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(2024, December 05). Omics Biology in Diagnosis of Diseases: Advances in Bioinformatics and Data Analyses. Life, Available online: https:\/\/www.mdpi.com\/journal\/life\/special_issues\/5BE4W6K4N3."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s13167-024-00353-9","article-title":"Promoting advanced medical services in the framework of 3PM\u2014A proof-of-concept by the \u201cCentro\u201d Region of Portugal","volume":"15","author":"Regateiro","year":"2024","journal-title":"EPMA J."},{"key":"ref_3","first-page":"67","article-title":"Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing","volume":"13","author":"Bao","year":"2014","journal-title":"Cancer Inform."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Maroilley, T., and Tarailo-Graovac, M. (2019). Uncovering Missing Heritability in Rare Diseases. Genes, 10.","DOI":"10.3390\/genes10040275"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.jmb.2005.08.020","article-title":"Loss of Protein Structure Stability as a Major Causative Factor in Monogenic Disease","volume":"353","author":"Yue","year":"2005","journal-title":"J. Mol. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Kingdom, R., and Wright, C.F. (2022). Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.920390"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Petersen, B.S., Fredrich, B., Hoeppner, M.P., Ellinghaus, D., and Franke, A. (2017). Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet., 18.","DOI":"10.1186\/s12863-017-0479-5"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.margen.2016.04.012","article-title":"Next-generation biology: Sequencing and data analysis approaches for non-model organisms","volume":"30","author":"Albrechtsen","year":"2016","journal-title":"Mar. Genom."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Athanasopoulou, K., Boti, M.A., Adamopoulos, P.G., Skourou, P.C., and Scorilas, A. (2022). Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life, 12.","DOI":"10.3390\/life12010030"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1002\/humu.24052","article-title":"Hypoparathyroidism, deafness, and renal dysplasia syndrome: 20 Years after the identification of the first GATA3 mutations","volume":"41","author":"Lemos","year":"2020","journal-title":"Hum. Mutat."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1161\/CIRCRESAHA.118.310998","article-title":"Epigenomics: Technologies and Applications","volume":"122","author":"Wang","year":"2018","journal-title":"Circ. Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/s41586-020-2329-2","article-title":"Transcript expression-aware annotation improves rare variant interpretation","volume":"581","author":"Cummings","year":"2020","journal-title":"Nature"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13073-017-0467-4","article-title":"A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications","volume":"9","author":"Haque","year":"2017","journal-title":"Genome Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.molcel.2017.01.023","article-title":"Comparative Analysis of Single-Cell RNA Sequencing Methods","volume":"65","author":"Ziegenhain","year":"2017","journal-title":"Mol. Cell."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Proteomics. Tissue-based map of the human proteome","volume":"347","author":"Uhlen","year":"2015","journal-title":"Science"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1177\/117693430700300004","article-title":"Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution","volume":"3","author":"Antunes","year":"2007","journal-title":"Evol. Bioinform."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Fernandes, M.Z., Caetano, C.F., Gaspar, C., Oliveira, A.S., Palmeira-de-Oliveira, R., Martinez-de-Oliveira, J., Rolo, J., and Palmeira-de-Oliveira, A. (2023). Uncovering the Yeast Diversity in the Female Genital Tract: An Exploration of Spatial Distribution and Antifungal Resistance. Pathogens, 12.","DOI":"10.3390\/pathogens12040595"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s11894-022-00859-0","article-title":"Gut Microbiome and Its Impact on Obesity and Obesity-Related Disorders","volume":"25","author":"Sankararaman","year":"2023","journal-title":"Curr. Gastroenterol. