My Bibliography

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Altwegg KA, Pratap UP, Liu Z, Liu J, Sanchez JR, Yang X, Ebrahimi B, Panneerdoss DM, Li X, Sareddy GR, Viswanadhapalli S, Rao MK, Vadlamudi RK. Targeting PELP1 oncogenic signaling in TNBC with the small molecule inhibitor SMIP34. Breast Cancer Res Treat. 2023 Jul;200(1):151-162. doi: 10.1007/s10549-023-06958-4. Epub 2023 May 18. PubMed PMID: 37199805; PubMed Central PMCID: PMC10224866.

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Subbarayalu P, Yadav P, Timilsina S, Medina D, Baxi K, Hromas R, Vadlamudi RK, Chen Y, Sung P, Rao MK. The RNA Demethylase ALKBH5 Maintains Endoplasmic Reticulum Homeostasis by Regulating UPR, Autophagy, and Mitochondrial Function. Cells. 2023 Apr 29;12(9). doi: 10.3390/cells12091283. PubMed PMID: 37174684; PubMed Central PMCID: PMC10177234.

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Altwegg KA, Viswanadhapalli S, Mann M, Chakravarty D, Krishnan S, Liu Z, Liu J, Pratap UP, Ebrahimi B, Sanchez JR, Li X, Ma S, Park BH, Santhamma B, Chen Y, Lai Z, Raj GV, Yuan Y, Zhou D, Sareddy GR, Tekmal RR, McHardy S, Huang TH, Rao MK, Vankayalapati H, Vadlamudi RK. A First-in-Class Inhibitor of ER Coregulator PELP1 Targets ER+ Breast Cancer. Cancer Res. 2022 Oct 17;82(20):3830-3844. doi: 10.1158/0008-5472.CAN-22-0698. PubMed PMID: 35950923; PubMed Central PMCID: PMC9588738.

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Timilsina S, Rajamanickam S, Rao A, Subbarayalu P, Nirzhor S, Abdelfattah N, Viswanadhapalli S, Chen Y, Jatoi I, Brenner A, Rao MK, Vadlamudi R, Kaklamani V. The antidepressant imipramine inhibits breast cancer growth by targeting estrogen receptor signaling and DNA repair events. Cancer Lett. 2022 Aug 1;540:215717. doi: 10.1016/j.canlet.2022.215717. Epub 2022 May 12. PubMed PMID: 35568265; PubMed Central PMCID: PMC10313451.

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Rajamanickam S, Park JH, Subbarayalu P, Timilsina S, Bates K, Yadav P, Nirzhor SSR, Eedunuri V, Mohammad TA, Jung KH, Onyeagucha B, Abdelfattah N, Benevides R, Lee G, Chen Y, Vadlamudi R, Brenner A, Kaklamani V, Jatoi I, Kuhn J, Hromas R, Gupta YK, Kaipparettu BA, Arbiser JL, Rao MK. Targeting aberrant replication and DNA repair events for treating breast cancers. Commun Biol. 2022 May 24;5(1):493. doi: 10.1038/s42003-022-03413-w. PubMed PMID: 35610507; PubMed Central PMCID: PMC9130234.

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Yadav P, Subbarayalu P, Medina D, Nirzhor S, Timilsina S, Rajamanickam S, Eedunuri VK, Gupta Y, Zheng S, Abdelfattah N, Huang Y, Vadlamudi R, Hromas R, Meltzer P, Houghton P, Chen Y, Rao MK. M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression. Cancer Res. 2022 May 16;82(10):1872-1889. doi: 10.1158/0008-5472.CAN-21-2106. PubMed PMID: 35303054; PubMed Central PMCID: PMC9336196.

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Li M, Viswanadhapalli S, Santhamma B, Pratap UP, Luo Y, Liu J, Altwegg KA, Tang W, Liu Z, Li X, Ebrahimi B, Yan H, Zou Y, Konda S, Sareddy GR, Xu Z, Chen Y, Rao MK, Brenner AJ, Kaklamani VG, Tekmal RR, Ahmed G, Raj GV, Nickisch KJ, Nair HB, Vadlamudi RK. LIFR inhibition enhances the therapeutic efficacy of HDAC inhibitors in triple negative breast cancer. Commun Biol. 2021 Oct 29;4(1):1235. doi: 10.1038/s42003-021-02741-7. PubMed PMID: 34716410; PubMed Central PMCID: PMC8556368.

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Altwegg KA, Vadlamudi RK. Role of estrogen receptor coregulators in endocrine resistant breast cancer. Explor Target Antitumor Ther. 2021;2(4):385-400. doi: 10.37349/etat.2021.00052. Epub 2021 Aug 30. PubMed PMID: 34528025; PubMed Central PMCID: PMC8439438.

