3D Genome

How the DNA folds in the Nucleus: a machine learning approach

A poster introducing 3D genome and matrix factorization to a general audience

Discovering structural units of chromosomal organization with matrix factorization and graph regularization

Three dimensional organization of the genome is emerging as an important determinant of cell-type specific expression and is implicated in many diseases, including cancer (Bouwman & de Laat 2015). Hi-C is a type of high-throughput chromosome …

GRINCH: Discovering structural units of chromosomes with graph-regularized matrix factorization

Three dimensional organization of the genome is emerging as an important determinant of cell-type specific expression and is implicated in many diseases, including cancer (Bouwman & de Laat 2015). Hi-C is a type of high-throughput chromosome …

A graph-regularized non-negative matrix factorization method to discover organizational units of chromosomes

Three dimensional organization of the genome is emerging as an important determinant of cell-type specific expression and is implicated in many diseases, including cancer. Hi-C is a type of high-throughput chromosome conformation capture (3C) assay …

Convolutional neural network (CNN) for predicting Hi-C interaction counts

Can deep learning model predict which regions of our genetic code influence each other?