Hugo Y. K. Lam
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View article: Insights from incorporating quantum computing into drug design workflows
Insights from incorporating quantum computing into drug design workflows Open
Motivation While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partiti…
View article: Insights from Incorporating Quantum Computing into Drug Design Workflows
Insights from Incorporating Quantum Computing into Drug Design Workflows Open
While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning betwe…
Gene Expression Scoring of Immune Activity Levels for Precision Use of Hydrocortisone in Vasodilatory Shock Open
Purpose: Among patients with vasodilatory shock, gene expression scores may identify different immune states. We aimed to test whether such scores are robust in identifying patients’ immune state and predicting response to hydrocortisone t…
View article: Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies Open
We characterized two reference samples for NGS technologies: a human triple-negative breast cancer cell line and a matched normal cell line. Leveraging several whole-genome sequencing (WGS) platforms, multiple sequencing replicates, and or…
ecTMB: a robust method to estimate and classify tumor mutational burden Open
Tumor Mutational Burden (TMB) is a measure of the abundance of somatic mutations in a tumor, which has been shown to be an emerging biomarker for both anti-PD-(L)1 treatment and prognosis. Nevertheless, multiple challenges still hinder the…
Deep convolutional neural networks for accurate somatic mutation detection Open
We present NeuSomatic, the first convolutional neural network approach for somatic mutation detection, which significantly outperforms previous methods on different sequencing platforms, sequencing strategies, and tumor purities. NeuSomati…
Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia Open
Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype—6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age—leading …
Lessons from the CAGI‐4 Hopkins clinical panel challenge Open
The CAGI-4 Hopkins clinical panel challenge was an attempt to assess state-of-the-art methods for clinical phenotype prediction from DNA sequence. Participants were provided with exonic sequences of 83 genes for 106 patients from the Johns…
LongISLND: <i>in silico</i> sequencing of lengthy and noisy datatypes Open
Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonst…
View article: svclassify: a method to establish benchmark structural variant calls
svclassify: a method to establish benchmark structural variant calls Open
We find that candidate SVs with high scores from multiple technologies have high concordance with PCR validation and an orthogonal consensus method MetaSV (99.7 % concordant), and candidate SVs with low scores are questionable. We distribu…