Alisandra K. Denton

Helixer, a hybrid convolutional/bLSTM network with a hidden Markov model post-processor, predicts eukaryotic primary gene models from DNA alone, outscoring GenemarkES and AUGUSTUS on most species.

Predmoter predicts ATAC-seq and ChIP-seq read coverage in plant genomes using DNA sequences, improving efficiency in identifying cis-regulatory elements.

This paper presents a chromosome-scale genome assembly for Solanum lycopersicoides and maps introgression lines to support genetic studies of traits in tomato.

The paper uses nanopore sequencing to assemble a high-quality genome of Solanum pennellii, achieving high gene completeness and structural similarity to a reference genome.

The paper introduces LOGAN, a memory-efficient, lossless data structure for sequence analysis, capable of handling large genomic datasets from multiple organisms.