Anindya Dutta

Anindya Dutta

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Anindya Dutta

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Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing.

J Biol Chem 2019 Oct 3. Epub 2019 Oct 3.

Biochem & Molec Genetics; Pathology, University of Virginia Health Sciences Center, United States.

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http://dx.doi.org/10.1074/jbc.RA119.009272DOI Listing
October 2019

A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs.

Mol Neurobiol 2019 Jul 3;56(7):4786-4798. Epub 2018 Nov 3.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Pinn Hall 1232, Charlottesville, VA, 22908, USA.

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http://link.springer.com/10.1007/s12035-018-1416-y
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http://dx.doi.org/10.1007/s12035-018-1416-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499716PMC
July 2019

The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients.

Mol Cancer Res 2019 May 16;17(5):1075-1086. Epub 2019 Jan 16.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.

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http://dx.doi.org/10.1158/1541-7786.MCR-18-0996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497557PMC
May 2019

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters.

Nucleic Acids Res 2019 May;47(9):4586-4596

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1093/nar/gkz155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511871PMC
May 2019

Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains.

Int J Biol Macromol 2019 Mar 2;124:903-914. Epub 2018 Dec 2.

Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India. Electronic address:

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http://dx.doi.org/10.1016/j.ijbiomac.2018.11.263DOI Listing
March 2019

The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers.

Mol Cell 2018 12 8;72(5):823-835.e5. Epub 2018 Nov 8.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.09.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294304PMC
December 2018

Promotes Invasion through a 3'-Hairpin Structure and Associates with Prognosis in Glioblastoma.

Mol Cancer Res 2018 10 10;16(10):1470-1482. Epub 2018 Jul 10.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.

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http://dx.doi.org/10.1158/1541-7786.MCR-18-0322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170721PMC
October 2018

MUNC, an Enhancer RNA Upstream from the Gene, Induces a Subgroup of Myogenic Transcripts in Independently of MyoD.

Mol Cell Biol 2018 10 28;38(20). Epub 2018 Sep 28.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/MCB.00655-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168980PMC
October 2018

tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner.

RNA 2018 08 29;24(8):1093-1105. Epub 2018 May 29.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22901, USA.

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http://dx.doi.org/10.1261/rna.066126.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6049499PMC
August 2018

Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System.

Adv Exp Med Biol 2017 ;1042:421-454

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.

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http://dx.doi.org/10.1007/978-981-10-6955-0_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933532PMC
July 2018

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells.

Trends Genet 2018 04 9;34(4):270-278. Epub 2018 Jan 9.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2017.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881399PMC
April 2018

ASF1a Promotes Non-homologous End Joining Repair by Facilitating Phosphorylation of MDC1 by ATM at Double-Strand Breaks.

Mol Cell 2017 Oct 21;68(1):61-75.e5. Epub 2017 Sep 21.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.08.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5743198PMC
October 2017

Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation.

Mol Cancer Res 2017 09 26;15(9):1197-1205. Epub 2017 May 26.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.

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http://dx.doi.org/10.1158/1541-7786.MCR-17-0095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581709PMC
September 2017

Two subunits of human ORC are dispensable for DNA replication and proliferation.

Elife 2016 12 1;5. Epub 2016 Dec 1.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, United States.

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http://dx.doi.org/10.7554/eLife.19084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5245961PMC
December 2016

Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis.

PLoS Med 2016 Dec 6;13(12):e1002192. Epub 2016 Dec 6.

Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pmed.1002192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140055PMC
December 2016

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs).

Trends Biochem Sci 2016 08 1;41(8):679-689. Epub 2016 Jun 1.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tibs.2016.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5173347PMC
August 2016

A Pro-metastatic tRNA Pathway.

Cell 2016 Jun;165(6):1314-1315

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.05.066DOI Listing
June 2016

A pan-cancer analysis of prognostic genes.

PeerJ 2015 16;3:e1499. Epub 2016 Feb 16.

Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA , United States.

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http://dx.doi.org/10.7717/peerj.1499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815555PMC
April 2016

Biological Processes Discovered by High-Throughput Sequencing.

Am J Pathol 2016 Apr 30;186(4):722-32. Epub 2016 Jan 30.

Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2015.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807928PMC
April 2016

Anindya Dutta.

