{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:03:07Z","timestamp":1792785787064,"version":"4.5.0"},"reference-count":77,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:00:00Z","timestamp":1791417600000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Science, Technology and Innovation Commission of Shenzhen Municipality grant","award":["JCYJ20170412152854656"],"award-info":[{"award-number":["JCYJ20170412152854656"]}]},{"name":"National Natural Science Foundation of China grant","award":["U23A20402"],"award-info":[{"award-number":["U23A20402"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Natural Science Foundation of China grant","award":["62207002"],"award-info":[{"award-number":["62207002"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Resolving cell-type contributions in cell-free RNA (cfRNA) profiles is important for liquid-biopsy research, but profiling many potential cellular sources remains computationally challenging. Here, we present Deconformer, a biologically informed deep-learning framework that integrates pathway knowledge into a Transformer architecture to estimate relative cfRNA contributions across 60 major human cell types. In systematic benchmarks using cross-platform simulations selected for similarity to real plasma cfRNA, Deconformer showed improved robustness from pathway-informed modeling and achieved competitive accuracy with substantially lower computational cost than established deconvolution methods. Applied to real cfRNA cohorts, it recapitulated known gestational trajectories and detected disease-associated composition shifts, supporting its use as a practical framework for large-scale cfRNA profiling.<\/jats:p>","DOI":"10.1093\/bib\/bbag544","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T19:24:32Z","timestamp":1789673072000},"source":"Crossref","is-referenced-by-count":0,"title":["Deconformer: efficient cell-type composition profiling of cfRNA across diverse cell types"],"prefix":"10.1093","volume":"27","author":[{"given":"Chaoxing","family":"Wang","sequence":"first","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuetao","family":"Tian","sequence":"additional","affiliation":[{"name":"Faculty of Psychology, Beijing Normal University , Xinjiekouwai Street, Haidian District, Beijing 100875, Beijing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Yan","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinghua","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sujun","family":"Zhu","sequence":"additional","affiliation":[{"name":"Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital , Hongli Road, Futian District, Shenzhen 518028, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chu","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]},{"name":"College of Life Science, Northeast Forestry University , Hexing Road, Xiangfang District, Harbin 150040, Heilongjiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingyu","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulong","family":"Qin","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongzhen","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Zeng","sequence":"additional","affiliation":[{"name":"Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital , Hongli Road, Futian District, Shenzhen 518028, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyue","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University , Weijin Road, Nankai District, Tianjin 300071, Tianjin ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Yuquan Road, Shijingshan District, Beijing 100049, Beijing ,","place":["China"]},{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengbin","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7554-4975","authenticated-orcid":false,"given":"Xin","family":"Jin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]},{"name":"Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4527-1168","authenticated-orcid":false,"given":"Wen-Jing","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Yunhua Road, Yantian District, Shenzhen 518083, Guangdong ,","place":["China"]},{"name":"College of Life Science, Northeast Forestry University , Hexing Road, Xiangfang District, Harbin 150040, Heilongjiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,8]]},"reference":[{"key":"2026100808260580500_ref1","doi-asserted-by":"publisher","first-page":"7361","DOI":"10.1073\/pnas.1405528111","article-title":"Noninvasive in vivo monitoring of tissue-specific global gene expression in humans","volume":"111","author":"Koh","year":"2014","journal-title":"Proc