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For: Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 2009;19:167-77. [PMID: 19056696 DOI: 10.1101/gr.080259.108] [Cited by in Crossref: 80] [Cited by in F6Publishing: 84] [Article Influence: 5.7] [Reference Citation Analysis]
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3 Nayak S, Calvo JA, Cong K, Peng M, Berthiaume E, Jackson J, Zaino AM, Vindigni A, Hadden MK, Cantor SB. Inhibition of the translesion synthesis polymerase REV1 exploits replication gaps as a cancer vulnerability. Sci Adv 2020;6:eaaz7808. [PMID: 32577513 DOI: 10.1126/sciadv.aaz7808] [Cited by in Crossref: 27] [Cited by in F6Publishing: 38] [Article Influence: 13.5] [Reference Citation Analysis]
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5 Amirfallah A, Arason A, Einarsson H, Gudmundsdottir ET, Freysteinsdottir ES, Olafsdottir KA, Johannsson OT, Agnarsson BA, Barkardottir RB, Reynisdottir I. High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer. PLoS One 2019;14:e0221413. [PMID: 31442252 DOI: 10.1371/journal.pone.0221413] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 0.7] [Reference Citation Analysis]
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8 Hayashi T, Hikichi M, Yukitake J, Wakatsuki T, Nishio E, Utsumi T, Harada N. Forskolin increases the effect of everolimus on aromatase inhibitor-resistant breast cancer cells. Oncotarget 2018;9:23451-61. [PMID: 29805747 DOI: 10.18632/oncotarget.25217] [Cited by in Crossref: 4] [Cited by in F6Publishing: 5] [Article Influence: 1.0] [Reference Citation Analysis]
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11 Borghei YS, Hosseini M, Ganjali MR. Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters. Methods Appl Fluoresc 2017;6:015001. [PMID: 28858858 DOI: 10.1088/2050-6120/aa8988] [Cited by in Crossref: 14] [Cited by in F6Publishing: 19] [Article Influence: 2.8] [Reference Citation Analysis]
12 Xie H, Rachakonda PS, Heidenreich B, Nagore E, Sucker A, Hemminki K, Schadendorf D, Kumar R. Mapping of deletion breakpoints at the CDKN2A locus in melanoma: detection of MTAP-ANRIL fusion transcripts. Oncotarget 2016;7:16490-504. [PMID: 26909863 DOI: 10.18632/oncotarget.7503] [Cited by in Crossref: 14] [Cited by in F6Publishing: 12] [Article Influence: 2.8] [Reference Citation Analysis]
13 Dobrolecki LE, Airhart SD, Alferez DG, Aparicio S, Behbod F, Bentires-Alj M, Brisken C, Bult CJ, Cai S, Clarke RB, Dowst H, Ellis MJ, Gonzalez-Suarez E, Iggo RD, Kabos P, Li S, Lindeman GJ, Marangoni E, McCoy A, Meric-Bernstam F, Piwnica-Worms H, Poupon MF, Reis-Filho J, Sartorius CA, Scabia V, Sflomos G, Tu Y, Vaillant F, Visvader JE, Welm A, Wicha MS, Lewis MT. Patient-derived xenograft (PDX) models in basic and translational breast cancer research. Cancer Metastasis Rev 2016;35:547-73. [PMID: 28025748 DOI: 10.1007/s10555-016-9653-x] [Cited by in Crossref: 117] [Cited by in F6Publishing: 122] [Article Influence: 23.4] [Reference Citation Analysis]
14 Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA. SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads. BMC Genomics 2017;18:691. [PMID: 28984202 DOI: 10.1186/s12864-017-4021-y] [Cited by in Crossref: 4] [Cited by in F6Publishing: 2] [Article Influence: 0.8] [Reference Citation Analysis]
15 Kumar S, Razzaq SK, Vo AD, Gautam M, Li H. Identifying fusion transcripts using next generation sequencing. Wiley Interdiscip Rev RNA 2016;7:811-23. [PMID: 27485475 DOI: 10.1002/wrna.1382] [Cited by in Crossref: 49] [Cited by in F6Publishing: 49] [Article Influence: 8.2] [Reference Citation Analysis]
16 Kalvala A, Gao L, Aguila B, Dotts K, Rahman M, Nana-Sinkam SP, Zhou X, Wang QE, Amann J, Otterson GA, Villalona-Calero MA, Duan W. Rad51C-ATXN7 fusion gene expression in colorectal tumors. Mol Cancer 2016;15:47. [PMID: 27296891 DOI: 10.1186/s12943-016-0527-1] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 1.0] [Reference Citation Analysis]
17 Rhoads A, Au KF. PacBio Sequencing and Its Applications. Genomics Proteomics Bioinformatics 2015;13:278-89. [PMID: 26542840 DOI: 10.1016/j.gpb.2015.08.002] [Cited by in Crossref: 923] [Cited by in F6Publishing: 835] [Article Influence: 131.9] [Reference Citation Analysis]
