Article
Biology
Max Karlsson, Evelina Sjostedt, Per Oksvold, Asa Sivertsson, Jinrong Huang, Maria Bueno Alvez, Muhammad Arif, Xiangyu Li, Lin Lin, Jiaying Yu, Tao Ma, Fengping Xu, Peng Han, Hui Jiang, Adil Mardinoglu, Cheng Zhang, Kalle von Feilitzen, Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, Wen Zhong, Linn Fagerberg, Cecilia Lindskog, Fredrik Ponten, Jan Mulder, Yonglun Luo, Mathias Uhlen
Summary: This study introduces a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering, and presents a whole-body map of protein-coding genes in the pig. The study provides insights into the expression patterns of these genes across different tissues and organs.
Article
Biotechnology & Applied Microbiology
Gaelle Lelandais, Damien Remy, Fabienne Malagnac, Pierre Grognet
Summary: This study conducted a comprehensive functional annotation of the P. anserina genome using RNA-seq data, including information about promoters, transcription starting sites, terminators, alternative splicing events, and transcription of non-coding regions. These new findings will enhance our understanding of gene regulation strategies in compact genomes, such as filamentous fungi.
Article
Neurosciences
Jordan D. Harper, Kang-Hsien Fan, M. Muaaz Aslam, Beth E. Snitz, Steven T. DeKosky, Oscar L. Lopez, Eleanor Feingold, M. Ilyas Kamboh
Summary: This study used genome-wide association analyses to investigate the genetic factors of Alzheimer's disease (AD) in older adults. The results confirmed the association of APOE*4 carriers with AD and identified a novel significant locus on chromosome 12. Gender-specific analyses also revealed two novel associations in males. These findings suggest the importance of community-based samples and incident dementia as phenotypes in the identification of novel genes for AD.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Article
Genetics & Heredity
Frieder Hadlich, Henry Reyer, Michael Oster, Nares Trakooljul, Eduard Murani, Siriluck Ponsuksili, Klaus Wimmers
Summary: Commercial and customized microarrays are valuable tools for analyzing holistic expression patterns, but require integration of the latest genomic information. This study presents a comprehensive workflow using the rePROBE R package to assign probes and annotate probe sets based on up-to-date genomic and transcriptomic data. The workflow reveals updated probe assignments and annotations for various livestock species and human, with a focus on providing a detailed basis for comprehensive analyses such as eQTL studies.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Plant Sciences
Muhammad Waseem, Xinxin Yang, Mehtab Muhammad Aslam, Mengna Li, Lian Zhu, Shanhan Chen, Guopeng Zhu, Yun Li, Pingwu Liu
Summary: This study aimed to identify potential long non-coding RNAs (lncRNAs) in Brassica napus under cold stress. The study identified a total of 11073 lncRNAs in B. napus varieties and found that their expression varied between different varieties and time points. Additionally, the study found correlations between some lncRNAs and miRNAs, as well as the expression status of protein-coding genes.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Moumita Roy Chowdhury, Ranjit Prasad Bahadur, Jolly Basak
Summary: This study predicted and validated miRNAs, their targets, and lncRNAs in the genome of cauliflower, providing insights into their roles in post-transcriptional gene regulation.
Article
Oncology
Theresa Jakobsen, Mette Dahl, Konstantinos Dimopoulos, Kirsten Gronbaek, Jorgen Kjems, Lasse Sommer Kristensen
Summary: Multiple myeloma (MM) is a common hematological malignancy with no cure currently available. Research has shown that circular RNA (circRNA) expression patterns are related to IMiD sensitivity, but certain circRNAs are not direct drivers of IMiD resistance.
Review
Genetics & Heredity
Diego Guerra-Almeida, Diogo Antonio Tschoeke, Rodrigo Nunes-da-Fonseca
Summary: This review proposes a classification of smORFs based on transcriptional features and discusses promising approaches to investigate them. SmORFs are potentially important coding sequences that have been historically overlooked, but are now gaining attention in systems biology.
Article
Biotechnology & Applied Microbiology
Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M. Hammon, Christa Kuhn
Summary: By combining transcriptomic and metabolomic analyses, long non-coding RNAs (lncRNAs) were identified to have potential regulatory functions in livestock, especially in divergent nutrient partitioning. These lncRNAs may play important roles in fine-tuning gene expression involved in metabolic pathways associated with different nutrient partitioning phenotypes.
Article
Forestry
Hainan Wu, Ziyuan Hao, Zhonghua Tu, Yaxian Zong, Lichun Yang, Chunfa Tong, Huogen Li
Summary: The structure and function of genes in the L. chinense genome were re-annotated based on PacBio long reads and Illumina short reads. The updated annotation, Lchi2.1, includes 42,831 gene models with a high proportion of complete BUSCOs. The study also identified genes related to leaf morphological processes. This research will contribute to gene functional studies in L. chinense and comparative genomic analysis.
