General information

Course Logistics

Prerequisites and Grading

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 Gradescope.

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.

Schedule

Date Content Reading Slides Assignments
Basics
9/26 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
10/1 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.
slides
10/3 Research showcase (Hanwen Xu, generative AI for cancer pathology) GigaPath.
pathologist–AI collaboration.
AI for pathology survey paper.
HW1 is here
10/8 Sequence aligment and analysis (Part 2) Deep-learning language models help to improve protein sequence alignment . Slides
10/10 Protein function prediction (part 1)
Graph to Sequence Alignment CAFA4 CAFA3 CAFA2
Slides
10/15 Protein function prediction (part 2) Protein family classification
10/17 Research showcase (Zixuan Liu, generative AI for optical coherence tomography) RETFound
OCTCube
Graph (systems biology)
10/22 Introduction to biomedical graph analysis (part 1) Graphs in molecular biology Slides HW2 is here
10/24 Introduction to biomedical graph analysis (part 2) HW1 due
10/29 Research showcase (Xiao Wang, generative AI for protein structure analysis) AlphaFold
10/31 Biomedical graph diffusion (part 1) Network-based tumor stratification
Supervised network-based tumor stratification
Slides
11/5 Research showcase (Patricia Xiao, generative AI for kidney transplant) AI for cardiovascular
11/7 Research showcase (Yu Zhang, generative AI for mamamgraph-based breast cancer diagnosis)
11/12 Biomedical graph diffusion (part 2)
Genomics
11/14 Genomics for precision medicine (drug repurposing) Towards precision medicine slides HW2 due! HW3 is released.
11/19 Genomics for precision medicine (drug combination)
11/21 Research showcase (Tangqi Fang, generative AI for Hi-C chromatin structure analysis) ORCA
11/26 Research showcase (Yongkang Li, generative AI for label-free mouse brain imaging) Cell Painting
12/3 Research showcase (Ran Zhang, generative AI for single cell foundation models) scFoundation,scGPT
12/5 Research showcase (Sheng Wang, generative AI for Medicine) Literature review and HW3 are due on Dec 10th!