Peng Zhou

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions

The paper tests gene regulatory network predictions in maize by analyzing transcriptomic and metabolic changes in TF mutants, finding limited phenotypic impacts but some altered target gene expression.

Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration

This paper develops a framework to prioritize maize metabolic gene regulators by integrating multi-omic data, identifying over 3,000 TFs and predicting new regulators of hormone, developmental, and metabolic processes.

Flnc: Machine Learning Improves the Identification of Novel Full-length Long Noncoding RNAs from RNA Sequencing Data Without Transcriptional Initiation Profiles

Flnc improves lncRNA identification from RNA-seq data by using machine learning, achieving over 85% accuracy without requiring H3K4me3 profiles.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

The paper uses DNA methylation profiles from a single tissue to identify unmethylated regions (UMRs) that mark expressed genes and cis-regulatory elements in plant genomes.

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

This study characterizes sRNA variation and inheritance in maize inbreds and F1 hybrids, revealing genotype and developmental influences on sRNA expression and non-additive inheritance patterns.

Dynamic patterns of transcript abundance of transposable element families in maize

This study characterizes TE family transcript abundance in maize using RNA-seq data from over 800 libraries, revealing dynamic and tissue-specific expression patterns.

Transposable elements contribute to dynamic genome content in maize

The paper identifies variable transposable element (TE) insertions across four maize genomes, showing their role in genome organization and gene content variation.

Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

The paper analyzes gene expression in maize hybrids and inbreds to show that single-parent expression is genotype- and tissue-specific, with implications for heterosis.

A Pandas complex adapted for piRNA-guided transposon silencing

The paper identifies a ternary complex involving Panx, dNxf2, and dNxt1 that suppresses transposon expression by inhibiting RNA export.