CV
WORK EXPERIENCE
Senior Bioinformatician (Operations)
Jan. 2023 - Present
Genomics England, London, UK
- Leading development of a new quality control monitoring system for pipeline runs using AWS systems and NextFlow Tower.
- Increased automation and security in team CI/CD pipeline, including developing a cookiecutter template for initialising future repositories.
- Line manage 1 junior member of Operations team, providing technical and professional mentorship with regular one-on-ones and semi-annual performance reviews.
- Led the team through both ISO 13485 and ISO15189 audits that returned no findings, ensuring team SOPs were up-to-date and answering auditor questions.
- Performed gap analysis to ensure team remained compliant with new ISO 15189:2022 standards.
- Represent the team at meetings with other squads, serving as a subject matter expert for company decisions that impact pipeline operations.
Bioinformatician (Operations)
June 2022 - Jan. 2023
Genomics England, London, UK
- Took initiative to improve documentation of team codebase by standardising docstrings across the repository to auto-build HTML documentation with Sphinx.
- Lead Operations support of Research Cohorts, creating a clearly defined protocol for testing in UAT and facilitating collaboration across teams to remove testing and production roadblocks.
- Ensured smooth operation of HPC pipeline by overseeing workflows to monitor for failures, intervening when necessary to apply ISO-certified fixes.
- Robust coding and teamwork skills refined by regular contribution and review of pull requests to implement process improvements.
Computational Biologist
Nov. 2020 - June 2022
Bioinformatics & Biostatistics (BIO2) Core, Institute for Metabolic Sciences, University of Cambridge, UK
Merkle Lab, Institute for Metabolic Sciences, University. of Cambridge, UK
- Provide expert analysis for key stakeholders to deliver critical recommendations that guide decision-making for future strategy.
- Wrote and implemented the Merkle Lab’s FAIR/O compliant data management policy to take advantage of remote storage and automation, which reduced overhead for wet-lab colleagues.
- Led the initiative to write the BIO2 Core’s external collaboration policy to guide future projects and ensure successful outcomes.
- Developed LipidTA, an open-source Python command line interface built to translate complex lipidomics data into meaningful insights.
- Constructed self-documenting, open-source pipelines for data analysis tasks ranging from external API queries to producing reports on diverse data anylses.
Computational Biologist
Oct. 2019 - Oct. 2020
National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- Developed a data-driven framework, ChooseR, in R that used a novel metric of cluster robustness to provide a quantitative measure of the quality of chosen clustering parameters. Led to a first-author publication in BMC Bioinformatics.
- Integrated diverse datasets to produce a reference atlas of spinal cord cell types and subsequently developed a machine learning pipeline to use this atlas to classify new cells. Led to a publication in Nature Communications.
- Worked in a team of wet-lab scientists to translate experimental data into meaningful interpretations and actionable recommendations. Regularly communicated these analyses to team members.
Masters Candidate
Sept. 2015 - Oct. 2019
Dept. of Physiology, Anatomy, and Genetics, University of Oxford, UK
National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
- Constructed applet in ImageJ Macro Language, a derivative of Java, to improve high-throughput analysis of super-resolution fluorescence microscopy data.
- Wove four years of experiments and data analysis into a cohesive story providing meaningful insight into the effects of autophagic perturbation on mitochondrial function in my thesis
- Strong organizational, teamwork, and collaboration skills expanded by managing an international, collaborative research project.
Dept. of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
Research Assistant, Sept. 2011 - May 2015
- Supervisor: Prof. Hey-Kyoung Lee
- Assisted in experiments examining the effects of visual deprivation on the strength of synapses in the primary auditory and visual cortices of mice that led to a Journal of Neuroscience publication.
TEACHING EXPERIENCE
EDUCATION
MSc by Research in Medical Science
March 2020
Universityof Oxford, UK
- Thesis: Investigating the effects of autophagic perturbations on mitochondrial function in Parkinson’s Disease
Foundation for Advanced Education in the Sciences, Bethesda, MD, USA
BIOF399, Deep Learning for Healthcare Image Analysis, Sept. - Dec. 2019
- Applications of convolutional neural networks (CNNs) to data to create GPU accelerated networks using Keras and TensorFlow.
BIOF509, Applied Machine Learning, Feb. - May 2019
- Broad, practical overview of machine learning, covering regression, random forest, K-means clustering, and deep learning using scikit-learn and tensorflow.
BIOF518, Theoretical and Applied Bioinformatics, Sept. - Dec. 2018
- Covering the theory and practice of a wide range of bioinformatic techniques, including BLAST, gene structure prediction, phylogenetics, and sequence alignments.
