| Year |
Citation |
Score |
| 2020 |
Huang H, Wang Y, Kandpal M, Zhao G, Cardenas H, Ji Y, Chaparala A, Tanner EJ, Chen J, Davuluri RV, Matei D. FTO-Dependent N6-Methyladenosine Modifications Inhibit Ovarian Cancer Stem Cell Self-Renewal by Blocking cAMP Signaling. Cancer Research. PMID 32606006 DOI: 10.1158/0008-5472.Can-19-4044 |
0.355 |
|
| 2020 |
Ji Y, Mishra RK, Davuluri RV. In silico analysis of alternative splicing on drug-target gene interactions. Scientific Reports. 10: 134. PMID 31924844 DOI: 10.1038/S41598-019-56894-X |
0.338 |
|
| 2020 |
Huang H, Wang Y, Kandpal M, Zhao G, Cardenas H, Ji Y, Tanner E, Chen J, Davuluri R, Matei D. Abstract 2449: A novel function of FTO in ovarian cancer stem cells through m6A RNA demethylation Cancer Research. 80: 2449-2449. DOI: 10.1158/1538-7445.Am2020-2449 |
0.353 |
|
| 2019 |
Ideozu JE, Rangaraj V, Abdala-Valencia H, Zhang X, Kandpal M, Sala MA, Davuluri RV, Levy H. Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing. Bmc Medical Genomics. 12: 66. PMID 31118097 DOI: 10.1186/S12920-019-0529-0 |
0.325 |
|
| 2019 |
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. IDH3α regulates one-carbon metabolism in glioblastoma. Science Advances. 5: eaat0456. PMID 30613765 DOI: 10.1126/Sciadv.Aat0456 |
0.342 |
|
| 2018 |
Malchenko S, Sredni ST, Boyineni J, Bi Y, Margaryan NV, Guda MR, Kostenko Y, Tomita T, Davuluri RV, Velpula K, Hendrix MJC, Soares MB. Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors. Oncotarget. 9: 13733-13747. PMID 29568390 DOI: 10.18632/Oncotarget.24460 |
0.321 |
|
| 2018 |
Huang H, Yu Q, Kandpal M, Davuluri RV, Matei D. Abstract 1396: Pathway-directed DNA demethylation as an epithelial to mesenchymal targeting strategy Cancer Research. 78: 1396-1396. DOI: 10.1158/1538-7445.Am2018-1396 |
0.445 |
|
| 2017 |
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, et al. Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nature Communications. 8: 1801. PMID 29180617 DOI: 10.1038/S41467-017-01562-9 |
0.383 |
|
| 2017 |
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, ... ... Davuluri RV, et al. Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation. Cell Reports. 19: 1858-1873. PMID 28564604 DOI: 10.1016/J.Celrep.2017.05.014 |
0.347 |
|
| 2017 |
Malchenko S, Sredni ST, Bi Y, Margaryan NV, Boyineni J, Mohanam I, Tomita T, Davuluri RV, Soares MB. Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model. Plos One. 12: e0173106. PMID 28249000 DOI: 10.1371/Journal.Pone.0173106 |
0.332 |
|
| 2017 |
Shilpi A, Bi Y, Jung S, Patra SK, Davuluri RV. Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis. Cancer Informatics. 16: 1-13. PMID 28096648 DOI: 10.4137/Cin.S39783 |
0.306 |
|
| 2016 |
Jin HJ, Jung S, DebRoy AR, Davuluri RV. Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer. Oncotarget. PMID 27409348 DOI: 10.18632/Oncotarget.10520 |
0.385 |
|
| 2016 |
Bell JB, Eckerdt F, 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, et al. MNK Inhibition Disrupts Mesenchymal Glioma Stem Cells and Prolongs Survival in a Mouse Model of Glioblastoma. Molecular Cancer Research : McR. PMID 27364770 DOI: 10.1158/1541-7786.Mcr-16-0172 |
0.371 |
|
| 2016 |
Dapas M, Kandpal M, Bi Y, Davuluri RV. Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. Briefings in Bioinformatics. PMID 26944083 DOI: 10.1093/Bib/Bbw016 |
0.38 |
|
| 2015 |
Jung S, Bi Y, Davuluri RV. Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi-class tumor subtyping. Bmc Genomics. 16: S3. PMID 26576613 DOI: 10.1186/1471-2164-16-S11-S3 |
