GEOMI: GEOmetry for Maximum Insight. - Adel Ahmed; Tim Dwyer; Michael Forster; Xiaoyan Fu; Joshua Wing Kei Ho; Seok-Hee Hong 001; Dirk Koschützki; Colin Murray; Nikola S. Nikolov; Ronnie Taib; Alexandre Tarassov; Kai Xu 003 (GD, 2005)

Drawing Clustered Graphs in Three Dimensions. - Joshua Wing Kei Ho; Seok-Hee Hong 001 (GD, 2005)

PathBank: Web-Based Querying and Visualziation of an Integrated Biological Pathway Database. - Joshua Wing Kei Ho; Tristan Manwaring; Seok-Hee Hong 001; Uwe Röhm; David Cho Yau Fung; Kai Xu 003; Tim Kraska; David Hart (CGIV, 2006)

SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides. - Joshua Wing Kei Ho; Cameron E. Adams; Jie Bin Lew; Timothy J. Matthews; Chiu Chin Ng; Arash Shahabi-Sirjani; Leng Hong Tan; Yu Zhao; Simon Easteal; Susan R. Wilson; Lars S. Jermiin (Bioinform., 2006)

Differential variability analysis of gene expression and its application to human diseases. - Joshua Wing Kei Ho; Maurizio Stefani; Cristobal G. dos Remedios; Michael A. Charleston (ISMB, 2008)

Application of Metamorphic Testing to Supervised Classifiers. - Xiaoyuan Xie; Joshua Wing Kei Ho; Christian Murphy; Gail E. Kaiser; Baowen Xu; Tsong Yueh Chen (QSIC, 2009)

An innovative approach for testing bioinformatics programs using metamorphic testing. - Tsong Yueh Chen; Joshua Wing Kei Ho; Huai Liu; Xiaoyuan Xie (BMC Bioinform., 2009)

A voting approach to identify a small number of highly predictive genes using multiple classifiers. - Md. Rafiul Hassan; M. Maruf Hossain; James Bailey 001; Geoff MacIntyre; Joshua Wing Kei Ho; Kotagiri Ramamohanarao (BMC Bioinform., 2009)

A genetic ensemble approach for gene-gene interaction identification. - Pengyi Yang; Joshua Wing Kei Ho; Albert Y. Zomaya; Bing Bing Zhou (BMC Bioinform., 2010)

Gene-gene interaction filtering with ensemble of filters. - Pengyi Yang; Joshua Wing Kei Ho; Jean Yee Hwa Yang; Bing Bing Zhou (BMC Bioinform., 2011)

Verification of phylogenetic Inference Programs Using Metamorphic Testing. - Md. Shaik Sadi; Fei-Ching Kuo; Joshua Wing Kei Ho; Michael A. Charleston; Tsong Yueh Chen (J. Bioinform. Comput. Biol., 2011)

Testing and validating machine learning classifiers by metamorphic testing. - Xiaoyuan Xie; Joshua Wing Kei Ho; Christian Murphy; Gail E. Kaiser; Baowen Xu; Tsong Yueh Chen (J. Syst. Softw., 2011)

Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. - Eleni Giannoulatou; Shin-Ho Park; David T. Humphreys; Joshua Wing Kei Ho (BMC Bioinform., 2014)

Comparative analysis of metazoan chromatin organization Open. - Joshua Wing Kei Ho; Youngsook L. Jung; Tao Liu 022; Burak Han Alver; Soohyun Lee; Kohta Ikegami; Kyung-Ah Sohn; Aki Minoda; Michael Y. Tolstorukov; Alex Appert; Stephen C. J. Parker; Tingting Gu; et al. (Nat., 2014)

hiHMM: Bayesian non-parametric joint inference of chromatin state maps. - Kyung-Ah Sohn; Joshua Wing Kei Ho; Djordje Djordjevic; Hyun-hwan Jeong; Peter J. Park; Ju Han Kim (Bioinform., 2015)

A cloud-based framework for applying metamorphic testing to a bioinformatics pipeline. - Michael Troup; Andrian Yang; Amir Hossein Kamali; Eleni Giannoulatou; Tsong Yueh Chen; Joshua Wing Kei Ho (MET@ICSE, 2016)

