Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hu Zhao, Jiacheng Li, Ling Yang, Gang Qin, Chunjiao Xia, Xingbing Xu, Yangmeng Su, Yinmeng Liu, Luchang Ming, Ling-Ling Chen, Lizhong Xiong, Weibo Xie
Summary: The study presented a functional impact map of genetic variants in rice, utilizing sequencing data and chromatin accessibility data from 4726 rice accessions. Through quantitative evaluation of missense mutations, a total of 918,848 non-redundant missense variants were identified. The study revealed that large-effect genetic variants in coding and regulatory regions may be subject to different directions of selection.
Article
Biochemical Research Methods
Konstantin Krismer, Jennifer Hammelman, David K. Gifford
Summary: Motivated by the poor interpretability of complex predictive models in regulatory genomics, this study introduces seqgra, a deep learning pipeline that incorporates rule-based simulation of biological sequence data to generate data based on hypothesized models of genome regulation. The pipeline also identifies neural network architectures capable of recovering the rules from the simulated data and analyzes the model's predictive performance in relation to training set size and the complexity of the simulated data.
Article
Multidisciplinary Sciences
Jinlei Han, Damar Lopez-Arredondo, Guangrun Yu, Yankun Wang, Baohua Wang, Sarah Brooke Wall, Xin Zhang, Hui Fang, Alfonso Carlos Barragan-Rosillo, Xiaoping Pan, Yanqin Jiang, Jingbo Chen, Hui Zhang, Bao-Liang Zhou, Luis Herrera-Estrella, Baohong Zhang, Kai Wang
Summary: This study examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton, revealing the interplay among transposable elements, cis-regulatory elements, and histone modifications during polyploidization. These findings advance our understanding of regulatory architecture in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Elias Orouji, Ayush T. Raman
Summary: The human genome is shaped by a variety of histone modifications, which play a crucial role in determining chromatin states and organization. Using statistical models and computational tools, noncoding regions of DNA can be annotated and combinatorial histone marks inferred. These marks enable the discovery of genomic function and activity, and their patterns change in different cell conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Yanding Zhao, Yadong Dong, Wei Hong, Chongming Jiang, Kevin Yao, Chao Cheng
Summary: Chromatin accessibility is crucial for transcriptional activation of the genome, with transcription factors and histone modifications playing important roles. In this study, a two-layer model was constructed to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. The results showed that TF binding and HM signals accurately predicted chromatin accessibility, while the predictive power of DNA sequences was limited.
Article
Genetics & Heredity
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
Summary: DeepCAGE is a deep learning framework that accurately predicts chromatin accessible regions in a variety of cell types, and exhibits superior performance in the classification and regression of chromatin accessibility signals.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Automation & Control Systems
Yinjing Liao, Hui Guo, Runyu Jing, Jiesi Luo, Menglong Li, Yizhou Li
Summary: Post-translational modifications of histone play a key role in gene expression regulation by controlling DNA accessibility and recruiting transcription factors. Developing computational methods to predict gene expression levels from histone modification data can enhance understanding of their function and contribute to the development of epigenetic drugs. Additionally, histone signals at the transcription termination site (TTS) provide valuable information to improve model performance, indicating potential regulatory mechanisms that need further exploration.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Multidisciplinary Sciences
Shuai Zhao, Kelly N. Chuh, Baichao Zhang, Barbara E. Dul, Robert E. Thompson, Lorna A. Farrelly, Xiaohui Liu, Ning Xu, Yi Xue, Robert G. Roeder, Ian Maze, Tom W. Muir, Haitao Li
Summary: The study found that the readers of H3K4me3 retain binding to H3K4me3Q5ser, while the erasers are significantly inhibited. The results suggest that H3Q5ser may potentially fine-tune critical gene expression programs by stabilizing H3K4me3 from dynamic turnover or enhancing its physical readout by downstream effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Tianjiao Zhang, Liangyu Li, Hailong Sun, Dali Xu, Guohua Wang
