{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T17:13:56Z","timestamp":1761844436959},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"S12","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-s12-s6","type":"journal-article","created":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T16:03:04Z","timestamp":1415289784000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data"],"prefix":"10.1186","volume":"15","author":[{"given":"Zijing","family":"Mao","sequence":"first","affiliation":[]},{"given":"Chifeng","family":"Ma","sequence":"additional","affiliation":[]},{"given":"Tim H-M","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Yidong","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Yufei","family":"Huang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,11,6]]},"reference":[{"key":"6677_CR1","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/B978-0-12-380866-0.60002-2","volume":"70","author":"M Kulis","year":"2010","unstructured":"Kulis M, Esteller M: DNA methylation and cancer. Adv Genet. 2010, 70: 27-56.","journal-title":"Adv Genet"},{"key":"6677_CR2","doi-asserted-by":"crossref","unstructured":"Yang AS: A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Research. 2004, 32 (3):","DOI":"10.1093\/nar\/gnh032"},{"issue":"2","key":"6677_CR3","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1101\/gr.125872.111","volume":"22","author":"GC Hon","year":"2012","unstructured":"Hon GC: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012, 22 (2): 246-58. 10.1101\/gr.125872.111.","journal-title":"Genome Res"},{"issue":"4","key":"6677_CR4","doi-asserted-by":"publisher","first-page":"e60980","DOI":"10.1371\/journal.pone.0060980","volume":"8","author":"F Gu","year":"2013","unstructured":"Gu F: CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. PLoS One. 2013, 8 (4): e60980-10.1371\/journal.pone.0060980.","journal-title":"PLoS One"},{"issue":"12","key":"6677_CR5","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1101\/gr.110601.110","volume":"20","author":"MD Robinson","year":"2010","unstructured":"Robinson MD: Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res. 2010, 20 (12): 1719-29. 10.1101\/gr.110601.110.","journal-title":"Genome Res"},{"issue":"10","key":"6677_CR6","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1038\/nbt.1681","volume":"28","author":"C Bock","year":"2010","unstructured":"Bock C: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010, 28 (10): 1106-14. 10.1038\/nbt.1681.","journal-title":"Nat Biotechnol"},{"issue":"12","key":"6677_CR7","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1038\/nbt.1508","volume":"26","author":"PV Kharchenko","year":"2008","unstructured":"Kharchenko PV, Tolstorukov MY, Park PJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008, 26 (12): 1351-9. 10.1038\/nbt.1508.","journal-title":"Nat Biotechnol"},{"issue":"9","key":"6677_CR8","doi-asserted-by":"publisher","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang Y: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9 (9): R137-10.1186\/gb-2008-9-9-r137.","journal-title":"Genome Biol"},{"key":"6677_CR9","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1186\/1471-2105-11-369","volume":"11","author":"ZS Qin","year":"2010","unstructured":"Qin ZS: HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics. 2010, 11: 369-10.1186\/1471-2105-11-369.","journal-title":"BMC Bioinformatics"},{"issue":"22","key":"6677_CR10","doi-asserted-by":"publisher","first-page":"2930","DOI":"10.1093\/bioinformatics\/bts562","volume":"28","author":"M Seifert","year":"2012","unstructured":"Seifert M: MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics. 2012, 28 (22): 2930-9. 10.1093\/bioinformatics\/bts562.","journal-title":"Bioinformatics"},{"issue":"8","key":"6677_CR11","doi-asserted-by":"publisher","first-page":"e39573","DOI":"10.1371\/journal.pone.0039573","volume":"7","author":"NU Nair","year":"2012","unstructured":"Nair NU: ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PLoS One. 2012, 7 (8): e39573-10.1371\/journal.pone.0039573.","journal-title":"PLoS One"},{"issue":"20","key":"6677_CR12","doi-asserted-by":"publisher","first-page":"2344","DOI":"10.1093\/bioinformatics\/btn402","volume":"24","author":"H Xu","year":"2008","unstructured":"Xu H: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics. 2008, 24 (20): 2344-9. 