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Items: 1 to 50 of 86

1.

CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.

Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y.

iScience. 2018 Dec 21;10:247-264. doi: 10.1016/j.isci.2018.11.029. Epub 2018 Dec 12.

2.

BRCA1 represses DNA replication initiation through antagonizing estrogen signaling and maintains genome stability in parallel with WEE1-MCM2 signaling during pregnancy.

Xu X, Chen E, Mo L, Zhang L, Shao F, Miao K, Liu J, Su SM, Valecha M, Chan UI, Zheng H, Chen M, Chen W, Chen Q, Fu H, Aladjem MI, He Y, Deng CX.

Hum Mol Genet. 2019 Mar 1;28(5):842-857. doi: 10.1093/hmg/ddy398.

PMID:
30445628
3.

Human Papillomavirus Integration: Analysis by Molecular Combing and Fiber-FISH.

Redmond CJ, Fu H, Aladjem MI, McBride AA.

Curr Protoc Microbiol. 2018 Nov;51(1):e61. doi: 10.1002/cpmc.61. Epub 2018 Aug 20.

PMID:
30129235
4.

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse.

Tubbs A, Sridharan S, van Wietmarschen N, Maman Y, Callen E, Stanlie A, Wu W, Wu X, Day A, Wong N, Yin M, Canela A, Fu H, Redon C, Pruitt SC, Jaszczyszyn Y, Aladjem MI, Aplan PD, Hyrien O, Nussenzweig A.

Cell. 2018 Aug 23;174(5):1127-1142.e19. doi: 10.1016/j.cell.2018.07.011. Epub 2018 Aug 2.

5.

The replication initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin.

Jang SM, Zhang Y, Utani K, Fu H, Redon CE, Marks AB, Smith OK, Redmond CJ, Baris AM, Tulchinsky DA, Aladjem MI.

Nat Commun. 2018 Jul 17;9(1):2782. doi: 10.1038/s41467-018-05177-6.

6.

Chromatin-Bound Cullin-Ring Ligases: Regulatory Roles in DNA Replication and Potential Targeting for Cancer Therapy.

Jang SM, Redon CE, Aladjem MI.

Front Mol Biosci. 2018 Mar 13;5:19. doi: 10.3389/fmolb.2018.00019. eCollection 2018. Review.

7.

Extra View: Sirt1 Acts As A Gatekeeper Of Replication Initiation To Preserve Genomic Stability.

Utani K, Aladjem MI.

Nucleus. 2018 Jan 1;9(1):261-267. doi: 10.1080/19491034.2018.1456218. Review.

8.

Replication timing and nuclear structure.

Fu H, Baris A, Aladjem MI.

Curr Opin Cell Biol. 2018 Jun;52:43-50. doi: 10.1016/j.ceb.2018.01.004. Epub 2018 Feb 4. Review.

9.

SLFN11 Blocks Stressed Replication Forks Independently of ATR.

Murai J, Tang SW, Leo E, Baechler SA, Redon CE, Zhang H, Al Abo M, Rajapakse VN, Nakamura E, Jenkins LMM, Aladjem MI, Pommier Y.

Mol Cell. 2018 Feb 1;69(3):371-384.e6. doi: 10.1016/j.molcel.2018.01.012.

10.

HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression.

Warburton A, Redmond CJ, Dooley KE, Fu H, Gillison ML, Akagi K, Symer DE, Aladjem MI, McBride AA.

PLoS Genet. 2018 Jan 24;14(1):e1007179. doi: 10.1371/journal.pgen.1007179. eCollection 2018 Jan.

11.

Regulation of Replication Origins.

Marks AB, Fu H, Aladjem MI.

Adv Exp Med Biol. 2017;1042:43-59. doi: 10.1007/978-981-10-6955-0_2. Review.

12.

Phase I Study of ATR Inhibitor M6620 in Combination With Topotecan in Patients With Advanced Solid Tumors.

Thomas A, Redon CE, Sciuto L, Padiernos E, Ji J, Lee MJ, Yuno A, Lee S, Zhang Y, Tran L, Yutzy W, Rajan A, Guha U, Chen H, Hassan R, Alewine CC, Szabo E, Bates SE, Kinders RJ, Steinberg SM, Doroshow JH, Aladjem MI, Trepel JB, Pommier Y.

J Clin Oncol. 2018 Jun 1;36(16):1594-1602. doi: 10.1200/JCO.2017.76.6915. Epub 2017 Dec 18.

13.

Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability.

Utani K, Fu H, Jang SM, Marks AB, Smith OK, Zhang Y, Redon CE, Shimizu N, Aladjem MI.

Nucleic Acids Res. 2017 Jul 27;45(13):7807-7824. doi: 10.1093/nar/gkx468.

14.

Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization.

Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG.

Nucleic Acids Res. 2017 Mar 17;45(5):2490-2502. doi: 10.1093/nar/gkw1211.

15.

Order from clutter: selective interactions at mammalian replication origins.

