- Zhou*, Johnson*, Morrison*, Beddows, Eapen, Katsman, Semwal, Abi-Habib, Heo, Laird, Berman, Triche, Shen# "BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies" Nucleic Acids Research (2024)
- Lee, Loo, Prasasya, Bartolomei, Kohli, Zhou# "Low-input and single-cell methods for Infinium DNA methylation BeadChips" Nucleic Acids Research (2024)
- Kaur*, Lee*, Goldberg, Spix, Hinoue, Li, Dwaraka, Smith, Shen, Liang, Renke, Laird, Zhou# "Comprehensive Evaluation of The Infinium Human MethylationEPIC v2 BeadChip" Epigenetics Communications (2023)
- Ding#, Goldberg, Zhou# "PyComplexHeatmap: a Python package to visualize multimodal genomics data" iMeta (2023)
- Ding, Kaur, Horvath, Zhou# "Comparative epigenome analysis using Infinium DNA methylation BeadChips" Briefing in Bioinformatics (2023)
- Iqbal, Zhou# "Computational methods for single-cell DNA methylome analysis." Genomics, Proteomics and Bioinformatics (2023) Review.
- Zhou#, Hinoue, Barnes, Mitchell, Iqbal, Lee, Foy, Lee, Moyer, VanderArk, Koeman, Ding, Kalkat, Spix, Eagleson, Pospisilik, Szabo, Bartolomei, Vander Schaaf, Kang, Wiseman, Jones, Krawczyk, Adams, Porecha, Chen, Shen#, Laird#. "DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse." Cell Genomics (2022)(also see Journal Highlight by Manel Esteller).
- Robertson, Yau, Carrot-Zhang, Damrauer, Knijnenburg, Chambwe, Hoadley, Kemal, Zenklusen, Cherniack#, Beroukhim#, Zhou#. "Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer." STAR Protoc (2021)
- Zhou#, Liang, Molloy, Jones#. "DNA Methylation Enables Transposable Element-Driven Genome Expansion." PNAS (2020)
- Carrot-Zhang*, Chambwe*, Damrauer*, Knijnenburg*, Robertson*, Yao*, Zhou*, Berger*, Huang*, et al. (co-first authors ordered alphabetically) “Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer.” Cancer Cell (2020)
- Gao*, Parker*, Reynolds*, Silva*, Wang*, Zhou* et al. (co-first authors ordered alphabetically) “Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons.” Cell Systems (2019)
- Carpenter*, Zhou* et al. “Mother-child transmission of epigenetic information by variable imprinting” PNAS (2018)
- Zhou#, Triche, Laird and Shen#. “SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.” Nucleic Acids Research (2018)
- Zhou*, Dinh*, Ramjan, Weisenberger, Nicolet, Shen#, Laird#, Berman#. “DNA methylation loss in late-replicating domains is linked to mitotic cell division.” Nature Genetics (2018) Supplemental Data: PMD Annotations
- Zhou, Laird and Shen. “Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes.” Nucleic Acids Research (2017) Supplemental Data: Infinium Annotation Hub
- Liu*, Ohtani*, Zhou* et al. “Vitamin C increases viral mimicry induced by 5-aza-2’-deoxycytidine.” PNAS (2016)
- Zhou*, Chen* et al. “TransVar: a multi-level variant annotator for precision genomics." Nature Methods (2015)
- Zhou, Zhao, Chong, Mark, Eterovic, Meric-Bernstam, Chen. "ClinSeK: a targeted variant characterization framework for clinical sequencing." Genome Medicine (2015)
- Zhou#, Chen, Zhao, Eterovic, Meric-Bernstam, Mills, Chen#. “Bias from removing read duplication in ultra-deep sequencing experiments.” Bioinformatics (2014)
- Zhou# and Nakhleh#. "Convergent evolution of modularity in metabolic networks through different community structures." BMC Evolutionary Biology (2012)
- Zhou# and Nakhleh#. "Quantifying and assessing the effect of chemical symmetry in metabolic pathways." Journal of Chemical Information and Modelling (2012)
- Zhou# and Nakhleh#. "The strength of chemical linkage as a criterion for pruning metabolic graphs." Bioinformatics (2011)
- Zhou# and Nakhleh#. "Properties of metabolic graphs: biological organization or representation artifacts?" BMC Bioinformatics (2011)
(#: corresponding author, *: co-first author, _: Zhou lab members)
--Prior to Zhou lab start--