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For: Andrighetti T, Bohar B, Lemke N, Sudhakar P, Korcsmaros T. MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. Cells 2020;9:cells9051278. [PMID: 32455748 PMCID: PMC7291277 DOI: 10.3390/cells9051278] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [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: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
2
George N, Bhandari P, Shruptha P, Jayaram P, Chaudhari S, Satyamoorthy K. Multidimensional outlook on the pathophysiology of cervical cancer invasion and metastasis. Mol Cell Biochem 2023;478:2581-2606. [PMID: 36905477 PMCID: PMC10006576 DOI: 10.1007/s11010-023-04686-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
3
Kumar R, Yadav G, Kuddus M, Ashraf GM, Singh R. Unlocking the microbial studies through computational approaches: how far have we reached? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023;30:48929-48947. [PMID: 36920617 PMCID: PMC10016191 DOI: 10.1007/s11356-023-26220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/24/2023] [Indexed: 04/16/2023]
4
Augustin J, McLellan PT, Calderaro J. Mise au point de l’utilisation de l’intelligence artificielle dans la prise en charge des maladies inflammatoires chroniques de l’intestin. Ann Pathol 2023:S0242-6498(23)00075-5. [PMID: 36997441 DOI: 10.1016/j.annpat.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023]
5
Duan H, Zhang X, Figeys D. An emerging field: Post-translational modification in microbiome. Proteomics 2023;23:e2100389. [PMID: 36239139 DOI: 10.1002/pmic.202100389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
6
Lim H, Tsai CJ, Keskin O, Nussinov R, Gursoy A. HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. Bioinformatics 2022;38:4962-4965. [PMID: 36124958 PMCID: PMC9620825 DOI: 10.1093/bioinformatics/btac633] [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: 03/14/2022] [Revised: 08/05/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]  Open
7
Sridhar S, Ajo-Franklin CM, Masiello CA. A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. ACS Synth Biol 2022;11:2909-2916. [PMID: 35961652 PMCID: PMC9486965 DOI: 10.1021/acssynbio.2c00079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
8
Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022;7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
9
Demeter A, Jacomin AC, Gul L, Lister A, Lipscombe J, Invernizzi R, Branchu P, Macaulay I, Nezis IP, Kingsley RA, Korcsmaros T, Hautefort I. Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Front Cell Infect Microbiol 2022;12:834895. [PMID: 36061866 PMCID: PMC9428466 DOI: 10.3389/fcimb.2022.834895] [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: 12/13/2021] [Accepted: 07/28/2022] [Indexed: 11/13/2022]  Open
10
Integrated analysis of microbe-host interactions in Crohn’s disease reveals potential mechanisms of microbial proteins on host gene expression. iScience 2022;25:103963. [PMID: 35479407 PMCID: PMC9035720 DOI: 10.1016/j.isci.2022.103963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/11/2021] [Accepted: 02/18/2022] [Indexed: 12/15/2022]  Open
11
Stidham RW, Takenaka K. Artificial Intelligence for Disease Assessment in Inflammatory Bowel Disease: How Will it Change Our Practice? Gastroenterology 2022;162:1493-1506. [PMID: 34995537 PMCID: PMC8997186 DOI: 10.1053/j.gastro.2021.12.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
12
Xue MY, Wu JJ, Xie YY, Zhu SL, Zhong YF, Liu JX, Sun HZ. Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing. MICROBIOME 2022;10:11. [PMID: 35057854 PMCID: PMC8772221 DOI: 10.1186/s40168-021-01211-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/07/2021] [Indexed: 05/23/2023]
13
Gul L, Modos D, Fonseca S, Madgwick M, Thomas JP, Sudhakar P, Booth C, Stentz R, Carding SR, Korcsmaros T. Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. J Extracell Vesicles 2022;11:e12189. [PMID: 35064769 PMCID: PMC8783345 DOI: 10.1002/jev2.12189] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 10/04/2021] [Accepted: 12/31/2021] [Indexed: 12/14/2022]  Open
14
Esvap E, Ulgen KO. Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome. ACS Synth Biol 2021;10:2121-2137. [PMID: 34402617 DOI: 10.1021/acssynbio.1c00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
15
Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends Microbiol 2021;29:621-633. [PMID: 33455849 PMCID: PMC8187264 DOI: 10.1016/j.tim.2020.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
16
Noman M, Ahmed T, Ijaz U, Shahid M, Azizullah, Li D, Manzoor I, Song F. Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants. Int J Mol Sci 2021;22:6852. [PMID: 34202205 PMCID: PMC8269294 DOI: 10.3390/ijms22136852] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]  Open
17
Sudhakar P, Machiels K, Verstockt B, Korcsmaros T, Vermeire S. Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. Front Microbiol 2021;12:618856. [PMID: 34046017 PMCID: PMC8148342 DOI: 10.3389/fmicb.2021.618856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/19/2021] [Indexed: 12/11/2022]  Open
18
Türei D, Valdeolivas A, Gul L, Palacio‐Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez‐Rodriguez J. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol Syst Biol 2021;17:e9923. [PMID: 33749993 PMCID: PMC7983032 DOI: 10.15252/msb.20209923] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022]  Open
19
Salvato F, Hettich RL, Kleiner M. Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PLoS Pathog 2021;17:e1009245. [PMID: 33630960 PMCID: PMC7906368 DOI: 10.1371/journal.ppat.1009245] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
20
Treveil A, Bohar B, Sudhakar P, Gul L, Csabai L, Olbei M, Poletti M, Madgwick M, Andrighetti T, Hautefort I, Modos D, Korcsmaros T. ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Comput Biol 2021;17:e1008685. [PMID: 33534793 PMCID: PMC7886129 DOI: 10.1371/journal.pcbi.1008685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/16/2021] [Accepted: 01/10/2021] [Indexed: 12/21/2022]  Open
21
Strand MA, Jin Y, Sandve SR, Pope PB, Hvidsten TR. Transkingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon. Comput Struct Biotechnol J 2021;19:1028-1034. [PMID: 33613868 PMCID: PMC7876536 DOI: 10.1016/j.csbj.2021.01.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 01/15/2023]  Open
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