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For: Lugo-Martinez J, Ruiz-Perez D, Narasimhan G, Bar-Joseph Z. Dynamic interaction network inference from longitudinal microbiome data. Microbiome 2019;7:54. [PMID: 30940197 PMCID: PMC6446388 DOI: 10.1186/s40168-019-0660-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 03/11/2019] [Indexed: 05/21/2023]
Number Cited by Other Article(s)
1
Creus-Martí I, Moya A, Santonja FJ. Methodology for microbiome data analysis: An overview. Comput Biol Med 2025;192:110157. [PMID: 40279974 DOI: 10.1016/j.compbiomed.2025.110157] [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: 06/30/2024] [Revised: 03/07/2025] [Accepted: 04/04/2025] [Indexed: 04/29/2025]
2
Chen S, Wang Y, Da Zhou, Hu J. Bayesian Inference of Phenotypic Plasticity of Cancer Cells Based on Dynamic Model for Temporal Cell Proportion Data. Biom J 2025;67:e70055. [PMID: 40298362 DOI: 10.1002/bimj.70055] [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: 06/15/2024] [Revised: 09/18/2024] [Accepted: 10/31/2024] [Indexed: 04/30/2025]
3
Hammond J, Smith VA. Bayesian networks for network inference in biology. J R Soc Interface 2025;22:20240893. [PMID: 40328299 PMCID: PMC12055290 DOI: 10.1098/rsif.2024.0893] [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: 12/13/2024] [Revised: 02/14/2025] [Accepted: 02/20/2025] [Indexed: 05/08/2025]  Open
4
Špiljak B, Ozretić P, Andabak Rogulj A, Lončar Brzak B, Brailo V, Škerlj M, Vidović Juras D. Oral Microbiome Research in Biopsy Samples of Oral Potentially Malignant Disorders and Oral Squamous Cell Carcinoma and Its Challenges. APPLIED SCIENCES 2024;14:11405. [DOI: 10.3390/app142311405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
5
Oh VKS, Li RW. Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2400458. [PMID: 39535493 DOI: 10.1002/advs.202400458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 09/16/2024] [Indexed: 11/16/2024]
6
Melkikh AV. Why does a cell function? New arguments in favor of quantum effects. Biosystems 2024;245:105311. [PMID: 39173899 DOI: 10.1016/j.biosystems.2024.105311] [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: 06/19/2024] [Revised: 08/18/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
7
Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G. Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA. mSystems 2024;9:e0130323. [PMID: 39240096 PMCID: PMC11494969 DOI: 10.1128/msystems.01303-23] [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: 12/19/2023] [Accepted: 07/10/2024] [Indexed: 09/07/2024]  Open
8
Peleg O, Borenstein E. Interpolation of microbiome composition in longitudinal data sets. mBio 2024;15:e0115024. [PMID: 39162569 PMCID: PMC11389371 DOI: 10.1128/mbio.01150-24] [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: 04/18/2024] [Accepted: 07/11/2024] [Indexed: 08/21/2024]  Open
9
Deek RA, Ma S, Lewis J, Li H. Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data. eLife 2024;13:e88956. [PMID: 38832759 PMCID: PMC11149933 DOI: 10.7554/elife.88956] [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: 04/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024]  Open
10
Xiao L, Zhou T, Zuo Z, Sun N, Zhao F. Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders. Sci Bull (Beijing) 2024;69:1275-1285. [PMID: 38388298 DOI: 10.1016/j.scib.2024.02.001] [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: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
11
Sizemore N, Oliphant K, Zheng R, Martin CR, Claud EC, Chattopadhyay I. A digital twin of the infant microbiome to predict neurodevelopmental deficits. SCIENCE ADVANCES 2024;10:eadj0400. [PMID: 38598636 PMCID: PMC11006218 DOI: 10.1126/sciadv.adj0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
12
Luo M, Zhu J, Jia J, Zhang H, Zhao J. Progress on network modeling and analysis of gut microecology: a review. Appl Environ Microbiol 2024;90:e0009224. [PMID: 38415584 PMCID: PMC11207142 DOI: 10.1128/aem.00092-24] [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] [Indexed: 02/29/2024]  Open
13
Tsamir-Rimon M, Borenstein E. A manifold-based framework for studying the dynamics of the vaginal microbiome. NPJ Biofilms Microbiomes 2023;9:102. [PMID: 38102172 PMCID: PMC10724123 DOI: 10.1038/s41522-023-00471-8] [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: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]  Open
14
Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G. Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571384. [PMID: 38168315 PMCID: PMC10760167 DOI: 10.1101/2023.12.12.571384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
15
Tsamir-Rimon M, Borenstein E. A Manifold-Based Framework for Studying the Dynamics of the Vaginal Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556518. [PMID: 37732273 PMCID: PMC10508760 DOI: 10.1101/2023.09.06.556518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
16
Muralitharan RR, Snelson M, Meric G, Coughlan MT, Marques FZ. Guidelines for microbiome studies in renal physiology. Am J Physiol Renal Physiol 2023;325:F345-F362. [PMID: 37440367 DOI: 10.1152/ajprenal.00072.2023] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]  Open
