À propos de ce cours
4.4
82 notes
25 avis
Spécialisation
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Niveau avancé

Niveau avancé

Heures pour terminer

Approx. 9 heures pour terminer

Recommandé : 5 hours/week...
Langues disponibles

Anglais

Sous-titres : Anglais...

Compétences que vous acquerrez

Data StructureAlgorithmsAlgorithm DesignString (Computer Science)
Spécialisation
100% online

100% online

Commencez dès maintenant et apprenez aux horaires qui vous conviennent.
Dates limites flexibles

Dates limites flexibles

Réinitialisez les dates limites selon votre disponibilité.
Niveau avancé

Niveau avancé

Heures pour terminer

Approx. 9 heures pour terminer

Recommandé : 5 hours/week...
Langues disponibles

Anglais

Sous-titres : Anglais...

Programme du cours : ce que vous apprendrez dans ce cours

Semaine
1
Heures pour terminer
5 heures pour terminer

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....
Reading
2 vidéos (Total 11 min), 2 lectures, 1 quiz
Video2 vidéos
Assembling phage genome4 min
Reading2 lectures
What does it mean to assemble a genome?10 min
Project Description10 min
Semaine
2
Heures pour terminer
4 heures pour terminer

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!...
Reading
5 vidéos (Total 24 min), 1 quiz
Video5 vidéos
Assembling genomes from k-mers4 min
De Bruijn graphs3 min
Bridges of Königsberg and universal strings4 min
Euler theorem6 min
Semaine
3
Heures pour terminer
8 heures pour terminer

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!...
Reading
3 vidéos (Total 11 min), 1 quiz
Video3 vidéos
From reads to read-pairs3 min
Genome assembly faces real sequencing data5 min
4.4

Meilleurs avis

par ASAug 5th 2018

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

par POAug 4th 2017

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

Enseignants

Avatar

Alexander S. Kulikov

Visiting Professor
Department of Computer Science and Engineering
Avatar

Michael Levin

Lecturer
Computer Science
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Pavel Pevzner

Professor
Department of Computer Science and Engineering
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Neil Rhodes

Adjunct Faculty
Computer Science and Engineering

À propos de University of California San Diego

UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory....

À propos de 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 communications, IT, mathematics, engineering, and more. Learn more on www.hse.ru...

À propos de la Spécialisation Data Structures and Algorithms

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....
Data Structures and Algorithms

Foire Aux Questions

  • Une fois que vous êtes inscrit(e) pour un Certificat, vous pouvez accéder à toutes les vidéos de cours, et à tous les quiz et exercices de programmation (le cas échéant). Vous pouvez soumettre des devoirs à examiner par vos pairs et en examiner vous-même uniquement après le début de votre session. Si vous préférez explorer le cours sans l'acheter, vous ne serez peut-être pas en mesure d'accéder à certains devoirs.

  • Lorsque vous vous inscrivez au cours, vous bénéficiez d'un accès à tous les cours de la Spécialisation, et vous obtenez un Certificat lorsque vous avez réussi. Votre Certificat électronique est alors ajouté à votre page Accomplissements. À partir de cette page, vous pouvez imprimer votre Certificat ou l'ajouter à votre profil LinkedIn. Si vous souhaitez seulement lire et visualiser le contenu du cours, vous pouvez accéder gratuitement au cours en tant qu'auditeur libre.

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