Article
Biochemical Research Methods
Zhourun Wu, Qing Liao, Shixi Fan, Bin Liu
Summary: A novel computational method idenPC-CAP was developed to identify protein complexes from the RNA-protein heterogeneous interaction network, reducing the false positive proteins ratio and outperforming other state-of-the-art methods in this field as demonstrated by experimental results.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Katarzyna Taylor, Agnieszka Piasecka, Arkadiusz Kajdasz, Aleksandra Brzek, Micaela Polay Espinoza, Cyril F. Bourgeois, Artur Jankowski, Malgorzata Borowiak, Katarzyna D. Raczynska, Lukasz J. Sznajder, Krzysztof Sobczak
Summary: This study aims to elucidate the mechanism of muscleblind-like splicing regulators (MBNLs) in alternative splicing (AS) processes. The findings indicate that DEAD-box (DDX) RNA helicases DDX5 and DDX17 play an important role in MBNL-dependent AS regulation. The helicases modulate MBNL splicing activity through changes in the ratio of MBNL splicing isoforms and accessibility of MBNL-binding sites. These findings contribute to a deeper understanding of the interdependencies between RNA-binding proteins and their implications in developmental homeostasis and pathological states.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Mansheng Li, Qiang He, Chunyuan Yang, Jie Ma, Fuchu He, Tao Chen, Yunping Zhu
Summary: The study introduces a well-designed schema PPIO for representing the biological context of Protein-Protein Interactions (PPIs), with a precision of 0.69, a recall of 0.72, and an F-score of 0.70 in experiment results from the BioCreAtIvE corpus.
Review
Biochemical Research Methods
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
Summary: Protein-RNA interactions play a vital role in cellular activities. Previous computational methods heavily rely on sequence data due to the lack of protein structure data. However, the emergence of AlphaFold is set to revolutionize protein-RNA interaction prediction. In this review, we provide a comprehensive overview of the field, covering binding site and binding preference prediction, as well as commonly used datasets, features, and models. We also discuss potential challenges and opportunities in this area.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Tejas Soni, Ashwani Sharma, Rajdeep Dutta, Annwesha Dutta, Senthilnath Jayavelu, Saikat Sarkar
Summary: This paper proposes a machine learning-based strategy to solve the computationally expensive fluid-structure interaction (FSI) problems. By introducing dissipation and time-varying forces to mimic the effect of fluid on an immersed beam, the authors utilize symbolic regression to generate computationally tractable functional forms for force/moment estimation. Numerical results demonstrate that the proposed machine learning approach accurately predicts the beam deflections under different discretizations.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Rui Yang, Haoquan Liu, Liu Yang, Ting Zhou, Xinyao Li, Yunjie Zhao
Summary: This study developed an easy-to-use bioinformatics resource called RPpocket for exploring and visualizing the structural interaction features of RNA-protein complexes. By analyzing sequence, secondary structure, and pocket topology, this database provides information on the interactions of RNA-protein complexes and reveals the binding mechanisms and related properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Xiaoyuan Tao, Sujuan Li, Guang Chen, Jian Wang, Shengchun Xu
Summary: Long non-coding RNAs (lncRNAs) are transcripts that are longer than 200 nucleotides (nt) and do not code for proteins. It is crucial to use appropriate research methodologies when studying lncRNAs with biological importance. While previous reviews have focused on lncRNA biogenesis, localization, functions, and potential applications, there has been limited discussion on leading strategies for lncRNA research. This article presents a comprehensive mind map for lncRNA research and explores the mechanisms and application scenarios of up-to-date techniques in studying the molecular functions of lncRNAs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Thao Vu, Elizabeth M. Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell P. Bowler, Farnoush Banaei-Kashani, Katerina J. Kechris
Summary: Biological networks provide a system-level understanding of underlying processes. In order to investigate the association between modules and variables of interest, a module summarization method that can explain the module's information and reduce dimensionality is needed. This article proposes NetSHy, a hybrid approach that incorporates topological properties to aid downstream analysis interpretation while reducing network dimensionality.
