Matthieu Miossec
PhD
Bioinformatics analyst @ Bioinformatics Core
Bioinformatics Core
Member of the Wellcome Centre's Bioinformatics Core since September 2020 with a full decade of bioinformatics and programming experience which encompasses whole-exome sequencing (particularly in relation to congenital heart disease), metagenomics and a recent growing amount of RNA sequencing. Happy to help with all your bioinformatics and Python-related queries in your language of choice: English, French or Spanish. I also provide teaching and training in whole exome/genome sequencing topics, Python and WDL, with plans to expand into machine learning.
I have some recent experience performing genomics in the cloud, using Google Cloud and the Broad Institute's genomics platform Terra. I have adopted the platform's workflow language of choice, WDL, for both cloud and HPC work. In 2018, I collaborated with the GATK dev team on a case study based on previous PhD/RA work which can be found here: reproducibility case study on Terra (see also chapter 14 of Genomics in the Cloud by Geraldine Van der Auwera & Brian O'Connor).
I am currently exploring metabolomics and machine learning. Happy to start receiving questions about either.
BACKGROUND
I earned a BSc in Computer Science from Durham University and an MSc in Bioinformatics and Computational Systems Biology from the University of Newcastle-Upon-Tyne. With support from the British Heart Foundation, I formally entered the field of genomic medicine in 2012, working at the Institute of Genetic Medicine in Newcastle, where I earned my PhD in 2016. My main focus was uncovering rare genetic variants predisposing to congenital heart diseases, such as Tetralogy of Fallot, using whole-exome sequencing data. After briefly working as a research associate at the Institute, I moved to Chile and joined the Centre for Bioinformatics and Integrative Biology (CBIB) where I delved into the world of metagenomics. During this time, I developed a growing passion for machine learning and gained a MOOC certificate on the subject.
Key publications
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Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot
Journal article
Page DJ. et al, (2019), Circulation Research, 124, 553 - 563
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Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells
Journal article
Groelly FJ. et al, (2022), Molecular Cell, 82, 3382 - 3397.e7
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Evaluation of computational methods for human microbiome analysis using simulated data
Journal article
Miossec MJ. et al, (2020), PeerJ, 8, e9688 - e9688
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Computational Methods for Human Microbiome Analysis
Journal article
Miossec MJ. et al, (2017), Current Protocols in Microbiology, 47
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Integration of target discovery, drug discovery and drug delivery: A review on computational strategies
Journal article
Duarte Y. et al, (2019), WIREs Nanomedicine and Nanobiotechnology, 11
Recent publications
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Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells
Journal article
Groelly FJ. et al, (2022), Molecular Cell, 82, 3382 - 3397.e7
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Evaluation of computational methods for human microbiome analysis using simulated data
Journal article
Miossec MJ. et al, (2020), PeerJ, 8, e9688 - e9688
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Scientific Business Abstracts of the 113th Annual Meeting of the Association of Physicians of Great Britain and Ireland
Journal article
Cacciottolo TM. et al, (2019), QJM: An International Journal of Medicine, 112, 724 - 729
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Integration of target discovery, drug discovery and drug delivery: A review on computational strategies
Journal article
Duarte Y. et al, (2019), WIREs Nanomedicine and Nanobiotechnology, 11
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In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential
Journal article
Orellana-Saez M. et al, (2019), Frontiers in Microbiology, 10