XGSA: A statistical method for cross-species gene set analysis. - Djordje Djordjevic; Kenro Kusumi; Joshua Wing Kei Ho (Bioinform., 2016)

Harnessing Multiple Source Test Cases in Metamorphic Testing: A Case Study in Bioinformatics. - Joshua Y. S. Tang; Andrian Yang; Tsong Yueh Chen; Joshua Wing Kei Ho (MET@ICSE, 2017)

Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. - Pengyi Yang; Andrew J. Oldfield; Taiyun Kim; Andrian Yang; Jean Yee Hwa Yang; Joshua Wing Kei Ho (Bioinform., 2017)

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud. - Andrian Yang; Michael Troup; Peijie Lin; Joshua Wing Kei Ho (Bioinform., 2017)

C3: An R package for cross-species compendium-based cell-type identification. - Md Humayun Kabir; Djordje Djordjevic; Michael D. O'Connor; Joshua Wing Kei Ho (Comput. Biol. Chem., 2018)

iSyTE 2.0: a database for expression-based gene discovery in the eye. - Atul Kakrana; Andrian Yang; Deepti Anand; Djordje Djordjevic; S. Deepthi Ramachandruni; Abhyudai Singh; Hongzhan Huang; Joshua Wing Kei Ho; Salil A. Lachke (Nucleic Acids Res., 2018)

Ultrafast clustering of single-cell flow cytometry data using FlowGrid. - Xiaoxin Ye; Joshua Wing Kei Ho (BMC Syst. Biol., 2019)

Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus. - Djordje Djordjevic; Joshua Y. S. Tang; Yun Xin Chen; Shu Lun Shannon Kwan; Raymond W. K. Ling; Gordon Qian; Chelsea Y. Y. Woo; Samuel J. Ellis; Joshua Wing Kei Ho (Comput. Biol. Chem., 2019)

Expression Clustering. - Xiaoxin Ye; Joshua W. K. Ho (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

dv-trio: a family-based variant calling pipeline using DeepVariant. - Eddie Ip; Clinton Hadinata; Joshua Wing Kei Ho; Eleni Giannoulatou (Bioinform., 2020)

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells. - Shobana V. Stassen; Dickson M. D. Siu; Kelvin C. M. Lee; Joshua W. K. Ho; Hayden K. H. So; Kevin K. Tsia (Bioinform., 2020)

Introduction to the Special Issue on GIW/ABACBS 2019. - Joshua W. K. Ho (J. Bioinform. Comput. Biol., 2020)

FlowGrid enables fast clustering of very large single-cell RNA-seq data. - Xiunan Fang; Joshua W. K. Ho (Bioinform., 2021)

Evaluation of Experimental Protocols for Shotgun Whole-Genome Metagenomic Discovery of Antibiotic Resistance Genes. - Ken Hung-On Yu; Xiunan Fang; Haobin Yao; Bond Ng; Tak Kwan Leung; Ling-Ling Wang; Chi Ho Lin; Agnes Sze Wah Chan; Wai Keung Leung; Suet Yi Leung; Joshua Wing Kei Ho (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning. - Weizhong Zheng; John H. C. Fong; Yuk Kei Wan; Athena H. Y. Chu; Yuanhua Huang; Alan S. L. Wong; Joshua W. K. Ho (RECOMB, 2023)

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. - Qiuchen Meng; Lei Wei; Kun Ma; Ming Shi; Xinyi Lin; Joshua W. K. Ho; Yinqing Li; Xuegong Zhang (Briefings Bioinform., 2024)

An edge-device-compatible algorithm for valvular heart diseases screening using phonocardiogram signals with a lightweight convolutional neural network and self-supervised learning. - Shichao Ma; Junyi Chen; Joshua W. K. Ho (Comput. Methods Programs Biomed., 2024)

Developing a named entity framework for thyroid cancer staging and risk level classification using large language models. - Matrix M. H. Fung; Eric H. M. Tang; Tingting Wu; Yan Luk; Ivan C. H. Au; Xiaodong Liu; Victor H. F. Lee; Chun Ka Wong; Zhili Wei; Wing Yiu Cheng; Isaac C. Y. Tai; Joshua W. K. Ho; et al. (npj Digit. Medicine, 2025)