Natl Acad Sci"},{"key":"2026100808260580500_ref2","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1126\/science.aar3819","article-title":"Noninvasive blood tests for fetal development predict gestational age and preterm delivery","volume":"360","author":"Ngo","year":"2018","journal-title":"Science"},{"key":"2026100808260580500_ref3","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1038\/s41467-019-14253-4","article-title":"Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing","volume":"11","author":"Ibarra","year":"2020","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref4","doi-asserted-by":"publisher","first-page":"eabb1654","DOI":"10.1126\/sciadv.abb1654","article-title":"Noninvasive characterization of Alzheimer\u2019s disease by circulating, cell-free messenger RNA next-generation sequencing","volume":"6","author":"Toden","year":"2020","journal-title":"Sci Adv"},{"key":"2026100808260580500_ref5","doi-asserted-by":"publisher","first-page":"2357","DOI":"10.1038\/s41467-021-22444-1","article-title":"A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection","volume":"12","author":"Larson","year":"2021","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref6","doi-asserted-by":"publisher","first-page":"108552","DOI":"10.1016\/j.celrep.2020.108552","article-title":"Charting extracellular transcriptomes in the human biofluid RNA atlas","volume":"33","author":"Hulstaert","year":"2020","journal-title":"Cell Rep"},{"key":"2026100808260580500_ref7","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1038\/s41587-021-01188-9","article-title":"Cell types of origin of the cell-free transcriptome","volume":"40","author":"Vorperian","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026100808260580500_ref8","doi-asserted-by":"publisher","first-page":"eabl4896","DOI":"10.1126\/science.abl4896","article-title":"The tabula sapiens: a multiple-organ, single-cell transcriptomic atlas of humans","volume":"376","author":"Tabula Sapiens Consortium*","year":"2022","journal-title":"Science"},{"key":"2026100808260580500_ref9","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1038\/s41586-022-04410-z","article-title":"Early prediction of preeclampsia in pregnancy with cell-free RNA","volume":"602","author":"Moufarrej","year":"2022","journal-title":"Nature"},{"key":"2026100808260580500_ref10","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1038\/s41586-021-04249-w","article-title":"RNA profiles reveal signatures of future health and disease in pregnancy","volume":"601","author":"Rasmussen","year":"2022","journal-title":"Nature"},{"key":"2026100808260580500_ref11","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","article-title":"Determining cell type abundance and expression from bulk tissues with digital cytometry","volume":"37","author":"Newman","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026100808260580500_ref12","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1038\/s41467-018-08023-x","article-title":"Bulk tissue cell type deconvolution with multi-subject single-cell expression reference","volume":"10","author":"Wang","year":"2019","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref13","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s43018-022-00356-3","article-title":"Cell type and gene expression deconvolution with BayesPrism enables bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology","volume":"3","author":"Chu","year":"2022","journal-title":"Nat Cancer"},{"key":"2026100808260580500_ref14","doi-asserted-by":"publisher","first-page":"bbaa317","DOI":"10.1093\/bib\/bbaa317","article-title":"Unveiling the immune infiltrate modulation in cancer and response to immunotherapy by MIXTURE\u2014an enhanced deconvolution method","volume":"22","author":"Fern\u00e1ndez","year":"2021","journal-title":"Brief Bioinform"},{"key":"2026100808260580500_ref15","doi-asserted-by":"publisher","first-page":"eaba2619","DOI":"10.1126\/sciadv.aba2619","article-title":"Deep learning\u2013based cell composition analysis from tissue expression profiles","volume":"6","author":"Menden","year":"2020","journal-title":"Sci Adv"},{"key":"2026100808260580500_ref16","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1038\/s41467-023-36961-8","article-title":"Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve","volume":"14","author":"Charytonowicz","year":"2023","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref17","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1038\/s41587-023-01905-6","article-title":"Predicting transcriptional outcomes of novel