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Items: 34

1.

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines.

Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, Beane G, Grubb S, Ananda G, Liu R, Stafford G, Chuang JH, Airhart SD, Karuturi RKM, George J, Bult CJ.

BMC Med Genomics. 2019 Jul 1;12(1):92. doi: 10.1186/s12920-019-0551-2.

2.

A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification.

Abrams D, Kumar P, Karuturi RKM, George J.

BMC Bioinformatics. 2019 Jun 6;20(Suppl 11):275. doi: 10.1186/s12859-019-2817-2.

3.

High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts.

Kim H, Kumar P, Menghi F, Noorbakhsh J, Cerveira E, Ryan M, Zhu Q, Ananda G, George J, Chen HC, Mockus S, Zhang C, Yang Y, Keck J, Karuturi RKM, Bult CJ, Lee C, Liu ET, Chuang JH.

Sci Rep. 2018 Dec 18;8(1):17937. doi: 10.1038/s41598-018-36184-8.

4.

MultiDCoX: Multi-factor analysis of differential co-expression.

Liany H, Rajapakse JC, Karuturi RKM.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):576. doi: 10.1186/s12859-017-1963-7.

5.

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles.

Lawlor N, Fabbri A, Guan P, George J, Karuturi RK.

Cancer Inform. 2016 Jun 12;15:103-14. doi: 10.4137/CIN.S38000. eCollection 2016. Review.

6.

Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors.

Ananda G, Mockus S, Lundquist M, Spotlow V, Simons A, Mitchell T, Stafford G, Philip V, Stearns T, Srivastava A, Barter M, Rowe L, Malcolm J, Bult C, Karuturi RK, Rasmussen K, Hinerfeld D.

Exp Mol Pathol. 2015 Feb;98(1):106-12. doi: 10.1016/j.yexmp.2014.12.009. Epub 2015 Jan 3.

7.

Systems consequences of amplicon formation in human breast cancer.

Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PÉ, Lee YF, Shreckengast PT, Soon WW, Malhotra A, Teo AS, Hillmer AM, Khng AJ, Ruan X, Ong SH, Bertrand D, Nagarajan N, Karuturi RK, Miranda AH, Liu ET.

Genome Res. 2014 Oct;24(10):1559-71. doi: 10.1101/gr.164871.113. Epub 2014 Sep 3.

8.

Identifying driver genes in cancer by triangulating gene expression, gene location, and survival data.

Rouam S, Miller LD, Karuturi RK.

Cancer Inform. 2015 Feb 3;13(Suppl 6):35-48. doi: 10.4137/CIN.S18302. eCollection 2014. Review.

9.

PDK1 signaling toward PLK1-MYC activation confers oncogenic transformation, tumor-initiating cell activation, and resistance to mTOR-targeted therapy.

Tan J, Li Z, Lee PL, Guan P, Aau MY, Lee ST, Feng M, Lim CZ, Lee EY, Wee ZN, Lim YC, Karuturi RK, Yu Q.

Cancer Discov. 2013 Oct;3(10):1156-71. doi: 10.1158/2159-8290.CD-12-0595. Epub 2013 Jul 25.

10.

Transcriptomic analyses of sexual dimorphism of the zebrafish liver and the effect of sex hormones.

Zheng W, Xu H, Lam SH, Luo H, Karuturi RK, Gong Z.

PLoS One. 2013;8(1):e53562. doi: 10.1371/journal.pone.0053562. Epub 2013 Jan 17.

11.

Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos.

Kraus P, Xing X, Lim SL, Fun ME, Sivakamasundari V, Yap SP, Lee H, Karuturi RK, Lufkin T.

BMC Res Notes. 2012 May 14;5:232. doi: 10.1186/1756-0500-5-232.

12.

Context-specific regulation of NF-κB target gene expression by EZH2 in breast cancers.

Lee ST, Li Z, Wu Z, Aau M, Guan P, Karuturi RK, Liou YC, Yu Q.

Mol Cell. 2011 Sep 2;43(5):798-810. doi: 10.1016/j.molcel.2011.08.011.

13.

ConReg-R: Extrapolative recalibration of the empirical distribution of p-values to improve false discovery rate estimates.

Li J, Paramita P, Choi KP, Karuturi RK.

Biol Direct. 2011 May 20;6:27. doi: 10.1186/1745-6150-6-27.

14.

Transcriptional consequences of genomic structural aberrations in breast cancer.

Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET.

Genome Res. 2011 May;21(5):676-87. doi: 10.1101/gr.113225.110. Epub 2011 Apr 5.

15.

FOXQ1 regulates epithelial-mesenchymal transition in human cancers.

Qiao Y, Jiang X, Lee ST, Karuturi RK, Hooi SC, Yu Q.

Cancer Res. 2011 Apr 15;71(8):3076-86. doi: 10.1158/0008-5472.CAN-10-2787. Epub 2011 Feb 23.

