ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.
Abbas A, Chandratre K, Gao Y, Yuan J, Zhang MQ, Mani RS, 2024 Jan Genome Biol 1 25 15
Yuan J, Houlahan KE, Ramanand SG, Lee S, Baek G, Yang Y, Chen Y, Strand DW, Zhang MQ, Boutros PC, Mani RS,
2022 Sep
Cancer Discov
Targeting radioresistance and replication fork stability in prostate cancer.
Li X, Baek G, Carreira S, Yuan W, Ma S, Hofstad M, Lee S, Gao Y, Bertan C, Fenor de la Maza MLD, Alluri PG, Burma S, Chen BP, Raj GV, de Bono J, Pommier Y, Mani RS, 2022 Mar JCI Insight
Sahoo SS, Ramanand SG, Gao Y, Abbas A, Kumar A, Cuevas IC, Li HD, Aguilar M, Xing C, Mani RS, Castrillon DH,
2022 Jun
J Clin Invest
12
132
Ramanand SG, Mani RS,
2022 Aug
Mol Cell
15
82
2730-2731
The landscape of RNA polymerase II associated chromatin interactions in prostate cancer.
Ramanand SG, Chen Y, Yuan J, Daescu K, Lambros M, Houlahan KE, Carreira S, Yuan W, Baek G, Sharp A, Paschalis A, Kanchwala M, Gao Y, Aslam A, Safdar N, Zhan X, Raj GV, Xing C, Boutros PC, de Bono J, Zhang MQ, Mani RS, 2020 Apr J. Clin. Invest.Genome-wide germline correlates of the epigenetic landscape of prostate cancer.
Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O'Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC, 2019 Oct Nat. Med.
Li X, Baek G, Ramanand SG, Sharp A, Gao Y, Yuan W, Welti J, Rodrigues DN, Dolling D, Figueiredo I, Sumanasuriya S, Crespo M, Aslam A, Li R, Yin Y, Mukherjee B, Kanchwala M, Hughes AM, Halsey WS, Chiang CM, Xing C, Raj GV, Burma S, de Bono J, Mani RS
2018 Jan
Cell Rep
3
22
796-808
Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer.
Mani RS, Amin MA, Li X, Kalyana-Sundaram S, Veeneman BA, Wang L, Ghosh A, Aslam A, Ramanand SG, Rabquer BJ, Kimura W, Tran M, Cao X, Roychowdhury S, Dhanasekaran SM, Palanisamy N, Sadek HA, Kapur P, Koch AE, Chinnaiyan AM 2016 Dec Cell Rep 10 17 2620-2631Induced chromosomal proximity and gene fusions in prostate cancer.
Mani RS, Tomlins SA, Callahan K, Ghosh A, Nyati MK, Varambally S, Palanisamy N, Chinnaiyan AM 2009 Nov Science 5957 326 1230
Lin CC, Chang TC, Wang Y, Guo L, Gao Y, Bikorimana E, Lemoff A, Fang YV, Zhang H, Zhang Y, Ye D, Soria-Bretones I, Servetto A, Lee KM, Luo X, Otto JJ, Akamatsu H, Napolitano F, Mani R, Cescon DW, Xu L, Xie Y, Mendell JT, Hanker AB, Arteaga CL,
2024 Mar
Nat Commun
1
15
2287
Critical role of antioxidant programs in enzalutamide-resistant prostate cancer.
Blatt EB, Parra K, Neeb A, Buroni L, Bogdan D, Yuan W, Gao Y, Gilbreath C, Paschalis A, Carreira S, DeBerardinis RJ, Mani RS, de Bono JS, Raj GV, 2023 Jul Oncogene 30 42 2347-2359
Udden SMN, Baek G, Pandey K, Vidal C, Liu Y, Rahimi AS, Kim DN, Nwachukwu CR, Mani RS, Alluri PG,
2023 Jan
NPJ Precis Oncol
1
7
11
Khan S, Kwak YT, Peng L, Hu S, Cantarel BL, Lewis CM, Gao Y, Mani RS, Kanneganti TD, Zaki H,
2023 Aug
J Clin Invest
Targeting ESR1 mutation-Induced transcriptional addiction in breast cancer with BET inhibition.
Udden SN, Wang Q, Kumar S, Malladi VS, Wu SY, Wei S, Posner BA, Geboers S, Williams NS, Liu YL, Sharma JK, Mani RS, Malladi S, Parra K, Hofstad M, Raj GV, Larios JM, Jagsi R, Wicha MS, Park BH, Gupta GP, Chinnaiyan AM, Chiang CM, Alluri PG, 2022 Jul JCI InsightAccurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q Zhang, Ram S Mani 2022 bioRxiv
de Bono JS, Guo C, Gurel B, De Marzo AM, Sfanos KS, Mani RS, Gil J, Drake CG, Alimonti A,
2020 Jun
Nat. Rev. Cancer
Genetic, Environmental, and Nuclear Factors Governing Genomic Rearrangements.
Ramanand SG, Mani RS, 2019 Adv. Exp. Med. Biol. 1210 57-66
Welti J, Sharp A, Yuan W, Dolling DI, Nava Rodrigues D, Figueiredo I, Gil V, Neeb A, Clarke M, Seed G, Crespo M, Sumanasuriya S, Ning J, Knight E, Francis JC, Hughes A, Halsey WS, Paschalis A, Mani RS, Raj GV, Plymate S, Carreira S, Boysen G, Chinnaiyan AM, Swain A, de Bono JS
2018 Mar
Clin. Cancer Res.
