MIT Deep Learning Genomics - Lecture 6 - Regulatory Genomics (Spring 2020)

MIT 6.874 Lecture 6. Spring 2020
Course website: mit6874.github...
Lecture slides:
Lecturer: Manolis Kellis
Lecture outline:
1. Biological foundations: Building blocks of Gene Regulation
- Gene regulation: Cell diversity, Epigenomics, Regulators (TFs), Motifs, Disease role
- Probing gene regulation: TFs/histones: ChIP-seq, Accessibility: DNase/ATAC-seq
2. Classical methods for Regulatory Genomics and Motif Discovery
- Enrichment-based motif discovery: Expectation Maximization, Gibbs Sampling
- Experimental: PBMs, SELEX. Comparative genomics: Evolutionary conservation.
3. Regulatory Genomics CNNs (Convolutional Neural Networks): Foundations
- Key idea: pixels == DNA letters. Patches/filters == Motifs. Higher == combinations
- Learning convolutional filters == Motif discovery. Applying them == Motif matches
4. Regulatory Genomics CNNs/RNNs in Practice: Diverse Architectures
- DeepBind: Learn motifs, use in (shallow) fully-connected layer, mutation impact
- DeepSea: Train model directly on mutational impact prediction
- Basset: Multi-task DNase prediction in 164 cell types, reuse/learn motifs
- ChromPuter: Multi-task prediction of different TFs, reuse partner motifs
- DeepLIFT: Model interpretation based on neuron activation properties
- DanQ: Recurrent Neural Network for sequential data analysis

[@ryanmedhaug163]

Your enthusiasm for your subject is contagious!! Such great lectures.

[@quantumcrash7266]

Your channel is a hidden goldmine!

[@toratora1983]

The dude expalining is class... beleive u me sir u can even xplain my grandmom genomics... u made the topic so simplified wow thanks from Bombay..and wish u all a great day

[@Tracks777]

amazing stuff

[@rohitgavirni3400]

Learned a lot today!

[@issacrussell4833]

Great lecture

[@lotuseyes3409]

Thank you!

[@madhusukumaran2634]

Basset - www.ncbi.nlm.nih.gov/pmc/articles/PMC4937568/pdf/990.pdf
DeepBind - www.researchgate.net/publication/280496611_Predicting_the_sequence_specificities_of_DNA-_and_RNA-binding_proteins_by_deep_learning
DeepSea - www.ncbi.nlm.nih.gov/pmc/articles/PMC4768299/pdf/nihms757739.pdf
Deep learning at base-resolution - www.biorxiv.org/content/10.1101/737981v1.full.pdf

[@zx4337]

Dr. Kellis, where can I obtain the reference for ChromPuter?