Article
Biochemical Research Methods
Ning Wang, Jun Zhang, Bin Liu
Summary: DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are important nucleic acid-binding proteins. A new computational predictor called IDRBP-PPCT was proposed to identify these proteins, and its effectiveness was proven.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Microbiology
Wenyue Hu, Yuli Wang, Bingxu Yang, Chen Lin, Hao Yu, Guang Liu, Zixin Deng, Hong-Yu Ou, Xinyi He
Summary: SRAP is an ancient protein superfamily found in various domains of life. YedK has a high affinity to DNA duplex with single strand segments. Mutants of YedK in Escherichia coli do not show differences in response to UV and DNA damaging reagents, indicating its non-essentiality or redundancy in E. coli.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Computer Science, Information Systems
Nina Evans, Andrej Miklosik, Rachelle Bosua, Athar Mahmood Ahmed Qureshi
Summary: This paper describes the experiences of experts who have adopted a holistic approach to driving transformation in various organizations. The primary goal is to outline key insights and observations that are critically important to implementing Digital Business Transformation (DBT). The authors conducted interviews to gather opinions and experiences related to organizational prerequisites, misconceptions, and challenges in implementing DBT. They identified six lessons learned during the transformations, including the importance of CEO commitment and change leadership, the right team to drive successful implementation, stakeholder perception and behavior, choosing the best digital platform, and the significance of relationships in the business ecosystem. The findings provide a holistic framework for organizations considering DBT implementation.
Article
Chemistry, Multidisciplinary
Andrej Miklosik, Alexander Bernhard Krah, Benjamim Fonseca, Ivo Pereira, Ana Madureira
Summary: This paper presents qualitative interpretative research on the experiences of German companies in the plastic extrusion machinery sector with digital transformation. The findings provide valuable insights into the progress of digital transformation initiatives in the pipe extrusion sector in Germany. The study also identifies several misconceptions about digital transformation, enhancing the existing literature on this topic.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Avigail Stokar-Avihail, Taya Fedorenko, Jens Hor, Jeremy Garb, Azita Leavitt, Adi Millman, Gabriela Shulman, Nicole Wojtania, Sarah Melamed, Gil Amitai, Rotem Sorek
Summary: In recent years, various defense systems against phages have been found in bacteria. However, the mechanism of how these systems sense phage infection remains unknown. To address this question, the researchers isolated 177 phage mutants that can evade 15 different defense systems. These mutants were found to have mutations in the gene sensed by the defense system, providing insights into the determinants of phage sensitivity. The study identifies specific determinants of different retron systems and reveals phage-encoded triggers for abortive infection systems, shedding light on how bacterial immune systems sense phage invaders.
Article
Multidisciplinary Sciences
Yuko Hasegawa, Kevin Struhl
Summary: The transcription factor SP1 exhibits varying binding dynamics at different target sites in the human genome, potentially influenced by factors such as location and cobinding factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Kashyap Chhatbar, John Connelly, Shaun Webb, Skirmantas Kriaucionis, Adrian Bird
Summary: The study found that CA repeats are not key mediators of MeCP2 function and there is no evidence to suggest that MeCP2 preferentially binds to CA repeat regions. Instead, CA repeat regions show typical CAC methylation levels similar to the surrounding genome and contribute modestly to MeCP2-mediated modulation of gene expression in accordance with their content of this canonical target motif.
LIFE SCIENCE ALLIANCE
(2022)
Article
Chemistry, Multidisciplinary
Sreejana Ray, Desiree Tillo, Stewart R. Durell, Syed Khund-Sayeed, Charles Vinson
Summary: NFATc2 is a DNA binding protein that shows differential binding to various types of DNA, with stronger binding observed when both cytosines in the CG dinucleotide are methylated.
Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Masayuki Oda
Summary: This article introduces a method called diffracted X-ray tracking (DXT) to study the structural dynamics of proteins in solution. The study found that structural fluctuations are suppressed when proteins bind to their ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Feifei Cui, Shuang Li, Zilong Zhang, Miaomiao Sui, Chen Cao, Abd El-Latif Hesham, Quan Zou
Summary: Nucleic acid-binding proteins (NABPs) are essential for gene expression. Accurate identification of these proteins is crucial but challenging. In this study, a computational predictor named DeepMC-iNABP was developed using multiclass classification and deep learning approaches. The results showed that DeepMC-iNABP effectively identified specific proteins and alleviated the cross-prediction problem.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Andrei G. Loiko, Alexander Sergeev, Adelya Genatullina, Mayya Monakhova, Elena A. Kubareva, Nina G. Dolinnaya, Elizaveta S. Gromova
Summary: This study reveals a potential link between G-quadruplex formation and the function of DNA methyltransferase Dnmt3a in mammals. G4s may play a role in epigenetic regulation by affecting the methylation of specific CpG sites and modulating the enzyme activity. Possible mechanisms include sequestration of Dnmt3a at G4 structures and disruption of Dnmt3a oligomerization on DNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Icaro Putinhon Caruso, Vitor dos Santos Almeida, Mariana Juliani do Amaral, Guilherme Caldas de Andrade, Gabriela Rocha de Araujo, Talita Stelling de Araujo, Jessica Moreira de Azevedo, Glauce Moreno Barbosa, Leonardo Bartkevihi, Peter Reis Bezerra, Katia Maria dos Santos Cabral, Isabella Otenio de Lourenco, Clara L. F. Malizia-Motta, Aline de Luna Marques, Nathane Cunha Mebus-Antunes, Thais Cristtina Neves-Martins, Jessica Marostica de Sa, Karoline Sanches, Marcos Caique Santana-Silva, Ariana Azevedo Vasconcelos, Marcius da Silva Almeida, Gisele Cardoso de Amorim, Cristiane Dinis Anobom, Andrea T. Da Poian, Francisco Gomes-Neto, Anderson S. Pinheiro, Fabio C. L. Almeida
Summary: This study investigates the binding characteristics of the SARS-CoV-2 nucleocapsid protein with nucleic acid sequences and reveals its role in RNA transcription and liquid-liquid phase separation. The findings suggest that the binding of the nucleocapsid protein to a specific sequence can induce DNA melting, which is crucial for viral infection. Additionally, the study shows a preference for the nucleocapsid protein to form liquid condensates with specific sequences, providing insights for the design of drugs targeting the nucleocapsid protein.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Biochemical Research Methods
Gulsen Betul Aktas, Arnau Ribera, Vasso Skouridou, Lluis Masip
Summary: The use of DNA binding proteins as universal anchors for DNA immobilization and detection offers a cost-effective and promising alternative to traditional immobilization methods. Additionally, a nucleic acid lateral flow assay based on two different DNA binding proteins has been developed for the detection of PCR amplicons, showing great potential for multiplex detection using various DNA binding proteins. Further research is needed to optimize the adsorption properties of these biomolecules on nitrocellulose and enhance assay sensitivities.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Biochemical Research Methods
Zhourun Wu, Qing Liao, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Chen-Chen Li, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Bin Liu, Chen-Chen Li, Ke Yan
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Bin Liu, Yulin Zhu, Ke Yan
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Medicine, Research & Experimental
Bin Liu, Zhihua Luo, Juan He
MOLECULAR THERAPY-NUCLEIC ACIDS
(2020)
Article
Biochemical Research Methods
Yi-Jun Tang, Yi-He Pang, Bin Liu
Article
Biochemical Research Methods
Jiangyi Shao, Ke Yan, Bin Liu
Summary: The FoldRec-C2C predictor globally incorporates protein interactions for protein fold recognition, treating it as an information retrieval task in natural language processing. Tested on the LINDAHL dataset, FoldRec-C2C outperforms 34 state-of-the-art methods in the field.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jiangyi Shao, Bin Liu
Summary: This study introduces a network-based predictor ProtFold-DFG for protein fold recognition, utilizing Directed Fusion Graph (DFG), KL divergence, and PageRank algorithm to enhance recognition accuracy. Experimental results demonstrate that ProtFold-DFG outperforms 35 other methods on the LINDAHL dataset, making it a promising approach for protein fold recognition.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Ke Yan, Jie Wen, Jin-Xing Liu, Yong Xu, Bin Liu
Summary: The study proposed two novel algorithms, TSVM-fold and ESVM-fold, utilizing sequence similarity scores generated by multiple template-based methods for protein fold recognition prediction. Experimental results showed that these algorithms outperform some state-of-the-art methods in rigorous benchmark datasets.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hang Wei, Qing Liao, Bin Liu
Summary: Identifying lncRNA-disease associations is crucial for exploring disease mechanisms and molecular drug discovery. However, current fusion strategies fail to remove noisy and irrelevant information, leading to low predictive performance. iLncRNAdis-FB proposes a new computational predictor based on CNN to integrate feature blocks from different data sources, achieving better prediction accuracy.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Yumeng Liu, Xiaolong Wang, Bin Liu
Summary: Intrinsically disordered proteins/regions (IDPs/IDRs) are important for biological functions, and accurate prediction is crucial for protein structure and function predictions. However, most existing methods tend to predict fully ordered proteins as disordered, ignoring the fact that most newly sequenced proteins are fully ordered. The proposed RFPR-IDP method, trained on both ordered and disordered proteins, outperforms existing predictors in predicting both ordered and disordered proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Zhourun Wu, Qing Liao, Bin Liu
Summary: Protein complexes are key units for studying a cell system, and high-throughput approaches have enabled the determination of PPI data. The proposed mutual important interacting partner relation and the new algorithm idenPC-MIIP show improved performance in identifying protein complexes compared to existing methods.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Ke Yan, Jie Wen, Yong Xu, Bin Liu
Summary: Protein fold recognition is crucial for understanding protein functions and drug design. New methods (MVLR and MLDH-Fold) were proposed to improve predictive performance by combining different views of protein sequences. Experimental results show that these computational methods outperform other predictors, indicating their usefulness for protein fold recognition.
Article
Biochemical Research Methods
Hang Wei, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Bin Liu, Shuangyan Jiang, Quan Zou
BRIEFINGS IN BIOINFORMATICS
(2020)