{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T02:42:07Z","timestamp":1791859327569,"version":"4.3.4"},"reference-count":65,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["BioEssays"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Artificial intelligence (AI) strategies are revolutionizing genomics by extracting complex patterns that traditional statistical pipelines are likely to miss. This mini\u2010review aims to provide a concise overview of how AI is transforming major genomic technologies including variant calling, gene expression analysis, single\u2010cell transcriptomics, CRISPR\u2010Cas9 optimization, and multi\u2010omics integration. In genome sequencing, machine learning variant callers greatly improve the accuracy and the rate at which single nucleotide and structural variants are called. In bulk RNA\u2010Seq, AI augmented quantification, denoising, and differential expression modules complement the highly established STAR\u2010featureCounts\u2010DESeq2 pipeline, revealing subtle signals in big data sets. In single cell transcriptomics, deep learning approaches enhance batch correction, automate cell type annotation, and track developmental trajectories, hence clarifying cellular heterogeneity. AI\u2010assisted guide RNA design, outcome prediction, and nuclease engineering enable more efficient CRISPR\u2010Cas9 editing, reducing experimental cycles, and off\u2010target effects. Finally, integrated platforms that combine genomic, transcriptomic, epigenomic, proteomic, and metabolomic layers provide an integrative view of cellular regulation and disease mechanisms. The review also covers current limitations, sparsity of data, model bias, privacy, and the need for standardized benchmarks and offers future directions in the form of interpretable models, collaborative learning, and open science practices. Together, these developments render AI an indispensable partner to unravel genomic complexity and accelerate precision medicine applications.<\/jats:p>","DOI":"10.1002\/bies.70160","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T07:06:53Z","timestamp":1782976013000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["AI in Genomics: From Variant Calling to Multi\u2010Omics Integration"],"prefix":"10.1002","volume":"48","author":[{"given":"Hina","family":"Sultana","sequence":"first","affiliation":[{"name":"Integrative Program in Biological and Genome Sciences University of North Carolina at Chapel Hill  Chapel Hill North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabyasachi","family":"Mohanty","sequence":"additional","affiliation":[{"name":"University of Nebraska\u2010Lincoln College of Engineering  Lincoln Nebraska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abhishikt David","family":"Solomon","sequence":"additional","affiliation":[{"name":"Division of Oral and Craniofacial Health Sciences Adams School of Dentistry University of North Carolina at Chapel Hill  Chapel Hill North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad Yamaan","family":"Iqbal","sequence":"additional","affiliation":[{"name":"East Chapel Hill High School  Chapel Hill North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atif Khurshid","family":"Wani","sequence":"additional","affiliation":[{"name":"Division of Veterinary Biochemistry Faculty of Veterinary Sciences and Animal Husbandry Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST\u2010K) Srinagar Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinay","family":"Kumar","sequence":"additional","affiliation":[{"name":"College of Medicine Hershey Medical Center Pennsylvania State University  Hershey Pennsylvania USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun","family":"Khattri","sequence":"additional","affiliation":[{"name":"Centre for Life Sciences Mahindra University  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"e_1_2_14_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddy115"},{"key":"e_1_2_14_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010018\u20100295\u20105"},{"key":"e_1_2_14_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073\u2010019\u20100689\u20108"},{"key":"e_1_2_14_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4235"},{"key":"e_1_2_14_6_1","doi-asserted-by":"publisher","DOI":"10.1101\/2022.05.20.492556"},{"key":"e_1_2_14_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/biom10010062"},{"key":"e_1_2_14_8_1","doi-asserted-by":"publisher","DOI":"10.3390\/biom12081133"},{"key":"e_1_2_14_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac191"},{"key":"e_1_2_14_10_1","doi-asserted-by":"publisher","DOI":"10.1259\/bjr.20230211"},{"key":"e_1_2_14_11_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_2_14_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_14_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_14_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100129"},{"key":"e_1_2_14_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_2_14_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"e_1_2_14_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010014\u20100550\u20108"},{"key":"e_1_2_14_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010015\u20102353\u2010z"},{"key":"e_1_2_14_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4197"},{"key":"e_1_2_14_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"},{"key":"e_1_2_14_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty1017"},{"key":"e_1_2_14_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010022\u201013665\u20105"},{"key":"e_1_2_14_23_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006076"},{"key":"e_1_2_14_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12874\u2010018\u20100482\u20101"},{"key":"e_1_2_14_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010025\u201010014\u20100"},{"key":"e_1_2_14_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt703"},{"key":"e_1_2_14_27_1","unstructured":"Partek.PartekTM FlowTM [Computer software](2024) https:\/\/www.illumina.com\/products\/by\u2010type\/informatics\u2010products\/partek\u2010flow.html."},{"key":"e_1_2_14_28_1","unstructured":"Illumina. 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