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CORaL: comparison of ranked lists for analysis of gene expression data.
Antosh M, Fox D, Cooper LN, Neretti N. Antosh M, et al. Among authors: neretti n. J Comput Biol. 2013 Jun;20(6):433-43. doi: 10.1089/cmb.2013.0017. Epub 2013 May 15. J Comput Biol. 2013. PMID: 23675929 Free PMC article.
Reduced expression of MYC increases longevity and enhances healthspan.
Hofmann JW, Zhao X, De Cecco M, Peterson AL, Pagliaroli L, Manivannan J, Hubbard GB, Ikeno Y, Zhang Y, Feng B, Li X, Serre T, Qi W, Van Remmen H, Miller RA, Bath KG, de Cabo R, Xu H, Neretti N, Sedivy JM. Hofmann JW, et al. Among authors: neretti n. Cell. 2015 Jan 29;160(3):477-88. doi: 10.1016/j.cell.2014.12.016. Epub 2015 Jan 22. Cell. 2015. PMID: 25619689 Free PMC article.
Regulation of gene expression in hepatic cells by the mammalian Target of Rapamycin (mTOR).
Jimenez RH, Lee JS, Francesconi M, Castellani G, Neretti N, Sanders JA, Sedivy J, Gruppuso PA. Jimenez RH, et al. Among authors: neretti n. PLoS One. 2010 Feb 5;5(2):e9084. doi: 10.1371/journal.pone.0009084. PLoS One. 2010. PMID: 20140209 Free PMC article.
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation.
Neretti N, Remondini D, Tatar M, Sedivy JM, Pierini M, Mazzatti D, Powell J, Franceschi C, Castellani GC. Neretti N, et al. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1(Suppl 1):S16. doi: 10.1186/1471-2105-8-S1-S16. BMC Bioinformatics. 2007. PMID: 17430560 Free PMC article.
LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation.
Simon M, Van Meter M, Ablaeva J, Ke Z, Gonzalez RS, Taguchi T, De Cecco M, Leonova KI, Kogan V, Helfand SL, Neretti N, Roichman A, Cohen HY, Meer MV, Gladyshev VN, Antoch MP, Gudkov AV, Sedivy JM, Seluanov A, Gorbunova V. Simon M, et al. Among authors: neretti n. Cell Metab. 2019 Apr 2;29(4):871-885.e5. doi: 10.1016/j.cmet.2019.02.014. Epub 2019 Mar 7. Cell Metab. 2019. PMID: 30853213 Free PMC article.
Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues.
De Cecco M, Criscione SW, Peterson AL, Neretti N, Sedivy JM, Kreiling JA. De Cecco M, et al. Among authors: neretti n. Aging (Albany NY). 2013 Dec;5(12):867-83. doi: 10.18632/aging.100621. Aging (Albany NY). 2013. PMID: 24323947 Free PMC article.
Transcriptional response to dietary restriction in Drosophila melanogaster.
Ding F, Gil MP, Franklin M, Ferreira J, Tatar M, Helfand SL, Neretti N. Ding F, et al. Among authors: neretti n. J Insect Physiol. 2014 Oct;69:101-6. doi: 10.1016/j.jinsphys.2014.05.002. Epub 2014 May 10. J Insect Physiol. 2014. PMID: 24819200 Free PMC article.
Profiling of the fetal and adult rat liver transcriptome and translatome reveals discordant regulation by the mechanistic target of rapamycin (mTOR).
Boylan JM, Sanders JA, Neretti N, Gruppuso PA. Boylan JM, et al. Among authors: neretti n. Am J Physiol Regul Integr Comp Physiol. 2015 Jul 1;309(1):R22-35. doi: 10.1152/ajpregu.00114.2015. Epub 2015 Apr 29. Am J Physiol Regul Integr Comp Physiol. 2015. PMID: 25924882 Free PMC article.
Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data.
Rosenthal M, Bryner D, Huffer F, Evans S, Srivastava A, Neretti N. Rosenthal M, et al. Among authors: neretti n. J Comput Biol. 2019 Nov;26(11):1191-1202. doi: 10.1089/cmb.2019.0100. Epub 2019 Jun 18. J Comput Biol. 2019. PMID: 31211598 Free PMC article.
GINOM: A statistical framework for assessing interval overlap of multiple genomic features.
Bryner D, Criscione S, Leith A, Huynh Q, Huffer F, Neretti N. Bryner D, et al. Among authors: neretti n. PLoS Comput Biol. 2017 Jun 15;13(6):e1005586. doi: 10.1371/journal.pcbi.1005586. eCollection 2017 Jun. PLoS Comput Biol. 2017. PMID: 28617797 Free PMC article.
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