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Items: 30

1.

Epigenetic Defects in the B cell lineage of Systemic Lupus Erythematosus Patients Display Population-Specific Patterns.

Breitbach M, Ramaker RC, Roberts K, Kimberly RP, Absher D.

Arthritis Rheumatol. 2019 Aug 20. doi: 10.1002/art.41083. [Epub ahead of print]

PMID:
31430064
2.

CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries.

Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM.

Nucleic Acids Res. 2019 Aug 22;47(14):e84. doi: 10.1093/nar/gkz425.

3.

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.

4.

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.

5.

Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD.

Prokop JW, Yeo NC, Ottmann C, Chhetri SB, Florus KL, Ross EJ, Sosonkina N, Link BA, Freedman BI, Coppola CJ, McDermott-Roe C, Leysen S, Milroy LG, Meijer FA, Geurts AM, Rauscher FJ 3rd, Ramaker R, Flister MJ, Jacob HJ, Mendenhall EM, Lazar J.

J Am Soc Nephrol. 2018 May;29(5):1525-1535. doi: 10.1681/ASN.2017080856. Epub 2018 Feb 23.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

Pharmacometabolomics reveals that serotonin is implicated in aspirin response variability.

Ellero-Simatos S, Lewis JP, Georgiades A, Yerges-Armstrong LM, Beitelshees AL, Horenstein RB, Dane A, Harms AC, Ramaker R, Vreeken RJ, Perry CG, Zhu H, Sànchez CL, Kuhn C, Ortel TL, Shuldiner AR, Hankemeier T, Kaddurah-Daouk R.

CPT Pharmacometrics Syst Pharmacol. 2014 Jul 16;3:e125. doi: 10.1038/psp.2014.22.

18.

Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling.

Ellero-Simatos S, Szymańska E, Rullmann T, Dokter WH, Ramaker R, Berger R, van Iersel TM, Smilde AK, Hankemeier T, Alkema W.

Genome Med. 2012 Nov 30;4(11):94. doi: 10.1186/gm395. eCollection 2012.

19.

Lipidomics reveals multiple pathway effects of a multi-components preparation on lipid biochemistry in ApoE*3Leiden.CETP mice.

Wei H, Hu C, Wang M, van den Hoek AM, Reijmers TH, Wopereis S, Bouwman J, Ramaker R, Korthout HA, Vennik M, Hankemeier T, Havekes LM, Witkamp RF, Verheij ER, Xu G, van der Greef J.

PLoS One. 2012;7(1):e30332. doi: 10.1371/journal.pone.0030332. Epub 2012 Jan 23.

20.

Cancer cell proliferation is inhibited by specific modulation frequencies.

Zimmerman JW, Pennison MJ, Brezovich I, Yi N, Yang CT, Ramaker R, Absher D, Myers RM, Kuster N, Costa FP, Barbault A, Pasche B.

Br J Cancer. 2012 Jan 17;106(2):307-13. doi: 10.1038/bjc.2011.523. Epub 2011 Dec 1.

21.

Lipidomic approach to evaluate rosuvastatin and atorvastatin at various dosages: investigating differential effects among statins.

Bergheanu SC, Reijmers T, Zwinderman AH, Bobeldijk I, Ramaker R, Liem AH, van der Greef J, Hankemeier T, Jukema JW.

Curr Med Res Opin. 2008 Sep;24(9):2477-87. doi: 10.1185/03007990802321709 . Epub 2008 Jul 24.

PMID:
18655752
22.

Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: compound class targeting in a metabolomics workflow.

Bobeldijk I, Hekman M, de Vries-van der Weij J, Coulier L, Ramaker R, Kleemann R, Kooistra T, Rubingh C, Freidig A, Verheij E.

J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):306-13. doi: 10.1016/j.jchromb.2008.05.008. Epub 2008 May 15.

PMID:
18511357
23.

Similarities and differences in lipidomics profiles among healthy monozygotic twin pairs.

Draisma HH, Reijmers TH, Bobeldijk-Pastorova I, Meulman JJ, Estourgie-Van Burk GF, Bartels M, Ramaker R, van der Greef J, Boomsma DI, Hankemeier T.

OMICS. 2008 Mar;12(1):17-31. doi: 10.1089/omi.2007.0048.

PMID:
18266560
24.
25.

Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation.

Bijlsma S, Bobeldijk I, Verheij ER, Ramaker R, Kochhar S, Macdonald IA, van Ommen B, Smilde AK.

Anal Chem. 2006 Jan 15;78(2):567-74.

PMID:
16408941
26.

Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis.

Verhoeckx KC, Bijlsma S, Jespersen S, Ramaker R, Verheij ER, Witkamp RF, van der Greef J, Rodenburg RJ.

Int Immunopharmacol. 2004 Nov;4(12):1499-514.

PMID:
15351319
27.

Determination of the 2H/1H, 17O/16O, and 18O/16O isotope ratios in water by means of tunable diode laser spectroscopy at 1.39 microm.

Kerstel ER, Gagliardi G, Gianfrani L, Meijer HA, van Trigt R, Ramaker R.

Spectrochim Acta A Mol Biomol Spectrosc. 2002 Sep;58(11):2389-96.

PMID:
12353687
28.

The psychological and social functioning of 14 children and 12 adolescents after Ilizarov leg lengthening.

Ramaker RR, Lagro SW, van Roermund PM, Sinnema G.

Acta Orthop Scand. 2000 Feb;71(1):55-9.

PMID:
10743994
29.

Breakup of the projectile at 35 MeV/nucleon.

Gonthier PL, Harper P, Bouma B, Ramaker R, Cebra DA, Koenig ZM, Fox D, Westfall GD.

Phys Rev C Nucl Phys. 1990 Jun;41(6):2635-2643. No abstract available.

PMID:
9966644
30.

Alpha emission at the Fermi energy.

Gonthier PL, Bouma B, Harper P, Ramaker R, Cebra DA, Koenig ZM, Fox D, Westfall GD.

Phys Rev C Nucl Phys. 1987 May;35(5):1946-1949. No abstract available.

PMID:
9953983

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