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Papers authored by Stoeckert CJ

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Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo.

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Civelek M, Grant GR, Irolla CR, Shi C, Riley RJ, Chiesa OA, Stoeckert CJ, Karanian JW, Pritchard WF, and Davies PF

American journal of physiology. Heart and circulatory physiology 298(1):H163-70, 2010 Jan - Who cited this? | PubMed ID: 19897713 | Fulltext

TriTrypDB: a functional genomic resource for the Trypanosomatidae.

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Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C,

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Nucleic acids research 38(Database issue):D457-62, 2010 Jan - Who cited this? | PubMed ID: 19843604 | Fulltext

EuPathDB: a portal to eukaryotic pathogen databases.

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Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA,

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Nucleic acids research 38(Database issue):D415-9, 2010 Jan - Who cited this? | PubMed ID: 19914931 | Fulltext

Conservation and divergence of known apicomplexan transcriptional regulons.

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Essien K and Stoeckert CJ

BMC genomics 11:147, 2010 - Who cited this? | PubMed ID: 20199665 | Fulltext

LKB1 regulates pancreatic beta cell size, polarity, and function.

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Granot Z, Swisa A, Magenheim J, Stolovich-Rain M, Fujimoto W, Manduchi E, Miki T, Lennerz JK, Stoeckert CJ, Meyuhas O, Seino S, Permutt MA, Piwnica-Worms H, Bardeesy N, and Dor Y

Cell metabolism 10(4):296-308, 2009 Oct - Who cited this? | PubMed ID: 19808022 | Fulltext

Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis.

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Civelek M, Manduchi E, Riley RJ, Stoeckert CJ, and Davies PF

Circulation research 105(5):453-61, 2009 Aug 28 - Who cited this? | PubMed ID: 19661457 | Fulltext

Renal gene and protein expression signatures for prediction of kidney disease progression.

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Ju W, Eichinger F, Bitzer M, Oh J, McWeeney S, Berthier CC, Shedden K, Cohen CD, Henger A, Krick S, Kopp JB, Stoeckert CJ, Dikman S, Schröppel B, Thomas DB, Schlondorff D,

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The American journal of pathology 174(6):2073-85, 2009 Jun - Who cited this? | PubMed ID: 19465643 | Fulltext

PlasmoDB: a functional genomic database for malaria parasites.

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Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W,

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Nucleic acids research 37(Database issue):D539-43, 2009 Jan - Who cited this? | PubMed ID: 18957442 | Fulltext

Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks.

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Bidaut G and Stoeckert CJ

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:356-67, 2009 - Who cited this? | PubMed ID: 19209714 | Fulltext

Large scale transcriptome data integration across multiple tissues to decipher stem cell signatures.

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Bidaut G and Stoeckert CJ

Methods in enzymology 467:229-45, 2009 - Who cited this? | PubMed ID: 19897095 | Fulltext

Much room for improvement in deposition rates of expression microarray datasets.

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Ochsner SA, Steffen DL, Stoeckert CJ, and McKenna NJ

Nature methods 5(12):991, 2008 Dec - Who cited this? | PubMed ID: 19034265 | Fulltext

PPAR{gamma} and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.

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Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ, Liu XS, and Lazar MA

Genes & development 22(21):2941-52, 2008 Nov 1 - Who cited this? | PubMed ID: 18981473 | Fulltext

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

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Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV,

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Nature 455(7214):757-63, 2008 Oct 9 - Who cited this? | PubMed ID: 18843361 | Fulltext

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.

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Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E,

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Nucleic acids research, 2008 Sep 29 - Who cited this? | PubMed ID: 18824479 | Fulltext

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

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Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J,

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Nature biotechnology 26(8):889-96, 2008 Aug - Who cited this? | PubMed ID: 18688244 | Fulltext

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

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Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T,

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Nature biotechnology 26(3):305, 2008 Mar - Who cited this? | PubMed ID: 18327244 | Fulltext

Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status.

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Yan B, Chen G, Saigal K, Yang X, Jensen ST, van Waes C, Stoeckert CJ, and Chen Z

Genome biology 9(3), 2008 - Who cited this? | PubMed ID: 18334025 | Fulltext

Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity.