0.36 |
|
| 2015 |
Campbell AR, Regan K, Bhave N, Pattanayak A, Parihar R, Stiff AR, Trikha P, Scoville SD, Liyanarachchi S, Kondadasula SV, Lele O, Davuluri R, Payne PR, Carson WE. Gene expression profiling of the human natural killer cell response to Fc receptor activation: unique enhancement in the presence of interleukin-12. Bmc Medical Genomics. 8: 66. PMID 26470881 DOI: 10.1186/S12920-015-0142-9 |
0.338 |
|
| 2015 |
Durrans A, Gao D, Gupta R, Fischer KR, Choi H, El Rayes T, Ryu S, Nasar A, Spinelli CF, Andrews W, Elemento O, Nolan D, Stiles B, Rafii S, Narula N, ... Davuluri R, et al. Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC. Plos One. 10: e0129123. PMID 26046767 DOI: 10.1371/Journal.Pone.0129123 |
0.378 |
|
| 2015 |
Walsh AM, Kapoor GS, Buonato JM, Mathew LK, Bi Y, Davuluri RV, Martinez-Lage M, Simon MC, O'Rourke DM, Lazzara MJ. Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma. Molecular Cancer Research : McR. PMID 25934697 DOI: 10.1158/1541-7786.Mcr-14-0183-T |
0.356 |
|
| 2015 |
Patro SC, Pal S, Bi Y, Lynn K, Mounzer KC, Kostman JR, Davuluri RV, Montaner LJ. Shift in monocyte apoptosis with increasing viral load and change in apoptosis-related ISG/Bcl2 family gene expression in chronically HIV-1-infected subjects. Journal of Virology. 89: 799-810. PMID 25355877 DOI: 10.1128/Jvi.02382-14 |
0.301 |
|
| 2015 |
He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A. Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2. The Journal of Clinical Endocrinology and Metabolism. 100: E164-72. PMID 25303483 DOI: 10.1210/Jc.2014-2147 |
0.317 |
|
| 2015 |
Roccograndi L, Bi Y, Davuluri R, Dahmane N, O'Rourke DM. Abstract 2247: SHP2 expression and function in different subtypes of glioblastoma Cancer Research. 75: 2247-2247. DOI: 10.1158/1538-7445.Am2015-2247 |
0.381 |
|
| 2015 |
Jung S, Bi Y, Davuluri RV. Abstract 2185: Informatics framework for clustering and deriving gene signatures for prognostic stratification of cancer patients Molecular and Cellular Biology. DOI: 10.1158/1538-7445.Am2015-2185 |
0.318 |
|
| 2014 |
Pal S, Gupta R, Davuluri RV. Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Methods in Molecular Biology (Clifton, N.J.). 1176: 1-9. PMID 25030914 DOI: 10.1007/978-1-4939-0992-6_1 |
0.338 |
|
| 2014 |
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. Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Research. 24: 1039-50. PMID 24676094 DOI: 10.1101/Gr.166983.113 |
0.354 |
|
| 2014 |
Pal S, Bi Y, Macyszyn L, Showe LC, O'Rourke DM, Davuluri RV. Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes. Nucleic Acids Research. 42: e64. PMID 24503249 DOI: 10.1093/Nar/Gku121 |
0.408 |
|
| 2014 |
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, et al. miR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma. Proceedings of the National Academy of Sciences of the United States of America. 111: 291-6. PMID 24368849 DOI: 10.1073/Pnas.1314341111 |
0.3 |
|
| 2014 |
Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Mamorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Research. 42: 774-89. PMID 24121688 DOI: 10.1093/Nar/Gkt910 |
0.32 |
|
| 2013 |
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, ... ... Davuluri RV, et al. HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts. Cell Death and Differentiation. 20: 1675-87. PMID 24037088 DOI: 10.1038/Cdd.2013.119 |
0.383 |
|
| 2013 |
