Nature Search

Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks

SUCCEED is a supervised multi-task DNA foundation model pretrained on 6,389 ENCODE tracks. It integrates CNN and Transformer architectures to model local motifs and long-range dependencies, enabling prediction of genomic regulatory features across tasks and cell types.

Canzhuang Sun
Zhijie He
Hebing Chen
ResearchOpen Access14 May 2026
Nature Communications

P: 1-19
CellLoop: Identifying single-cell 3D genome chromatin loops

CellLoop maps 3D chromatin loops in single cells, revealing how distinct DNA folding patterns shape gene activity, define cell identity, and organize spatial genome domains, providing new insights into cellular diversity and genome function.

Yusen Ye
Yiheng Wang
Lin Gao
ResearchOpen Access06 Apr 2026
Nature Communications

P: 1-15
Human pluripotent stem cell-derived skin organoids enabled pathophysiological model of Mycobacterium tuberculosis infection

Cutaneous tuberculosis is an infectious disease associated with extracellular matrix remodeling and granuloma-driven fibrosis. Here, the authors present an in vitro model of this disease using skin organoids infected with Mycobacterium tuberculosis, and describe infection-induced alterations in specific pathways and cell populations.

Liang Yue
Yating Liang
Yingxia Tan
ResearchOpen Access02 Dec 2025
Nature Communications

Volume: 16, P: 1-16
TP63 mediates the generation of tumour-specific chromatin loops that underlie MYC activation in radiation-induced tumorigenesis

Radiation-induced malignantly transformed cells undergo multi-scale 3D genome reorganization. TP63 acts as a key mediator, creating accessible chromatin sites that form tumour-specific loops activating the MYC oncogene during malignant transformation.

Qiaowei Liu
Shuai Jiang
Yi Hu
ResearchOpen Access30 Sept 2025
Nature Communications

Volume: 16, P: 1-18
Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions

Here the authors developed a nucleolus Hi-C technique (nHi-C) for enriching nucleolus-associated interactions, and revealed specific heterochromatin interaction patterns within and around nucleoli in human cells at high resolution.

Ting Peng
Yingping Hou
Cheng Li
ResearchOpen Access21 Jan 2023
Nature Communications

Volume: 14, P: 1-15
mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer

Lv, Wang, Lin, Ye et al. report that mTORC2 phosphorylates cGAS to promote its chromatin localization and SWI/SNF recruitment to regulate target gene expression, thereby mediating plasticity and chemoresistance in colorectal cancer.

Guoqing Lv
Qian Wang
Lin Yuan
ResearchOpen Access30 Jul 2024
Nature Cell Biology

Volume: 26, P: 1585-1596
The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation

CTCF, which is known to play critical role in chromatin structure, undergoes post-translational modifications (PTMs). In this research, O-GlcNAcylation was found to inhibit CTCF binding, impacting 3D chromatin structure, gene expression and cellular development.

Xiuxiao Tang
Pengguihang Zeng
Junjun Ding
ResearchOpen Access01 Apr 2024
Nature Communications

Volume: 15, P: 1-15
General features to enhance enzymatic activity of poly(ethylene terephthalate) hydrolysis

In the face of global plastic pollution, enzymatic degradation of poly(ethylene terephthalate) (PET) has attracted much attention. Now, structural and biochemical studies reveal a minimal mutational strategy to increase the activity of PET-degrading enzymes, with potential evolutionary implications.

Chun-Chi Chen
Xu Han
Rey-Ting Guo
Research20 May 2021
Nature Catalysis

Volume: 4, P: 425-430
Calibration of physical and mechanical property parameters of broccoli seedling stalks

Liming Qin
Yikang Gong
Di Wang
ResearchOpen Access09 Feb 2026
Scientific Reports

Volume: 16, P: 1-17
CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection

Gene modules are widespread and important for studying cancer. Here, authors propose an explainable deep learning-based framework, CGMega, which incorporates multi-omics information from the three-dimensional genome, epigenome, and protein-protein interactions to dissect cancer gene modules.

Hao Li
Zebei Han
Xiaochen Bo
ResearchOpen Access17 Jul 2024
Nature Communications

Volume: 15, P: 1-15
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains

TAD hierarchy demonstrates cell-to-cell variability, leading to the development of numerous callers. Here, authors present a comprehensive benchmark of TAD hierarchy callers and introduce the ‘air conditioner’ model to illustrate TAD hierarchy’s role in transcription.

Jingxuan Xu
Xiang Xu
Hebing Chen
ResearchOpen Access23 May 2024
Nature Communications

Volume: 15, P: 1-19
Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks

Transcription factor regulatory networks underlie major features of cellular identity and complex function such as pluripotency, development and differentiation. Li and colleagues develop a graph neural network to predict transcription factor regulatory networks based on single-cell ATAC-seq data.

