Article
Biochemistry & Molecular Biology
Wirawan Adikusuma, Wan-Hsuan Chou, Min-Rou Lin, Jafit Ting, Lalu Muhammad Irham, Dyah Aryani Perwitasari, Wei-Pin Chang, Wei-Chiao Chang
Summary: By analyzing genomic data, we identified 139 biological asthma risk genes and identified 64 drugs that target these genes. Additionally, we found 17 drugs with clinical evidence for treating asthma and further identified 11 promising candidate drugs.
Article
Mathematical & Computational Biology
Zequn Sun, Dongjun Chung, Brian Neelon, Andrew Millar-Wilson, Stephen P. Ethier, Feifei Xiao, Yinan Zheng, Kristin Wallace, Gary Hardiman
Summary: This article proposes a pathway-guided Bayesian sparse latent factor model for the simultaneous identification of cancer patient subgroups and key molecular features. By utilizing pathway information, this model enhances the accuracy and robustness of cancer patient subgroup and key molecular feature identification, and also promotes biological understanding and interpretation. An alternative Gibbs sampler for logistic and negative binomial models is proposed to facilitate efficient posterior sampling.
STATISTICS IN MEDICINE
(2023)
Article
Cell Biology
Huang Yaoxing, Yu Danchun, Sun Xiaojuan, Jiang Shuman, Yan Qingqing, Jia Lin
Summary: Gastric cancer is a common cause of cancer-related deaths worldwide, with its molecular mechanisms still poorly understood. A machine learning-based study identified 787 novel susceptibility genes related to gastric cancer, providing new insights into the genetic and biological basis of gastric cancer development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Yuexun Xu, Hui Luo, Qunchao Hu, Haiyan Zhu
Summary: Integrative multi-platform analysis revealed the wide range of mutations and complex molecular characteristics of cervical cancer. Unsupervised clustering identified four significant expression subtypes, and 10 potential driver genes were identified through multidimensional dataset integration.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Mahdieh Ghasemi, Maseud Rahgozar, Kaveh Kavousi
Summary: This article proposes a new heterogeneous biological network embedding approach, NetEM, to identify disease-associated genes. The experiments and case studies using real data demonstrate the superior performance of NetEM in identifying disease genes compared to three other algorithms.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Kader Salifou, Callum Burnard, Poornima Basavarajaiah, Giuseppa Grasso, Marion Helsmoortel, Victor Mac, David Depierre, Celine Franckhauser, Emmanuelle Beyne, Xavier Contreras, Jerome Dejardin, Sylvie Rouquier, Olivier Cuvier, Rosemary Kiernan
Summary: MRN-MDC1 plays a central role in DNA damage response and repair, interacting with factors involved in gene expression and RNA processing, as well as DDR factors. Association of MRN with the transcriptional machinery scans active genes for transcription-induced DNA damage to preserve genome integrity.
Article
Multidisciplinary Sciences
Gang Wei, Youhong Dong, Zhongshi He, Hu Qiu, Yong Wu, Yongshun Chen
Summary: This study identified hub genes and constructed an mRNA-miRNA-lncRNA regulatory network in gastric cancer, providing new insights into the underlying mechanisms of gastric carcinogenesis. The hub genes CTHRC1, FNDC1, and INHBA may serve as novel prognostic biomarkers and therapeutic targets.
Article
Computer Science, Artificial Intelligence
Justin Engelmann, Alice D. McTrusty, Ian J. C. MacCormick, Emma Pead, Amos Storkey, Miguel O. Bernabeu
Summary: This study proposes an improved deep learning model for recognizing multiple retinal diseases under more realistic conditions and uses global explainability methods to identify the relevant regions in ultra-widefield (UWF) images. The model performs well in distinguishing between healthy and diseased retinas and identifies the posterior pole as the most important region.