Bi Y, Davuluri RV. NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. Bmc Bioinformatics. 14: 262. PMID 23981227 DOI: 10.1186/1471-2105-14-262 |
0.326 |
|
| 2013 |
Glass C, Wuertzer C, Cui X, Bi Y, Davuluri R, Xiao YY, Wilson M, Owens K, Zhang Y, Perkins A. Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia. Plos One. 8: e67134. PMID 23826213 DOI: 10.1371/Journal.Pone.0067134 |
0.434 |
|
| 2013 |
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, ... ... Davuluri RV, et al. CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer. Genome Research. 23: 1446-61. PMID 23796952 DOI: 10.1101/Gr.152942.112 |
0.385 |
|
| 2013 |
Zhang Z, Pal S, Bi Y, Tchou J, Davuluri RV. Isoform level expression profiles provide better cancer signatures than gene level expression profiles. Genome Medicine. 5: 33. PMID 23594586 DOI: 10.1186/Gm437 |
0.42 |
|
| 2013 |
Bi Y, Pal S, Macyszyn L, O'Rourke D, Davuluri R. Abstract C06: Translation of isoform-level gene signature into robust diagnostic assay for glioblastoma subtyping Cancer Research. 73. DOI: 10.1158/1538-7445.Fbcr13-C06 |
0.38 |
|
| 2013 |
Pal S, Bi Y, Macyszyn L, Showe LC, O'Rourke DM, Davuluri RV. Abstract 5597: Molecular classification of glioblastoma multiforme using isoform-level gene expression signatures. Cancer Research. 73: 5597-5597. DOI: 10.1158/1538-7445.Am2013-5597 |
0.386 |
|
| 2013 |
Bi Y, Pal S, Macyszyn L, Showe LC, O'Rourke D, Davuluri RV. Abstract A26: Translation of isoform-level gene signature into robust diagnostic assay for glioblastoma subtyping. Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Targ-13-A26 |
0.38 |
|
| 2012 |
Bhattacharjee M, Gupta R, Davuluri R. Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling Frontiers in Genetics. 3: 239-239. PMID 23293650 DOI: 10.3389/Fgene.2012.00239 |
0.357 |
|
| 2012 |
Deng Z, Wang Z, Stong N, Plasschaert R, Moczan A, Chen HS, Hu S, Wikramasinghe P, Davuluri RV, Bartolomei MS, Riethman H, Lieberman PM. A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection. The Embo Journal. 31: 4165-78. PMID 23010778 DOI: 10.1038/Emboj.2012.266 |
0.335 |
|
| 2012 |
Pal S, Gupta R, Davuluri RV. Alternative transcription and alternative splicing in cancer. Pharmacology & Therapeutics. 136: 283-94. PMID 22909788 DOI: 10.1016/J.Pharmthera.2012.08.005 |
0.473 |
|
| 2012 |
Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proceedings of the National Academy of Sciences of the United States of America. 109: 8646-51. PMID 22586128 DOI: 10.1073/Pnas.1205654109 |
0.347 |
|
| 2012 |
Lu F, Tsai K, Chen HS, Wikramasinghe P, Davuluri RV, Showe L, Domsic J, Marmorstein R, Lieberman PM. Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA. Journal of Virology. 86: 5752-62. PMID 22419807 DOI: 10.1128/Jvi.07216-11 |
0.385 |
|
| 2012 |
Xiang C, Baubet V, Pal S, Holderbaum L, Tatard V, Jiang P, Davuluri RV, Dahmane N. RP58/ZNF238 directly modulates proneurogenic gene levels and is required for neuronal differentiation and brain expansion Cell Death & Differentiation. 19: 692-702. PMID 22095278 DOI: 10.1038/Cdd.2011.144 |
0.315 |
|
| 2012 |
Pal S, Zhang Z, Gupta R, Bi Y, Fetting HH, O'Rourke DM, Davuluri RV. Abstract 2990: Molecular subtyping of glioblastoma based on isoform level network modeling Cancer Research. 72: 2990-2990. DOI: 10.1158/1538-7445.Am2012-2990 |
0.429 |
|
| 2011 |
Bi Y, Kim H, Gupta R, Davuluri RV. Tree-based position weight matrix approach to model transcription factor binding site profiles. Plos One. 6: e24210. PMID 21912677 DOI: 10.1371/Journal.Pone.0024210 |
