jhhung

PEAT. An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.

EARRINGS. EARRINGS: An efficient and ingenious adapter removal design for large-scale NGS meta-analyses

sBWT. A highly hardware-acceleration friendly k-ordered FM-index for exact string matching, overlap graph construction for de novo assembly, and more.

Tailor. Tailor is a fast short read aligner like bowtie/BWA/SOAP2 but is designed specifically to discovering trimming and tailing events for small silencing RNAs.

EpiVerse. EpiVerse is an innovative three-stage pipeline designed to impute chromatin structures across various cell types. By enabling cross cell-type Hi-C imputations, EpiVerse facilitates unique "epigenome-level" perturbational Hi-C experiments, offering valuable insights into chromatin architecture dynamics under diverse epigenetic conditions.

PS2MS. PS²MS is an AI-driven predictive system designed to identify new psychoactive substances (NPS) using mass spectrometry. It generates a synthetic NPS database by enumerating feasible derivatives of known substances and employs deep learning to predict their mass spectra and chemical fingerprints.

kISS. k-ordered Induced Suffix Sorting (kISS) is an algorithm tailored to efficiently construct and leverage k-ordered FM-indexes, particularly for high-speed read mapping in extensive genome datasets. The innovation behind k-ordered FM-indexes aims to enhance the efficiency and speed of pattern matching tasks in genomics.

Premnas. A Framework to Estimate Intraclonal Heterogeneity and Subpopulation Changes from Perturbational Bulk Gene Expression Profiles