Article
Biochemistry & Molecular Biology
Konstantin Zaytsev, Alexey Fedorov, Eugene Korotkov
Summary: We have developed a new method for classifying promoter sequences using a genetic algorithm and the MAHDS sequence alignment method. Four classes of human promoters were created, using 17,310 sequences from the EPD database. A search for potential promoter sequences (PPSs) in the human genome was conducted, resulting in 3,065,317 PPSs, with only 1,241,206 located in unannotated regions. Intersections were found between PPSs and true promoters, transposable elements, and interspersed repeats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yousra Yahia, Alexia Pigeot, Amal Zine El Aabidine, Nilay Shah, Nezih Karasu, Ignasi Forne, Stefan Krebs, Helmut Blum, Cyril Esnault, Tom Sexton, Axel Imhof, Dirk Eick, Jean-Christophe Andrau
Summary: This study shows that the largest subunit of RNA polymerase II (Pol II), known as the C-terminal domain (CTD), plays a crucial role in the transcriptional process. Using a CTD-& UDelta;5 mutant in human cells, it was found that this mutant can transcribe genes but has impaired termination. The mutant lacks interaction with the Mediator and Integrator complexes and does not affect the overall genomic organization.
Article
Biochemical Research Methods
Xin Bai, Jie Ren, Yingying Fan, Fengzhu Sun
Summary: The study developed a new model KIMI for distinguishing genetic materials of different microbial communities based on k-mer frequency computation while controlling FDR, achieving better performance compared to other widely used FDR control methods. Simulation results show that KIMI is effective in controlling FDR and improving power simultaneously.
Article
Chemistry, Analytical
Heilym Ramirez, Sergio A. Velastin, Paulo Aguayo, Ernesto Fabregas, Gonzalo Farias
Summary: In recent years, there has been a lot of effort in developing applications to detect various human activities, with a particular emphasis on fall detection, especially for the elderly. Some applications use wearable sensors integrated into devices like cell phones, necklaces, or smart bracelets to detect sudden movements, but these devices can be uncomfortable and are limited to personal use. On the other hand, vision-based algorithms that analyze video camera images offer advantages as they do not require wearing sensors and can be implemented in open spaces and with unfamiliar people. This paper presents a vision-based algorithm for activity recognition using human skeleton pose estimation as a feature extraction method.
Article
Chemistry, Multidisciplinary
Abhi Das, Sanjay Dutta
Summary: The study demonstrated that aloe emodin and aloe emodin-8-glucoside are potent quadruplex-binding molecules, especially showing higher binding affinity towards c-KIT and c-MYC sequences compared to their duplex DNA binding ability. This finding may be related to the anticancer activity of these aloe-active compounds and could be beneficial for the potential therapeutic application of natural compound-based molecules.
Article
Biochemistry & Molecular Biology
Juan F. Santana, Geoffrey S. Collins, Mrutyunjaya Parida, Donal S. Luse, David H. Price
Summary: The effects of depleting different components of RNA polymerase II general transcription factors vary in their impact on promoter activity and are regulated by both core promoter elements and the recruitment of TFIID.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Linyan Nie, Anggrek C. Nusantara, Viraj G. Damle, Maxim Baranov, Mayeul Chipaux, Claudia Reyes-San-Martin, Thamir Hamoh, Chandra Prakash Epperla, Miroslava Guricova, Petr Cigler, Geert van den Bogaart, Romana Schirhagl
Summary: Free radicals are important indicators for stress and pathogenic conditions, and are difficult to detect due to their reactivity and low abundance. A novel relaxometry method using a fluorescent defect in a diamond has been developed for subcellular detection of radicals with nanoscale MRI capabilities. Variability in radical production was observed in primary dendritic cells from healthy donors, and their response to stimulation or inhibition was investigated.
Article
Chemistry, Multidisciplinary
Bo-Chen Zhu, Juan He, Xiao-Yu Xia, Jingxing Jiang, Wenting Liu, Liu-Yi Liu, Bing-Bing Liang, Hua-Gang Yao, Zhuofeng Ke, Wei Xia, Zong-Wan Mao
Summary: Research found that a quasi-cross-shaped platinum (II) compound (L' 2LPt) has selective affinity to bind the TBA G-quadruplex and can abrogate the inhibitory activity of TBA against thrombin. The complex structure of L' 2LPt-TBA was solved by NMR, revealing the self-adaptive property of L' 2LPt upon binding to TBA.
Article
Agriculture, Multidisciplinary
Renjun Huang, Wei Zheng, Baohua Zhang, Jun Zhou, Zhengshan Cui, Zhen Zhang
Summary: In this paper, a special neural network utilizing the improved Transformer structure is proposed to achieve damage-free grasping of deformable objects. The network achieves a fruit recognition accuracy of 97.33% on a tactile dataset containing 9375 grasp of 15 fruits, outperforming the traditional recurrent neural network model. The performance of the proposed model is evaluated from various aspects, and the prediction of the subsequent grasp force is explored. This work contributes to robotic haptic perception and damage-free grasping in the agricultural field, and provides technical reference for other researches on grasp tactile data.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2023)
Article
Biochemistry & Molecular Biology
Tomasz Fraczyk
Summary: Proteins mainly anchor copper(II) ions through imidazole clusters from histidine residues, with motifs containing histidine in the first three N-terminal positions showing unique Cu(II)-binding properties. These sequences are beneficial for fast Cu(II) exchange between ligands and may play a role in redox reactions.
