{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T22:52:07Z","timestamp":1773096727602,"version":"3.50.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T00:00:00Z","timestamp":1564099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFA0505500"],"award-info":[{"award-number":["2017YFA0505500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB13040700"],"award-info":[{"award-number":["XDB13040700"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61372138"],"award-info":[{"award-number":["61372138"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771476"],"award-info":[{"award-number":["31771476"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the National Science and Technology Major Project","award":["2018ZX10201002"],"award-info":[{"award-number":["2018ZX10201002"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The growth and survival of myeloma cells are greatly affected by their surrounding microenvironment. To understand the molecular mechanism and the impact of stiffness on the fate of myeloma-initiating cells (MICs), we develop a systems biological model to reveal the dynamic regulations by integrating reverse-phase protein array data and the stiffness-associated pathway.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We not only develop a stiffness-associated signaling pathway to describe the dynamic regulations of the MICs, but also clearly identify three critical proteins governing the MIC proliferation and death, including FAK, mTORC1 and NF\u03baB, which are validated to be related with multiple myeloma by our immunohistochemistry experiment, computation and manually reviewed evidences. Moreover, we demonstrate that the systematic model performs better than widely used parameter estimation algorithms for the complicated signaling pathway.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>We can not only use the systems biological model to infer the stiffness-associated genetic signaling pathway and locate the critical proteins, but also investigate the important pathways, proteins or genes for other type of the cancer. Thus, it holds universal scientific significance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz542","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T11:27:00Z","timestamp":1563967620000},"page":"1554-1561","source":"Crossref","is-referenced-by-count":31,"title":["Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3708-1727","authenticated-orcid":false,"given":"Le","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer Science"},{"name":"Medical Big Data Center, Sichuan University , Chengdu 610065, China"},{"name":"Chongqqing Zhongdi Medical Information Technology Co., Ltd , Chongqing 401320, China"}]},{"given":"Guangdi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science, Southwest University , Chongqing 400715, China"},{"name":"Library of Chengdu University, Chengdu University , Chengdu 610106, China"}]},{"given":"Meijing","family":"Kong","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science, Southwest University , Chongqing 400715, China"}]},{"given":"Tingting","family":"Li","sequence":"additional","affiliation":[{"name":"College of Mathematics and Statistics, Southwest University , Chongqing 400715, China"}]},{"given":"Dan","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Radiology, Wake Forest University School of Medicine , Winston-Salem, NC 27157, USA"}]},{"given":"Xiaobo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Radiology, Wake Forest University School of Medicine , Winston-Salem, NC 27157, USA"}]},{"given":"Chuanwei","family":"Yang","sequence":"additional","affiliation":[{"name":"Systems Biology, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}]},{"given":"Lei","family":"Xia","sequence":"additional","affiliation":[{"name":"Cancer Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University , Chongqing 400042, China"}]},{"given":"Zhenzhou","family":"Yang","sequence":"additional","affiliation":[{"name":"Cancer Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University , Chongqing 400042, China"}]},{"given":"Luonan","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"Center for Excellence in Animal Evolution and Genetics , Chinese Academy of Sciences, Kunming 650223, China"},{"name":"Shanghai Research Center for Brain Science and Brain-Inspired Intelligence , Shanghai 201210, China"}]}],"member":"286","published-online":{"date-parts":[[2019,7,26]]},"reference":[{"key":"2023051709452635100_btz542-B1","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1007\/s12185-011-0949-x","article-title":"Targeting