0.314 |
|
| 2011 |
Kim H, Bi Y, Pal S, Gupta R, Davuluri RV. IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. Bmc Bioinformatics. 12: 305. PMID 21794104 DOI: 10.1186/1471-2105-12-305 |
0.351 |
|
| 2011 |
Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe LC, Dahmane N, Davuluri RV. Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Research. 21: 1260-72. PMID 21712398 DOI: 10.1101/Gr.120535.111 |
0.402 |
|
| 2011 |
Gupta R, Bhattacharyya A, Agosto-Perez FJ, Wickramasinghe P, Davuluri RV. MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. Nucleic Acids Research. 39: D92-7. PMID 21097880 DOI: 10.1093/Nar/Gkq1171 |
0.429 |
|
| 2011 |
Sun H, Wu J, Wickramasinghe P, Pal S, Gupta R, Bhattacharyya A, Agosto-Perez FJ, Showe LC, Huang TH, Davuluri RV. Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Research. 39: 190-201. PMID 20843783 DOI: 10.1093/Nar/Gkq775 |
0.389 |
|
| 2011 |
Zhang Z, Davuluri RV. Abstract 31: Isoform level gene expression signature is a better discriminator of cancer from normal cells than gene level expression signature Cancer Research. 71: 31-31. DOI: 10.1158/1538-7445.Am2011-31 |
0.442 |
|
| 2010 |
Lu F, Wikramasinghe P, Norseen J, Tsai K, Wang P, Showe L, Davuluri RV, Lieberman PM. Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1). Virology Journal. 7: 262. PMID 20929547 DOI: 10.1186/1743-422X-7-262 |
0.355 |
|
| 2010 |
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, ... ... Davuluri RV, et al. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Research. 70: 2789-98. PMID 20332227 DOI: 10.1158/0008-5472.Can-09-3541 |
0.331 |
|
| 2010 |
Herz HM, Madden LD, Chen Z, Bolduc C, Buff E, Gupta R, Davuluri R, Shilatifard A, Hariharan IK, Bergmann A. The H3K27me3 demethylase dUTX is a suppressor of Notch- and Rb-dependent tumors in Drosophila. Molecular and Cellular Biology. 30: 2485-97. PMID 20212086 DOI: 10.1128/Mcb.01633-09 |
0.329 |
|
| 2010 |
Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV. Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. Bmc Bioinformatics. 11: S65. PMID 20122241 DOI: 10.1186/1471-2105-11-S1-S65 |
0.407 |
|
| 2010 |
Chou JL, Su HY, Chen LY, Liao YP, Hartman-Frey C, Lai YH, Yang HW, Deatherage DE, Kuo CT, Huang YW, Yan PS, Hsiao SH, Tai CK, Lin HJ, Davuluri RV, et al. Promoter hypermethylation of FBXO32, a novel TGF-beta/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer. Laboratory Investigation; a Journal of Technical Methods and Pathology. 90: 414-25. PMID 20065949 DOI: 10.1038/Labinvest.2009.138 |
0.38 |
|
| 2010 |
Rossi S, Kopetz S, Davuluri R, Hamilton SR, Calin GA. MicroRNAs, ultraconserved genes and colorectal cancers The International Journal of Biochemistry & Cell Biology. 42: 1291-1297. PMID 19497386 DOI: 10.1016/J.Biocel.2009.05.018 |
0.401 |
|
| 2010 |
Chou J, Su H, Chen L, Liao Y, Hartman-Frey C, Lai Y, Yang H, Deatherage DE, Kuo C, Huang Y, Yan PS, Hsiao S, Tai C, Lin HL, Davuluri RV, et al. Abstract 3072: Promoter hypermethylation of FBXO32, a novel TGF-β/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer Cancer Research. 70: 3072-3072. DOI: 10.1158/1538-7445.Am10-3072 |
0.364 |
|
| 2009 |
Chen SS, Raval A, Johnson AJ, Hertlein E, Liu TH, Jin VX, Sherman MH, Liu SJ, Dawson DW, Williams KE, Lanasa M, Liyanarachchi S, Lin TS, Marcucci G, Pekarsky Y, ... Davuluri R, et al. Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America. 106: 13433-8. PMID 19666576 DOI: 10.1073/Pnas.0906455106 |
0.388 |
|
