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For: Bravo-Merodio L, Williams JA, Gkoutos GV, Acharjee A. -Omics biomarker identification pipeline for translational medicine. J Transl Med 2019;17:155. [PMID: 31088492 PMCID: PMC6518609 DOI: 10.1186/s12967-019-1912-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/08/2019] [Indexed: 01/31/2023]  Open
Number Cited by Other Article(s)
1
Hernández-Lemus E, Ochoa S. Methods for multi-omic data integration in cancer research. Front Genet 2024;15:1425456. [PMID: 39364009 PMCID: PMC11446849 DOI: 10.3389/fgene.2024.1425456] [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: 04/29/2024] [Accepted: 08/28/2024] [Indexed: 10/05/2024]  Open
2
Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024;74:108400. [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
3
Onwuka S, Bravo-Merodio L, Gkoutos GV, Acharjee A. Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations. iScience 2024;27:110298. [PMID: 39040076 PMCID: PMC11261406 DOI: 10.1016/j.isci.2024.110298] [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: 02/12/2024] [Revised: 04/29/2024] [Accepted: 06/14/2024] [Indexed: 07/24/2024]  Open
4
Kleftogiannis D, Gavasso S, Tislevoll BS, van der Meer N, Motzfeldt IK, Hellesøy M, Gullaksen SE, Griessinger E, Fagerholt O, Lenartova A, Fløisand Y, Schuringa JJ, Gjertsen BT, Jonassen I. Automated cell type annotation and exploration of single-cell signaling dynamics using mass cytometry. iScience 2024;27:110261. [PMID: 39021803 PMCID: PMC11253510 DOI: 10.1016/j.isci.2024.110261] [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: 10/16/2023] [Revised: 04/20/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]  Open
5
Alqahtani T, Deore SL, Kide AA, Shende BA, Sharma R, Chakole RD, Nemade LS, Kale NK, Borah S, Deokar SS, Behera A, Dhawal Bhandari D, Gaikwad N, Azad AK, Ghosh A. Mitochondrial dysfunction and oxidative stress in Alzheimer's disease, and Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis -An updated review. Mitochondrion 2023:S1567-7249(23)00051-X. [PMID: 37269968 DOI: 10.1016/j.mito.2023.05.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
6
Al-Tashi Q, Saad MB, Muneer A, Qureshi R, Mirjalili S, Sheshadri A, Le X, Vokes NI, Zhang J, Wu J. Machine Learning Models for the Identification of Prognostic and Predictive Cancer Biomarkers: A Systematic Review. Int J Mol Sci 2023;24:7781. [PMID: 37175487 PMCID: PMC10178491 DOI: 10.3390/ijms24097781] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]  Open
7
Bosch S, Acharjee A, Quraishi MN, Bijnsdorp IV, Rojas P, Bakkali A, Jansen EEW, Stokkers P, Kuijvenhoven J, Pham TV, Beggs AD, Jimenez CR, Struys EA, Gkoutos GV, de Meij TGJ, de Boer NKH. Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer. Gut Microbes 2022;14:2139979. [PMID: 36369736 PMCID: PMC9662191 DOI: 10.1080/19490976.2022.2139979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
8
Zhou M, Bian K, Hu F, Lai W. A New Strategy for Identification of Coal Miners With Abnormal Physical Signs Based on EN-mRMR. Front Bioeng Biotechnol 2022;10:935481. [PMID: 35898648 PMCID: PMC9310099 DOI: 10.3389/fbioe.2022.935481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022]  Open
9
Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EEW, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TGJ, de Boer NKH. The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma. Gut Microbes 2022;14:2038863. [PMID: 35188868 PMCID: PMC8865277 DOI: 10.1080/19490976.2022.2038863] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
10
Verissimo T, Faivre A, Sgardello S, Naesens M, de Seigneux S, Criton G, Legouis D. Estimated Renal Metabolomics at Reperfusion Predicts One-Year Kidney Graft Function. Metabolites 2022;12:57. [PMID: 35050179 PMCID: PMC8778290 DOI: 10.3390/metabo12010057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023]  Open
11
Gautam Y, Johansson E, Mersha TB. Multi-Omics Profiling Approach to Asthma: An Evolving Paradigm. J Pers Med 2022;12:jpm12010066. [PMID: 35055381 PMCID: PMC8778153 DOI: 10.3390/jpm12010066] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023]  Open
12
Smith BJ, Silva-Costa LC, Martins-de-Souza D. Human disease biomarker panels through systems biology. Biophys Rev 2021;13:1179-1190. [PMID: 35059036 PMCID: PMC8724340 DOI: 10.1007/s12551-021-00849-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022]  Open
13
De San-Martin BS, Ferreira VG, Bitencourt MR, Pereira PCG, Carrilho E, de Assunção NA, de Carvalho LRS. Metabolomics as a potential tool for the diagnosis of growth hormone deficiency (GHD): a review. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2021;64:654-663. [PMID: 33085993 PMCID: PMC10528619 DOI: 10.20945/2359-3997000000300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/25/2020] [Indexed: 11/23/2022]
