{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T13:01:40Z","timestamp":1790427700517,"version":"4.1.0"},"reference-count":81,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011332","name":"UCAS","doi-asserted-by":"publisher","award":["2022ZZ01013 and 2024HIAS-Y016"],"award-info":[{"award-number":["2022ZZ01013 and 2024HIAS-Y016"]}],"id":[{"id":"10.13039\/501100011332","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFA1004800"],"award-info":[{"award-number":["2022YFA1004800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62573147 and T2341024"],"award-info":[{"award-number":["62573147 and T2341024"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"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>Accurately inferring cell-type-specific gene regulatory networks (GRNs) is crucial for understanding cellular heterogeneity, lineage determination, and disease progression mechanisms. Although single-cell RNA sequencing (scRNA-seq) enables high-resolution expression profiling, its inherent sparsity and high noise levels pose challenges to reliable GRN reconstruction. To address these issues, we propose cell type-specific gene regulatory network (CTN), a regulatory inference framework based on bilateral self-representation matrix decomposition, which integrates bulk RNA-seq data with scRNA-seq data to decompose global regulatory relationships and intercellular communication, thereby reconstructing GRNs at the cell type level. CTN demonstrates high inference accuracy and strong performance in functional module identification. In the analysis of real biological processes, CTN reveals the key regulators and functional modules in the differentiation process for different lineages of the hematopoietic system, identifies differentially perturbed regulatory networks for tumor-related cell types, and depicts potential functional mechanisms in the tumor microenvironment.<\/jats:p>","DOI":"10.1093\/bib\/bbag525","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T11:47:54Z","timestamp":1789040874000},"source":"Crossref","is-referenced-by-count":0,"title":["Constructing cell-type-specific gene regulatory networks from cell\u2013cell communication and a global gene regulatory network"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-0463-0573","authenticated-orcid":false,"given":"Yuke","family":"Xie","sequence":"first","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bowen","family":"Fu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laijun","family":"Zhong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haorong","family":"Li","sequence":"additional","affiliation":[{"name":"School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Chang","sequence":"additional","affiliation":[{"name":"Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics , No. 962 Caoshan Road, Longzihu District, Bengbu 233030, Anhui ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3246-4227","authenticated-orcid":false,"given":"Xiaoping","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , No. 1 Xiangshan Branch Road, Xihu District, Hangzhou 310024, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"2026092608232866300_ref1","doi-asserted-by":"publisher","first-page":"3335","DOI":"10.1016\/j.csbj.2020.10.022","article-title":"Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks","volume":"18","author":"Wang","year":"2020","journal-title":"Comput Struct Biotechnol J"},{"key":"2026092608232866300_ref2","doi-asserted-by":"publisher","first-page":"bbab325","DOI":"10.1093\/bib\/bbab325","article-title":"DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data","volume":"22","author":"Chen","year":"2021","journal-title":"Brief Bioinform"},{"key":"2026092608232866300_ref3","doi-asserted-by":"publisher","first-page":"e1010942","DOI":"10.1371\/journal.pgen.1010942","article-title":"Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model","volume":"19","author":"Wang","year":"2023","journal-title":"PLoS Genet"},{"key":"2026092608232866300_ref4","doi-asserted-by":"publisher","first-page":"100911","DOI":"10.1016\/j.patter.2023.100911","article-title":"MDIC3: matrix decomposition to infer cell-cell communication","volume":"5","author":"Liu","year":"2024","journal-title":"Patterns (N Y)"},{"key":"2026092608232866300_ref5","doi-asserted-by":"publisher","first-page":"103006","DOI":"10.1016\/j.xpro.2024.103006","article-title":"Protocol for unsupervised inference of cell-cell