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Items: 1 to 50 of 90

1.

In silico analysis of alternative splicing on drug-target gene interactions.

Ji Y, Mishra RK, Davuluri RV.

Sci Rep. 2020 Jan 10;10(1):134. doi: 10.1038/s41598-019-56894-x.

2.

Multivariate Analysis of Preoperative Magnetic Resonance Imaging Reveals Transcriptomic Classification of de novo Glioblastoma Patients.

Rathore S, Akbari H, Bakas S, Pisapia JM, Shukla G, Rudie JD, Da X, Davuluri RV, Dahmane N, O'Rourke DM, Davatzikos C.

Front Comput Neurosci. 2019 Dec 12;13:81. doi: 10.3389/fncom.2019.00081. eCollection 2019.

3.

Immune landscapes associated with different glioblastoma molecular subtypes.

Martinez-Lage M, Lynch TM, Bi Y, Cocito C, Way GP, Pal S, Haller J, Yan RE, Ziober A, Nguyen A, Kandpal M, O'Rourke DM, Greenfield JP, Greene CS, Davuluri RV, Dahmane N.

Acta Neuropathol Commun. 2019 Nov 29;7(1):203. doi: 10.1186/s40478-019-0803-6.

4.

Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing.

Ideozu JE, Rangaraj V, Abdala-Valencia H, Zhang X, Kandpal M, Sala MA, Davuluri RV, Levy H.

BMC Med Genomics. 2019 May 22;12(1):66. doi: 10.1186/s12920-019-0529-0.

5.

Platform-Independent Classification System to Predict Molecular Subtypes of High-Grade Serous Ovarian Carcinoma.

Shilpi A, Kandpal M, Ji Y, Seagle BL, Shahabi S, Davuluri RV.

JCO Clin Cancer Inform. 2019 Apr;3:1-9. doi: 10.1200/CCI.18.00096.

6.

IDH3α regulates one-carbon metabolism in glioblastoma.

May JL, Kouri FM, Hurley LA, Liu J, Tommasini-Ghelfi S, Ji Y, Gao P, Calvert AE, Lee A, Chandel NS, Davuluri RV, Horbinski CM, Locasale JW, Stegh AH.

Sci Adv. 2019 Jan 2;5(1):eaat0456. doi: 10.1126/sciadv.aat0456. eCollection 2019 Jan.

7.

Metastatic cancers promote cachexia through ZIP14 upregulation in skeletal muscle.

Wang G, Biswas AK, Ma W, Kandpal M, Coker C, Grandgenett PM, Hollingsworth MA, Jain R, Tanji K, Lόpez-Pintado S, Borczuk A, Hebert D, Jenkitkasemwong S, Hojyo S, Davuluri RV, Knutson MD, Fukada T, Acharyya S.

Nat Med. 2018 Jun;24(6):770-781. doi: 10.1038/s41591-018-0054-2. Epub 2018 Jun 6.

8.

Radiomic MRI signature reveals three distinct subtypes of glioblastoma with different clinical and molecular characteristics, offering prognostic value beyond IDH1.

Rathore S, Akbari H, Rozycki M, Abdullah KG, Nasrallah MP, Binder ZA, Davuluri RV, Lustig RA, Dahmane N, Bilello M, O'Rourke DM, Davatzikos C.

Sci Rep. 2018 Mar 23;8(1):5087. doi: 10.1038/s41598-018-22739-2.

9.

Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors.

Malchenko S, Sredni ST, Boyineni J, Bi Y, Margaryan NV, Guda MR, Kostenko Y, Tomita T, Davuluri RV, Velpula K, Hendrix MJC, Soares MB.

Oncotarget. 2018 Feb 9;9(17):13733-13747. doi: 10.18632/oncotarget.24460. eCollection 2018 Mar 2.

10.

Publisher Correction: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs.

Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M.

Nat Commun. 2018 Jan 8;9(1):160. doi: 10.1038/s41467-017-02485-1.

11.

Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs.

Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M.

Nat Commun. 2017 Nov 27;8(1):1801. doi: 10.1038/s41467-017-01562-9. Erratum in: Nat Commun. 2018 Jan 8;9(1):160.

12.

Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation.

Calvert AE, Chalastanis A, Wu Y, Hurley LA, Kouri FM, Bi Y, Kachman M, May JL, Bartom E, Hua Y, Mishra RK, Schiltz GE, Dubrovskyi O, Mazar AP, Peter ME, Zheng H, James CD, Burant CF, Chandel NS, Davuluri RV, Horbinski C, Stegh AH.