TREE GENETICS & GENOMES
(2023)
Article
Genetics & Heredity
Xian Wei, Man Xu, Chao Wang, Shengjian Fang, Yu Zhang, Weihua Wang
Summary: The study analyzed the expression profile of lncRNAs in nasal mucosa tissue of patients with allergic rhinitis (AR) and identified dysregulation of 57 lncRNAs and 127 mRNAs. The results suggest that lncRNAs play a role in biological pathways related to AR, with leukocyte transepithelial migration being a potential target for regulating allergic inflammation and the CXCL12/CXCR4 axis playing an important role in the inflammatory process of AR.
BMC MEDICAL GENOMICS
(2021)
Article
Biotechnology & Applied Microbiology
Daniel C. Shippy, Jyoti J. Watters, Tyler K. Ulland
Summary: The study revealed that AD activates multiple signaling pathways that regulate numerous genes in microglia, contributing to Aβ phagocytosis and neuroinflammation. These findings identified several regulatory factors and biomarkers in microglia, which could be beneficial for further comprehension of AD neuropathology.
Article
Biochemical Research Methods
Lars Gabriel, Katharina J. Hoff, Tomas Bruna, Mark Borodovsky, Mario Stanke
Summary: TSEBRA is a software tool that selects gene predictions from BRAKER1 and BRAKER2 sets based on RNA-seq and homologous protein evidence support. Computational experiments show that TSEBRA achieves higher accuracy compared to running BRAKER1 and BRAKER2 alone, and it performs favorably against EVidenceModeler.
BMC BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Yu Hu, Rong Li, Hongyin Chen, Lihao Chen, Xuyue Zhou, Linxi Liu, Mei Ju, Kun Chen, Dan Huang
Summary: This study aimed to identify cSCC-specific lncRNAs and found that six unstudied lncRNAs may play an important role in the progression of cSCC by modulating ACY3, NR1D1, and MZB1, and being involved in endoplasmic reticulum stress apoptosis and autophagy processes.
Article
Multidisciplinary Sciences
Abbas Saad Alatrany, Wasiq Khan, Abir Hussain, Dhiya Al-Jumeily
Summary: The increasing incidence of Alzheimer's disease (AD) poses socioeconomic challenges. In this study, a hybrid feature selection approach and neural network models are used to predict AD. The approach outperformed existing methods with 99% accuracy and f1-score, providing impactful outcomes for other chronic diseases.
Article
Chemistry, Multidisciplinary
Jin-ping Pang, Chao Shen, Wen-fang Zhou, Yun-xia Wang, Lu-hu Shan, Xin Chai, Ying Shao, Xue-ping Hu, Feng Zhu, Dan-yan Zhu, Li Xiao, Lei Xu, Xiao-hong Xu, Dan Li, Ting-jun Hou
Summary: The androgen receptor (AR) is a crucial transcription factor in prostate cancer development, and finding novel anti-AR therapeutics to combat mutation-induced resistance is challenging. In this study, a virtual screening strategy based on the crystal structure of the DNA binding domain (DBD) of AR identified a potential hit, Cpd39, that could block the binding of AR DBD to DNA and inhibit AR transcriptional activity effectively. Cpd39 also demonstrated safety and potency in inhibiting the proliferation of various prostate cancer cell lines, suggesting it could be a promising starting point for new therapeutics for castration-resistant PCa.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Rheumatology
Wanlong Wu, Wenwen Xu, Wenjia Sun, Danting Zhang, Jiangfeng Zhao, Qun Luo, Xiaodong Wang, Feng Zhu, Yu Zheng, Yu Xue, Weiguo Wan, Huaxiang Wu, Qian Han, Shuang Ye
Summary: This study aimed to establish and validate a clinical prediction model for 6-month all-cause mortality in Chinese patients with anti-MDA5 positive DM-ILD. The results showed that a categorical predictor based on forced vital capacity (FVC)% was identified and validated as an independent prognostic factor, which could effectively distinguish the risk stages in patients and facilitate risk stratification in clinical practice.
Review
Biochemistry & Molecular Biology
Fengyuan Yang, Jingyi Yang, Zhao Zhang, Gao Tu, Xiaojun Yao, Weiwei Xue, Feng Zhu
Summary: This review summarizes the recent advances in the design of single- and dual-target inhibitors against HIV-1 IN or/and RT-RNase H, as well as the prediction of mutation-induced drug resistance based on computational methods. CADD plays a significant role in accelerating antiviral drug development.
