{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:17:51Z","timestamp":1763468271347,"version":"3.37.3"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,10,7]],"date-time":"2015-10-07T00:00:00Z","timestamp":1444176000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2015,10,7]],"date-time":"2015-10-07T00:00:00Z","timestamp":1444176000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIP-1265265"],"award-info":[{"award-number":["IIP-1265265"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Netw Model Anal Health Inform Bioinforma"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1007\/s13721-015-0099-9","type":"journal-article","created":{"date-parts":[[2015,10,7]],"date-time":"2015-10-07T11:42:55Z","timestamp":1444218175000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A gene expression-based mathematical modeling approach for breast cancer tumor growth and shrinkage"],"prefix":"10.1007","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0792-1251","authenticated-orcid":false,"given":"Aydin","family":"Saribudak","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen","family":"Gundry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianmin","family":"Zou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. \u00dcmit","family":"Uyar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,10,7]]},"reference":[{"issue":"6","key":"99_CR1","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/0895-7177(96)00018-0","volume":"23","author":"Z Bajzer","year":"1996","unstructured":"Bajzer Z, Maru\u0161i\u0107 M, Vuk-Pavlovi\u0107 S (1996) Conceptual frameworks for mathematical modeling of tumor growth dynamics. Math Comput Model 23(6):31\u201346","journal-title":"Math Comput Model"},{"issue":"5","key":"99_CR2","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1002\/jps.3000","volume":"91","author":"A Chakraborty","year":"2002","unstructured":"Chakraborty A, Jusko WJ (2002) Pharmacodynamic interaction of recombinant human interleukin-10 and prednisolone using in vitro whole blood lymphocyte proliferation. J Pharm Sci 91(5):1334\u20131342","journal-title":"J Pharm Sci"},{"key":"99_CR3","first-page":"1","volume":"7","author":"J Dem\u0161ar","year":"2006","unstructured":"Dem\u0161ar J (2006) Statistical comparisons of classifiers over multiple data sets. J Mach Learn Res 7:1\u201330","journal-title":"J Mach Learn Res"},{"issue":"1","key":"99_CR4","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: Ncbi gene expression and hybridization array data repository. Nucleic Acids Res 30(1):207\u2013210","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"99_CR5","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1007\/s10549-011-1895-2","volume":"132","author":"LJ Esserman","year":"2012","unstructured":"Esserman LJ, Berry DA, Cheang MC, Yau C, Perou CM, Carey L, DeMichele A, Gray JW, Conway-Dorsey K, Lenburg ME et al (2012) Chemotherapy response and recurrence-free survival in neoadjuvant breast cancer depends on biomarker profiles: results from the i-spy 1 trial (calgb 150007\/150012; acrin 6657). Breast Cancer Res Treatment 132(3):1049\u20131062","journal-title":"Breast Cancer Res Treatment"},{"issue":"26","key":"99_CR6","doi-asserted-by":"publisher","first-page":"3242","DOI":"10.1200\/JCO.2011.39.2779","volume":"30","author":"LJ Esserman","year":"2012","unstructured":"Esserman LJ, Berry DA, DeMichele A, Carey L, Davis SE, Buxton M, Hudis C, Gray JW, Perou C, Yau C et al (2012) Pathologic complete response predicts recurrence-free survival more effectively by cancer subset: results from the i-spy 1 trial-calgb 150007\/150012, acrin 6657. J Clin Oncol 30(26):3242\u20133249","journal-title":"J Clin Oncol"},{"issue":"7","key":"99_CR7","first-page":"1551","volume":"56","author":"JL Falany","year":"1996","unstructured":"Falany JL, Falany CN (1996) Expression of cytosolic sulfotransferases in normal mammary epithelial cells and breast cancer cell lines. Cancer Res 56(7):1551\u20131555","journal-title":"Cancer Res"},{"key":"99_CR8","unstructured":"Ganic E, Gundry S, Zou J, Uyar MU (2014) Evaluation of anticancer therapy using in silico analysis of treatments for HER2+ breast cancer. In: IEEE international symposium on medical measurements and applications (MeMeA 2014). Lisbon, pp 211\u2013216"},{"issue":"16","key":"99_CR9","first-page":"5979","volume":"61","author":"S Gruvberger","year":"2001","unstructured":"Gruvberger S, Ringn\u00e9r M, Chen Y, Panavally S, Saal LH, Borg \u00c5, Fern\u00f6 M, Peterson C, Meltzer PS (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 61(16):5979\u20135984","journal-title":"Cancer Res"},{"key":"99_CR10","doi-asserted-by":"crossref","unstructured":"Gundry S, Zou J, Urrea E, Sahin C, Kusyk J, Uyar M (2012) Analysis of emergent behavior for ga-based topology control mechanism for self-spreading nodes in MANETs, vol 422. In: Advances in intelligent modelling and simulation, series studies in computational intelligence. Springer, Berlin, pp 