Director, Bioinformatics

• Feb 2023 - Present

Associate Director, Bioinformatics

• Feb 2022 - Mar 2023

Team Leader of Bioinformatics Research

• May 2018 - Feb 2022

Principal Bioinformatics Scientist

• Oct 2017 - Apr 2018

Design, development and delivery of research initiatives that optimize the performance of the PELEUS™ bioinformatics platform. This platform guides the production of clonal neoantigen targeting T cells, a personalized therapy for advanced non-small-cell lung carcinoma and melanoma being evaluated in successive Phase I/II trials (NCT03517917; NCT03997474; NCT04032847). Projects include: * Complex mutation identification and validation * State-of-the-art clonality prediction *… Show more Design, development and delivery of research initiatives that optimize the performance of the PELEUS™ bioinformatics platform. This platform guides the production of clonal neoantigen targeting T cells, a personalized therapy for advanced non-small-cell lung carcinoma and melanoma being evaluated in successive Phase I/II trials (NCT03517917; NCT03997474; NCT04032847). Projects include: * Complex mutation identification and validation * State-of-the-art clonality prediction * Effective neoantigen ranking * Efficient neoantigen immunogenicity screening

Senior Research Scientist

• Dec 2016 - Sep 2017

Research Scientist

• Oct 2014 - Nov 2016

Discovery Science Group • Project manager and lead analyst in genomic and transcriptomics projects focusing on biomarker identification and patient stratification for four leading pharmaceutical companies. Techniques regularly applied include unsupervised and supervised machine learning techniques such as NMF and RF. Projects include: ◦ Robust reproducible pipelines for higher-order feature engineering from oncogenomic variant data (e.g. mutation signature activity & microsatellite… Show more Discovery Science Group • Project manager and lead analyst in genomic and transcriptomics projects focusing on biomarker identification and patient stratification for four leading pharmaceutical companies. Techniques regularly applied include unsupervised and supervised machine learning techniques such as NMF and RF. Projects include: ◦ Robust reproducible pipelines for higher-order feature engineering from oncogenomic variant data (e.g. mutation signature activity & microsatellite instability prediction), applied to complete TCGA and PDx consortium datasets. ◦ Development and benchmarking of Somatic Copy Number Analysis Strategies from second-generation sequencing data (whole exome sequencing and targeted panel) ◦ Development and benchmarking of scalable state-of-the-art RNA-seq pipelines ◦ Biomarker discovery and patient stratification in a multicenter Phase 2 clinical trial of an autoimmune disease treatment, focusing primarily on WES-derived MHC data.

Bioinformatician

• Dec 2011 - Oct 2014

Bioinformatics and Biostatistics Group • Analysis of large-scale tumour DNA sequencing projects, including primary (e.g. alignment, quality control), secondary (e.g. SNV, indel, SCNA & SV calling) and tertiary analyses (e.g. estimation of phylogeny and clonality). Projects included: ◦ Comprehensive genomic characterisation of patient-derived Acute Myeloid Leukemia xenograft models by whole genome sequencing ◦ Characterisation of intra-tumour heterogeneity by multi-region whole exome… Show more Bioinformatics and Biostatistics Group • Analysis of large-scale tumour DNA sequencing projects, including primary (e.g. alignment, quality control), secondary (e.g. SNV, indel, SCNA & SV calling) and tertiary analyses (e.g. estimation of phylogeny and clonality). Projects included: ◦ Comprehensive genomic characterisation of patient-derived Acute Myeloid Leukemia xenograft models by whole genome sequencing ◦ Characterisation of intra-tumour heterogeneity by multi-region whole exome sequencing in five projects, focusing primarily on chromosomal copy-number aberrations ◦ Collaborator in the multidisciplinary, nationwide TracerX project, a longitudinal study of lung tumour evolution (https://www.nature.com/collections/haffgaicaf) • Regular consultation on experimental design • Developed various bioinformatics tools, including: ◦ A package to identify false positive mutations in sequencing data ◦ A pipeline to detect retrotransposon integration sites in sequencing data ◦ An approach to identify allelic imbalance in sequencing and/or array data Show less Bioinformatics and Biostatistics Group • Analysis of large-scale tumour DNA sequencing projects, including primary (e.g. alignment, quality control), secondary (e.g. SNV, indel, SCNA & SV calling) and tertiary analyses (e.g. estimation of phylogeny and clonality). Projects included: ◦ Comprehensive genomic characterisation of patient-derived Acute Myeloid Leukemia xenograft models by whole genome sequencing ◦ Characterisation of intra-tumour heterogeneity by multi-region whole exome… Show more Bioinformatics and Biostatistics Group • Analysis of large-scale tumour DNA sequencing projects, including primary (e.g. alignment, quality control), secondary (e.g. SNV, indel, SCNA & SV calling) and tertiary analyses (e.g. estimation of phylogeny and clonality). Projects included: ◦ Comprehensive genomic characterisation of patient-derived Acute Myeloid Leukemia xenograft models by whole genome sequencing ◦ Characterisation of intra-tumour heterogeneity by multi-region whole exome sequencing in five projects, focusing primarily on chromosomal copy-number aberrations ◦ Collaborator in the multidisciplinary, nationwide TracerX project, a longitudinal study of lung tumour evolution (https://www.nature.com/collections/haffgaicaf) • Regular consultation on experimental design • Developed various bioinformatics tools, including: ◦ A package to identify false positive mutations in sequencing data ◦ A pipeline to detect retrotransposon integration sites in sequencing data ◦ An approach to identify allelic imbalance in sequencing and/or array data Show less

