Article
Biochemical Research Methods
Chunyan Ao, Quan Zou, Liang Yu
Summary: This study developed a predictor based on machine learning to identify 2'-O-methylation modification sites in RNA. The predictor showed high efficiency and accuracy in identifying modification sites across multiple species, outperforming existing tools.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Hongyu Li, Li Chen, Zaoli Huang, Xiaotong Luo, Huiqin Li, Jian Ren, Yubin Xie
Summary: 2'-O-methylations play a crucial role in regulating gene expression, and a novel hybrid deep-learning algorithm named DeepOMe has been proposed to accurately predict 2'-O-Me sites in human transcriptome, showing high performance in cross-validation and outperforming existing methods.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Summary: The article discusses the importance of analyzing RNA modifications through deep sequencing methods, describes common analytical approaches and issues, and explores the feasibility of using machine learning algorithms to establish predictive models.
Article
Astronomy & Astrophysics
Zhi Qin, Peigen Hu, Jing Li, Linhua Liu
Summary: Phosphorus is a crucial element for life development and researchers are now investigating the formation of phosphorus-bearing species in interstellar environments. Due to practical constraints, theoretical calculations using quantum mechanics are essential for understanding the formation mechanism of phosphorus monoxide ion (PO+). Various contributing processes were considered, leading to a total rate coefficient that remains relatively constant across temperatures of 1-10,000 K. The 2 (1)sigma(+) -> X (1)sigma(+) transition process dominates the formation of PO+ and can be used to model phosphorus astrochemistry in interstellar mediums.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2023)
Article
Computer Science, Hardware & Architecture
Mohammad Rahmani Fadiheh, Alex Wezel, Johannes Mueller, Joerg Bormann, Sayak Ray, Jason M. Fung, Subhasish Mitra, Dominik Stoffel, Wolfgang Kunz
Summary: Hardware security issues, especially transient execution attacks like Spectre and Meltdown, pose a genuine threat to modern computing systems. This paper introduces a new approach to HW sign-off verification that guarantees processor security at the RTL level by presenting a formal definition of security and a proof methodology based on Unique Program Execution Checking (UPEC). UPEC is capable of systematically detecting vulnerabilities to transient execution attacks in various HW designs.
IEEE TRANSACTIONS ON COMPUTERS
(2023)
Article
Chemistry, Analytical
Wei Li, Hongmei Yang, Yafen Wang, Xiaocheng Weng, Fang Wang
Summary: This method demonstrates the selective recognition of 6mA through DNA ligase's selective ligation reaction towards A-C mismatch and 6mA-C mismatch, further combined with RCA amplification to achieve highly sensitive identification of 6mA in dsDNA at single-base resolution.
Article
Multidisciplinary Sciences
Timothy Bondoc, Troy Lowe, Steven Clarke
Summary: PRMT7 targets substrates with specific amino acid motif, and it has inhibitory activity on human histone H2B with RXR motif. The difference in activity is due to changes in V-max rather than binding affinity. Ionic strength affects the activity by decreasing substrate-enzyme binding affinity.
Review
Biochemical Research Methods
Hong Wang, Shuyu Wang, Yong Zhang, Shoudong Bi, Xiaolei Zhu
Summary: Thanks to the advancement of deep sequencing and large-scale profiling, epitranscriptomics has become a rapidly growing field. This review comprehensively explores machine learning based approaches for predicting 10 types of RNA methylation, discussing data, features, learning algorithms, and future perspectives for RNA methylation sites prediction.
Article
Biotechnology & Applied Microbiology
Zeeshan Abbas, Mobeen ur Rehman, Hilal Tayara, Quan Zou, Kil To Chong
Summary: The article introduces a novel model called m5C-pred, which combines multiple feature encoding techniques to extract features from RNA sequences and accurately identify m5C methylation sites using SHapley Additive exPlanations and XGBoost as a classifier. The authors used the optimization method Optuna to determine the best hyperparameters and validated the accuracy and superiority of the model through comparisons with other methods.
Article
Biochemistry & Molecular Biology
Bo Xu, Can Zhang, Ao Jiang, Xianhong Zhang, Fenfei Liang, Xueqing Wang, Danni Li, Chenglong Liu, Xiaomei Liu, Jing Xia, Yang Li, Yirong Wang, Zelan Yang, Jia Chen, Yu Zhou, Liang Chen, Hui Sun
Summary: This study reveals that the interaction between O-GlcNAc transferase (OGT) and histone methyltransferase Dot1L facilitates OGT-dependent histone O-GlcNAcylation. Moreover, depletion of Dot1L decreases the levels of OGT associated with chromatin and affects gene transcription regulation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Shang Liang, Joana C. Silva, Olga Suska, Radoslaw Lukoszek, Rajaei Almohammed, Victoria H. Cowling
Summary: CMTR1 plays a critical role in RNA expression and differentiation, particularly in histone and ribosomal protein gene regulation. Repression of CMTR1 leads to decreased RNA expression, translation inhibition, and induction of DNA replication stress and damage. CMTR1 is upregulated during neural differentiation and is essential for gene expression and proliferation during this process.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Shama Parween, Thilina T. Alawathugoda, Ashok D. Prabakaran, S. Thameem Dheen, Randall H. Morse, Bright Starling Emerald, Suraiya A. Ansari
Summary: Protein O-GlcNAcylation is an important nutrient-sensitive glycosylation modification that plays a role in neurodevelopment. Up-regulation of O-GlcNAc levels using pharmacological methods can enhance the expression of key neurogenic transcription factor genes and affect chromatin modifications.
