Providing advanced bioinformatic services for investigators to leverage genomics, proteomics and metabolomics (omics) data
The core’s focus is to help researchers identify and interpret patterns in RNA and DNA by placing omics data into a biologically meaningful context. This encompasses assisting with experimental design, developing reproducible workflows, analyzing next-generation sequencing data and supporting manuscript development/publication. Additionally, we offer consultation meetings to discuss the types of analysis and support bioinformatics can provide. We also assist with experimental design to best answer the biological questions of interest. The core is also responsible for designing and preparing materials for training lab scientists on various bioinformatics software and databases.
The core provides an extraordinary amount of personal custom bioinformatic support to the Development Neurobiology department. The core maintains a wide range of general services but creates individualized services and analyses to meet the needs of the specific laboratory, staff member or project. The core has access to three dedicated workstations, an Ubuntu server and the St. Jude high-performance computational cluster, consisting of 6,400+ cores, totaling 10+ PB of storage memory. The core is staffed and operated by PhD-level full-time staff with expertise in WGS, WGBS, WES, PCR amplicon sequencing, ChIP-Seq, bulk RNA-Seq and single-cell/nuclear RNA-Seq technologies. Additionally, the core staff is equipped with analysis expertise in next-generation sequencing alignment, germline/somatic variant (SNV, Indels, CNV and structural) calling, germline HLA typing, manual review of variants, variant annotation, personalized cancer vaccine design, differential gene expression analysis, fusion detection, integration of single-cell data and single-cell pseudotime analysis.
Provide consultation to optimize experimental design at the project planning stage for studies that involve the generation of omics data
Assist in coordinating and managing bioinformatic projects between the end users, software developers, system designers, and different departments
Provide one-on-one training and resources to staff
Provide routine and customized bioinformatic omics analysis
Dr. Cody Alexander Ramirez was born and raised in Austin, TX, and later attended St. Edward’s University, where he obtained his BS in Bioinformatics with a concentration in Biomathematics. He then moved on to Washington University in St. Louis, where he obtained his Ph.D. under the mentorship of Dr. Obi L. Griffith and Todd A. Fehniger, investigating the genomic landscape and neoepitope vaccine candidates in follicular lymphoma. In 2021, Ramirez began leading the Bioinformatic Core, where he continues to pursue his passion for advanced bioinformatic analysis and mentoring core users to equip the next generation of bioinformaticians at St. Jude and beyond.
Cody Alexander Ramirez, PhD
Lead Bioinformatics Analyst