multigene perturbations with GEARS","volume":"42","author":"Roohani","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026100808260580500_ref18","doi-asserted-by":"publisher","first-page":"4761","DOI":"10.1093\/nar\/gkae267","article-title":"Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges","volume":"52","author":"Nguyen","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100808260580500_ref19","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1186\/s13059-024-03292-w","article-title":"Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods","volume":"25","author":"Hu","year":"2024","journal-title":"Genome Biol"},{"key":"2026100808260580500_ref20","doi-asserted-by":"publisher","first-page":"255","DOI":"10.2307\/2532051","article-title":"A concordance correlation coefficient to evaluate reproducibility","volume":"45","author":"Lin","year":"1989","journal-title":"Biometrics"},{"key":"2026100808260580500_ref21","article-title":"BERT: pre-training of deep bidirectional transformers for language understanding","author":"Devlin","year":"2019","journal-title":"Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)"},{"key":"2026100808260580500_ref22","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1038\/s41592-024-02201-0","article-title":"scGPT: toward building a foundation model for single-cell multi-omics using generative AI","volume":"21","author":"Cui","year":"2024","journal-title":"Nat Methods"},{"key":"2026100808260580500_ref23","doi-asserted-by":"publisher","first-page":"4117","DOI":"10.1038\/s41467-021-24360-w","article-title":"Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity","volume":"12","author":"Vanderbeke","year":"2021","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref24","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1101\/gr.276175.121","article-title":"Plasma cell-free RNA characteristics in COVID-19 patients","volume":"32","author":"Wang","year":"2022","journal-title":"Genome Res"},{"key":"2026100808260580500_ref25","doi-asserted-by":"publisher","first-page":"e29","DOI":"10.1111\/bjh.16817","article-title":"The association between severe COVID-19 and low platelet count: evidence from 31 observational studies involving 7613 participants","volume":"190","author":"Jiang","year":"2020","journal-title":"Br J Haematol"},{"key":"2026100808260580500_ref26","doi-asserted-by":"publisher","first-page":"20254","DOI":"10.1038\/s41598-021-99705-y","article-title":"Dynamic alterations in monocyte numbers, subset frequencies and activation markers in acute and convalescent COVID-19 individuals","volume":"11","author":"Rajamanickam","year":"2021","journal-title":"Sci Rep"},{"key":"2026100808260580500_ref27","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1093\/nsr\/nwaa041","article-title":"Pathogenic T-cells and inflammatory monocytes incite inflammatory storms in severe COVID-19 patients","volume":"7","author":"Zhou","year":"2020","journal-title":"Natl Sci Rev"},{"key":"2026100808260580500_ref28","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1002\/JLB.4HI0720-470R","article-title":"Frontline science: COVID-19 infection induces readily detectable morphologic and inflammation-related phenotypic changes in peripheral blood monocytes","volume":"109","author":"Zhang","year":"2021","journal-title":"J Leukoc Biol"},{"key":"2026100808260580500_ref29","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1038\/s41591-020-0944-y","article-title":"A single-cell atlas of the peripheral immune response in patients with severe COVID-19","volume":"26","author":"Wilk","year":"2020","journal-title":"Nat Med"},{"key":"2026100808260580500_ref30","doi-asserted-by":"publisher","first-page":"103967","DOI":"10.1016\/j.ebiom.2022.103967","article-title":"T cell response against SARS-CoV-2 persists after one year in patients surviving severe COVID-19","volume":"78","author":"Venet","year":"2022","journal-title":"eBioMedicine"},{"key":"2026100808260580500_ref31","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/s41421-020-00225-2","article-title":"The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing","volume":"6","author":"Xu","year":"2020","journal-title":"Cell Discov"},{"key":"2026100808260580500_ref32","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/s41591-021-01329-2","article-title":"Single-cell multi-omics analysis of the immune response in COVID-19","volume":"27","author":"Stephenson","year":"2021","journal-title":"Nat Med"},{"key":"2026100808260580500_ref33","doi-asserted-by":"publisher","first-page":"030501","DOI":"10.11613\/BM.2021.030501","article-title":"Complete