{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:51:24Z","timestamp":1791363084701,"version":"4.3.1"},"reference-count":174,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T00:00:00Z","timestamp":1768262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Carol Davila University of Medicine and Pharmacy, Genomics Research and Development Institute, Ministry of Investment and European Projects","award":["PS\/272\/PS_P5\/OP1\/RSO1.1\/PS_P5_RSO1.1_A9-ROGEN Project (MySMIS 324809)"],"award-info":[{"award-number":["PS\/272\/PS_P5\/OP1\/RSO1.1\/PS_P5_RSO1.1_A9-ROGEN Project (MySMIS 324809)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Omics research is changing the way medicine develops new strategies for diagnosis, prevention, and treatment. With the surge of advanced machine learning models tailored for omicss analysis, recent research has shown improved results and pushed the progress towards personalized medicine. The dissection of multiple layers of genetic information has provided new insights into precision medicine, at the same time raising issues related to data abundance. Studies focusing on single-cell scale have upgraded the knowledge about gene expression, revealing the heterogeneity that governs the functioning of multicellular organisms. The amount of information gathered through such sequencing techniques often exceeds the human capacity for analysis. Understanding the underlying network of gene expression regulation requires advanced computational tools that can deal with the complex analytical data provided. The recent emergence of artificial intelligence-based frameworks, together with advances in quantum algorithms, has the potential to enhance multiomicsc analyses, increasing the efficiency and reliability of the gene expression profile prediction. The development of more accurate computational models will significantly reduce the error rates in interpreting large datasets. By making analytical workflows faster and more precise, these innovations make it easier to integrate and interrogate multi-omics data at scale. Deep learning (DL) networks perform well in terms of recognizing complex patterns and modeling non-linear relationships that enable the inference of gene expression profiles. Applications range from direct prediction of DNA sequence-informed predictive modeling to transcriptomic and epigenetic analysis. Quantum computing, particularly through quantum machine learning methods, is being explored as a complementary approach for predictive modeling, with potential applications to complex gene interactions in increasingly large and high-dimensional biological datasets. Together, these tools are reshaping the study of complex biological data, while ongoing innovation in this field is driving progress towards personalized medicine. Overall, the combination of high-resolution omics and advanced computational tools marks an important shift toward more precise and data-driven clinical decision-making.<\/jats:p>","DOI":"10.3390\/ijms27020801","type":"journal-article","created":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T18:40:09Z","timestamp":1768329609000},"page":"801","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["AI-Based Prediction of Gene Expression in Single-Cell and Multiscale Genomics and Transcriptomics"],"prefix":"10.3390","volume":"27","author":[{"given":"Ema Andreea","family":"P\u0103l\u0103\u0219tea","sequence":"first","affiliation":[{"name":"Genomics Research and Development Institute, Bucharest 030167, Romania"},{"name":"Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 030167, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7870-4791","authenticated-orcid":false,"given":"Irina-Mihaela","family":"Matache","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 030167, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5642-9979","authenticated-orcid":false,"given":"Eugen","family":"Radu","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 030167, Romania"},{"name":"Emergency University Hospital, Bucharest 050098, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8971-1049","authenticated-orcid":false,"given":"Octavian","family":"Henegariu","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06520, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Octavian","family":"Bucur","sequence":"additional","affiliation":[{"name":"Genomics Research and Development Institute, Bucharest 030167, Romania"},{"name":"Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 030167, Romania"},{"name":"Viron Molecular Medicine Institute, Boston, MA 02108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e694","DOI":"10.1002\/ctm2.694","article-title":"Single-cell RNA Sequencing Technologies and Applications: A Brief Overview","volume":"12","author":"Jovic","year":"2022","journal-title":"Clin. 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