This is a 3 session course meeting on:
Saturdays February 18th, February 25th, & March 4th from 11am - 2pm
Session 1: Introduction to DNA Sequencing & Analysis
The first session in this series will be an introduction to the molecular structure of DNA, and basics of transcription and translation. We will learn about the current methods of “reading” it: short- and long- read DNA sequencing technologies.
Using a provided sample dataset including metagenomic and human data, we will use online tools to perform sequence alignments and searches to gain an understanding of the applications and interpretations of this data for both human genomics and environmental metagenomics.
Session 2: Bioinformatics for Environmental Metagenomics
We are increasingly aware of the invisible and ubiquitous microbial component of our lives – in and on our bodies, in our environment. But, how do you actually measure that? What if you wanted to find out what bacteria are living around you? In this workshop we will learn the methods for identifying microbial species with DNA sequencing data, and understand what their functions are and how that can inform decisions or urban design.
We will use the Pathomap dataset and each participant will obtain the metagenomic sequences of their favorite subway station. We will explain the file formats used for sequencing data and how to manipulate them, and gain hands-on experience on using the computational tools to identify bacterial species and their genes with that data, and visualize the results.
Session 3: Bioinformatics for Human Genomics
The Human Genome Project released the human reference genome in 2003, and since then DNA sequencing has become ubiquitous tool in biomedical research. In this workshop we will learn about the file formats describing human DNA sequencing data and its annotation. We will use data from the Genome in a Bottle (Joint Initiative for Metrology in Biology) standard datasets, and learn to use tools from the open source BEDTOOLS suite to analyze it.
Dr. Elizabeth Hénaff was born of French/American parents in Austin in 1981, grew up in France, and has since lived in the US, Japan and Spain. She received a BS in Computer Science, an MS in Plant Biology (both from UT Austin) and a PhD in Bioinformatics from the University of Barcelona. The impetus behind her research is a fascination with the way living beings interact with their environment. She has made contributions to understanding how plants respond to the force of gravity, how plant genome structure changes in response to stress, and most recently has turned her attention to the ubiquitous and invisible microbial component of our environment. She has consistently made the tools – software, wetware, hardware – needed to answer her research questions, and enjoys both this process and the goal equally. Her interests in biological interactions and data visualization have inspired her to create interactive installations, and she has collaborated with artists and musicians in Barcelona, Paris and New York designing custom interactive visuals for their events. She currently works as a postdoc at the Weill Cornell Medical College in New York City.