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Items: 38

1.

Renal cell tumors with clear cell histology and intact VHL and chromosome 3p: a histological review of tumors from the Cancer Genome Atlas database.

Favazza L, Chitale DA, Barod R, Rogers CG, Kalyana-Sundaram S, Palanisamy N, Gupta NS, Williamson SR.

Mod Pathol. 2017 Nov;30(11):1603-1612. doi: 10.1038/modpathol.2017.72. Epub 2017 Jul 21.

2.

A First-Time-in-Human Study of GSK2636771, a Phosphoinositide 3 Kinase Beta-Selective Inhibitor, in Patients with Advanced Solid Tumors.

Mateo J, Ganji G, Lemech C, Burris HA, Han SW, Swales K, Decordova S, DeYoung MP, Smith DA, Kalyana-Sundaram S, Wu J, Motwani M, Kumar R, Tolson JM, Rha SY, Chung HC, Eder JP, Sharma S, Bang YJ, Infante JR, Yan L, de Bono JS, Arkenau HT.

Clin Cancer Res. 2017 Oct 1;23(19):5981-5992. doi: 10.1158/1078-0432.CCR-17-0725. Epub 2017 Jun 23.

3.

Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes.

Zhao W, Beers DR, Hooten KG, Sieglaff DH, Zhang A, Kalyana-Sundaram S, Traini CM, Halsey WS, Hughes AM, Sathe GM, Livi GP, Fan GH, Appel SH.

JAMA Neurol. 2017 Jun 1;74(6):677-685. doi: 10.1001/jamaneurol.2017.0357.

4.

Renal Cell Carcinoma With Chromosome 6p Amplification Including the TFEB Gene: A Novel Mechanism of Tumor Pathogenesis?

Williamson SR, Grignon DJ, Cheng L, Favazza L, Gondim DD, Carskadon S, Gupta NS, Chitale DA, Kalyana-Sundaram S, Palanisamy N.

Am J Surg Pathol. 2017 Mar;41(3):287-298. doi: 10.1097/PAS.0000000000000776.

PMID:
28009604
5.

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.

Cell Rep. 2016 Dec 6;17(10):2620-2631. doi: 10.1016/j.celrep.2016.11.019.

6.

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease.

Chung C, Elrick MJ, Dell'Orco JM, Qin ZS, Kalyana-Sundaram S, Chinnaiyan AM, Shakkottai VG, Lieberman AP.

PLoS Genet. 2016 May 6;12(5):e1006042. doi: 10.1371/journal.pgen.1006042. eCollection 2016 May.

7.

Non-coding RNA LINC00857 is predictive of poor patient survival and promotes tumor progression via cell cycle regulation in lung cancer.

Wang L, He Y, Liu W, Bai S, Xiao L, Zhang J, Dhanasekaran SM, Wang Z, Kalyana-Sundaram S, Balbin OA, Shukla S, Lu Y, Lin J, Reddy RM, Carrott PW Jr, Lynch WR, Chang AC, Chinnaiyan AM, Beer DG, Zhang J, Chen G.

Oncotarget. 2016 Mar 8;7(10):11487-99. doi: 10.18632/oncotarget.7203.

8.

Landscape of gene fusions in epithelial cancers: seq and ye shall find.

Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM.

Genome Med. 2015 Dec 18;7:129. doi: 10.1186/s13073-015-0252-1. Review.

9.

Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes.

Dhanasekaran SM, Balbin OA, Chen G, Nadal E, Kalyana-Sundaram S, Pan J, Veeneman B, Cao X, Malik R, Vats P, Wang R, Huang S, Zhong J, Jing X, Iyer M, Wu YM, Harms PW, Lin J, Reddy R, Brennan C, Palanisamy N, Chang AC, Truini A, Truini M, Robinson DR, Beer DG, Chinnaiyan AM.

Nat Commun. 2014 Dec 22;5:5893. doi: 10.1038/ncomms6893.

10.

Primary urethral clear-cell adenocarcinoma: comprehensive analysis by surgical pathology, cytopathology, and next-generation sequencing.

Mehra R, Vats P, Kalyana-Sundaram S, Udager AM, Roh M, Alva A, Pan J, Lonigro RJ, Siddiqui J, Weizer A, Lee C, Cao X, Wu YM, Robinson DR, Dhanasekaran SM, Chinnaiyan AM.

Am J Pathol. 2014 Mar;184(3):584-91. doi: 10.1016/j.ajpath.2013.11.023. Epub 2014 Jan 3.

11.

Activating ESR1 mutations in hormone-resistant metastatic breast cancer.

Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, Gursky A, Siddiqui J, Tomlins SA, Roychowdhury S, Pienta KJ, Kim SY, Roberts JS, Rae JM, Van Poznak CH, Hayes DF, Chugh R, Kunju LP, Talpaz M, Schott AF, Chinnaiyan AM.

Nat Genet. 2013 Dec;45(12):1446-51. doi: 10.1038/ng.2823. Epub 2013 Nov 3.

12.

Identification of targetable FGFR gene fusions in diverse cancers.

Wu YM, Su F, Kalyana-Sundaram S, Khazanov N, Ateeq B, Cao X, Lonigro RJ, Vats P, Wang R, Lin SF, Cheng AJ, Kunju LP, Siddiqui J, Tomlins SA, Wyngaard P, Sadis S, Roychowdhury S, Hussain MH, Feng FY, Zalupski MM, Talpaz M, Pienta KJ, Rhodes DR, Robinson DR, Chinnaiyan AM.

Cancer Discov. 2013 Jun;3(6):636-47. doi: 10.1158/2159-8290.CD-13-0050. Epub 2013 Apr 4.

13.

miRConnect 2.0: identification of oncogenic, antagonistic miRNA families in three human cancers.

Hua Y, Larsen N, Kalyana-Sundaram S, Kjems J, Chinnaiyan AM, Peter ME.

BMC Genomics. 2013 Mar 15;14:179. doi: 10.1186/1471-2164-14-179.

14.

Outlier kinase expression by RNA sequencing as targets for precision therapy.

Kothari V, Wei I, Shankar S, Kalyana-Sundaram S, Wang L, Ma LW, Vats P, Grasso CS, Robinson DR, Wu YM, Cao X, Simeone DM, Chinnaiyan AM, Kumar-Sinha C.

Cancer Discov. 2013 Mar;3(3):280-93. doi: 10.1158/2159-8290.CD-12-0336. Epub 2013 Feb 5.

15.

Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia.

Velusamy T, Palanisamy N, Kalyana-Sundaram S, Sahasrabuddhe AA, Maher CA, Robinson DR, Bahler DW, Cornell TT, Wilson TE, Lim MS, Chinnaiyan AM, Elenitoba-Johnson KS.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):3035-40. doi: 10.1073/pnas.1214326110. Epub 2013 Feb 4.

16.

Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing.

Robinson DR, Wu YM, Kalyana-Sundaram S, Cao X, Lonigro RJ, Sung YS, Chen CL, Zhang L, Wang R, Su F, Iyer MK, Roychowdhury S, Siddiqui J, Pienta KJ, Kunju LP, Talpaz M, Mosquera JM, Singer S, Schuetze SM, Antonescu CR, Chinnaiyan AM.

Nat Genet. 2013 Feb;45(2):180-5. doi: 10.1038/ng.2509. Epub 2013 Jan 13.

17.

Gene Fusion Markup Language: a prototype for exchanging gene fusion data.

Kalyana-Sundaram S, Shanmugam A, Chinnaiyan AM.

BMC Bioinformatics. 2012 Oct 16;13:269. doi: 10.1186/1471-2105-13-269.

18.

Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer.

Kalyana-Sundaram S, Shankar S, Deroo S, Iyer MK, Palanisamy N, Chinnaiyan AM, Kumar-Sinha C.

Neoplasia. 2012 Aug;14(8):702-8.

19.

SLC45A3-ELK4 chimera in prostate cancer: spotlight on cis-splicing.

Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM.

Cancer Discov. 2012 Jul;2(7):582-5. doi: 10.1158/2159-8290.CD-12-0212.

20.

Expressed pseudogenes in the transcriptional landscape of human cancers.

Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu YM, Cao X, Asangani IA, Kothari V, Prensner JR, Lonigro RJ, Iyer MK, Barrette T, Shanmugam A, Dhanasekaran SM, Palanisamy N, Chinnaiyan AM.

Cell. 2012 Jun 22;149(7):1622-34. doi: 10.1016/j.cell.2012.04.041.

21.

Personalized oncology through integrative high-throughput sequencing: a pilot study.

Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, Kalyana-Sundaram S, Sam L, Balbin OA, Quist MJ, Barrette T, Everett J, Siddiqui J, Kunju LP, Navone N, Araujo JC, Troncoso P, Logothetis CJ, Innis JW, Smith DC, Lao CD, Kim SY, Roberts JS, Gruber SB, Pienta KJ, Talpaz M, Chinnaiyan AM.

Sci Transl Med. 2011 Nov 30;3(111):111ra121. doi: 10.1126/scitranslmed.3003161.

22.

Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer.