17
Lyu X, Du Y, Liu G, Mai T, Li Y, Zhang Z, Bei C. Prevalence and influencing factors of hyperuricemia in middle-aged and older adults in the Yao minority area of China: a cross-sectional study. Sci Rep 2023;13:10185. [PMID: 37349536 PMCID: PMC10287663 DOI: 10.1038/s41598-023-37274-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]  Open
18
Valdes C, Stebliankin V, Ruiz-Perez D, Park JI, Lee H, Narasimhan G. Microbiome maps: Hilbert curve visualizations of metagenomic profiles. FRONTIERS IN BIOINFORMATICS 2023;3:1154588. [PMID: 37405310 PMCID: PMC10317073 DOI: 10.3389/fbinf.2023.1154588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/22/2023] [Indexed: 07/06/2023]  Open
19
Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B, Van Steen K. Capturing the dynamics of microbial interactions through individual-specific networks. Front Microbiol 2023;14:1170391. [PMID: 37256048 PMCID: PMC10225591 DOI: 10.3389/fmicb.2023.1170391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]  Open
20
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
21
Aldirawi H, Morales FG. Univariate and Multivariate Statistical Analysis of Microbiome Data: An Overview. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
22
Yang L, Chen J. Benchmarking differential abundance analysis methods for correlated microbiome sequencing data. Brief Bioinform 2023;24:bbac607. [PMID: 36617187 PMCID: PMC9851339 DOI: 10.1093/bib/bbac607] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/09/2023]  Open
23
Stebliankin V, Sazal M, Valdes C, Mathee K, Narasimhan G. A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis. Microb Genom 2022;8:mgen000899. [PMID: 36748547 PMCID: PMC9837561 DOI: 10.1099/mgen.0.000899] [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: 12/21/2021] [Accepted: 09/11/2022] [Indexed: 12/24/2022]  Open
24
Saha S, Perrin L, Röder L, Brun C, Spinelli L. Epi-MEIF: detecting higher order epistatic interactions for complex traits using mixed effect conditional inference forests. Nucleic Acids Res 2022;50:e114. [PMID: 36107776 PMCID: PMC9639209 DOI: 10.1093/nar/gkac715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 12/04/2022]  Open
25
Yuan Y, Cosme C, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. CINS: Cell Interaction Network inference from Single cell expression data. PLoS Comput Biol 2022;18:e1010468. [PMID: 36095011 PMCID: PMC9499239 DOI: 10.1371/journal.pcbi.1010468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/22/2022] [Accepted: 08/03/2022] [Indexed: 12/05/2022]  Open
26
Kim H, Jeon J, Lee KK, Lee YH. Longitudinal transmission of bacterial and fungal communities from seed to seed in rice. Commun Biol 2022;5:772. [PMID: 35915150 PMCID: PMC9343636 DOI: 10.1038/s42003-022-03726-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/14/2022] [Indexed: 12/22/2022]  Open
27
Kodikara S, Ellul S, Lê Cao KA. Statistical challenges in longitudinal microbiome data analysis. Brief Bioinform 2022;23:bbac273. [PMID: 35830875 PMCID: PMC9294433 DOI: 10.1093/bib/bbac273] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/28/2022] [Accepted: 06/12/2022] [Indexed: 11/13/2022]  Open
28
Armoni R, Borenstein E. Temporal Alignment of Longitudinal Microbiome Data. Front Microbiol 2022;13:909313. [PMID: 35814702 PMCID: PMC9257075 DOI: 10.3389/fmicb.2022.909313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]  Open
29
Explainable Machine Learning for Longitudinal Multi-Omic Microbiome. MATHEMATICS 2022. [DOI: 10.3390/math10121994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
30
Sunkavalli A, McClure R, Genco C. Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae. Microorganisms 2022;10:922. [PMID: 35630366 PMCID: PMC9147433 DOI: 10.3390/microorganisms10050922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/05/2022]  Open
31
Kaiser T, Jahansouz C, Staley C. Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data. Future Microbiol 2022;17:621-631. [PMID: 35360922 DOI: 10.2217/fmb-2021-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
32
Li D, Velazquez JJ, Ding J, Hislop J, Ebrahimkhani MR, Bar-Joseph Z. TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. Genome Biol 2022;23:73. [PMID: 35255944 PMCID: PMC8900372 DOI: 10.1186/s13059-022-02629-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/09/2022] [Indexed: 02/08/2023]  Open
33
He L, Wang C, Hu J, Gao Z, Falcone E, Holland SM, Blaser MJ, Li H. ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study. Front Genet 2022;13:777877. [PMID: 35281829 PMCID: PMC8914110 DOI: 10.3389/fgene.2022.777877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022]  Open
34
Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022;25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
35
Lugo-Martinez J, Xu S, Levesque J, Gallagher D, Parker LA, Neu J, Stewart CJ, Berrington JE, Embleton ND, Young G, Gregory KE, Good M, Tandon A, Genetti D, Warren T, Bar-Joseph Z. Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants. J Biomed Inform 2022;128:104031. [DOI: 10.1016/j.jbi.2022.104031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/20/2021] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