Postdoctoral Researcher

• Nov 2009 - Nov 2011

Cardiovascular Genomics Group • Design, implementation and analysis of a cardiovascular disease linkage & association project based on STR/SNP data • Advanced sequence analysis to identify inversion-mediated breakpoints in repetitive complex segmental duplications, coupled with iterative in vitro breakpoint validation • Characterised population genetic and phylogenetic attributes of a polymorphic inversion using large public datasets (e.g. 1000 genome project) Cardiovascular Genomics Group • Design, implementation and analysis of a cardiovascular disease linkage & association project based on STR/SNP data • Advanced sequence analysis to identify inversion-mediated breakpoints in repetitive complex segmental duplications, coupled with iterative in vitro breakpoint validation • Characterised population genetic and phylogenetic attributes of a polymorphic inversion using large public datasets (e.g. 1000 genome project)

Research Assistant

• Jan 2003 - Sep 2005

Audiovestibular Genomics Group • Investigated age-related hearing loss in mouse models. Projects included: ◦ STR-based linkage analysis and candidate gene Sanger sequencing ◦ Establishing a mutagenesis screen, ensuring strict compliance with the Animals (Scientific Procedures) Act as a Personal Licence holder ◦ Managing two team members at all stages of the project ◦ Supporting construction of a dual recombinase-based gene-targeting vector ◦ Training two junior doctors in… Show more Audiovestibular Genomics Group • Investigated age-related hearing loss in mouse models. Projects included: ◦ STR-based linkage analysis and candidate gene Sanger sequencing ◦ Establishing a mutagenesis screen, ensuring strict compliance with the Animals (Scientific Procedures) Act as a Personal Licence holder ◦ Managing two team members at all stages of the project ◦ Supporting construction of a dual recombinase-based gene-targeting vector ◦ Training two junior doctors in basic molecular biology techniques Show less Audiovestibular Genomics Group • Investigated age-related hearing loss in mouse models. Projects included: ◦ STR-based linkage analysis and candidate gene Sanger sequencing ◦ Establishing a mutagenesis screen, ensuring strict compliance with the Animals (Scientific Procedures) Act as a Personal Licence holder ◦ Managing two team members at all stages of the project ◦ Supporting construction of a dual recombinase-based gene-targeting vector ◦ Training two junior doctors in… Show more Audiovestibular Genomics Group • Investigated age-related hearing loss in mouse models. Projects included: ◦ STR-based linkage analysis and candidate gene Sanger sequencing ◦ Establishing a mutagenesis screen, ensuring strict compliance with the Animals (Scientific Procedures) Act as a Personal Licence holder ◦ Managing two team members at all stages of the project ◦ Supporting construction of a dual recombinase-based gene-targeting vector ◦ Training two junior doctors in basic molecular biology techniques Show less