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Untertitel: Englisch

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Data StructureAlgorithmsAlgorithm DesignString (Computer Science)

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Untertitel: Englisch

Lehrplan - Was Sie in diesem Kurs lernen werden

5 Stunden zum Abschließen

The 2011 European E. coli Outbreak

In April 2011, hundreds of people in Germany were hospitalized with a deadly disease that often started as food poisoning with bloody diarrhea. 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. Within a few months, the outbreak had infected thousands and killed 53 people. To prevent the further spread of the outbreak, computational biologists all over the world had to answer the question “What is the genome sequence of E. coli X?” in order to figure out what new genes it acquired to become pathogenic. The 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this Genome Assembly Programming Challenge, you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the deadly E. coli X strain. However, before you embark on building a program for assembling the E. coli X strain, we have to explain some genomic concepts and warm you up by having you solve a simpler problem of assembling a small virus.

2 Videos (Gesamt 11 min), 2 Lektüren, 1 Quiz
2 Videos
Assembling phage genome4m
2 Lektüren
What does it mean to assemble a genome?10m
Project Description10m
4 Stunden zum Abschließen

Assembling Genomes Using de Bruijn Graphs

DNA sequencing approach that led to assembly of a small virus in 1977 went through a series of transformations that contributed to the emergence of personalized medicine a few years ago. By the late 1980s, biologists were routinely sequencing viral genomes containing hundreds of thousands of nucleotides, but the idea of sequencing a bacterial (let alone the human) genome containing millions (or even billions) of nucleotides remained preposterous and would cost billions of dollars. In 1988, three biologists (independently and simultaneously!) came up with an idea to reduce sequencing cost and proposed the futuristic and at the time completely implausible method of DNA arrays. None of these three biologists could have possibly imagined that the implications of his own experimental research would eventually bring him face-to-face with challenging algorithmic problems. In this module you will learn about the algorithmic challenge of DNA sequencing using information about short k-mers provided by DNA arrays. You will also travel to the 18the century to learn about the Bridges of Konigsberg and solve a related problem of assembling a jigsaw puzzle!

5 Videos (Gesamt 24 min), 1 Quiz
5 Videos
Assembling genomes from k-mers4m
De Bruijn graphs3m
Bridges of Königsberg and universal strings4m
Euler theorem6m
8 Stunden zum Abschließen

Genome Assembly Faces Real Sequencing Data

Our discussion of genome assembly has thus far relied upon various assumptions. In this module, we will face practical challenges introduced by quirks in modern sequencing technologies and discuss some algorithmic techniques that have been devised to address these challenges. Afterwards, you will assemble the smallest bacterial genome that lives symbiotically inside leafhoppers. Its sheltered life has allowed it to reduce its genome to only about 112,091 nucleotides and 137 genes. And afterwards, you will be ready to assemble the E. coli X genome!

3 Videos (Gesamt 11 min), 1 Quiz
3 Videos
From reads to read-pairs3m
Genome assembly faces real sequencing data5m
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Top reviews from Genome Assembly Programming Challenge

von ASAug 5th 2018

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

von POAug 4th 2017

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



Alexander S. Kulikov

Visiting Professor
Department of Computer Science and Engineering

Michael Levin

Computer Science

Pavel Pevzner

Department of Computer Science and Engineering

Neil Rhodes

Adjunct Faculty
Computer Science and Engineering

Über University of California San Diego

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Über National Research University Higher School of Economics

National Research University - Higher School of Economics (HSE) is one of the top research universities in Russia. Established in 1992 to promote new research and teaching in economics and related disciplines, it now offers programs at all levels of university education across an extraordinary range of fields of study including business, sociology, cultural studies, philosophy, political science, international relations, law, Asian studies, media and communicamathematics, engineering, and more. Learn more on www.hse.ru...

Über die Spezialisierung Datenstrukturen und Algorithmen

This specialization is a mix of theory and practice: you will learn algorithmic techniques for solving various computational problems and will implement about 100 algorithmic coding problems in a programming language of your choice. No other online course in Algorithms even comes close to offering you a wealth of programming challenges that you may face at your next job interview. To prepare you, we invested over 3000 hours into designing our challenges as an alternative to multiple choice questions that you usually find in MOOCs. Sorry, we do not believe in multiple choice questions when it comes to learning algorithms...or anything else in computer science! For each algorithm you develop and implement, we designed multiple tests to check its correctness and running time — you will have to debug your programs without even knowing what these tests are! It may sound difficult, but we believe it is the only way to truly understand how the algorithms work and to master the art of programming. The specialization contains two real-world projects: Big Networks and Genome Assembly. You will analyze both road networks and social networks and will learn how to compute the shortest route between New York and San Francisco (1000 times faster than the standard shortest path algorithms!) Afterwards, you will learn how to assemble genomes from millions of short fragments of DNA and how assembly algorithms fuel recent developments in personalized medicine....
Datenstrukturen und Algorithmen

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