Analysis of CDNA Microarray Images. - Yee Hwa Yang; Michael J. Buckley; Terence P. Speed (Briefings Bioinform., 2001)

Identifying differentially expressed genes from microarray experiments via statistic synthesis. - Yee Hwa Yang; Yuanyuan Xiao; Mark R. Segal (Bioinform., 2005)

Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing. - Yuanyuan Xiao; Yee Hwa Yang; Todd A. Burckin; Lily Shiue; Grant A. Hartzog; Mark R. Segal (PLoS Comput. Biol., 2005)

A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. - Yuanyuan Xiao; Mark R. Segal; Yee Hwa Yang; Ru-Fang Yeh (Bioinform., 2007)

A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. - Penghao Wang; Pengyi Yang; Jonathan Arthur; Jean Yee Hwa Yang (Bioinform., 2010)

Comparison study of microarray meta-analysis methods. - Anna Campain; Yee Hwa Yang (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)

Two-Step Cross-Entropy Feature Selection for Microarrays - Power Through Complementarity. - Tim Peters; David W. Bulger; To-ha Loi; Jean Yee Hwa Yang; David Ma (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

OCAP: an open comprehensive analysis pipeline for iTRAQ. - Penghao Wang; Pengyi Yang; Jean Yee Hwa Yang (Bioinform., 2012)

Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator. - Pengyi Yang; Jie Ma; Penghao Wang; Yunping Zhu; Bing Bing Zhou; Jean Yee Hwa Yang (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Latin square dataset for evaluating the accuracy of mass spectrometry-based protein identification and quantification. - Penghao Wang; Jean Yee Hwa Yang; Mark Raftery; Ling Zhong; Susan R. Wilson (BIBM, 2013)

Estimation of data-specific constitutive exons with RNA-Seq data. - Ellis Patrick; Michael J. Buckley; Yee Hwa Yang (BMC Bioinform., 2013)

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. - Ellis Patrick; Michael J. Buckley; David M. Lin; Yee Hwa Yang (BMC Genom., 2013)

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. - Pengyi Yang; Ellis Patrick; Shi-Xiong Tan; Daniel J. Fazakerley; James G. Burchfield; Christopher Gribben; Matthew J. Prior; David E. James; Yee Hwa Yang (Bioinform., 2014)

Network-based biomarkers enhance classical approaches to prognostic gene expression signatures. - Rebecca L. Barter; Sarah-Jane Schramm; Graham J. Mann; Yee Hwa Yang (BMC Syst. Biol., 2014)

Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data. - Ellis Patrick; Michael J. Buckley; Samuel Müller 001; David M. Lin; Jean Yee Hwa Yang (Bioinform., 2015)

ClassifyR: an R package for performance assessment of classification with applications to transcriptomics. - Dario Strbenac; Graham J. Mann; John T. Ormerod; Jean Yee Hwa Yang (Bioinform., 2015)

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. - Pengyi Yang; Xiaofeng Zheng; Vivek Jayaswal; Guang Hu 005; Jean Yee Hwa Yang; Raja Jothi (PLoS Comput. Biol., 2015)

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. - Pengyi Yang; Sean J. Humphrey; David E. James; Yee Hwa Yang; Raja Jothi (Bioinform., 2016)

Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. - Shila Ghazanfar; Adam J. Bisogni; John T. Ormerod; David M. Lin; Jean Yee Hwa Yang (BMC Syst. Biol., 2016)

Characterizing mutation-expression network relationships in multiple cancers. - Shila Ghazanfar; Jean Yee Hwa Yang (Comput. Biol. Chem., 2016)

Positive unlabeled learning via wrapper-based adaptive sampling. - Pengyi Yang; Wei Liu 007; Jean Yee Hwa Yang (IJCAI, 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)

Diagonal Discriminant Analysis with Feature Selection for High Dimensional Data. - Sarah Elizabeth Romanes; John Thomas Ormerod; Jean Yee Hwa Yang (CoRR, 2018)

Challenges for Brain Data Analysis in VR Environments. - Sabrina Jaeger; Karsten Klein 001; Lucas Joos; Johannes Zagermann; Michael de Ridder; Jinman Kim; Jean Yee Hwa Yang; Ulrike Pfeil; Harald Reiterer; Falk Schreiber (PacificVis, 2019)

Impact of similarity metrics on single-cell RNA-seq data clustering. - Taiyun Kim; Irene Rui Chen; Yingxin Lin; Andy Yi-Yang Wang; Jean Yee Hwa Yang; Pengyi Yang (Briefings Bioinform., 2019)

DCARS: differential correlation across ranked samples. - Shila Ghazanfar; Dario Strbenac; John T. Ormerod; Jean Yee Hwa Yang; Ellis Patrick (Bioinform., 2019)

bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays. - Kevin Y. X. Wang; Alexander M. Menzies; Ines P. Silva; James S. Wilmott; Yibing Yan; Matthew Wongchenko; Richard F. Kefford; Richard A. Scolyer; Georgina V. Long; Garth Tarr; Samuel Müller 001; Jean Yee Hwa Yang (Bioinform., 2019)

scDC: single cell differential composition analysis. - Yue Cao; Yingxin Lin; John T. Ormerod; Pengyi Yang; Jean Yee Hwa Yang; Kitty K. Lo (BMC Bioinform., 2019)

