Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Deep learning infrastructure for genomics

Test genes for Spatial Variation

xHLA: Fast and accurate HLA typing from short read sequence data

snakemake pipeline for creating trees from sequence sets

A simple neural network for calling het-/hom-variants from alignments of single molecule reads to a reference

HLA-TAPAS pipeline for HLA association and fine-mapping studies

Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* et al., Nature Biotech 2021)

Deep learning in genomics

Detecting Evolutionary Patterns of Cancers using Consensus Trees

xHLA: Fast and accurate HLA typing from short read sequence data