CHEMISTRY & BIODIVERSITY
(2021)
Article
Virology
Yujing Huang, Xin Guo, Jing Zhang, Jianming Li, Mingyi Xu, Qing Wang, Zhongyang Liu, Yanping Ma, Ying Qi, Qiang Ruan
Summary: This study investigated the functions of HCMV RNA2.7 by comparing the host cellular transcriptomes between cells infected with HCMV clinical strain and RNA2.7 deleted mutant. The results showed that the removal of RNA2.7 significantly activated host gene transcriptions, leading to facilitated viral DNA replication.
Article
Genetics & Heredity
Qiuhui Li, Bin Yan, Tak-Wah Lam, Ruibang Luo
Summary: In this study, an assembly-free approach was designed to identify novel sequences from Oxford Nanopore Technology long reads. This approach discovered a significant number of novel sequences that were missed by other methods, and revealed their association with transcription factor binding motifs. Additionally, the placement of novel sequences showed enrichment in repeat regions and generated new sequences related to the evolution of a specific subpopulation.
Article
Computer Science, Artificial Intelligence
Xiaopeng Ji, Qingsong Zhao, Jun Cheng, Chenfei Ma
Summary: This paper proposes a method for human action recognition based on depth map sequences, capturing spatial and temporal information through short-term and long-term dependencies, achieving efficient recognition and state-of-the-art performance.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Multidisciplinary Sciences
Benjamin M. Spector, Mrutyunjaya Parida, Ming Li, Christopher B. Ball, Jeffery L. Meier, Donal S. Luse, David H. Price
Summary: Interactions between the RNA polymerase II preinitiation complex (PIC) and paused early elongation complexes with the +1 nucleosome are functionally important. However, there are differences in these interactions between cellular chromatin and the human cytomegalovirus (HCMV) genome. Host PICs and paused Pol II complexes frequently interact with the +1 nucleosome, while viral transcription complexes have limited nucleosomal interactions.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Information Systems
Lang Deng, Jianfei Yang, Shenghai Yuan, Han Zou, Chris Xiaoxuan Lu, Lihua Xie
Summary: In this article, a novel multimodal gait recognition method called GaitFi is proposed, which combines WiFi signals and videos for human identification. The GaitFi outperforms state-of-the-art gait recognition methods and achieves excellent results in real-world experiments.
IEEE INTERNET OF THINGS JOURNAL
(2023)
Article
Biochemical Research Methods
Hong Su, Zhenling Peng, Jianyi Yang
Summary: A novel method called RNAsite was developed to predict small molecule-RNA binding sites, showing competitive and superior performance compared to other methods. The study investigated the influence of RNA structure's flexibility and conformational changes caused by ligand binding on RNAsite, as well as explored the possibility of improving RNAsite through geometry-based binding pocket detection.
Article
Biochemical Research Methods
Lisha Ye, Peikun Wu, Zhenling Peng, Jianzhao Gao, Jian Liu, Jianyi Yang
Summary: Protein model quality assessment is crucial in structure prediction, and QDistance is a new approach using inter-residue distances to estimate both global and local qualities. By comparing with reference models and incorporating predicted distances, QDistance proves to be competitive and robust in predicting protein structure quality.
Article
Biochemical Research Methods
Xingjian Chen, Lingjing Liu, Weitong Zhang, Jianyi Yang, Ka-Chun Wong
Summary: This study proposes a deep learning-based framework to infer human host status using longitudinal microbiome data. Results show that the method achieves robust performance compared to other classifiers and significantly reduces prediction time.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Ruiyang Song, Baixin Cao, Zhenling Peng, Christopher J. Oldfield, Lukasz Kurgan, Ka-Chun Wong, Jianyi Yang
Summary: The article introduces a new sequence-based predictor, DMBS, which improves the accurate prediction of deleterious nsSNPs by optimizing conservation estimates and utilizing functional/binding residue annotations. Empirical results show that DMBS outperforms current methods in various benchmarks, demonstrating its effectiveness in guiding wet-lab experiments.
Article
Biochemical Research Methods
Zongyang Du, Zhenling Peng, Jianyi Yang
Summary: The study proposed 19 metrics to measure the accuracy of protein distance prediction, with some metrics showing high correlation with model accuracy. Experimental results showed that the metrics largely coincided with the official version when ranking distance prediction groups in CASP14. These findings suggest that the proposed metrics are effective in measuring distance prediction.
