# SemiBin notes & more information

## Manuscripts

SemiBin1 (also introduces the architecture):

> Pan, S.; Zhu, C.; Zhao, XM.; Coelho, LP. [A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments](https://doi.org/10.1038/s41467-022-29843-y). Nat Commun 13, 2326 (2022). https://doi.org/10.1038/s41467-022-29843-y

SemiBin2 (self-supervised approach & long-reads):

> Pan, S.; Zhao, XM; Coelho, LP. [SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing](https://doi.org/10.1093/bioinformatics/btad209). *Bioinformatics* Volume 39, Issue Supplement 1, June 2023, Pages i21–i29; [https://doi.org/10.1093/bioinformatics/btad209](https://doi.org/10.1093/bioinformatics/btad209)

## Tool links

- SemiBin github: https://github.com/BigDataBiology/SemiBin
- SemiBin docs: https://semibin.rtfd.io/
- SemiBin mailing-list (to keep up to date & ask questions): https://groups.google.com/g/semibin-users
- Software commitments: https://www.big-data-biology.org/software/commitments/

## Videos

1. Tutorial: https://youtu.be/L7YWtYVoI8U?si=ZqmogqW8HzwlR2Sm
2. Introduction to SemiBin: https://youtu.be/4sj4VrpXARs?si=fpdky7PrklJmjsSE

## Text-based tutorials:
1. https://github.com/BigDataBiology/VideoTutorials/tree/main/1__NGLessSemiBin
2. https://github.com/BigDataBiology/SemiBin_tutorial

## Other SemiBin notes

- Presentation (does **not** work on mobile, on a computer, press `?` to get help and `F11` to make it full screen): https://2023-07-25-talk-semibin.big-data-biology.org/

## Our contact information

- Luis Pedro Coelho: [e-mail] (or schedule a [video call](https://cal.com/luis-pedro-coelho/zoom-15))
- Shaojun Pan: [e-mail]
- Group website: https://big-data-biology.org/
- We are looking for PhD students (see https://big-data-biology.org/manual)
- There are other groups in the Centre for Microbiome Research too! It's a great environment