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lauraluebbert authored Oct 29, 2024
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Expand Up @@ -11,25 +11,25 @@ Harvard's Artificial Intelligence for Medicine and Science lab.
A LLM powered chatbot for bioinformatics ([documentation](https://brad-bioinformatics-retrieval-augmented-data.readthedocs.io/en/latest/index.html), [project main page](https://brad-bioinformatics-retrieval-augmented-data.readthedocs.io/_/downloads/en/latest/pdf/)).
- [scPRINT](https://www.jkobject.com/scPRINT/)
scPRINT is a large transformer model built for the inference of gene networks (connections between genes explaining the cell's expression profile) from scRNAseq data ([preprint](https://www.biorxiv.org/content/10.1101/2024.07.29.605556v1)).
- [AnoPrimer](https://sanjaynagi.github.io/AnoPrimer/landing-page.html):
- [AnoPrimer](https://sanjaynagi.github.io/AnoPrimer/landing-page.html)
AnoPrimer is a python package for primer design in An. gambiae and An. funestus, whilst considering genetic variation in wild whole-genome sequenced specimens in malariagen_data.
- [AvaTaR](https://github.com/zou-group/avatar)
Optimizing LLM Agents for Tool-Assisted Knowledge Retrieval (NeurIPS 2024) by James Zou Lab at Stanford University.
- [GRLDrugProp](https://github.com/Madscba/GRLDrugProp)
Graph representation learning for modelling drug properties.
- Rust implementation of gget: https://github.com/noamteyssier/ggetrs
- https://github.com/Superbio-ai/getbio
- https://github.com/yonniejon/AchillesPrediction
- https://github.com/ELELAB/cancermuts
- https://github.com/Benoitdw/SNPrimer
- https://github.com/louisjoecodes/a16z-hackathon-project
- https://github.com/EvX57/BACE1-Drug-Discovery
- https://github.com/vecerkovakaterina/hidden-genes-msc
- https://github.com/vecerkovakaterina/llm_bioinfo_agent
- https://github.com/greedjar74/upstage_AI_Lab
- https://github.com/alphavector/all
- Rust implementation of gget: [https://github.com/noamteyssier/ggetrs](https://github.com/noamteyssier/ggetrs)
- [https://github.com/Superbio-ai/getbio](https://github.com/Superbio-ai/getbio)
- [https://github.com/yonniejon/AchillesPrediction](https://github.com/yonniejon/AchillesPrediction)
- [https://github.com/ELELAB/cancermuts](https://github.com/ELELAB/cancermuts)
- [https://github.com/Benoitdw/SNPrimer](https://github.com/Benoitdw/SNPrimer)
- [https://github.com/louisjoecodes/a16z-hackathon-project](https://github.com/louisjoecodes/a16z-hackathon-project)
- [https://github.com/EvX57/BACE1-Drug-Discovery](https://github.com/EvX57/BACE1-Drug-Discovery)
- [https://github.com/vecerkovakaterina/hidden-genes-msc](https://github.com/vecerkovakaterina/hidden-genes-msc)
- [https://github.com/vecerkovakaterina/llm_bioinfo_agent](https://github.com/vecerkovakaterina/llm_bioinfo_agent)
- [https://github.com/greedjar74/upstage_AI_Lab](https://github.com/greedjar74/upstage_AI_Lab)
- [https://github.com/alphavector/all](https://github.com/alphavector/all)

Also see: https://github.com/pachterlab/gget/network/dependents
Also see: [https://github.com/pachterlab/gget/network/dependents](https://github.com/pachterlab/gget/network/dependents)

# 📃 Featured publications
- David Bradley et al., [The fitness cost of spurious phosphorylation.](https://doi.org/10.1038/s44318-024-00200-7) *The EMBO Journal* (2024). DOI: 10.1038/s44318-024-00200-7
Expand All @@ -49,6 +49,6 @@ Also see: https://github.com/pachterlab/gget/network/dependents
- Mingze Dong et al., [Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states.](https://doi.org/10.1101/2023.11.11.566161) *bioRxiv* (2023). DOI: 10.1101/2023.11.11.566161

# 📰 News
- Documentary short film about *gget*: https://youtu.be/cVR0k6Mt97o
- Podcast episode for the Prototype Fund Public Interest Podcast about the importance of open-source software and its role in academic research (in German): https://public-interest-podcast.podigee.io/33-pips4e4
- Prototype Fund announcement: https://prototypefund.de/project/gget-genomische-datenbanken/
- Documentary short film about *gget*: [https://youtu.be/cVR0k6Mt97o](https://youtu.be/cVR0k6Mt97o)
- Podcast episode for the Prototype Fund Public Interest Podcast about the importance of open-source software and its role in academic research (in German): [https://public-interest-podcast.podigee.io/33-pips4e4](https://public-interest-podcast.podigee.io/33-pips4e4)
- Prototype Fund announcement: [https://prototypefund.de/project/gget-genomische-datenbanken](https://prototypefund.de/project/gget-genomische-datenbanken/)

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