Article
Biochemical Research Methods
Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang
Summary: In this study, the protein-ligand interactions in monomeric and quaternary structures were compared using molecular docking experiments and binding free energy estimations. The results showed that ligands in quaternary structures can simultaneously interact with multiple protein chains, and quaternary structures have lower binding free energy and more accurate ligand conformations compared to monomeric structures. Therefore, it is recommended to use quaternary structures in future studies on protein-ligand interactions.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Zongyang Du, Hong Su, Wenkai Wang, Lisha Ye, Hong Wei, Zhenling Peng, Ivan Anishchenko, David Baker, Jianyi Yang
Summary: The trRosetta server is a web-based platform for fast and accurate protein structure prediction using deep learning and Rosetta, which distinguishes itself from other similar servers in terms of rapid and accurate prediction of novel structures.
Article
Biochemistry & Molecular Biology
Saisai Sun, Jianyi Yang, Zhaolei Zhang
Summary: RNA molecules can fold into complex three-dimensional structures and interact with small molecule ligands. Researchers have established a database of RNA secondary structural motifs and bound small molecule ligands. They also developed a computational pipeline to predict RNA secondary structures and search for similar motifs and interacting small molecules. The server was successfully used to identify potential matches for a specific RNA sequence.
Article
Chemistry, Multidisciplinary
Hong Su, Wenkai Wang, Zongyang Du, Zhenling Peng, Shang-Hua Gao, Ming-Ming Cheng, Jianyi Yang
Summary: The accuracy of de novo protein structure prediction has been significantly improved in recent years with the introduction of deep learning techniques. The improved version trRosettaX utilizes a new multi-scale network and attention-based module to enhance prediction accuracy. trRosettaX shows significant improvements in contact precision and TM-score compared to trRosetta in CASP and CAMEO tests.
Article
Multidisciplinary Sciences
Syed Nabeel-Shah, Hyunmin Lee, Nujhat Ahmed, Giovanni L. Burke, Shaghayegh Farhangmehr, Kanwal Ashraf, Shuye Pu, Ulrich Braunschweig, Guoqing Zhong, Hong Wei, Hua Tang, Jianyi Yang, Edyta Marcon, Benjamin J. Blencowe, Zhaolei Zhang, Jack F. Greenblatt
Summary: The imbalance in immune response observed in SARS-CoV-2 infected patients may be due to the altered interaction between the nucleocapsid protein (N protein) and stress granule resident proteins, which in turn affects the stress response of host cells.
Article
Multidisciplinary Sciences
Xingjian Chen, Zifan Zhu, Weitong Zhang, Yuchen Wang, Fuzhou Wang, Jianyi Yang, Ka-Chun Wong
Summary: Predicting human diseases from microbiome data is important in medical applications. Existing methods often overlook the abundance profiles of known and unknown microbial organisms, as well as the taxonomic relationships among them, resulting in information loss. To address these issues, we developed a comprehensive machine learning framework called MetaDR that combines deep learning and various information sources to predict human diseases.
Review
Biochemistry & Molecular Biology
Zhenling Peng, Wenkai Wang, Renmin Han, Fa Zhang, Jianyi Yang
Summary: This article reviews the progress of deep learning-based protein structure prediction methods in the past two years, analyzes the advantages and disadvantages of the two-step and end-to-end approaches, emphasizes the value of developing both approaches, and points out the challenges in function-oriented protein structure prediction.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zhenling Peng, Wenkai Wang, Hong Wei, Xiaoge Li, Jianyi Yang
Summary: We present the results of our monomer and multimer structure prediction methods in CASP15. By utilizing complementary sequence databases and advanced database searching algorithms, we generated high-quality multiple sequence alignments (MSAs) and selected top MSAs for structure prediction. Our methods, named Yang-Server and Yang-Multimer, ranked first and fourth for monomer and multimer structure prediction, respectively. The predicted structure models by Yang-Server showed an average TM-score of 0.876 for 94 monomers, compared to 0.798 by the default AlphaFold2, while the predicted structure models by Yang-Multimer showed an average DockQ score of 0.464 for 42 multimers, compared to 0.389 by the default AlphaFold-Multimer. Factors such as improved MSAs, iterated modeling, and interplay between monomer and multimer structure prediction contributed to the improvement.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Wenkai Wang, Zhenling Peng, Jianyi Yang
Summary: trRosettaX-Single is an automated algorithm for single-sequence protein structure prediction that predicts two-dimensional geometry and reconstructs three-dimensional structures using a multi-scale network and knowledge distillation. It outperforms AlphaFold2 and RoseTTAFold on orphan proteins and works well on human-designed proteins.
NATURE COMPUTATIONAL SCIENCE
(2022)
Article
Biochemical Research Methods
Hong Wei, Boling Wang, Jianyi Yang, Jianzhao Gao
Summary: In this study, a new method called RNAbval was proposed to predict RNA B-factors using random forest and a comprehensive set of features. The method achieved a significant improvement of 9.2-20.5 percent over the state-of-the-art method on two benchmark test datasets. The proposed method is available for access online.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