| 2009 |
Qin H, Chan MW, Liyanarachchi S, Balch C, Potter D, Souriraj IJ, Cheng AS, Agosto-Perez FJ, Nikonova EV, Yan PS, Lin HJ, Nephew KP, Saltz JH, Showe LC, Huang TH, ... Davuluri RV, et al. An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. Bmc Systems Biology. 3: 73. PMID 19615063 DOI: 10.1186/1752-0509-3-73 |
0.32 |
|
| 2008 |
Chan MW, Huang YW, Hartman-Frey C, Kuo CT, Deatherage D, Qin H, Cheng AS, Yan PS, Davuluri RV, Huang TH, Nephew KP, Lin HJ. Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer. Neoplasia (New York, N.Y.). 10: 908-19. PMID 18714391 DOI: 10.1593/Neo.08540 |
0.314 |
|
| 2008 |
Singer GA, Wu J, Yan P, Plass C, Huang TH, Davuluri RV. Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. Bmc Genomics. 9: 349. PMID 18655706 DOI: 10.1186/1471-2164-9-349 |
0.437 |
|
| 2008 |
Whitman SP, Hackanson B, Liyanarachchi S, Liu S, Rush LJ, Maharry K, Margeson D, Davuluri R, Wen J, Witte T, Yu L, Liu C, Bloomfield CD, Marcucci G, Plass C, et al. DNA hypermethylation and epigenetic silencing of the tumor suppressor gene, SLC5A8, in acute myeloid leukemia with the MLL partial tandem duplication. Blood. 112: 2013-6. PMID 18566324 DOI: 10.1182/Blood-2008-01-128595 |
0.393 |
|
| 2008 |
Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH. The functional consequences of alternative promoter use in mammalian genomes. Trends in Genetics : Tig. 24: 167-77. PMID 18329129 DOI: 10.1016/J.Tig.2008.01.008 |
0.42 |
|
| 2008 |
Kulshreshtha R, Davuluri RV, Calin GA, Ivan M. A microRNA component of the hypoxic response Cell Death and Differentiation. 15: 667-671. PMID 18219318 DOI: 10.1038/Sj.Cdd.4402310 |
0.358 |
|
| 2007 |
Davuluri RV. Bioinformatics tools for modeling transcription factor target genes and epigenetic changes. Methods in Molecular Biology (Clifton, N.J.). 408: 129-51. PMID 18314581 DOI: 10.1007/978-1-59745-547-3_8 |
0.41 |
|
| 2007 |
Opavsky R, Wang SH, Trikha P, Raval A, Huang Y, Wu YZ, Rodriguez B, Keller B, Liyanarachchi S, Wei G, Davuluri RV, Weinstein M, Felsher D, Ostrowski M, Leone G, et al. CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells. Plos Genetics. 3: 1757-69. PMID 17907813 DOI: 10.1371/Journal.Pgen.0030167 |
0.375 |
|
| 2007 |
Kulshreshtha R, Ferracin M, Negrini M, Calin GA, Davuluri RV, Ivan M. Regulation of microRNA expression: the hypoxic component. Cell Cycle (Georgetown, Tex.). 6: 1426-31. PMID 17582223 DOI: 10.4161/Cc.6.12.4410 |
0.398 |
|
| 2007 |
Sevignani C, Calin GA, Nnadi SC, Shimizu M, Davuluri RV, Hyslop T, Demant P, Croce CM, Siracusa LD. MicroRNA genes are frequently located near mouse cancer susceptibility loci. Proceedings of the National Academy of Sciences of the United States of America. 104: 8017-22. PMID 17470785 DOI: 10.1073/Pnas.0702177104 |
0.337 |
|
| 2007 |
Wang H, Hertlein E, Bakkar N, Sun H, Acharyya S, Wang J, Carathers M, Davuluri R, Guttridge DC. NF-kappaB regulation of YY1 inhibits skeletal myogenesis through transcriptional silencing of myofibrillar genes. Molecular and Cellular Biology. 27: 4374-87. PMID 17438126 DOI: 10.1128/Mcb.02020-06 |
0.341 |
|
| 2007 |
Yoon H, He H, Nagy R, Davuluri R, Suster S, Schoenberg D, Pellegata N, Chapelle Ade L. Identification of a novel noncoding RNA gene, NAMA, that is downregulated in papillary thyroid carcinoma with BRAF mutation and associated with growth arrest. International Journal of Cancer. 121: 767-75. PMID 17415708 DOI: 10.1002/Ijc.22701 |
0.398 |
|
| 2007 |
