Explanipedia

BioLogical: a universal analysis framework for biosystem logical dynamic Open

Yuxiang Yao, Dong Liu, Z.P. Zhang, Chengchen Zhao, Duanqing Pei · 2025

Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R pack…

Innovative Approaches to Combat Duck Viral Hepatitis: Dual-Specific Anti-DHAV-1 and DHAV-3 Yolk Antibodies Open

Siqi Lei, Yuanhe Yang, Chengchen Zhao, Anguo Liu, Pingli He · 2025

Background and Objectives: Duck viral hepatitis (DVH), a highly contagious and acutely fatal avian disease, is characterized by convulsions, acute death, liver swelling, and hemorrhage, leading to substantial losses in the duck industry. H…

Cpt1a Drives primed-to-naïve pluripotency transition through lipid remodeling Open

Zhaoyi Ma, Xingnan Huang, Junqi Kuang, Qiannan Wang, Yue Qin , et al. · 2024

Metabolism has been implicated in cell fate determination, particularly through epigenetic modifications. Similarly, lipid remodeling also plays a role in regulating cell fate. Here, we present comprehensive lipidomics analysis during BMP4…

ALKBH5 governs human endoderm fate by regulating the DKK1/4-mediated Wnt/β-catenin activation Open

Zechuan Liang, Tao Huang, Wei Li, Zhaoyi Ma, Kaipeng Wang , et al. · 2024

N6-methyladenonsine (m6A) is ubiquitously distributed in mammalian mRNA. However, the precise involvement of m6A in early development has yet to be fully elucidated. Here, we report that deletion of the m6A demethylase ALKBH5 in human embr…

Cell fate decision by a morphogen-transcription factor-chromatin modifier axis Open

Ming Jin, Lihui Lin, Jiajun Li, Linlin Wu, Shicai Fang , et al. · 2024

Engineering mouse cell fate controller by rational design Open

Tao Huang, Dong Liu, Xiaomin Wang, Junqi Kuang, Manqi Wu , et al. · 2024

Pig blastocyst-like structure models from embryonic stem cells Open

Jinzhu Xiang, Hanning Wang, Bingbo Shi, Jiajun Li, Dong Liu , et al. · 2024

Pluripotent stem cells have the potential to generate embryo models that can recapitulate developmental processes in vitro. Large animals such as pigs may also benefit from stem-cell-based embryo models for improving breeding. Here, we rep…

Exclusion of HDAC1/2 complexes by oncogenic nuclear condensates Open

Junqi Kuang, Pengli Li, Ziwei Zhai, Yixin Fan, Huaiyuan Xu , et al. · 2024

Cell fate decision by a morphogen-transcription factor-chromatin modifier axis Open

Duanqing Pei, Ming Jin, Lihui Lin, Linlin Wu, Shicai Fang , et al. · 2023

Cell fate decision remains poorly understood at the molecular level. Embryogenesis provides a unique opportunity to analyse molecular details associated cell fate decisions. Works based on model organisms have provided a conceptual framewo…

The NuRD complex cooperates with SALL4 to orchestrate reprogramming Open

Bo Wang, Chen Li, Ming Jin, Linlin Wu, Shicai Fang , et al. · 2023

Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. Here, we report that chromatin remodeling complex NuRD participates in closing open chromatin in the early phase of somatic reprogram…

Mechanical strain treatment improves nuclear transfer reprogramming efficiency by enhancing chromatin accessibility Open

Yujie Chen, Ruimin Xu, Shuang Zhou, Chengchen Zhao, Ziyue Hu , et al. · 2023

UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution Open

Liudan Jiang, Jiayong Yin, Maoxiang Qian, Shaoqin Rong, Shengqi Zhang , et al. · 2022

As an aberrant base in DNA, uracil is generated by either deoxyuridine (dU) misincorporation or cytosine deamination, and involved in multiple physiological and pathological processes. Genome-wide profiles of uracil are important for study…

Single‐cell transcriptomics of LepR‐positive skeletal cells reveals heterogeneous stress‐dependent stem and progenitor pools Open

Chunyang Mo, Jingxin Guo, Jiachen Qin, Xiaoying Zhang, Yuxi Sun , et al. · 2021

Sequencing uracil in DNA at single-nucleotide resolution Open

Liudan Jiang, Jiayong Yin, Maoxiang Qian, Shaoqin Rong, Kejing Chen , et al. · 2021

As an aberrant base in DNA, uracil is generated by dUMP misincorporation or cytosine deamination, and involved in multiple physiological and pathological processes. Current methods for whole-genome mapping of uracil all rely on uracil-DNA …

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization Open

Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu, Chengchen Zhao · 2021

A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos Open

Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao , et al. · 2020

Identification of ALPPL2 as a Naive Pluripotent State-Specific Surface Protein Essential for Human Naive Pluripotency Regulation Open

Yan Bi, Zhifen Tu, Yanping Zhang, Peng Yang, Mingyue Guo , et al. · 2020

Human naive pluripotent stem cells established from the epiblasts of preimplantation blastocysts provide a useful model for mechanistic studies of pluripotency regulation and lineage differentiation. Important advances have been made to op…

Additional file 2 of A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos Open

Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao , et al. · 2020

Additional file 2: Table S1. A total of 64 genes showed both high DNA methylation heterogeneity at promoters and expression heterogeneity in human 8-cell stage embryos.

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state Open

Yixuan Wang, Chengchen Zhao, Zhenzhen Hou, Yuanyuan Yang, Yan Bi , et al. · 2018

Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental biology studies and therapeutic manipulations. However, the molecular mechanisms involved in the establishment and maintenance…

Author response: Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state Open

Yixuan Wang, Chengchen Zhao, Zhenzhen Hou, Yuanyuan Yang, Yan Bi , et al. · 2017

CAM: A quality control pipeline for MNase-seq data Open

Shengen Shawn Hu, Xiaolan Chen, Liao Ji, Yiqing Chen, Chengchen Zhao , et al. · 2017

Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organiza…

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data Open

Chengchen Zhao, Shengen Shawn Hu, Xiao Huo, Yong Zhang · 2017

An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. Howe…

CAM: a quality control pipeline for MNase-seq data Open

Shengen Shawn Hu, Xiaolan Chen, Liao Ji, Yiqing Chen, Chengchen Zhao , et al. · 2017

Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organiza…

Dr.seq2: a quality control and analysis pipeline for parallel single cell transcriptome and epigenome data Open

Chengchen Zhao, Shengen Shawn Hu, Xiao Huo, Yong Zhang · 2017

An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. Howe…

Dr.seq: a quality control and analysis pipeline for droplet sequencing Open

Xiao Huo, Shengen Shawn Hu, Chengchen Zhao, Yong Zhang · 2016

Motivation: Drop-seq has recently emerged as a powerful technology to analyze gene expression from thousands of individual cells simultaneously. Currently, Drop-seq technology requires refinement and quality control (QC) steps are critical…

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