Authors:
Anindya Dutta

Curr Biol 2015 Dec;25(23):R1112-4

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http://dx.doi.org/10.1016/j.cub.2015.10.035DOI Listing
December 2015

Initiation of replication in Xenopus egg extracts at a spatially defined origin.

Cell Cycle 2015 Aug 19;14(15):2391. Epub 2015 Jun 19.

a Department of Biochemistry and Molecular Genetics ; University of Virginia ; Charlottesville , VA USA.

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http://dx.doi.org/10.1080/15384101.2015.1063306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612457PMC
August 2015

Sequential replication-coupled destruction at G1/S ensures genome stability.

Genes Dev 2015 Aug 13;29(16):1734-46. Epub 2015 Aug 13.

Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;

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http://dx.doi.org/10.1101/gad.263731.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561482PMC
August 2015

Long non-coding RNAs as emerging regulators of differentiation, development, and disease.

Transcription 2014 30;5(4):e944014. Epub 2014 Oct 30.

a Department of Biochemistry and Molecular Genetics ; University of Virginia School of Medicine ; Charlottesville , VA USA.

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http://dx.doi.org/10.4161/21541272.2014.944014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581346PMC
July 2015

MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex.

Nat Commun 2015 Jul 28;6:7744. Epub 2015 Jul 28.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Jordan Hall, 1300 Jefferson Park Avenue, Charlottesville, Virginia 22908 USA.

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http://dx.doi.org/10.1038/ncomms8744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525285PMC
July 2015

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity.

Cell Rep 2015 Jun 4;11(11):1749-59. Epub 2015 Jun 4.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.05.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481157PMC
June 2015

The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus.

Mol Cancer Res 2015 May 20;13(5):828-38. Epub 2015 Feb 20.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.

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http://mcr.aacrjournals.org/content/early/2015/02/20/1541-77
Web Search
http://mcr.aacrjournals.org/cgi/doi/10.1158/1541-7786.MCR-15
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http://dx.doi.org/10.1158/1541-7786.MCR-15-0016-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456356PMC
May 2015

The AAA+ proteins Pontin and Reptin enter adult age: from understanding their basic biology to the identification of selective inhibitors.

Front Mol Biosci 2015 5;2:17. Epub 2015 May 5.

INSERM, U1053 Bordeaux, France ; Groupe de Recherches pour l'Etude du Foie, Université de Bordeaux Bordeaux, France.

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http://dx.doi.org/10.3389/fmolb.2015.00017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428354PMC
May 2015

The acetyltransferase Tip60 is a critical regulator of the differentiation-dependent amplification of human papillomaviruses.

J Virol 2015 Apr 11;89(8):4668-75. Epub 2015 Feb 11.

Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA

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http://dx.doi.org/10.1128/JVI.03455-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442364PMC
April 2015

MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis.

Mol Cell Biol 2015 Feb 17;35(3):498-513. Epub 2014 Nov 17.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/MCB.01079-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285423PMC
February 2015

Novel anti-apoptotic microRNAs 582-5p and 363 promote human glioblastoma stem cell survival via direct inhibition of caspase 3, caspase 9, and Bim.

PLoS One 2014 7;9(5):e96239. Epub 2014 May 7.

Division of Neuro-Oncology, Departments of Neurology, Microbiology, and Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096239PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013090PMC
January 2015

tRFdb: a database for transfer RNA fragments.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D141-5. Epub 2014 Nov 11.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA

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http://dx.doi.org/10.1093/nar/gku1138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383946PMC
January 2015

14-3-3 proteins play a role in the cell cycle by shielding cdt2 from ubiquitin-mediated degradation.

Mol Cell Biol 2014 Nov 25;34(21):4049-61. Epub 2014 Aug 25.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA

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http://mcb.asm.org/cgi/doi/10.1128/MCB.00838-14
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http://dx.doi.org/10.1128/MCB.00838-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386460PMC
November 2014

Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets.

BMC Biol 2014 Oct 1;12:78. Epub 2014 Oct 1.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville 22901, VA, USA.

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http://dx.doi.org/10.1186/s12915-014-0078-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203973PMC
October 2014

CRL4Cdt2 E3 ubiquitin ligase and proliferating cell nuclear antigen (PCNA) cooperate to degrade thymine DNA glycosylase in S phase.

J Biol Chem 2014 Aug 24;289(33):23056-64. Epub 2014 Jun 24.