the interplay between myeloma cells and the bone marrow microenvironment in myeloma","volume":"94","author":"Abe","year":"2011","journal-title":"Int. J. Hematol"},{"key":"2023051709452635100_btz542-B2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.exphem.2007.01.024","article-title":"Targeted therapy of multiple myeloma based upon tumor-microenvironmental interactions","volume":"35","author":"Anderson","year":"2007","journal-title":"Exp. Hematol"},{"key":"2023051709452635100_btz542-B3","author":"Apostolos","year":"2014"},{"key":"2023051709452635100_btz542-B4","first-page":"301","article-title":"Rigid microenvironments promote cardiac differentiation of mouse and human embryonic stem cells","volume":"14","author":"Arshi","year":"2016","journal-title":"Sci. Technol. Adv. Mater"},{"key":"2023051709452635100_btz542-B5","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1093\/bib\/bbm029","article-title":"Petri net modelling of biological networks","volume":"8","author":"Chaouiya","year":"2007","journal-title":"Brief. Bioinform"},{"key":"2023051709452635100_btz542-B6","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/msb.2008.74","article-title":"Input\u2013output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data","volume":"5","author":"Chen","year":"2009","journal-title":"Mol. Syst. Biol"},{"key":"2023051709452635100_btz542-B7","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1158\/1535-7163.MCT-13-0022","article-title":"Genetic and pharmacologic evidence that mTOR targeting outweighs mTORC1 inhibition as an antimyeloma strategy","volume":"13","author":"Chen","year":"2014","journal-title":"Mol. Cancer Ther"},{"key":"2023051709452635100_btz542-B8","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1074\/jbc.M113.526335","article-title":"Hyperactivation of mammalian target of rapamycin complex 1 (mTORC1) promotes breast cancer progression through enhancing glucose starvation-induced autophagy and Akt signaling","volume":"289","author":"Chen","year":"2014","journal-title":"J. Biol. Chem"},{"key":"2023051709452635100_btz542-B9","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.bbamcr.2014.11.019","article-title":"CD138-negative myeloma cells regulate mechanical properties of bone marrow stromal cells through SDF-1\/CXCR4\/AKT signaling pathway","volume":"1853","author":"Dan","year":"2015","journal-title":"Biochim. Biophys. Acta"},{"key":"2023051709452635100_btz542-B10","first-page":"1921","article-title":"The role of the bone marrow microenvironment in multiple myeloma","volume":"17","author":"De Raeve","year":"2002","journal-title":"Histol. Histopathol"},{"key":"2023051709452635100_btz542-B11","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1111\/apm.12733","article-title":"The expression profile and prognostic value of APE\/Ref-1 and NPM1 in high-grade serous ovarian adenocarcinoma","volume":"125","author":"Fan","year":"2017","journal-title":"APMIS"},{"key":"2023051709452635100_btz542-B12","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.pbiomolbio.2009.10.004","article-title":"Unique biomechanical interactions between myeloma cells and bone marrow stroma cells","volume":"103","author":"Feng","year":"2010","journal-title":"Prog. Biophys. Mol. Biol"},{"key":"2023051709452635100_btz542-B13","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/nrc1072","article-title":"The circadian clock: pacemaker and tumour suppressor","volume":"3","author":"Fu","year":"2003","journal-title":"Nat. Rev. Cancer"},{"key":"2023051709452635100_btz542-B14","doi-asserted-by":"crossref","first-page":"2209","DOI":"10.3390\/molecules22122209","article-title":"Developing an agent-based drug model to investigate the synergistic effects of drug combinations","volume":"22","author":"Gao","year":"2017","journal-title":"Molecules"},{"key":"2023051709452635100_btz542-B15","first-page":"2104","article-title":"Genetic algorithms in search, optimization, and machine learning","volume-title":"Addison-Wesley","author":"Goldberg","year":"1989"},{"key":"2023051709452635100_btz542-B16","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1109\/MPER.2002.4312424","article-title":"An efficient simulated annealing algorithm for network reconfiguration in large-scale distribution systems","volume":"22","author":"Jeon","year":"2002","journal-title":"IEEE Power Eng. Rev"},{"key":"2023051709452635100_btz542-B17","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.semcancer.2010.04.003","article-title":"Adhesion molecules: the lifelines of multiple myeloma cells","volume":"20","author":"Katz","year":"2010","journal-title":"Semin. Cancer