About Us

Clinical Genomics & Precision Health

Services
Resources
Team Members

Services

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.

Resources

GENOMESEER: CLINICAL GENOMICS ANALYSIS WORKFLOWS

  • Docker Images for GenomeSeer
  • Trim Galore
  • BWA Alignment
  • Variant Calling
  • Variant Annotation
  • DNA Nexus Applets
  • GenomeSeer

THE UTSW – DATA ANALYSIS WORKFLOWS IN SEQUENCING (U-DAWS)

  • Germline Variant Calling (Exome, Whole Genome, Gene Panel)
  • Somatic Mutation Variant Calling
  • RNA-Seq Differential Gene Expression
  • Microbiome 16S rRNA Sequence Analysis

CLIA LAB TOOLS

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Team Members

Brandi Cantarel, Ph.D.
Assistant Professor

Brandi Cantarel

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.
Faculty Profile
Publications
LinkedIn Profile

 Guillaume Jimenez
Scientific Programmer II

Guillaume Jimenez

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.
LinkedIn Profile

Chelsea Raulerson, Ph.D. 
Computational Biologist III

 Chelsea Raulerson

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.
LinkedIn Profile

Benjamin Wakeland, M.S.
Data Scientist III

 Benjamin Wakeland

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).
Publications

Jeremy Mathews, B.S.
Computational Biologist Intern

 Jeremy Mathews

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.
LinkedIn Profile

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