{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T03:28:54Z","timestamp":1767065334128,"version":"build-2065373602"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T00:00:00Z","timestamp":1691366400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"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"}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB38040400"],"award-info":[{"award-number":["XDB38040400"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200520","12131020","31930022","T2341007","T2350003","62132015"],"award-info":[{"award-number":["32200520","12131020","31930022","T2341007","T2350003","62132015"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Fund for Science and Technology Innovation Strategy of Guangdong Province","award":["2021B0909050004","2021B0909060002"],"award-info":[{"award-number":["2021B0909050004","2021B0909060002"]}]},{"DOI":"10.13039\/501100020963","name":"JST Moonshot Research and Development Program","doi-asserted-by":"publisher","award":["JPMJMS2021"],"award-info":[{"award-number":["JPMJMS2021"]}],"id":[{"id":"10.13039\/501100020963","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Gene regulatory networks (GRNs) reveal the complex molecular interactions that govern cell state. However, it is challenging for identifying causal relations among genes due to noisy data and molecular nonlinearity. Here, we propose a novel causal criterion, neighbor cross-mapping entropy (NME), for inferring GRNs from both steady data and time-series data. NME is designed to quantify \u2018continuous causality\u2019 or functional dependency from one variable to another based on their function continuity with varying neighbor sizes. NME shows superior performance on benchmark datasets, comparing with existing methods. By applying to scRNA-seq datasets, NME not only reliably inferred GRNs for cell types but also identified cell states. Based on the inferred GRNs and further their activity matrices, NME showed better performance in single-cell clustering and downstream analyses. In summary, based on continuous causality, NME provides a powerful tool in inferring causal regulations of GRNs between genes from scRNA-seq data, which is further exploited to identify novel cell types\/states and predict cell type-specific network modules.<\/jats:p>","DOI":"10.1093\/bib\/bbad281","type":"journal-article","created":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T00:26:54Z","timestamp":1691368014000},"source":"Crossref","is-referenced-by-count":10,"title":["Single-cell causal network inferred by cross-mapping entropy"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3558-323X","authenticated-orcid":false,"given":"Lin","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Systems Biology , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Xia","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Biology , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Biology , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Biology , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Tao","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, Chinese Academy of Sciences , Hangzhou 310024 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3960-0068","authenticated-orcid":false,"given":"Luonan","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Biology , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Center for Excellence in Molecular Cell Science, , Shanghai 200031 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"},{"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, Chinese Academy of Sciences , Hangzhou 310024 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,8,7]]},"reference":[{"key":"2023092216535654500_ref1","doi-asserted-by":"crossref","first-page":"D97","DOI":"10.1093\/nar\/gkaa995","article-title":"GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions","volume":"49","author":"Fang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023092216535654500_ref2","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1186\/s12864-019-6298-5","article-title":"D3GRN: a data driven dynamic network construction method to infer gene regulatory networks","volume":"20","author":"Chen","year":"2019","journal-title":"BMC Genomics"},{"key":"2023092216535654500_ref3","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1007\/s00018-022-04208-2","article-title":"Gene regulatory network from cranial neural crest cells to osteoblast differentiation and calvarial bone development","volume":"79","author":"Liao","year":"2022","journal-title":"Cell Mol Life Sci"},{"key":"2023092216535654500_ref4","doi-asserted-by":"crossref","first-page":"bbab009","DOI":"10.1093\/bib\/bbab009","article-title":"A comprehensive overview and critical evaluation of gene regulatory network inference technologies","volume":"22","author":"Zhao","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023092216535654500_ref5","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/0022-5193(73)90247-6","article-title":"Boolean formalization of genetic control circuits","volume":"42","author":"Thomas","year":"1973","journal-title":"J Theor Biol"},{"key":"2023092216535654500_ref6","doi-asserted-by":"crossref","first-page":"511","DOI":"10.2174\/138920209789208237","article-title":"A tutorial on analysis and simulation of Boolean gene regulatory network models","volume":"10","author":"Xiao","year":"2009","journal-title":"Curr Genomics"},{"key":"2023092216535654500_ref7","doi-asserted-by":"crossref","first-page":"Ii138","DOI":"10.1093\/bioinformatics\/btg1071","article-title":"Gene