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Essien K, Hannenhalli S, and Stoeckert CJ

PLoS ONE 3(9), 2008 - Who cited this? | PubMed ID: 18769675 | Fulltext

ToxoDB: an integrated Toxoplasma gondii database resource.

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Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ, Wang H, and Brunk BP

Nucleic acids research 36(Database issue):D553-6, 2008 Jan - Who cited this? | PubMed ID: 18003657 | Fulltext

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

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Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG,

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Nature biotechnology 25(10):1127, 2007 Oct - Who cited this? | PubMed ID: 17921998 | Fulltext

Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays.

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Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ, and Grant GR

PLoS genetics 3(8):e143, 2007 Aug 24 - Who cited this? | PubMed ID: 17722985 | Fulltext

Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha.

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Gupta RK, Gao N, Gorski RK, White P, Hardy OT, Rafiq K, Brestelli JE, Chen G, Stoeckert CJ, and Kaestner KH

Genes & development 21(7):756-69, 2007 Apr 1 - Who cited this? | PubMed ID: 17403778 | Fulltext

Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents.

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Hardy OT, Hohmeier HE, Becker TC, Manduchi E, Doliba NM, Gupta RK, White P, Stoeckert CJ, Matschinsky FM, Newgard CB, and Kaestner KH

Molecular endocrinology (Baltimore, Md.) 21(3):765-73, 2007 Mar - Who cited this? | PubMed ID: 17185391 | Fulltext

Analysis and management of microarray gene expression data.

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Grant GR, Manduchi E, and Stoeckert CJ

Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Chapter 19, 2007 Jan - Who cited this? | PubMed ID: 18265395 | Fulltext

Clustering of genes into regulons using integrated modeling-COGRIM.

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Chen G, Jensen ST, and Stoeckert CJ

Genome biology 8(1):R4, 2007 - Who cited this? | PubMed ID: 17204163 | Fulltext

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

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Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, and Stoeckert CJ

Nucleic acids research 35(Database issue):D751-5, 2007 Jan - Who cited this? | PubMed ID: 17071715 | Fulltext

ApiDB: integrated resources for the apicomplexan bioinformatics resource center.

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Aurrecoechea C, Heiges M, Wang H, Wang Z, Fischer S, Rhodes P, Miller J, Kraemer E, Stoeckert CJ, Roos DS, and Kissinger JC

Nucleic acids research 35(Database issue):D427-30, 2007 Jan - Who cited this? | PubMed ID: 17098930 | Fulltext

Novel genes identified by manual annotation and microarray expression analysis in the pancreas.

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Mazzarelli JM, White P, Gorski R, Brestelli J, Pinney DF, Arsenlis A, Katokhin A, Belova O, Bogdanova V, Elisafenko E, Gubina M, Nizolenko L, Perelman P, Puzakov M, Shilov A, Trifonoff V,

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Genomics 88(6):752-61, 2006 Dec - Who cited this? | PubMed ID: 16725306 | Fulltext

PlasmoDB v5: new looks, new genomes.

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Stoeckert CJ, Fischer S, Kissinger JC, Heiges M, Aurrecoechea C, Gajria B, and Roos DS

Trends in parasitology 22(12):543-6, 2006 Dec - Who cited this? | PubMed ID: 17029963 | Fulltext

STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments.

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Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ, Weber BL, Maris JM, and Grant GR

Genome research 16(9):1149-58, 2006 Sep - Who cited this? | PubMed ID: 16899652 | Fulltext

The MGED Ontology: a resource for semantics-based description of microarray experiments.

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Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, and Stoeckert CJ

Bioinformatics (Oxford, England) 22(7):866, 2006 Apr 1 - Who cited this? | PubMed ID: 16428806 | Fulltext

Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale.

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Date SV and Stoeckert CJ

Genome research 16(4):542-9, 2006 Apr - Who cited this? | PubMed ID: 16520460 | Fulltext

Defining the mammalian CArGome.

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Sun Q, Chen G, Streb JW, Long X, Yang Y, Stoeckert CJ, and Miano JM

Genome research 16(2):197-207, 2006 Feb - Who cited this? | PubMed ID: 16365378 | Fulltext

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.

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Chen F, Mackey AJ, Stoeckert CJ, and Roos DS

Nucleic acids research 34(Database issue), 2006 Jan 1 - Who cited this? | PubMed ID: 16381887 | Fulltext

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

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Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC,

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Omics : a journal of integrative biology 10(2):205, 2006 Summer - Who cited this? | PubMed ID: 16901227 | Fulltext

Plasmodium research in the postgenomic era.