Hao Li
Yu Sun
Xiaochen Bo
Research11 Apr 2022
Nature Machine Intelligence

Volume: 4, P: 389-400
An EGFR/HER2-targeted conjugate sensitizes gemcitabine-sensitive and resistant pancreatic cancer through different SMAD4-mediated mechanisms

Chemoresistance is a main limitation for the treatment of pancreatic ductal adenocarcinoma (PDAC). Here, the authors show that an antibody drug conjugate-like compound targeting both EGFR and HER2 overcomes gemcitabine resistance in PDAC preclinical models by mechanisms involving the tumour suppressor SMAD4.

Hongjuan Yao
Wenping Song
Liang Li
ResearchOpen Access20 Sept 2022
Nature Communications

Volume: 13, P: 1-24
Ablation alone is noninferior to radiotherapy plus ablation in the patients with early-stage hepatocellular carcinoma: a population-based study

Yusheng Guo
Hebing Chen
Chuansheng Zheng
ResearchOpen Access10 Jan 2024
Scientific Reports

Volume: 14, P: 1-11
Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold

Rui Chen
Xinpeng Guo
Bing He
ResearchOpen Access23 Oct 2025
Scientific Reports

Volume: 15, P: 1-14
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape

Hebing Chen
Hao Li
Wenjie Shu
ResearchOpen Access16 Feb 2015
Scientific Reports

Volume: 5, P: 1-13
3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression

Multi-omics profiling of matched normal colon, primary tumor, and liver metastasis from colorectal carcinoma patients based on Hi-C, ATAC-seq and RNA-seq technologies sheds light on the changes and regulatory mechanisms of 3D genomics during the tumorigenesis and metastasis of colorectal carcinoma.

Xiang Xu
Jingbo Gan
Jin Gu
ResearchOpen Access04 Mar 2025
Communications Biology

Volume: 8, P: 1-16
Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance

An integrated analysis of RNA editing events in human embryo development suggests that recurrent RNA edits might enhance maternal mRNA clearance.

Yang Ding
Yang Zheng
Xiaochen Bo
ResearchOpen Access21 Dec 2022
Communications Biology

Volume: 5, P: 1-13
CLIC3 interacts with NAT10 to inhibit N4-acetylcytidine modification of p21 mRNA and promote bladder cancer progression

Yujun Shuai
Hui Zhang
Guosong Jiang
ResearchOpen Access05 Jan 2024
Cell Death & Disease

Volume: 15, P: 1-14
Phase II study of novel orally PI3Kα/δ inhibitor TQ-B3525 in relapsed and/or refractory follicular lymphoma

Huaqing Wang
Jifeng Feng
Zhiming Li
ResearchOpen Access17 Apr 2024
Signal Transduction and Targeted Therapy

Volume: 9, P: 1-9
Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework

Junting Wang
Chengyue Zhang
Liang Li
Research25 Dec 2023
Cancer Gene Therapy

Volume: 31, P: 439-453
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development

TimeTalk is a computational approach that uses time-course single-cell RNA-seq data to identify ligand-receptor pairs for studying cell-cell communications in early embryo development.

Longteng Wang
Yang Zheng
Hebing Chen
ResearchOpen Access02 Sept 2023
Communications Biology

Volume: 6, P: 1-16
Functional annotation of HOT regions in the human genome: implications for human disease and cancer

Hao Li
Hebing Chen
Wenjie Shu
ResearchOpen Access26 Jun 2015
Scientific Reports

Volume: 5, P: 1-16
Author Correction: 3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression

Xiang Xu
Jingbo Gan
Jin Gu
Amendments and CorrectionsOpen Access31 Mar 2025
Communications Biology

Volume: 8, P: 1

Search

Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks

CellLoop: Identifying single-cell 3D genome chromatin loops

Human pluripotent stem cell-derived skin organoids enabled pathophysiological model of Mycobacterium tuberculosis infection

TP63 mediates the generation of tumour-specific chromatin loops that underlie MYC activation in radiation-induced tumorigenesis

Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions

mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer

The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation

General features to enhance enzymatic activity of poly(ethylene terephthalate) hydrolysis

Calibration of physical and mechanical property parameters of broccoli seedling stalks

CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection

A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains

Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks

An EGFR/HER2-targeted conjugate sensitizes gemcitabine-sensitive and resistant pancreatic cancer through different SMAD4-mediated mechanisms

Ablation alone is noninferior to radiotherapy plus ablation in the patients with early-stage hepatocellular carcinoma: a population-based study

Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold

An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape

3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression

Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance

CLIC3 interacts with NAT10 to inhibit N4-acetylcytidine modification of p21 mRNA and promote bladder cancer progression

Phase II study of novel orally PI3Kα/δ inhibitor TQ-B3525 in relapsed and/or refractory follicular lymphoma

Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework

TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development

Functional annotation of HOT regions in the human genome: implications for human disease and cancer

Author Correction: 3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression

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