From the Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908

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http://dx.doi.org/10.1074/jbc.M114.574210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132804PMC
August 2014

ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks.

Genes Dev 2014 Apr 3;28(8):875-87. Epub 2014 Apr 3.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1101/gad.239194.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4003279PMC
April 2014

The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration.

Genes Dev 2014 Mar 14;28(5):491-501. Epub 2014 Feb 14.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA;

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http://dx.doi.org/10.1101/gad.234419.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950346PMC
March 2014

Human Primpol1: a novel guardian of stalled replication forks.

EMBO Rep 2013 Dec 5;14(12):1032-3. Epub 2013 Nov 5.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.

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http://embor.embopress.org/cgi/doi/10.1038/embor.2013.171
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http://dx.doi.org/10.1038/embor.2013.171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981087PMC
December 2013

Overcoming platinum resistance in preclinical models of ovarian cancer using the neddylation inhibitor MLN4924.

Mol Cancer Ther 2013 Oct 12;12(10):1958-67. Epub 2013 Aug 12.

Corresponding Author: Amir A. Jazaeri, Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Virginia Health System, Box 800712, Charlottesville, VA 22908.

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http://dx.doi.org/10.1158/1535-7163.MCT-12-1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795967PMC
October 2013

Degradation of p12 subunit by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage.

J Biol Chem 2013 Oct 10;288(42):30509-14. Epub 2013 Sep 10.

From the Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908.

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http://dx.doi.org/10.1074/jbc.C113.505586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798521PMC
October 2013

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes.

Cancer Biol Ther 2013 Sep 26;14(9):840-52. Epub 2013 Jul 26.

Department of Biochemistry and Molecular Genetics; University of Virginia School of Medicine; Charlottesville, VA USA.

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http://dx.doi.org/10.4161/cbt.25329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3909553PMC
September 2013

MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab.

J Transl Med 2013 Sep 18;11:218. Epub 2013 Sep 18.

Department of Surgery, Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, VA, USA.

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http://dx.doi.org/10.1186/1479-5876-11-218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853033PMC
September 2013

Deubiquitination of Tip60 by USP7 determines the activity of the p53-dependent apoptotic pathway.

Mol Cell Biol 2013 Aug 17;33(16):3309-20. Epub 2013 Jun 17.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1128/MCB.00358-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753911PMC
August 2013

Regulation of TGF-β signaling, exit from the cell cycle, and cellular migration through cullin cross-regulation: SCF-FBXO11 turns off CRL4-Cdt2.

Cell Cycle 2013 Jul;12(14):2175-82

Department of Radiation Oncology; School of Medicine, University of Virginia, Charlottesville, VA, USA.

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http://dx.doi.org/10.4161/cc.25314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755067PMC
July 2013

Defective nuclear import of Tpr in Progeria reflects the Ran sensitivity of large cargo transport.

J Cell Biol 2013 May 6;201(4):541-57. Epub 2013 May 6.

Center for Cell Signaling, University of Virginia, Charlottesville, VA 22903, USA.

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http://dx.doi.org/10.1083/jcb.201212117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653351PMC
May 2013

The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination.

Mol Cell Biol 2013 Apr 11;33(8):1632-44. Epub 2013 Feb 11.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1128/MCB.01503-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624244PMC
April 2013

RVBs are required for assembling a functional TIP60 complex.

Mol Cell Biol 2013 Mar 7;33(6):1164-74. Epub 2013 Jan 7.

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1128/MCB.01567-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592018PMC
March 2013

Genomic instability in cancer.

Cold Spring Harb Perspect Biol 2013 Mar 1;5(3):a012914. Epub 2013 Mar 1.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1101/cshperspect.a012914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578360PMC
March 2013

CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration.

Mol Cell 2013 Mar 7;49(6):1147-58. Epub 2013 Mar 7.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615078PMC
March 2013

The emergence of the conserved AAA+ ATPases Pontin and Reptin on the signaling landscape.

Sci Signal 2013 Mar 12;6(266):mr1. Epub 2013 Mar 12.

Université Bordeaux, Physiopathologie du Cancer du Foie, U1053, F-33000 Bordeaux, France.

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http://dx.doi.org/10.1126/scisignal.2003906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201591PMC
March 2013

Non-micro-short RNAs: the new kids on the block.

Mol Biol Cell 2012 Dec;23(24):4664-7

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1091/mbc.E12-10-0716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521675PMC
December 2012

Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts.