communication using matrix decomposition","volume":"5","author":"Liu","year":"2024","journal-title":"STAR Protoc"},{"key":"2026092608232866300_ref6","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41592-019-0690-6","article-title":"Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data","volume":"17","author":"Pratapa","year":"2020","journal-title":"Nat Methods"},{"key":"2026092608232866300_ref7","doi-asserted-by":"publisher","first-page":"e12776","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"key":"2026092608232866300_ref8","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1039\/c5mb00560d","article-title":"Large scale gene regulatory network inference with a multi-level strategy","volume":"12","author":"Wu","year":"2016","journal-title":"Mol BioSyst"},{"key":"2026092608232866300_ref9","doi-asserted-by":"publisher","first-page":"665","DOI":"10.5351\/CSAM.2015.22.6.665","article-title":"Ppcor: an R package for a fast calculation to semi-partial correlation coefficients","volume":"22","author":"Kim","year":"2015","journal-title":"Commun Stat Appl Methods"},{"key":"2026092608232866300_ref10","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/s43588-021-00099-8","article-title":"Modeling gene regulatory networks using neural network architectures","volume":"1","author":"Shu","year":"2021","journal-title":"Nat Comput Sci"},{"key":"2026092608232866300_ref11","doi-asserted-by":"publisher","first-page":"108690","DOI":"10.1016\/j.compbiomed.2024.108690","article-title":"SLIVER: unveiling large scale gene regulatory networks of single-cell transcriptomic data through causal structure learning and modules aggregation","volume":"178","author":"Jiang","year":"2024","journal-title":"Comput Biol Med"},{"key":"2026092608232866300_ref12","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/s12015-013-9486-8","article-title":"Wnt signaling and the control of human stem cell fate","volume":"10","author":"Van Camp","year":"2014","journal-title":"Stem Cell Rev Rep"},{"key":"2026092608232866300_ref13","doi-asserted-by":"publisher","first-page":"328372","DOI":"10.1155\/2012\/328372","article-title":"The MAPK MEK1\/2-ERK1\/2 pathway and its implication in hepatocyte cell cycle control","volume":"2012","author":"Gu\u00e9gan","year":"2012","journal-title":"Int J Hepatol"},{"key":"2026092608232866300_ref14","doi-asserted-by":"publisher","first-page":"1458","DOI":"10.1038\/s41587-019-0332-7","article-title":"Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia","volume":"37","author":"Granja","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026092608232866300_ref15","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1038\/ng.3646","article-title":"Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution","volume":"48","author":"Corces","year":"2016","journal-title":"Nat Genet"},{"key":"2026092608232866300_ref16","doi-asserted-by":"publisher","first-page":"5608","DOI":"10.1182\/bloodadvances.2022009313","article-title":"ETV6 represses inflammatory response genes and regulates HSPC function during stress hematopoiesis in mice","volume":"7","author":"Bloom","year":"2023","journal-title":"Blood Adv"},{"key":"2026092608232866300_ref17","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1182\/blood-2005-09-008656","article-title":"E2f4 regulates fetal erythropoiesis through the promotion of cellular proliferation","volume":"108","author":"Kinross","year":"2006","journal-title":"Blood"},{"key":"2026092608232866300_ref18","doi-asserted-by":"publisher","first-page":"4721","DOI":"10.1182\/blood-2009-04-216390","article-title":"The transcription factors STAT5A\/B regulate GM-CSF-mediated granulopoiesis","volume":"114","author":"Kimura","year":"2009","journal-title":"Blood"},{"key":"2026092608232866300_ref19","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1093\/intimm\/11.7.1075","article-title":"STAT1 activation during monocyte to macrophage maturation: role of adhesion molecules","volume":"11","author":"Coccia","year":"1999","journal-title":"Int Immunol"},{"key":"2026092608232866300_ref20","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1111\/j.1365-3083.2006.01827.x","article-title":"Inhibition of monocytic differentiation by phosphorylation-deficient Stat1 is associated with impaired expression of Stat2, ICSBP\/IRF8 and C\/EBPepsilon","volume":"64","author":"Dimberg","year":"2006","journal-title":"Scand J