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Tong K, Chen X, Yan S, Dai L, Liao Y, Li Z, Wang T. PlantMine: A Machine-Learning Framework to Detect Core SNPs in Rice Genomics. Genes (Basel) 2024; 15:603. [PMID: 38790232 PMCID: PMC11120712 DOI: 10.3390/genes15050603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
As a fundamental global staple crop, rice plays a pivotal role in human nutrition and agricultural production systems. However, its complex genetic architecture and extensive trait variability pose challenges for breeders and researchers in optimizing yield and quality. Particularly to expedite breeding methods like genomic selection, isolating core SNPs related to target traits from genome-wide data reduces irrelevant mutation noise, enhancing computational precision and efficiency. Thus, exploring efficient computational approaches to mine core SNPs is of great importance. This study introduces PlantMine, an innovative computational framework that integrates feature selection and machine learning techniques to effectively identify core SNPs critical for the improvement of rice traits. Utilizing the dataset from the 3000 Rice Genomes Project, we applied different algorithms for analysis. The findings underscore the effectiveness of combining feature selection with machine learning in accurately identifying core SNPs, offering a promising avenue to expedite rice breeding efforts and improve crop productivity and resilience to stress.
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Affiliation(s)
- Kai Tong
- School of Biological Engineering, Sichuan University of Science & Engineering, Yibin 644000, China; (K.T.); (L.D.); (Y.L.)
| | - Xiaojing Chen
- National Agriculture Science Data Center, Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Shen Yan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Liangli Dai
- School of Biological Engineering, Sichuan University of Science & Engineering, Yibin 644000, China; (K.T.); (L.D.); (Y.L.)
| | - Yuxue Liao
- School of Biological Engineering, Sichuan University of Science & Engineering, Yibin 644000, China; (K.T.); (L.D.); (Y.L.)
| | - Zhaoling Li
- School of Biological Engineering, Sichuan University of Science & Engineering, Yibin 644000, China; (K.T.); (L.D.); (Y.L.)
| | - Ting Wang
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Big Agri-Data, Ministry of Agriculture and Rural Areas, Beijing 100081, China
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Xu M, Zhang X, Li Y, Chen S, Zhang Y, Zhou Z, Lin S, Dong T, Hou G, Qiu Y. Identification of suicidality in patients with major depressive disorder via dynamic functional network connectivity signatures and machine learning. Transl Psychiatry 2022; 12:383. [PMID: 36097160 PMCID: PMC9467986 DOI: 10.1038/s41398-022-02147-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
Major depressive disorder (MDD) is a severe brain disease associated with a significant risk of suicide. Identification of suicidality is sometimes life-saving for MDD patients. We aimed to explore the use of dynamic functional network connectivity (dFNC) for suicidality detection in MDD patients. A total of 173 MDD patients, including 48 without suicide risk (NS), 74 with suicide ideation (SI), and 51 having attempted suicide (SA), participated in the present study. Thirty-eight healthy controls were also recruited for comparison. A sliding window approach was used to derive the dFNC, and the K-means clustering method was used to cluster the windowed dFNC. A linear support vector machine was used for classification, and leave-one-out cross-validation was performed for validation. Other machine learning methods were also used for comparison. MDD patients had widespread hypoconnectivity in both the strongly connected states (states 2 and 5) and the weakly connected state (state 4), while the dysfunctional connectivity within the weakly connected state (state 4) was mainly driven by suicidal attempts. Furthermore, dFNC matrices, especially the weakly connected state, could be used to distinguish MDD from healthy controls (area under curve [AUC] = 82), and even to identify suicidality in MDD patients (AUC = 78 for NS vs. SI, AUC = 88 for NS vs. SA, and AUC = 74 for SA vs. SI), with vision-related and default-related inter-network connectivity serving as important features. Thus, the dFNC abnormalities observed in this study might further improve our understanding of the neural substrates of suicidality in MDD patients.
