{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T18:47:47Z","timestamp":1785782867447,"version":"3.56.0"},"reference-count":81,"publisher":"Cold Spring Harbor Laboratory","issue":"8","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62531006"],"award-info":[{"award-number":["62531006"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62271173"],"award-info":[{"award-number":["62271173"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82401214"],"award-info":[{"award-number":["82401214"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["124B2027"],"award-info":[{"award-number":["124B2027"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["LH2022H041"],"award-info":[{"award-number":["LH2022H041"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["JQ2023A003"],"award-info":[{"award-number":["JQ2023A003"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017366","name":"Key Research and Development Program of Heilongjiang","doi-asserted-by":"publisher","award":["2022ZX01A19"],"award-info":[{"award-number":["2022ZX01A19"]}],"id":[{"id":"10.13039\/100017366","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science and Technology Program of XPCC","award":["2025AB050"],"award-info":[{"award-number":["2025AB050"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["HIT.DZJJ.2024043"],"award-info":[{"award-number":["HIT.DZJJ.2024043"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"General Postdoctoral Funding Program of Heilongjiang Province","award":["LBH-Z22206"],"award-info":[{"award-number":["LBH-Z22206"]}]},{"name":"Science and Technology Innovation Talent Program for Advanced Manufacturing of Harbin City","award":["CXRC20231117155"],"award-info":[{"award-number":["CXRC20231117155"]}]},{"name":"State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology","award":["MSWJ-24M15"],"award-info":[{"award-number":["MSWJ-24M15"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,6,9]]},"published-print":{"date-parts":[[2026,8]]},"abstract":"<jats:p>Single-cell multiomic technology makes it possible to profile both the transcriptome and epigenome within individual cells. The detection of rare cell states from such data is crucial for exploring novel disease biomarkers with clinical potential. However, existing methods typically focus on the gene and peak counts while ignoring the underlying genomic sequence at accessible sites. Here, we propose ComicGTN, an innovative computational framework that integrates single-cell multiomic data with DNA sequence information via enhanced graph transformer networks to accurately identify rare cell clusters. ComicGTN consistently outperforms nine state-of-the-art methods in identifying rare cells across multiple complex scenarios. In mouse breast cancer data, ComicGTN detects several functionally distinct immune subpopulations. In cerebral cortex of epilepsy patients, it uncovers oligodendrocytes undergoing particular differentiation states. For polycystic kidney disease patient\u2013derived organoids, ComicGTN elaborates pathological pathways in a captured rare glomerular subgroup. Overall, ComicGTN accelerates the localization of disease-associated rare cell populations, facilitating the derivation of clinical insights in development and disease progression.<\/jats:p>","DOI":"10.1101\/gr.281661.125","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T16:40:18Z","timestamp":1784306418000},"page":"1652-1667","source":"Crossref","is-referenced-by-count":0,"title":["ComicGTN infers disease-associated rare cell states from single-cell multiomic data using DNA sequence\u2013augmented graph transformer networks"],"prefix":"10.1101","volume":"36","author":[{"given":"Boran","family":"Yang","sequence":"first","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiao","family":"Hua","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guanghua","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhui","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Qi","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiyuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danshu","family":"Sheng","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuilin","family":"Jin","sequence":"additional","affiliation":[{"name":"School of Mathematics, Harbin Institute of Technology, Harbin 150000, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"key":"2026080311251241000_36.8.1652.1","doi-asserted-by":"publisher","DOI":"10.2337\/db15-1413"},{"key":"2026080311251241000_36.8.1652.2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad7969"},{"key":"2026080311251241000_36.8.1652.3","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2688"},{"key":"2026080311251241000_36.8.1652.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau0730"},{"key":"2026080311251241000_36.8.1652.5","doi-asserted-by":"publisher","DOI":"10.1002\/cne.24206"},{"key":"2026080311251241000_36.8.1652.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1710964114"},{"key":"2026080311251241000_36.8.1652.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature12305"},{"key":"2026080311251241000_36.8.1652.8","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80093-8"},{"key":"2026080311251241000_36.8.1652.9","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02998-7"},{"key":"2026080311251241000_36.8.1652.10","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23010262"},{"key":"2026080311251241000_36.8.1652.11","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-020-3482-1"},{"key":"2026080311251241000_36.8.1652.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24489-8"},{"key":"2026080311251241000_36.8.1652.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-026-71180-x"},{"key":"2026080311251241000_36.8.1652.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21583-9"},{"key":"2026080311251241000_36.8.1652.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2022.09.015"},{"key":"2026080311251241000_36.8.1652.16","doi-asserted-by":"publisher","DOI":"10.1111\/epi.18413"},{"key":"2026080311251241000_36.8.1652.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-29530-0"},{"key":"2026080311251241000_36.8.1652.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0367-1"},{"key":"2026080311251241000_36.8.1652.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01938-4"},{"key":"2026080311251241000_36.8.1652.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0332-7"},{"key":"2026080311251241000_36.8.1652.21","doi-asserted-by":"publisher","DOI":"10.1038\/nature14966"},{"key":"2026080311251241000_36.8.1652.22","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.cellbio.20.010403.095114"},{"key":"2026080311251241000_36.8.1652.23","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4662"},{"key":"2026080311251241000_36.8.1652.24","doi-asserted-by":"publisher","DOI":"10.1186\/s40364-024-00705-7"},{"key":"2026080311251241000_36.8.1652.25","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202304360"},{"key":"2026080311251241000_36.8.1652.