机器学习/深度学习与基因组学资源搜罗

作为一个genomics方向的研究者，在AI的浪潮中总是避免不了焦虑。担心被时代抛弃。

在以前，不识字的我们称之为文盲；

再后来，英语不好是地球村的文盲；

接着到了信息时代，不会编程也是某种意义上的“文盲”；

那到了AI的时代呢？

焦虑解决不了任何问题，战胜焦虑的最好办法就是面对焦虑!

所以我今天整理了一下目前机器学习/深度学习与基因组相关的研究的一些资源供自己学习，也分享给各位同路人。

论文：

1. Nature Reviews Genetics

Deep learning: new computational modelling techniques for genomics

• https://www.nature.com/articles/s41576-019-0122-6

2. Nature Reviews Genetics

Obtaining genetics insights from deep learning via explainable artificial intelligence

• https://www.nature.com/articles/s41576-022-00532-2

3. Briefings in Bioinformatics

Interpretation of deep learning in genomics and epigenomics

• https://doi.org/10.1093/bib/bbaa177

4. BMC Human Genomics

review of deep learning applications in human genomics using next-generation sequencing data

• https://humgenomics.biomedcentral.com/articles/10.1186/s40246-022-00396-x

5. Frontiers in Systems Biology

A Brief Review on Deep Learning Applications in Genomic Studies

• https://www.frontiersin.org/journals/systems-biology/articles/10.3389/fsysb.2022.877717/full

6. PeerJ

Genomics enters the deep learning era

• https://peerj.com/articles/13613/

7. Communications Biology

A self-supervised deep learning method for data-efficient training in genomics

• https://www.nature.com/articles/s42003-023-05310-2

• https://github.com/GenomeNet/self-genomenet/

8. International Journal of Molecular Sciences

Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models

• https://www.mdpi.com/1422-0067/24/21/15858

9. Current Opinion in Biotechnology

Deep learning in regulatory genomics: from identification to design

• https://linkinghub.elsevier.com/retrieve/pii/S095816692200221X

10. Nature Computational Science

A software framework for end-to-end genomic sequence analysis with deep learning

• https://www.nature.com/articles/s43588-023-00557-5

• https://eugene-tools.readthedocs.io/en/latest/index.html

• https://today.ucsd.edu/story/introducing-eugene-an-easy-to-use-deep-learning-genomics-software

教程/工具

1. 斯坦福大学 Deep Learning Tutorial

• http://ufldl.stanford.edu/tutorial/

2. 布朗大学 Deep Learning in Genomics的slides

• https://cs.brown.edu/courses/csci1850/lectures.html

3. Deep Learning Genomics Primer

• https://github.com/abidlabs/deep-learning-genomics-primer

4. Janggu - Deep learning for Genomics

• https://github.com/BIMSBbioinfo/janggu
• https://www.deepgenomics.com/AI-Platform/

视频

1. Deep Learning in Life Sciences

• https://www.youtube.com/watch?v=0jWOZoTsYzI&list=PLypiXJdtIca5sxV7aE3-PS9fYX3vUdIOX

2. Session 1: Algorithm development and machine learning approaches in genomics

• https://www.youtube.com/watch?v=6WEBnAXbiWY

3. James Zou: "Deep learning for genomics

• Introduction and examples": https://www.youtube.com/watch?v=JYt1IqdDAPc

4. Deep learning for genomics - Anshul Kundaje

• https://www.youtube.com/watch?v=X5mdoxR9qag

5. Genomics with Deep Learning: A Concise Overview | AISC

• https://www.youtube.com/live/8SYDJ_62paM

6. Interpretable machine learning for genomics: examples, opportunities, and challenges: David Watson

• https://www.youtube.com/watch?v=tdn0L5KbkK8

7. NNFC Workshop: Deep learning for genomic discovery

• https://www.broadinstitute.org/videos/nnfc-workshop-deep-learning-genomic-discovery

8. 一个MIT的视频课程的播放列表，包含了好多视频课程

• https://compbio.mit.edu/videos.html