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Items: 49

1.

Author Correction: L1 drives IFN in senescent cells and promotes age-associated inflammation.

De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD, Le O, Beauséjour C, Ambati J, Ambati K, Simon M, Seluanov A, Gorbunova V, Slagboom PE, Helfand SL, Neretti N, Sedivy JM.

Nature. 2019 Aug;572(7767):E5. doi: 10.1038/s41586-019-1350-9.

PMID:
31296937
2.

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.

J Comput Biol. 2019 Jun 18. doi: 10.1089/cmb.2019.0100. [Epub ahead of print]

PMID:
31211598
3.

Single cell RNA-seq in the sea urchin embryo show marked cell-type specificity in the Delta/Notch pathway.

Foster S, Teo YV, Neretti N, Oulhen N, Wessel GM.

Mol Reprod Dev. 2019 Aug;86(8):931-934. doi: 10.1002/mrd.23181. Epub 2019 Jun 14.

PMID:
31199038
4.

Notch Signaling Mediates Secondary Senescence.

Teo YV, Rattanavirotkul N, Olova N, Salzano A, Quintanilla A, Tarrats N, Kiourtis C, Müller M, Green AR, Adams PD, Acosta JC, Bird TG, Kirschner K, Neretti N, Chandra T.

Cell Rep. 2019 Apr 23;27(4):997-1007.e5. doi: 10.1016/j.celrep.2019.03.104.

5.

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.

Cell Metab. 2019 Apr 2;29(4):871-885.e5. doi: 10.1016/j.cmet.2019.02.014. Epub 2019 Mar 7.

PMID:
30853213
6.

L1 drives IFN in senescent cells and promotes age-associated inflammation.

De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD, Le O, Beauséjour C, Ambati J, Ambati K, Simon M, Seluanov A, Gorbunova V, Slagboom PE, Helfand SL, Neretti N, Sedivy JM.

Nature. 2019 Feb;566(7742):73-78. doi: 10.1038/s41586-018-0784-9. Epub 2019 Feb 6. Erratum in: Nature. 2019 Aug;572(7767):E5.

7.

Cell-free DNA as a biomarker of aging.

Teo YV, Capri M, Morsiani C, Pizza G, Faria AMC, Franceschi C, Neretti N.

Aging Cell. 2019 Feb;18(1):e12890. doi: 10.1111/acel.12890. Epub 2018 Dec 20.

8.

Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells.

Gruppuso PA, Boylan JM, Zabala V, Neretti N, Abshiru NA, Sikora JW, Doud EH, Camarillo JM, Thomas PM, Kelleher NL, Sanders JA.

PLoS One. 2018 Sep 7;13(9):e0203351. doi: 10.1371/journal.pone.0203351. eCollection 2018.

9.

The three-dimensional organization of the genome in cellular senescence and age-associated diseases.

Evans SA, Horrell J, Neretti N.

Semin Cell Dev Biol. 2019 Jun;90:154-160. doi: 10.1016/j.semcdb.2018.07.022. Epub 2018 Jul 27. Review.

10.

Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage- and Histone Methylation-Dependent Pathways.

Ito T, Teo YV, Evans SA, Neretti N, Sedivy JM.

Cell Rep. 2018 Mar 27;22(13):3480-3492. doi: 10.1016/j.celrep.2018.03.002.

11.

GINOM: A statistical framework for assessing interval overlap of multiple genomic features.

Bryner D, Criscione S, Leith A, Huynh Q, Huffer F, Neretti N.

PLoS Comput Biol. 2017 Jun 15;13(6):e1005586. doi: 10.1371/journal.pcbi.1005586. eCollection 2017 Jun.

12.

The Chromatin Landscape of Cellular Senescence.

Criscione SW, Teo YV, Neretti N.

Trends Genet. 2016 Nov;32(11):751-761. doi: 10.1016/j.tig.2016.09.005. Epub 2016 Sep 28. Review.

13.

Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span in Drosophila.

Wood JG, Jones BC, Jiang N, Chang C, Hosier S, Wickremesinghe P, Garcia M, Hartnett DA, Burhenn L, Neretti N, Helfand SL.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11277-11282. Epub 2016 Sep 12.

14.

Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability.

Nelson DM, Jaber-Hijazi F, Cole JJ, Robertson NA, Pawlikowski JS, Norris KT, Criscione SW, Pchelintsev NA, Piscitello D, Stong N, Rai TS, McBryan T, Otte GL, Nixon C, Clark W, Riethman H, Wu H, Schotta G, Garcia BA, Neretti N, Baird DM, Berger SL, Adams PD.

Genome Biol. 2016 Jul 25;17(1):158. doi: 10.1186/s13059-016-1017-x.

15.

