The clinical genomics and precision health team is part of the UTSW Next Generation Sequencing (NGS) clinical service. The team created and validated all the bioinformatics pipelines for the CAP/CLIA –certified genomic tests that UTSW offers to clinical oncologists. The BICF NGS team also developed the Annotation Software for Electronic Reporting (ANSWER) tool, which allows molecular pathologists to visualize raw data, annotate genes and variants and to create the report used by the clinical oncologists to make treatment decisions.
- Docker Images for GenomeSeer
- Trim Galore
- BWA Alignment
- Variant Calling
- Variant Annotation
- DNA Nexus Applets
- Germline Variant Calling (Exome, Whole Genome, Gene Panel)
- Somatic Mutation Variant Calling
- RNA-Seq Differential Gene Expression
- Microbiome 16S rRNA Sequence Analysis
Brandi Cantarel, Ph.D.
Brandi Cantarel is a computational biologist, who bridges the gap between clinical and basic biomedical research. Dr. Cantarel is an expert in high-throughput sequence analysis including WGS/WES, RNA-seq, Methyl-seq, metagenomics and the integration of data. Her technical skills include: a) methods and pipeline development for complex data analysis, b) custom database development, and c) web development for data exploration and visualization. She has set up BICF’s Nanocourse and fellowship programs and established the foundations of the Clinical NGS laboratory. She coordinates Nanocourses and Data Science Summer School and directs all aspects of the Clinical NGS development.
Scientific Programmer II
Guillaume Jimenez is a software engineer with a specialization in high-throughput data management and visualization. Mr. Jimenez is developing tools for the querying and visualization of sequence data to help researchers identify tends in protocol development. He is also the lead developer for the development of a UTSW clinical annotation database.
Chelsea Raulerson, Ph.D.
Computational Biologist III
Chelsea Raulerson is a computational biologist who specializes in in next generation sequence (NGS) analysis in genomics, metagenomics and transcriptomics Dr. Raulerson is the lead bioinformatics analysis for the data processing of clinical samples to identify genetic variation including SNVs, InDels, translocation and gene fusions in patient samples.
Benjamin Wakeland, M.S.
Data Scientist III
Benjamin Wakeland is a member of the Immunology Department embedded with the BICF team. He is a lead software engineer with specialization in genomics. Mr. Wakeland has been developing packages for high-throughput genomics analysis for over 10 years. Mr. Wakeland oversees LIMS workflow development and instrument integration. He is also the lead developer of the UTSW Clinically Operable Interpretations kNowledgebase (U-COIN).
Jeremy Mathews, B.S.
Computational Biologist Intern
Jeremy Mathews is a computational biologist intern with a specialization in cloud computing. Mr. Mathews is developing software containers (docker, singularity) and converting existing bioinformatics workflows for deployment on the cloud, on platforms including AWS, Azure and platforms such as DNA Nexus.