J Biol Chem 2012 Nov 10;287(48):40360-70. Epub 2012 Oct 10.

Department of Biochemistry and Molecular Genetics, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1074/jbc.M112.378414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504751PMC
November 2012

miR-26a is required for skeletal muscle differentiation and regeneration in mice.

Genes Dev 2012 Oct;26(19):2180-91

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1101/gad.198085.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465739PMC
October 2012

MicroRNAs regulate and provide robustness to the myogenic transcriptional network.

Curr Opin Pharmacol 2012 Jun 2;12(3):383-8. Epub 2012 Mar 2.

Department of Biochemistry and Molecular Genetics, University of Virginia, 1300 Jefferson Park Ave, Jordan Hall 1240, University of Virginia School of Medicine, Charlottesville, VA 22908, United States.

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http://dx.doi.org/10.1016/j.coph.2012.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369106PMC
June 2012

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues.

Science 2012 Apr 8;336(6077):82-6. Epub 2012 Mar 8.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.

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http://dx.doi.org/10.1126/science.1213307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703515PMC
April 2012

The role of microRNAs in glioma initiation and progression.

Front Biosci (Landmark Ed) 2012 Jan 1;17:700-12. Epub 2012 Jan 1.

University of Virginia, Department of Microbiology, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.2741/3952DOI Listing
January 2012

Molecular requirements for transformation of fallopian tube epithelial cells into serous carcinoma.

Neoplasia 2011 Oct;13(10):899-911

W. Norman Thornton Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Virginia Health System, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1593/neo.11138DOI Listing
October 2011

The SKP1-Cul1-F-box and leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A) protein.

J Biol Chem 2011 Sep 8;286(35):30462-70. Epub 2011 Jul 8.

Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts 02129, USA.

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http://dx.doi.org/10.1074/jbc.M111.273508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162406PMC
September 2011

Selective ubiquitylation of p21 and Cdt1 by UBCH8 and UBE2G ubiquitin-conjugating enzymes via the CRL4Cdt2 ubiquitin ligase complex.

Mol Cell Biol 2011 Aug 31;31(15):3136-45. Epub 2011 May 31.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147600PMC
August 2011

DNA replication: mammalian Treslin-TopBP1 interaction mirrors yeast Sld3-Dpb11.

Curr Biol 2011 Aug;21(16):R638-40

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1016/j.cub.2011.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523092PMC
August 2011

MicroRNA-378 targets the myogenic repressor MyoR during myoblast differentiation.

J Biol Chem 2011 Jun 6;286(22):19431-8. Epub 2011 Apr 6.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1074/jbc.M111.219006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103322PMC
June 2011

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription.

Genome Res 2011 Mar 20;21(3):377-89. Epub 2010 Dec 20.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044852PMC
March 2011

The effect of the intra-S-phase checkpoint on origins of replication in human cells.

Genes Dev 2011 Mar;25(6):621-33

Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virigina 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059835PMC
March 2011

Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

PLoS One 2011 Mar 14;6(3):e17912. Epub 2011 Mar 14.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056778PMC
March 2011

miR-206 and -486 induce myoblast differentiation by downregulating Pax7.

Mol Cell Biol 2011 Jan 1;31(1):203-14. Epub 2010 Nov 1.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Jordan Hall 1232, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019853PMC
January 2011

CRL4Cdt2: master coordinator of cell cycle progression and genome stability.

Cell Cycle 2011 Jan 15;10(2):241-9. Epub 2011 Jan 15.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025761PMC
http://dx.doi.org/10.4161/cc.10.2.14530DOI Listing
January 2011

CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation.

Mol Cell 2010 Oct;40(1):9-21

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.molcel.2010.09.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966975PMC
October 2010

Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET.

Genome Med 2010 Sep 22;2(9):70. Epub 2010 Sep 22.

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1300 Jefferson Pk Ave, Charlottesville, VA 22908-0733, USA.

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http://dx.doi.org/10.1186/gm191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092121PMC
September 2010

Evaluation of EVI1 and EVI1s (Delta324) as potential therapeutic targets in ovarian cancer.

Gynecol Oncol 2010 Aug 11;118(2):189-95. Epub 2010 May 11.

W. Norman Thornton Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Virginia Health System, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.ygyno.2010.04.007DOI Listing
August 2010

MiR-322/424 and -503 are induced during muscle differentiation and promote cell cycle quiescence and differentiation by down-regulation of Cdc25A.

Mol Biol Cell 2010 Jul 12;21(13):2138-49. Epub 2010 May 12.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1091/mbc.e10-01-0062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893979PMC
July 2010

Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection.

Mol Biol Cell 2010 Feb 2;21(3):393-404. Epub 2009 Dec 2.

Departments of *Biochemistry and Molecular Genetics and Computer Science, University of Virginia, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814785PMC
February 2010

CRL4(Cdt2) E3 ubiquitin ligase monoubiquitinates PCNA to promote translesion DNA synthesis.

Mol Cell 2010 Jan;37(1):143-9

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818832PMC
January 2010

The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1.

J Biol Chem 2009 Dec 8;284(49):34179-88. Epub 2009 Oct 8.

Division of Oncology Research, Mayo College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797188PMC
December 2009

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs).

Genes Dev 2009 Nov;23(22):2639-49

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://genesdev.cshlp.org/lookup/doi/10.1101/gad.1837609
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779758PMC
November 2009

Microarray analysis of DNA replication timing.

Methods Mol Biol 2009 ;556:191-203

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201590PMC
September 2009

p21 in cancer: intricate networks and multiple activities.

Nat Rev Cancer 2009 Jun;9(6):400-14

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722839PMC
June 2009

The evolution of guanylyl cyclases as multidomain proteins: conserved features of kinase-cyclase domain fusions.

J Mol Evol 2009 Jun 3;68(6):587-602. Epub 2009 Jun 3.

Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.

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http://dx.doi.org/10.1007/s00239-009-9242-5DOI Listing
June 2009

RVB1/RVB2: running rings around molecular biology.

Mol Cell 2009 Jun;34(5):521-33

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Jordan 1240, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733251PMC
June 2009

Surface treatment of pure and PEG-4000 blended fibroin films and their characterizations as matrices for in vitro fibroblast culture.

J Biomater Appl 2009 May 18;23(6):497-517. Epub 2008 Sep 18.

Department of Biotechnology, Indian Institute of Technology Kharagpur-721302, India.

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http://dx.doi.org/10.1177/0885328208094261DOI Listing
May 2009

MicroRNAs in cancer.

Annu Rev Pathol 2009 ;4:199-227

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1146/annurev.pathol.4.110807.092222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2769253PMC
May 2009

Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes.

Structure 2008 Oct;16(10):1511-20

Centro de Investigaciones Biológicas/Centre for Biological Research, Spanish National Research Council (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577609PMC
October 2008

DNA replication and genomic instability.

Adv Exp Med Biol 2005 ;570:249-79

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1007/1-4020-3764-3_9DOI Listing
September 2008

PCNA-dependent regulation of p21 ubiquitylation and degradation via the CRL4Cdt2 ubiquitin ligase complex.

Genes Dev 2008 Sep;22(18):2496-506

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1101/gad.1676108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2546691PMC
September 2008

Human Rvb1/Tip49 is required for the histone acetyltransferase activity of Tip60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage.

Mol Cell Biol 2008 Apr 19;28(8):2690-700. Epub 2008 Feb 19.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Jordan 1240, 1300 Jefferson Park Ave., Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2293106PMC
April 2008

Human Cdt1 lacking the evolutionarily conserved region that interacts with MCM2-7 is capable of inducing re-replication.

J Biol Chem 2008 Mar 8;283(11):6817-25. Epub 2008 Jan 8.

Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts 02115, USA.

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March 2008

Mechanisms to control rereplication and implications for cancer.

Curr Opin Cell Biol 2007 Dec 28;19(6):663-71. Epub 2007 Nov 28.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.ceb.2007.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174913PMC
December 2007

The origin recognition complex localizes to telomere repeats and prevents telomere-circle formation.

Curr Biol 2007 Nov;17(22):1989-95

The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.

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November 2007

ATR pathway is the primary pathway for activating G2/M checkpoint induction after re-replication.

J Biol Chem 2007 Oct 22;282(42):30357-62. Epub 2007 Aug 22.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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October 2007

Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication.

Genes Dev 2007 Sep 30;21(18):2288-99. Epub 2007 Aug 30.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1101/gad.1585607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1973143PMC
September 2007

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas.

Genome Res 2007 Jun;17(6):865-76

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5427007
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891345PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007