Genome-wide characterization of human L1 antisense promoter-driven transcripts.

Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N.

BMC Genomics. 2016 Jun 14;17:463. doi: 10.1186/s12864-016-2800-5.

16.

Reorganization of chromosome architecture in replicative cellular senescence.

Criscione SW, De Cecco M, Siranosian B, Zhang Y, Kreiling JA, Sedivy JM, Neretti N.

Sci Adv. 2016 Feb 5;2(2):e1500882. doi: 10.1126/sciadv.1500882. eCollection 2016 Feb.

17.

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.

Am J Physiol Regul Integr Comp Physiol. 2015 Jul 1;309(1):R22-35. doi: 10.1152/ajpregu.00114.2015. Epub 2015 Apr 29.

18.

Enhancement of radiation effect on cancer cells by gold-pHLIP.

Antosh MP, Wijesinghe DD, Shrestha S, Lanou R, Huang YH, Hasselbacher T, Fox D, Neretti N, Sun S, Katenka N, Cooper LN, Andreev OA, Reshetnyak YK.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5372-6. doi: 10.1073/pnas.1501628112. Epub 2015 Apr 13.

19.

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.

Cell. 2015 Jan 29;160(3):477-88. doi: 10.1016/j.cell.2014.12.016. Epub 2015 Jan 22.

20.

Drosophila melanogaster show a threshold effect in response to radiation.

Antosh M, Fox D, Hasselbacher T, Lanou R, Neretti N, Cooper LN.

Dose Response. 2014 May 5;12(4):551-81. doi: 10.2203/dose-response.13-047.Antosh. eCollection 2014 Dec.

21.

Transcriptional landscape of repetitive elements in normal and cancer human cells.

Criscione SW, Zhang Y, Thompson W, Sedivy JM, Neretti N.

BMC Genomics. 2014 Jul 11;15:583. doi: 10.1186/1471-2164-15-583.

22.

Dietary switch reveals fast coordinated gene expression changes in Drosophila melanogaster.

Whitaker R, Gil MP, Ding F, Tatar M, Helfand SL, Neretti N.

Aging (Albany NY). 2014 May;6(5):355-68.

23.

Transcriptional response to dietary restriction in Drosophila melanogaster.

Ding F, Gil MP, Franklin M, Ferreira J, Tatar M, Helfand SL, Neretti N.

J Insect Physiol. 2014 Oct;69:101-6. doi: 10.1016/j.jinsphys.2014.05.002. Epub 2014 May 10.

24.

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.

Aging (Albany NY). 2013 Dec;5(12):867-83.

25.

Dietary and genetic effects on age-related loss of gene silencing reveal epigenetic plasticity of chromatin repression during aging.

Jiang N, Du G, Tobias E, Wood JG, Whitaker R, Neretti N, Helfand SL.

Aging (Albany NY). 2013 Nov;5(11):813-24.

26.

Death by transposition - the enemy within?

Sedivy JM, Kreiling JA, Neretti N, De Cecco M, Criscione SW, Hofmann JW, Zhao X, Ito T, Peterson AL.

Bioessays. 2013 Dec;35(12):1035-43. doi: 10.1002/bies.201300097. Epub 2013 Oct 15.

27.

Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2).

Lamming DW, Demirkan G, Boylan JM, Mihaylova MM, Peng T, Ferreira J, Neretti N, Salomon A, Sabatini DM, Gruppuso PA.

FASEB J. 2014 Jan;28(1):300-15. doi: 10.1096/fj.13-237743. Epub 2013 Sep 26.

28.

CORaL: comparison of ranked lists for analysis of gene expression data.

Antosh M, Fox D, Cooper LN, Neretti N.

J Comput Biol. 2013 Jun;20(6):433-43. doi: 10.1089/cmb.2013.0017. Epub 2013 May 15.

29.

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements.

De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM.

Aging Cell. 2013 Apr;12(2):247-56. doi: 10.1111/acel.12047. Epub 2013 Jan 30.

30.

takeout-dependent longevity is associated with altered Juvenile Hormone signaling.

Chamseddin KH, Khan SQ, Nguyen ML, Antosh M, Morris SN, Kolli S, Neretti N, Helfand SL, Bauer JH.

Mech Ageing Dev. 2012 Nov-Dec;133(11-12):637-46. doi: 10.1016/j.mad.2012.08.004. Epub 2012 Aug 30.

31.

Transcriptome variance in single oocytes within, and between, genotypes.

Reich A, Neretti N, Freiman RN, Wessel GM.

Mol Reprod Dev. 2012 Aug;79(8):502-3. doi: 10.1002/mrd.22061. Epub 2012 Jul 9. No abstract available.

32.