155\u2013183","DOI":"10.1007\/978-3-642-30154-4_8"},{"issue":"12","key":"99_CR11","doi-asserted-by":"publisher","first-page":"2042","DOI":"10.1016\/j.compchemeng.2009.06.005","volume":"33","author":"J Harrold","year":"2009","unstructured":"Harrold J, Parker R (2009) Clinically relevant cancer chemotherapy dose scheduling via mixed-integer optimization. Comput Chem Eng 33(12):2042\u20132054","journal-title":"Comput Chem Eng"},{"issue":"4","key":"99_CR12","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1186\/bcr2889","volume":"13","author":"DL Holliday","year":"2011","unstructured":"Holliday DL, Speirs V (2011) Choosing the right cell line for breast cancer research. Breast Cancer Res 13(4):215","journal-title":"Breast Cancer Res"},{"issue":"9","key":"99_CR13","doi-asserted-by":"publisher","first-page":"3196","DOI":"10.1158\/0008-5472.CAN-10-3471","volume":"71","author":"D Iliopoulos","year":"2011","unstructured":"Iliopoulos D, Hirsch HA, Struhl K (2011) Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types. Cancer Res 71(9):3196\u20133201","journal-title":"Cancer Res"},{"key":"99_CR14","doi-asserted-by":"crossref","unstructured":"Kayano M, Shiga M, Mamitsuka H (2014) Detecting differentially coexpressed genes from labeled expression data: a brief review","DOI":"10.1109\/TCBB.2013.2297921"},{"key":"99_CR15","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/s10928-009-9117-9","volume":"36","author":"G Koch","year":"2009","unstructured":"Koch G, Walz A, Lahu G et al (2009) Modeling of tumor growth and anticancer effects of combination therapy. J Pharmacokinet Pharmacodyn 36:179\u2013197","journal-title":"J Pharmacokinet Pharmacodyn"},{"issue":"3","key":"99_CR16","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.jare.2011.04.006","volume":"2","author":"J Kusyk","year":"2011","unstructured":"Kusyk J, Sahin C, Uyar M, Urrea E, Gundry S (2011) Self organization of nodes in mobile ad hoc networks using evolutionary games and genetic algorithms. J Adv Res 2(3):253\u2013264","journal-title":"J Adv Res"},{"issue":"8","key":"99_CR17","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1200\/JCO.2007.14.4147","volume":"26","author":"C Liedtke","year":"2008","unstructured":"Liedtke C, Mazouni C, Hess KR, Andr\u00e9 F, Tordai A, Mejia JA, Symmans WF, Gonzalez-Angulo AM, Hennessy B, Green M et al (2008) Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J Clin Oncol 26(8):1275\u20131281","journal-title":"J Clin Oncol"},{"key":"99_CR18","doi-asserted-by":"crossref","unstructured":"Louangrath PI (2014) Correlation coefficient according to data classification. SSRN 2417910","DOI":"10.2139\/ssrn.2417910"},{"issue":"1","key":"99_CR19","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/bcr2222","volume":"11","author":"X-J Ma","year":"2009","unstructured":"Ma X-J, Dahiya S, Richardson E, Erlander M, Sgroi DC (2009) Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res 11(1):R7","journal-title":"Breast Cancer Res"},{"issue":"2","key":"99_CR20","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1006\/jmaa.1993.1361","volume":"179","author":"M Marusic","year":"1993","unstructured":"Marusic M, Bajzer Z (1993) Generalized two-parameter equation of growth. J Math Anal Appl 179(2):446\u2013462","journal-title":"J Math Anal Appl"},{"issue":"4","key":"99_CR21","first-page":"428","volume":"5","author":"WL McGuire","year":"1978","unstructured":"McGuire WL (1978) Hormone receptors: their role in predicting prognosis and response to endocrine therapy. Semin Oncol 5(4):428\u2013433","journal-title":"Semin Oncol"},{"issue":"7050","key":"99_CR22","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/nature03799","volume":"436","author":"AJ Minn","year":"2005","unstructured":"Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB, Gerald WL, Massagu\u00e9 J (2005) Genes that mediate breast cancer metastasis to lung. Nature 436(7050):518\u2013524","journal-title":"Nature"},{"issue":"Suppl 1","key":"99_CR23","first-page":"1009","volume":"53","author":"A Nicholas","year":"2012","unstructured":"Nicholas A, Mulhern P, Siegel E (2012) The National Biomedical Imaging Archive: a repository of advanced imaging information. J Nucl Med 53(Suppl 1):1009","journal-title":"J Nucl Med"},{"issue":"4","key":"99_CR24","first-page":"835","volume":"4","author":"LL Nielsen","year":"1998","unstructured":"Nielsen LL, Lipari P, Dell J, Gurnani M, Hajian G (1998) Adenovirus-mediated p53 gene therapy and paclitaxel have synergistic efficacy in models of human head and neck, ovarian, prostate, and breast cancer. Clin Cancer Res 4(4):835\u2013846","journal-title":"Clin Cancer Res"},{"issue":"6","key":"99_CR25","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1634\/theoncologist.10-6-370","volume":"10","author":"L Norton","year":"2005","unstructured":"Norton L (2005) Conceptual and practical implications of breast tissue geometry: toward a more effective, less toxic therapy. Oncologist 