David Tse

Activation of Multiple Eph Receptors on Neuronal Membranes Correlates with The Onset of Traumatic Optic Neuropathy

This study identifies Eph receptor activation in postnatal mouse retinas and shows its correlation with traumatic optic neuropathy onset and neuroprotective effects upon inhibition.

Systematic characterization of genome editing in primary T cells reveals proximal genomic insertions and enables machine learning prediction of CRISPR-Cas9 DNA repair outcomes

This study systematically characterizes genome editing in primary T cells, identifies proximal genomic insertions, and develops a machine learning model to predict CRISPR-Cas9 DNA repair outcomes.

Do Read Errors Matter for Genome Assembly?

The paper investigates the tradeoff between read length and error rate for genome assembly using an adversarial erasure error model and verifies results on real genomes.

Shannon: An Information-Optimal de Novo RNA-Seq Assembler

Shannon is an RNA-Seq assembler that uses information theory to optimally reconstruct transcripts, achieving higher sensitivity and specificity than existing methods.

FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads

FinisherSC improves de-novo assembly using long reads by addressing repeats, producing longer and higher quality contigs with high concordance.

Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

The paper develops a formula for haplotype assembly from mate-pair reads using a generative model and connects it to decoding convolutional codes.