Androgen receptor variants mediate DNA repair after prostate cancer irradiation.
Yin Y, Li R, Xu K, Ding S, Li J, Baek G, Ramanand SG, Ding S, Liu Z, Gao Y, Kanchwala MS, Li X, Hutchinson R, Liu X, Woldu SL, Xing C, Desai NB, Feng FY, Burma S, de Bono JS, Dehm SM, Mani RS, Chen BPC, Raj GV 2017 Jul Cancer Res.
Pandey N, Xavier DF, Chatterjee A, Mani RS, Hiremagalore R, Tharakan A, Rajashekhar B, Anand A
2015 Nov
Ann. Hum. Genet.
The emerging role of speckle-type POZ protein (SPOP) in cancer development.
Mani RS 2014 Jul Drug Discov. Today
Banerjee R, Russo N, Liu M, Basrur V, Bellile E, Palanisamy N, Scanlon CS, van Tubergen E, Inglehart RC, Metwally T, Mani RS, Yocum A, Nyati MK, Castilho RM, Varambally S, Chinnaiyan AM, D'Silva NJ
2014
Nat Commun
5
4527
He S, Xie F, Liu Y, Tong Q, Mochizuki K, Lapinski PE, Mani RS, Reddy P, Mochizuki I, Chinnaiyan AM, Mineishi S, King PD, Zhang Y
2013 Dec
Blood
25
122
4119-28
Role of transcriptional corepressor CtBP1 in prostate cancer progression.
Wang R, Asangani IA, Chakravarthi BV, Ateeq B, Lonigro RJ, Cao Q, Mani RS, Camacho DF, McGregor N, Schumann TE, Jing X, Menawat R, Tomlins SA, Zheng H, Otte AP, Mehra R, Siddiqui J, Dhanasekaran SM, Nyati MK, Pienta KJ, Palanisamy N, Kunju LP, Rubin MA, Chinnaiyan AM, Varambally S 2012 Oct Neoplasia 10 14 905-14
He S, Wang J, Kato K, Xie F, Varambally S, Mineishi S, Kuick R, Mochizuki K, Liu Y, Nieves E, Mani RS, Chinnaiyan AM, Marquez VE, Zhang Y
2012 Feb
Blood
5
119
1274-82
Banerjee R, Mani RS, Russo N, Scanlon CS, Tsodikov A, Jing X, Cao Q, Palanisamy N, Metwally T, Inglehart RC, Tomlins S, Bradford C, Carey T, Wolf G, Kalyana-Sundaram S, Chinnaiyan AM, Varambally S, D'Silva NJ
2011 Oct
Oncogene
42
30
4339-49
Coordinated regulation of polycomb group complexes through microRNAs in cancer.
Cao Q, Mani RS, Ateeq B, Dhanasekaran SM, Asangani IA, Prensner JR, Kim JH, Brenner JC, Jing X, Cao X, Wang R, Li Y, Dahiya A, Wang L, Pandhi M, Lonigro RJ, Wu YM, Tomlins SA, Palanisamy N, Qin Z, Yu J, Maher CA, Varambally S, Chinnaiyan AM 2011 Aug Cancer Cell 2 20 187-99TMPRSS2-ERG-mediated feed-forward regulation of wild-type ERG in human prostate cancers.
Mani RS, Iyer MK, Cao Q, Brenner JC, Wang L, Ghosh A, Cao X, Lonigro RJ, Tomlins SA, Varambally S, Chinnaiyan AM 2011 Aug Cancer Res. 16 71 5387-92
Yu J, Yu J, Mani RS, Cao Q, Brenner CJ, Cao X, Wang X, Wu L, Li J, Hu M, Gong Y, Cheng H, Laxman B, Vellaichamy A, Shankar S, Li Y, Dhanasekaran SM, Morey R, Barrette T, Lonigro RJ, Tomlins SA, Varambally S, Qin ZS, Chinnaiyan AM
2010 May
Cancer Cell
5
17
443-54
Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences.
Mani RS, Chinnaiyan AM 2010 Dec Nat. Rev. Genet. 12 11 819-29Functional consequences of novel connexin 26 mutations associated with hereditary hearing loss.
Mani RS, Ganapathy A, Jalvi R, Srikumari Srisailapathy CR, Malhotra V, Chadha S, Agarwal A, Ramesh A, Rangasayee RR, Anand A 2009 Apr Eur. J. Hum. Genet. 4 17 502-9Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer.
Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, Brenner JC, Yu J, Kim JH, Han B, Tan P, Kumar-Sinha C, Lonigro RJ, Palanisamy N, Maher CA, Chinnaiyan AM 2008 Dec Science 5908 322 1695-9Repression of E-cadherin by the polycomb group protein EZH2 in cancer.
Cao Q, Yu J, Dhanasekaran SM, Kim JH, Mani RS, Tomlins SA, Mehra R, Laxman B, Cao X, Yu J, Kleer CG, Varambally S, Chinnaiyan AM 2008 Dec Oncogene 58 27 7274-84Implications in disclosing auditory genetic mutation to a family: a case study.
Shekhawat GS, RamShankar M, Jalvi RR, Rangasayee R, Anand A 2007 Jul Int J Audiol 7 46 384-7
RamShankar M, Girirajan S, Dagan O, Ravi Shankar HM, Jalvi R, Rangasayee R, Avraham KB, Anand A
2003 May
J. Med. Genet.
5
40
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