Cell Rep. 2017 May 30;19(9):1858-1873. doi: 10.1016/j.celrep.2017.05.014.

13.

Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model.

Malchenko S, Sredni ST, Bi Y, Margaryan NV, Boyineni J, Mohanam I, Tomita T, Davuluri RV, Soares MB.

PLoS One. 2017 Mar 1;12(3):e0173106. doi: 10.1371/journal.pone.0173106. eCollection 2017.

14.

Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes.

Liu X, Zhao B, Sun L, Bhuripanyo K, Wang Y, Bi Y, Davuluri RV, Duong DM, Nanavati D, Yin J, Kiyokawa H.

Nat Commun. 2017 Jan 30;8:14286. doi: 10.1038/ncomms14286.

15.

Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis.

Shilpi A, Bi Y, Jung S, Patra SK, Davuluri RV.

Cancer Inform. 2017 Jan 9;16:1-13. doi: 10.4137/CIN.S39783. eCollection 2017.

16.

Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers.

Van Roosbroeck K, Fanini F, Setoyama T, Ivan C, Rodriguez-Aguayo C, Fuentes-Mattei E, Xiao L, Vannini I, Redis RS, D'Abundo L, Zhang X, Nicoloso MS, Rossi S, Gonzalez-Villasana V, Rupaimoole R, Ferracin M, Morabito F, Neri A, Ruvolo PP, Ruvolo VR, Pecot CV, Amadori D, Abruzzo L, Calin S, Wang X, You MJ, Ferrajoli A, Orlowski R, Plunkett W, Lichtenberg TM, Davuluri RV, Berindan-Neagoe I, Negrini M, Wistuba II, Kantarjian HM, Sood AK, Lopez-Berestein G, Keating MJ, Fabbri M, Calin GA.

Clin Cancer Res. 2017 Jun 1;23(11):2891-2904. doi: 10.1158/1078-0432.CCR-16-1025. Epub 2016 Nov 30.

17.

Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer.

Jin HJ, Jung S, DebRoy AR, Davuluri RV.

Oncotarget. 2016 Aug 23;7(34):54616-54626. doi: 10.18632/oncotarget.10520.

18.

MNK Inhibition Disrupts Mesenchymal Glioma Stem Cells and Prolongs Survival in a Mouse Model of Glioblastoma.

Bell JB, Eckerdt FD, Alley K, Magnusson LP, Hussain H, Bi Y, Arslan AD, Clymer J, Alvarez AA, Goldman S, Cheng SY, Nakano I, Horbinski C, Davuluri RV, James CD, Platanias LC.

Mol Cancer Res. 2016 Oct;14(10):984-993. Epub 2016 Jun 30.

19.

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.

Dapas M, Kandpal M, Bi Y, Davuluri RV.

Brief Bioinform. 2017 Mar 1;18(2):260-269. doi: 10.1093/bib/bbw016.

20.

Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi-class tumor subtyping.

Jung S, Bi Y, Davuluri RV.

BMC Genomics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2164-16-S11-S3. Epub 2015 Nov 10.

21.

Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques.

Macyszyn L, Akbari H, Pisapia JM, Da X, Attiah M, Pigrish V, Bi Y, Pal S, Davuluri RV, Roccograndi L, Dahmane N, Martinez-Lage M, Biros G, Wolf RL, Bilello M, O'Rourke DM, Davatzikos C.

Neuro Oncol. 2016 Mar;18(3):417-25. doi: 10.1093/neuonc/nov127. Epub 2015 Jul 16.

22.

Correction for Patro et al., Shift in Monocyte Apoptosis with Increasing Viral Load and Change in Apoptosis-Related ISG/Bcl2 Family Gene Expression in Chronically HIV-1-Infected Subjects.

Patro SC, Pal S, Bi Y, Lynn K, Mounzer KC, Kostman JR, Davuluri RV, Montaner LJ.

J Virol. 2015 Jul;89(13):6970. doi: 10.1128/JVI.00735-15. No abstract available.

23.

Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma.

Walsh AM, Kapoor GS, Buonato JM, Mathew LK, Bi Y, Davuluri RV, Martinez-Lage M, Simon MC, O'Rourke DM, Lazzara MJ.

Mol Cancer Res. 2015 Aug;13(8):1227-37. doi: 10.1158/1541-7786.MCR-14-0183-T. Epub 2015 May 1.

24.

