Brooks Paige

ProFam: Open-Source Protein Family Language Modelling for Fitness Prediction and Design

ProFam is an open-source protein family language model that improves fitness prediction and design by leveraging evolutionary context through homologous sequences.

Design in Voxel Space Decode in SMILES Space: Plixer Generates Drug-Like Molecules for Protein Pockets

Plixer generates drug-like molecules for protein pockets using a two-stage model that decouples spatial interaction learning from chemical grammar learning.

Approximated Gene Expression Trajectories (AGETs) for Gene Regulatory Network Inference on Cell Tracks

This paper introduces a framework to infer gene regulatory networks (GRNs) during tissue morphogenesis by integrating cell movement and gene expression data.

Chainsaw: protein domain segmentation with fullyconvolutional neural networks

Chainsaw uses a fully convolutional neural network to predict protein domain boundaries, achieving higher accuracy than existing methods in domain segmentation.

Cell Rearrangement Generates Pattern Emergence as a Function of Temporal Morphogen Exposure.

The paper shows cell rearrangement during mesoderm elongation generates gene expression patterns through temporal Wnt and FGF exposure.

Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores

This paper shows that genetic risk scores can be used to reconstruct genotypes in private genomic databases when models are trained on overlapping participant sets.