blood count alterations in COVID-19 patients: a narrative review","volume":"31","author":"Palladino","year":"2021","journal-title":"Biochem Med (Zagreb)"},{"key":"2026100808260580500_ref34","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1016\/S1473-3099(20)30434-5","article-title":"Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study","volume":"20","author":"Carsana","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"2026100808260580500_ref35","doi-asserted-by":"publisher","first-page":"4713","DOI":"10.1016\/j.cell.2021.07.023","article-title":"Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19","volume":"184","author":"Ziegler","year":"2021","journal-title":"Cell"},{"key":"2026100808260580500_ref36","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1038\/s41587-020-0602-4","article-title":"COVID-19 severity correlates with airway epithelium\u2013immune cell interactions identified by single-cell analysis","volume":"38","author":"Chua","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026100808260580500_ref37","doi-asserted-by":"publisher","first-page":"e75181","DOI":"10.7554\/eLife.75181","article-title":"Cancer type classification using plasma cell-free RNAs derived from human and microbes","volume":"11","author":"Chen","year":"2022","journal-title":"eLife"},{"key":"2026100808260580500_ref38","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1038\/s41698-022-00270-y","article-title":"Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies","volume":"6","author":"Roskams-Hieter","year":"2022","journal-title":"Npj Precis Oncol"},{"key":"2026100808260580500_ref39","doi-asserted-by":"publisher","first-page":"101281","DOI":"10.1016\/j.xcrm.2023.101281","article-title":"Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients\u2019 blood","volume":"4","author":"Tao","year":"2023","journal-title":"Cell Rep Med"},{"key":"2026100808260580500_ref40","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1038\/s41586-025-08834-1","article-title":"An ultrasensitive method for detection of cell-free RNA","volume":"641","author":"Nesselbush","year":"2025","journal-title":"Nature"},{"key":"2026100808260580500_ref41","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/s41591-019-0379-5","article-title":"Platelet GPIb\u03b1 is a mediator and potential interventional target for NASH and subsequent liver cancer","volume":"25","author":"Malehmir","year":"2019","journal-title":"Nat Med"},{"key":"2026100808260580500_ref42","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.12659\/MSM.909474","article-title":"Platelet distribution width in hepatocellular carcinoma","volume":"24","author":"Guo","year":"2018","journal-title":"Med Sci Monit"},{"key":"2026100808260580500_ref43","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1159\/000489833","article-title":"Association of platelet count and mean platelet volume with overall survival in patients with cirrhosis and unresectable hepatocellular carcinoma","volume":"8","author":"Scheiner","year":"2019","journal-title":"Liver Cancer"},{"key":"2026100808260580500_ref44","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/s41586-019-0915-y","article-title":"Neutrophils escort circulating tumour cells to enable cell cycle progression","volume":"566","author":"Szczerba","year":"2019","journal-title":"Nature"},{"key":"2026100808260580500_ref45","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/s41586-022-05400-x","article-title":"Liver tumour immune microenvironment subtypes and neutrophil heterogeneity","volume":"612","author":"Xue","year":"2022","journal-title":"Nature"},{"key":"2026100808260580500_ref46","doi-asserted-by":"publisher","first-page":"102463","DOI":"10.1016\/j.redox.2022.102463","article-title":"Inhibition of APOC1 promotes the transformation of M2 into M1 macrophages via the ferroptosis pathway and enhances anti-PD1 immunotherapy in hepatocellular carcinoma based on single-cell RNA sequencing","volume":"56","author":"Hao","year":"2022","journal-title":"Redox Biol"},{"key":"2026100808260580500_ref47","doi-asserted-by":"publisher","first-page":"1424","DOI":"10.1038\/nm.4438","article-title":"Human primary liver cancer\u2013derived organoid cultures for disease modeling and drug screening","volume":"23","author":"Broutier","year":"2017","journal-title":"Nat Med"},{"key":"2026100808260580500_ref48","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1007\/s10555-023-10084-4","article-title":"Hepatocellular carcinoma: molecular mechanism, targeted therapy, and