Teaching

Drs Griffith guest lecture regularly for a number of traditional courses at Washington University School of Medicine. Drs Griffith also coordinate the Cancer Informatics Journal Club and Dr Obi Griffith is course master for a Genomics in Medicine course. The Griffith Lab is deeply committed to providing open source educational resources to aid the bioinformatics community. To this end we maintain several online courses and tutorials. We also deliver periodic workshops based on these materials (see below). To date we have led 34 workshops held in 7 cities and 5 countries. Furthermore, we and many members of the lab are actively engaged in community forums such as BioStars.

Upcoming Workshops

1. Canadian Bioinformatics Workshops - RNA-seq Analysis, Dates TBD, 2025
2. Cold Spring Harbor Laboratory - Advanced Sequencing Technologies & Bioinformatics Analysis, November 10-23, 2024

Past Workshops

1. RNA-seq analysis and cloud computing (CBW, Toronto)
2. Advanced Sequencing Technologies and Applications (CSHL, New York)
3. Cancer Research Institute Bioinformatics Bootcamp (CRI, Orlando)
4. Genomic Data Visualization/Interpretation (Physalia Courses, Berlin)
5. Precision Medicine Bioinformatics (PR Informatics, Glasgow)
6. High-Throughput Biology: From Sequence to Networks (CSHL / CBW, New York)
7. Workshop on Genomics (Evomics, Český Krumlov)

Online Courses

1. rnabio.org - Informatics for RNA-seq: A web resource for analysis on the cloud.
   Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
2. genviz.org - Genomic Data Visualization and Interpretation.
   In-depth tutorials for the interpretation and visualization of omic data including: genome browsing and interpretation, introduction to BioMart, liftover, ProteinPaint, COSMIC, introduction to R, ggplot2, R Markdown, Shiny, GenVisR, differential expression and pathway analysis, variant annotation and interpretation, and others.
3. pmbio.org - Precision Medicine Bioinformatics.
   An end-to-end precision medicine analysis of real human genome (WGS and Exome) and transcriptome (RNA-seq) data for a hypothetical patient. The goal of the analysis is to identify personalized therapeutic options for this patient as well as identifying any prognostic or diagnostic implications in the data.

Online tutorials (Selected)

• Introduction to AWS Cloud Computing
• Creating Heatmaps in R
• Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
• How to Download Raw Sequence Data from GEO/SRA
• Analysing Microarray Data In Bioconductor
• Tools For Alternative Splicing Detection From Rna-Seq Data
• Databases Of Tumor Suppressors and Oncogenes
• Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
• Machine Learning For Cancer Classification
• Individualized medicine in cancer by whole genome, exome or transcriptome sequencing
• Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
• Packages For Visualization Of Biological Data In R
• How to Create a Mutation Landscape (Waterfall) Plot with GenVisR
• How To Install A Specific Cdf Package For Use In Bioconductor
• How to View Gene Annotations For Non-Standard (E.G., Virus) Genome In IGV
• Exploring cancer mutation data portals
• Using The Biomart Perl Api For Simple Queries
• How to Create a Mutation Lolliplot with GenVisR

Washington University Courses

• Special Topics in Molecular Genetics: Molecular Basis of Cancer (BIO5288)
• Genetics and Genomics of Disease (BIO5487)
• Human Linkage and Association (M21-5483/L41-5483)
• Genomics in Medicine I/II (M17-532/533)
• Cancer Informatics Journal Club (L41-BIOL5499)