scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer, Jing Xu, De-Shuang Huang, Xiujun Zhang, 2024
Genome-Wide Identification and Expression Analysis of Kiwifruit Leucine-Rich Repeat Receptor-like Proteins Reveal Their Roles in Biotic and Abiotic Stress Responses, Yingying Cao, Congxiao Zhang, Fang Liu, Dawei Li, Aidi Zhang, Li Li, Xiujun Zhang, 2024
Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and dissects important economic traits, Xuemei Lu, Xiaofen Yu, Xiujun Zhang, 2024
A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress, Zhang, Aidi, Yuhong Xiong, Fang Liu, Xiujun Zhang, 2023
CIForm as a Transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data, Jing Xu, Aidi Zhang, Fang Liu, Liang Chen, Xiujun Zhang, 2023
EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors, Huixiang Peng, Jing Xu, Kangchen Liu, Fang Liu, Aidi Zhang, Xiujun Zhang, 2023
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data, Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang, 2023
Genome assembly of the snow lotus species Saussurea involucrata provides insights into acacetin and rutin biosynthesis and tolerance to an alpine environment, Yanxia Sun, Aidi Zhang, Jacob B Landis, Wei Shi, Xiujun Zhang, Hang Sun, Hengchang Wang, 2023
CIForm as a Transformer-based model for cell type annotation of large-scale single-cell RNA-seq data, Xu J, Zhang A, Liu F, Chen L, Zhang X, 2023
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data, Xu J, Zhang A, Liu F, Zhang X, 2023
Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch), Jiang X, Liu K, Peng H, Fang J, Zhang A, Han Y, Zhang X, 2023
EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors, Peng H, Xu J, Liu K, Liu F, Zhang A, Zhang X, 2023
Diversity of RNA editing in chloroplast transcripts across three main plant clades, Zhang A, Fang J, Zhang X, 2023
Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing, Sun Y, Zhang A, Zhang X, Landis JB, Zhang H, Zhang X, Sun H, Wang H, 2023
Genome-wide identification and expression analysis of peach multiple organellar RNA editing factors reveals the roles of RNA editing in plant immunity, Zhang A, Xiong Y, Fang J, Liu K, Peng H, Zhang X, 2022
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique, Jiang X, Zhang X, 2022
Dynamic network biomarker analysis reveals the critical phase transition of fruit ripening in grapevine, Wang T, Peng H, Cao Y, Xu J, Xiong Y, Liu K, Fang J, Liu F, Zhang A, Zhang X, 2022
PiTLiD: Identification of plant disease from leaf images based on convolutional neural network, Liu K, Zhang X, 2022
Diversity and functional evolution of terpene synthases in rosaceae, Zhang A, Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X, 2022
Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity, Fang J, Jiang X, Wang T, Deng Z, Zhang A, Zhang X, 2022
Genome-wide analysis of multiple organellar RNA editing factor (MORF) family in kiwifruit (actinidia chinensis) reveals its roles in chloroplast RNA editing and pathogens stress, Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X, Zhang A, 2022
Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes, Jia Z, Zhang X, 2022
Identification of genes involved in celastrol biosynthesis by comparative transcriptome analysis in tripterygium wilfordii, Zhu Y, Zhang X, Zhang Y, Lü S, Li C, 2022
Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition, Wang T, Zhang X, 2021
Application of deep learning in plant–microbiota association analysis, Deng Z, Zhang J, Li J, Zhang X, 2021
The draft genome of a flat peach (Prunus persica L. cv.‘124 Pan’) provides insights into its good fruit flavor traits, Zhang A, Zhou H, Jiang X, Han Y, Zhang X, 2021
Tissue-specificity of RNA editing in plant: analysis of transcripts from three tobacco (Nicotiana tabacum) varieties, Fang J, Jiang X, Wang T, Zhang X, Zhang A, 2021
Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis, Zhang F, Liu X, Zhang A, Jiang Z, Chen L, Zhang X, 2019
Assessment of organic acid accumulation and its related genes in peach, Zheng B, Zhao L, Jiang X, Cherono S, Liu J, Ogutu C, Ntini C, Zhang X, Han Y, 2021
A 1.7‐Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach, Zhou H, Ma R, Gao L, Zhang J, Zhang A, Zhang X, Ren F, Zhang W, Liao L, Yang Q, 2021
Genome sequencing of the endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms of evolutionary specialization, Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X, Sun H, Wang H, 2020
Dynamic response of RNA editing to temperature in grape by RNA deep sequencing, Zhang A, Jiang X, Zhang F, Wang T, Zhang X, 2020
Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis, Zhang F, Liu X, Zhang A, Jiang Z, Chen L, Zhang X, 2019
SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates, Shanmugam R, Zhang F, Srinivasan H, Charles Richard JL, Liu KI, Zhang X, Woo CWA, Chua ZHM, Buschdorf JP, Meaney MJ, 2018
Part mutual information for quantifying direct associations in networks, Zhao J, Zhou Y, Zhang X, Chen L, 2016
A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing, Liu KI, Ramli MNB, Woo CWA, Wang Y, Zhao T, Zhang X, Yim GRD, Chong BY, Gowher A, Chua MZH, 2016
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data, Zheng G, Xu Y, Zhang X, Liu Z-P, Wang Z, Chen L, Zhu X-G, 2016
CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test, Aghdam R, Ganjali M, Zhang X, Eslahchi C, 2015
Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks, Zhang X, Zhao J, Hao J-K, Zhao X-M, Chen L, 2015
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference, Zhang X, Liu K, Liu Z-P, Duval B, Richer J-M, Zhao X-M, Hao J-K, Chen L, 2013
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information, Zhang X, Zhao X-M, He K, Lu L, Cao Y, Liu J, Hao J-K, Liu Z-P, Chen L, 2012
Area of Focus
Ai | Omics | Precision Medicine | Bioinformatics | Data Analysis | Genomics | Crispr | Machine Learning | Drug Design | Single-Cell Analysis