14
Monaghan TM, Biswas RN, Nashine RR, Joshi SS, Mullish BH, Seekatz AM, Blanco JM, McDonald JAK, Marchesi JR, Yau TO, Christodoulou N, Hatziapostolou M, Pucic-Bakovic M, Vuckovic F, Klicek F, Lauc G, Xue N, Dottorini T, Ambalkar S, Satav A, Polytarchou C, Acharjee A, Kashyap RS. Multiomics Profiling Reveals Signatures of Dysmetabolism in Urban Populations in Central India. Microorganisms 2021;9:1485. [PMID: 34361920 PMCID: PMC8307859 DOI: 10.3390/microorganisms9071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]  Open
15
Hartl D, de Luca V, Kostikova A, Laramie J, Kennedy S, Ferrero E, Siegel R, Fink M, Ahmed S, Millholland J, Schuhmacher A, Hinder M, Piali L, Roth A. Translational precision medicine: an industry perspective. J Transl Med 2021;19:245. [PMID: 34090480 PMCID: PMC8179706 DOI: 10.1186/s12967-021-02910-6] [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: 02/02/2021] [Accepted: 05/25/2021] [Indexed: 02/08/2023]  Open
16
Koch M, Acharjee A, Ament Z, Schleicher R, Bevers M, Stapleton C, Patel A, Kimberly WT. Machine Learning-Driven Metabolomic Evaluation of Cerebrospinal Fluid: Insights Into Poor Outcomes After Aneurysmal Subarachnoid Hemorrhage. Neurosurgery 2021;88:1003-1011. [PMID: 33469656 PMCID: PMC8046589 DOI: 10.1093/neuros/nyaa557] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/04/2020] [Indexed: 11/14/2022]  Open
17
UPLC-Q-TOF/MS-based plasma metabolome to identify biomarkers and time of injury in traumatic brain injured rats. Neuroreport 2021;32:415-422. [PMID: 33788810 DOI: 10.1097/wnr.0000000000001576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
18
Krokidis MG, Exarchos TP, Vlamos P. Data-driven biomarker analysis using computational omics approaches to assess neurodegenerative disease progression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021;18:1813-1832. [PMID: 33757212 DOI: 10.3934/mbe.2021094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
19
Investigation of Genetic Variations of IL6 and IL6R as Potential Prognostic and Pharmacogenetics Biomarkers: Implications for COVID-19 and Neuroinflammatory Disorders. Life (Basel) 2020;10:life10120351. [PMID: 33339153 PMCID: PMC7765585 DOI: 10.3390/life10120351] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022]  Open
20
Stapleton CJ, Acharjee A, Irvine HJ, Wolcott ZC, Patel AB, Kimberly WT. High-throughput metabolite profiling: identification of plasma taurine as a potential biomarker of functional outcome after aneurysmal subarachnoid hemorrhage. J Neurosurg 2020;133:1842-1849. [PMID: 31756713 DOI: 10.3171/2019.9.jns191346] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/11/2019] [Indexed: 01/28/2023]
21
Acharjee A, Larkman J, Xu Y, Cardoso VR, Gkoutos GV. A random forest based biomarker discovery and power analysis framework for diagnostics research. BMC Med Genomics 2020;13:178. [PMID: 33228632 PMCID: PMC7685541 DOI: 10.1186/s12920-020-00826-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 11/15/2020] [Indexed: 11/25/2022]  Open
22
Aziz F, Acharjee A, Williams JA, Russ D, Bravo-Merodio L, Gkoutos GV. Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference. Int J Mol Sci 2020;21:E7886. [PMID: 33114263 PMCID: PMC7660606 DOI: 10.3390/ijms21217886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]  Open
23
Translational biomarkers in the era of precision medicine. Adv Clin Chem 2020;102:191-232. [PMID: 34044910 DOI: 10.1016/bs.acc.2020.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
24
Xiong XF, Chen DD, Zhu HJ, Ge WH. Prognostic value of endogenous and exogenous metabolites in liver transplantation. Biomark Med 2020;14:1165-1181. [PMID: 32969246 DOI: 10.2217/bmm-2020-0073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
25
Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes. Front Oncol 2020;10:845. [PMID: 32528899 PMCID: PMC7259379 DOI: 10.3389/fonc.2020.00845] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022]  Open
26
Machine learning for the detection of early immunological markers as predictors of multi-organ dysfunction. Sci Data 2019;6:328. [PMID: 31857590 PMCID: PMC6923383 DOI: 10.1038/s41597-019-0337-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]  Open
27
Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019;10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022]  Open
28
Loo JFC, Ho HP, Kong SK, Wang TH, Ho YP. Technological Advances in Multiscale Analysis of Single Cells in Biomedicine. ACTA ACUST UNITED AC 2019;3:e1900138. [PMID: 32648696 DOI: 10.1002/adbi.201900138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/25/2019] [Indexed: 12/20/2022]
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