Biol"},{"key":"2023051709452635100_btz542-B18","doi-asserted-by":"crossref","first-page":"48","DOI":"10.18632\/aging.100633","article-title":"BMAL1-dependent regulation of the mTOR signaling pathway delays aging","volume":"6","author":"Khapre","year":"2014","journal-title":"Aging"},{"key":"2023051709452635100_btz542-B19","doi-asserted-by":"crossref","first-page":"e271","DOI":"10.1093\/bioinformatics\/btl264","article-title":"A decompositional approach to parameter estimation in pathway modeling","volume":"22","author":"Koh","year":"2006","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B20","doi-asserted-by":"crossref","first-page":"1610","DOI":"10.1182\/blood-2013-01-481457","article-title":"Pim2 is required for maintaining multiple myeloma cell growth through modulating TSC2 phosphorylation","volume":"122","author":"Lu","year":"2013","journal-title":"Blood"},{"key":"2023051709452635100_btz542-B21","doi-asserted-by":"crossref","first-page":"e00393-17","DOI":"10.1128\/IAI.00393-17","article-title":"SipA activation of caspase-3 is a decisive mediator of host cell survival at early stages of Salmonella enterica serovar Typhimurium infection","volume":"85","author":"McIntosh","year":"2017","journal-title":"Infect. Immun"},{"key":"2023051709452635100_btz542-B22","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/nrc1647","article-title":"The role of focal-adhesion kinase in cancer. A new therapeutic opportunity","volume":"5","author":"Mclean","year":"2005","journal-title":"Nat. Rev. Cancer"},{"key":"2023051709452635100_btz542-B23","doi-asserted-by":"crossref","first-page":"10853","DOI":"10.1073\/pnas.0804821105","article-title":"mTORC1 promotes survival through translational control of Mcl-1","volume":"105","author":"Mills","year":"2008","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"2023051709452635100_btz542-B24","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/msb.2008.53","article-title":"Models from experiments: combinatorial drug perturbations of cancer cells","volume":"4","author":"Nelander","year":"2008","journal-title":"Mol. Syst. Biol"},{"key":"2023051709452635100_btz542-B25","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1093\/bioinformatics\/btv040","article-title":"Factor graph analysis of live cell\u2013imaging data reveals mechanisms of cell fate decisions","volume":"31","author":"Niederberger","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B26","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1093\/bioinformatics\/btt083","article-title":"Systematic parameter estimation in data-rich environments for cell signalling dynamics","volume":"29","author":"Nim","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B27","doi-asserted-by":"crossref","first-page":"313.","DOI":"10.1007\/s12307-011-0086-3","article-title":"The immune microenvironment of myeloma","volume":"4","author":"Noonan","year":"2011","journal-title":"Cancer Microenviron"},{"key":"2023051709452635100_btz542-B28","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1111\/ejn.13553","article-title":"NF-\u03baB signalling is involved in immune-modulation, but not basal functioning, of the mouse suprachiasmatic circadian clock","volume":"45","author":"O\u2019Keeffe","year":"2017","journal-title":"Eur. J. Neurosci"},{"key":"2023051709452635100_btz542-B29","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1111\/j.1349-7006.2009.01467.x","article-title":"Inhibition of mTORCI activity by REDD1 induction in myeloma cells resistant to bortezomib cytotoxicity","volume":"101","author":"Olivier Decaux","year":"2010","journal-title":"Cancer Sci"},{"key":"2023051709452635100_btz542-B30","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1038\/s41598-018-38246-3","article-title":"Neuronal message passing using mean-field, bethe, and marginal approximations","volume":"9","author":"Parr","year":"2019","journal-title":"Sci. Rep"},{"key":"2023051709452635100_btz542-B31","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ccr.2005.08.010","article-title":"Tensional homeostasis and the malignant phenotype","volume":"8","author":"Paszek","year":"2005","journal-title":"Cancer Cell"},{"key":"2023051709452635100_btz542-B32","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1093\/bioinformatics\/btu133","article-title":"Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach","volume":"30","author":"Peng","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B33","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/j.ccell.2016.02.018","article-title":"mTORC1-dependent metabolic reprogramming underlies escape from