10.1093\/bioinformatics\/btn402.","journal-title":"Bioinformatics"},{"issue":"18","key":"6677_CR13","doi-asserted-by":"publisher","first-page":"2334","DOI":"10.1093\/bioinformatics\/btp384","volume":"25","author":"C Taslim","year":"2009","unstructured":"Taslim C: Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics. 2009, 25 (18): 2334-40. 10.1093\/bioinformatics\/btp384.","journal-title":"Bioinformatics"},{"key":"6677_CR14","first-page":"126","volume-title":"Channel state testing in information decoding","author":"HL Yudkin","year":"1965","unstructured":"Yudkin HL: Channel state testing in information decoding. 1965, 126-leaves"},{"issue":"12","key":"6677_CR15","doi-asserted-by":"publisher","first-page":"e86","DOI":"10.1093\/nar\/gkp383","volume":"37","author":"F Malentacchi","year":"2009","unstructured":"Malentacchi F: Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol. Nucleic Acids Res. 2009, 37 (12): e86-10.1093\/nar\/gkp383.","journal-title":"Nucleic Acids Res"},{"issue":"7-8","key":"6677_CR16","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.1016\/j.biocel.2007.03.006","volume":"39","author":"J Lewin","year":"2007","unstructured":"Lewin J: Comparative DNA methylation analysis in normal and tumour tissues and in cancer cell lines using differential methylation hybridisation. Int J Biochem Cell Biol. 2007, 39 (7-8): 1539-50. 10.1016\/j.biocel.2007.03.006.","journal-title":"Int J Biochem Cell Biol"},{"issue":"14","key":"6677_CR17","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-60. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"issue":"23","key":"6677_CR18","doi-asserted-by":"publisher","first-page":"6569","DOI":"10.1093\/emboj\/19.23.6569","volume":"19","author":"P Ajuh","year":"2000","unstructured":"Ajuh P: Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry. EMBO J. 2000, 19 (23): 6569-81. 10.1093\/emboj\/19.23.6569.","journal-title":"EMBO J"},{"issue":"2","key":"6677_CR19","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1006\/geno.1998.5254","volume":"49","author":"PM Groenen","year":"1998","unstructured":"Groenen PM: Rearrangement of the human CDC5L gene by a t(6;19)(p21;q13.1) in a patient with multicystic renal dysplasia. Genomics. 1998, 49 (2): 218-29. 10.1006\/geno.1998.5254.","journal-title":"Genomics"},{"issue":"19","key":"6677_CR20","doi-asserted-by":"publisher","first-page":"17091","DOI":"10.1074\/jbc.M110.208769","volume":"286","author":"K Ganesh","year":"2011","unstructured":"Ganesh K: CTNNBL1 is a novel nuclear localization sequence-binding protein that recognizes RNA-splicing factors CDC5L and Prp31. Journal of Biological Chemistry. 2011, 286 (19): 17091-102. 10.1074\/jbc.M110.208769.","journal-title":"Journal of Biological Chemistry"},{"issue":"6","key":"6677_CR21","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1158\/1541-7786.MCR-07-2115","volume":"6","author":"XY Lu","year":"2008","unstructured":"Lu XY: Cell cycle regulator gene CDC5L, a potential target for 6p12-p21 amplicon in osteosarcoma. Mol Cancer Res. 2008, 6 (6): 937-46. 10.1158\/1541-7786.MCR-07-2115.","journal-title":"Mol Cancer Res"},{"issue":"2","key":"6677_CR22","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1158\/0008-5472.CAN-12-1321","volume":"73","author":"A Wakefield","year":"2013","unstructured":"Wakefield A: Bcl3 selectively promotes metastasis of ERBB2-driven mammary tumors. Cancer Res. 2013, 73 (2): 745-55. 10.1158\/0008-5472.CAN-12-1321.","journal-title":"Cancer Res"},{"issue":"1-2","key":"6677_CR23","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.mce.2011.07.021","volume":"345","author":"T Mitsui","year":"2011","unstructured":"Mitsui T: Inhibition of Bcl3 gene expression mediates the anti-proliferative action of estrogen in pituitary lactotrophs in primary culture. Mol Cell Endocrinol. 