Aladjem MI, Redon CE.

Nat Rev Genet. 2017 Feb;18(2):101-116. doi: 10.1038/nrg.2016.141. Epub 2016 Nov 21. Review.

16.

A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells.

Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan M, Kim R, You Y, Hanna H, Boisclair Y, Long Q, Aladjem MI.

Nat Commun. 2016 Jun 8;7:11748. doi: 10.1038/ncomms11748.

17.

Distinct epigenetic features of differentiation-regulated replication origins.

Smith OK, Kim R, Fu H, Martin MM, Lin CM, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlain S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WS, Aladjem MI.

Epigenetics Chromatin. 2016 May 10;9:18. doi: 10.1186/s13072-016-0067-3. eCollection 2016.

18.

Replication origins: determinants or consequences of nuclear organization?

Marks AB, Smith OK, Aladjem MI.

Curr Opin Genet Dev. 2016 Apr;37:67-75. doi: 10.1016/j.gde.2015.11.008. Epub 2016 Feb 2. Review.

19.

Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response.

Luna A, McFadden GB, Aladjem MI, Kohn KW.

PLoS Comput Biol. 2015 May 28;11(5):e1004144. doi: 10.1371/journal.pcbi.1004144. eCollection 2015 May.

20.

Allele-specific analysis of DNA replication origins in mammalian cells.

Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE.

Nat Commun. 2015 May 19;6:7051. doi: 10.1038/ncomms8051.

21.

ColoWeb: a resource for analysis of colocalization of genomic features.

Kim R, Smith OK, Wong WC, Ryan AM, Ryan MC, Aladjem MI.

BMC Genomics. 2015 Feb 28;16:142. doi: 10.1186/s12864-015-1345-3.

22.

The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage.

Fu H, Martin MM, Regairaz M, Huang L, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, Aladjem MI.

Nat Commun. 2015 Apr 16;6:6746. doi: 10.1038/ncomms7746.

23.

Mapping replication origin sequences in eukaryotic chromosomes.

Fu H, Besnard E, Desprat R, Ryan M, Kahli M, Lemaitre JM, Aladjem MI.

Curr Protoc Cell Biol. 2014 Dec 1;65:22.20.1-17. doi: 10.1002/0471143030.cb2220s65. Review.

24.

Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome.

Erliandri I, Fu H, Nakano M, Kim JH, Miga KH, Liskovykh M, Earnshaw WC, Masumoto H, Kouprina N, Aladjem MI, Larionov V.

Nucleic Acids Res. 2014 Oct;42(18):11502-16. doi: 10.1093/nar/gku835. Epub 2014 Sep 16.

25.

Best practices for mapping replication origins in eukaryotic chromosomes.

Besnard E, Desprat R, Ryan M, Kahli M, Aladjem MI, Lemaitre JM.

Curr Protoc Cell Biol. 2014 Sep 2;64:22.18.1-13. doi: 10.1002/0471143030.cb2218s64. Review.

26.

DNA double-strand break repair genes and oxidative damage in brain metastasis of breast cancer.

Woditschka S, Evans L, Duchnowska R, Reed LT, Palmieri D, Qian Y, Badve S, Sledge G Jr, Gril B, Aladjem MI, Fu H, Flores NM, Gökmen-Polar Y, Biernat W, Szutowicz-Zielińska E, Mandat T, Trojanowski T, Och W, Czartoryska-Arlukowicz B, Jassem J, Mitchell JB, Steeg PS.

J Natl Cancer Inst. 2014 Jun 19;106(7). pii: dju145. doi: 10.1093/jnci/dju145. Print 2014 Jul.

27.

Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization.

Smith OK, Aladjem MI.

J Mol Biol. 2014 Oct 9;426(20):3330-41. doi: 10.1016/j.jmb.2014.05.027. Epub 2014 Jun 4. Review.

28.

Inactivation of Rb and E2f8 synergizes to trigger stressed DNA replication during erythroid terminal differentiation.

Ghazaryan S, Sy C, Hu T, An X, Mohandas N, Fu H, Aladjem MI, Chang VT, Opavsky R, Wu L.

Mol Cell Biol. 2014 Aug;34(15):2833-47. doi: 10.1128/MCB.01651-13. Epub 2014 May 27.

29.

Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization.

Mukhopadhyay R, Lajugie J, Fourel N, Selzer A, Schizas M, Bartholdy B, Mar J, Lin CM, Martin MM, Ryan M, Aladjem MI, Bouhassira EE.

PLoS Genet. 2014 May 1;10(5):e1004319. doi: 10.1371/journal.pgen.1004319. eCollection 2014 May.

30.

A new light on DNA replication from the inactive X chromosome.

Aladjem MI, Fu H.

Bioessays. 2014 Jun;36(6):591-7. doi: 10.1002/bies.201400021. Epub 2014 Apr 6. Review.

31.

A chromatin structure-based model accurately predicts DNA replication timing in human cells.