networks inference using dynamic Bayesian networks","volume":"19","author":"Perrin","year":"2003","journal-title":"Bioinformatics"},{"key":"2023092216535654500_ref8","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/bib\/4.3.228","article-title":"Inferring gene networks from time series microarray data using dynamic Bayesian networks","volume":"4","author":"Kim","year":"2003","journal-title":"Brief Bioinform"},{"key":"2023092216535654500_ref9","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/bioinformatics\/btx605","article-title":"A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data","volume":"34","author":"Sanchez-Castillo","year":"2018","journal-title":"Bioinformatics"},{"key":"2023092216535654500_ref10","doi-asserted-by":"crossref","first-page":"e1005024","DOI":"10.1371\/journal.pcbi.1005024","article-title":"Inference of gene regulatory network based on local Bayesian networks","volume":"12","author":"Liu","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2023092216535654500_ref11","doi-asserted-by":"crossref","first-page":"5","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":"2023092216535654500_ref12","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","article-title":"GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks","volume":"35","author":"Moerman","year":"2019","journal-title":"Bioinformatics"},{"key":"2023092216535654500_ref13","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/j.1475-6773.2011.01243.x","article-title":"Statistics and causality: separated to reunite-commentary on Bryan Dowd\u2019s \u201cseparated at birth\u201d","volume":"46","author":"Pearl","year":"2011","journal-title":"Health Serv Res"},{"key":"2023092216535654500_ref14","first-page":"9870149","article-title":"Continuity scaling: a rigorous framework for detecting and quantifying causality accurately","volume":"2022","author":"Ying","year":"2022","journal-title":"Research (Wash D C)"},{"key":"2023092216535654500_ref15","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1103\/PhysRevA.33.1134","article-title":"Independent coordinates for strange attractors from mutual information","volume":"33","author":"Fraser","year":"1986","journal-title":"Phys Rev A Gen Phys"},{"key":"2023092216535654500_ref16","doi-asserted-by":"crossref","first-page":"066208","DOI":"10.1103\/PhysRevE.71.066208","article-title":"Statistical validation of mutual information calculations: comparison of alternative numerical algorithms","volume":"71","author":"Cellucci","year":"2005","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"2023092216535654500_ref17","doi-asserted-by":"crossref","first-page":"2318","DOI":"10.1103\/PhysRevE.52.2318","article-title":"Estimation of mutual information using kernel density estimators","volume":"52","author":"Moon","year":"1995","journal-title":"Physical Review E"},{"key":"2023092216535654500_ref18","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevE.66.051903","article-title":"Binless strategies for estimation of information from neural data","volume":"66","author":"Victor","year":"2002","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"2023092216535654500_ref19","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevE.69.066138","article-title":"Estimating mutual information","volume":"69","author":"Kraskov","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"2023092216535654500_ref20","doi-asserted-by":"crossref","first-page":"1903","DOI":"10.1162\/0899766054323026","article-title":"Edgeworth approximation of multivariate differential entropy","volume":"17","author":"Van Hulle","year":"2005","journal-title":"Neural Comput"},{"key":"2023092216535654500_ref21","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1109\/MLSP.2005.1532920","volume-title":"2005 IEEE Workshop on Machine Learning for Signal Processing (Mlsp)","author":"Van Hulle","year":"2005"},{"key":"2023092216535654500_ref22","doi-asserted-by":"crossref","first-page":"10555","DOI":"10.1073\/pnas.152046799","article-title":"Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics","volume":"99","author":"Ronen","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023092216535654500_ref23","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/ng881","article-title":"Network motifs in the transcriptional regulation network of Escherichia coli","volume":"31","author":"Shen-Orr","year":"2002","journal-title":"Nat Genet"},{"key":"2023092216535654500_ref24","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1016\/j.cell.2020.07.017","article-title":"Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing","volume":"182","author":"Maynard","year":"2020","journal-title":"Cell"},{"key":"2023092216535654500_ref25","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat Commun"},{"key":"2023092216535654500_ref26","doi-asserted-by":"crossref","first-page":"W556","DOI":"10.1093\/nar\/gkz430","article-title":"GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis","volume":"47","author":"Tang","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023092216535654500_ref27","doi-asserted-by":"crossref","first-page":"4885","DOI":"10.1093\/bioinformatics\/btaa032","article-title":"Inference of gene regulatory networks based on nonlinear ordinary differential equations","volume":"36","author":"Ma","year":"2020","journal-title":"Bioinformatics"},{"key":"2023092216535654500_ref28","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1111\/j.1749-6632.2009.04497.x","article-title":"Lessons from the DREAM2 challenges","volume":"1158","author":"Stolovitzky","year":"2009","journal-title":"Ann