Graham D Rose

PhD educated bioinformatics scientist with over ten year’s experience in high-throughput sequencing from doctoral training, research, and government level positions, including Imperial College Healthcare NHS Trust, Wellcome Trust Sanger Institute and Public Health England, providing a wide analytical and applied skill set in the genomics space, coupled to a strong molecular biology training.

Current

I am currently based within the GOSH Bioinformatics group at Great Ormond Street Hospital for Children NHS Foundation Trust, which is the lead centre for the North Thames Genomic Labortory Hub. Initially funded through Genomics England, this now permanent role involves software development, analysis and management skill sets for the high-throughput sequencing data generated as part of routine diagnostic service, and previously the 100,000 genomes project.

Employment

09.2019-present Great Ormond Street Hospital Permanent bioinformatician within the diagnostic bioinfomatics team, combining the development and maintenance of a suite of bespoke web based applications and analytical pipelines, and to facilitate Clinical Scientists and researchers within interogating genomic datasets.

04.2019-04.2019 Springer Nature Freelance Scientific Editor, taking on the developmental editing of research articles and reports.

04.2019-09.2019 Great Ormond Street Hospital Contract bioinformatician role to help develop and maintain a software management tool for handling clinical data retrieved from Genomics England as part of the 100,000 genomes project. As well as wider integration across the Bioinformatics group software projects.

10.2018-04.2019 Great Ormond Street Hospital Honorary bioinformatician role involving a collaboration to build on a bioinformatics management tool for handling clinical data retrieved from Genomics England as part of the 100,000 genomes project.

05.2018-present Imperial College London Honorary research fellow within the National Heart Lung Institute, providing bioinformatics support for several rare disease datasets generated as part of the 100,000 genomes project.

01.2018-04.2019 Imperial College Healthcare NHS Trust Bioinformatics scientist working on the 100,000 Genomes Project, and part of the West London Genomic Medicine Centre (GMC).

04.2016-04.2018 Faculty of Genomic Medicine, Queen Mary University London Visiting lecturer, responsible for delivering part of the HEE MSc in Genomic Medicine ‘Application of Genomics in Infectious Disease’ module.

07.2014-01.2018 Public Health England Computational Biologist role, responsible for building and delivering genomic and metagenomic research and development projects using a range of NGS platforms.

09.2013-07.2014 The Pirbright Institute Characterising terabase-scale sequence data from the transcriptome of Anopheles gambiae, as part of the Vector Molecular Biology group

02.2008-07.2009 Wellcome Trust Sanger Institute Finishing and comparative analysis within the Pathogen Genomics group, including Clostridium difficile and Mycobacterium tuberculosis.

Education

09.2009-06.2013 MRC National Institute of Medical Research Pathogen Genomics PhD (supervisors: Prof. Douglas Young and Prof. Sebastein Gagneux). My thesis was entitled A genomic and transcriptomic study of lineage-specific variation in Mycobacterium tuberculosis, available via UCL Senate House

09.2006-08.2007 University of Leeds MRes Bioinformatics and Computational Biology (Distinction)

09.2003-06.2006 University of Leeds BSc Microbiology (Hons) 2.1

Presentations

National

2017 Microbiology Society event: Microbiome session at Porton Down, “Challenges of the Unknown”

2016 Illumina User General Meeting: Invited scientific talk session, “The preterm infant gut microbiome”

Publications

2017 Complete Genome Sequences of BK Polyomavirus Strains from Two Patients with Urinary Tract Infection, Sequenced Using the Ion Torrent Platform. G. Rose, K. Ranellou, R. Misra, C. Crump, D. Wooldridge, S. Parmar, C. Maddren, S. Gharbia, H. Jalal. Genome Announcements. 2017

The Challenges of Identifying Mycobacterium to the Species Level using MALDI‐TOF MS G. Rose, R. Culak, T. Chambers, S. E. Gharbia, H. N. Shah, Y. Kim, JS. Kim. MALDI‐TOF and Tandem MS for Clinical Microbiology. 2017.

Antibiotic resistance potential of the healthy preterm infant gut microbiome. G. Rose, A. G. Shaw, K. Sim, D. J. Wooldridge, M. Li, S. Gharbia, R. Misra, J. S. Kroll. PeerJ. 2017.