NATURE MACHINE INTELLIGENCE
(2022)
Editorial Material
Multidisciplinary Sciences
Alexander Bernier, Hanshi Liu, Bartha Maria Knoppers
Summary: Computational tools to limit the identifiability of genomic data show promise in protecting privacy and ensuring legal compliance. Even if they do not eliminate all risks of individual identification, the law may still classify the data as anonymized.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Yang Liu, Lanlan Chen, Xiangbo Meng, Shujun Ye, Lianjun Ma
Summary: This study identified hub genes associated with colorectal adenocarcinoma and constructed a 3-gene signature to predict the prognosis of patients. The findings provide valuable insights into the molecular mechanisms and potential prognosis factors of colorectal adenocarcinoma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Peter Larsson, Daniella Pettersson, Hanna Engqvist, Elisabeth Werner Ronnerman, Eva Forssell-Aronsson, Aniko Kovacs, Per Karlsson, Khalil Helou, Toshima Z. Parris
Summary: The study analyzed the genetic alterations and prognostic value of PSM gene expression in various cancer types using TCGA data. High frequency of PSM genetic alterations, especially DNA amplification, was observed in certain cancer types. Overexpression of most PSM genes in cancer and their association with adverse clinical outcomes were also reported.
Article
Plant Sciences
Akshay Singh, Ajay Kumar Mahato, Avantika Maurya, S. Rajkumar, A. K. Singh, Rakesh Bhardwaj, S. K. Kaushik, Sandeep Kumar, Veena Gupta, Kuldeep Singh, Rakesh Singh
Summary: Amaranth is a highly nutritious food crop grown worldwide. The Amaranth Genomic Resource Database (AGRDB) has been developed to provide access to genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters. The database allows for various types of searches and includes tools like JBrowse and BLAST search. AGRDB will be a valuable platform for genetic improvement and characterization of this future crop.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Shuya ma, Le Liu, Huiyun Shi, Yu Gu, Yujun Li, Ghulam Qanmber
Summary: In this study, 157 SAC genes were identified for the first time in eight cotton species. These genes play important roles in flower, ovule, and fiber development, as well as in the response to abiotic stress conditions.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Zhiwen Shi, Bolin Chen, Xiao Han, Weiyue Gu, Shuzhi Liang, Lin Wu
Summary: In this study, computational analysis of genetic data from 10,619 cancer patients revealed the prevalence of Homologous Recombination Deficiency (HRD) across multiple cancer types and its clinical prognostic value. HRD is associated with high mutation or deletion frequency of homologous recombination-related genes. Additionally, HRD is positively correlated with DNA damage response and immune-related signaling pathways. Furthermore, HRD can be utilized to predict pan-cancer patients' responses to PD-1 immunotherapy.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Meng Wang, Ishani Banik, A. Hunter Shain, Iwei Yeh, Boris C. Bastian
Summary: This study conducted a meta-analysis of sequencing data from acral and mucosal melanoma samples and identified important genetic mutations and gene amplifications, providing important clues for understanding the pathogenesis and therapeutic targets of these difficult-to-treat cancers.
Article
Genetics & Heredity
Feng Zhang, Lanlan Dai, Weimin Lin, Wenyu Wang, Xuanzhu Liu, Jianguo Zhang, Tielin Yang, Xiaogang Liu, Hui Shen, Xiangding Chen, Lijun Tan, Qing Tian, Hong-Wen Deng, Xun Xu, Xiong Guo
FUNCTIONAL & INTEGRATIVE GENOMICS
(2016)
Article
Endocrinology & Metabolism
Tianhua Niu, Ning Liu, Xun Yu, Ming Zhao, Hyung Jin Choi, Paul J. Leo, Matthew A. Brown, Lei Zhang, Yu-Fang Pei, Hui Shen, Hao He, Xiaoying Fu, Shan Lu, Xiang-Ding Chen, Li-Jun Tan, Tie-Lin Yang, Yan Guo, Nam H. Cho, Jie Shen, Yan-Fang Guo, Geoffrey C. Nicholson, Richard L. Prince, John A. Eisman, Graeme Jones, Philip N. Sambrook, Qing Tian, Xue-Zhen Zhu, Christopher J. Papasian, Emma L. Duncan, Andre G. Uitterlinden, Chan Soo Shin, Shuanglin Xiang, Hong-Wen Deng
