Computational Methods in Genomics & Medicine

约 435 个字 预计阅读时间 1 分钟

这门课是 UCB 的 COMPSCI 194/294-172。

Instructor: Nilah Ioannidis, nilah@berkeley.edu

Course description: This special topics course will cover the computational, statistical and biological background required for students to understand recent research in the field of computational genomics. Each course topic will be motivated by one or more key research papers in the field. We will cover computational methods including hidden Markov models, machine learning approaches for classification and regression, convolutional neural networks, and their application to genome annotation, genome-wide association studies, clinical variant interpretation, and predicting the impact of genetic variation on molecular phenotypes such as transcription factor binding, histone modifications, chromatin accessibility, and gene expression.

---

授课老师是白人美女AP老师，除了华裔剩下的要素都齐全了，还是非常有意思的身份。授课时间是每周一下午的3点到6点，总共就12节课，每次的上课时间会比较久，整体听下来感觉英语是最能听懂的。课程主要涉及到用 AI 方法去做生信方面的一些工作，然后中间有大量读论文训练，作业是代码+数学题，实践性和科研性都有涉及到，非常不错的一门课程。

Date	Topics
9/2	NO CLASS (Labor Day)
9/9	1. Course introduction 2. Lecture 1.1 (HMMs and genome annotation)
9/16	1. Lecture 1.2 (HMMs and genome annotation) 2. Lecture 1.3 (Genomics background) [HW1 assigned - due Friday 9/27]
9/23	1. Instructor-led paper presentation GENSCAN 2. Lecture 2.1 (Linear/logistic regression and GWAS)
9/30	1. Student paper presentation ChromHMM 2. Lecture 2.2 (Linear/logistic regression and GWAS) [HW2 assigned - due Friday 10/11]
10/7	1. Student paper presentation COVID-19 GWAS 2. Lecture 3.1 (Machine learning and variant effect prediction)
10/14	1. Student paper presentation Polygenic risk scores 2. Lecture 3.2 (Machine learning and variant effect prediction) [HW3 assigned - due Friday 10/25]
10/21	1. Student paper presentation VEST 2. Lecture 4.1 (CNNs and sequence-to-function models)
10/28	1. Student paper presentation CADD 2. Lecture 4.2 (CNNs and sequence-to-function models) [HW4 assigned - due Friday 11/15]
11/4	1. Student paper presentation DeepSEA 2. Lecture 4.3 (CNNs and sequence-to-function models)
11/11	NO CLASS (Veterans Day)
11/18	1. Student paper presentation Basenji 2. Lecture 5.1 (Language models for proteins and DNA) [HW5 assigned - due Friday 12/6]
11/25	1. Student paper presentation SpliceAI 2. Lecture 5.2 (Language models for proteins and DNA)
12/2	1. Student paper presentation ESM-1b 2. Guest speaker: TBA