18 Li H, Chen H, Liu F, Ren C, Wang S, Bo X, Shu W. Functional annotation of HOT regions in the human genome: implications for human disease and cancer. Sci Rep 2015;5:11633. [PMID: 26113264 DOI: 10.1038/srep11633] [Cited by in Crossref: 19] [Cited by in F6Publishing: 14] [Article Influence: 2.7] [Reference Citation Analysis]
19 Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res 2015;43:e116. [PMID: 26040699 DOI: 10.1093/nar/gkv562] [Cited by in Crossref: 68] [Cited by in F6Publishing: 65] [Article Influence: 9.7] [Reference Citation Analysis]
20 Mourad R, Hsu PY, Juan L, Shen C, Koneru P, Lin H, Liu Y, Nephew K, Huang TH, Li L. Estrogen induces global reorganization of chromatin structure in human breast cancer cells. PLoS One 2014;9:e113354. [PMID: 25470140 DOI: 10.1371/journal.pone.0113354] [Cited by in Crossref: 34] [Cited by in F6Publishing: 37] [Article Influence: 4.3] [Reference Citation Analysis]
21 Węsierska-Gądek J, Heinzl S. Interactions Between Ataxia Telangiectasia Mutated Kinase Inhibition, Poly(ADP-ribose) Polymerase-1 Inhibition and BRCA1 Status in Breast Cancer Cells. J Cancer Prev 2014;19:125-36. [PMID: 25337581 DOI: 10.15430/JCP.2014.19.2.125] [Cited by in Crossref: 4] [Cited by in F6Publishing: 5] [Article Influence: 0.5] [Reference Citation Analysis]
22 Rai A, Menon AV, Jalan S. Randomness and preserved patterns in cancer network. Sci Rep 2014;4:6368. [PMID: 25220184 DOI: 10.1038/srep06368] [Cited by in Crossref: 19] [Cited by in F6Publishing: 14] [Article Influence: 2.4] [Reference Citation Analysis]
23 Cope LM, Fackler MJ, Lopez-Bujanda Z, Wolff AC, Visvanathan K, Gray JW, Sukumar S, Umbricht CB. Do breast cancer cell lines provide a relevant model of the patient tumor methylome? PLoS One 2014;9:e105545. [PMID: 25157401 DOI: 10.1371/journal.pone.0105545] [Cited by in Crossref: 13] [Cited by in F6Publishing: 13] [Article Influence: 1.6] [Reference Citation Analysis]
24 Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A. Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools. BMC Bioinformatics 2014;15 Suppl 7:S2. [PMID: 25080362 DOI: 10.1186/1471-2105-15-S7-S2] [Cited by in Crossref: 12] [Cited by in F6Publishing: 11] [Article Influence: 1.5] [Reference Citation Analysis]
25 Yang H, Volfovsky N, Rattray A, Chen X, Tanaka H, Strathern J. GAP-Seq: a method for identification of DNA palindromes. BMC Genomics 2014;15:394. [PMID: 24885769 DOI: 10.1186/1471-2164-15-394] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 0.9] [Reference Citation Analysis]
26 Speers C, Feng FY, Pierce LJ. PARP-1 inhibitors and radiotherapy sensitivity: future prospects for therapy? Breast Cancer Management 2014;3:281-96. [DOI: 10.2217/bmt.14.6] [Cited by in Crossref: 2] [Article Influence: 0.3] [Reference Citation Analysis]
27 Patel A, Schwab R, Liu YT, Bafna V. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Res 2014;24:318-28. [PMID: 24307551 DOI: 10.1101/gr.161497.113] [Cited by in Crossref: 13] [Cited by in F6Publishing: 12] [Article Influence: 1.4] [Reference Citation Analysis]
28 Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, Heerema N, Hsiao TH, Chiu YC, Chen Y, Liu Y, Li L, Li R, Thompson IM, Nephew KP, Sharp ZD, Kirma NB, Jin VX, Huang TH. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell 2013;24:197-212. [PMID: 23948299 DOI: 10.1016/j.ccr.2013.07.007] [Cited by in Crossref: 42] [Cited by in F6Publishing: 40] [Article Influence: 4.7] [Reference Citation Analysis]
29 Wu J, Zhang W, Huang S, He Z, Cheng Y, Wang J, Lam T, Peng Z, Yiu S. SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads. Bioinformatics 2013;29:2971-8. [DOI: 10.1093/bioinformatics/btt522] [Cited by in Crossref: 18] [Cited by in F6Publishing: 15] [Article Influence: 2.0] [Reference Citation Analysis]
30 Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One 2013;8:e73974. [PMID: 24019942 DOI: 10.1371/journal.pone.0073974] [Cited by in Crossref: 31] [Cited by in F6Publishing: 24] [Article Influence: 3.4] [Reference Citation Analysis]
31 Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res 2013;41:e165. [PMID: 23892400 DOI: 10.1093/nar/gkt641] [Cited by in Crossref: 89] [Cited by in F6Publishing: 65] [Article Influence: 9.9] [Reference Citation Analysis]