glycolysis addiction in cancer cells","volume":"29","author":"Pusapati","year":"2016","journal-title":"Cancer Cell"},{"key":"2023051709452635100_btz542-B34","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1093\/bioinformatics\/btm510","article-title":"Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference","volume":"23","author":"Quach","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B35","first-page":"162","article-title":"Regulation of NF-kB in multiple myeloma: therapeutic implications","volume":"2","author":"Rena","year":"2004","journal-title":"Clin. Adv. Hematol. Oncol"},{"key":"2023051709452635100_btz542-B36","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1038\/msb.2009.87","article-title":"Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction","volume":"5","author":"Saez-Rodriguez","year":"2009","journal-title":"Mol. Syst. Biol"},{"key":"2023051709452635100_btz542-B37","doi-asserted-by":"crossref","first-page":"6704","DOI":"10.1158\/0008-5472.CAN-10-0460","article-title":"Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis","volume":"70","author":"Sergio","year":"2010","journal-title":"Cancer Res"},{"key":"2023051709452635100_btz542-B38","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.cell.2015.09.001","article-title":"Nuclear FAK controls chemokine transcription, Tregs, and evasion of anti-tumor immunity","volume":"163","author":"Serrels","year":"2015","journal-title":"Cell"},{"key":"2023051709452635100_btz542-B39","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1093\/bioinformatics\/btx626","article-title":"PyDREAM: high-dimensional parameter inference for biological models in python","volume":"34","author":"Shockley","year":"2018","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B40","doi-asserted-by":"crossref","first-page":"1886","DOI":"10.3390\/ijms13021886","article-title":"The mTOR signalling pathway in human cancer","volume":"13","author":"Soares","year":"2012","journal-title":"Int. J. Mol. Sci"},{"key":"2023051709452635100_btz542-B41","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nrc3792","article-title":"FAK in cancer: mechanistic findings and clinical applications","volume":"14","author":"Sulzmaier","year":"2014","journal-title":"Nat. Rev. Cancer"},{"key":"2023051709452635100_btz542-B42","doi-asserted-by":"crossref","first-page":"8265","DOI":"10.1016\/j.biomaterials.2012.07.041","article-title":"Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway","volume":"33","author":"Sun","year":"2012","journal-title":"Biomaterials"},{"key":"2023051709452635100_btz542-B43","first-page":"1","article-title":"Emerging roles of focal adhesion kinase in cancer","volume":"2015","author":"Tai","year":"2015","journal-title":"Biomed Res. Int"},{"key":"2023051709452635100_btz542-B44","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S0022-1759(99)00199-4","article-title":"Isolation and characterization of human multiple myeloma cell enriched populations","volume":"235","author":"Tai","year":"2000","journal-title":"J. Immunol. Methods"},{"key":"2023051709452635100_btz542-B45","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/nrc2189","article-title":"Understanding multiple myeloma pathogenesis in the bone marrow to identify new therapeutic targets","volume":"7","author":"Teru","year":"2007","journal-title":"Nat. Rev. Cancer"},{"key":"2023051709452635100_btz542-B46","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1093\/bioinformatics\/btv655","article-title":"BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments","volume":"32","author":"Thomas","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051709452635100_btz542-B47","first-page":"2512","volume-title":"Mol. Cancer Ther","author":"Tibes","year":"2006"},{"key":"2023051709452635100_btz542-B48","doi-asserted-by":"crossref","first-page":"e12905","DOI":"10.1371\/journal.pone.0012905","article-title":"Matrix rigidity regulates cancer cell growth and cellular phenotype","volume":"5","author":"Tilghman","year":"2010","journal-title":"PLoS One"},{"key":"2023051709452635100_btz542-B49","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.semcancer.2007.08.002","article-title":"Focal adhesion kinase as a regulator of cell tension in the progression of cancer","volume":"18","author":"Tilghman","year":"2008","journal-title":"Semin. Cancer Biol"},{"key":"2023051709452635100_btz542-B50","doi-asserted-by":"crossref","first-page":"4167","DOI":"10.1158\/0008-5472.CAN-08-4859","article-title":"The mechanical rigidity of the extracellular matrix regulates the structure, motility, and proliferation of glioma