Article
Physiology
Long Li, Qingxu Jing, Sen Yan, Xuxu Liu, Yuanyuan Sun, Defu Zhu, Dawei Wang, Chenjun Hao, Dongbo Xue
Summary: The Amadis database provides experimentally supported microbiota-disease associations, dynamic network construction methods, and a user-friendly interface for researchers to explore the relationships between gastrointestinal microbiota and human diseases. It serves as a valuable resource for researchers to obtain specific microbe-based human disease networks.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yimeng Zhang, Yuexin Zhang, Chao Song, Xilong Zhao, Bo Ai, Yuezhu Wang, Liwei Zhou, Jiang Zhu, Chenchen Feng, Liyan Xu, Qiuyu Wang, Hong Sun, Qiaoli Fang, Xiaozheng Xu, Enmin Li, Chunquan Li
Summary: The study established an integrative CR resource, CRdb, to curate a large number of available resources for chromatin regulators (CRs) and provide extensive annotations and analyses to help researchers understand the regulatory mechanisms and functions of CRs. CRdb contains a comprehensive collection of CRs and ChIP-seq samples from various human tissues and cell types, along with genetic annotations and functional analyses. It serves as a useful tool for exploring the potential functions and regulatory mechanisms of CRs in diseases and biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Oncology
Maria Pia Campagna, Alexandre Xavier, Jeannette Lechner-Scott, Vicky Maltby, Rodney J. Scott, Helmut Butzkueven, Vilija G. Jokubaitis, Rodney A. Lea
Summary: The interaction between genetic and environmental factors drives the development of complex diseases, with the role of the epigenome in disease pathophysiology gaining attention. Epigenome-wide association studies (EWASes) investigating the association between phenotype and epigenetic variants, particularly DNA methylation, have increased in number in recent years due to advancements in technology. Studies focusing on methylation data in blood samples have been recommended as a cost-effective approach, with novel areas of EWAS analysis expanding to include longitudinal study designs and statistical deconvolution for identifying cell-specific differential methylation.
CLINICAL EPIGENETICS
(2021)
Article
Biochemistry & Molecular Biology
Kaixuan Diao, Jing Chen, Tao Wu, Xuan Wang, Guangshuai Wang, Xiaoqin Sun, Xiangyu Zhao, Chenxu Wu, Jinyu Wang, Huizi Yao, Casimiro Gerarduzzi, Xue-Song Liu
Summary: Seq2Neo is a pipeline that predicts the immunogenicity of neoantigens by providing a solution for neoepitope feature prediction using raw sequencing data. It supports different types of genome DNA alterations and includes a CNN-based model that shows improved performance in immunogenicity prediction compared to currently available tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Vishal B. Siramshetty, Ivan Grishagin, Dac-Trung Nguyen, Tyler Peryea, Yulia Skovpen, Oleg Stroganov, Daniel Katzel, Timothy Sheils, Ajit Jadhav, Ewy A. Mathe, Noel T. Southall
Summary: The United States has a complex regulatory scheme for marketing drugs. NCATS has developed Inxight Drugs, a web resource that integrates data from FDA, US government publications, and other sources to provide a wealth of manually curated literature data on drug ingredients and regulatory status. The database contains over 125,000 product ingredients, including approved, marketed, and investigational drugs, and is regularly updated using automated data aggregation tools.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Lili Duan, Lu Cao, Rui Zhang, Liaoran Niu, Wanli Yang, Weibo Feng, Wei Zhou, Junfeng Chen, Xiaoqian Wang, Yiding Li, Yujie Zhang, Jinqiang Liu, Qingchuan Zhao, Daiming Fan, Liu Hong
Summary: The study identified the biological functions and prognostic value of autophagy-related genes (ARGs) in esophageal adenocarcinoma (EAC), establishing a prognostic prediction model based on nine overall survival (OS)-related ARGs. The model successfully stratified patient outcomes and was confirmed in an independent validation cohort, highlighting ERBB2 as a potential therapeutic target. The study contributes to individualized survival prediction and optimization of treatment strategies for EAC patients.
Review
Food Science & Technology
Phaniendra Alugoju, V. K. D. Krishna Swamy, Naga Venkata Anusha Anthikapalli, Tewin Tencomnao
Summary: The translation section discusses the impact of age-related diseases on societal and healthcare expenditure, as well as the importance of anti-aging strategies. It then lists the various protective effects of astaxanthin, covering multiple organs and diseases, including neurodegenerative diseases, bone-related diseases, cancers, cardiovascular disorders, diabetes-associated complications, eye disorders, gastric disorders, kidney disorders, liver diseases, pulmonary disorders, muscle disorders, and skin diseases.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Biochemical Research Methods
Linlin Gong, Rui Zhang, Mengying Han, Qian-Nan Hu
Summary: The comprehensive cosmetic ingredients bioinformatics platform (CCIBP) is a unique database that provides information on regulations, physicochemical properties, metabolic pathways, and safe concentrations of cosmetic molecules. It also correlates plant information in natural products, supports formulation and efficacy component analysis, and combines synthetic biology knowledge to facilitate access to natural molecules and biosynthetic production. CCIBP, empowered with chemoinformatics, bioinformatics, and synthetic biology data and tools, is a valuable platform for cosmetic research and development of ingredients.
