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Items: 13

1.

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay.

Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM.

PLoS Genet. 2018 Nov 30;14(11):e1007671. doi: 10.1371/journal.pgen.1007671. eCollection 2018 Nov.

2.

Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing.

Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM.

Clin Cancer Res. 2018 May 1;24(9):2092-2099. doi: 10.1158/1078-0432.CCR-17-1960. Epub 2018 Feb 28.

3.

R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R.

Ramaker RC, Gordon ER, Cooper SJ.

Bioinformatics. 2018 May 15;34(10):1789-1791. doi: 10.1093/bioinformatics/btx825.

PMID:
29280991
4.

A genome-wide interactome of DNA-associated proteins in the human liver.

Ramaker RC, Savic D, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ.

Genome Res. 2017 Nov;27(11):1950-1960. doi: 10.1101/gr.222083.117. Epub 2017 Oct 11.

5.

Post-mortem molecular profiling of three psychiatric disorders.

Ramaker RC, Bowling KM, Lasseigne BN, Hagenauer MH, Hardigan AA, Davis NS, Gertz J, Cartagena PM, Walsh DM, Vawter MP, Jones EG, Schatzberg AF, Barchas JD, Watson SJ, Bunney BG, Akil H, Bunney WE, Li JZ, Cooper SJ, Myers RM.

Genome Med. 2017 Jul 28;9(1):72. doi: 10.1186/s13073-017-0458-5.

6.

RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature.

Ramaker RC, Lasseigne BN, Hardigan AA, Palacio L, Gunther DS, Myers RM, Cooper SJ.

Oncotarget. 2017 Jun 13;8(24):38668-38681. doi: 10.18632/oncotarget.16961.

7.

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns.

Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM.

BMC Cancer. 2017 Apr 17;17(1):273. doi: 10.1186/s12885-017-3252-2.

8.

aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments.

Alonso A, Lasseigne BN, Williams K, Nielsen J, Ramaker RC, Hardigan AA, Johnston B, Roberts BS, Cooper SJ, Marsal S, Myers RM.

Bioinformatics. 2017 Jun 1;33(11):1727-1729. doi: 10.1093/bioinformatics/btx023.

9.

Genomic regulation of invasion by STAT3 in triple negative breast cancer.

McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM.

Oncotarget. 2017 Jan 31;8(5):8226-8238. doi: 10.18632/oncotarget.14153.

10.

Differential stress induced c-Fos expression and identification of region-specific miRNA-mRNA networks in the dorsal raphe and amygdala of high-responder/low-responder rats.

Cohen JL, Ata AE, Jackson NL, Rahn EJ, Ramaker RC, Cooper S, Kerman IA, Clinton SM.

Behav Brain Res. 2017 Feb 15;319:110-123. doi: 10.1016/j.bbr.2016.11.015. Epub 2016 Nov 16.

11.

Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets.

Ghatalia P, Yang ES, Lasseigne BN, Ramaker RC, Cooper SJ, Chen D, Sudarshan S, Wei S, Guru AS, Zhao A, Cooper T, Della Manna DL, Naik G, Myers RM, Sonpavde G.

PLoS One. 2016 Aug 30;11(8):e0160924. doi: 10.1371/journal.pone.0160924. eCollection 2016.

12.

Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation.

Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM.

Genome Med. 2016 Jul 11;8(1):74. doi: 10.1186/s13073-016-0328-6.

13.

RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4.

Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM.

Mol Oncol. 2016 Oct;10(8):1169-82. doi: 10.1016/j.molonc.2016.05.004. Epub 2016 May 26.

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