LIFE SCIENCE ALLIANCE
(2022)
Article
Cell Biology
Jean-Sebastien Parent, Jonathan Cahn, Rowan P. Herridge, Daniel Grimanelli, Robert A. Martienssen
Summary: This study demonstrates that small RNAs guide histone H3 lysine 9 dimethylation and asymmetric DNA methylation during Arabidopsis thaliana embryonic development, revealing a novel silencing mechanism. This de novo silencing mechanism depends on the catalytic domain of SUVH9, a Su(Var)3-9 homolog previously thought to be catalytically inactive.
GENES & DEVELOPMENT
(2021)
Review
Chemistry, Multidisciplinary
Yue Huang, Wenyang Xia, Ze Dong, Cai-Guang Yang
Summary: Epigenetics, including the N-6-methyladenosine (m(6)A) modification, plays a critical role in gene expression regulation. Understanding the biology of RNA epigenetics and developing drugs targeting m(6)A modifying proteins is important for cancer research and therapy.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biology
Xin-Jian Xu, Hong-Xiang Gao, Liu-Cun Zhu, Rui Zhu
Summary: Network theory has been of great interest in the biological community for its effectiveness in identifying tumor-associated genes. However, most studies have focused on single networks of single omics, which have limited predictive power. This study constructs a bilayer network of DNA methylation sites and RNAs and applies it to five types of tumor data to identify key genes associated with tumors. Compared to single networks, the proposed bilayer network yields more tumor-associated DNA methylation sites and genes, which are validated through prognostic and KEGG enrichment analyses.
Article
Biochemistry & Molecular Biology
Ling-Ling Zheng, Jun-Hao Li, Jie Wu, Wen-Ju Sun, Shun Liu, Ze-Lin Wang, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Peng Shao, Qi Liu, Peterson Kariuki Maina, Jiayue Cui, Thomas B. Bair, Tiandao Li, Shaikamjad Umesalma, Weizhou Zhang, Hank Heng Qi
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
NUCLEIC ACIDS RESEARCH
(2017)
Article
Cell Biology
Zhuo Yao, Fuhua Xie, Min Li, Zirui Liang, Wenli Xu, Jianhua Yang, Chang Liu, Hongwangwang Li, Hui Zhou, Liang-Hu Qu
CELL DEATH & DISEASE
(2017)
Article
Multidisciplinary Sciences
Huilin Huang, Hengyou Weng, Bowen Dong, Panpan Zhao, Hui Zhou, Lianghu Qu
Scientific Reports
(2017)
Article
Microbiology
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
FRONTIERS IN MICROBIOLOGY
(2017)
Article
Cell Biology
Ze-Lin Wang, Bin Li, Yu-Xia Luo, Qiao Lin, Shu-Rong Liu, Xiao-Qin Zhang, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
Article
Immunology
Shaojun Xing, Peng Shao, Fengyin Li, Xudong Zhao, Wooseok Seo, Justin C. Wheat, Selvi Ramasamy, Jianfeng Wang, Xiang Li, Weiqun Peng, Shuyang Yu, Chengyu Liu, Ichiro Taniuchi, David A. Sweetser, Hai-Hui Xue
JOURNAL OF EXPERIMENTAL MEDICINE
(2018)
Article
Microbiology
Isaac J. Jensen, Christina S. Winborn, Micaela G. Fosdick, Peng Shao, Mikaela M. Tremblay, Qiang Shan, Sandeep Kumar Tripathy, Christopher M. Snyder, Hai-Hui Xue, Thomas S. Griffith, Jon C. Houtman, Vladimir P. Badovinac
Article
Immunology
Shaojun Xing, Kexin Gai, Xiang Li, Peng Shao, Zhouhao Zeng, Xudong Zhao, Xin Zhao, Xia Chen, William J. Paradee, David K. Meyerholz, Weiqun Peng, Hai-Hui Xue
JOURNAL OF EXPERIMENTAL MEDICINE
(2019)
Article
Immunology
Peng Shao, Fengyin Li, Jinyong Wang, Xia Chen, Chengyu Liu, Hai-Hui Xue
JOURNAL OF IMMUNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Qi Liu, Nicholas Borcherding, Peng Shao, Huojun Cao, Weizhou Zhang, Hank Heng Qi
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2019)
Article
Medicine, General & Internal
Qi Liu, Nicholas C. Borcherding, Peng Shao, Peterson K. Maina, Weizhou Zhang, Hank H. Qi
Article
Biochemistry & Molecular Biology
Peterson Kariuki Maina, Peng Shao, Xiongfei Jia, Qi Liu, Shaikamjad Umesalma, Maximo Marin, Donald Long, Samantha Concepcion-Roman, Hank Heng Qi
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2017)