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Chiu YC, Zheng S, Wang LJ, Iskra BS, Rao MK, Houghton PJ, Huang Y, Chen Y. Predicting and characterizing a cancer dependency map of tumors with deep learning. Sci Adv. 2021 Aug;7(34). doi: 10.1126/sciadv.abh1275. Print 2021 Aug. PubMed PMID: 34417181; PubMed Central PMCID: PMC8378822.

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Tang W, Ramasamy K, Pillai SMA, Santhamma B, Konda S, Pitta Venkata P, Blankenship L, Liu J, Liu Z, Altwegg KA, Ebrahimi B, Pratap UP, Li X, Valente PT, Kost E, Sareddy GR, Vadlamudi RK, Nair HB, Tekmal RR, Viswanadhapalli S. LIF/LIFR oncogenic signaling is a novel therapeutic target in endometrial cancer. Cell Death Discov. 2021 Aug 16;7(1):216. doi: 10.1038/s41420-021-00603-z. PubMed PMID: 34400617; PubMed Central PMCID: PMC8367961.

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Lee JH, Hong J, Zhang Z, de la Peña Avalos B, Proietti CJ, Deamicis AR, Guzmán G P, Lam HM, Garcia J, Roudier MP, Sisk AE, De La Rosa R, Vu K, Yang M, Liao Y, Scheirer J, Pechacek D, Yadav P, Rao MK, Zheng S, Johnson-Pais TL, Leach RJ, Elizalde PV, Dray E, Xu K. Regulation of telomere homeostasis and genomic stability in cancer by N (6)-adenosine methylation (m(6)A). Sci Adv. 2021 Jul;7(31). doi: 10.1126/sciadv.abg7073. Print 2021 Jul. PubMed PMID: 34321211; PubMed Central PMCID: PMC8318370.

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Pratap UP, Sareddy GR, Liu Z, Venkata PP, Liu J, Tang W, Altwegg KA, Ebrahimi B, Li X, Tekmal RR, Viswanadhapalli S, McHardy S, Brenner AJ, Vadlamudi RK. Histone deacetylase inhibitors enhance estrogen receptor beta expression and augment agonist-mediated tumor suppression in glioblastoma. Neurooncol Adv. 2021 Jan-Dec;3(1):vdab099. doi: 10.1093/noajnl/vdab099. eCollection 2021 Jan-Dec. PubMed PMID: 34485908; PubMed Central PMCID: PMC8412056.

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Liu J, Liu Z, Li M, Tang W, Pratap UP, Luo Y, Altwegg KA, Li X, Zou Y, Zhu H, Sareddy GR, Viswanadhapalli S, Vadlamudi RK. Interaction of transcription factor AP-2 gamma with proto-oncogene PELP1 promotes tumorigenesis by enhancing RET signaling. Mol Oncol. 2021 Apr;15(4):1146-1161. doi: 10.1002/1878-0261.12871. Epub 2021 Feb 9. PubMed PMID: 33269540; PubMed Central PMCID: PMC8024722.

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Luo Y, Li M, Pratap UP, Viswanadhapalli S, Liu J, Venkata PP, Altwegg KA, Palacios BE, Li X, Chen Y, Rao MK, Brenner AJ, Sareddy GR, Vadlamudi RK. PELP1 signaling contributes to medulloblastoma progression by regulating the NF-κB pathway. Mol Carcinog. 2020 Mar;59(3):281-292. doi: 10.1002/mc.23152. Epub 2019 Dec 24. PubMed PMID: 31872914; PubMed Central PMCID: PMC7021561.

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Abdelfattah N, Rajamanickam S, Panneerdoss S, Timilsina S, Yadav P, Onyeagucha BC, Garcia M, Vadlamudi R, Chen Y, Brenner A, Houghton P, Rao MK. MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma. Nat Commun. 2018 Oct 31;9(1):4541. doi: 10.1038/s41467-018-06808-8. PubMed PMID: 30382096; PubMed Central PMCID: PMC6208371.

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Panneerdoss S, Eedunuri VK, Yadav P, Timilsina S, Rajamanickam S, Viswanadhapalli S, Abdelfattah N, Onyeagucha BC, Cui X, Lai Z, Mohammad TA, Gupta YK, Huang TH, Huang Y, Chen Y, Rao MK. Cross-talk among writers, readers, and erasers of m(6)A regulates cancer growth and progression. Sci Adv. 2018 Oct;4(10):eaar8263. doi: 10.1126/sciadv.aar8263. eCollection 2018 Oct. PubMed PMID: 30306128; PubMed Central PMCID: PMC6170038.

