Haidong Yan

The CCCH Zinc Finger Gene PgCCCH50 from Pearl Millet Confers Drought and Salt Tolerance through an ABA-Dependent PgAREB1-PgCCCH50 Module

This study identifies PgCCCH50 as a drought and salt tolerance gene in pearl millet, showing it is regulated by the ABA-responsive transcription factor PgAREB1.

The genetic architecture of cell-type-specific cis-regulation in maize

The paper identifies cell-type-specific cis-regulatory variants in maize using single-cell genomics and population genetics, revealing their role in local adaptation and flowering.

A spatially resolved multiomic single-cell atlas of soybean development

The paper constructs a spatially resolved multiomic single-cell atlas of soybean development, identifying cell types, chromatin regions, and gene regulatory networks involved in growth and nitrogen fixation.

Haplotype-resolved genome assembly of upland switchgrass provides insights into cold tolerance

This study presents a haplotype-resolved genome of upland switchgrass and identifies genetic factors associated with cold tolerance through multi-omics analysis.

Mono-allelic epigenetic regulation of bi-directional silencing of RNA Polymerase II polycistronic transcription initiation in Trypanosoma brucei.

The paper shows that epigenetic mechanisms, including base J modification, regulate mono-allelic transcriptional silencing of adjacent polycistronic gene clusters in Trypanosoma brucei.

Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

The paper introduces scifi-ATAC-seq, a method that increases single-cell ATAC-seq throughput by 20-fold using combinatorial fluidic indexing.

Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes.

This study shows that PP1-1 modulates Pol II termination in T. brucei by dephosphorylating the Pol II large subunit, leading to readthrough transcription and pervasive genome transcription.

Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods

The paper introduces SPmarker, an interpretable machine learning pipeline to identify new cell-type marker genes in Arabidopsis root single-cell RNA-seq data, finding hundreds of novel markers and expanding trichoblast markers across species.

DeepTE: a computational method for de novo classification of transposons with convolu-tional neural network

DeepTE classifies transposable elements using convolutional neural networks, outperforming existing tools in benchmark tests.