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01187-9"},{"key":"2026080311251241000_36.8.1652.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0903-2"},{"key":"2026080311251241000_36.8.1652.28","doi-asserted-by":"publisher","DOI":"10.1152\/ajprenal.00173.2005"},{"key":"2026080311251241000_36.8.1652.29","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.92.10.4392"},{"key":"2026080311251241000_36.8.1652.30","doi-asserted-by":"publisher","DOI":"10.7150\/thno.29617"},{"key":"2026080311251241000_36.8.1652.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9"},{"key":"2026080311251241000_36.8.1652.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07234-6"},{"key":"2026080311251241000_36.8.1652.33","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05688-9"},{"key":"2026080311251241000_36.8.1652.34","doi-asserted-by":"publisher","DOI":"10.1038\/nrd4100"},{"key":"2026080311251241000_36.8.1652.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.04.005"},{"key":"2026080311251241000_36.8.1652.36","doi-asserted-by":"publisher","DOI":"10.1038\/s41583-023-00711-y"},{"key":"2026080311251241000_36.8.1652.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.04.050"},{"key":"2026080311251241000_36.8.1652.38","doi-asserted-by":"publisher","DOI":"10.3390\/cells12010045"},{"key":"2026080311251241000_36.8.1652.39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2311854121"},{"key":"2026080311251241000_36.8.1652.40","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35031-9"},{"key":"2026080311251241000_36.8.1652.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2023.12.003"},{"key":"2026080311251241000_36.8.1652.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.056"},{"key":"2026080311251241000_36.8.1652.43","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-63921-1"},{"key":"2026080311251241000_36.8.1652.44","doi-asserted-by":"publisher","DOI":"10.7150\/thno.81847"},{"key":"2026080311251241000_36.8.1652.45","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2009121244"},{"key":"2026080311251241000_36.8.1652.46","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3392"},{"key":"2026080311251241000_36.8.1652.47","doi-asserted-by":"publisher","DOI":"10.1038\/nri.2017.49"},{"key":"2026080311251241000_36.8.1652.48","doi-asserted-by":"publisher","DOI":"10.3390\/ijms252111340"},{"key":"2026080311251241000_36.8.1652.49","doi-asserted-by":"publisher","DOI":"10.1038\/nm1731"},{"key":"2026080311251241000_36.8.1652.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29366-6"},{"key":"2026080311251241000_36.8.1652.51","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-024-01883-0"},{"key":"2026080311251241000_36.8.1652.52","doi-asserted-by":"publisher","DOI":"10.1038\/nrneph.2012.291"},{"key":"2026080311251241000_36.8.1652.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2022.03.008"},{"key":"2026080311251241000_36.8.1652.54","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4401"},{"key":"2026080311251241000_36.8.1652.55","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0748-5"},{"key":"2026080311251241000_36.8.1652.56","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02313-2"},{"key":"2026080311251241000_36.8.1652.57","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1207238109"},{"key":"2026080311251241000_36.8.1652.58","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03347-y"},{"key":"2026080311251241000_36.8.1652.59","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan8546"},{"key":"2026080311251241000_36.8.1652.60","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2017.149"},{"key":"2026080311251241000_36.8.1652.61","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02274-x"},{"key":"2026080311251241000_36.8.1652.62","doi-asserted-by":"publisher","DOI":"10.1038\/nature11232"},{"key":"2026080311251241000_36.8.1652.63","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2922-4"},{"key":"2026080311251241000_36.8.1652.64","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-59529-0"},{"key":"2026080311251241000_36.8.1652.65","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.07.039"},{"key":"2026080311251241000_36.8.1652.66","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004371"},{"key":"2026080311251241000_36.8.1652.67","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2008.17.1462"},{"key":"2026080311251241000_36.8.1652.68","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2018.05.013"},{"key":"2026080311251241000_36.8.1652.69","doi-asserted-by":"publisher","DOI":"10.1126\/science.aah4573"},{"key":"2026080311251241000_36.8.1652.70","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-024-02073-2"},{"key":"2026080311251241000_36.8.1652.71","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44570-8"},{"key":"2026080311251241000_36.8.1652.72","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1739-7"},{"key":"2026080311251241000_36.8.1652.73","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1332808100"},{"key":"2026080311251241000_36.8.1652.74","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2018.10.010"},{"key":"2026080311251241000_36.8.1652.75","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-61337-5"},{"key":"2026080311251241000_36.8.1652.76","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51891-9"},{"key":"2026080311251241000_36.8.1652.77","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202309885"},{"key":"2026080311251241000_36.8.1652.78","doi-asserted-by":"publisher","DOI":"10.1109\/ICDM65498.2025.00179"},{"key":"2026080311251241000_36.8.1652.79","doi-asserted-by":"publisher","DOI":"10.1038\/s43588-024-00622-7"},{"key":"2026080311251241000_36.8.1652.80","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01060-3"},{"key":"2026080311251241000_36.8.1652.81","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1117374108"}],"container-title":["Genome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/gr.281661.125","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T18:25:20Z","timestamp":1785781520000},"score":1,"resource":{"primary":{"URL":"http:\/\/genome.cshlp.org\/lookup\/doi\/10.1101\/gr.281661.125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,17]]},"references-count":81,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,3]]},"published-print":{"date-parts":[[2026,8]]}},"alternative-id":["10.1101\/gr.281661.125"],"URL":"https:\/\/doi.org\/10.1101\/gr.281661.125","relation":{},"ISSN":["1088-9051","1549-5469"],"issn-type":[{"value":"1088-9051","type":"print"},{"value":"1549-5469","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,17]]}}}