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For: Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE. PLoS One 2011;6:e21750. [PMID: 21789178 PMCID: PMC3137602 DOI: 10.1371/journal.pone.0021750] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/05/2011] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Xie Y, Yang J, Ouyang JF, Petretto E. scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets. Brief Bioinform 2024;25:bbae482. [PMID: 39350339 PMCID: PMC11442147 DOI: 10.1093/bib/bbae482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/30/2024] [Accepted: 09/12/2024] [Indexed: 10/04/2024]  Open
2
Karimi-Fard A, Saidi A, TohidFar M, Emami SN. Novel candidate genes for environmental stresses response in Synechocystis sp. PCC 6803 revealed by machine learning algorithms. Braz J Microbiol 2024;55:1219-1229. [PMID: 38705959 PMCID: PMC11153407 DOI: 10.1007/s42770-024-01338-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024]  Open
3
Murmu S, Sinha D, Chaurasia H, Sharma S, Das R, Jha GK, Archak S. A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions. FRONTIERS IN PLANT SCIENCE 2024;15:1292054. [PMID: 38504888 PMCID: PMC10948452 DOI: 10.3389/fpls.2024.1292054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024]
4
Tahmasebi A, Niazi A, Akrami S. Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species. Sci Rep 2023;13:847. [PMID: 36646724 PMCID: PMC9842770 DOI: 10.1038/s41598-023-27746-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023]  Open
5
Favreau E, Geist KS, Wyatt CDR, Toth AL, Sumner S, Rehan SM. Co-expression Gene Networks and Machine-learning Algorithms Unveil a Core Genetic Toolkit for Reproductive Division of Labour in Rudimentary Insect Societies. Genome Biol Evol 2023;15:evac174. [PMID: 36527688 PMCID: PMC9830183 DOI: 10.1093/gbe/evac174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]  Open
6
Chataika BY, Akundabweni LSM, Sibiya J, Achigan-Dako EG, Sogbohossou DEO, Kwapata K, Awala S. Major Production Constraints and Spider Plant [Gynandropsis gynandra (L.) Briq.] Traits Preferences Amongst Smallholder Farmers of Northern Namibia and Central Malawi. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.831821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
7
Gene Correlation Guided Gene Selection for Microarray Data Classification. BIOMED RESEARCH INTERNATIONAL 2021;2021:6490118. [PMID: 34435048 PMCID: PMC8382518 DOI: 10.1155/2021/6490118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022]
8
Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021;1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
9
Das S, Rai SN. Statistical Approach for Biologically Relevant Gene Selection from High-Throughput Gene Expression Data. ENTROPY (BASEL, SWITZERLAND) 2020;22:E1205. [PMID: 33286973 PMCID: PMC7712650 DOI: 10.3390/e22111205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
10
Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges. ENTROPY 2020;22:e22040427. [PMID: 33286201 PMCID: PMC7516904 DOI: 10.3390/e22040427] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/18/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022]
11
Sun S, Wang C, Ding H, Zou Q. Machine learning and its applications in plant molecular studies. Brief Funct Genomics 2019;19:40-48. [DOI: 10.1093/bfgp/elz036] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/06/2019] [Accepted: 09/15/2019] [Indexed: 01/16/2023]  Open
12
Rahaman MM, Ahsan MA, Chen M. Data-mining Techniques for Image-based Plant Phenotypic Traits Identification and Classification. Sci Rep 2019;9:19526. [PMID: 31862925 PMCID: PMC6925301 DOI: 10.1038/s41598-019-55609-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/21/2019] [Indexed: 11/09/2022]  Open
13
Gene selection for microarray data classification via adaptive hypergraph embedded dictionary learning. Gene 2019;706:188-200. [DOI: 10.1016/j.gene.2019.04.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 01/19/2023]
14
Olohan L, Gardiner LJ, Lucaci A, Steuernagel B, Wulff B, Kenny J, Hall N, Hall A. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample. BMC Genomics 2018;19:250. [PMID: 29653520 PMCID: PMC5899405 DOI: 10.1186/s12864-018-4640-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 04/03/2018] [Indexed: 01/01/2023]  Open
15
Statistical approach for selection of biologically informative genes. Gene 2018;655:71-83. [PMID: 29458166 DOI: 10.1016/j.gene.2018.02.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/26/2017] [Accepted: 02/14/2018] [Indexed: 11/23/2022]
16
Statistical Approach for Gene Set Analysis with Trait Specific Quantitative Trait Loci. Sci Rep 2018;8:2391. [PMID: 29402907 PMCID: PMC5799309 DOI: 10.1038/s41598-018-19736-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 12/06/2017] [Indexed: 11/20/2022]  Open
17
