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For: Fujimoto MS, Suvorov A, Jensen NO, Clement MJ, Bybee SM. Detecting false positive sequence homology: a machine learning approach. BMC Bioinformatics 2016;17:101. [PMID: 26911862 PMCID: PMC4765110 DOI: 10.1186/s12859-016-0955-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 02/19/2016] [Indexed: 01/12/2023]  Open
Number Cited by Other Article(s)
1
Loreto ELS, Melo ESD, Wallau GL, Gomes TMFF. The good, the bad and the ugly of transposable elements annotation tools. Genet Mol Biol 2024;46:e20230138. [PMID: 38373163 PMCID: PMC10876081 DOI: 10.1590/1678-4685-gmb-2023-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024]  Open
2
Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023;151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
3
Singh D, Roy J. A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs. Nucleic Acids Res 2022;50:12094-12111. [PMID: 36420898 PMCID: PMC9757047 DOI: 10.1093/nar/gkac1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022]  Open
4
Nawade B, Kumar A, Maurya R, Subramani R, Yadav R, Singh K, Rangan P. Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield-Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame. PLANTS (BASEL, SWITZERLAND) 2022;11:2980. [PMID: 36365434 PMCID: PMC9657858 DOI: 10.3390/plants11212980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
5
Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021;71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]  Open
6
Suvorov A, Hochuli J, Schrider DR. Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning. Syst Biol 2020;69:221-233. [PMID: 31504938 PMCID: PMC8204903 DOI: 10.1093/sysbio/syz060] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/28/2019] [Indexed: 11/13/2022]  Open
7
A Systematic Review on Supervised and Unsupervised Machine Learning Algorithms for Data Science. UNSUPERVISED AND SEMI-SUPERVISED LEARNING 2020. [DOI: 10.1007/978-3-030-22475-2_1] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
8
Garcia DC, Cheng X, Land ML, Standaert RF, Morrell-Falvey JL, Doktycz MJ. Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways. ACS Chem Biol 2019;14:2867-2875. [PMID: 31693336 DOI: 10.1021/acschembio.9b00725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
9
Hong J, Luo Y, Zhang Y, Ying J, Xue W, Xie T, Tao L, Zhu F. Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. Brief Bioinform 2019;21:1437-1447. [PMID: 31504150 PMCID: PMC7412958 DOI: 10.1093/bib/bbz081] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/12/2022]  Open
10
Yu CY, Li XX, Yang H, Li YH, Xue WW, Chen YZ, Tao L, Zhu F. Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate. Int J Mol Sci 2018;19:E183. [PMID: 29316706 PMCID: PMC5796132 DOI: 10.3390/ijms19010183] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/09/2017] [Accepted: 01/04/2018] [Indexed: 12/27/2022]  Open
11
Sharkey CR, Fujimoto MS, Lord NP, Shin S, McKenna DD, Suvorov A, Martin GJ, Bybee SM. Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles. Sci Rep 2017;7:8. [PMID: 28127058 PMCID: PMC5428366 DOI: 10.1038/s41598-017-00061-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022]  Open
12
Suvorov A, Jensen NO, Sharkey CR, Fujimoto MS, Bodily P, Wightman HMC, Ogden TH, Clement MJ, Bybee SM. Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata. Mol Ecol 2016;26:1306-1322. [DOI: 10.1111/mec.13884] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/24/2016] [Accepted: 10/04/2016] [Indexed: 02/04/2023]
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