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Affiliation(s)
- Manxi Xu
- grid.410737.60000 0000 8653 1072Department of Radiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Duobao AVE 56, Liwan district, Guangzhou, People’s Republic of China ,grid.33199.310000 0004 0368 7223Department of Radiology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000 People’s Republic of China
| | - Xiaojing Zhang
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060 People’s Republic of China
| | - Yanqing Li
- grid.410737.60000 0000 8653 1072Department of Radiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Duobao AVE 56, Liwan district, Guangzhou, People’s Republic of China
| | - Shengli Chen
- grid.33199.310000 0004 0368 7223Department of Radiology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000 People’s Republic of China
| | - Yingli Zhang
- grid.452897.50000 0004 6091 8446Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020 People’s Republic of China
| | - Zhifeng Zhou
- grid.452897.50000 0004 6091 8446Department of Radiology, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020 People’s Republic of China
| | - Shiwei Lin
- grid.33199.310000 0004 0368 7223Department of Radiology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000 People’s Republic of China
| | - Tianfa Dong
- grid.410737.60000 0000 8653 1072Department of Radiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Duobao AVE 56, Liwan district, Guangzhou, People’s Republic of China
| | - Gangqiang Hou
- Department of Radiology, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020, People's Republic of China.
| | - Yingwei Qiu
- Department of Radiology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000, People's Republic of China.
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Ao C, Jiao S, Wang Y, Yu L, Zou Q. Biological Sequence Classification: A Review on Data and General Methods. RESEARCH 2022. [DOI: 10.34133/research.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
With the rapid development of biotechnology, the number of biological sequences has grown exponentially. The continuous expansion of biological sequence data promotes the application of machine learning in biological sequences to construct predictive models for mining biological sequence information. There are many branches of biological sequence classification research. In this review, we mainly focus on the function and modification classification of biological sequences based on machine learning. Sequence-based prediction and analysis are the basic tasks to understand the biological functions of DNA, RNA, proteins, and peptides. However, there are hundreds of classification models developed for biological sequences, and the quite varied specific methods seem dizzying at first glance. Here, we aim to establish a long-term support website (
http://lab.malab.cn/~acy/BioseqData/home.html
), which provides readers with detailed information on the classification method and download links to relevant datasets. We briefly introduce the steps to build an effective model framework for biological sequence data. In addition, a brief introduction to single-cell sequencing data analysis methods and applications in biology is also included. Finally, we discuss the current challenges and future perspectives of biological sequence classification research.
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Affiliation(s)
- Chunyan Ao
- School of Computer Science and Technology, Xidian University, Xi’an, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Shihu Jiao
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi’an, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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Malik A, Subramaniyam S, Kim CB, Manavalan B. SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information. Comput Struct Biotechnol J 2021; 20:165-174. [PMID: 34976319 PMCID: PMC8703055 DOI: 10.1016/j.csbj.2021.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Sortase enzymes are cysteine transpeptidases that embellish the surface of Gram-positive bacteria with various proteins thereby allowing these microorganisms to interact with their neighboring environment. It is known that several of their substrates can cause pathological implications, so researchers have focused on the development of sortase inhibitors. Currently, six different classes of sortases (A-F) are recognized. However, with the extensive application of bacterial genome sequencing projects, the number of potential sortases in the public databases has exploded, presenting considerable challenges in annotating these sequences. It is very laborious and time-consuming to characterize these sortase classes experimentally. Therefore, this study developed the first machine-learning-based two-layer predictor called SortPred, where the first layer predicts the sortase from the given sequence and the second layer predicts their class from the predicted sortase. To develop SortPred, we constructed an original benchmarking dataset and investigated 31 feature descriptors, primarily on five feature encoding algorithms. Afterward, each of these descriptors were trained using a random forest classifier and their robustness was evaluated with an independent dataset. Finally, we selected the final model independently for both layers depending on the performance consistency between cross-validation and independent evaluation. SortPred is expected to be an effective tool for identifying bacterial sortases, which in turn may aid in designing sortase inhibitors and exploring their functions. The SortPred webserver and a standalone version are freely accessible at: https://procarb.org/sortpred.
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Affiliation(s)
- Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Republic of Korea
| | | | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea
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