Deep learning in biology

计算基因组学工具解析肿瘤与免疫细胞的互作

参考：https://www.jianshu.com/p/04428f4f0c30

Tasks

重要的计算生物学和生物信息学paper：(深度学习应用)

知乎专栏的帖子（重要，系统的介绍，仁者见仁）：

目前机器学习在生物学领域有应用吗https://www.zhihu.com/question/41428117?from=profile_question_card
网络生物学与机器学习（上）：什么是机器学习https://zhuanlan.zhihu.com/p/38980158

非常重要！全部的参考列表在：https://github.com/hussius/deeplearning-biology部分paper提供code和tutorial，非常diverse

比如关于基因组：加粗的表示先看，暂时不看神经网络

A primer on deep learning in genomics：https://doi.org/10.1038/s41588-018-0295-5

Deep learning: new computational modelling techniques for genomics：https://www.nature.com/articles/s41576-019-0122-6

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics：https://doi.org/10.1371/journal.pone.0141287

Machine learning applications in genetics and genomics:https://doi.org/10.1038/nrg3920

一篇关于植物的，适合加深对机器学习的理解：

Machine learning for Big Data analytics in plants：https://doi.org/10.1016/j.tplants.2014.08.004

Machine learning and complex biological data：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1689-0

Recent Advances of Deep Learning in Bioinformatics and Computational Biology：https://www.frontiersin.org/articles/10.3389/fgene.2019.00214/full

Ten quick tips for machine learning in computational biology：https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0155-3#article-info

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State：这篇文章是在任兵老师 Integrative analysis of haplotype-resolved epigenomes across human tissues的参考文献中的，因为涉及随机森林所以放在这里，haplotype的原文解析记录在我的citavi6：https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002968

GWAS分析完整介绍：https://www.cnblogs.com/leezx/p/9013615.html