Anthony Cox Email & Phone Number

Cambridge, England, United Kingdom

I provide expert consulting services to startups in the UK, US and mainland Europe, advising on scientific computing and bioinformatics strategy and tackling short-term and long-term data analysis and bioinformatics projects that arise in early-stage technology development.Recent projects:• Bactobio (Apr-Jul 24, extended to Sep 24) Productizing research data science code for microbial genomics. Tech: Python, pandas, MLflow, Hydra, CI/CD• Resolve Biosciences (Jan 24 - present): Image analysis and algorithm design for spatial genomics. Tech: Python, OpenCV• Next-generation sequencing data analysis and interpretation - experienced in Illumina, Oxford Nanopore and PacBio• Advised on NGS adoption and scaleup - data strategy and implementation• Built and deployed NGS pipelines - using Docker, AWS and Nextflow I combine specialized bioinformatics knowledge with deep expertise in software engineering, computer science and high-performance computing, delivering innovative solutions to the most challenging problems in bioinformatics and genomics.

Cambridge, England, United Kingdom

• Working with the Tree of Life project and Professor Richard Durbin's group from the University of Cambridge on novel assembly algorithms for complex genomes using PacBio Hifi long read sequencing data• Collaborating with Strelchuk and Durbin groups at University of Cambridge to develop quantum speedups of bioinformatics algorithms as part of Wellcome Leap grant “Human and Pathogen Quantum Pangenomics”

Cambridge, England, United Kingdom

Led expansion of AI and machine learning capabilities at Illumina's UK site.• Grew UK AI team from 3 to 15 members.• Built data pipeline for de novo assembly of 556 primate genomes as part of large study in machine learning and comparative genomics, accepted for publication in Nature.• Software prototyping, algorithm design and bioinformatics for new product development.

Cambridge, England, United Kingdom

Technical lead of team of 7 on DRAGEN (FPGA-based processing platform for DNA data).• Integrated new population genotyping module into DRAGEN and successfully delivered two releases.• Published white paper comparing accuracy with competitors (GATK and DeepVariant).• Collaborated with Genomics England to genotype 80,000 human genomes with our software.

Cambridge, England, United Kingdom

Novel algorithms, software development and data analysis for Illumina's next-generation DNA sequencing technology. Hands on technical lead of software team of 5 enabling human genome analysis at population scale. • Built cloud framework for joint variant calling and statistical genetics on cohorts of human genomes.• Initiated research program into compression and indexing of DNA data, leading to 8 peer-reviewed publications and open-source software package (http://beetl.github.io/BEETL/ ).• Led interdisciplinary process improvement effort for DNA mutation detection algorithms.Other research interests included: • Bacterial genome assembly.• Cancer genomics. • Metagenomics.• Detection of copy number and structural variants.

Cambridge, England, United Kingdom

Pioneered the bioinformatics and data analysis of Solexa DNA sequencing technology• Created ELAND, first sequence alignment program to address the 1000-fold increase in throughput achieved by “next-generation” sequencing technologies. • Architecture, design and implementation of the first data analysis pipeline for Solexa DNA sequencers.

Co-developed SSAHA, pioneering software for ultra-fast search of large DNA sequence databases (more than 1,200 citations in Genome Research)

Algorithm and software development for the ground segment of the Meteosat Second Generation series of geostationary weather satellites.