Article
Computer Science, Information Systems
Lubna Riaz, Hafiz Muhammad Qadir, Ghulam Ali, Mubashir Ali, Muhammad Ahsan Raza, Anca D. Jurcut, Jehad Ali
Summary: Skin, the body's largest organ, can be affected by various diseases. Early identification of skin diseases is crucial to prevent their growth and spread. This research proposes a joint learning system using Convolutional Neural Networks (CNN) and Local Binary Pattern (LBP) to detect skin diseases at an early stage with high accuracy. The system is trained and tested using a publicly accessible dataset and achieves a robust fusion architecture with an accuracy of 98.60% and a validation accuracy of 97.32%. Comparative results are also included for further analysis.
Article
Obstetrics & Gynecology
Rezvan Asgari, Mitra Bakhtiari, Davood Rezazadeh, Reza Yarani, Farzaneh Esmaeili, Kamran Mansouri
Summary: The study evaluated the role of TSGA10 gene in spermatid differentiation/maturation and found that the expression of TSGA10 decreased in patients with teratospermia, affecting the expression of genes related to sperm maturation and autophagy, while the ROS levels increased.
REPRODUCTIVE SCIENCES
(2021)
Article
Computer Science, Theory & Methods
Joao Bachiega, Breno Costa, Leonardo R. Carvalho, Michel J. F. Rosa, Aleteia Araujo
Summary: This article provides a comprehensive review of resource allocation for fog computing, based on a systematic literature review. The results offer an updated and comprehensive view on this subject, discussing the main challenges and open research questions.
ACM COMPUTING SURVEYS
(2023)
Review
Biochemical Research Methods
Li Liu, Kaiyuan Han, Huimin Sun, Lu Han, Dong Gao, Qilemuge Xi, Lirong Zhang, Hao Lin
Summary: This review provides an overview of loop-calling tools for various 3C-based techniques. It categorizes and summarizes these tools, discusses background biases and denoising algorithms, and helps researchers select the most appropriate method for loop calling and downstream analysis. It is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Immunology
Hannan Ai, Fanmei Meng, Yuncan Ai
Summary: Characterizing immune landscapes at the systems level is important in modern medicine. This article introduces the PathwayKO platform, which integrates advanced methods of pathway enrichment analysis, statistics analysis, and visualizing analysis to conduct cutting-edge integrative pathway analysis and decipher target KO signaling pathways. The platform is demonstrated to comprehensively analyze real-world mouse KO transcriptomes and effectively evaluate the performance of pathway analysis methods. These advances in deciphering biological insights at the systems-level have potential applications in bioinformatics and systems immunology.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemical Research Methods
Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Minyoung Kim, Aditya Sarkar, Sei Chang, Angela Lu, Neha Rajkumar, Nicholas Darfci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul
Summary: This article evaluates the performance of SV detection tools on mouse and human WGS data, using a comprehensive polymerase chain reaction-confirmed gold standard set of SVs and the genome-in-a-bottle variant set. In contrast to previous studies, their gold standard dataset includes a complete set of SVs to report precision and sensitivity rates of the SV detection methods. The study finds wide variation in performance among SV detection tools.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sen Yang, Wenting Zong, Lingling Shi, Ruisi Li, Zhenshu Ma, Shubao Ma, Jingna Si, Zhijing Wu, Jinglan Zhai, Yingke Ma, Zhuojing Fan, Sisi Chen, Huahong Huang, Deqiang Zhang, Yiming Bao, Rujiao Li, Jianbo Xie
Summary: PPGR is a comprehensive resource that integrates and analyzes genomic, gene regulation, and functional data of perennial plants. It includes extensive information from 60 species and provides various multi-omics search and analysis tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cardiac & Cardiovascular Systems
Ruo-Gu Li, Ying-Jia Xu, Juan Wang, Xing-Yuan Liu, Fang Yuan, Ri-Tai Huang, Song Xue, Li Li, Hua Liu, Yan-Jie Li, Xin-Kai Qu, Hong-Yu Shi, Min Zhang, Xing-Biao Qiu, Yi-Qing Yang