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Wei Z, Panneerdoss S, Timilsina S, Zhu J, Mohammad TA, Lu ZL, de Magalhães JP, Chen Y, Rong R, Huang Y, Rao MK, Meng J. Topological Characterization of Human and Mouse m(5)C Epitranscriptome Revealed by Bisulfite Sequencing. Int J Genomics. 2018;2018:1351964. doi: 10.1155/2018/1351964. eCollection 2018. PubMed PMID: 30009162; PubMed Central PMCID: PMC6020461.

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Cui X, Zhang L, Meng J, Rao MK, Chen Y, Huang Y. MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):526-534. doi: 10.1109/TCBB.2015.2403355. PubMed PMID: 29610101.

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Onyeagucha B, Subbarayalu P, Abdelfattah N, Rajamanickam S, Timilsina S, Guzman R, Zeballos C, Eedunuri V, Bansal S, Mohammad T, Chen Y, Vadlamudi RK, Rao MK. Novel post-transcriptional and post-translational regulation of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 determine the fate of breast cancer cells to survive or die. Oncotarget. 2017 Oct 17;8(49):85984-85996. doi: 10.18632/oncotarget.20841. eCollection 2017 Oct 17. PubMed PMID: 29156771; PubMed Central PMCID: PMC5689661.

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Panneerdoss S, Viswanadhapalli S, Abdelfattah N, Onyeagucha BC, Timilsina S, Mohammad TA, Chen Y, Drake M, Vuori K, Kumar TR, Rao MK. Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells. Nat Commun. 2017 Sep 19;8(1):598. doi: 10.1038/s41467-017-00590-9. PubMed PMID: 28928467; PubMed Central PMCID: PMC5605700.

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Cui X, Meng J, Zhang S, Rao MK, Chen Y, Huang Y. A hierarchical model for clustering m(6)A methylation peaks in MeRIP-seq data. BMC Genomics. 2016 Aug 22;17 Suppl 7(Suppl 7):520. doi: 10.1186/s12864-016-2913-x. PubMed PMID: 27556597; PubMed Central PMCID: PMC5001242.

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Rajamanickam S, Panneerdoss S, Gorthi A, Timilsina S, Onyeagucha B, Kovalskyy D, Ivanov D, Hanes MA, Vadlamudi RK, Chen Y, Bishop AJ, Arbiser JL, Rao MK. Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis. Clin Cancer Res. 2016 Jul 15;22(14):3524-36. doi: 10.1158/1078-0432.CCR-15-2535. Epub 2016 Feb 29. PubMed PMID: 26927663; PubMed Central PMCID: PMC4947433.

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Welborn JP, Davis MG, Ebers SD, Stodden GR, Hayashi K, Cheatwood JL, Rao MK, MacLean JA 2nd. Rhox8 Ablation in the Sertoli Cells Using a Tissue-Specific RNAi Approach Results in Impaired Male Fertility in Mice. Biol Reprod. 2015 Jul;93(1):8. doi: 10.1095/biolreprod.114.124834. Epub 2015 May 13. PubMed PMID: 25972016; PubMed Central PMCID: PMC4706311.

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Cui X, Meng J, Rao MK, Chen Y, Huang Y. HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data. BMC Genomics. 2015;16 Suppl 4(Suppl 4):S2. doi: 10.1186/1471-2164-16-S4-S2. Epub 2015 Apr 21. PubMed PMID: 25917296; PubMed Central PMCID: PMC4416174.

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Liu H, Flores MA, Meng J, Zhang L, Zhao X, Rao MK, Chen Y, Huang Y. MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res. 2015 Jan;43(Database issue):D197-203. doi: 10.1093/nar/gku1024. Epub 2014 Nov 6. PubMed PMID: 25378335; PubMed Central PMCID: PMC4383883.

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Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone-induced and DNA demethylation-induced relief of a tissue-specific and developmentally regulated block in transcriptional elongation. J Biol Chem. 2014 Dec 19;289(51):35087-101. doi: 10.1074/jbc.M114.615435. Epub 2014 Oct 20. PubMed PMID: 25331959; PubMed Central PMCID: PMC4271199.

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Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y, Rao MK, Huang Y. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods. 2014 Oct 1;69(3):274-81. doi: 10.1016/j.ymeth.2014.06.008. Epub 2014 Jun 27. PubMed PMID: 24979058; PubMed Central PMCID: PMC4194139.

