Hong Kong JC STEM Lab
Genomics and AI in Healthcare

The software tools here were developed in the Zhang lab over many years by grant support from NSF, NIH, The Alzheimer's Association and Monsanto Corporation.

Computational Biology

AmpSeq-SSR
An accurate and efficient method for large-scale SSR genotyping and applications (software, supplemental table)
miRvial
A computational method and software package for detecting and characterizing microRNAs of diverse genomic origins (software)
BlocBuster
An allele-specific and network-based GWAS method (paper1, paper2, software)
mgRF
Module-guided Random Forests for integration of genotypic variation and gene expression for analyzing complex traits (paper, software)
miRank
MicroRNA prediction with a novel ranking algorithm based on random walks (paper, software and data files)
Qcut and HQcut
Finding communities in networks; also with scripts for visualizing clustering results and for constructing and clustering gene co-expression networks (paper1, paper2, software)
WordSpy
A steganalysis-based, genome scale motif finding method (software)
Rearrangement clustering
A method with application to gene expression analysis (paper, software)
DBTree
A bi-directional regression tree approach to modeling transcriptional regulation (paper, software)
Iterated loop matching
A method for RNA folding with pseudonots (software)
Degenerate multiple PCR primers
A method for selecting degenerate multiple PCR primers (software)

Optimization and Search

Cut-and-solve for the ATSP
(software)
MaxSolver
An exact max-SAT solver (software)
Backbone guided WalkSAT
A method with dynamic noise strategy for SAT and Max-SAT (software)