AMERICAN JOURNAL OF CARDIOLOGY
(2018)
Article
Mathematical & Computational Biology
Wen-Jing Wang, Yu-Mei Wang, Yi Hu, Qin Lin, Rou Chen, Huan Liu, Wen-Ze Cao, Hui-Fang Zhu, Chang Tong, Li Li, Lu-Ying Peng
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)
Article
Cell Biology
Tianyou Yuan, Shiyi Wang, Chaoyue Hu, Yufei Wu, Dandan Liang, Li Li, Yi Liu, Jun Li, Yi-Han Chen
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2018)
Article
Cell Biology
Yi Guan, Xueting Gao, Qiuyu Tang, Lin Huang, Siyun Gao, Shuai Yu, Jiale Huang, Jun Li, Daizhan Zhou, Yangyang Zhang, Dan Shi, Dandan Liang, Yi Liu, Li Li, Yingyu Cui, Liang Xu, Yi-Han Chen
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Xueting Gao, Siyun Gao, Yi Guan, Lin Huang, Jiale Huang, Li Lin, Yuan Liu, Hong Zhao, Bijun Huang, Tianyou Yuan, Yi Liu, Dandan Liang, Yangyang Zhang, Xiue Ma, Li Li, Jun Li, Daizhan Zhou, Dan Shi, Liang Xu, Yi-Han Chen
Article
Cell Biology
Duo Wang, Yumei Wang, Huan Liu, Chang Tong, Qilong Ying, Agapios Sachinidis, Li Li, Luying Peng
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2019)
Article
Cell & Tissue Engineering
Rou Chen, Jun He, Yumei Wang, You Guo, Juan Zhang, Luying Peng, Duo Wang, Qin Lin, Jie Zhang, Zheng Guo, Li Li
STEM CELL RESEARCH & THERAPY
(2019)
Article
Cardiac & Cardiovascular Systems
Li Geng, Shuo Wang, Fulei Zhang, Ke Xiong, Jian Huang, Tingting Zhao, Dan Shi, Fei Lv, Li Li, Dandan Liang, Yingyu Cui, Yi Liu, Duanyang Xie, Yi-Han Chen
CIRCULATION-ARRHYTHMIA AND ELECTROPHYSIOLOGY
(2019)
Article
Cell Biology
Zhigang Li, Huifang Zhu, Chang Liu, Yumei Wang, Duo Wang, Huan Liu, Wenze Cao, Yi Hu, Qin Lin, Chang Tong, Min Lu, Agapios Sachinidis, Li Li, Luying Peng
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2019)
Article
Cell & Tissue Engineering
Li-Xiao Zhen, Yu-Ying Gu, Qian Zhao, Hui-Fang Zhu, Jin-Hui Lv, Shu-Jun Li, Zhen Xu, Li Li, Zuo-Ren Yu
WORLD JOURNAL OF STEM CELLS
(2019)
Article
Cardiac & Cardiovascular Systems
Duanyang Xie, Li Geng, Ke Xiong, Tingting Zhao, Shuo Wang, Jinfeng Xue, Cheng Wang, Guanghua Wang, Zhiqiang Feng, Huixing Zhou, Yini Li, Li Li, Yi Liu, Zhigang Xue, Jian Yang, Honghui Ma, Dandan Liang, Yi-Han Chen
CIRCULATION RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Juan Wang, Xiaojuan Xu, Xiujuan Shi, Jieping Zhang, Furong Gao, Jiao Li, Song Jia, Jie Xu, Junfang Zhang, Luying Peng, Li Li, Jianjun Chen, Siguang Li, Lixia Lu
Summary: The instructional model that combines literature-based learning with experimental design was introduced in 2018 to help undergraduate medical students enhance their self-learning and scientific research skills. This model led to better student-centered teaching and self-directed learning, as well as a significant increase in final scores. Students enjoyed the group work and gained experience in organization and presentation.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2021)
Article
Medicine, Research & Experimental
Yumei Wang, Na Yi, Yi Hu, Xianxiao Zhou, Hanyu Jiang, Qin Lin, Rou Chen, Huan Liu, Yanqiong Gu, Chang Tong, Min Lu, Junfang Zhang, Bin Zhang, Luying Peng, Li Li
MOLECULAR THERAPY-NUCLEIC ACIDS
(2020)
Article
Cell Biology
Zhigang Li, Yilei Meng, Chang Liu, Huan Liu, Wenze Cao, Chang Tong, Min Lu, Li Li, Luying Peng
Summary: Myocardial dysfunction is a significant manifestation in sepsis, with Kcnh2 potentially playing a protective role in sepsis-induced cardiac dysfunction by regulating FAK/AKT-FOXO3A signaling pathway to block LPS-induced myocardium apoptosis.Survival outcome in Kcnh2(+/-) septic rats was markedly deteriorated, compared with Kcnh2(+/+) rats. Activation of AKT or knockdown of FOXO3A attenuated the pathological manifestations mediated by Kcnh2 defect.
CELL PROLIFERATION
(2021)
Article
Cardiac & Cardiovascular Systems
Yu-Han Guo, Jun Wang, Xiao-Juan Guo, Ri-Feng Gao, Chen-Xi Yang, Li Li, Yu-Min Sun, Xing-Biao Qiu, Ying-Jia Xu, Yi-Qing Yang
Summary: This study identified a new gene locus for DCM and identified three mutations associated with DCM. The findings provide novel insights into the molecular pathogenesis of DCM and have potential implications for prenatal prevention and precision treatment in a subset of patients.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2022)