BIOF309, Introduction to Python, Sept. - Dec. 2018
- Developing core Python principles such as syntax, reading/writing files, debugging, regular expressions, and creating modules.
Scientists Teaching Science, Mar. - Apr. 2018
- Teaching course for scientists that developed principles of effective teaching and communication, including enquiry-based learning, course planning, and exam writing.
BSc in Neuroscience and Molecular & Cellular Biology
May 2015
_Johns Hopkins University, Baltimore. MD, USA__
- General Honors (GPA: 3.91) - First equivalent
Minor in Spanish for the Professions
May 2015
_Johns Hopkins University, Baltimore. MD, USA__
Core Skills
Technical
- Full stack data analysis with Pandas/Numpy/Tidyverse
- Data visualisation with Matplotlib/Seaborn/ggplot2
- App development for data exploration in R (Shiny) and Python (dash)
- Command-line-interface (CLI) tool development in Python and Shell
- Pipeline development using Snakemake
- Continuous integration with Github Actions, Travis CI, CodeCov, PyUp, PyTest, and Read the Docs
- Shell scripting in various dialects (Bash, Zsh, Fish)
- Single cell RNA sequencing analysis in R (Seurat/Scran) and Python (Scanpy/scVI)
- High-throughput data analysis scripts in ImageJ using a derivative of Java
- Software version control with git/GitHub
- Remote, high performance computing experience (AWS)
Laboratory
- Airy scan microscopy (Zeis 880 platform)
- High-throughput laser confocal microscopy (Perkin Elmer Phenix platform)
- Immunofluorescence
- General cell culture
- Chemical differentiation of iPSCs
- Plasmid and viral vector design and construction
- Western blotting
- DNA gel electrophoresis
- Mouse surgery and dissection
- Biotinylation
- Golgi staining
- Brain slice preparation for electrophysiology
AWARDS
Intramural Research Training Award
National Institutes of Health, Sept 2015 - Jan 2020
Bethesda, MD, USA
Barry Goldwater Scholarship
The Barry Goldwater Scholarship and Excellence in Education Foundation, 2014
PUBLICATIONS
Vision loss shifts the balance of feedforward and intracortical circuits in opposite directions in mouse primary auditory and visual cortices
Petrus E, Rodriguez G, Patterson R, Connor B, Kanold PO, Lee HK. (2015). "Vision loss shifts the balance of feedforward and intracortical circuits in opposite directions in mouse primary auditory and visual cortices." J Neurosci. 35(23).
Selecting single cell clustering parameter values using subsampling-based clustering metrics
Patterson-Cross RB, Levine AJ, Menon V. Selecting single cell clustering parameter values using subsampling-based robustness metrics. BMC Bioinformatics. 2021 Feb 1;22(1):39.
A Harmonized Atlas of Spinal Cord Cell Types and Their Spatial Organization
Russ DE, Cross RBP, Li L, Koch SC, Matson KJE, Yadav A, Alkaslasi MR, Lee DI, Le Pichon CE, Menon V, Levine AJ. A harmonized atlas of mouse spinal cord cell types and their spatial organization. Nat Commun. 2021 Sep 29;12(1):5722. doi: 10.1038/s41467-021-25125-1. Erratum in: Nat Commun. 2022 Feb 18;13(1):1033. Erratum in: Nat Commun. 2022 Oct 19;13(1):6184. PMID: 34588430; PMCID: PMC8481483.
A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns
Arokiaraj, Cynthia Mary and Kleyman, Michael and Chamessian, Alexander and Shiers, Stephanie and Kang, Byungsoo and Kennedy, Meaghan M. and Patterson, Ryan and Lewis, David A. and Qadri, Yawar and Levine, Ariel J. and Price, Theodore and Pfenning, Andreas R. and Seal, Rebecca P., A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns. Available at SSRN: https://ssrn.com/abstract=3924596 or http://dx.doi.org/10.2139/ssrn.3924596
A comparative transcriptomic analysis of glucagon-like peptide-1 receptor- and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus
Smith C, Patterson-Cross R, Woodward O, Lewis J, Chiarugi D, Merkle F, Gribble F, Reimann F, Adriaenssens A. A comparative transcriptomic analysis of glucagon-like peptide-1 receptor- and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus. Appetite. 2022 Jul 1;174:106022. doi: 10.1016/j.appet.2022.106022. Epub 2022 Apr 14. PMID: 35430298; PMCID: PMC7614381.