Alexander Murray Email and Phone Number

Bioinformatics Analyst Fellow with Food & Drug Administration's High-performance Integrated Virtual Environment (HIVE) team, leading complex Next Generation Sequencing (NGS) analyses and collaborating with scientists across multiple FDA offices and centers.Developed and implemented comprehensive bioinformatics pipelines specializing in bulk and single-cell RNA-seq and ChIP-seq data analysis, utilizing BASH, R (Tidyverse, Seurat, DESeq2, etc.), and Python (NumPy, Pandas, ScanPy, etc.) frameworks.Team member pioneering machine learning initiatives to create an in-house, balanced, cell-type annotation tool for FDA-CBER-HIVE; leveraging open source LLMs (SQLCoder-8b, Mistral-8B) to process and analyze scRNA-seq data through curated public datasets.Managed complete analysis workflows including data wrangling, quality control, and statistical modeling, delivering actionable insights through customized HTML reports and visualizations/figures utilizing RMarkdown and Quarto packages.Demonstrated expertise in High Performance Computing (HPC) through technical seminars and client presentations, showcasing advanced capabilities in multi-spectral data analysis and FDA-validated bioinformatics approaches.Maintained high standards of reproducibility and code quality through meticulous environment documentation (renv) and version control practices (Gitlab) while effectively operating within Agile sprint methodologies.Regularly presented research findings at internal and external conferences, delivering clear technical communications and strategic advisory services for project planning, statistical power analysis, and goal achievement.

R&D Biologist for ATCC's contribution to Human Cancer Models Initiative Consortium. Studied, developed, and expanded patient tumor-derived 3D organoid cancer models in-vitro, maintained meticulous batch records.

• Analyzed sequencing data from the epigenomic and computational biology lab at VMCVM. Managed and processed RNA-seq/single-cell RNA-seq data utilizing bash within a High-Performance Compute Linux cluster and leveraging R to visualize data of expression profiles from neurons within transgenic animals. Provided feedback for further exploration of gene expression changes with regards to neural tissue in different biological conditions.• Designed and implemented a pipeline for future analytic work. Constructed a workflow pipeline within a Linux cluster for wet lab scientists to analyze their data without assistance. This enabled basic analysis work to be completed in the future without the need to contract a bioinformatician.

Identified the interaction of two proteins involved in development, learning, memory, and behavior within mammalians brain. Combined numerous epigenetic bioinformatics datasets, reviewed relevant background literature, drew inferences, and completed an experiment to confirm a previously unexplored protein interaction within mammalian brains. Confirming this interaction provided a secure foundation for understanding how early-life experiences pre-dispose mammals to neuropsychiatric disorders such as post-traumatic stress disorder, major depressive disorder, and schizophrenia.

• Led novice laboratory scientists and contributed to the successful application for multiple National Institutes of Health (NIH) R01/R21 grants. Coordinated a team of three Ph.D. candidates to generate preliminary data necessary for NIH R01 & R21 grants. Produced data utilizing biological and molecular techniques, then provided follow-up analysis utilizing ImageJ and R. Composed proposals and edited submissions for successfully funded NIH grant applications to the National Institute of Mental Health (NIMH).• Optimized several techniques for generation of neuroscience-based data and bioinformatics. Optimized biologically-based techniques (e.g. brain region isolation, neural stem-cell isolation, primary ganglionic neuron isolation and culture, circularized chromosome conformation capture, and low-input ChIP-seq), informatic pipelines (e.g. 10X Genomics single-cell RNA-seq, 10X multi-omic data pipeline), behavioral studies (e.g. fear operant conditioning, elevated plus maze, and open field test) and incorporated said techniques into lab SOPs and repertoires for data generation. • Managed a transgenic mouse breeding program. Generated and maintained numerous lines of transgenic knock-out mice. Organized and evaluated up to 400 animals weekly. Identified and implemented a new organizational system for tracking multiple generations of mice over a multi-year study. Generated specific gene knock-outs to evaluate NIH grant aims over a 4-year period. Expanded lab SOPs and vivarium caretaking guidelines to include mouse behavioral studies.

• Managed finances for the BMVS program. Managed budgets, prepared reports, organized fundraisers, and updated officers on the financial state of the organization. Collected and disbursed organizational funds, planned and executed fundraising events while following COVID-19 safety protocols.

• Served as the intermediary between students and executive board to address issues hindering inclusivity and causing conflict. Planned and launched initiatives to identify long-lasting challenges to diversity in an international graduate community. Connected students to forgotten or underutilized services, such as on-campus therapists and support groups. Ensured international students received necessary bureaucratic support from the program.

• Served as BMVS liaison to the main campus Graduate Student Assembly. Planned university-wide events to phase out antiquated charters, as well as increase inclusion, mental well-being, and student safety. Led financial services committee to identify and eliminate gratuitous fees. Instituted bi-weekly newsletter to disseminate information about free physical fitness events and groups. Disseminated information to BMVS program and relayed responses back to main campus organization.

• Identified protein-protein interactions involving Egr1. Designed and implemented gene knock-down experiments using cultured primary embryonic mouse neuro-stem cells and recombinant adenovirus. Oversaw planning and care of transgenic mouse colonies. Analyzed data generated from experiments utilizing R. Wrote standard operating procedures for new techniques, experiment design, and lab safety. Contributed towards and edited a manuscript for Nature Communications publication. • Supervised undergraduate research students. Guided three undergraduate students in their research experiments on epigenetics and biological sciences. Monitored lab conditions, resources, and safety procedures. Instituted bi-weekly journal club to present contemporary publications. Prepared students to successfully present in Dennis Dean Undergraduate Research and Creative Scholarship Conference.

• Cloned a mammalian gene and tested a protein-protein interaction. Cloned Egr4 gene from the C57BL/6J mouse genome into a plasmid vector utilizing PCR primers & restriction enzymes. Transfected the plasmid into cultured cells and tested protein-protein interactions via co-immunoprecipitation. Examined the interaction of Egr4 with Tet1, a DNA demethylation enzyme.