New comparative genomics approach reveals a conserved health span signature across species.

Antosh M, Fox D, Helfand SL, Cooper LN, Neretti N.

Aging (Albany NY). 2011 Jun;3(6):576-83.

33.

Kinetic profiling of the c-Myc transcriptome and bioinformatic analysis of repressed gene promoters.

Yap CS, Peterson AL, Castellani G, Sedivy JM, Neretti N.

Cell Cycle. 2011 Jul 1;10(13):2184-96. Epub 2011 Jul 1.

34.

Comparative transcriptional pathway bioinformatic analysis of dietary restriction, Sir2, p53 and resveratrol life span extension in Drosophila.

Antosh M, Whitaker R, Kroll A, Hosier S, Chang C, Bauer J, Cooper L, Neretti N, Helfand SL.

Cell Cycle. 2011 Mar 15;10(6):904-11. Epub 2011 Mar 15.

35.

Chromatin remodeling in the aging genome of Drosophila.

Wood JG, Hillenmeyer S, Lawrence C, Chang C, Hosier S, Lightfoot W, Mukherjee E, Jiang N, Schorl C, Brodsky AS, Neretti N, Helfand SL.

Aging Cell. 2010 Dec;9(6):971-8. doi: 10.1111/j.1474-9726.2010.00624.x. Epub 2010 Oct 21.

36.

Comparative transcriptional profiling identifies takeout as a gene that regulates life span.

Bauer J, Antosh M, Chang C, Schorl C, Kolli S, Neretti N, Helfand SL.

Aging (Albany NY). 2010 May;2(5):298-310.

37.

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.

PLoS One. 2010 Feb 5;5(2):e9084. doi: 10.1371/journal.pone.0009084.

38.

Long-lived Indy and calorie restriction interact to extend life span.

Wang PY, Neretti N, Whitaker R, Hosier S, Chang C, Lu D, Rogina B, Helfand SL.

Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9262-7. doi: 10.1073/pnas.0904115106. Epub 2009 May 22.

39.

Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage.

Neretti N, Wang PY, Brodsky AS, Nyguyen HH, White KP, Rogina B, Helfand SL.

Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2277-82. doi: 10.1073/pnas.0812484106. Epub 2009 Jan 21.

40.

Global regulation of nucleotide biosynthetic genes by c-Myc.

Liu YC, Li F, Handler J, Huang CR, Xiang Y, Neretti N, Sedivy JM, Zeller KI, Dang CV.

PLoS One. 2008 Jul 16;3(7):e2722. doi: 10.1371/journal.pone.0002722.

41.

Reconstructing networks of pathways via significance analysis of their intersections.

Francesconi M, Remondini D, Neretti N, Sedivy JM, Cooper LN, Verondini E, Milanesi L, Castellani G.

BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S9. doi: 10.1186/1471-2105-9-S4-S9.

42.

The oncogene c-Myc coordinates regulation of metabolic networks to enable rapid cell cycle entry.

Morrish F, Neretti N, Sedivy JM, Hockenbery DM.

Cell Cycle. 2008 Apr 15;7(8):1054-66. Epub 2008 Feb 8.

43.

Exon expression profiling reveals stimulus-mediated exon use in neural cells.

McKee AE, Neretti N, Carvalho LE, Meyer CA, Fox EA, Brodsky AS, Silver PA.

Genome Biol. 2007;8(8):R159.

44.

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.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S16.

45.

Multiple ping sonar accuracy improvement using robust motion estimation and ping fusion.

Yu L, Neretti N, Intrator N.

J Acoust Soc Am. 2006 Apr;119(4):2106-13.

PMID:
16642825
46.

Targeting c-Myc-activated genes with a correlation method: detection of global changes in large gene expression network dynamics.

Remondini D, O'Connell B, Intrator N, Sedivy JM, Neretti N, Castellani GC, Cooper LN.

Proc Natl Acad Sci U S A. 2005 May 10;102(19):6902-6. Epub 2005 May 2.

47.

Delay accuracy in bat sonar is related to the reciprocal of normalized echo bandwidth, or Q.

Simmons JA, Neretti N, Intrator N, Altes RA, Ferragamo MJ, Sanderson MI.

Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3638-43. Epub 2004 Feb 27.

48.

Evaluation of an auditory model for echo delay accuracy in wideband biosonar.

Sanderson MI, Neretti N, Intrator N, Simmons JA.

J Acoust Soc Am. 2003 Sep;114(3):1648-59.

PMID:
14514218
49.

Time-frequency model for echo-delay resolution in wideband biosonar.

Neretti N, Sanderson MI, Intrator N, Simmons JA.

J Acoust Soc Am. 2003 Apr;113(4 Pt 1):2137-45.

PMID:
12703724

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