cells","volume":"69","author":"Ulrich","year":"2009","journal-title":"Cancer Res"},{"key":"2023051709452635100_btz542-B51","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1109\/18.910585","article-title":"On the optimality of solutions of the max-product belief propagation algorithm in arbitrary graphs","volume":"47","author":"Weiss","year":"2001","journal-title":"IEEE Trans. Inf. Theory"},{"key":"2023051709452635100_btz542-B52","doi-asserted-by":"crossref","first-page":"313","DOI":"10.3233\/CBM-160643","article-title":"APE1 overexpression promotes the progression of ovarian cancer and serves as a potential therapeutic target","volume":"17","author":"Wen","year":"2016","journal-title":"Cancer Biomark"},{"key":"2023051709452635100_btz542-B53","author":"Yamashita","year":"2012"},{"key":"2023051709452635100_btz542-B54","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1634\/stemcells.2004-0226","article-title":"Characterization and localization of side population cells in mouse skin","volume":"23","author":"Yano","year":"2005","journal-title":"Stem Cells"},{"key":"2023051709452635100_btz542-B55","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.3892\/ol.2013.1597","article-title":"Asiatic acid, a triterpene, inhibits cell proliferation through regulating the expression of focal adhesion kinase in multiple myeloma cells","volume":"6","author":"Zhang","year":"2013","journal-title":"Oncol. Lett"},{"key":"2023051709452635100_btz542-B56","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.jtbi.2006.06.034","article-title":"Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer","volume":"244","author":"Zhang","year":"2007","journal-title":"J. Theor. Biol"},{"key":"2023051709452635100_btz542-B57","doi-asserted-by":"crossref","first-page":"14877","DOI":"10.1039\/C6NR01637E","article-title":"Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization\/validation","volume":"8","author":"Zhang","year":"2016","journal-title":"Nanoscale"},{"key":"2023051709452635100_btz542-B58","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/jmcb\/mjx056","article-title":"EZH2-, CHD4-, and IDH-linked epigenetic perturbation and its association with survival in glioma patients","volume":"9","author":"Zhang","year":"2017","journal-title":"J. Mol. Cell Biol"},{"key":"2023051709452635100_btz542-B59","first-page":"1","article-title":"Building up a robust risk mathematical platform to predict colorectal cancer","volume":"2017","author":"Zhang","year":"2017","journal-title":"Complexity"},{"key":"2023051709452635100_btz542-B60","doi-asserted-by":"crossref","first-page":"e1007069","DOI":"10.1371\/journal.pcbi.1007069","article-title":"Comprehensively benchmarking applications for detecting copy number variation","volume":"15","author":"Zhang","year":"2019","journal-title":"PLoS Comput. Biol"},{"key":"2023051709452635100_btz542-B61","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/s12859-019-2741-5","article-title":"Computed tomography angiography-based analysis of high-risk intracerebral haemorrhage patients by employing a mathematical model","volume":"20 (Suppl. 7)","author":"Zhang","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2023051709452635100_btz542-B62","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.plrev.2017.01.007","article-title":"Using game theory to investigate the epigenetic control mechanisms of embryo development: comment on: \u201cEpigenetic game theory: how to compute the epigenetic control of maternal-to-zygotic transition\u201d by Qian Wang et al","volume":"20","author":"Zhang","year":"2017","journal-title":"Phys. Life Rev"},{"key":"2023051709452635100_btz542-B63","doi-asserted-by":"crossref","first-page":"17046","DOI":"10.1038\/srep17046","article-title":"PRL-3 activates mTORC1 in cancer progression","volume":"5","author":"Zu","year":"2015","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz542\/29106893\/btz542.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/11\/1554\/50361121\/btz542.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/11\/1554\/50361121\/btz542.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T10:28:03Z","timestamp":1684319283000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/11\/1554\/5539692"}},"subtitle":[],"editor":[{"given":"Kelso","family":"Janet","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,7,26]]},"references-count":63,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2021,7,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz542","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,6,1]]},"published":{"date-parts":[[2019,7,26]]}}}