2016 Dosage compensation in the African malaria mosquito Anopheles gambiae. G. Rose, E. Krzywinska, J. Kim, L. Revuelta, L. Ferretti, and J. Krzywinski. Genome Biology and Evolution. 2016.

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. ET Mee, MD Preston, PD Minor, S Schepelmann; CS533 Study Participants. Vaccine. 2016.

2015 Genomic diversity of BK polyomavirus in East of England–Preliminary data. K Ranellou, C Crump, R Misra, D Wooldridge, G Rose, S Gharbia, S Parmar, M Curran, N Verlander, H Zhang, H Jalal. Journal of Clinical Virology. 2015.

Challenges of the Unknown: Clinical Application of Microbial Metagenomics. G. Rose, D. J. Wooldridge, C. Anscombe, E. T. Mee, R. V. Misra, and S. Gharbia. International Journal of Genomics. 2015.

Complete genome sequence of the hypervirulent bacterium Clostridium difficile strain G46, ribotype 027. T. Gaulton, R. Misra, G. Rose, P. Baybayan, R. Hall, J. Freeman, J. Turton, S. Picton, J. Korlach, S. Gharbia, and H. Shah. Genome Announcements. 2015.

2013 A genomic and transcriptomic study of lineage-specific variation in Mycobacterium tuberculosis. GD. Rose. University College London. 2013.

Mapping of Genotype-Phenotype Diversity among Clinical Isolates of Mycobacterium tuberculosis by Sequence-Based Transcriptional Profiling. G. Rose, T. Cortes, I. Comas, M. Coscolla, S. Gagneux, and D. B. Young. Genome Biology and Evolution. 2013.

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis. T. Cortes, O. T. Schubert, G. Rose, K. B. Arnvig, I. Comas, R. Aebersold, and D. B. Young Cell Reports. 2013.

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis is Induced during Starvation and Infection. J. Houghton, T. Cortes, O. Schubert, G. Rose, A. Rodgers, M. De Ste Croix, R. Aebersold, D. B. Young, and K. B. Arnvig. PLoS ONE. 2013.

Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. M. Kato-Maeda, C. Ho, B. Passarelli, N. Banaei, J. Grinsdale, L. Flores, J. Anderson, M. Murray, G. Rose, L. M. Kawamura, N. Pourmand, M. a. Tariq, S. Gagneux, and P. C. Hopewell. PLoS One. 2013.

2012 The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis. B. Müller, S. Borrell, G. Rose, and S. Gagneux. Trends Genet. 2012.

2011 Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. I. Comas, S. Borrell, A. Roetzer, G. Rose, B. Malla, M. Kato-Maeda, J. Galagan, S. Niemann, and S. Gagneux. Nature Genetics 2011.

Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. K. B. Arnvig, I. Comas, N. R. Thomson, J. Houghton, H. I. Boshoff, N. J. Croucher, G. Rose, T. T. Perkins, J. Parkhill, G. Dougan, and D. B. Young. PLoS Pathogens. 2011.

Genotypic and phenotypic modifications of Neisseria meningitidis after an accidental human passage. H. Omer, G. Rose, K. a. Jolley, E. Frapy, J. R. Zahar, M. C. J. Maiden, S. D. Bentley, C. R. Tinsley, X. Nassif, and E. Bille. PLoS One. 2011.

2010 Evolutionary dynamics of Clostridium difficile over short and long time scales. M. He, M. Sebaihia, T. D. Lawley, R. A. Stabler, L. F. Dawson, M. J. Martin, K. E. Holt, H. M. B. Seth-Smith, M. a Quail, R. Rance, K. Brooks, C. Churcher, D. Harris, S. D. Bentley, C. Burrows, L. Clark, C. Corton, V. Murray, G. Rose, S. Thurston, A. van Tonder, D. Walker, B. W. Wren, G. Dougan, and J. Parkhill. PNAS. 2010.

2009 Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. R. A. Stabler, M. He, L. Dawson, M. Martin, E. Valiente, C. Corton, T. D. Lawley, M. Sebaihia, M. A. Quail, G. Rose, D. N. Gerding, M. Gibert, M. R. Popoff, J. Parkhill, G. Dougan, and B. W. Wren. Genome Biology. 2009.

Technical skills

Areas of expertise

Awards

Public Health England Pump Prime Funding (PPF) round 2017 (viral surveillance study)

MRC scholarship (PhD fees + stipend)

BBSRC postgraduate scholarship (MRes fees + stipend)