Gindin Y, Valenzuela MS, Aladjem MI, Meltzer PS, Bilke S.

Mol Syst Biol. 2014 Mar 28;10:722. doi: 10.1002/msb.134859.

32.

Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome.

Yudkin D, Hayward BE, Aladjem MI, Kumari D, Usdin K.

Hum Mol Genet. 2014 Jun 1;23(11):2940-52. doi: 10.1093/hmg/ddu006. Epub 2014 Jan 12.

PMID:
24419320
33.

SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism.

Luna A, Aladjem MI, Kohn KW.

Genome Integr. 2013 Dec 20;4(1):6. doi: 10.1186/2041-9414-4-6.

34.

Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle.

Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI.

PLoS Genet. 2013 Jun;9(6):e1003542. doi: 10.1371/journal.pgen.1003542. Epub 2013 Jun 6. Erratum in: PLoS Genet. 2013 Jul;;9(7). doi:10.1371/annotation/2b2d77ee-6d39-4685-b2e5-ebba0b793902.

35.

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.

Fried JY, van Iersel MP, Aladjem MI, Kohn KW, Luna A.

Bioinformatics. 2013 Jun 1;29(11):1465-6. doi: 10.1093/bioinformatics/btt146. Epub 2013 Apr 1.

36.

ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin.

Lee KY, Fu H, Aladjem MI, Myung K.

J Cell Biol. 2013 Jan 7;200(1):31-44. doi: 10.1083/jcb.201206084. Epub 2012 Dec 31.

37.

Rif1 choreographs DNA replication timing.

Aladjem MI.

EMBO J. 2012 Sep 12;31(18):3650-2. doi: 10.1038/emboj.2012.238. Epub 2012 Aug 14. No abstract available.

38.

Software support for SBGN maps: SBGN-ML and LibSBGN.

van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.

Bioinformatics. 2012 Aug 1;28(15):2016-21. Epub 2012 May 10.

39.

The chromatin backdrop of DNA replication: lessons from genetics and genome-scale analyses.

Conner AL, Aladjem MI.

Biochim Biophys Acta. 2012 Jul;1819(7):794-801. doi: 10.1016/j.bbagrm.2012.01.017. Epub 2012 Feb 8. Review.

40.

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.

Chandan K, van Iersel MP, Aladjem MI, Kohn KW, Luna A.

Bioinformatics. 2012 Mar 15;28(6):889-90. doi: 10.1093/bioinformatics/btr694. Epub 2011 Dec 22.

41.

Mus81-mediated DNA cleavage resolves replication forks stalled by topoisomerase I-DNA complexes.

Regairaz M, Zhang YW, Fu H, Agama KK, Tata N, Agrawal S, Aladjem MI, Pommier Y.

J Cell Biol. 2011 Nov 28;195(5):739-49. doi: 10.1083/jcb.201104003.

42.

Genome-wide depletion of replication initiation events in highly transcribed regions.

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI.

Genome Res. 2011 Nov;21(11):1822-32. doi: 10.1101/gr.124644.111. Epub 2011 Aug 3.

43.

Prevention of transcriptional silencing by a replicator-binding complex consisting of SWI/SNF, MeCP1, and hnRNP C1/C2.

Huang L, Fu H, Lin CM, Conner AL, Zhang Y, Aladjem MI.

Mol Cell Biol. 2011 Aug;31(16):3472-84. doi: 10.1128/MCB.05587-11. Epub 2011 Jun 20.

44.

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).

Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.

Bioinformatics. 2011 Aug 1;27(15):2165-6. doi: 10.1093/bioinformatics/btr336. Epub 2011 Jun 2.

45.

Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences.

Valenzuela MS, Chen Y, Davis S, Yang F, Walker RL, Bilke S, Lueders J, Martin MM, Aladjem MI, Massion PP, Meltzer PS.

PLoS One. 2011;6(5):e17308. doi: 10.1371/journal.pone.0017308. Epub 2011 May 13.

46.

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.

BMC Bioinformatics. 2011 May 17;12:167. doi: 10.1186/1471-2105-12-167.

47.

Interactions of MCP1 with components of the replication machinery in mammalian cells.

Bronze-da-Rocha E, Lin CM, Shimura T, Aladjem MI.

Int J Biol Sci. 2011 Feb 17;7(2):193-208.

48.

Inhibition of histone deacetylase in cancer cells slows down replication forks, activates dormant origins, and induces DNA damage.

Conti C, Leo E, Eichler GS, Sordet O, Martin MM, Fan A, Aladjem MI, Pommier Y.

Cancer Res. 2010 Jun 1;70(11):4470-80. doi: 10.1158/0008-5472.CAN-09-3028. Epub 2010 May 11.

49.

Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage.

Kim S, Aladjem MI, McFadden GB, Kohn KW.

PLoS Comput Biol. 2010 Feb 5;6(2):e1000665. doi: 10.1371/journal.pcbi.1000665.

50.

The Systems Biology Graphical Notation.

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.

Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.

PMID:
19668183

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