DESCRIPTION
This intermediate-level workshop will provide bioinformatics and genomic epidemiology training to public health laboratorians with a microbiology and bioinformatics background, with a focus on individuals with basic bioinformatic skills and those who work closely with epidemiologic personnel. This training will give the theory and background on next generation sequencing (NGS) and the fundamental analytical approaches. In addition to the theory, this course will give hands-on experience with some of the common analysis and data visualization tools along side epidemiologists from other jurisdictions. Attendees are expected to complete some prerequisite materials prior to the workshop.
AUDIENCE
This course is intended for microbiologists and early career bioinformaticians who routinely generate and analyze NGS data, have some experience with basic bioinformatic analysis and work closely with epidemiologists. Participants should have access to at least some of the tools discussed during the course and/or have the infrastructure in place to utilize the tools discussed in this course upon return to the laboratory. Much of the training will be in conjunction with epidemiologists.
OBJECTIVES
At the conclusion of the program, the participant will be able to:
- Utilize the basic theory quality management and sequence quality metrics for next generation sequencing for both surveillance and clinical testing
- Explain sequencing and bioinformatics results to public health professionals and epidemiologists
- Discuss the strengths and weaknesses of the specific types of tools used for different pathogens
- Explain how strength and weaknesses of different tools can impact interpretation
FACULTY
Laura Bankers, PhD, bioinformatics and genomic analysis supervisor, Colorado DPEH
John Barnes, PhD, deputy director, CDC
Heather Blankenship, PhD, genomics technical director, Michigan DHHS
Christopher Carter, MPH, genomic epidemiologist, Kansas DHE
Dan Evans, MS, genomic epidemiologist, Minnesota DOH
Logan Fink, MS, bioinformatics lead scientist, Virginia DCLS
Christopher Jossart, MPH, data scientist II, Wisconsin SLH
Henry Kunerth, PhD, research scientist II, Minnesota DOH
Alexandra Lorentz, PhD, lead scientist, Virginia DCLS
Abbey Marye, MPH, genomic epidemiologist, Utah DHHS
Meghan Maloney, MPH, epidemiologist IV, Connecticut DPH
Molly Mitchell, PhD, bioinformatics supervisor, Florida DPH
Kelly Oakeson, PhD, chief scientist, Utah DHHS
Anupama Shankar, PhD, microbiologist, CDC
Mayra Trujillo, MS, epidemiologist, Kansas DHE
Hayley Yaglom, MS, MPH, genomic epidemiologist III, TGen North
ACCESSIBILITY
In compliance with the Americans with Disabilities Act, individuals seeking special accommodations must email a request to Shannon Mahoney at least three weeks prior to the workshop’s start date.
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