Alexander Titus

tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets

The paper introduces tfboot, an R package for statistically evaluating TFBS disruption in gene sets using bootstrapping methods.

FLAG: Find, Label Annotate Genomes, a fully automated tool for genome gene structural and functional annotation of highly fragmented non-model species

FLAG is an automated genome annotation tool that improves gene structure and functional annotations for fragmented non-model genomes, outperforming existing methods in accuracy and completeness.

MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Network, Inspired by Capsule Networks

The paper introduces MethylCapsNet and MethylSPWNet, deep learning models that organize DNA methylation data into biologically relevant capsules to improve interpretability in classifying CNS tumors.

MethylNet: An Automated and Modular Deep Learning Approach for DNA Methylation Analysis

MethylNet is a deep learning framework for DNA methylation analysis that constructs embeddings, makes predictions, and uncovers heterogeneity with minimal user input.

Unsupervised deep learning with variational autoencoders applied to breast tumor genome-wide DNA methylation data with biologic feature extraction

This study applies variational autoencoders to breast tumor DNA methylation data to identify differential methylation patterns and regulatory regions.

Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes