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Our Science – Aladjem Website

Mirit I. Aladjem, Ph.D.

Selected Publications

1)  Gindin Y, Valenzuela MS, Aladjem MI, Meltzer PS, Bilke S.
A chromatin structure-based model accurately predicts DNA replication timing in human cells.
Mol. Syst. Biol. 10: 722, 2014.
[Journal]
2)  Aladjem MI, Fu H.
A new light on DNA replication from the inactive X chromosome.
Bioessays. [Epub ahead of print], 2014.
[Journal]
3)  Yudkin D, Hayward BE, Aladjem MI, Kumari D, Usdin K.
Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome.
Hum. Mol. Genet. [Epub ahead of print], 2014.
[Journal]
4)  Lee KY, Fu H, Aladjem MI, Myung K.
ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin.
J. Cell Biol. 200: 31-44, 2013.
[Journal]
5)  Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI.
Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle.
PLoS Genet. 9: e1003542, 2013.
[Journal]
6)  Fried JY, van Iersel MP, Aladjem MI, Kohn KW, Luna A.
PathVisio-Faceted Search: An Exploration Tool for Multi-Dimensional Navigation of Large Pathways.
Bioinformatics. 29: 1465-6, 2013.
[Journal]
7)  Luna A, Aladjem MI, Kohn KW.
SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism.
Genome Integr. 4: 6, 2013.
[Journal]
8)  Kouprina N, Samoshkin A, Erliandri I, Nakano M, Lee HS, Fu H, Iida Y, Aladjem M, Oshimura M, Masumoto H, Earnshaw WC, Larionov V.
Organization of Synthetic Alphoid DNA Array in Human Artificial Chromosome (HAC) with a Conditional Centromere.
ACS Synth Biol. 1: 590-601, 2012.
[Journal]
9)  Chandan K, van Iersel MP, Aladjem MI, Kohn KW, Luna A.
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.
Bioinformatics. 28: 889-90, 2012.
[Journal]
10)  Aladjem MI.
Rif1 choreographs DNA replication timing.
EMBO J. 31: 3650-2, 2012.
[Journal]
11)  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.
Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinformatics. 28: 2016-21, 2012.
[Journal]
12)  Conner AL, Aladjem MI.
The chromatin backdrop of DNA replication: Lessons from genetics and genome-scale analyses.
Biochim. Biophys. Acta. 1819: 794-801, 2012.
[Journal]
13)  Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.
A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method.
BMC Bioinformatics. 12: 167, 2011.
[Journal]
14)  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-wide depletion of replication initiation events in highly transcribed regions.
Genome Res. 21: 1822-32, 2011.
[Journal]
15)  Bronze-da-Rocha E, Lin CM, Shimura T, Aladjem MI.
Interactions of MCP1 with components of the replication machinery in mammalian cells.
Int. J. Biol. Sci. 7: 193-208, 2011.
[Journal]
16)  Regairaz M, Zhang YW, Fu H, Agama KK, Tata N, Agrawal S, Aladjem MI, Pommier Y.
Mus81-mediated DNA cleavage resolves replication forks stalled by topoisomerase I-DNA complexes.
J. Cell Biol. 195: 739-49, 2011.
[Journal]
17)  Luna A, Sunshine M, van Iersel MP, Aladjem MI, Kohn KW.
PathVisio-MIM: PathVisio plugin for creating and editing Molecu-lar Interaction Maps (MIMs).
Bioinformatics. 27: 2165-6, 2011.
[Journal]
18)  Valenzuela MS, Chen Y, Davis S, Yang F, Walker RL, Bilke S, Lueders J, Martin MM, Aladjem MI, Massion PP, Meltzer PS.
Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences.
PLoS ONE. 6: e17308, 2011.
[Journal]
19)  Huang L, Fu H, Lin CM, Conner A, Zhang Y, Aladjem MI.
Prevention of transcriptional silencing by a replicator-binding complex consisting of SWI/SNF, MeCP1 and hnRNP C1/C2.
Mol Cell Biol. 31: 3472-84, 2011.
[Journal]
20)  Conti C, Leo E, Eichler GS, Sordet O, Martin MM, Fan A, Aladjem MI, Pommier Y.
Inhibition of histone deacetylase in cancer cells slows down replication forks, activates dormant origins, and induces DNA damage.
Cancer Res. 70: 4470-80, 2010.
[Journal]
21)  Kim S, Aladjem MI, McFadden GB, Kohn KW.
Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage.
PLoS Comput. Biol. 6: e1000665, 2010.
[Journal]
22)  Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.
The BioPAX community standard for pathway data sharing.
Nat. Biotechnol. 28: 935-42, 2010.
[Journal]
23)  Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.
Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis.
Cell Cycle. 8: 2281-99, 2009.
[Journal]
24)  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.
The Systems Biology Graphical Notation.
Nat. Biotechnol. 27: 735-41, 2009.
[Journal]
25)  Shimura T, Torres MJ, Martin MM, Rao VA, Pommier Y, Katsura M, Miyagawa K, Aladjem MI.
Bloom's syndrome helicase and Mus81 are required to induce transient double-strand DNA breaks in response to DNA replication stress.
J. Mol. Biol. 375: 1152-64, 2008.
[Journal]
26)  Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.
Chromatin Challenges during DNA Replication: A Systems Representation.
Mol. Biol. Cell. 19: 1-7, 2008.
[Journal]
27)  Aladjem M, Chattoraj DK.
EMBO Conference on Replication and Segregation of Chromosomes, Geilo, Norway, June 16-20 Replication and segregation of chromosomes in the three domains of life: EMBO conference reports common grounds Meeting Report.
Plasmid. 61: 89-93, 2008.
[Journal]
28)  Shimura T, Martin MM, Torres MJ, Gu C, Pluth JM, DiBernardi MA, McDonald JS, Aladjem MI.
DNA-PK is involved in repairing a transient surge of DNA breaks induced by deceleration of DNA replication.
J. Mol. Biol. 367: 665-80, 2007.
[Journal]
29)  Miao ZH, Player A, Shankavaram U, Wang YH, Zimonjic DB, Lorenzi PL, Liao ZY, Liu H, Shimura T, Zhang HL, Meng LH, Zhang YW, Kawasaki ES, Popescu NC, Aladjem MI, Goldstein DJ, Weinstein JN, Pommier Y.
Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses.
Cancer Res. 67: 8752-61, 2007.
[Journal]
30)  Aladjem MI.
Replication in Context: Dynamic Regulation of DNA Replication Patterns in Metazoans.
Nature Reviews Genetics. 8: 588-600, 2007.
Full Text Article. [Journal]
31)  Hong A, Narbonne-Reveau K, Riesgo-Escovar J, Fu H, Aladjem MI, Lilly MA.
The cyclin-dependent kinase inhibitor Dacapo promotes replication licensing during Drosophila endocycles.
EMBO J. 26: 2071-82, 2007.
[Journal]
32)  Seiler JA, Conti C, Syed A, Aladjem MI, Pommier Y.
The Intra-S-phase Checkpoint Affects Both DNA Replication Initiation and Elongation: Single-Cell and -DNA Fiber Analyses.
Mol Cell Biol. 27: 5806-18, 2007.
[Journal]
33)  Pommier Y, Weinstein JN, Aladjem MI, Kohn KW.
Chk2 molecular interaction map and rationale for Chk2 inhibitors.
Clin. Cancer Res. 12: 2657-61, 2006.
[Journal]
34)  Kohn KW, Aladjem MI.
Circuit diagrams for biological networks.
Mol. Syst. Biol. 2: 2006.0002, 2006.
[Journal]
35)  Wang L, Lin CM, Lopreiato JO, Aladjem MI.
Cooperative sequence modules determine replication initiation sites at the human {beta}-globin locus.
Hum. Mol. Genet. 15: 2613-22, 2006.
[Journal]
36)  Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y.
Depicting combinatorial complexity with the molecular interaction map notation.
Mol. Syst. Biol. 2: 51, 2006.
[Journal]
37)  Feng YQ, Desprat R, Fu H, Olivier E, Lin CM, Lobell A, Gowda SN, Aladjem MI, Bouhassira EE.
DNA methylation supports intrinsic epigenetic memory in mammalian cells.
PLoS Genet. 2: e65, 2006.
[Journal]
38)  Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.
Mol. Biol. Cell. 17: 1-13, 2006.
[Journal]
39)  Furuta T, Hayward RL, Meng LH, Takemura H, Aune GJ, Bonner WM, Aladjem MI, Kohn KW, Pommier Y.
p21CDKN1A allows the repair of replication-mediated DNA double-strand breaks induced by topoisomerase I and is inactivated by the checkpoint kinase inhibitor 7-hydroxystaurosporine.
Oncogene. 25: 2839-49, 2006.
[Journal]
40)  Fu H, Wang L, Lin CM, Singhania S, Bouhassira EE, Aladjem MI.
Preventing gene silencing with human replicators.
Nat. Biotechnol. 24: 572-6, 2006.
[Journal]
41)  Buzina A, Aladjem MI, Kolman JL, Wahl GM, Ellis J.
Initiation of DNA replication at the human beta-globin 3' enhancer.
Nucleic Acids Res. 33: 4412-24, 2005.
[Journal]
42)  Wang J, Liu H, Lin CM, Aladjem MI, Epner EM.