Brena RM, Morrison C, Liyanarachchi S, Jarjoura D, Davuluri RV, Otterson GA, Reisman D, Glaros S, Rush LJ, Plass C. Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancer. Plos Medicine. 4: e108. PMID 17388669 DOI: 10.1371/Journal.Pmed.0040108 |
0.312 |
|
| 2006 |
Kulshreshtha R, Ferracin M, Wojcik SE, Garzon R, Alder H, Agosto-Perez FJ, Davuluri R, Liu CG, Croce CM, Negrini M, Calin GA, Ivan M. A microRNA signature of hypoxia. Molecular and Cellular Biology. 27: 1859-67. PMID 17194750 DOI: 10.1128/Mcb.01395-06 |
0.363 |
|
| 2006 |
Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP. A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics (Oxford, England). 22: 2210-6. PMID 16809387 DOI: 10.1093/Bioinformatics/Btl329 |
0.35 |
|
| 2006 |
Wei SH, Balch C, Paik HH, Kim YS, Baldwin RL, Liyanarachchi S, Li L, Wang Z, Wan JC, Davuluri RV, Karlan BY, Gifford G, Brown R, Kim S, Huang TH, et al. Prognostic DNA methylation biomarkers in ovarian cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 12: 2788-94. PMID 16675572 DOI: 10.1158/1078-0432.Ccr-05-1551 |
0.342 |
|
| 2006 |
Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E. AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiology. 140: 818-29. PMID 16524982 DOI: 10.1104/Pp.105.072280 |
0.413 |
|
| 2006 |
Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH. Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Molecular Cell. 21: 393-404. PMID 16455494 DOI: 10.1016/J.Molcel.2005.12.016 |
0.366 |
|
| 2006 |
Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV. MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. Nucleic Acids Research. 34: D98-103. PMID 16381984 DOI: 10.1093/Nar/Gkj096 |
0.386 |
|
| 2005 |
Jin VX, Sun H, Pohar TT, Liyanarachchi S, Palaniswamy SK, Huang TH, Davuluri RV. ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes. Journal of Molecular Endocrinology. 35: 225-30. PMID 16216904 DOI: 10.1677/Jme.1.01839 |
0.382 |
|
| 2005 |
Cunningham D, Swartzlander D, Liyanarachchi S, Davuluri RV, Herman GE. Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblasts. Journal of Lipid Research. 46: 1150-62. PMID 15805545 DOI: 10.1194/Jlr.M400462-Jlr200 |
0.353 |
|
| 2005 |
Palaniswamy SK, Jin VX, Sun H, Davuluri RV. OMGProm: a database of orthologous mammalian gene promoters. Bioinformatics (Oxford, England). 21: 835-6. PMID 15531605 DOI: 10.1093/Bioinformatics/Bti119 |
0.373 |
|
| 2004 |
Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV. Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Research. 32: 6627-35. PMID 15608294 DOI: 10.1093/Nar/Gkh1005 |
0.418 |
|
| 2004 |
Leu YW, Yan PS, Fan M, Jin VX, Liu JC, Curran EM, Welshons WV, Wei SH, Davuluri RV, Plass C, Nephew KP, Huang TH. Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Research. 64: 8184-92. PMID 15548683 DOI: 10.1158/0008-5472.Can-04-2045 |
0.387 |
|
| 2004 |
Yu L, Liu C, Bennett K, Wu YZ, Dai Z, Vandeusen J, Opavsky R, Raval A, Trikha P, Rodriguez B, Becknell B, Mao C, Lee S, Davuluri RV, Leone G, et al. A NotI-EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignancies. Genomics. 84: 647-60. PMID 15475242 DOI: 10.1016/J.Ygeno.2004.06.010 |
0.406 |
|
| 2004 |
Nakagawa H, Liyanarachchi S, Davuluri RV, Auer H, Martin EW, de la Chapelle A, Frankel WL. Role of cancer-associated stromal fibroblasts in metastatic colon cancer to the liver and their expression profiles. Oncogene. 23: 7366-77. PMID 15326482 DOI: 10.1038/Sj.Onc.1208013 |
0.34 |
|
| 2004 |