An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity. - Michael de Ridder; Karsten Klein 001; Jean Yee Hwa Yang; Pengyi Yang; Jim Lagopoulos; Ian B. Hickie; Max Bennett; Jinman Kim (Neuroinformatics, 2019)

AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications. - Pengyi Yang; John T. Ormerod; Wei Liu 007; Chendong Ma; Albert Y. Zomaya; Jean Yee Hwa Yang (IEEE Trans. Cybern., 2019)

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. - Thomas Andrew Geddes; Taiyun Kim; Lihao Nan; James G. Burchfield; Jean Yee Hwa Yang; Dacheng Tao; Pengyi Yang (BMC Bioinform., 2019)

CiteFuse enables multi-modal analysis of CITE-seq data. - Hani Jieun Kim; Yingxin Lin; Thomas Andrew Geddes; Jean Yee Hwa Yang; Pengyi Yang (Bioinform., 2020)

LC-N2G: a local consistency approach for nutrigenomics data analysis. - Xiangnan Xu; Samantha Solon-Biet; Alistair M. Senior; David Raubenheimer; Stephen J. Simpson; Luigi Fontana; Samuel Müller 001; Jean Yee Hwa Yang (BMC Bioinform., 2020)

Ensemble deep learning in bioinformatics. - Yue Cao; Thomas Andrew Geddes; Jean Yee Hwa Yang; Pengyi Yang (Nat. Mach. Intell., 2020)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Uncovering cell identity through differential stability with Cepo. - Hani Jieun Kim; Kevin Y. X. Wang; Carissa Chen; Yingxin Lin; Patrick P. L. Tam; David M. Lin; Jean Y. H. Yang; Pengyi Yang (Nat. Comput. Sci., 2021)

The health digital twin to tackle cardiovascular disease - a review of an emerging interdisciplinary field. - Genevieve Coorey; Gemma A. Figtree; David F. Fletcher; Victoria J. Snelson; Stephen T. Vernon; David S. Winlaw; Stuart M. Grieve; Alistair Lee McEwan; Jean Yee Hwa Yang; Pierre Qian; Kieran O'Brien; Jessica Orchard; et al. (npj Digit. Medicine, 2022)

Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine. - Kevin Y. X. Wang; Gulietta M. Pupo; Varsha Tembe; Ellis Patrick; Dario Strbenac; Sarah-Jane Schramm; John F. Thompson; Richard A. Scolyer; Samuel Müller 001; Garth Tarr; Graham J. Mann; Jean Yee Hwa Yang (npj Digit. Medicine, 2022)

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. - Yue Cao; Yingxin Lin; Ellis Patrick; Pengyi Yang; Jean Yee Hwa Yang (Bioinform., 2022)

Scalable workflow for characterization of cell-cell communication in COVID-19 patients. - Yingxin Lin; Lipin Loo; Andy Tran; David M. Lin; Cesar Moreno; Daniel Hesselson; G. Gregory Neely; Jean Y. H. Yang (PLoS Comput. Biol., 2022)

scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data. - Jie Hao; Jiawei Zou; Jiaqiang Zhang; Ke Chen; Duojiao Wu; Wei Cao; Guoguo Shang; Jean Yee Hwa Yang; KongFatt Wong-Lin; Hourong Sun; Zhen Zhang; Xiangdong Wang; et al. (Briefings Bioinform., 2023)

Deep multimodal graph-based network for survival prediction from highly multiplexed images and patient variables. - Xiaohang Fu; Ellis Patrick; Jean Y. H. Yang; David Dagan Feng; Jinman Kim (Comput. Biol. Medicine, 2023)

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. - Yue Cao; Shila Ghazanfar; Pengyi Yang; Jean Y. H. Yang (Briefings Bioinform., 2023)

eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions. - Xiangnan Xu; Alistair M. Senior; David G. Le Couteur; Victoria C. Cogger; David Raubenheimer; David E. James; Benjamin Parker; Stephen J. Simpson; Samuel Müller 001; Jean Y. H. Yang (Briefings Bioinform., 2024)

CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data. - Daniel Kim; Carissa Chen; Lijia Yu; Jean Yee Hwa Yang; Pengyi Yang (Bioinform., 2025)

IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits. - Daniel Mechtersheimer; Wenze Ding; Xiangnan Xu; Sanghyun Kim; Carolyn Sue; Yue Cao; Jean Y. H. Yang (Bioinform., 2025)

Improving lesion segmentation in medical images by global and regional feature compensation. - Chuhan Wang; Zhenghao Chen; Jean Y. H. Yang; Jinman Kim (Pattern Recognit., 2026)