Embedded Files
Lectures (CSB 004)
Lectures (CSB 004)
- Monday, Wednesday, Friday: 3:00 - 3:50 pm
- Friday: 4:00 - 4:50 pm, discussion
Logistics
Logistics
Course staff
Course staff
- Yana Safonova, instructor: isafonova at ucsd dot edu
- Owen Chapman, TA: ochapman at eng dot ucsd dot edu
- Arya Kaul, tutor: a1kaul at ucsd dot edu
Office hours
Office hours
- Yana: Wednesday, 1:30 pm – 2:30 pm, Atkinson Hall, room 4105
- Arya: Tuesday, 11 am – 12 pm, CSE dungeon
- Owen: Wednesday, 7pm – 8pm, CSE dungeon B240
CSE 180 syllabus and schedule
CSE 180 syllabus and schedule
UCSD Academic and Administrative Calendar 2018–2019
Week 1. Introduction
Week 1. Introduction
- Jan 7th, Monday: Course Introduction.
- Jan 9th, Wednesday: Introduction to Bioinformatics, part I.
- Jan 11th, Friday: Introduction to Bioinformatics, part II.
Week 2. Chapter 1: Where in the Genome Does DNA Replication Begin? (Part 1)
Week 2. Chapter 1: Where in the Genome Does DNA Replication Begin? (Part 1)
- Jan 14th, Monday
- 1.1. A Journey of a Thousand Miles...
- 1.2. Hidden Messages in the Replication Origin, Part 1.
- Homework for Jan14th: Chapters 1.1 and 1.2. Rosalind problems "Installing Python", "Variables and Some Arithmetic", "Strings and Lists", "Conditions and Loops", "Working with Files", and "Dictionaries".
- Quiz 1.
- Programming practice “Counting nucleotides in a string”.
- Jan 16th, Wednesday
- 1.3. Hidden Messages in the Replication Origin (Part 2).
- 1.4. Some Hidden Messages are More Surprising than Others.
- Homework for Jan 16th: Chapters 1.3 and 1.4. Rosalind problems "Counting DNA Nucleotides" and "Complementing a Strand of DNA".
- Quiz 2.
- Programming practice “Counting k-mers in a string”.
- Jan 18th, Friday
- 1.5. An Explosion of Hidden Messages.
- 1.6. Detour: The Most Beautiful Experiment in Biology.
- 1.7. Detour: Directionality of DNA Strands.
- Homework for Jan 18th: Chapters 1.5 - 1.7.
- Programming practice “A naive algorithm for finding oriC”.
Week 3. Chapter 2: Where in the Genome Does DNA Replication Begin? (Part 2)
Week 3. Chapter 2: Where in the Genome Does DNA Replication Begin? (Part 2)
- Jan 21st, Monday: Martin Luther King, Jr. Holiday
- Jan 23rd, Wednesday.
- 2.1. The Simplest Way to Replicate DNA.
- 2.2. Asymmetry of Replication.
- 2.3. Peculiar Statistics of the Forward and Reverse Half-Strands.
- Homework for Jan 23rd: Chapters 2.1 - 2.3. Rosalind problems "Transcribing DNA into RNA", "Computing GC Content", "Find All Occurrences of a Pattern in a String", and "Find the Most Frequent Words in a String".
- Quiz 3 and Python data structures, part I.
- Jan 25th, Friday
- 2.4. The Skew Diagram.
- 2.5. Some Hidden Messages Are More Elusive than Others.
- 2.6. A Final Attempt at Finding DnaA Boxes in E. coli.
- Homework for Jan 25th: Chapters 2.4 - 2.6. Rosalind problems "Compute the Hamming Distance Between Two Strings" and "k-Mer Composition".
- Quiz 4 and Python data structures, part II.
Week 4. Chapter 3: Which DNA Patterns Play The Role of Molecular Clocks? (Part 1)
Week 4. Chapter 3: Which DNA Patterns Play The Role of Molecular Clocks? (Part 1)
- Jan 28th, Monday:
- Discussion of peer-reviewed questions to Chapters 1 and 2.
- Homework to Jan 28th: Rosalind problems "Find Frequent Words with Mismatches and Reverse Complements" and "Find the Most Frequent Words with Mismatches in a String".
Please also prepare up to 5 questions about Chapters 1 and 2 and send it to Yana by Monday, Jan 28th, 9:00 am. Questions may cover various aspects of finding the origin of replication (limitation of methods, alternative approaches, biomedical applications) or express concerns about the quality of the explanations provided in Chapters 1, 2. Each reasonable question will be awarded by 1 point (max 5 points) and the points will be included to Quiz part during the final grading. IMPORTANT: Questions sent after the deadline won't be considered.
- Jan 30th, Wednesday.
- 3.1 Do We Have a "Clock" Gene?
- 3.2 Motif Finding is More Difficult Than You Think.
- 3.3 Scoring Motifs.
- Homework to Jan 30th: Chapters 3.1 - 3.3.
- Big-O notation and fast algorithms for exact string matching.
