Burstein lab

4/4 To allow standardized benchmarking for future tool development, we also released B-PPI-DB, a curated bacterial PPI database derived from STRING: doi.org/10.5281/zeno...

We hope B-PPI is just the first of many efficient bacterial PPI predictors!

3/4 B-PPI outperforms other rapid methods for bacterial PPI prediction without the high cost of structural folding and generalizes to unseen interactions with minimal fine-tuning.

2/4 B-PPI is a cross-attention model for bacterial PPI prediction at scale. Given protein pairs, it leverages ProstT5, a structure-aware protein language model, to generate embeddings, and outputs the interaction probability.

1/4 Ever wanted to predict bacterial protein-protein interactions (PPI) on a large scale?
We wanted to, but realized there’s no such algorithm that is both rapid and optimized for bacterial protein analysis.
This led our ⭐️Chen Agassy⭐️ to develop B-PPI: doi.org/10.64898/202...

Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review ...

6/6 🔮 What's next for NLP in biology? We discuss future directions as well. Join us in exploring the future of this exciting field! arxiv.org/abs/2506.02212

5/6 💡 Discover how NLP is being applied to:
• Protein structure prediction 🏗️
• Taxonomic classification 🌳
• Mutational effect prediction 🔀
• Gene expression prediction 📈
And much more!

4/6 🧩 Tokenization challenges? We've got that covered too! Explore different approaches to breaking down biological sequences and their impact on model performance.

3/6 📚 We break down the evolution of NLP models in biology, from classic word2vec to cutting-edge transformers and hyena operators. Understand their strengths, limitations, and exciting applications!

2/6 🔬 We dive deep into how NLP techniques are revolutionizing the analysis of biological 'languages':
• DNA 🧬
• RNA 🧬
• Proteins 💪
• Entire genomes 🔍
Learn how these methods are unlocking new insights in genomics!

1/6 🧬📊 Curious about the buzz around NLP in biology? Feeling overwhelmed by the rapid developments? We've got you covered! Our review on NLP applications in genomics, by the wonderful Ella Rannon, is now out as a pre-print! #NLP #Bioinformatics arxiv.org/abs/2506.02212

Hello Bluesky! Burstein lab just joined - are we too late for the party 👀 ??