Sogbohossou EOD, Achigan-Dako EG, Maundu P, Solberg S, Deguenon EMS, Mumm RH, Hale I, Van Deynze A, Schranz ME. A roadmap for breeding orphan leafy vegetable species: a case study of Gynandropsis gynandra (Cleomaceae). HORTICULTURE RESEARCH 2018;5:2. [PMID: 29423232 PMCID: PMC5798814 DOI: 10.1038/s41438-017-0001-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/23/2017] [Accepted: 11/29/2017] [Indexed: 05/24/2023]
18
Kumar A, Jeya Sundara Sharmila D, Singh S. SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes. GENOMICS DATA 2017;12:28-37. [PMID: 28275550 PMCID: PMC5331150 DOI: 10.1016/j.gdata.2017.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/07/2017] [Accepted: 02/15/2017] [Indexed: 12/22/2022]
19
Gene selection for tumor classification using neighborhood rough sets and entropy measures. J Biomed Inform 2017;67:59-68. [PMID: 28215562 DOI: 10.1016/j.jbi.2017.02.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/25/2017] [Accepted: 02/09/2017] [Indexed: 01/04/2023]
20
Transcriptomic basis for drought-resistance in Brassica napus L. Sci Rep 2017;7:40532. [PMID: 28091614 PMCID: PMC5238399 DOI: 10.1038/srep40532] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/07/2016] [Indexed: 01/06/2023]  Open
21
Das S, Meher PK, Rai A, Bhar LM, Mandal BN. Statistical Approaches for Gene Selection, Hub Gene Identification and Module Interaction in Gene Co-Expression Network Analysis: An Application to Aluminum Stress in Soybean (Glycine max L.). PLoS One 2017;12:e0169605. [PMID: 28056073 PMCID: PMC5215982 DOI: 10.1371/journal.pone.0169605] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/19/2016] [Indexed: 11/30/2022]  Open
22
Lu X, Yang Y, Wu F, Gao M, Xu Y, Zhang Y, Yao Y, Du X, Li C, Wu L, Zhong X, Zhou Y, Fan N, Zheng Y, Xiong D, Peng H, Escudero J, Huang B, Li X, Ning Y, Wu K. Discriminative analysis of schizophrenia using support vector machine and recursive feature elimination on structural MRI images. Medicine (Baltimore) 2016;95:e3973. [PMID: 27472673 PMCID: PMC5265810 DOI: 10.1097/md.0000000000003973] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/16/2016] [Accepted: 05/26/2016] [Indexed: 12/11/2022]  Open
23
D'Andrea RM, Triassi A, Casas MI, Andreo CS, Lara MV. Identification of genes involved in the drought adaptation and recovery in Portulaca oleracea by differential display. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015;90:38-49. [PMID: 25767913 DOI: 10.1016/j.plaphy.2015.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/28/2015] [Indexed: 06/04/2023]
24
Chen Y, Zhou W, Wang H, Yuan Z. Prediction of O-glycosylation sites based on multi-scale composition of amino acids and feature selection. Med Biol Eng Comput 2015;53:535-44. [PMID: 25752770 DOI: 10.1007/s11517-015-1268-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022]
25
Meng J, Zhang J, Luan Y. Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:433-444. [PMID: 26357229 DOI: 10.1109/tcbb.2014.2361329] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
26
Gene selection using rough set based on neighborhood for the analysis of plant stress response. Appl Soft Comput 2014. [DOI: 10.1016/j.asoc.2014.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
27
Zhang X, Lu G, Long W, Zou X, Li F, Nishio T. Recent progress in drought and salt tolerance studies in Brassica crops. BREEDING SCIENCE 2014;64:60-73. [PMID: 24987291 PMCID: PMC4031111 DOI: 10.1270/jsbbs.64.60] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/19/2014] [Indexed: 05/19/2023]
28
Shaik R, Ramakrishna W. Machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice. PLANT PHYSIOLOGY 2014;164:481-95. [PMID: 24235132 PMCID: PMC3875824 DOI: 10.1104/pp.113.225862] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
29
Bhardwaj J, Chauhan R, Swarnkar MK, Chahota RK, Singh AK, Shankar R, Yadav SK. Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC Genomics 2013;14:647. [PMID: 24059455 PMCID: PMC3853109 DOI: 10.1186/1471-2164-14-647] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/13/2013] [Indexed: 11/10/2022]  Open
30
Wang J, Chen L, Wang Y, Zhang J, Liang Y, Xu D. A computational systems biology study for understanding salt tolerance mechanism in rice. PLoS One 2013;8:e64929. [PMID: 23762267 PMCID: PMC3676415 DOI: 10.1371/journal.pone.0064929] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/19/2013] [Indexed: 01/22/2023]  Open
31
Hu C, Wang J, Zheng C, Xu S, Zhang H, Liang Y, Bi L, Fan Z, Han B, Xu W. Raman spectra exploring breast tissues: Comparison of principal component analysis and support vector machine-recursive feature elimination. Med Phys 2013;40:063501. [DOI: 10.1118/1.4804054] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]  Open
32
Landschoot S, Waegeman W, Audenaert K, Vandepitte J, Haesaert G, De Baets B. Toward a Reliable Evaluation of Forecasting Systems for Plant Diseases: A Case Study Using Fusarium Head Blight of Wheat. PLANT DISEASE 2012;96:889-896. [PMID: 30727362 DOI: 10.1094/pdis-08-11-0665] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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