Rush LJ, Raval A, Funchain P, Johnson AJ, Smith L, Lucas DM, Bembea M, Liu TH, Heerema NA, Rassenti L, Liyanarachchi S, Davuluri R, Byrd JC, Plass C. Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Research. 64: 2424-33. PMID 15059895 DOI: 10.1158/0008-5472.Can-03-2870 |
0.368 |
|
| 2004 |
Besco J, Popesco MC, Davuluri RV, Frostholm A, Rotter A. Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2). Bmc Genomics. 5: 14. PMID 15040814 DOI: 10.1186/1471-2164-5-14 |
0.335 |
|
| 2004 |
Baldus CD, Liyanarachchi S, Mrózek K, Auer H, Tanner SM, Guimond M, Ruppert AS, Mohamed N, Davuluri RV, Caligiuri MA, Bloomfield CD, de la Chapelle A. Acute myeloid leukemia with complex karyotypes and abnormal chromosome 21: Amplification discloses overexpression of APP, ETS2, and ERG genes. Proceedings of the National Academy of Sciences of the United States of America. 101: 3915-20. PMID 15007164 DOI: 10.1073/Pnas.0400272101 |
0.37 |
|
| 2004 |
de Stanchina E, Querido E, Narita M, Davuluri RV, Pandolfi PP, Ferbeyre G, Lowe SW. PML is a direct p53 target that modulates p53 effector functions. Molecular Cell. 13: 523-35. PMID 14992722 DOI: 10.1016/S1097-2765(04)00062-0 |
0.322 |
|
| 2004 |
Sun H, Davuluri RV. Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics (Oxford, England). 20: 727-34. PMID 14751988 DOI: 10.1093/Bioinformatics/Btg476 |
0.35 |
|
| 2004 |
Pohar TT, Sun H, Davuluri RV. HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. Nucleic Acids Research. 32: D86-90. PMID 14681365 DOI: 10.1093/Nar/Gkh056 |
0.421 |
|
| 2003 |
Davuluri RV. Application of FirstEF to find promoters and first exons in the human genome. Current Protocols in Bioinformatics. Unit4.7. PMID 18428702 DOI: 10.1002/0471250953.Bi0407S01 |
0.364 |
|
| 2003 |
Davuluri RV, Zhang MQ. Computer software to find genes in plant genomic DNA. Methods in Molecular Biology (Clifton, N.J.). 236: 87-108. PMID 14501060 DOI: 10.1385/1-59259-413-1:87 |
0.521 |
|
| 2003 |
Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. Bmc Bioinformatics. 4: 25. PMID 12820902 DOI: 10.1186/1471-2105-4-25 |
0.396 |
|
| 2002 |
Yoon H, Liyanarachchi S, Wright FA, Davuluri R, Lockman JC, de la Chapelle A, Pellegata NS. Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. Proceedings of the National Academy of Sciences of the United States of America. 99: 15632-7. PMID 12438652 DOI: 10.1073/Pnas.242597299 |
0.395 |
|
| 2002 |
Nahle Z, Polakoff J, Davuluri RV, McCurrach ME, Jacobson MD, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D, Lowe SW. Direct coupling of the cell cycle and cell death machinery by E2F. Nature Cell Biology. 4: 859-64. PMID 12389032 DOI: 10.1038/Ncb868 |
0.466 |
|
| 2002 |
Dai Z, Weichenhan D, Wu YZ, Hall JL, Rush LJ, Smith LT, Raval A, Yu L, Kroll D, Muehlisch J, Frühwald MC, de Jong P, Catanese J, Davuluri RV, Smiraglia DJ, et al. An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Research. 12: 1591-8. PMID 12368252 DOI: 10.1101/Gr.197402 |
0.395 |
|
| 2001 |
Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nature Genetics. 29: 412-7. PMID 11726928 DOI: 10.1038/Ng780 |
0.504 |
|
| 2001 |
Tabaska JE, Davuluri RV, Zhang MQ. Identifying the 3'-terminal exon in human DNA. Bioinformatics (Oxford, England). 17: 602-7. PMID 11448878 DOI: 10.1093/Bioinformatics/17.7.602 |
0.379 |
|
| 2000 |
Davuluri RV, Suzuki Y, Sugano S, Zhang MQ. CART Classification of Human 5′ UTR Sequences Genome Research. 10: 1807-1816. PMID 11076865 DOI: 10.1101/Gr.Gr-1460R |
0.462 |
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