RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Authors


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.


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.


Brian Haas

Brian Haas earned a master’s degree in molecular biology and biochemistry at the State University of Albany, N.Y., and after discovering his passion for deciphering the genetic blueprint of life, decided to enter the then-burgeoning field of bioinformatics. He has since been pursuing his dream of doing bioinformatics and genome research, along the way earning a separate master’s degree in computer science at Johns Hopkins University. Brian has been working in the genomics field since 1999, first with The Institute for Genomic Research in Rockville, Md. He joined the Broad Institute in 2007 and is currently a senior computational biologist within the Klarman Cell Observatory. His research is focused on developing and supporting open source bioinformatics software tools and using computational techniques to explore aspects of molecular biology, particularly in the study of transcriptomes.


Jason Walker

Jason Walker is a Biomedical Informatics Project Manager at the McDonnell Genome Institute. He works with the Griffith Lab to translate grant objectives and analysis goals into well defined development milestones for software engineers to iterate on projects, achieving consistent progress while maintaining best practices in software development methodologies. His responsibilities include overseeing the integration and adaptation of numerous bioinformatics tools for cancer genomics automated analysis of high-throughput DNA and RNA sequence data. In addition to large-scale research projects, he works with a CLIA licensed laboratory on clinical-grade, CAP-accredited analysis workflows for reporting somatic variants in cancer patient genomes.’


Alex Wagner

Dr. Wagner is an NCI Ruth L. Kirschstein NRSA Postdoctoral Fellow at the McDonnell Genome Institute and Washington University School of Medicine. His research interests are in facilitating the interpretation of genomic variants in a clinical context. He leads development of the Drug Gene Interaction Database, and is a primary contributor to other projects centered on interpretations of genomic variants (Database of Curated Mutations, Clinical Interpretations of Variants in Cancer) and Genomic Visualizations in R. Alex is an active member of the Global Alliance for Genomics and Health (GA4GH), and is leading an effort to aggregate and normalize the disparate knowledgebases of the GA4GH Variant Interpretation for Cancer Consortium. He is also currently studying the role of genomic variants in cancers and leading a study characterizing relapsed Small Cell Lung Cancers with Drs. Obi Griffith, Malachi Griffith, and Ramaswamy Govindan.


Kelsy C. Cotto

Kelsy is a PhD candidate in the Molecular Cell Biology program at Washington University in St. Louis. She completed her undergraduate degree at Mercer University in 2016, where she earned a B.S. in Biochemistry and Molecular Biology. She is interested in developing methods to analyze multiple types of sequencing data in order to better understand regulatory mutations and splicing within cancer, particularly with respect to personalized cancer vaccine design. Currently, she is involved with DGIdb, RegTools, ORegAnno and analysis of several breast cancer clinical cohorts. She is also part of the Precision Medicine Pathway and Cancer Biology Pathway at WashU, which allows to better understand how she can translate genomics and informatics into the clinic more efficiently.


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.