Immunol"},{"key":"2026092608232866300_ref21","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1084\/jem.20112084","article-title":"ZBTB1 is a determinant of lymphoid development","volume":"209","author":"Siggs","year":"2012","journal-title":"J Exp Med"},{"key":"2026092608232866300_ref22","first-page":"3769","article-title":"Fli1 is essential for the maintenance of hematopoietic stem cell homeostasis and function","volume":"130","author":"Badwe","year":"2017","journal-title":"Blood"},{"key":"2026092608232866300_ref23","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1182\/blood-2021-154353","article-title":"Ing4-deficiency enhances hematopoietic stem cell quiescence and confers resistance to inflammatory stress","volume":"138","author":"Thompson","year":"2021","journal-title":"Blood"},{"key":"2026092608232866300_ref24","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.1093\/abbs\/gmw109","article-title":"ZFX modulates the growth of human leukemic cells via B4GALT1","volume":"48","author":"Wu","year":"2016","journal-title":"Acta Biochim Biophys Sin (Shanghai)"},{"key":"2026092608232866300_ref25","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1007\/s13258-024-01540-8","article-title":"A novel study on CXXC5: unraveling its regulatory mechanisms in hematopoietic stem cell biology through proteomics and gene editing","volume":"46","author":"Liu","year":"2024","journal-title":"Genes Genomics"},{"key":"2026092608232866300_ref26","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/s41418-024-01305-6","article-title":"DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner","volume":"31","author":"Yang","year":"2024","journal-title":"Cell Death Differ"},{"key":"2026092608232866300_ref27","doi-asserted-by":"publisher","first-page":"9385","DOI":"10.1093\/nar\/gkad619","article-title":"CSDE1 promotes miR-451 biogenesis","volume":"51","author":"Kakumani","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026092608232866300_ref28","doi-asserted-by":"publisher","first-page":"11897","DOI":"10.1074\/jbc.M709569200","article-title":"Splenomegaly and modified erythropoiesis in KLF13\u2212\/\u2212 mice","volume":"283","author":"Gordon","year":"2008","journal-title":"J Biol Chem"},{"key":"2026092608232866300_ref29","doi-asserted-by":"publisher","first-page":"e33474","DOI":"10.1371\/journal.pone.0033474","article-title":"Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts","volume":"7","author":"Suzuki","year":"2012","journal-title":"PLoS One"},{"key":"2026092608232866300_ref30","doi-asserted-by":"publisher","first-page":"11425","DOI":"10.1016\/S0021-9258(19)78141-1","article-title":"Sp1 is a critical factor for the monocytic specific expression of human CD14","volume":"269","author":"Zhang","year":"1994","journal-title":"J Biol Chem"},{"key":"2026092608232866300_ref31","doi-asserted-by":"publisher","first-page":"10107","DOI":"10.1073\/pnas.1711058114","article-title":"Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation","volume":"114","author":"Gao","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092608232866300_ref32","doi-asserted-by":"publisher","first-page":"16917","DOI":"10.1038\/s41598-019-53141-1","article-title":"mTORC1 activity is essential for erythropoiesis and B cell lineage commitment","volume":"9","author":"Malik","year":"2019","journal-title":"Sci Rep"},{"key":"2026092608232866300_ref33","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1083\/jcb.200307056","article-title":"FoxO3a regulates erythroid differentiation and induces BTG1, an activator of protein arginine methyl transferase 1","volume":"164","author":"Bakker","year":"2004","journal-title":"J Cell Biol"},{"key":"2026092608232866300_ref34","doi-asserted-by":"publisher","first-page":"4731","DOI":"10.1182\/blood.V120.21.4731.4731","article-title":"Functional analysis of FOXO3A involved in erythroid differentiation","volume":"120","author":"Wang","year":"2012","journal-title":"Blood"},{"key":"2026092608232866300_ref35","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1007\/s12026-010-8187-5","article-title":"Role of Ras\/Raf\/MEK\/ERK signaling in physiological hematopoiesis and leukemia development","volume":"49","author":"Chung","year":"2011","journal-title":"Immunol Res"},{"key":"2026092608232866300_ref36","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/nrc2694","article-title":"Signal integration by JNK and p38 MAPK pathways in cancer development","volume":"9","author":"Wagner","year":"2009","journal-title":"Nat