# CCTB Deep Learning Journal Club

The idea is not only to discuss papers about deep learning and its applications, but also to use it as learning opportunity and to try out implementations - anyone is welcome to join, regardless of experience.

## Next DLJC

Thursday, July 7th, at 13:00

https://go.uniwue.de/cia-zoom

Vaishnav et al, [*The evolution, evolvability and engineering of gene regulatory DNA*](https://www.nature.com/articles/s41586-022-04506-6), Nature (2022)
> detecting signatures of natural selection in non-coding DNA

## Paper selection

Please vote for your favourite by adding :+1: or make your own suggestions:

- *your suggestion here...*

## Zotero group

We have a [Zotero group](https://www.zotero.org/groups/2172420/cctb_deep_learning_journal_club/library) to collect papers - you can join with your Zotero login to add your own suggestions, or just [view it on the web](https://www.zotero.org/groups/2172420/cctb_deep_learning_journal_club/library).

## Mattermost

The [deep-learning](https://cctb-intern.biologie.uni-wuerzburg.de/cctb/channels/deep-learning) channel is for suggesting and selecting papers, and for announcements.

## Past and future DLJC meetings

since the relaunch 2022:

| Date | Paper | Presenter |
| -------- | -------- | -------- |
| 03/02/22 | [Highly accurate protein structure prediction with AlphaFold](https://www.nature.com/articles/s41586-021-03819-2) | Philip |
| 10/03/22 | [Biologically informed deep neural network for prostate cancer discovery](https://www.nature.com/articles/s41586-021-03922-4) | Markus |
| 07/04/22 | [Magnetic control of tokamak plasmas through deep reinforcement learning](https://www.nature.com/articles/s41586-021-04301-9) | Chris |
| 19/05/22 | [Using deep learning to annotate the protein universe](https://www.nature.com/articles/s41587-021-01179-w) | |
| 07/07/22 | [The evolution, evolvability and engineering of gene regulatory DNA](https://www.nature.com/articles/s41586-022-04506-6) | |

2017-2020:

| Date | Paper |
| -------- | -------- |
| 28/04/17 | [Automated synaptic connectivity inference for volume electron microscopy](http://www.nature.com/nmeth/journal/v14/n4/pdf/nmeth.4206.pdf) |
| 16/03/18 | [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://link.springer.com/chapter/10.1007%2F978-3-319-46723-8_49) |
| 20/04/18 | [Genome-enabled prediction using probabilistic neural network classifiers](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2553-1) |
| 15/11/19 | [Grandmaster level in StarCraft II using multi-agent reinforcement learning](https://doi.org/10.1038/s41586-019-1724-z) |
| 13/12/19 | [The Unreasonable Effectiveness of Recurrent Neural Networks](http://karpathy.github.io/2015/05/21/rnn-effectiveness/) |
| 31/01/20 | [High-precision automated reconstruction of neurons with flood-filling networks](https://doi.org/10.1038/s41592-018-0049-4) |