Lesley Gray Email and Phone Number

AGRF is a not-for-profit core genomics facility offering extraction, sequencing, genotyping and bioinformatics services to academic researchers, commercial genomics companies and clinical groups. The bioinformatics team service a wide range of industries and analysis types. As senior bioinformatician I have a key role in driving the growth and quality improvements of our pipeline implementations of common bioinformatics analysis, such as RNA-Seq, WGS and metagenomic diversity profiling. I have extensive experience with Illumina sequencing and genotyping arrays, as well as experience with sanger sequencing, nanopore and ion torrent data. I am responsible for conducting feasibilities and cost estimates for custom bioinformatics projects and large NGS experiments and also assist with preparation of contracts for new routine service agreements and commercial clients. Another part of my role is to contribute to internal I&D efforts, such as assessment of novel off-the-shelf bioinformatics workflows, performance of new library preparations and validation of established workflows for new sequencing instruments. I also played a key role in the accreditation and maintenance of our ISO:15189 clinical pipelines. During my time at AGRF I have delivered on over 100 bioinformatics projects. My projects are mostly custom bioinformatics solutions for clients requiring a publication-ready analysis or other in-depth exploration or interpretation of their data. Some examples include:- Karotyping and SV analysis- Population genetics (GBS and array-based)- Metagenomics and bacterial genomics - Primer design- Clinical genomics- Complex statistical designs for RNA-Seq/WGBS/arrays such as family studies, matched samples designs and multivariate analyses- RRBS/WGBS- Cancer genomics such as TMB, somatic variant calling and genotyping approaches- Analysis of non-model organisms- Genome Assembly - CRISPR editing- QTL-Seq and 3D pooling- GWAS analysis

Contributed novel research in the field of medical genomics. Some key research areas included identifying the genetic factors contributing to rheumatic heart disease in indigenous Australians and researching the spread of antimicrobial resistance genes in bacteria, one of the top international WHO concerns. These projects involved a range of bioinformatic techniques not limited to genome assembly and annotation, network analyses, GWAS, meta-analyses, phylogenetics and candidate gene fine-mapping.- Conducted the first GWAS of Rheumatic heart disease in Australia, as part of a larger meta-analysis into RHD genetics internationally. I was the core individual coordinating the analysis across Australia and responsible for collating and analysing clinical and genetic data. - Detailed understanding of immunology, vaccine development and laboratory and bioinformatics techniques to analysing HLA- Developed a range of expertise in analysis of genetic information specific to human and bacterial samples. i.e. Databases, software, web applications and statistical genetic techniques.- Management of a large consortium, communicating and integrating needs from a diverse range of parties from medical practice, research and ethical-science governance groups - Direct experience dealing with Indigenous authorities in governance of genetic information, modifying research direction to comply with ethical standards and communicating with elders and community representatives to deliver ethical research- Guidance of PhD students and colleagues- Publication in international peer-reviewed journals- Delivering seminars, participation in international conferences- General administration as required, some systems administration and maintenance of online repositories

Reviewing research outcomes from STIUP medical device funding in collaboration with the Department of Business- Liaising with small business owners and manufacturers in understanding and reporting progress towards commercialising technologies- Due diligence analysis and report writing for future medical investments

PhD student with La Trobe University and the Department of Environment and Primary Industries (DEPI, formerly DPI). My doctorate was completed in the Computational Biology group at DEPI headed by Prof Ben Cocks and Prof Ben Hayes. This bioinformatics and systems biology project involved identifying genes for lactation improvement in dairy cattle and included genome wide association studies (GWAS), novel methods for analysis of biological pathways and target-gene fine mapping.- Data analysis, management and sharing in a high-performance computing environment - Analysis and visualization of NGS, transcriptomic and proteomic data. Specialties in dealing with fine and high-density SNP data in structured data sets- Developed novel genetic and statistical techniques to quantify the genetic contribution to a production trait, assessing antagonistic pleiotropy, assessing biological systems driving production traits and filtering epistatic interactions - Quantifying the genetic component of production traits using mixed models in ASReml and R. Understanding of common dairy genomics techniques for fitting breed structure including the GRM and GBLUP. Familiar with Bayesian statistical methodology and common dairy terminology and production measures. - Formal training and experience in communicating complex information to non-specialist audiences. Published 4 manuscripts in peer-reviewed journals- Experience in a range of bioinformatics techniques, software and web applications- Participation in the Dairy Futures CRC education program, including regular industry interaction through policy/strategy discussion, seminars, conferences and community involvement events- Detailed understanding of the dairy industry including on-farm experience, manufacturing, policy and research.

General laboratory maintenance and support for a team of ~40 scientists. - Recording usage of laboratory consumables, purchasing and logistics - Using molecular biological techniques to create chemical stocks - Maintaining, calibrating and cleaning laboratory equipment- Training and compliance with OH&S guidelines and OGTR regulation. Compliance with PC2 laboratory standards and GMO regulations- Running autoclaves, training and experience in disposal of biohazard and radioactive waste