Summary: This article introduces a deep learning framework called DeepICSH for identifying silencers in specific cells. DeepICSH leverages multiple biological data sources and a convolutional neural network to capture biologically relevant signal combinations associated with silencers. Through extensive experiments, DeepICSH has shown superior performance in silencer identification.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agriculture, Multidisciplinary
Si-di Xie, Ran Tian, Jun-jie Zhang, Han-mei Liu, Yang-ping Li, Yu-feng Hu, Guo-wu Yu, Yu-bi Huang, Ying-hong Liu
Summary: Chromatin accessibility plays a crucial role in gene transcriptional regulation. Using a maize kernel mutant called dek219, researchers identified the DICER-LIKE1 (DCL1) protein as an important enzyme in miRNA biogenesis that affects the expression of miRNAs and histone genes. They also found that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be involved in regulating histone gene expression. ATAC-seq experiments showed that the chromatin accessibility of dek219 is altered compared to wild type, potentially impacting the expression of crucial genes in kernel development. Analysis revealed 119 candidate genes regulated by chromatin accessibility, including some known to play a role in kernel development.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Multidisciplinary Sciences
Parashar Dhapola, Johan Rodhe, Rasmus Olofzon, Thomas Bonald, Eva Erlandsson, Shamit Soneji, Goran Karlsson
Summary: Scarf is a modularly designed Python package that enables memory-efficient single-cell analysis and can run on low-cost devices. It provides efficient implementations for memory and computation and supports accurate reference-anchored mapping and subsampling of large single-cell datasets.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz
Summary: Compared to its predecessors, the Telomere-to-Telomere CHM13 genome has significant improvements in sequence length and structural accuracy, enabling more comprehensive study of the human genome. The application of the T2T-CHM13 reference has demonstrated improved accuracy in read mapping and variant calling for globally diverse samples, leading to the discovery of previously unresolved variants and the removal of false positives. These advancements position T2T-CHM13 as a potential replacement for GRCh38 as the dominant reference for human genetics.
Review
Plant Sciences
Rocio Nunez-Vazquez, Benedicte Desvoyes, Crisanto Gutierrez
Summary: Plants have developed various mechanisms to adapt to abiotic stresses, which involve transcriptional regulation and chromatin modifications. Understanding and manipulating these regulatory networks are crucial for enhancing crop resilience and performance against stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Liying Wang, Zhiliang Xu, Libin Wang, Chao Liu, Huafang Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Sai Xiao, Wei Li, Wei Li
Summary: The study reveals that RNF20 is crucial for early stage somatic cell reprogramming, with Rnf20 knockout leading to failure in reprogramming at the initial stage. The absence of RNF20 affects the transcription of MET-related genes and early pluripotency genes, ultimately hindering the establishment of a pluripotent gene network.
CELL PROLIFERATION
(2021)
Article
Microbiology
Congmin Zhu, Xin Wang, Jianchu Li, Rui Jiang, Hui Chen, Ting Chen, Yuqing Yang
Summary: The study reveals the significant impact of gut microbiota on human disease risk, proposing the use of machine learning models to accurately infer the associations between human variables and gut microbiota. Analysis on the American Gut Project dataset shows distinct association strengths between gut microbiota and various diseases, with significant improvement in classification performance for diseases like inflammatory bowel disease by adding gut microbiota into human variables.
Article
Biochemistry & Molecular Biology
Yanhong Wu, Qifan Hu, Shicheng Wang, Changyi Liu, Yiran Shan, Wenbo Guo, Rui Jiang, Xiaowo Wang, Jin Gu
Summary: In this study, a feature selection method called Highly Regional Genes (HRG) is proposed based on the cell-cell similarity network to identify informative genes that exhibit regional expression patterns. The HRG method demonstrates high accuracy and robustness compared to other unsupervised methods, and it improves the performance of cell clustering and gene correlation analysis.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Editorial Material
Multidisciplinary Sciences
Sijie Chen, Yanting Luo, Haoxiang Gao, Fanhong Li, Jiaqi Li, Yixin Chen, Renke You, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang
Summary: This perspective discusses the need and directions for the development of a unified information framework to enable the assembly of cell atlases and revolutionize medical research on the virtual body of assembled cell systems.