N Y Acad Sci"},{"key":"2023092216535654500_ref29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1196\/annals.1407.021","article-title":"Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference","volume":"1115","author":"Stolovitzky","year":"2007","journal-title":"Ann N Y Acad Sci"},{"key":"2023092216535654500_ref30","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1089\/cmb.2008.09TT","article-title":"Generating realistic in silico gene networks for performance assessment of reverse engineering methods","volume":"16","author":"Marbach","year":"2009","journal-title":"J Comput Biol"},{"key":"2023092216535654500_ref31","doi-asserted-by":"crossref","first-page":"4703","DOI":"10.1038\/s41467-019-12253-y","article-title":"Microbe-host interplay in atopic dermatitis and psoriasis","volume":"10","author":"Fyhrquist","year":"2019","journal-title":"Nat Commun"},{"key":"2023092216535654500_ref32","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nature25177","article-title":"Skin microbiota-host interactions","volume":"553","author":"Chen","year":"2018","journal-title":"Nature"},{"key":"2023092216535654500_ref33","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nature06245","article-title":"An ecological and evolutionary perspective on human\u2013microbe mutualism and disease","volume":"449","author":"Dethlefsen","year":"2007","journal-title":"Nature"},{"key":"2023092216535654500_ref34","doi-asserted-by":"crossref","first-page":"6348","DOI":"10.1038\/s41598-017-05740-z","article-title":"The resident pathobiont Staphylococcus xylosus in Nfkbiz-deficient skin accelerates spontaneous skin inflammation","volume":"7","author":"Kim","year":"2017","journal-title":"Sci Rep"},{"key":"2023092216535654500_ref35","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2021.102575","article-title":"Porphyrins produced by acneic Cutibacterium acnes strains activate the inflammasome by inducing K(+) leakage","volume":"24","author":"Spittaels","year":"2021","journal-title":"iScience"},{"key":"2023092216535654500_ref36","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00793-19","article-title":"Porphyrin production and regulation in cutaneous Propionibacteria","volume":"5","author":"Barnard","year":"2020","journal-title":"mSphere"},{"key":"2023092216535654500_ref37","doi-asserted-by":"crossref","first-page":"e01725","DOI":"10.1128\/mBio.01725-15","article-title":"Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols","volume":"7","author":"Bomar","year":"2016","journal-title":"MBio"},{"key":"2023092216535654500_ref38","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1186\/s13059-016-1033-x","article-title":"Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm","volume":"17","author":"Chu","year":"2016","journal-title":"Genome Biol"},{"key":"2023092216535654500_ref39","article-title":"Dynamic network biomarker factors orchestrate cell-fate determination at tipping points during hESC differentiation","volume":"4","author":"Lin","year":"2022","journal-title":"Innovation"},{"key":"2023092216535654500_ref40","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1111\/j.1742-4658.2009.07509.x","article-title":"Roles of AP-2 transcription factors in the regulation of cartilage and skeletal development","volume":"277","author":"Wenke","year":"2010","journal-title":"FEBS J"},{"key":"2023092216535654500_ref41","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1186\/gb-2005-6-13-246","article-title":"The AP-2 family of transcription factors","volume":"6","author":"Eckert","year":"2005","journal-title":"Genome Biol"},{"key":"2023092216535654500_ref42","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.201800124","article-title":"Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions","volume":"1","author":"Tuck","year":"2018","journal-title":"Life Sci Alliance"},{"key":"2023092216535654500_ref43","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.cmet.2019.06.001","article-title":"Macrophages and metabolism in the tumor microenvironment","volume":"30","author":"Vitale","year":"2019","journal-title":"Cell Metab"},{"key":"2023092216535654500_ref44","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.ccell.2018.07.009","article-title":"Notch signaling in the tumor microenvironment","volume":"34","author":"Meurette","year":"2018","journal-title":"Cancer Cell"},{"key":"2023092216535654500_ref45","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1158\/2159-8290.CD-19-0499","article-title":"Tumor microenvironment dynamics in clear-cell renal cell carcinoma","volume":"9","author":"Vuong","year":"2019","journal-title":"Cancer Discov"},{"key":"2023092216535654500_ref46","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.addr.2016.07.012","article-title":"Molecular imaging of the tumor microenvironment","volume":"113","author":"Zhou","year":"2017","journal-title":"Adv Drug Deliv Rev"},{"key":"2023092216535654500_ref47","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/nm.4494","article-title":"Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling","volume":"24","author":"Roswall","year":"2018","journal-title":"Nat Med"},{"key":"2023092216535654500_ref48","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/s12935-022-02599-7","article-title":"Cancer-associated fibroblasts and resistance to anticancer therapies: status, mechanisms, and countermeasures","volume":"22","author":"Feng","year":"2022","journal-title":"Cancer Cell Int"},{"key":"2023092216535654500_ref49","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/s10555-011-9340-x","article-title":"Cancer-associated-fibroblasts