DeMontfort University, UK
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.
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).
University of New Hampshire
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.
BC Centre for Disease Control
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”.
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
University of Nottingham
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.
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