Review
Biochemical Research Methods
Karin Elimelech-Zohar, Yaron Orenstein
Summary: Nucleic-acid G-quadruplexes (G4s) are crucial in cellular processes, and experimental assays have been developed to measure them in high throughput. This has enabled the development of machine-learning-based methods, particularly deep neural networks, to predict G4s in any nucleic-acid sequence and species.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Chemistry, Medicinal
Tiago Santos, Gilmar F. Salgado, Eurico J. Cabrita, Carla Cruz
Summary: This article discusses the progress in the design of G-quadruplex binding ligands and the various methods available to assess the binding interactions. Different experimental approaches, such as structure-based, affinity-based, and high-throughput methods, each have their unique advantages and drawbacks. The combination of these techniques has led to the discovery of numerous G4 ligands for diagnostic and therapeutic purposes.
Correction
Infectious Diseases
Zhangkai J. Cheng, Jing Shan
Summary: The original version of the article contained a mistake.
Correction
Multidisciplinary Sciences
Terry Plank, Craig E. Manning
Summary: The paper has an updated version available for access.
Correction
Statistics & Probability
Behdad Mostafaiy
Summary: This article discusses the discrete Linnik Weibull distribution and uses the method of maximum likelihood to estimate its unknown parameters. The authors made some mistakes in the estimation procedure and section 7, and this article presents the corrections.
COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Yuexu Jiang, Duolin Wang, Weiwei Wang, Dong Xu
Summary: Accurate annotation of protein localization plays a crucial role in understanding protein function. Computational prediction, especially with recent advancements in machine learning, has been a key research area for over two decades. This review paper categorizes main features and algorithms, summarizes existing prediction tools, evaluates their performance, and provides future outlook for protein localization methods.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Esra Bagda, Efkan Bagda, Abdulkadir Kocak, Mahmut Durmus
Summary: In this study, the affinity and binding mechanisms of water-soluble gallium phthalocyanine with DNA were investigated using various experimental techniques and computational studies. The results showed higher affinity of GaPc towards G-quadruplex DNA, leading to reduced aggregation of GaPc and conformational changes in the G-quadruplex DNA structure. Both experimental and computational findings indicated the potential of GaPc-G-quadruplex DNA conjugates for applications in photodynamic therapy.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Correction
Chemistry, Multidisciplinary
Caiyan Liu, Yongli Shen, Zihui Xiao, Hui Yang, Xue Han, Kedong Yuan, Yi Ding
Summary: The researchers corrected a method for the direct synthesis of aldehydes with alcohols (thiols) under neutral conditions, and provided computational insights into the electrochemical formation of acetals.
Review
Biochemical Research Methods
Jing Wang, Qinglong Zhang, Junshan Han, Yanpeng Zhao, Caiyun Zhao, Bowei Yan, Chong Dai, Lianlian Wu, Yuqi Wen, Yixin Zhang, Dongjin Leng, Zhongming Wang, Xiaoxi Yang, Song He, Xiaochen Bo
Summary: This review article discusses the recent applications of computational methods in synthetic lethality (SL) prediction. It introduces the concept and screening methods of SL, summarizes various SL-related data resources, and provides an overview of computational methods including statistical-based methods, network-based methods, classical machine learning methods, and deep learning methods for SL prediction. The article also highlights the use of negative sampling methods in these models. Representative tools for SL prediction are introduced, and the challenges and future work for SL prediction are discussed.
BRIEFINGS IN BIOINFORMATICS
(2022)
Correction
Soil Science
Ernesto Saiz, Fotis Sgouridis, Falko P. Drijfhout, Sami Ullah
Summary: The results showed significant inconsistencies in carbon abundance across species, sites, and time.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Correction
Robotics
Shuzhi Sam Ge, Agnieszka Wykowska, Oussama Khatib
Summary: This is to inform you that a sentence was accidentally left out from the final version.
INTERNATIONAL JOURNAL OF SOCIAL ROBOTICS
(2023)
Correction
Medicine, General & Internal
Karim Fizazi, Neal Shore, Teuvo L. Tammela, Albertas Ulys, Egils Vjaters, Sergey Polyakov, Mindaugas Jievaltas, Murilo Luz, Boris Alekseev, Iris Kuss, Christian Kappeler, Amir Snapir, Toni Sarapohja, Matthew R. Smith
Summary: This article points out incorrect data regarding the application of Darolutamide in nonmetastatic, castration-resistant prostate cancer.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Correction
Biochemistry & Molecular Biology
Yonghua Bao, Yongchen Guo, Yiqiong Yang, Xiaonan Wei, Shanshan Zhang, Yongmeng Zhang, Kai Li, Ming Yuan, Dongli Guo, Virgilia Macias, Xiangdong Zhu, Wei Zhang, Wancai Yang
Summary: A correction to this paper has been published.
Correction
Biochemistry & Molecular Biology
V. K. Vashistha, A. Mittal, P. K. Upadhyay, H. Nagar, R. Kumar, H. Gupta, R. Bala, D. K. Das
Summary: An erratum for this paper has been published, with the link https://doi.org/10.1134/S1068162023330014.
RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Yizhi Cui, Hongzhi Liu, Yutong Ming, Zheng Zhang, Li Liu, Ruijun Liu
Summary: G-quadruplex (G4) is a non-classical DNA structure that plays an important role in biological processes. Computational methods are necessary for predicting G4s due to their distribution in functional regions in a cell-type-specific manner. In this study, we developed a new prediction model based on machine learning and constructed a dataset using high-resolution sequencing data from G4 CUT & Tag. Our results demonstrate the influence of flanking sequences on G4 formation and the higher GC content of G4 flanking sequences. Furthermore, we identified G4 motifs for known transcription factors in the high-resolution dataset.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
