Regulatory Genomics - Deep Learning in Life Sciences - Lecture 07 (Spring 2021)

Deep Learning in Life Sciences - Lecture 07 - Regulatory Genomics (Spring 2021)
6.874/6.802/20.390/20.490/HST.506 Spring 2021 Prof. Manolis Kellis
Deep Learning in the Life Sciences / Computational Systems Biology
Playlist: • MIT Deep Learning in L...
Latest slides and course today: compbio.mit.edu/6874
Spring 2021 slides and materials: mit6874.github.io/
0:00 Logistics
2:30 Overview
3:09 Biological foundations of gene regulation
16:21 DNA motifs
21:05 Technologies for probing gene regulation
26:07 Deep learning at base-resolution reveals cis-regulatory motif syntax
31:42 BPNet: predicting base-resolution profiles from DNA sequence
43:00 Interpreting the predictions of BPNet
55:42 Experimental validation of BPNet predictions
58:38 Enchancing epigenomic data with deep learning
1:04:54 AtacWorks: Improving the quality of ATAC-seq signals
1:09:24 Performance of AtacWorks
1:19:35 Applying AtacWorks to investigate lineage priming

[@constantlychangin]

Great!

[@janwaska521]

Professor Kellis,
Thank you for the excellent lectures,
Off topic:
How are the morphogen sources determined?
How are their type, activation time, secretion rate and stop time determined and established?

[@janwaska4081]

Professor Kellis, how do the bioelectrical networks / morphogenetic code that Dr Michael Levin presents in several videos available on CZcams relate to the regulatory genomics? Thanks.

[@janwaska521]

How are the epigenetic markers established?

[@janwaska521]

How are the TFBS motifs established in the DNA?

[@janwaska4081]

Why does the CZcams headline says "Regulatory Genomics - Deep Learning in Life Sciences - Lecture 07 (Spring 2021)" but the front slide shows: "Lecture 6: Regulatory Genomics" ? Is it lecture 6 or 7?

[@ManolisKellis1]

The slide has the mistake. It's lecture 7

[@janwaska4081]

@@ManolisKellis1 Thank you professor Kellis.