RavenCAD: a DNA assebly planning tool
Published:
RavenCAD is a dynamic programing algorithm for planing DNA synthesis protocols that is accessible as a web application
Portfolio
TBA: a Transcription Factor Binding Analysis
Published:
TBA is a multi-functional machine learning tool for identifying words in the genome (aka transcription factor motifs) associated with genomic features.
Genomic Grammar
Published:
A series of neural networks and algorithms for identifying a genomic grammar that can be used to classify regulatory circuits in the mammalian genome. The current model, is a convolutional network that uses a dot-product attention mechanism. This network has performance on par with or exceeding current state-of-the-art methods such as DeepBind at distinguishing regulatory circuits from random genomic background. Additionally, the attention mechanism of the model can be used to extract the architectures of regulatory circuits in the genome via a post-processing step performed on the output of the model.