32 Malhotra A, Shibata Y, Hall IM, Dutta A. Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes. Cancer Biol Ther 2013;14:840-52. [PMID: 23792589 DOI: 10.4161/cbt.25329] [Cited by in Crossref: 9] [Cited by in F6Publishing: 13] [Article Influence: 1.0] [Reference Citation Analysis]
33 Balic M, Schwarzenbacher D, Stanzer S, Heitzer E, Auer M, Geigl JB, Cote RJ, Datar RH, Dandachi N. Genetic and epigenetic analysis of putative breast cancer stem cell models. BMC Cancer 2013;13:358. [PMID: 23883436 DOI: 10.1186/1471-2407-13-358] [Cited by in Crossref: 21] [Cited by in F6Publishing: 20] [Article Influence: 2.3] [Reference Citation Analysis]
34 Zhang X, Claerhout S, Prat A, Dobrolecki LE, Petrovic I, Lai Q, Landis MD, Wiechmann L, Schiff R, Giuliano M, Wong H, Fuqua SW, Contreras A, Gutierrez C, Huang J, Mao S, Pavlick AC, Froehlich AM, Wu MF, Tsimelzon A, Hilsenbeck SG, Chen ES, Zuloaga P, Shaw CA, Rimawi MF, Perou CM, Mills GB, Chang JC, Lewis MT. A renewable tissue resource of phenotypically stable, biologically and ethnically diverse, patient-derived human breast cancer xenograft models. Cancer Res. 2013;73:4885-4897. [PMID: 23737486 DOI: 10.1158/0008-5472.can-12-4081] [Cited by in Crossref: 292] [Cited by in F6Publishing: 271] [Article Influence: 32.4] [Reference Citation Analysis]
35 Jiao X, Hooper SD, Djureinovic T, Larsson C, Wärnberg F, Tellgren-Roth C, Botling J, Sjöblom T. Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. BMC Genomics 2013;14:165. [PMID: 23496902 DOI: 10.1186/1471-2164-14-165] [Cited by in Crossref: 18] [Cited by in F6Publishing: 21] [Article Influence: 2.0] [Reference Citation Analysis]
36 Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res 2013;23:762-76. [PMID: 23410887 DOI: 10.1101/gr.143677.112] [Cited by in Crossref: 128] [Cited by in F6Publishing: 113] [Article Influence: 14.2] [Reference Citation Analysis]
37 Albrecht JC, Kotani A, Lin JS, Soper SA, Barron AE. Simultaneous detection of 19 K-ras mutations by free-solution conjugate electrophoresis of ligase detection reaction products on glass microchips. Electrophoresis 2013;34:590-7. [PMID: 23192597 DOI: 10.1002/elps.201200462] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 1.3] [Reference Citation Analysis]
38 Raphael BJ. Chapter 6: Structural variation and medical genomics. PLoS Comput Biol 2012;8:e1002821. [PMID: 23300412 DOI: 10.1371/journal.pcbi.1002821] [Cited by in Crossref: 24] [Cited by in F6Publishing: 21] [Article Influence: 2.4] [Reference Citation Analysis]
39 Schulte I, Batty EM, Pole JC, Blood KA, Mo S, Cooke SL, Ng C, Howe KL, Chin SF, Brenton JD, Caldas C, Howarth KD, Edwards PA. Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. BMC Genomics 2012;13:719. [PMID: 23260012 DOI: 10.1186/1471-2164-13-719] [Cited by in Crossref: 20] [Cited by in F6Publishing: 27] [Article Influence: 2.0] [Reference Citation Analysis]
40 Qi M, Li Y, Liu J, Yang X, Wang L, Zhou Z, Han B. Morphologic features of carcinomas with recurrent gene fusions. Adv Anat Pathol 2012;19:417-24. [PMID: 23060067 DOI: 10.1097/PAP.0b013e318273baae] [Cited by in Crossref: 6] [Cited by in F6Publishing: 4] [Article Influence: 0.6] [Reference Citation Analysis]
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42 Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet 2012;8:e1002692. [PMID: 22615578 DOI: 10.1371/journal.pgen.1002692] [Cited by in Crossref: 63] [Cited by in F6Publishing: 59] [Article Influence: 6.3] [Reference Citation Analysis]
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44 Sakarya O, Breu H, Radovich M, Chen Y, Wang YN, Barbacioru C, Utiramerur S, Whitley PP, Brockman JP, Vatta P, Zhang Z, Popescu L, Muller MW, Kudlingar V, Garg N, Li CY, Kong BS, Bodeau JP, Nutter RC, Gu J, Bramlett KS, Ichikawa JK, Hyland FC, Siddiqui AS. RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput Biol 2012;8:e1002464. [PMID: 22496636 DOI: 10.1371/journal.pcbi.1002464] [Cited by in Crossref: 37] [Cited by in F6Publishing: 36] [Article Influence: 3.7] [Reference Citation Analysis]
45 Edwards PA, Howarth KD. Are breast cancers driven by fusion genes? Breast Cancer Res 2012;14:303. [PMID: 22424054 DOI: 10.1186/bcr3122] [Cited by in Crossref: 9] [Cited by in F6Publishing: 10] [Article Influence: 0.9] [Reference Citation Analysis]
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