Robinson DR, Kalyana-Sundaram S, Wu YM, Shankar S, Cao X, Ateeq B, Asangani IA, Iyer M, Maher CA, Grasso CS, Lonigro RJ, Quist M, Siddiqui J, Mehra R, Jing X, Giordano TJ, Sabel MS, Kleer CG, Palanisamy N, Natrajan R, Lambros MB, Reis-Filho JS, Kumar-Sinha C, Chinnaiyan AM.

Nat Med. 2011 Nov 20;17(12):1646-51. doi: 10.1038/nm.2580.

23.

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS, Chinnaiyan AM.

Genome Res. 2011 Jul;21(7):1028-41. doi: 10.1101/gr.119347.110.

24.

The tumor suppressor gene rap1GAP is silenced by miR-101-mediated EZH2 overexpression in invasive squamous cell carcinoma.

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.

Oncogene. 2011 Oct 20;30(42):4339-49. doi: 10.1038/onc.2011.141. Epub 2011 May 2.

25.

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.

Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM.

BMC Bioinformatics. 2010 Jul 2;11:369. doi: 10.1186/1471-2105-11-369.

26.

Re: Florian Jentzmik, Carsten Stephan, Kurt Miller, et al. Sarcosine in urine after digital rectal examination fails as a marker in prostate cancer detection and identification of aggressive tumours. Eur Urol 2010;58:12-8.

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghoshd D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM.

Eur Urol. 2010 Sep;58(3):e29-30; author reply e31-2. doi: 10.1016/j.eururo.2010.05.003. Epub 2010 May 18. No abstract available.

27.

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma.

Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Suleman K, Kumar-Sinha C, Dhanasekaran SM, Chen YB, Esgueva R, Banerjee S, LaFargue CJ, Siddiqui J, Demichelis F, Moeller P, Bismar TA, Kuefer R, Fullen DR, Johnson TM, Greenson JK, Giordano TJ, Tan P, Tomlins SA, Varambally S, Rubin MA, Maher CA, Chinnaiyan AM.

Nat Med. 2010 Jul;16(7):793-8. doi: 10.1038/nm.2166. Epub 2010 Jun 6.

28.

Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer.

Khan AP, Poisson LM, Bhat VB, Fermin D, Zhao R, Kalyana-Sundaram S, Michailidis G, Nesvizhskii AI, Omenn GS, Chinnaiyan AM, Sreekumar A.

Mol Cell Proteomics. 2010 Feb;9(2):298-312. doi: 10.1074/mcp.M900159-MCP200. Epub 2009 Nov 9.

29.

Chimeric transcript discovery by paired-end transcriptome sequencing.

Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8. doi: 10.1073/pnas.0904720106. Epub 2009 Jul 10.

30.

AGTR1 overexpression defines a subset of breast cancer and confers sensitivity to losartan, an AGTR1 antagonist.

Rhodes DR, Ateeq B, Cao Q, Tomlins SA, Mehra R, Laxman B, Kalyana-Sundaram S, Lonigro RJ, Helgeson BE, Bhojani MS, Rehemtulla A, Kleer CG, Hayes DF, Lucas PC, Varambally S, Chinnaiyan AM.

Proc Natl Acad Sci U S A. 2009 Jun 23;106(25):10284-9. doi: 10.1073/pnas.0900351106. Epub 2009 Jun 1.

31.

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression.

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM.

Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. Erratum in: Nature. 2013 Jul 25;499(7459):504.

32.

Transcriptome sequencing to detect gene fusions in cancer.

Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM.

Nature. 2009 Mar 5;458(7234):97-101. doi: 10.1038/nature07638. Epub 2009 Jan 11.

33.

Humoral response profiling reveals pathways to prostate cancer progression.

Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A.

Mol Cell Proteomics. 2008 Mar;7(3):600-11. Epub 2007 Dec 11.

34.

Molecular concepts analysis links tumors, pathways, mechanisms, and drugs.

Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, Kasper N, Varambally R, Barrette TR, Ghosh D, Varambally S, Chinnaiyan AM.

Neoplasia. 2007 May;9(5):443-54.

35.

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.

Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM.

Neoplasia. 2007 Feb;9(2):166-80.

36.

Integrative molecular concept modeling of prostate cancer progression.

Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, Dhanasekaran SM, Kalyana-Sundaram S, Wei JT, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM.

Nat Genet. 2007 Jan;39(1):41-51. Epub 2006 Dec 17.

PMID:
17173048
37.

Probabilistic model of the human protein-protein interaction network.

Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM.

Nat Biotechnol. 2005 Aug;23(8):951-9.

PMID:
16082366
38.

Mining for regulatory programs in the cancer transcriptome.

Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Barrette TR, Ghosh D, Chinnaiyan AM.

Nat Genet. 2005 Jun;37(6):579-83.

PMID:
15920519

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