biomarkers","volume":"42","author":"Wang","year":"2023","journal-title":"Cancer Metastasis Rev"},{"key":"2026100808260580500_ref49","doi-asserted-by":"publisher","first-page":"3665","DOI":"10.3390\/cancers15143665","article-title":"Image-guided ablation therapies for extrahepatic metastases from hepatocellular carcinoma: a review","volume":"15","author":"Umakoshi","year":"2023","journal-title":"Cancers (Basel)"},{"key":"2026100808260580500_ref50","doi-asserted-by":"publisher","first-page":"100479","DOI":"10.1016\/j.jhepr.2022.100479","article-title":"Lipid alterations in chronic liver disease and liver cancer","volume":"4","author":"Paul","year":"2022","journal-title":"JHEP Rep"},{"key":"2026100808260580500_ref51","doi-asserted-by":"publisher","first-page":"eaaz0131","DOI":"10.1126\/scitranslmed.aaz0131","article-title":"Circulating transcripts in maternal blood reflect a molecular signature of early-onset preeclampsia","volume":"12","author":"Munchel","year":"2020","journal-title":"Sci Transl Med"},{"key":"2026100808260580500_ref52","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/j.placenta.2021.05.002","article-title":"Syncytiotrophoblast stress in early onset preeclampsia: the issues perpetuating the syndrome","volume":"113","author":"Carrasco-Wong","year":"2021","journal-title":"Placenta"},{"key":"2026100808260580500_ref53","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1161\/HYPERTENSIONAHA.124.23362","article-title":"Senescent syncytiotrophoblast secretion during early onset preeclampsia","volume":"82","author":"Nonn","year":"2025","journal-title":"Hypertension"},{"key":"2026100808260580500_ref54","doi-asserted-by":"publisher","first-page":"1864","DOI":"10.3389\/fimmu.2020.01864","article-title":"Mechanisms of key innate immune cells in early- and late-onset preeclampsia","volume":"11","author":"Aneman","year":"2020","journal-title":"Front Immunol"},{"key":"2026100808260580500_ref55","doi-asserted-by":"publisher","first-page":"112","DOI":"10.4274\/tjod.galenos.2019.93708","article-title":"First trimester complete blood cell indices in early and late onset preeclampsia","volume":"16","author":"\u00d6rg\u00fcl","year":"2019","journal-title":"Turk J Obstet Gynecol"},{"key":"2026100808260580500_ref56","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1038\/s41581-022-00670-0","article-title":"The role of immune cells and mediators in preeclampsia","volume":"19","author":"Deer","year":"2023","journal-title":"Nat Rev Nephrol"},{"key":"2026100808260580500_ref57","doi-asserted-by":"publisher","first-page":"1336764","DOI":"10.3389\/fmed.2024.1336764","article-title":"A meta-analysis on first-trimester blood count parameters-is the neutrophil-to-lymphocyte ratio a potentially novel method for first-trimester preeclampsia screening?","volume":"11","author":"M\u00e9sz\u00e1ros","year":"2024","journal-title":"Front Med (Lausanne)"},{"key":"2026100808260580500_ref58","doi-asserted-by":"publisher","first-page":"4326","DOI":"10.1038\/s41467-025-58533-8","article-title":"Maternal gut microbiota influences immune activation at the maternal-fetal interface affecting pregnancy outcome","volume":"16","author":"Giugliano","year":"2025","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref59","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1016\/j.jhep.2019.08.005","article-title":"Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development","volume":"71","author":"Mouries","year":"2019","journal-title":"J Hepatol"},{"key":"2026100808260580500_ref60","doi-asserted-by":"publisher","first-page":"575197","DOI":"10.3389\/fimmu.2020.575197","article-title":"Maternal immunological adaptation during normal pregnancy","volume":"11","author":"Abu-Raya","year":"2020","journal-title":"Front Immunol"},{"key":"2026100808260580500_ref61","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.molimm.2012.08.025","article-title":"Reproductive immunology","volume":"55","author":"Christiansen","year":"2013","journal-title":"Mol Immunol"},{"key":"2026100808260580500_ref62","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.molimm.2023.07.005","article-title":"Dissecting human placental cells heterogeneity in preeclampsia and gestational diabetes using single-cell sequencing","volume":"161","author":"Jiao","year":"2023","journal-title":"Mol Immunol"},{"key":"2026100808260580500_ref63","doi-asserted-by":"publisher","first-page":"e21423","DOI":"10.1096\/fj.202000326RR","article-title":"Hyperglycemia and gestational diabetes suppress placental glycolysis and mitochondrial function and alter lipid