Shift in monocyte apoptosis with increasing viral load and change in apoptosis-related ISG/Bcl2 family gene expression in chronically HIV-1-infected subjects.

Patro SC, Pal S, Bi Y, Lynn K, Mounzer KC, Kostman JR, Davuluri RV, Montaner LJ.

J Virol. 2015 Jan;89(1):799-810. doi: 10.1128/JVI.02382-14. Epub 2014 Oct 29. Erratum in: J Virol. 2015 Jul;89(13):6970.

25.

Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2.

He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A.

J Clin Endocrinol Metab. 2015 Jan;100(1):E164-72. doi: 10.1210/jc.2014-2147.

26.

Protein kinase A activation enhances β-catenin transcriptional activity through nuclear localization to PML bodies.

Zhang M, Mahoney E, Zuo T, Manchanda PK, Davuluri RV, Kirschner LS.

PLoS One. 2014 Oct 9;9(10):e109523. doi: 10.1371/journal.pone.0109523. eCollection 2014.

27.

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.

Pal S, Gupta R, Davuluri RV.

Methods Mol Biol. 2014;1176:1-9. doi: 10.1007/978-1-4939-0992-6_1.

PMID:
25030914
28.

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline.

Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman PM, Davuluri RV, Riethman H.

Genome Res. 2014 Jun;24(6):1039-50. doi: 10.1101/gr.166983.113. Epub 2014 Mar 27.

29.

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes.

Pal S, Bi Y, Macyszyn L, Showe LC, O'Rourke DM, Davuluri RV.

Nucleic Acids Res. 2014 Apr;42(8):e64. doi: 10.1093/nar/gku121. Epub 2014 Feb 6.

30.

miR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma.

Mathew LK, Skuli N, Mucaj V, Lee SS, Zinn PO, Sathyan P, Imtiyaz HZ, Zhang Z, Davuluri RV, Rao S, Venneti S, Lal P, Lathia JD, Rich JN, Keith B, Minn AJ, Simon MC.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):291-6. doi: 10.1073/pnas.1314341111. Epub 2013 Dec 24.

31.

HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts.

Ferdin J, Nishida N, Wu X, Nicoloso MS, Shah MY, Devlin C, Ling H, Shimizu M, Kumar K, Cortez MA, Ferracin M, Bi Y, Yang D, Czerniak B, Zhang W, Schmittgen TD, Voorhoeve MP, Reginato MJ, Negrini M, Davuluri RV, Kunej T, Ivan M, Calin GA.

Cell Death Differ. 2013 Dec;20(12):1675-87. doi: 10.1038/cdd.2013.119. Epub 2013 Sep 13.

32.

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.

Bi Y, Davuluri RV.

BMC Bioinformatics. 2013 Aug 27;14:262. doi: 10.1186/1471-2105-14-262.

33.

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer.

Ling H, Spizzo R, Atlasi Y, Nicoloso M, Shimizu M, Redis RS, Nishida N, Gafà R, Song J, Guo Z, Ivan C, Barbarotto E, De Vries I, Zhang X, Ferracin M, Churchman M, van Galen JF, Beverloo BH, Shariati M, Haderk F, Estecio MR, Garcia-Manero G, Patijn GA, Gotley DC, Bhardwaj V, Shureiqi I, Sen S, Multani AS, Welsh J, Yamamoto K, Taniguchi I, Song MA, Gallinger S, Casey G, Thibodeau SN, Le Marchand L, Tiirikainen M, Mani SA, Zhang W, Davuluri RV, Mimori K, Mori M, Sieuwerts AM, Martens JW, Tomlinson I, Negrini M, Berindan-Neagoe I, Foekens JA, Hamilton SR, Lanza G, Kopetz S, Fodde R, Calin GA.

Genome Res. 2013 Sep;23(9):1446-61. doi: 10.1101/gr.152942.112. Epub 2013 Jun 24.

34.

ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing.

Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV, Nishikura K.

Cell. 2013 Apr 25;153(3):575-89. doi: 10.1016/j.cell.2013.03.024.

35.

Isoform level expression profiles provide better cancer signatures than gene level expression profiles.

Zhang Z, Pal S, Bi Y, Tchou J, Davuluri RV.

Genome Med. 2013 Apr 17;5(4):33. doi: 10.1186/gm437. eCollection 2013.

36.

Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling.

Bhattacharjee M, Gupta R, Davuluri RV.

Front Genet. 2012 Nov 27;3:239. doi: 10.3389/fgene.2012.00239. eCollection 2012.

37.