16.

Deconvolution of chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF occupancies reveals the temporal recruitment of Rep2 at the MBF target genes.

Eshaghi M, Zhu L, Chu Z, Li J, Chan CS, Shahab A, Karuturi RK, Liu J.

Eukaryot Cell. 2011 Jan;10(1):130-41. doi: 10.1128/EC.00218-10. Epub 2010 Nov 12.

17.

Genomic binding profiling of the fission yeast stress-activated MAPK Sty1 and the bZIP transcriptional activator Atf1 in response to H2O2.

Eshaghi M, Lee JH, Zhu L, Poon SY, Li J, Cho KH, Chu Z, Karuturi RK, Liu J.

PLoS One. 2010 Jul 16;5(7):e11620. doi: 10.1371/journal.pone.0011620.

18.

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms.

Chia BK, Karuturi RK.

Algorithms Mol Biol. 2010 May 28;5:23. doi: 10.1186/1748-7188-5-23.

19.

Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data.

Luo H, Li J, Eshaghi M, Liu J, Karuturi RK.

BMC Bioinformatics. 2010 May 13;11:247. doi: 10.1186/1471-2105-11-247.

20.
21.

An oestrogen-receptor-alpha-bound human chromatin interactome.

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y.

Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.

22.

The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish.

Chatterjee S, Min L, Karuturi RK, Lufkin T.

Transgenic Res. 2010 Apr;19(2):299-304. doi: 10.1007/s11248-009-9312-x. Epub 2009 Aug 7.

PMID:
19662507
23.

Ablation of phosphoinositide-3-kinase class II alpha suppresses hepatoma cell proliferation.

Ng SK, Neo SY, Yap YW, Karuturi RK, Loh ES, Liau KH, Ren EC.

Biochem Biophys Res Commun. 2009 Sep 18;387(2):310-5. doi: 10.1016/j.bbrc.2009.07.013. Epub 2009 Jul 8.

PMID:
19591801
24.

CDKN1C (p57) is a direct target of EZH2 and suppressed by multiple epigenetic mechanisms in breast cancer cells.

Yang X, Karuturi RK, Sun F, Aau M, Yu K, Shao R, Miller LD, Tan PB, Yu Q.

PLoS One. 2009;4(4):e5011. doi: 10.1371/journal.pone.0005011. Epub 2009 Apr 2. Erratum in: PLoS One. 2009;4(4). doi: 10.1371/annotation/e70583a2-3581-4848-b1e3-b518ac07d3a6.

25.

REST regulates distinct transcriptional networks in embryonic and neural stem cells.

Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM, Karuturi RK, Wei CL, Buckley NJ, Stanton LW.

PLoS Biol. 2008 Oct 28;6(10):e256. doi: 10.1371/journal.pbio.0060256.

26.

The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis.

Sim SH, Yu Y, Lin CH, Karuturi RK, Wuthiekanun V, Tuanyok A, Chua HH, Ong C, Paramalingam SS, Tan G, Tang L, Lau G, Ooi EE, Woods D, Feil E, Peacock SJ, Tan P.

PLoS Pathog. 2008 Oct;4(10):e1000178. doi: 10.1371/journal.ppat.1000178. Epub 2008 Oct 17.

27.

Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

Lam SH, Mathavan S, Tong Y, Li H, Karuturi RK, Wu Y, Vega VB, Liu ET, Gong Z.

PLoS Genet. 2008 Jul 11;4(7):e1000121. doi: 10.1371/journal.pgen.1000121.

28.

Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome.

Chu Z, Li J, Eshaghi M, Karuturi RK, Lin K, Liu J.

BMC Genomics. 2007 Sep 15;8:323.

29.
30.

Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells.

Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q.

Genes Dev. 2007 May 1;21(9):1050-63. Epub 2007 Apr 16.

31.
32.

Global map of growth-regulated gene expression in Burkholderia pseudomallei, the causative agent of melioidosis.

Rodrigues F, Sarkar-Tyson M, Harding SV, Sim SH, Chua HH, Lin CH, Han X, Karuturi RK, Sung K, Yu K, Chen W, Atkins TP, Titball RW, Tan P.

J Bacteriol. 2006 Dec;188(23):8178-88. Epub 2006 Sep 22.

33.

Systematic deletion analysis of fission yeast protein kinases.

Bimbó A, Jia Y, Poh SL, Karuturi RK, den Elzen N, Peng X, Zheng L, O'Connell M, Liu ET, Balasubramanian MK, Liu J.

Eukaryot Cell. 2005 Apr;4(4):799-813.

34.

Identification of cell cycle-regulated genes in fission yeast.

Peng X, Karuturi RK, Miller LD, Lin K, Jia Y, Kondu P, Wang L, Wong LS, Liu ET, Balasubramanian MK, Liu J.

Mol Biol Cell. 2005 Mar;16(3):1026-42. Epub 2004 Dec 22.

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