and tumour cells: a diabolic liaison driving cancer progression","volume":"31","author":"Cirri","year":"2012","journal-title":"Cancer Metastasis Rev"},{"key":"2023092216535654500_ref50","doi-asserted-by":"crossref","first-page":"3173","DOI":"10.1038\/onc.2010.92","article-title":"TWISTing an embryonic transcription factor into an oncoprotein","volume":"29","author":"Ansieau","year":"2010","journal-title":"Oncogene"},{"key":"2023092216535654500_ref51","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/sj.bjc.6602876","article-title":"A twist for survival and cancer progression","volume":"94","author":"Puisieux","year":"2006","journal-title":"Br J Cancer"},{"key":"2023092216535654500_ref52","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1016\/j.cell.2004.06.006","article-title":"Twist, a master regulator of morphogenesis, plays an essential role in tumor metastasis","volume":"117","author":"Yang","year":"2004","journal-title":"Cell"},{"key":"2023092216535654500_ref53","doi-asserted-by":"crossref","first-page":"2497","DOI":"10.1007\/s13277-013-1002-x","article-title":"Twist: a molecular target in cancer therapeutics","volume":"34","author":"Khan","year":"2013","journal-title":"Tumour Biol"},{"key":"2023092216535654500_ref54","doi-asserted-by":"crossref","first-page":"e179","DOI":"10.1038\/cddis.2011.61","article-title":"Transcription factors that mediate epithelial-mesenchymal transition lead to multidrug resistance by upregulating ABC transporters","volume":"2","author":"Saxena","year":"2011","journal-title":"Cell Death Dis"},{"key":"2023092216535654500_ref55","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1158\/1078-0432.CCR-08-2372","article-title":"Twist1-mediated adriamycin-induced epithelial-mesenchymal transition relates to multidrug resistance and invasive potential in breast cancer cells","volume":"15","author":"Li","year":"2009","journal-title":"Clin Cancer Res"},{"key":"2023092216535654500_ref56","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.3892\/ijo.2016.3342","article-title":"Twist mediates an aggressive phenotype in human colorectal cancer cells","volume":"48","author":"Deng","year":"2016","journal-title":"Int J Oncol"},{"key":"2023092216535654500_ref57","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1002\/ijc.22489","article-title":"Anti-apoptotic role of TWIST and its association with Akt pathway in mediating taxol resistance in nasopharyngeal carcinoma cells","volume":"120","author":"Zhang","year":"2007","journal-title":"Int J Cancer"},{"key":"2023092216535654500_ref58","doi-asserted-by":"crossref","DOI":"10.1038\/cddis.2012.63","article-title":"Silencing of Twist1 sensitizes NSCLC cells to cisplatin via AMPK-activated mTOR inhibition","volume":"3","author":"Jin","year":"2012","journal-title":"Cell Death Dis"},{"key":"2023092216535654500_ref59","doi-asserted-by":"crossref","first-page":"20380","DOI":"10.18632\/oncotarget.14608","article-title":"Multiple biological functions of Twist1 in various cancers","volume":"8","author":"Zhao","year":"2017","journal-title":"Oncotarget"},{"key":"2023092216535654500_ref60","doi-asserted-by":"crossref","first-page":"2791","DOI":"10.1002\/jcb.27703","article-title":"Cancer-associated fibroblasts: secretions, interactions, and therapy","volume":"120","author":"Farhood","year":"2019","journal-title":"J Cell Biochem"},{"key":"2023092216535654500_ref61","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/s41575-019-0115-0","article-title":"Cancer-associated fibroblasts in gastrointestinal cancer","volume":"16","author":"Kobayashi","year":"2019","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2023092216535654500_ref62","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.semcancer.2014.01.005","article-title":"Catabolic cancer-associated fibroblasts transfer energy and biomass to anabolic cancer cells, fueling tumor growth","volume":"25","author":"Martinez-Outschoorn","year":"2014","journal-title":"Semin Cancer Biol"},{"key":"2023092216535654500_ref63","doi-asserted-by":"crossref","DOI":"10.1186\/s12943-021-01428-1","article-title":"Crosstalk between cancer-associated fibroblasts and immune cells in the tumor microenvironment: new findings and future perspectives","volume":"20","author":"Mao","year":"2021","journal-title":"Mol Cancer"},{"key":"2023092216535654500_ref64","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1080\/10799893.2020.1811325","article-title":"Agrin promotes the proliferation, invasion and migration of rectal cancer cells via the WNT signaling pathway to contribute to rectal cancer progression","volume":"41","author":"Wang","year":"2021","journal-title":"J Recept Signal Transduct Res"},{"key":"2023092216535654500_ref65","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0115004","article-title":"Agrin and perlecan mediate tumorigenic processes in oral squamous cell carcinoma","volume":"9","author":"Kawahara","year":"2014","journal-title":"PloS One"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/5\/bbad281\/51710650\/bbad281.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/5\/bbad281\/51710650\/bbad281.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T17:15:06Z","timestamp":1695402906000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad281\/7237942"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,7]]},"references-count":65,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad281","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,9]]},"published":{"date-parts":[[2023,8,7]]},"article-number":"bbad281"}}