Rev Cancer"},{"key":"2026092608232866300_ref37","doi-asserted-by":"publisher","first-page":"aab2116","DOI":"10.1126\/science.aab2116","article-title":"Distinct routes of lineage development reshape the human blood hierarchy across ontogeny","volume":"351","author":"Notta","year":"2016","journal-title":"Science"},{"key":"2026092608232866300_ref38","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1038\/ncb3493","article-title":"Human haematopoietic stem cell lineage commitment is a continuous process","volume":"19","author":"Velten","year":"2017","journal-title":"Nat Cell Biol"},{"key":"2026092608232866300_ref39","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.stem.2020.11.015","article-title":"Integrative single-cell RNA-seq and ATAC-seq analysis of human developmental hematopoiesis","volume":"28","author":"Ranzoni","year":"2021","journal-title":"Cell Stem Cell"},{"key":"2026092608232866300_ref40","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1182\/blood.2019001289","article-title":"Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs","volume":"134","author":"O\u2019Byrne","year":"2019","journal-title":"Blood"},{"key":"2026092608232866300_ref41","doi-asserted-by":"publisher","first-page":"42106","DOI":"10.1074\/jbc.M308586200","article-title":"HMGA1 co-activates transcription in B cells through indirect association with DNA","volume":"278","author":"McCarthy","year":"2003","journal-title":"J Biol Chem"},{"key":"2026092608232866300_ref42","doi-asserted-by":"publisher","first-page":"4884","DOI":"10.1038\/s41388-020-1331-3","article-title":"Bptf determines oncogenic addiction in aggressive B-cell lymphomas","volume":"39","author":"Richart","year":"2020","journal-title":"Oncogene"},{"key":"2026092608232866300_ref43","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S1074-7613(01)00085-1","article-title":"NFATc1 and NFATc2 together control both T and B cell activation and differentiation","volume":"14","author":"Peng","year":"2001","journal-title":"Immunity"},{"key":"2026092608232866300_ref44","doi-asserted-by":"publisher","first-page":"228","DOI":"10.3389\/fimmu.2012.00228","article-title":"Akt and mTOR in B cell activation and differentiation","volume":"3","author":"Limon","year":"2012","journal-title":"Front Immunol"},{"key":"2026092608232866300_ref45","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1002\/eji.201242912","article-title":"B-cell receptor signal strength influences terminal differentiation","volume":"43","author":"Lechouane","year":"2013","journal-title":"Eur J Immunol"},{"key":"2026092608232866300_ref46","doi-asserted-by":"publisher","first-page":"9573","DOI":"10.1073\/pnas.1314562111","article-title":"PDK1 regulates B cell differentiation and homeostasis","volume":"111","author":"Baracho","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092608232866300_ref47","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1038\/ni.1712","article-title":"CD98hc facilitates B cell proliferation and adaptive humoral immunity","volume":"10","author":"Cantor","year":"2009","journal-title":"Nat Immunol"},{"key":"2026092608232866300_ref48","doi-asserted-by":"publisher","first-page":"117146","DOI":"10.1016\/j.biopha.2024.117146","article-title":"FNIP1: a key regulator of mitochondrial function","volume":"177","author":"Zeng","year":"2024","journal-title":"Biomed Pharmacother"},{"key":"2026092608232866300_ref49","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.cytogfr.2017.04.005","article-title":"Control of B lymphocyte development and functions by the mTOR signaling pathways","volume":"35","author":"Iwata","year":"2017","journal-title":"Cytokine Growth Factor Rev"},{"key":"2026092608232866300_ref50","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/s41423-018-0185-x","article-title":"Sin1\/mTORC2 regulate B cell growth and metabolism by activating mTORC1 and Myc","volume":"16","author":"Li","year":"2019","journal-title":"Cell Mol Immunol"},{"key":"2026092608232866300_ref51","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1182\/blood-2013-01-477505","article-title":"Requirement for Rictor in homeostasis and function of mature B lymphoid cells","volume":"122","author":"Lee","year":"2013","journal-title":"Blood"},{"key":"2026092608232866300_ref52","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s13045-018-0558-8","article-title":"SF3B1 deficiency impairs human erythropoiesis via activation of p53 pathway: implications