36
Wang C, Hu J, Blaser MJ, Li H. Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study. BMC Genomics 2021;22:667. [PMID: 34525957 PMCID: PMC8442444 DOI: 10.1186/s12864-021-07948-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/25/2021] [Indexed: 12/26/2022]  Open
37
Sharma D, Xu W. phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data. Bioinformatics 2021;37:3707-3714. [PMID: 34213529 DOI: 10.1093/bioinformatics/btab482] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/24/2021] [Accepted: 06/30/2021] [Indexed: 11/12/2022]  Open
38
Matchado MS, Lauber M, Reitmeier S, Kacprowski T, Baumbach J, Haller D, List M. Network analysis methods for studying microbial communities: A mini review. Comput Struct Biotechnol J 2021;19:2687-2698. [PMID: 34093985 PMCID: PMC8131268 DOI: 10.1016/j.csbj.2021.05.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/01/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022]  Open
39
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data. mSystems 2021;6:6/2/e01105-20. [PMID: 33785573 PMCID: PMC8546994 DOI: 10.1128/msystems.01105-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
40
Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation effect selection in high-dimensional and compositional microbiome data. Stat Med 2021;40:885-896. [PMID: 33205470 PMCID: PMC7855955 DOI: 10.1002/sim.8808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/31/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023]
41
Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Loncar Turukalo T, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, Klammsteiner T, Kolev M, Lahti L, Lopes MB, Moreno V, Naskinova I, Org E, Paciência I, Papoutsoglou G, Shigdel R, Stres B, Vilne B, Yousef M, Zdravevski E, Tsamardinos I, Carrillo de Santa Pau E, Claesson MJ, Moreno-Indias I, Truu J. Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Front Microbiol 2021;12:634511. [PMID: 33737920 PMCID: PMC7962872 DOI: 10.3389/fmicb.2021.634511] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022]  Open
42
Zaura E, Pappalardo VY, Buijs MJ, Volgenant CMC, Brandt BW. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. Periodontol 2000 2021;85:210-236. [PMID: 33226702 PMCID: PMC7756869 DOI: 10.1111/prd.12359] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Sazal M, Mathee K, Ruiz-Perez D, Cickovski T, Narasimhan G. Inferring directional relationships in microbial communities using signed Bayesian networks. BMC Genomics 2020;21:663. [PMID: 33349235 PMCID: PMC7751116 DOI: 10.1186/s12864-020-07065-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
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Lee CY, Cheu RK, Lemke MM, Gustin AT, France MT, Hampel B, Thurman AR, Doncel GF, Ravel J, Klatt NR, Arnold KB. Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. Nat Commun 2020;11:6147. [PMID: 33262350 PMCID: PMC7708644 DOI: 10.1038/s41467-020-19880-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]  Open
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Park SY, Ufondu A, Lee K, Jayaraman A. Emerging computational tools and models for studying gut microbiota composition and function. Curr Opin Biotechnol 2020;66:301-311. [PMID: 33248408 PMCID: PMC7744364 DOI: 10.1016/j.copbio.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
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Cosma-Grigorov A, Meixner H, Mrochen A, Wirtz S, Winkler J, Marxreiter F. Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates. Front Neurol 2020;11:1041. [PMID: 33071933 PMCID: PMC7538808 DOI: 10.3389/fneur.2020.01041] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]  Open
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A network approach to elucidate and prioritize microbial dark matter in microbial communities. ISME JOURNAL 2020;15:228-244. [PMID: 32963345 PMCID: PMC7852563 DOI: 10.1038/s41396-020-00777-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/18/2020] [Accepted: 09/10/2020] [Indexed: 01/13/2023]
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020;171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Jang BS, Chang JH, Chie EK, Kim K, Park JW, Kim MJ, Song EJ, Nam YD, Kang SW, Jeong SY, Kim HJ. Gut Microbiome Composition Is Associated with a Pathologic Response After Preoperative Chemoradiation in Patients with Rectal Cancer. Int J Radiat Oncol Biol Phys 2020;107:736-746. [PMID: 32315676 DOI: 10.1016/j.ijrobp.2020.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022]
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Peñalver Bernabé B, Maki PM, Dowty SM, Salas M, Cralle L, Shah Z, Gilbert JA. Precision medicine in perinatal depression in light of the human microbiome. Psychopharmacology (Berl) 2020;237:915-941. [PMID: 32065252 DOI: 10.1007/s00213-019-05436-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/11/2019] [Indexed: 12/17/2022]
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