exome sequencing. Leukemia 25, 1519–1522 (2011) doi: 10.1038/leu.2011.114.

PromethION: Unleash the power of nanopore sequencing

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Helmut Blum heads the Genomics group in the Laboratory for Functional Genome Analyses at the Gene Center of the Ludwig-Maximilians-University of Munich. This group operates a technology platform for short and long-read sequencing and bioinformatic analysis. The platform provides a variety of library preparation methods and comprehensive sequencing for their own scientific projects and various collaborations in the field of life sciences. Currently the group extends its field of action towards high-output long-read sequencing with the PromethION sequencer.

Rapid bacterial identification from clinical samples using nanopore sequencing

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Jangsup Moon, MD, PhD is a neurologist interested in metagenomic pathogen detection using nanopore sequencing. He received his MD in 2005 and finished his Neurology residency training at Seoul National University Hospital in 2013. He received his PhD in Neuroscience at the College of Medicine, Seoul National University School in 2015. He is currently working as an Assistant Professor in the Department of Neurosurgery and Neurology at Seoul National University Hospital.

Recent publications

Moon, J. et al. Campylobacter fetus meningitis confirmed by a 16S rRNA gene analysis using the MinION nanopore sequencer, South Korea, 2016. Emerging Microbes and Infections 6,(2017)

Real-time selective sequencing with RUBRIC

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Redefining the Arabidopsis thaliana transcriptome with DRS sequencing

Resistome accumulation induced by discharge of treated domestic wastewater - an overlooked aspect of modern wastewater treatment

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Yu Xia is Assistant Professor of Southern University of Science and Technology (SUSTech), and received her PhD from the University of Hong Kong. Her research interest focuses on utilizing nanopore sequencing to understand the community ecology and functional synergy among microbes that are crucial for biological wastewater treatment or important for nature material cycles. The topics she currently works on include: environmental dissemination of antibiotic resistance genes (ARGs); direct interspecies electron transfer (DIET) capable microbes in anaerobic sludge digestion; sulfate/nitrate reduction mediated anaerobic methane oxidation (AOM) in coastal sediment. Additionally, she has served as the Young Ambassador of Hong Kong region for American Society for Microbiology (ASM) and the General Secretary for the Postgraduate Student Association (PGSA) of the University of Hong Kong.

Sequencing everything with PromethION

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Sally is a Technical Specialist in Genomics for the University of York’s Bioscience Technology Facility. She completed her PhD in medical science at the University of Birmingham in 2008, and held post-doctoral positions studying stem cell biology and gene regulation at the University of Leeds, and then the University of York. She plays a key role in providing next-generation sequencing services and solutions to users within the University and further afield, and was an early adopter of nanopore sequencing technologies.

Shaking up the short reads - using MinION sequencing to enhance an outbreak investigation

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Hayley Wilson is a post-doctoral research associate for Dr Estée Török in her newly established research group at the University of Cambridge. She completed her PhD in 2016 under the supervision of Professor Sharon Peacock, also at the University of Cambridge. She is currently working on investigating the carriage, transmission and infection of multidrug-resistant bacteria in various patient groups at the Cambridge University Hospitals NHS Foundation Trust. Her work utilises genomic techniques to provide high resolution data in investigating these pathogens and has recently begun working with long-read data produced by the Oxford Nanopore MinION.

Simultaneous methylation and chromatin accessibility profiling on breast cancer models

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Isac Lee is a PhD student in the department of Biomedical Engineering at Johns Hopkins School of Medicine. He is being trained in the lab of Dr. Winston Timp, studying the epigenome and genome of cancer. He is interested in epigenomic reprogramming and its association with gene expression and genomic aberrations during cancer progression. He is working on integrating and developing genomic and epigenomic methodologies, and applying them on cancer models and clinical samples.

Single cell transcriptome sequencing with the 10x Genomics Chromium and the MinION

Soup and nuts: nanopore applications

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Dan Turner is Vice President of Applications at Oxford Nanopore Technologies and is a highly experienced scientist who has worked in the field of next-generation sequencing for the last 11 years. Dan provides scientific leadership for multi-disciplinary teams in Oxford, New York and San Francisco. The Applications group aims to bring together sample prep technologies, genomics applications and bioinformatics, to expand the utility of Oxford Nanopore Technologies devices and illustrate the benefits of these technologies to the wider world.

Before joining Oxford Nanopore Technologies, Dan was Head of Sequencing Technology Development at the Wellcome Trust Sanger Institute, and prior to this he held postdoctoral positions at the Sanger Institute and Cornell University Medical College in Manhattan.

