My Research Work

“Application of a comprehensive platform technology for detection of cancer-associated genomic alterations and viral DNA in liquid biopsies”. Annals of Oncology, 2018. (Second Author)
“An enhanced next-generation sequencing liquid biopsy assay for simultaneous detection of somatic variants, microsatellite instability and viral DNA.”. Journal of Clinical Oncology, 2018. (Second Author)
“LDSplitDB: A database for studies of meiotic recombination hotspots in MHC using human genomic data”. BMC Medical Genomics, 2018. (Second Author)
“Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline”. PLoS Comput Biol, 2016. (First Author)
“flowAI: automatic and interactive anomaly discerning tools for flow cytometry”. Bioinformatics, 2016. (Second Author)
“ARG-walker: Inference of Individual Specific Strengths of Meiotic Recombination Hotspots by Population Genomics Analysis”. BMC Genomics, 2015. (First Author)
“Optimization of production conditions for mushroom polysaccharides with high yield and antitumor activity”. Carbohydrate Polymers, 2012. (Third Author)

“Method for Detection and Quantification of Genetic Alterations”. 10201805450Y, 2018.
“Methods for Identifying Clusters in a Dataset, Methods of Analyzing Cytometry Data with the Aid of a Computer and Methods of Detecting Cell Sub-populations in a Plurality of Cells”. US 2017-0371886 A1, 2017.
“ModalGATE: An Efficient Gating Algorithm Facilitating Automated and Reproducible Analysis of Flow Cytometry Data”. SIGN/P/09834/00/SG, 2017.

R packages

cytofkit An integrated analysis pipeline for high-dimensional and high-throughput mass cytometry data. (Ranked among top 20% on Bioconductor, with average 300 download times per month)
flowAI Automatic and interactive quality control for flow cytometry data. (Ranked among top 50% on Bioconductor, with average 100 download times per month)
ClusterX A tool for visualizing the high-dimensional mass cytometry data as well as automatically detecting cell populations by fast density-based clustering, generally applicable to any multi-parametric data.
RphenoGraph R implementation of PhenoGraph , a fast and accurate high-dimensional clustering algorithm.
uSORT A self-refining ordering pipeline for gene selection.
StackedDensityPlot A flexible and easy-to-use function for building stacked density plot based on ggplot2.

Shiny APP

flowAIshinyAPP A web application for interactive quality control of flow cytometry data
cytofkitShinyAPP A web application for interactive visualization and exploration of cytofkit analysis results

Perl Tool

ARGwalker Ancestral Recombination Graph (ARG) mining based estimation of individual recombination strength