JOURNAL OF BONE AND MINERAL RESEARCH
(2016)
Article
Biochemical Research Methods
Wenyu Wang, Jingcan Hao, Shuyu Zheng, Qianrui Fan, Awen He, Yan Wen, Xiong Guo, Cuiyan Wu, Sen Wang, Tielin Yang, Hui Shen, Xiangding Chen, Qing Tian, Lijun Tan, Hong-Wen Deng, Feng Zhang
Article
Genetics & Heredity
Chao Xu, Kehao Wu, Ji-Gang Zhang, Hui Shen, Hong-Wen Deng
GENETIC EPIDEMIOLOGY
(2017)
Article
Endocrinology & Metabolism
W. Zhu, H. Shen, J-G Zhang, L. Zhang, Y. Zeng, H-L Huang, Y-C Zhao, H. He, Y. Zhou, K-H Wu, Q. Tian, L-J Zhao, F-Y Deng, H-W Deng
OSTEOPOROSIS INTERNATIONAL
(2017)
Article
Multidisciplinary Sciences
Yan Guo, Shan-Shan Dong, Xiao-Feng Chen, Ying-Aisha Jing, Man Yang, Han Yan, Hui Shen, Xiang-Ding Chen, Li-Jun Tan, Qing Tian, Hong-Wen Deng, Tie-Lin Yang
SCIENTIFIC REPORTS
(2016)
Article
Multidisciplinary Sciences
Jingcan Hao, Wenyu Wang, Yan Wen, Xiao Xiao, Awen He, Xiong Guo, Tielin Yang, Xiaogang Liu, Hui Shen, Xiangding Chen, Qing Tian, Hong-Wen Deng, Feng Zhang
SCIENTIFIC REPORTS
(2016)
Article
Cell Biology
Yong Zeng, Fei-Yan Deng, Wei Zhu, Lan Zhang, Hao He, Chao Xu, Qing Tian, Ji-Gang Zhang, Li-Shu Zhang, Hong-Gang Hu, Hong-Wen Deng
Article
Endocrinology & Metabolism
Yu-Fang Pei, Hai-Gang Ren, Lu Liu, Xiao Li, Chen Fang, Yun Huang, Wen-Zhu Hu, Wei-Wen Kong, An-Ping Feng, Xin-Yi You, Wen Zhao, Hui Shen, Qing Tian, Yong-Hong Zhang, Hong-Wen Deng, Lei Zhang
Article
Orthopedics
C. Wu, Y. Wen, X. Guo, T. Yang, H. Shen, X. Chen, Q. Tian, L. Tan, H. -W. Deng, F. Zhang
OSTEOARTHRITIS AND CARTILAGE
(2017)
Article
Endocrinology & Metabolism
Chun-Ping Zeng, Yuan-Cheng Chen, Xu Lin, Jonathan Greenbaum, You-Ping Chen, Cheng Peng, Xia-Fang Wang, Rou Zhou, Wei-Min Deng, Jie Shen, Hong-Wen Deng
JOURNAL OF DIABETES
(2017)
Article
Physics, Applied
Xiao-Juan Ye, Qiang Gao, Hong-Bao Cao, Xiao-Han Wang, Chun-Sheng Liu
Summary: The study predicts a two-dimensional material named Be2B monolayer as an excellent anode material for magnesium-ion batteries, with superior structural stability and excellent performance.
APPLIED PHYSICS LETTERS
(2023)
Article
Chemistry, Medicinal
Shuang Liang, Danyang Liu, Zhengwu Xiao, Jonathan Greenbaum, Hui Shen, Hongmei Xiao, Hongwen Deng
Summary: Sarcopenia, a condition characterized by age-related muscle loss, is a growing public health concern. This study used different approaches to identify potential drugs for repurposing, including analysis of gene expression in skeletal muscle, assessment of drug similarity, and validation in vitro. Vorinostat was found to be a promising drug for promoting muscle fiber formation. Although further validation is needed, this suggests a potential strategy for treating and preventing sarcopenia.
Review
Biology
Martin Nwadiugwu, Hui Shen, Hong-Wen Deng
Summary: This study systematically reviewed genetic research on Alzheimer's disease (AD) using single-cell transcriptomics (scRNA-seq) or spatial genomics to identify potential molecular mechanisms and explore differences from previous findings. It presented an overview of molecular imbalances in AD and their mechanisms across different factors. The study highlighted the importance of continuing research to identify common causes and solutions for AD. scRNA-seq and spatial transcriptomics provide more in-depth results, which are crucial for AD-modifying investigations.
Review
Biology
Lei Huang, Meng Song, Hui Shen, Huixiao Hong, Ping Gong, Hong-Wen Deng, Chaoyang Zhang
Summary: This review provides an overview of deep learning-based methods for imputing missing omics data, focusing on model architectures and multi-omics data imputation. These methods can model complex patterns and relationships in large and high-dimensional omics datasets, making them an increasingly popular choice for imputation. The review also discusses the challenges and opportunities associated with deep learning methods in this field.