Accessibility and statistics
- Conesa A, Beck S. Making multi-omics data accessible to researchers. Sci Data. 2019 Oct 31;6(1):251. doi: 10.1038/s41597-019-0258-4. PMID: 31672978
- Wilkinson MD, ET AL The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18. Erratum in: Sci Data. 2019 Mar 19;6(1):6. PMID: 26978244
Statistical significance
- Timmons JA, Szkop KJ, Gallagher IJ. Multiple sources of bias confound functional enrichment analysis of global -omics data. Genome Biol. 2015 Sep 7;16:186. doi: 10.1186/s13059-015-0761-7. PMID: 26346307
Pathway mapping and data integration
- Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R. A Comparison of Microbial Genome Web Portals. Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019. Review. PMID: 30853946
- Hofmann JD, Otto A, Berges M, Biedendieck R, Michel AM, Becher D, Jahn D, Neumann-Schaal M. Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production. Front Microbiol. 2018 Aug 21;9:1970. doi: 10.3389/fmicb.2018.01970. eCollection 2018. PMID: 30186274
- Reimand J, Isserlin R, Voisin V, et al. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols. 2019 Feb;14(2):482-517. DOI: 10.1038/s41596-018-0103-9.
Regulatory networks
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Rodionov DA. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev. 2007 Aug;107(8):3467-97. Epub 2007 Jul 18. Review. PMID: 17636889.
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Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res. 2021 Jan 8;49(D1):D112-D120. doi: 10.1093/nar/gkaa810. PMID: 33045728; PMCID: PMC7778901.
MultiOmics data integration
- Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics Data Integration, Interpretation, and Its Application. Bioinform Biol Insights. 2020 Jan 31;14:1177932219899051 (For Human mainly) . PMID: 32076369.
- Wörheide MA, Krumsiek J, Kastenmüller G, Arnold M. Multi-omics integration in biomedical research - A metabolomics-centric review. Anal Chim Acta. 2021 Jan 2;1141:144-162. PMCID: PMC7701361
- Krassowski M, Das V, Sahu SK, Misra BB. State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. Front Genet. 2020 Dec 10;11:610798. doi: 10.3389/fgene.2020.610798.PMID: 33362867