Grading: Your grade will be based on two parts: 3 homework assignments, literature review, and discussion in three research Showcase lectures. There are no credit given for attending other lectures. There are no exams and no quizzes.
Homework assigments: Only written assignments, no programming assignments. Submit to Canvas.
Research Showcase: 45-minute invited presentation about ongoing computational biology research by Allen School PhD students and the instructor. The instructor will then lead the discussion about the limitation, potential improvement and future directions.
Late Policy: We will allow 3 total late days. If an assignment is submitted late and this exceeds your 3 late days, that assignment will receive 0 credit. Late days may be spread over any number of assignments, but the total number may not exceed 3. Late days are rounded up so that an assignment that is 28 hours late accumulated 2 late days.
| Date | Content | Reading | Slides | Assignments |
|---|---|---|---|---|
| Basics | ||||
| 9/25 | Welcome/overview. Introduction to computational biology. | Molecular Biology for Computer Scientists
Central dogma (10 mins) Transcription/translation Yu, Michael Ku, et al. "Translation of genotype to phenotype by a hierarchy of cell subsystems." Cell systems 2.2 (2016): 77-88. |
slides | |
| Sequence | ||||
| 9/30 |
Sequence aligment and analysis (Part 1) |
A survey of best practices for RNA-seq data analysis. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. | ||
| 10/2 | Sequence aligment and analysis (Part 2) | Deep-learning language models help to improve protein sequence alignment . | HW1 is here | |
| 10/7 | Protein function prediction (part 1) | Protein family classification | slides | |
| 10/9 | Protein function prediction (part 2) | Graph to Sequence Alignment CAFA4 CAFA3 CAFA2 |
||
| Graph (systems biology) | ||||
| 10/14 | Introduction to biomedical graph analysis (part 1) | Graphs in molecular biology | slides | hw 2 is here |
| 10/16 | Research showcase (Wei Qiu, generative AI for aging research) | |||
| 10/21 | Introduction to biomedical graph analysis (part 2) | |||
| 10/23 | Research showcase (Zixuan Liu, generative AI for retinal imaging analysis) |
RETFound OCTCube |
||
| 10/28 | Biomedical graph diffusion (part 1) | Network-based tumor stratification Supervised network-based tumor stratification |
slides | HW1 due |
| 10/30 | Research showcase (Hanwen Xu, generative AI for cancer pathology) | |||
| 11/4 | Biomedical graph diffusion (part 2) | |||
| 11/6 | Research showcase (Yongkang Li, generative AI for label-free mouse brain imaging) | Cell Painting | ||
| 11/11 | UW Holiday, no class, Veterans Day | |||
| Genomics | ||||
| 11/13 | Research showcase (Shengqi Hang, generative AI for chromatin structure analysis) | HW2 due! | ||
| 11/18 | Genomics for precision medicine | Towards precision medicine | slides | HW3 is here |
| 11/20 | Research showcase (Chanwoo Kim, interpretable AI for pathology data analysis) | MONET | ||
| 11/25 | Research showcase (Sheng Wang, generative AI for Medicine) | |||
| 12/2 | Research showcase (Patricia Xiao, generative AI for cardiovascular disease analysis) | AI for cardiovascular | ||
| 12/4 | Research showcase (Tangqi Fang, generative AI for genomic data analysis) | ORCALiterature review and HW3 are due on Dec 10th! | ||