Article
Biochemical Research Methods
Xueyan Liu, Yong Xu, Ran Wang, Sheng Liu, Jun Wang, YongLun Luo, Kwong-Sak Leung, Lixin Cheng
Summary: MoonFinder v2.0 is an algorithm dedicated to predicting human mlncRNAs, providing a comprehensive framework and a moonlighting coefficient for assessing their cellular functions. Studies have shown that mlncRNAs exhibit specific expression characteristics in sepsis and tend to be mutually exclusive in terms of coexpression compared to other lncRNAs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Marc Horlacher, Nils Wagner, Lambert Moyon, Klara Kuret, Nicolas Goedert, Marco Salvatore, Jernej Ule, Julien Gagneur, Ole Winther, Annalisa Marsico
Summary: RBPNet is a new deep learning method that predicts CLIP-seq crosslink count distribution from RNA sequence. Training on millions of regions, RBPNet shows high generalization on eCLIP, iCLIP, and miCLIP assays, outperforming state-of-the-art classifiers. RBPNet performs bias correction by modeling the raw signal as a mixture of protein-specific and background signal. By using Integrated Gradients for model interrogation, RBPNet identifies predictive sub-sequences corresponding to known and novel binding motifs and enables variant-impact scoring through in silico mutagenesis. Overall, RBPNet improves the imputation of protein-RNA interactions and enhances mechanistic interpretation of predictions.
Review
Biochemistry & Molecular Biology
Dennis Wicke, Janek Meissner, Robert Warneke, Christoph Elfmann, Joerg Stuelke
Summary: Model organisms like Bacillus subtilis have been extensively studied, but a significant number of proteins in these organisms still have unknown functions. The Understudied Proteins Initiative aims to address this issue. Highly expressed proteins that are poorly studied are likely to play important roles in cellular processes and should be a priority for further research.
MOLECULAR MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Takumi Yokoyama, Takehiro Ando, Yukio Takamori, Daisuke Fuji, Masashi Sato, Santhana Vedi, Mizuki Yamamoto, Takashi Kawakami
Summary: This study reports a novel linker for SELEX of mRNA-displayed unnatural peptides, forming thioethers through intramolecular reactions.
CHEMICAL COMMUNICATIONS
(2022)
Review
Virology
Arpita Kar, Abhisekh Samanta, Soumyadeep Mukherjee, Subhasis Barik, Avik Biswas
Summary: Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), the most common primary liver malignancy. The study of HBV-host interactions has identified various mechanisms involved in the development and progression of HBV-associated HCC. This review provides a comprehensive summary of the existing knowledge on HBV-host interplay and highlights new therapeutic strategies for HBV-induced HCC.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Chemistry, Analytical
Alexander Wiorek, Maria Cuartero, Gaston A. Crespo
Summary: This study presents the synergistic effects of carbon nanotubes and an ion-selective membrane, demonstrating the selective ion capture from a solution. By manipulating the charge generation on the carbon nanotubes lattice, controlled ion uptake is achieved. This concept has potential applications in removing ionic interferences in samples to enhance the precision of analytical assessments with sensors.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Georg L. L. Goebel, Lisa Hohnen, Lydia Borgelt, Pascal Hommen, Xiaqiu Qiu, Helen Lightfoot, Peng Wu
Summary: The study reports the inhibitory activities of a series of small molecules with tricyclic tetrahydroquinoline structure against LIN28. It identifies the structural features required for LIN28 inhibition and emphasizes the importance of developing small molecules with new scaffolds as LIN28-targeting probes and therapeutic candidates.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Cell Biology
WeiWei Zhang, HuiLi Tong, ZiHeng Zhang, ShuLi Shao, Dan Liu, ShuFeng Li, YunQin Yan
JOURNAL OF CELLULAR PHYSIOLOGY
(2018)
Article
Cell Biology
Sanlan Li, Yuhan Shi, Xuan Yao, Xing Wang, Libing Shen, Zhiping Rao, Jiacheng Yuan, Yueguang Liu, Zhenning Zhou, Ziheng Zhang, Fei Liu, Sue Han, Junlan Geng, Hui Yang, Leping Cheng
Article
Oncology
Zhe Sun, Ziheng Zhang, Qiao-Qi Wang, Ji-Long Liu
Summary: Inhibition of CTP synthase selectively decreases cell viability and induces DNA replication stress in MYC-overexpressing cells. Combined inhibition of CTP synthase and ATR is synthetically lethal in MYC-overexpressing cells, leading to cell death in vitro and decreased tumor growth in vivo. Interfering with CTPS1 but not CTPS2 is necessary to induce replication stress and cell death in MYC-deregulated cancer cells in the presence of an ATR inhibitor.
Article
Biology
Weiping Sun, Ziheng Zhang, Ji-Long Liu, Min Zhuang
Summary: A novel method CRUIS is introduced in this study, combining the RNA-binding capacity of CRISPR/Cas13 and the proximity-tagging activity of PUP-IT for capturing RNA-protein interactions in living cells.
Article
Cell Biology
Yusheng Pang, Ziheng Zhang, Zhao Wang, Yuxin Wang, Yunqin Yan, Shufeng Li, Huili Tong
CELL ADHESION & MIGRATION
(2019)