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For: Asgari E, Münch PC, Lesker TR, McHardy AC, Mofrad MRK. DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinformatics 2020;35:2498-2500. [PMID: 30500871 DOI: 10.1093/bioinformatics/bty954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/21/2018] [Accepted: 11/28/2018] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023;24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]  Open
2
Shtossel O, Isakov H, Turjeman S, Koren O, Louzoun Y. Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy. Gut Microbes 2023;15:2224474. [PMID: 37345233 PMCID: PMC10288916 DOI: 10.1080/19490976.2023.2224474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/08/2023] [Indexed: 06/23/2023]  Open
3
Chrisman BS, Paskov KM, Stockham N, Jung JY, Varma M, Washington PY, Tataru C, Iwai S, DeSantis TZ, David M, Wall DP. Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers. BMC Bioinformatics 2021;22:509. [PMID: 34666677 PMCID: PMC8527694 DOI: 10.1186/s12859-021-04427-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/06/2021] [Indexed: 12/31/2022]  Open
4
Abbasi K, Razzaghi P, Poso A, Ghanbari-Ara S, Masoudi-Nejad A. Deep Learning in Drug Target Interaction Prediction: Current and Future Perspectives. Curr Med Chem 2021;28:2100-2113. [PMID: 32895036 DOI: 10.2174/0929867327666200907141016] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 11/22/2022]
5
Song K, Wright FA, Zhou YH. Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction. Front Mol Biosci 2020;7:610845. [PMID: 33392266 PMCID: PMC7772236 DOI: 10.3389/fmolb.2020.610845] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]  Open
6
Kwak MS, Cha JM, Shin HP, Jeon JW, Yoon JY. Development of a Novel Metagenomic Biomarker for Prediction of Upper Gastrointestinal Tract Involvement in Patients With Crohn's Disease. Front Microbiol 2020;11:1162. [PMID: 32582102 PMCID: PMC7283919 DOI: 10.3389/fmicb.2020.01162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/06/2020] [Indexed: 12/28/2022]  Open
7
Peng H. CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification. PeerJ 2020;8:e8965. [PMID: 32341900 PMCID: PMC7179567 DOI: 10.7717/peerj.8965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]  Open
8
Meola M, Rifa E, Shani N, Delbès C, Berthoud H, Chassard C. DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. BMC Genomics 2019;20:560. [PMID: 31286860 PMCID: PMC6615214 DOI: 10.1186/s12864-019-5914-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022]  Open
9
Madani A, Bakhaty A, Kim J, Mubarak Y, Mofrad M. Bridging finite element and machine learning modeling: stress prediction of arterial walls in atherosclerosis. J Biomech Eng 2019;141:2729617. [PMID: 30912802 DOI: 10.1115/1.4043290] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 11/08/2022]
10
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX). Sci Rep 2019;9:3577. [PMID: 30837494 PMCID: PMC6401088 DOI: 10.1038/s41598-019-38746-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/19/2018] [Indexed: 12/28/2022]  Open
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