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Mishra S, Deng JJ, Gowda PS, Rao MK, Lin CL, Chen CL, Huang T, Sun LZ. Androgen receptor and microRNA-21 axis downregulates transforming growth factor beta receptor II (TGFBR2) expression in prostate cancer. Oncogene. 2014 Jul 31;33(31):4097-106. doi: 10.1038/onc.2013.374. Epub 2013 Sep 16. PubMed PMID: 24037531; PubMed Central PMCID: PMC3962713.

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Roy SS, Gonugunta VK, Bandyopadhyay A, Rao MK, Goodall GJ, Sun LZ, Tekmal RR, Vadlamudi RK. Significance of PELP1/HDAC2/miR-200 regulatory network in EMT and metastasis of breast cancer. Oncogene. 2014 Jul 10;33(28):3707-16. doi: 10.1038/onc.2013.332. Epub 2013 Aug 26. PubMed PMID: 23975430; PubMed Central PMCID: PMC3935988.

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Bansal H, Yihua Q, Iyer SP, Ganapathy S, Proia DA, Penalva LO, Uren PJ, Suresh U, Carew JS, Karnad AB, Weitman S, Tomlinson GE, Rao MK, Kornblau SM, Bansal S. WTAP is a novel oncogenic protein in acute myeloid leukemia. Leukemia. 2014 May;28(5):1171-4. doi: 10.1038/leu.2014.16. Epub 2014 Jan 13. PubMed PMID: 24413322; PubMed Central PMCID: PMC4369791.

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MacLean JA 2nd, Hu Z, Welborn JP, Song HW, Rao MK, Wayne CM, Wilkinson MF. The RHOX homeodomain proteins regulate the expression of insulin and other metabolic regulators in the testis. J Biol Chem. 2013 Nov 29;288(48):34809-25. doi: 10.1074/jbc.M113.486340. Epub 2013 Oct 11. PubMed PMID: 24121513; PubMed Central PMCID: PMC3843094.

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Meng J, Cui X, Rao MK, Chen Y, Huang Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 2013 Jun 15;29(12):1565-7. doi: 10.1093/bioinformatics/btt171. Epub 2013 Apr 14. PubMed PMID: 23589649; PubMed Central PMCID: PMC3673212.

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Cui X, Meng J, Chen Y, Huang Y. Differential analysis of RNA Methylation sequencing data. Differential analysis of RNA Methylation sequencing data. 2013. doi: 0.1109/GlobalSIP.2013.6736806.

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Meng J, Cui X, Liu H, Zhang L, Zhang S, Rao MK, Chen Y, Huang Y. Unveiling the dynamics in RNA epigenetic regulations. Bioinformatics and Biomedicine. 2013; :139-144 144. doi: 10.1109/BIBM.2013.6732477.

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Imam JS, Plyler JR, Bansal H, Prajapati S, Bansal S, Rebeles J, Chen HI, Chang YF, Panneerdoss S, Zoghi B, Buddavarapu KC, Broaddus R, Hornsby P, Tomlinson G, Dome J, Vadlamudi RK, Pertsemlidis A, Chen Y, Rao MK. Genomic loss of tumor suppressor miRNA-204 promotes cancer cell migration and invasion by activating AKT/mTOR/Rac1 signaling and actin reorganization. PLoS One. 2012;7(12):e52397. doi: 10.1371/journal.pone.0052397. Epub 2012 Dec 21. PubMed PMID: 23285024; PubMed Central PMCID: PMC3528651.

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Bansal H, Seifert T, Bachier C, Rao M, Tomlinson G, Iyer SP, Bansal S. The transcription factor Wilms tumor 1 confers resistance in myeloid leukemia cells against the proapoptotic therapeutic agent TRAIL (tumor necrosis factor α-related apoptosis-inducing ligand) by regulating the antiapoptotic protein Bcl-xL. J Biol Chem. 2012 Sep 21;287(39):32875-80. doi: 10.1074/jbc.C112.366559. Epub 2012 Aug 16. PubMed PMID: 22898820; PubMed Central PMCID: PMC3463302.

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Panneerdoss S, Chang YF, Buddavarapu KC, Chen HI, Shetty G, Wang H, Chen Y, Kumar TR, Rao MK. Androgen-responsive microRNAs in mouse Sertoli cells. PLoS One. 2012;7(7):e41146. doi: 10.1371/journal.pone.0041146. Epub 2012 Jul 20. PubMed PMID: 22911753; PubMed Central PMCID: PMC3401116.

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Chang YF, Lee-Chang JS, Imam JS, Buddavarapu KC, Subaran SS, Sinha-Hikim AP, Gorospe M, Rao MK. Interaction between microRNAs and actin-associated protein Arpc5 regulates translational suppression during male germ cell differentiation. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5750-5. doi: 10.1073/pnas.1117837109. Epub 2012 Mar 23. PubMed PMID: 22447776; PubMed Central PMCID: PMC3326518.

