- GIMSAN - web application/server for motif-discovery equipped with a practical and reliable statistical significance analysis. It is also available as a stand-alone application on Unix.
- ALICO - Alignment Constrained null set generator: a framework to generate randomized versions of an input multiple sequence alignment that preserve some of its crucial features including its dependence structure.
- GibbsILR - motif-finder that optimizes for the incomplete likelihood ratio (ILR)
- Patrick Ng (2017). dna2vec: Consistent vector representations of variable-length k-mers. arXiv preprint arXiv:1701.06279.
- A Chaiboonchoe, Patrick Ng*, et al. (2016) Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.Molecular BioSystems. (pubmed) [* co-first author contribution]
- Chun Nin Wong, Patrick Ng, Angela E Douglas. (2011) Low-diversity bacterial community in the gut of the fruitfly Drosophila melanogaster. Environmental Microbiology. (pubmed)
- Patrick Ng, Uri Keich. (2010) Alignment Constrained Sampling. Journal of Computational Biology, 18(2): 155-168. RECOMB on Regulatory Genomics. (pubmed)
- Patrick Ng, Uri Keich. (2008) GIMSAN: A Gibbs motif finder with significance analysis. Bioinformatics, 24 (19): 2256-2257. (pubmed)
- Patrick Ng, Uri Keich. (2008) Factoring local sequence composition in motif significance analysis. Genome Informatics 21:15-26. International Conference on Genome Informatics (GIW), Gold Coast Australia. (pubmed)
- Uri Keich, Patrick Ng. (2007) A conservative parametric approach to motif significance analysis. Genome Informatics 19:61-72. International Conference on Genome Informatics (GIW), Singapore. (pubmed)
- Patrick Ng, Niranjan Nagarajan, Neil Jones, Uri Keich. (2006) Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone. Bioinformatics 22 (14): e393-e401. International Conference on Intelligent Systems for Molecular Biology (ISMB). (pubmed)
- Niranjan Nagarajan, Patrick Ng, Uri Keich. (2006) Refining motif finders with E-value calculations. RECOMB on Regulatory Genomics. (citeseer)