Precision Medicine Bioinformatics

Introduction to bioinformatics for DNA and RNA sequence analysis

Authors

Obi L. Griffith

Dr. Obi Griffith is Assistant Professor of Medicine and Assistant Director at the McDonnell Genome Institute. Dr. Griffith’s research is focused on the development of personalized medicine strategies for cancer using genomic technologies with a particular focus on gene regulatory changes associated with breast cancer. He develops and uses bioinformatics and statistical methods for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction. Dr. Griffith has developed and instructs a workshop on RNA sequence analysis for Cold Spring Harbor Laboratories and is a regular instructor for the Canadian Bioinformatics Workshops series. Before coming to Washington University, Dr. Griffith completed bioinformatics post-doctoral fellowships at Lawrence Berkeley National Laboratory in Berkeley, California and at the BC Cancer Agency Genome Sciences Centre in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2008) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.

Malachi Griffith

Dr. Malachi Griffith is an Assistant Director of the McDonnell Genome Institute and an Assistant Professor in the Department of Medicine. Dr. Griffith’s research is focused on the development of genomics, bioinformatics and statistical methods as they apply to the study of cancer biology and medicine. A particular focus of his work is in the translation of genomics data from whole genome, exome and transcriptome sequencing into clinically actionable observations and personalized cancer therapies. Dr. Griffith is a regular instructor for the Canadian Bioinformatics Workshops series and Cold Spring Harbor Laboratories. Dr. Griffith is currently supported by an NIH R00 pathway to independence grant. Before coming to Washington University Dr. Griffith was a bioinformatics post-doctoral fellow at the BC Cancer Agency Genome Sciences center in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2009) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.

Zachary L. Skidmore

Zachary Skidmore is a staff scientist at the McDonell Genome Institute at Washington University in Saint Louis. His undergraduate work was completed at the Ohio State University where he obtained a B.Sc. in molecular biology. Graduate work was performed at the University of Illinois where he obtained a M.eng in bioinformatics. His research focus is in the realm of cancer biology where he uses and develops tools and techniques to aid in the analysis and interpretation of cancer sequencing data. He has worked on several large sequencing projects across many cancer types and has expertise in a variety of languages (perl, R, bash, python, typescript, angular2). He is the creator and maintainer of the bioconductor package GenVisR, a graphics program designed to help visualize cohort level genomic data.

Huiming Xia

Huiming Xia is a graduate student in the Computational Systems & Biology program at Washington University in St. Louis. She graduated from Carnegie Mellon University in 2017 with a dual degree in Computational Biology and Chemistry. She is interested in developing machine learning models for improving current strategies of neoantigen design for cancer immunotherapy.



Erica Barnell

Erica Barnell is an MD/PhD candidate at the Washington University School of Medicine and is completing her PhD at the McDonnell Genome Institute in the Griffith lab. Her thesis research surrounds building tools to improve the annotation bottleneck within precision oncology. She has worked on several research project including: assisting with building the Clinical Interpretation of Cancer Variant (CIViC) database, implementing a deep learning approach to automate somatic variant refinement (DeepSVR), and creating a standard operating procedure for manual review of sequencing data. Her undergraduate work was completed at Cornell University where she obtained a B.S. in Biological Sciences and Applied Economics and Management.

Sharon Freshour

Sharon Freshour is a graduate student in the Human and Statistical Genetics program at Washington University in St. Louis. She received her B.S. in Mathematics from St. Edward’s University in 2016. She is interested in uncovering mechanisms of immunotherapy resistance in cancer.




Jeff Szymanski

Jeff Szymanski is a clinical and molecular pathologist and clinical informatics fellow at Washington Univeristy in St. Louis. Jeff is interested in developing computational tools to improve interpretation of clinical laboratory and genomic data and is currently applying machine learning to complex clinical decision support problems.






Katie Campbell

Katie recently received her PhD in Molecular Cell Biology from Washington University in St. Louis. She graduated from Penn State University in 2014 with honors in Biochemistry. Katie is interested in utilizing genomics and informatics approaches to study cancer and tumor immunology in order to understand mechanisms of drug and treatment sensitivity. Her graduate research was focused on characterizing models of and defining targeted and immunotherapeutic opportunities in head and neck cancer. Katie has also contributed to other projects in the lab, including CIViC, GenVisR, pVACtools, and DGIdb, as well as analyzing cancer case studies for the Washington University Genomics Tumor Board. Katie’s additional talents include saying the alphabet backwards, standing on her head, and regularly drinking large amounts of coffee.