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Chang YF, Lee-Chang JS, Harris KY, Sinha-Hikim AP, Rao MK. Role of β-catenin in post-meiotic male germ cell differentiation. PLoS One. 2011;6(11):e28039. doi: 10.1371/journal.pone.0028039. Epub 2011 Nov 18. PubMed PMID: 22125654; PubMed Central PMCID: PMC3220672.

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Chang YF, Lee-Chang JS, Panneerdoss S, MacLean JA 2nd, Rao MK. Isolation of Sertoli, Leydig, and spermatogenic cells from the mouse testis. Biotechniques. 2011 Nov;51(5):341-2, 344. doi: 10.2144/000113764. PubMed PMID: 22054547; PubMed Central PMCID: PMC3774005.

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Bansal H, Bansal S, Rao M, Foley KP, Sang J, Proia DA, Blackman RK, Ying W, Barsoum J, Baer MR, Kelly K, Swords R, Tomlinson GE, Battiwalla M, Giles FJ, Lee KP, Padmanabhan S. Heat shock protein 90 regulates the expression of Wilms tumor 1 protein in myeloid leukemias. Blood. 2010 Nov 25;116(22):4591-9. doi: 10.1182/blood-2009-10-247239. Epub 2010 Jul 22. PubMed PMID: 20651072; PubMed Central PMCID: PMC2996117.

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Imam JS, Buddavarapu K, Lee-Chang JS, Ganapathy S, Camosy C, Chen Y, Rao MK. MicroRNA-185 suppresses tumor growth and progression by targeting the Six1 oncogene in human cancers. Oncogene. 2010 Sep 2;29(35):4971-9. doi: 10.1038/onc.2010.233. Epub 2010 Jul 5. PubMed PMID: 20603620.

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Bhardwaj A, Rao MK, Kaur R, Buttigieg MR, Wilkinson MF. GATA factors and androgen receptor collaborate to transcriptionally activate the Rhox5 homeobox gene in Sertoli cells. Mol Cell Biol. 2008 Apr;28(7):2138-53. doi: 10.1128/MCB.01170-07. Epub 2008 Jan 22. PubMed PMID: 18212046; PubMed Central PMCID: PMC2268436.

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Rao MK, Pham J, Imam JS, MacLean JA, Murali D, Furuta Y, Sinha-Hikim AP, Wilkinson MF. Tissue-specific RNAi reveals that WT1 expression in nurse cells controls germ cell survival and spermatogenesis. Genes Dev. 2006 Jan 15;20(2):147-52. doi: 10.1101/gad1367806. PubMed PMID: 16418481; PubMed Central PMCID: PMC1356106.

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Rao MK, Wilkinson MF. Tissue-specific and cell type-specific RNA interference in vivo. Nat Protoc. 2006;1(3):1494-501. doi: 10.1038/nprot.2006.260. PubMed PMID: 17406440.

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Rao MK, Wilkinson MF. RNAi As A Tool to Silence Genes of Interest in Specific Tissues or Cell types. Drug Discovery. 2006; :35-36.

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MacLean JA 2nd, Rao MK, Doyle KM, Richards JS, Wilkinson MF. Regulation of the Rhox5 homeobox gene in primary granulosa cells: preovulatory expression and dependence on SP1/SP3 and GABP. Biol Reprod. 2005 Dec;73(6):1126-34. doi: 10.1095/biolreprod.105.042747. Epub 2005 Aug 10. PubMed PMID: 16093360.

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Maclean JA 2nd, Chen MA, Wayne CM, Bruce SR, Rao M, Meistrich ML, Macleod C, Wilkinson MF. Rhox: a new homeobox gene cluster. Cell. 2005 Feb 11;120(3):369-82. doi: 10.1016/j.cell.2004.12.022. PubMed PMID: 15707895.

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Rao MK, Wayne CM, Meistrich ML, Wilkinson MF. Pem homeobox gene promoter sequences that direct transcription in a Sertoli cell-specific, stage-specific, and androgen-dependent manner in the testis in vivo. Mol Endocrinol. 2003 Feb;17(2):223-33. doi: 10.1210/me.2002-0232. PubMed PMID: 12554750.

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Rao MK, Wayne CM, Wilkinson MF. Pem homeobox gene regulatory sequences that direct androgen-dependent developmentally regulated gene expression in different subregions of the epididymis. J Biol Chem. 2002 Dec 13;277(50):48771-8. doi: 10.1074/jbc.M209417200. Epub 2002 Sep 25. PubMed PMID: 12351657.