2011, 345 (1-2): 68-78. 10.1016\/j.mce.2011.07.021.","journal-title":"Mol Cell Endocrinol"},{"issue":"3","key":"6677_CR24","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1016\/j.bbrc.2010.08.084","volume":"400","author":"HJ Choi","year":"2010","unstructured":"Choi HJ: Bcl3-dependent stabilization of CtBP1 is crucial for the inhibition of apoptosis and tumor progression in breast cancer. Biochem Biophys Res Commun. 2010, 400 (3): 396-402. 10.1016\/j.bbrc.2010.08.084.","journal-title":"Biochem Biophys Res Commun"},{"issue":"32","key":"6677_CR25","doi-asserted-by":"publisher","first-page":"3709","DOI":"10.1038\/onc.2011.529","volume":"31","author":"Z Huang","year":"2012","unstructured":"Huang Z: Tumor suppressor Alpha B-crystallin (CRYAB) associates with the cadherin\/catenin adherens junction and impairs NPC progression-associated properties. Oncogene. 2012, 31 (32): 3709-20. 10.1038\/onc.2011.529.","journal-title":"Oncogene"},{"issue":"20","key":"6677_CR26","doi-asserted-by":"publisher","first-page":"8390","DOI":"10.1073\/pnas.1101747108","volume":"108","author":"AK Cheung","year":"2011","unstructured":"Cheung AK: Cysteine-rich intestinal protein 2 (CRIP2) acts as a repressor of NF-kappaB-mediated proangiogenic cytokine transcription to suppress tumorigenesis and angiogenesis. Proc Natl Acad Sci USA. 2011, 108 (20): 8390-5. 10.1073\/pnas.1101747108.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6677_CR27","volume-title":"Pathol Oncol Res","author":"LS Zhang","year":"2014","unstructured":"Zhang LS: Association of Genetic Polymorphisms in HSD17B1, HSD17B2 and SHBG Genes with Hepatocellular Carcinoma Risk. Pathol Oncol Res. 2014"},{"issue":"2","key":"6677_CR28","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1007\/s10549-013-2448-7","volume":"138","author":"O Obazee","year":"2013","unstructured":"Obazee O: Confirmation of the reduction of hormone replacement therapy-related breast cancer risk for carriers of the HSD17B1_937_G variant. Breast Cancer Res Treat. 2013, 138 (2): 543-8. 10.1007\/s10549-013-2448-7.","journal-title":"Breast Cancer Res Treat"},{"issue":"1","key":"6677_CR29","doi-asserted-by":"publisher","first-page":"e85592","DOI":"10.1371\/journal.pone.0085592","volume":"9","author":"RZ Luo","year":"2014","unstructured":"Luo RZ: Decreased Expression of PTPN12 Correlates with Tumor Recurrence and Poor Survival of Patients with Hepatocellular Carcinoma. PLoS One. 2014, 9 (1): e85592-10.1371\/journal.pone.0085592.","journal-title":"PLoS One"},{"issue":"1-2","key":"6677_CR30","first-page":"151","volume":"375","author":"E Villa-Moruzzi","year":"2013","unstructured":"Villa-Moruzzi E: PTPN12 controls PTEN and the AKT signalling to FAK and HER2 in migrating ovarian cancer cells. Mol Cell Biochem. 2013, 375 (1-2): 151-7.","journal-title":"Mol Cell Biochem"},{"issue":"5","key":"6677_CR31","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/j.cell.2011.02.003","volume":"144","author":"T Sun","year":"2011","unstructured":"Sun T: Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase. Cell. 2011, 144 (5): 703-18. 10.1016\/j.cell.2011.02.003.","journal-title":"Cell"},{"issue":"7","key":"6677_CR32","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1162\/neco.2006.18.7.1527","volume":"18","author":"GE Hinton","year":"2006","unstructured":"Hinton GE, Osindero S, Teh YW: A fast learning algorithm for deep belief nets. Neural Computation. 2006, 18 (7): 1527-1554. 10.1162\/neco.2006.18.7.1527.","journal-title":"Neural Computation"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S12-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T14:51:34Z","timestamp":1650552694000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S12-S6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,6]]},"references-count":32,"journal-issue":{"issue":"S12","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6677"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s12-s6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,6]]},"assertion":[{"value":"6 November 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S6"}}