processing","volume":"35","author":"Valent","year":"2021","journal-title":"FASEB J"},{"key":"2026100808260580500_ref64","doi-asserted-by":"publisher","first-page":"99","DOI":"10.47162\/RJME.63.1.09","article-title":"Maternal obesity and placental pathology in correlation with adverse pregnancy outcome","volume":"63","author":"Tabacu","year":"2022","journal-title":"Rom J Morphol Embryol"},{"key":"2026100808260580500_ref65","doi-asserted-by":"publisher","first-page":"8087","DOI":"10.3390\/ijms22158087","article-title":"Immunoendocrine dysregulation during gestational diabetes mellitus: the central role of the placenta","volume":"22","author":"Olmos-Ortiz","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026100808260580500_ref66","doi-asserted-by":"publisher","first-page":"1907","DOI":"10.1210\/en.2019-00232","article-title":"Gestational diabetes adversely affects pancreatic islet architecture and function in the male rat offspring","volume":"160","author":"Agarwal","year":"2019","journal-title":"Endocrinology"},{"key":"2026100808260580500_ref67","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1007\/s00125-020-05155-y","article-title":"Decreased pancreatic acinar cell number in type 1 diabetes","volume":"63","author":"Wright","year":"2020","journal-title":"Diabetologia"},{"key":"2026100808260580500_ref68","doi-asserted-by":"publisher","first-page":"bbac430","DOI":"10.1093\/bib\/bbac430","article-title":"MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data","volume":"23","author":"Fan","year":"2022","journal-title":"Brief Bioinform"},{"key":"2026100808260580500_ref69","doi-asserted-by":"publisher","first-page":"bbag184","DOI":"10.1093\/bib\/bbag184","article-title":"Evaluating reference-mixture matching in cell-type deconvolution with single-cell RNA-seq references","volume":"27","author":"Zhao","year":"2026","journal-title":"Brief Bioinform"},{"key":"2026100808260580500_ref70","doi-asserted-by":"publisher","first-page":"5650","DOI":"10.1038\/s41467-020-19015-1","article-title":"Benchmarking of cell type deconvolution pipelines for transcriptomics data","volume":"11","author":"Avila Cobos","year":"2020","journal-title":"Nat Commun"},{"key":"2026100808260580500_ref71","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s40364-022-00409-w","article-title":"Current challenges and best practices for cell-free long RNA biomarker discovery","volume":"10","author":"Cab\u00fas","year":"2022","journal-title":"Biomark Res"},{"key":"2026100808260580500_ref72","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-026-03218-w","article-title":"High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples","author":"Yao","year":"2026","journal-title":"Nat Biotechnol"},{"key":"2026100808260580500_ref73","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41586-018-0698-6","article-title":"Single-cell reconstruction of the early maternal\u2013fetal interface in humans","volume":"563","author":"Vento-Tormo","year":"2018","journal-title":"Nature"},{"key":"2026100808260580500_ref74","doi-asserted-by":"publisher","first-page":"10892","DOI":"10.1038\/s41598-022-14516-z","article-title":"Single-cell transcriptional profiling reveals cellular and molecular divergence in human maternal\u2013fetal interface","volume":"12","author":"Wang","year":"2022","journal-title":"Sci Rep"},{"key":"2026100808260580500_ref75","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The genome sequence archive family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2026100808260580500_ref76","doi-asserted-by":"publisher","first-page":"D18","DOI":"10.1093\/nar\/gkad1078","article-title":"Database resources of the national genomics data center, China national center for bioinformation in 2024","volume":"52","author":"CNCB-NGDC Members and Partners","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100808260580500_ref77","doi-asserted-by":"publisher","first-page":"e987","DOI":"10.1002\/ctm2.987","article-title":"Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids","volume":"12","author":"Liu","year":"2022","journal-title":"Clin Transl Med"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag544\/71717994\/bbag544.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag544\/71717994\/bbag544.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T12:26:14Z","timestamp":1791462374000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag544\/8885516"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":77,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag544","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,9,1]]},"article-number":"bbag544"}}