NATIONAL SCIENCE REVIEW
(2022)
Article
Biochemical Research Methods
Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv
Summary: Single-cell technologies have significantly advanced biological research, and the scGraph algorithm improves cell-type identification performance by leveraging gene interaction relationships, providing important insights into cellular characteristics.
Article
Biochemical Research Methods
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang
Summary: Drug resistance is a major challenge in cancer therapy, and studying cancer cell lines has limitations. This article proposes a new method, DualGCN, to predict cancer drug response using a dual graph convolutional network model, which outperforms existing methods without using large-scale SNV data. This method has the potential to be applied to clinical and single-cell tumor samples, advancing precision medicine.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
Summary: DeepCAGE is a deep learning framework that accurately predicts chromatin accessible regions in a variety of cell types, and exhibits superior performance in the classification and regression of chromatin accessibility signals.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Xi Xi, Haochen Li, Shengquan Chen, Tingting Lv, Tianxing Ma, Rui Jiang, Ping Zhang, Wing Hung Wong, Xuegong Zhang
Summary: This article introduces a machine-learning-based cross-scale framework GRPath to decipher putative causal paths from genetic variants to disease phenotypes. Applied to cardiovascular diseases, a large number of pcPaths were identified, providing new insights into genetic variants for types of heart failure.
Article
Biology
Yaowen Gu, Si Zheng, Qijin Yin, Rui Jiang, Jiao Li
Summary: Computational drug repositioning is an effective method to find new indications for existing drugs. The heterogeneous graph neural network REDDA enhances drug-disease association prediction by utilizing biological entity relations. Experimental results show that REDDA outperforms other methods, indicating its potential in drug development.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong
Summary: HiChIPdb is a comprehensive database based on HiChIP interactions, which allows for standardized categorization and annotation of functional interactions across diverse cell types and tissues, and provides a unified pipeline for data analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Rui Jiang, Zhen Li, Yuhang Jia, Siyu Li, Shengquan Chen
Summary: Recent advances in spatial transcriptomics have led to a better understanding of tissue organization. In this study, we propose a scalable method called SINFONIA for identifying spatially variable genes using ensemble strategies. The method, implemented in Python, demonstrates superior performance compared to baseline methods in various evaluation metrics, and can be easily integrated into existing analysis workflows, aiding the analysis of spatial transcriptomics.
Article
Multidisciplinary Sciences
Shuo Li, Weihua Zeng, Xiaohui Ni, Qiao Liu, Wenyuan Li, Mary L. Stackpole, Yonggang Zhou, Arjan Gower, Kostyantyn Krysan, Preeti Ahuja, David S. Lu, Steven S. Raman, William Hsu, Denise R. Aberle, Clara E. Magyar, Samuel W. French, Steven -Huy B. Han, Edward B. Garon, Vatche G. Agopian, Wing Hung Wong, Steven M. Dubinett, Xianghong Jasmine Zhoua
Summary: Plasma cell-free DNA (cfDNA) is a noninvasive biomarker that can be used to detect abnormal cell death due to diseases. By establishing a comprehensive tissue methylation atlas and utilizing the cfSort deep-learning model, the performance of tissue deconvolution in cfDNA can be significantly improved, enabling disease detection and longitudinal treatment monitoring.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong
Summary: scREG is a dimension reduction methodology for single cell multiome data based on the concept of cis-regulatory potential, used for constructing subpopulation-specific cis-regulatory networks. It demonstrates increased accuracy in inferring regulatory networks and enrichment of GWAS variants in cis-regulatory elements for specific diseases.
Article
Computer Science, Artificial Intelligence
Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang
Summary: The authors propose a probabilistic generative model called EpiAnno to automatically annotate single-cell chromatin accessibility sequencing (scCAS) data. The model is validated on multiple datasets and demonstrates advantages in interpretable embedding and biological implications.
NATURE MACHINE INTELLIGENCE
(2022)