Targeted deletion of the chicken beta-globin regulatory elements reveals a cooperative gene silencing activity.
J Biol Chem. 280: 23340-8, 2005.
[Journal]
43)  Feng YQ, Warin R, Li T, Olivier E, Besse A, Lobell A, Fu H, Lin CM, Aladjem MI, Bouhassira EE.
The human beta-globin locus control region can silence as well as activate gene expression.
Mol Cell Biol. 25: 3864-74, 2005.
[Journal]
44)  Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW.
Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks.
Sci STKE. 2004: pe8, 2004.
[Journal]
45)  Wang L, Lin CM, Brooks S, Cimbora D, Groudine M, Aladjem MI.
The human beta-globin replication initiation region consists of two modular independent replicators.
Mol Cell Biol. 24: 3373-86, 2004.
[Journal]
46)  Aladjem MI.
The mammalian beta globin origin of DNA replication.
Front. Biosci. 9: 2540-7, 2004.
[Journal]
47)  Aladjem MI, Fanning E.
The replicon revisited: an old model learns new tricks in metazoan chromosomes.
EMBO Rep. 5: 686-91, 2004.
[Journal]
48)  Indig FE, Partridge JJ, von Kobbe C, Aladjem MI, Latterich M, Bohr VA.
Werner syndrome protein directly binds to the AAA ATPase p97/VCP in an ATP-dependent fashion.
J Struct Biol. 146: 251-9, 2004.
[Journal]
49)  Nenguke T, Aladjem MI, Gusella JF, Wexler NS, Arnheim N, Venezuela HD Project .
Candidate DNA replication initiation regions at human trinucleotide repeat disease loci.
Hum Mol Genet. 12: 1021-8, 2003.
[Journal]
50)  Lin CM, Fu H, Martinovsky M, Bouhassira E, Aladjem MI.
Dynamic Alterations of Replication Timing in Mammalian Cells.
Current Biology. 13: 1019-28, 2003.
[Journal]
51)  Furuta T, Takemura H, Liao ZY, Aune GJ, Redon C, Sedelnikova OA, Pilch DR, Rogakou EP, Celeste A, Chen HT, Nussenzweig A, Aladjem MI, Bonner WM, Pommier Y.
Phosphorylation of histone H2AX and activation of Mre11, Rad50, and Nbs1 in response to replication-dependent DNA double-strand breaks induced by mammalian DNA topoisomerase I cleavage complexes.
J Biol Chem. 278: 20303-12, 2003.
[Journal]
52)  Aladjem MI, Rodewald LW, Lin CM, Bowman S, Cimbora DM, Brody LL, Epner EM, Groudine M, Wahl GM.
Replication initiation patterns in the beta-globin loci of totipotent and differentiated murine cells: evidence for multiple initiation regions.
Mol Cell Biol. 22: 442-452, 2002.
[Journal]
53)  Aladjem MI, Spike BT, Rodewald LW, Hope TJ, Klemm M, Jaenisch R, Wahl GM.
ES cells do not activate p53-dependent stress responses and undergo p53-independent apoptosis in response to DNA damage.
Curr Biol. 8: 145-155, 1998.
[Journal]
54)  Aladjem MI, Rodewald LW, Kolman JL, Wahl GM.
Genetic dissection of a mammalian replicator in the human beta-globin locus.
Science. 281: 1005-1009, 1998.
[Journal]
55)  Aladjem MI, Wahl GM.
Mapping replication fork direction by leading strand analysis.
Methods. 13: 281-92, 1997.
[Journal]
56)  Aladjem MI, Brody LL, O'Gorman S, Wahl GM.
Positive selection of FLP-mediated unequal sister chromatid exchange products in mammalian cells.
Mol. Cell. Biol. 17: 857-61, 1997.
[Journal]
57)  Aladjem MI, Groudine M, Brody LL, Dieken ES, Fournier RE, Wahl GM, Epner EM.
Participation of the human beta-globin locus control region in initiation of DNA replication.
Science. 270: 815-819, 1995.
[Journal]
58)  Aladjem MI, Lavi S.
Carcinogen-induced activation of SV40 gene expression in a semi-permissive environment.
Virology. 189: 493-9, 1992.
[Journal]
59)  Aladjem MI, Lavi S.
The mechanism of carcinogen-induced DNA amplification: in vivo and in vitro studies.
Mutat. Res. 276: 339-44, 1992.
[Journal]
60)  Aladjem MI, Koltin Y, Lavi S.
Enhancement of copper resistance and CupI amplification in carcinogen-treated yeast cells.
Mol. Gen. Genet. 211: 88-94, 1988.
[Journal]
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This page was last updated on 4/21/2014.