The beauty and the beast

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Hans Jansen is CTO at Future Genomics Technologies based in Leiden in the Netherlands. A molecular biologist with broad experience, his focus has been on the use of next generation sequencing and bioinformatics for genome assembly and transcriptome analysis. As CTO he is responsible for the translation of academic knowledge and novel technologies into usable applications, providing early and easy access to these applications.

Leading the implementation of the MinION at ZF screens, he has been a member of the MARC consortium since it started in 2014. This group was formed to provide independent evaluation of the platform, pool data and analysis techniques, and exchange ideas for how to improve the sequencing protocol or bioinformatic processing.

Having used the MinION, GridION X5, and PromethION in their various genome projects, Hans has a wealth of experience in using the growing number of tools available for nanopore reads, and all from a biologists view point.

The complex architecture of plant T-DNA transgene insertions

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Dr. Todd Michael is Professor and Director of Informatics at the J. Craig Venter Institute (JCVI) in San Diego, CA USA. At JCVI, Dr. Michael’s group builds genome sequencing, editing and analysis tools with a specific focus on developing synthetic plants. Current projects include sequencing minimal and specialized plant genomes, computationally designing a minimal plant genome, booting-up plant artificial chromosomes, and leveraging nanopore sequencing for complete genomes and epigenomic analysis.

Recent publications

Jupe, F. et al. The complex architecture of plant transgene insertions. bioRxiv 282772 (2018). doi:10.1101/282772

Michael, T. P. et al. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications 9, (2018).

The detection of 7-deazaguanine in both RNA and DNA using MinION: progress towards studying the function of G-quadruplexes

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Dr Carika Weldon is a lecturer in Biomedical Science at De Montfort University in Leicester. Prior to joining the faculty as the youngest lecturer in the university’s history, she obtained her BSc (Hons) Medical Biochemistry in 2011 and her PhD in Biochemistry in 2015 from the University of Leicester.

Dr Weldon’s doctoral work focused on alternative splicing of the apoptotic gene Bcl-X. By creating the new FOLDeR method, she discovered that G-quadruplexes shifts the XS/XL ratio to favour the pro-apoptotic XS isoform. By screening over 30 G-quadruplex ligands, her work identified a suitable drug that could be used for treating cancers, based on its ability to shift the ratio almost 40-fold. In her own lab now she looks at how the presence of G-quadruplexes in pre-mRNA can influence alternative splicing in other genes. She is utilizing the versatile technique of nanopore technology to detect modified guanine with the hopes of gaining more insight into the exciting fields of splicing and G-quadruplexes.

Recent publications

Weldon, C. et al. Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X. Nucleic Acids Research (2017). doi:10.1093/nar/gkx1122

Weldon, C. et al. Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA. Nature Chemical Biology 13, 18–20 (2017).

Tombo: detection of non-standard nucleotides using raw nanopore signal

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Michael’s graduate and postdoctoral work at Portland State University and Oregon Health Sciences University focused on the biology of gene expression and regulation. Michael then worked as a senior scientific specialist for a leading next-generation sequencing company. He joined Oxford Nanopore Technologies in September 2014 as Technical Applications Manager. He is currently responsible for overseeing US technical support operations.

Tracking movement and evolution of antibiotic resistance plasmids in a hospital over a decade

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TractION LIMS

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Understanding transmission dynamics of TB and AMR in the farmland environment

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Dr Robert James is currently working as a post-doctoral research fellow with Prof. E. Wellington as lead investigator on the BBSRC funded project; “Mycobacterium bovis and the farmland ecosystem: understanding transmission dynamics between animals and the environment.” This collaborative project between the University of Warwick, the Zoological society of London and Imperial College, aims to identify the environmental reservoirs of infection in agricultural land use types, and routes of transmission between mammalian hosts and the environment. Furthermore, Robert has an interest in the evolution and selection of antimicrobial resistance genes in the environment and has recently undertaken work to quantify AMR gene abundances in farmland and residential areas of Karatchi, Pakistan.

Using MinKNOW to assess the quality of your run - The Duty Time Plot

VirION: Towards long-read viral metagenomics

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Ben Temperton spent 7 years as a professional software engineer before retraining as a marine microbiologist, gaining his PhD from Queens University Belfast. He spent two years as a postdoctoral scholar at Oregon State University with Prof. Steve Giovannoni using metagenomics and metaproteomics to understand the role of the SAR11 clade in global marine carbon biogeochemistry. During this time, he identified four new viruses infecting SAR11 as the most abundant viruses on Earth. Upon his return to the UK, he established the first UK environmental Single Cell Genomics Laboratory at Plymouth Marine Laboratory, before moving to the University of Exeter to set up his own research group studying marine viral ecology and the global impact of predator-prey interactions on carbon remineralisation.