10(6):370\u2013381","journal-title":"Oncologist"},{"issue":"4","key":"99_CR26","first-page":"1172","volume":"8","author":"JW Park","year":"2002","unstructured":"Park JW, Hong K, Kirpotin DB, Colbern G, Shalaby R, Baselga J, Shao Y, Nielsen UB, Marks JD, Moore D et al (2002) Anti-her2 immunoliposomes enhanced efficacy attributable to targeted delivery. Clin Cancer Res 8(4):1172\u20131181","journal-title":"Clin Cancer Res"},{"issue":"12","key":"99_CR27","doi-asserted-by":"publisher","first-page":"1862","DOI":"10.1016\/j.ejca.2007.05.011","volume":"43","author":"M Rocchetti","year":"2007","unstructured":"Rocchetti M, Simeoni M, Pesenti E et al (2007) Predicting the active doses in humans from animal studies: a novel approach in oncology. Eur J Cancer 43(12):1862\u20131868","journal-title":"Eur J Cancer"},{"key":"99_CR28","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1007\/s10846-011-9649-2","volume":"67","author":"CS Sahin","year":"2012","unstructured":"Sahin CS, Gundry S, Uyar MU (2012) Markov chain analysis of self-organizing mobile nodes. J Intell Robot Sys 67:133\u2013153","journal-title":"J Intell Robot Sys"},{"key":"99_CR29","doi-asserted-by":"crossref","unstructured":"Sahin C, Uyar MU, Gundry S, Urrea E (2012) Self organization for area coverage maximization and energy conservation in mobilead hoc networks. In: Transactions on computational science XV. Springer, pp 49\u201373","DOI":"10.1007\/978-3-642-28525-7_2"},{"key":"99_CR30","unstructured":"Saribudak A, Ganic E, Zou J, Gundry S, Uyar MU (2014) Toward genomic based personalized mathematical models for reast cancer tumor growth. In: IEEE 14th International conference on bioinformatics and bioengineering (BIBE), Nov 2014, pp 115\u2013119"},{"key":"99_CR31","doi-asserted-by":"publisher","first-page":"1094","DOI":"10.1158\/0008-5472.CAN-03-2524","volume":"64","author":"M Simeoni","year":"2004","unstructured":"Simeoni M, Magni P, Cammia C et al (2004) Predictive pharmacokinetic pharmacodynamic modeling of tumor growth kinetics in xenograft models after administration of anticancer agents. Cancer Res 64:1094\u20131101","journal-title":"Cancer Res"},{"issue":"18","key":"99_CR32","doi-asserted-by":"publisher","first-page":"10393","DOI":"10.1073\/pnas.1732912100","volume":"100","author":"C Sotiriou","year":"2003","unstructured":"Sotiriou C, Neo S-Y, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET (2003) Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci 100(18):10393\u201310398","journal-title":"Proc Natl Acad Sci"},{"issue":"5643","key":"99_CR33","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1126\/science.1087447","volume":"302","author":"JM Stuart","year":"2003","unstructured":"Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302(5643):249\u2013255","journal-title":"Science"},{"issue":"6871","key":"99_CR34","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1038\/415530a","volume":"415","author":"LJ van\u2019t Veer","year":"2002","unstructured":"van\u2019t Veer LJ, Dai H, Van De Vijver MJ et al (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871):530\u2013536","journal-title":"Nature"},{"issue":"3","key":"99_CR35","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1016\/j.ygyno.2013.03.008","volume":"129","author":"AE Wagner","year":"2013","unstructured":"Wagner AE, Pappas L, Ghia AJ, Gaffney DK (2013) Impact of tumor size on survival in cancer of the cervix and validation of stage iia1 and iia2 subdivisions. Gynecol Oncol 129(3):517\u2013521","journal-title":"Gynecol Oncol"},{"key":"99_CR36","unstructured":"Zou J, Gundry S, Ganic E, Uyar MU (2014) Mathematical models for absorption and efficacy of ovarian cancer treatments. In: Proceedings 36th IEEE engineering in medicine and biology society conference (EMBC), Aug 2014, pp 3442\u20133445"}],"container-title":["Network Modeling Analysis in Health Informatics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-015-0099-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s13721-015-0099-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-015-0099-9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-015-0099-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T08:37:56Z","timestamp":1589445476000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s13721-015-0099-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,7]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["99"],"URL":"https:\/\/doi.org\/10.1007\/s13721-015-0099-9","relation":{},"ISSN":["2192-6662","2192-6670"],"issn-type":[{"type":"print","value":"2192-6662"},{"type":"electronic","value":"2192-6670"}],"subject":[],"published":{"date-parts":[[2015,10,7]]},"assertion":[{"value":"9 March 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 July 2015","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2015","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 October 2015","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors do not declare any conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"28"}}