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University of California San Diego

Genome Assembly Programming Challenge

In Spring 2011, thousands of people in Germany were hospitalized with a deadly disease that started as food poisoning with bloody diarrhea and often led to kidney failure. It was the beginning of the deadliest outbreak in recent history, caused by a mysterious bacterial strain that we will refer to as E. coli X. Soon, German officials linked the outbreak to a restaurant in Lübeck, where nearly 20% of the patrons had developed bloody diarrhea in a single week. At this point, biologists knew that they were facing a previously unknown pathogen and that traditional methods would not suffice – computational biologists would be needed to assemble and analyze the genome of the newly emerged pathogen. To investigate the evolutionary origin and pathogenic potential of the outbreak strain, researchers started a crowdsourced research program. They released bacterial DNA sequencing data from one of a patient, which elicited a burst of analyses carried out by computational biologists on four continents. They even used GitHub for the project: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki The 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this online course you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the E. coli X from millions of overlapping substrings of the E.coli X genome.

Status: Algorithms
Status: Molecular Biology
AdvancedCourse17 hours

Featured reviews

PO

5.0Reviewed Aug 3, 2017

Good course and final capstone project. Would recommend anyone from beginner to professional.

PB

5.0Reviewed Jul 27, 2019

May be the course would have given more hints. But a learned a lot from the projects.

PA

5.0Reviewed Jul 13, 2017

Really tough and enjoyable Project. Learnt something very special.

AS

5.0Reviewed Aug 4, 2018

I would like to say thank you to all who have created this course and specialization! Good material, excellent lecturers!

FS

5.0Reviewed Sep 5, 2020

It's a great experience with learning a Genome Assembly.

SH

5.0Reviewed Oct 20, 2020

Really enjoyable and also challenging specialization. I also enjoyed this capstone too. I gathered my interest in Algorithms and Bioinformatics field.

SA

4.0Reviewed Aug 11, 2020

hi, this is a hard course and the videos are not sufficient. but finally i finished. thanks a lot

AG

5.0Reviewed Jul 28, 2020

very challenging course, but still very good and you learn a lot

All reviews

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John Berkowitz
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Евгений Семченко
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Alexander Chertov
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Tamilarasu S
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Michael O
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