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Duraisingh M, Ferdig MT, Stoeckert CJ, Volkman SK, and McGovern VP

Trends in parasitology 22(1):1-4, 2006 Jan - Who cited this? | PubMed ID: 16311071 | Fulltext

Development of FuGO: an ontology for functional genomics investigations.

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Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B,

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Omics : a journal of integrative biology 10(2):199-204, 2006 - Who cited this? | PubMed ID: 16901226 | Fulltext

Using ontologies to annotate microarray experiments.

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Whetzel PL, Parkinson H, and Stoeckert CJ

Methods in enzymology 411:325-39, 2006 - Who cited this? | PubMed ID: 16939798 | Fulltext

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

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Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL,

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BMC bioinformatics 7:489, 2006 - Who cited this? | PubMed ID: 17087822 | Fulltext

Functional genomics databases on the web.

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Stoeckert CJ

Cellular microbiology 7(8):1053, 2005 Aug - Who cited this? | PubMed ID: 16008573 | Fulltext

Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet.

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Passerini AG, Shi C, Francesco NM, Chuan P, Manduchi E, Grant GR, Stoeckert CJ, Karanian JW, Wray-Cahen D, Pritchard WF, and Davies PF

Biochemical and biophysical research communications 332(1):142-8, 2005 Jun 24 - Who cited this? | PubMed ID: 15896310 | Fulltext

A practical false discovery rate approach to identifying patterns of differential expression in microarray data.

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Grant GR, Liu J, and Stoeckert CJ

Bioinformatics (Oxford, England) 21(11):2684-90, 2005 Jun 1 - Who cited this? | PubMed ID: 15797908 | Fulltext

Promoter features related to tissue specificity as measured by Shannon entropy.

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Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, and Stoeckert CJ

Genome biology 6(4), 2005 - Who cited this? | PubMed ID: 15833120 | Fulltext

An object model and database for functional genomics.

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Jones A, Hunt E, Wastling JM, Pizarro A, and Stoeckert CJ

Bioinformatics (Oxford, England) 20(10):1583, 2004 Jul 10 - Who cited this? | PubMed ID: 15145818 | Fulltext

Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury.

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Marciano PG, Brettschneider J, Manduchi E, Davis JE, Eastman S, Raghupathi R, Saatman KE, Speed TP, Stoeckert CJ, Eberwine JH, and McIntosh TK

The Journal of neuroscience : the official journal of the Society for Neuroscience 24(12):2866-76, 2004 Mar 24 - Who cited this? | PubMed ID: 15044525 | Fulltext

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

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Manduchi E, Grant GR, He H, Liu J, Mailman MD, Pizarro AD, Whetzel PL, and Stoeckert CJ

Bioinformatics (Oxford, England) 20(4):452, 2004 Mar 1 - Who cited this? | PubMed ID: 14990441 | Fulltext

Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta.

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Passerini AG, Polacek DC, Shi C, Francesco NM, Manduchi E, Grant GR, Pritchard WF, Powell S, Chang GY, Stoeckert CJ, and Davies PF

Proceedings of the National Academy of Sciences of the United States of America 101(8):2482-7, 2004 Feb 24 - Who cited this? | PubMed ID: 14983035 | Fulltext

The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data.

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Parkinson H, Aitken S, Baldock RA, Bard JB, Burger A, Hayamizu TF, Rector A, Ringwald M, Rogers J, Rosse C, Stoeckert CJ, and Davidson D

Comparative and functional genomics 5(6-7):521, 2004 - Who cited this? | PubMed ID: 18629134 | Fulltext

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites.

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Li L, Crabtree J, Fischer S, Pinney D, Stoeckert CJ, Sibley LD, and Roos DS

Nucleic acids research 32(Database issue):D326-8, 2004 Jan 1 - Who cited this? | PubMed ID: 14681425 | Fulltext

Maintaining data integrity in microarray data management.

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Grant GR, Manduchi E, Pizarro A, and Stoeckert CJ

Biotechnology and bioengineering 84(7):795-800, 2003 Dec 30 - Who cited this? | PubMed ID: 14708120 | Fulltext

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