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A course on genomics and bioinformatics from WU

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Welcome to the Fall 2024 and Spring 2025 Bioinformatics (BFX) Workshop! It can be taken for credit under the WUSTL course titles: Applied Bioinformatics for Genomics I and II.

Objectives

This workshop series is designed for people who want to:

  • learn the fundamentals of computational genomics
  • use this information to improve and expedite their research
  • expand their knowledge by hearing from experts in other subject areas

By the end of this series, participants will be able to:

  • Demonstrate basic competency in running key bioinformatics software
  • Analyze sequencing data, going from raw data to biologically interpretable results
  • Draw upon a diverse set of genomic technologies to answer specific research questions
  • Apply critical thinking and analytic competencies to genomics research

Registration

You are welcome to join at any time byregistering on this form. After registering, you'll be added to an email distribution list and slack channel for the course. See theCommunications section below for details. There is no obligation to complete the course if you register, but it helps us with planning and securing appropriate resources.

Schedule

Weekly workshops are held on Mondays @ 10am inMid-Campus Center (MCC) 11th floor Main Conference Room (Room #11504)

The BFX Workshop schedule,subject to change, is available below. Previous years' course materials can still be accessed in thearchive folder. Westrongly encourage in-person participation, but a Zoom recording of each Workshop session will also be made available shortly after each session. SeeParticipation for more details about external or remote participation.

Time will be set aside before and after lectures for "office hours", where you can get help with assignments, or ask for advice about your own projects.

Fall 2024

DateTimeTopicPresenter
08/26/2410:00amIntro to Bioinformatics and Computer SetupChris Miller
11:00amExtra hands-on help with setup
09/02/24NO SEMINAR - LABOR DAY
09/09/249:00amExtra hands-on help with setup
10:00amIntroduction to Unix and the command lineChris Miller
11:00amExtra hands-on help with setup/unix
09/16/2410:00amSequence data generation/manipulationChris Miller
09/23/2410:00amDNA Alignment FundamentalsJason Walker
09/30/2410:00amSequence data visualization/IGVChris Miller
10/07/2410:00amData manipulation and basic plotting with RChris Miller
10/14/2410:00amNO SEMINAR – FALL BREAK
10/21/2410:00amRNA sequencing I – Data and AlignmentKartik Singhal
10/28/2410:00amRNA sequencing II – Transcript QuantificationMy Hoang
11/04/2410:00amRNA sequencing III – Differential ExpressionMariam Khanfar
11/11/2410:00amGermline and Somatic Variant CallingChris Miller
11/18/2410:00amNO SEMINAR
11/25/2410:00amParsing, Filtering, and Annotating VCFsJohn Garza
12/02/2410:00amTroubleshooting bioinformatics, Semester wrap-upChris Miller

Spring 2025

DateTimeTopicPresenter
01/13/2510:00amIntro/prereqs, Genomic Intervals and BedtoolsChris Miller
01/20/25NO SEMINAR - MLK DAY
01/27/2510:00amEpigenomics, ChIP/ATAC/WGBSChris Miller
02/03/2510:00amData visualization with R and ggplot2 - part 1Chris Miller
02/10/2510:00amData visualization with R and ggplot2 - part 2Chris Miller
02/17/2510:00amGenome Assembly, PangenomeJuan Macias
02/24/2510:00amSingle-cell RNAseq part 1Jennifer Foltz
03/03/2510:00amSingle-cell RNAseq part 2Jennifer Foltz
03/10/25NO SEMINAR - SPRING BREAK
03/17/2510:00amGenomic Workflows/Cloud ComputingJason Walker
03/24/2510:00amMicrobial GenomicsBrigida Rusconi
03/31/2510:00amMachine Learning/AI in GenomicsObi Griffith
04/07/25NO SEMINAR
04/14/2510:00amLong Read SequencingChris Miller
04/21/2510:00amGenomic Medicine, course wrap-upChris Miller

Participation

There are no requirements or qualifications to participate in the BFX Workshop. However, this course ramps up quickly and you will need to have basic competency at the unix command line within the first three weeks. We will cover some of these skills in the first two weeks of class, but if you are new to working at a terminal, westrongly recommend that you work through the command-line exercises listed on the prerequisites page ahead of the course, and/or block out some substantial time to work through them in the first two weeks.

If you are not taking the course for credit, there are no attendance requirements. There will be "assignments" given during most lectures and we strongly encourage you to complete them in order to get the most out of the course - lectures are no substitute for hands-on learning!

For external or remote asyncronous participation, we suggest watching each weekly Zoom recording (available shortly after each in-person session) and strongly encourage interaction viaSlack. The #bfx_workshop Slack channel is the primary form of interaction between workshop attendees, external participants, organizers, and presenters.

Organizers

This workshop is a collaborative effort between the Institute for Clinical and Translational Sciences (ICTS), the Department of Medicine, McDonnell Genome Institute (MGI), the Division of Hematology & Oncology, and the Department of Pediatrics with faculty, staff, and student representation and participation from many other Institutes, Departments, and Divisions at Washington University School of Medicine in St. Louis.

The course director isChris Miller (c.a.miller@wustl dot edu) and John Garza (johnegarza@wustl dot edu) is our dedicated teaching assistant.

Folks giving lectures in this workshop have multi-disciplinary backgrounds in Bioinformatics, Medicine, Computational Biology, Genetics, Computer Science, Oncology, Virology, Information Systems, Microbiology, Immunology, and many other combinations of both Data and Biological Sciences. They share best practices, technology, and knowledge from decades of experience working in these fields of study. Each year, the course evolves to match the rapidly evolving landscape of tools and techniques.

The organizers would like to specifically thank theICTS Precision Health function for supporting the Bioinformatics Workshop. (NIH CTSA Grant Number UL1TR002345)

Communications

Slack

Announcements, discussion, and homework help all take place primarily via Slack. For members of the ICTS Precision Health Slack organizationictsprecisionhealth.slack.com, please use the#bfx-workshop channel. If you do not have access to the ICTS Precision Health Slack, please email [johnegarza at wustl.edu]

Email

An Office 365 email group will be created for general announcements, schedule changes, etc from those thatregister.

Archived Lectures

If you'd like to look back at past sessions, course info and lectures from previous academic years are available in the archives:

Banner image adapted fromNHGRI (public domain)


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