for understanding of ineffective erythropoiesis in MDS","volume":"11","author":"Huang","year":"2018","journal-title":"J Hematol Oncol"},{"key":"2026092608232866300_ref53","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1186\/1471-2164-14-587","article-title":"Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Kr\u00fcppel-like factors","volume":"14","author":"Xiong","year":"2013","journal-title":"BMC Genomics"},{"key":"2026092608232866300_ref54","doi-asserted-by":"publisher","first-page":"1522","DOI":"10.4161\/auto.29197","article-title":"PRKAA1\/AMPK\u03b11 is required for autophagy-dependent mitochondrial clearance during erythrocyte maturation","volume":"10","author":"Zhu","year":"2014","journal-title":"Autophagy"},{"key":"2026092608232866300_ref55","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/s41588-020-0636-z","article-title":"Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer","volume":"52","author":"Lee","year":"2020","journal-title":"Nat Genet"},{"key":"2026092608232866300_ref56","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1136\/amiajnl-2011-000658","article-title":"Identifying disease genes and module biomarkers by differential interactions","volume":"19","author":"Liu","year":"2012","journal-title":"J Am Med Inform Assoc"},{"key":"2026092608232866300_ref57","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.1172\/JCI80005","article-title":"Myeloid-derived suppressor cells in the tumor microenvironment: expect the unexpected","volume":"125","author":"Marvel","year":"2015","journal-title":"J Clin Invest"},{"key":"2026092608232866300_ref58","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1158\/2326-6066.CIR-16-0297","article-title":"Myeloid-derived suppressor cells","volume":"5","author":"Gabrilovich","year":"2017","journal-title":"Cancer Immunol Res"},{"key":"2026092608232866300_ref59","doi-asserted-by":"publisher","first-page":"1581","DOI":"10.32604\/or.2025.060063","article-title":"Plasticity of myeloid-derived suppressor cells in cancer and cancer therapy","volume":"33","author":"Lv","year":"2025","journal-title":"Oncol Res"},{"key":"2026092608232866300_ref60","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/s41568-019-0238-1","article-title":"A framework for advancing our understanding of cancer-associated fibroblasts","volume":"20","author":"Sahai","year":"2020","journal-title":"Nat Rev Cancer"},{"key":"2026092608232866300_ref61","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1038\/nrc.2016.73","article-title":"The biology and function of fibroblasts in cancer","volume":"16","author":"Kalluri","year":"2016","journal-title":"Nat Rev Cancer"},{"key":"2026092608232866300_ref62","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1158\/1940-6207.CAPR-09-0105","article-title":"STAT2 contributes to promotion of colorectal and skin carcinogenesis","volume":"3","author":"Gamero","year":"2010","journal-title":"Cancer Prev Res (Phila)"},{"key":"2026092608232866300_ref63","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1016\/j.bbrc.2012.12.145","article-title":"PES1 regulates sensitivity of colorectal cancer cells to anticancer drugs","volume":"431","author":"Xie","year":"2013","journal-title":"Biochem Biophys Res Commun"},{"key":"2026092608232866300_ref64","doi-asserted-by":"publisher","first-page":"70214","DOI":"10.18632\/oncotarget.19603","article-title":"TGF\u03b2 induced factor homeobox 1 promotes colorectal cancer development through activating Wnt\/\u03b2-catenin signaling","volume":"8","author":"Wang","year":"2017","journal-title":"Oncotarget"},{"key":"2026092608232866300_ref65","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1007\/s12032-024-02349-x","article-title":"YWHAG promotes colorectal cancer progression by regulating the CTTN-Wnt\/\u03b2-catenin signaling axis","volume":"41","author":"Wang","year":"2024","journal-title":"Med Oncol"},{"key":"2026092608232866300_ref66","doi-asserted-by":"publisher","first-page":"1901278","DOI":"10.1002\/advs.201901278","article-title":"Granulocytic myeloid-derived suppressor cells promote the stemness of colorectal cancer cells through exosomal S100A9","volume":"6","author":"Wang","year":"2019","journal-title":"Adv Sci (Weinh)"},{"key":"2026092608232866300_ref67","doi-asserted-by":"publisher","first-page":"4094","DOI":"10.1172\/JCI64115","article-title":"TNF signaling drives myeloid-derived suppressor cell accumulation","volume":"122","author":"Zhao","year":"2012","journal-title":"J