CURRENT MEDICINAL CHEMISTRY
(2022)
Editorial Material
Biochemical Research Methods
Chenyang Zhang, Minjie Mou, Ying Zhou, Wei Zhang, Xichen Lian, Shuiyang Shi, Mingkun Lu, Huaicheng Sun, Fengcheng Li, Yunxia Wang, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Yunqing Qiu, Feng Zhu, Jianqing Gao
Summary: This study conducted a comprehensive assessment and analysis on the biological activities of DIGs in drug formulations, providing the first comprehensive activities for both DIGs and DFMs to the pharmaceutical community. The biological targets of each DIG and formulation were fully referenced to available databases, and popular artificial intelligence techniques were used to evaluate the predictive potential of DIGs' activity data. The findings of this work are expected to have significant implications for the future practice of drug discovery and precision medicine.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Weiqi Xia, Lingyan Zheng, Jiebin Fang, Fengcheng Li, Ying Zhou, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu
Summary: This study presents a novel protein function annotation strategy, PFmulDL, which integrates multiple deep learning methods to address the limitations of existing methods in annotating proteins in "rare classes". The new model is capable of annotating a larger number of protein families and significantly improving prediction performance.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Engineering, Environmental
Feng Zhu, Xianjia Peng, Xingyun Hu, Linghao Kong
Summary: This study investigated the effects of sulfuration factors on the particle size and settling performance of metal sulfides, and revealed the involved mechanisms. The results showed that the H2S release rate played a critical role in determining the particle size and settling performance.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biochemical Research Methods
Jing Wu, He Liu, Haiquan Wang, Yuqi Wang, Qi Cheng, Ruochen Zhao, Hongliang Gao, Lei Fang, Feng Zhu, Bin Xue
Summary: In this study, we used iTRAQ-based proteomic analysis to study the key regulatory factors in the termination phase of liver regeneration (LR). The findings provide a foundation for further research on the molecular mechanism and biomarkers of the termination phase of LR, and can guide the perioperative management of patients after hepatectomy.
JOURNAL OF PROTEOMICS
(2022)
Article
Clinical Neurology
Floriane Calocer, Huah Shin Ng, Feng Zhu, Yinshan Zhao, Olivier Dejardin, Emmanuelle Leray, Gilles Defer, Charity Evans, John D. Fisk, Ruth Ann Marrie, Helen Tremlett
Summary: The study found that lower socioeconomic status is associated with a higher mortality risk in persons with multiple sclerosis (PwMS).
MULTIPLE SCLEROSIS JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiuna Sun, Yintao Zhang, Hanyang Li, Ying Zhou, Shuiyang Shi, Zhen Chen, Xin He, Hanyu Zhang, Fengcheng Li, Jiayi Yin, Minjie Mou, Yunzhu Wang, Yunqing Qiu, Feng Zhu
Summary: Drug resistance has become a major global healthcare issue. This study introduces a comprehensive database called 'DRESIS' that provides information on all types of drug resistance mechanisms and covers a wide range of diseases. The database includes extensively validated resistance data, making it a valuable resource for future drug discovery and clinical treatment optimization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Fengcheng Li, Jiayi Yin, Mingkun Lu, Minjie Mou, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen, Feng Zhu
Summary: The efficacy and safety of drugs depend on their interactions with various pharmacologically important molecules. To better understand this information, a new database called DrugMAP has been developed, which provides a comprehensive list of interacting molecules for over 30,000 drugs/drug candidates. It also includes differential expression patterns for over 5,000 interacting molecules in different disease sites, ADME-relevant organs, and physiological tissues. With over 200,000 interactions among drugs and molecules, DrugMAP is expected to be a valuable resource for drug discovery and network analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kuerbannisha Amahong, Wei Zhang, Ying Zhou, Song Zhang, Jiayi Yin, Fengcheng Li, Hongquan Xu, Tianci Yan, Zixuan Yue, Yuhong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han, Feng Zhu
Summary: This study constructed a new database (CovInter) to describe the interactions between coronavirus RNAs and host proteins. The unique feature of this database lies in the explicit characterization of these interactions and the comprehensive provision of experimentally validated biological functions for important host proteins, as well as the systematic quantification of differential expression patterns of these key proteins before and after infection.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Chemistry, Medicinal
Kenneth M. Merz, Guo-Wei Wei, Feng Zhu
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Gao Tu, Binbin Xu, Ding Luo, Jin Liu, Zerong Liu, Gang Chen, Weiwei Xue
Summary: Serotonin transporter (SERT) plays a vital role in reuptake of serotonin and its allosteric modulation has potential for developing new medications for psychiatric disorders. Using cryo-EM structures and molecular dynamics simulations, the functional structures of SERT in complex with ibogaine and serotonin were characterized, revealing interaction variations and identifying novel allosteric sites. These findings provide insights into the molecular mechanism of serotonin reuptake and offer opportunities for the development of new therapeutics.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Environmental Sciences
Shengguo Xue, Ramon Korna, Jiarong Fan, Wenshun Ke, Wei Lou, Jinting Wang, Feng Zhu
Summary: The rapid development of the smelting industry has led to increased release of antimony into the soil environment, posing a threat to human health and ecosystems. A study on an abandoned antimony smelting site revealed the pollution characteristics and environmental risks of potentially toxic elements. The findings highlight the significant influence of anthropogenic sources on pollutant accumulation.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2023)
Article
Chemistry, Medicinal
Shengzhe Deng, Haiwei Zhang, Rongpei Gou, Ding Luo, Zerong Liu, Feng Zhu, Weiwei Xue
Summary: The study investigates the molecular mechanism underlying the transportation of human dopamine transporter (hDAT), which regulates the reuptake of extracellular dopamine (DA) and is an essential target for CNS diseases. Using a structure-based method, allosteric sites on hDAT in inward-open conformation were explored and compounds with allosteric affinity were screened. The discovery of a new allosteric inhibitor for hDAT provides a starting point for lead optimization and demonstrates the usability of the method for discovering novel allosteric modulators of other therapeutic targets.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)