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Caetano, C.F., Gaspar, C., Oliveira, A.S., Palmeira-de-Oliveira, R., Rodrigues, L., Gon\u00e7alves, T., Martinez-de-Oliveira, J., Palmeira-de-Oliveira, A., and Rolo, J. (2023). Study of Ecological Relationship of Yeast Species with Candida albicans in the Context of Vulvovaginal Infections. Microorganisms, 11.","DOI":"10.3390\/microorganisms11102398"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00033-22","DOI":"10.1128\/msystems.00033-22","article-title":"Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas","volume":"7","author":"Kwan","year":"2022","journal-title":"mSystems"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bonif\u00e1cio, M., Mateus, C., Alves, A.R., Maldonado, E., Duarte, A.P., Domingues, F., Oleastro, M., and Ferreira, S. (2021). Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleri. Pathogens, 10.","DOI":"10.3390\/pathogens10070909"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"75","DOI":"10.3103\/S0891416819020022","article-title":"Human Bacterial Microflora Composition: Genotoxic and Carcinogenic Effects Associated with Its Changes in Various Organs","volume":"34","author":"Baranova","year":"2019","journal-title":"Mol. Genet. Microbiol. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.mrrev.2018.04.002","article-title":"Induction and modulation of genotoxicity by the bacteriome in mammals","volume":"776","author":"Druzhinin","year":"2018","journal-title":"Mutat. Res. Rev. Mutat. Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1007\/s11892-018-1057-6","article-title":"Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence?","volume":"18","author":"Sircana","year":"2018","journal-title":"Curr. Diabetes Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1093\/bfgp\/3.1.84","article-title":"Computational resources for metabolomics","volume":"3","author":"Arita","year":"2004","journal-title":"Brief Funct. Genom."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/d41586-024-03276-7","article-title":"\u2018Phenomenal\u2019 tool sequences DNA and tracks proteins\u2014Without cracking cells open","volume":"634","author":"Ledford","year":"2024","journal-title":"Nature"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"487","DOI":"10.4137\/EBO.S11335","article-title":"EASER: Ensembl Easy Sequence Retriever","volume":"9","author":"Maldonado","year":"2013","journal-title":"Evol. Bioinform. Online"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Maldonado, E., Sunagar, K., Almeida, D., Vasconcelos, V., and Antunes, A. (2014). IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0096243"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Maldonado, E., and Antunes, A. (2019). LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinform., 20.","DOI":"10.1186\/s12859-019-3292-5"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/nrg3046","article-title":"Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data","volume":"12","author":"Cooper","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"Zhang","year":"2014","journal-title":"Science"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1101\/gr.103663.109","article-title":"Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution","volume":"20","author":"Skinner","year":"2010","journal-title":"Genome Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"125","DOI":"10.2307\/4444260","article-title":"Nothing in Biology Makes Sense except in the Light of Evolution","volume":"35","author":"Dobzhansky","year":"1973","journal-title":"Am. Biol. Teach."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"20220054","DOI":"10.1360\/nso\/20220054","article-title":"Exploring mysteries of life and their great values in biomedicine through evolutionary genomics","volume":"2","author":"Wang","year":"2023","journal-title":"Natl. Sci. Open"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"121","DOI":"10.4137\/EBO.S597","article-title":"Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology","volume":"4","author":"Levasseur","year":"2008","journal-title":"Evol. Bioinform."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Li, P., Liu, M., and He, W.M. (2024). Integrated Transcriptomic Analysis Reveals Reciprocal Interactions between SARS-CoV-2 Infection and Multi-Organ Dysfunction, Especially the Correlation of Renal Failure and COVID-19. Life, 14.","DOI":"10.3390\/life14080960"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Hasin, Y., Seldin, M., and Lusis, A. (2017). Multi-omics approaches to disease. Genome Biol., 18.","DOI":"10.1186\/s13059-017-1215-1"},{"key":"ref_40","unstructured":"Maldonado, E., and Khan, I. (2024, July 11). Multi-Omics for Diagnosing Diseases: Bioinformatics Approaches and Integrative Data Analyses. Life, Available online: https:\/\/www.mdpi.com\/journal\/life\/special_issues\/15JSWLKS45."},{"key":"ref_41","unstructured":"Maldonado, E., and Khan, I. (2024, July 11). Multi-Omics for Diagnosing Diseases: Bioinformatics Approaches and Integrative Data Analyses. 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