02-604 Fundamentals of Bioinformatics
02-604 COURSE PROFILE
| Course Level | Graduate |
| Units | 12 |
| Special Permission Required? (If yes, see “Notes:) | No |
| Frequency Offered | Spring |
| Course Relevance (who should take this course?) | This course is designed for first-year MS students in computational biology or students from other disciplines who desire a broad introduction to some of the most fundamental algorithmic approaches in analyzing the large datasets generated from experiments in molecular biology. |
| Key Topics |
Identifying replication origins in bacterial genomesRandomized algorithms for motif finding in DNA sequences Graph-based algorithms for genome assembly Brute-force algorithms for antibiotic analysis Dynamic programming algorithms for sequence alignment Combinatorial algorithms for genome rearrangement analyses Evolutionary tree construction algorithms Clustering algorithms for gene expression analyses Combinatorial pattern matching algorithms applied to DNA read mapping Hidden Markov models for comparing rapidly mutating genetic sequences Statistical analysis for computational proteomics |
| Background Knowledge | A solid background in introductory programming (such as that provided by 02-601) is essential. Some knowledge of basic algorithms and data structures is also helpful. Background biology knowledge is not needed. |
| Assessment Structure | Comprehension quizzes. (10% of grade)Weekly write up and participation (10% of grade) Programming assignments. (40% of grade) Bioinformatics Software challenges. (10% of grade) Midterm. (10% of grade) Final exam (20% of grade) |
| Most Recent Syllabus | http://compeau.cbd.cmu.edu/wp-content/uploads/2018/01/syllabus_604.pdf |
| Sample Lecture Recordings | http://youtube.com/user/bioinfalgorithms |
| Learning Resources | The course companion can be found at http://bioinformaticsalgorithms.com |
| Department Website | https://cbd.cmu.edu |
| College Website | https://cs.cmu.edu |
| Updated January 2018 | |