Author

Cindy Q. Yao

Ontario Institute for Cancer Research

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Research Focus:differential expression· 3 Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Paul Christopher BoutrosiD· 5 shared Kathleen E. HoulahaniD· 3 shared Ren SuniD· 3 shared Stephenie D. ProkopeciD· 3 shared Aileen LuiD· 2 shared Francis NguyeniD· 2 shared Jianxin WangiD· 2 shared Lawrence E. HeisleriD· 2 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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5 shared papersBioinformatics

Paul Christopher BoutrosORCID

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Author profile →

5 papers

Recent·Most cited

The Landscape of Prostate Tumour Methylation

Jaron Arbet, Takafumi N. Yamaguchi, Yu-Jia Shiah, Rupert Hugh-White, Adriana Wiggins, Jieun Oh, Nicole Zeltser, Tsumugi Gebo, Adrien Foucal, Robert Lesurf, Chol-Hee Jung, Rachel M.A. Dang, Raag Agrawal, Julie Livingstone, Adriana Salcedo, , Paul Christopher Boutros

This study maps epigenomic heterogeneity in prostate cancer by analyzing 3,001 methylomes and identifies four subtypes with distinct clinical and molecular features.

Cancer Discovery · Jun 17, 2026Peer-reviewedCancer Biology

Identifying TCDD-resistance genes via murine and rat comparative genomics and transcriptomics

Stephenie D. Prokopec, Aileen Lu, Sandy Che-Eun S. Lee, Cindy Q. Yao, Ren Sun, John D. Watson, Rabah Soliymani, Richard de Borja, Ada Wong, Michelle Sam, Philip C. Zuzarte, John D. McPherson, Allan B. Okey, Raimo Pohjanvirta, Paul Christopher Boutros

The paper identifies genes associated with TCDD-response phenotypes by comparing genomic and transcriptomic data from transgenic mice and rats.

Archives of Toxicology · Sep 11, 2019Peer-reviewedGenomics

BPG: Seamless, Automated and Interactive Visualization of Scientific Data

Christine P’ng, Jeffrey J. Green, Lauren C. Chong, Daryl M. Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle Chan‐Seng‐Yue, Cindy Q. Yao, , Paul Christopher Boutros

BPG is an R package that generates publication-quality, customizable plots and offers an interactive web tool for figure customization and integration with computational pipelines.

BMC Bioinformatics · Jan 21, 2019Peer-reviewedBioinformatics

Network-Based Biomarkers Enable Cross-Disease Biomarker Discovery

Syed Aleem Haider, Cindy Q. Yao, Vicky S. Sabine, Michal R. Grzadkowski, Vincent Stimper, Maud H. W. Starmans, Jianxin Wang, Francis Nguyen, Nathalie C. Moon, Xihui Lin, Camilla Drake, Cheryl Crozier, Cassandra L. Brookes, Cornelis J.�H. van de Velde, Annette Hasenburg, , Paul Christopher Boutros

The paper introduces SIMMS, a method that identifies biomarkers by analyzing molecular data and biological networks, showing improved performance in predicting disease subtypes and outcomes.

Nature Communications · Nov 6, 2018Peer-reviewedBioinformatics

Accurate Reference-Free Somatic Variant-Calling by Integrating Genomic, Sequencing and Population Data

Ren Sun, Christopher M. Lalansingh, Shadrielle M. G. Espiritu, Cindy Q. Yao, Takafumi N. Yamaguchi, Stephenie D. Prokopec, Lesia Szyca, Kathleen E. Houlahan, Lawrence E. Heisler, Morgan D Black, Constance H. Li, John W. Barrett, Anthony Charles Nichols, Paul Christopher Boutros

S22S is a reference-free method for somatic variant calling that uses genomic and population data to accurately identify SNVs without matched normal samples.

bioRxiv · Aug 2, 2018 · PreprintBioinformatics