A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection.

Deng Z, Wang Z, Stong N, Plasschaert R, Moczan A, Chen HS, Hu S, Wikramasinghe P, Davuluri RV, Bartolomei MS, Riethman H, Lieberman PM.

EMBO J. 2012 Nov 5;31(21):4165-78. doi: 10.1038/emboj.2012.266. Epub 2012 Sep 25.

38.

Sequencing and analysis of a South Asian-Indian personal genome.

Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G.

BMC Genomics. 2012 Aug 31;13:440. doi: 10.1186/1471-2164-13-440.

39.

Alternative transcription and alternative splicing in cancer.

Pal S, Gupta R, Davuluri RV.

Pharmacol Ther. 2012 Dec;136(3):283-94. doi: 10.1016/j.pharmthera.2012.08.005. Epub 2012 Aug 14. Review.

PMID:
22909788
40.

The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type.

Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A.

Proc Natl Acad Sci U S A. 2012 May 29;109(22):8646-51. doi: 10.1073/pnas.1205654109. Epub 2012 May 14.

41.

Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA.

Lu F, Tsai K, Chen HS, Wikramasinghe P, Davuluri RV, Showe L, Domsic J, Marmorstein R, Lieberman PM.

J Virol. 2012 May;86(10):5752-62. doi: 10.1128/JVI.07216-11. Epub 2012 Mar 14.

42.

RP58/ZNF238 directly modulates proneurogenic gene levels and is required for neuronal differentiation and brain expansion.

Xiang C, Baubet V, Pal S, Holderbaum L, Tatard V, Jiang P, Davuluri RV, Dahmane N.

Cell Death Differ. 2012 Apr;19(4):692-702. doi: 10.1038/cdd.2011.144. Epub 2011 Nov 18.

43.

Tree-based position weight matrix approach to model transcription factor binding site profiles.

Bi Y, Kim H, Gupta R, Davuluri RV.

PLoS One. 2011;6(9):e24210. doi: 10.1371/journal.pone.0024210. Epub 2011 Sep 2.

44.

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.

Kim H, Bi Y, Pal S, Gupta R, Davuluri RV.

BMC Bioinformatics. 2011 Jul 27;12:305. doi: 10.1186/1471-2105-12-305.

45.

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.

Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe LC, Dahmane N, Davuluri RV.

Genome Res. 2011 Aug;21(8):1260-72. doi: 10.1101/gr.120535.111. Epub 2011 Jun 28.

46.

Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of B-cell chronic lymphocytic leukemia.

Fabbri M, Bottoni A, Shimizu M, Spizzo R, Nicoloso MS, Rossi S, Barbarotto E, Cimmino A, Adair B, Wojcik SE, Valeri N, Calore F, Sampath D, Fanini F, Vannini I, Musuraca G, Dell'Aquila M, Alder H, Davuluri RV, Rassenti LZ, Negrini M, Nakamura T, Amadori D, Kay NE, Rai KR, Keating MJ, Kipps TJ, Calin GA, Croce CM.

JAMA. 2011 Jan 5;305(1):59-67. doi: 10.1001/jama.2010.1919.

47.

MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.

Gupta R, Bhattacharyya A, Agosto-Perez FJ, Wickramasinghe P, Davuluri RV.

Nucleic Acids Res. 2011 Jan;39(Database issue):D92-7. doi: 10.1093/nar/gkq1171. Epub 2010 Nov 21.

48.

Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1).

Lu F, Wikramasinghe P, Norseen J, Tsai K, Wang P, Showe L, Davuluri RV, Lieberman PM.

Virol J. 2010 Oct 7;7:262. doi: 10.1186/1743-422X-7-262.

49.

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.

Sun H, Wu J, Wickramasinghe P, Pal S, Gupta R, Bhattacharyya A, Agosto-Perez FJ, Showe LC, Huang TH, Davuluri RV.

Nucleic Acids Res. 2011 Jan;39(1):190-201. doi: 10.1093/nar/gkq775. Epub 2010 Sep 14.

50.

Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility.

Nicoloso MS, Sun H, Spizzo R, Kim H, Wickramasinghe P, Shimizu M, Wojcik SE, Ferdin J, Kunej T, Xiao L, Manoukian S, Secreto G, Ravagnani F, Wang X, Radice P, Croce CM, Davuluri RV, Calin GA.

Cancer Res. 2010 Apr 1;70(7):2789-98. doi: 10.1158/0008-5472.CAN-09-3541. Epub 2010 Mar 23.

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