Clin Invest"},{"key":"2026092608232866300_ref68","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1038\/s41423-020-00610-7","article-title":"The kinase AKT1 potentiates the suppressive functions of myeloid-derived suppressor cells in inflammation and cancer","volume":"18","author":"Jia","year":"2021","journal-title":"Cell Mol Immunol"},{"key":"2026092608232866300_ref69","doi-asserted-by":"publisher","first-page":"817800","DOI":"10.3389\/fcell.2022.956604","article-title":"Mapk14 is a prognostic biomarker and correlates with the clinicopathological features and immune infiltration of colorectal cancer","volume":"10","author":"Wang","year":"2022","journal-title":"Front Cell Dev Biol"},{"key":"2026092608232866300_ref70","doi-asserted-by":"publisher","first-page":"3108933","DOI":"10.1155\/2021\/3108933","article-title":"AEBP1 is one of the epithelial-mesenchymal transition regulatory genes in colon adenocarcinoma","volume":"2021","author":"Li","year":"2021","journal-title":"Biomed Res Int"},{"key":"2026092608232866300_ref71","doi-asserted-by":"publisher","first-page":"2295","DOI":"10.1007\/s12094-022-02910-y","article-title":"Significant position of C-myc in colorectal cancer: a promising therapeutic target","volume":"24","author":"Tan","year":"2022","journal-title":"Clin Transl Oncol"},{"key":"2026092608232866300_ref72","doi-asserted-by":"publisher","first-page":"e15602","DOI":"10.7717\/peerj.15602","article-title":"Role of ELK1 in regulating colorectal cancer progression: miR-31-5p\/CDIP1 axis in CRC pathogenesis","volume":"11","author":"Yan","year":"2023","journal-title":"PeerJ"},{"key":"2026092608232866300_ref73","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1158\/2159-8290.CD-15-0730","article-title":"ERBB2 emerges as a new target for colorectal cancer","volume":"5","author":"Pectasides","year":"2015","journal-title":"Cancer Discov"},{"key":"2026092608232866300_ref74","doi-asserted-by":"publisher","first-page":"5369","DOI":"10.3390\/ijms20215369","article-title":"BRAF-mutated colorectal cancer: clinical and molecular insights","volume":"20","author":"Caputo","year":"2019","journal-title":"Int J Mol Sci"},{"key":"2026092608232866300_ref75","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1038\/s42005-025-02091-4","article-title":"Causal network inference based on cross-validation predictability","volume":"8","author":"Zhang","year":"2025","journal-title":"Commun Phys"},{"key":"2026092608232866300_ref76","doi-asserted-by":"publisher","first-page":"e2409170","DOI":"10.1002\/advs.202409170","article-title":"Reconstructing molecular networks by causal diffusion do-calculus analysis with deep learning","volume":"11","author":"Wang","year":"2024","journal-title":"Adv Sci (Weinh)"},{"key":"2026092608232866300_ref77","doi-asserted-by":"publisher","first-page":"2423","DOI":"10.1093\/bioinformatics\/btab099","article-title":"Inference of gene regulatory networks using pseudo-time series data","volume":"37","author":"Zhang","year":"2021","journal-title":"Bioinformatics"},{"key":"2026092608232866300_ref78","doi-asserted-by":"publisher","first-page":"e95276","DOI":"10.1371\/journal.pone.0095276","article-title":"Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations","volume":"9","author":"Wu","year":"2014","journal-title":"PLoS One"},{"key":"2026092608232866300_ref79","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"2026092608232866300_ref80","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1093\/bioinformatics\/bts619","article-title":"NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference","volume":"29","author":"Zhang","year":"2013","journal-title":"Bioinformatics"},{"key":"2026092608232866300_ref81","doi-asserted-by":"publisher","first-page":"3064","DOI":"10.1038\/s41467-023-38637-9","article-title":"Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets","volume":"14","author":"Zhang","year":"2023","journal-title":"Nat Commun"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag525\/71402351\/bbag525.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag525\/71402351\/bbag525.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T12:31:37Z","timestamp":1790425897000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag525\/8836544"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":81,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag525","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":"bbag525"}}