- Feb 1st, Friday
- 3.4 Greedy Motif Search.
- Homework to Feb 1st: Chapter 3.4.
- Motif representation and sequence alignment.
Week 5. Chapter 4: Which DNA Patterns Play The Role of Molecular Clocks? (Part 2)
Week 5. Chapter 4: Which DNA Patterns Play The Role of Molecular Clocks? (Part 2)
- Feb 4st, Monday:
- 4.1 Motif Finding Meets Oliver Cromwell.
- Homework to Feb 4th: Chapter 4.1.
- Quiz 5 and introduction to probability theory, part I.
- Feb 6st, Wednesday:
- 4.2 Randomized Motif Search.
- Homework to Feb 6th: Chapter 4.2.
- Introduction to probability theory, part II.
- Feb 8st, Friday:
- 4.3 How Can a Randomized Algorithm Perform So Well?
- Homework to Feb 8th: Chapter 4.3.
- Programming practice to Midterm 1.
Week 6. Midterm 1. Topics of final projects. Chapter 5: Unix command line
Week 6. Midterm 1. Topics of final projects. Chapter 5: Unix command line
- Feb 11th, Monday
- Midterm 1 [practice test].
- Homework to Feb 11th: Rosalind problems Consensus and Profile, Find a Profile-most Probable k-mer in a String, and New Motif Discovery.
- Feb 13th, Wednesday:
- 5.1 The Blinking Cursor
- Command line practice, part I.
- Feb 15th, Friday:
- 5.2 Data, Applications, and Scripts.
- 5.3 Git, the "Undo" Button of Software Development.
- Homework to Feb 15th: Chapters 5.1.
- Command line practice, part II. Applications of sequencing data to biological problems.
- Final project examples
Week 7. Chapter 6: Investigating the Foodborne Outbreak (Genome Assembly Project)
Week 7. Chapter 6: Investigating the Foodborne Outbreak (Genome Assembly Project)
- Feb 18th, Monday, Presidents' Day Holiday
- Feb 20th, Wednesday:
- Homework to Feb 20th: Chapters 5.2 and 5.3.
- Genome assembly, part I
- Feb 22nd, Friday:
- 6.1. The Start of the Outbreak
- 6.2. The Mysterious Strain
- 6.3. A Puzzle of Million Pieces
- Genome assembly, part II
- Homework to Feb 22nd: Chapters 6.1 - 6.3
Week 8. Chapter 7: Of Mice and Men (RNA Sequencing and Gene Expression Analysis)
Week 8. Chapter 7: Of Mice and Men (RNA Sequencing and Gene Expression Analysis)
- Feb 25th, Monday:
- 6.4. Eyewitness Identification
- 6.5 What is the genetic cause of HUS?
- 6.6. Antibiotic Resistance and its Origin
- 6.7. Detour: Tools, Databases and Formats
- Quiz. Genome assembly, part III
- Homework to Feb 25th: Chapters 6.4 - 6.7
- Feb 27th, Wednesday
- 7.1. Are gene expression profiles in human and mouse brains similar?
- 7.2. Studying the Brain
- Genome assembly challenges. Alignment tools, part I
- Homework to Feb 27th: Chapters 7.1 - 7.2
- Mar 1st, Friday
- 7.3. Comparing Expression Levels
- 7.4. Comparing Workflows
- Alignment tools, part II
- Homework to Mar 1st: Chapters 7.3 - 7.4
Week 9. Chapter 8: 65 Roses (Whole Genome and Whole Exome Sequencing)
Week 9. Chapter 8: 65 Roses (Whole Genome and Whole Exome Sequencing)
- Mar 4th, Monday
- 7.5. Detour: Tools, Databases and Formats
- Quiz. Alignment tools, part III. Analysis of RNA-seq data, part I
- Homework for Mar 4th: Chapter 7.5. Genome assembly homework.
- Mar 6th, Wednesday
- 8.1. Can We Find All Mutations Causing Cystic Fibrosis?
- 8.2. Pros and Cons of Exome Sequencing
- Analysis of RNA-seq data, part II
- Homework to Mar 6th: Chapters 8.1, 8.2
- Mar 8th, Friday
- 8.3 Looking for Genetic Diseases
- 8.4. Detour: Tools, Databases and Formats.
- 8.5 Detour: Walkthroughs
- Practice to Midterm 2
- Homework to Mar 8th: Chapters 8.3 - 8.5.
Week 10. Midterm 2. Chapter 9: Learning from a Trio
Week 10. Midterm 2. Chapter 9: Learning from a Trio
- Mar 11th, Monday
- 9.1 Sequencing Trios
- Finding genomic variations: haplotype assembly, sequencing trio, GWAS
- Homework to Mar 11th: Chapter 9.1. Alignment homework
- Mar 13th, Wednesday
- Midterm 2 [practice test].
- Mar 15th, Friday
Final week, presentations of final projects
Final week, presentations of final projects
- Wednesday, Mar 20th, 3:00 - 5:59 PM, CSB 004
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