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Results: 1 to 20 of 115

1.

Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3.

Osipovich AB, Long Q, Manduchi E, Gangula R, Hipkens SB, Schneider J, Okubo T, Stoeckert CJ Jr, Takada S, Magnuson MA.

Development. 2014 Aug;141(15):2939-49. doi: 10.1242/dev.104810.

PMID:
25053427
[PubMed - in process]
Free Article
2.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

PMID:
24936976
[PubMed - in process]
Free PMC Article
3.

Emerging topic: Flow-related epigenetic regulation of endothelial phenotype through DNA methylation.

Davies PF, Manduchi E, Stoeckert CJ, Jiménez JM, Jiang YZ.

Vascul Pharmacol. 2014 Aug;62(2):88-93. doi: 10.1016/j.vph.2014.05.007. Epub 2014 May 27. Review.

PMID:
24874278
[PubMed - as supplied by publisher]
4.

Ontodog: a web-based ontology community view generation tool.

Zheng J, Xiang Z, Stoeckert CJ Jr, He Y.

Bioinformatics. 2014 May 1;30(9):1340-2. doi: 10.1093/bioinformatics/btu008. Epub 2014 Jan 9.

PMID:
24413522
[PubMed - indexed for MEDLINE]
5.

Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis.

Greenfest-Allen E, Malik J, Palis J, Stoeckert CJ Jr.

BMC Syst Biol. 2013 May 15;7:38. doi: 10.1186/1752-0509-7-38.

PMID:
23675896
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Ontogeny of erythroid gene expression.

Kingsley PD, Greenfest-Allen E, Frame JM, Bushnell TP, Malik J, McGrath KE, Stoeckert CJ, Palis J.

Blood. 2013 Feb 7;121(6):e5-e13. doi: 10.1182/blood-2012-04-422394. Epub 2012 Dec 12.

PMID:
23243273
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

EuPathDB: the eukaryotic pathogen database.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. doi: 10.1093/nar/gks1113. Epub 2012 Nov 21.

PMID:
23175615
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Dual lineage-specific expression of Sox17 during mouse embryogenesis.

Choi E, Kraus MR, Lemaire LA, Yoshimoto M, Vemula S, Potter LA, Manduchi E, Stoeckert CJ Jr, Grapin-Botton A, Magnuson MA.

Stem Cells. 2012 Oct;30(10):2297-308. doi: 10.1002/stem.1192.

PMID:
22865702
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.

Parikh PP, Zheng J, Logan-Klumpler F, Stoeckert CJ Jr, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS.

J Biomed Semantics. 2012 May 23;3(1):5. doi: 10.1186/2041-1480-3-5.

PMID:
22621763
[PubMed]
Free PMC Article
10.

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.

Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr.

Database (Oxford). 2011 Dec 21;2011:bar045. doi: 10.1093/database/bar045. Print 2011.

PMID:
22190598
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

FungiDB: an integrated functional genomics database for fungi.

Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS.

Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81. doi: 10.1093/nar/gkr918. Epub 2011 Nov 7.

PMID:
22064857
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.

Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19. doi: 10.1002/0471250953.bi0612s35.

PMID:
21901743
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Transcriptomes of the major human pancreatic cell types.

Dorrell C, Schug J, Lin CF, Canaday PS, Fox AJ, Smirnova O, Bonnah R, Streeter PR, Stoeckert CJ Jr, Kaestner KH, Grompe M.

Diabetologia. 2011 Nov;54(11):2832-44. doi: 10.1007/s00125-011-2283-5. Epub 2011 Sep 1. Erratum in: Diabetologia. 2013 May;56(5):1192.

PMID:
21882062
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA.

Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.

PMID:
21775302
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.

Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ.

Database (Oxford). 2011 Jun 23;2011:bar027. doi: 10.1093/database/bar027. Print 2011.

PMID:
21705364
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis.

Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF.

Circ Cardiovasc Genet. 2011 Jun;4(3):243-52. doi: 10.1161/CIRCGENETICS.110.958926. Epub 2011 Apr 14.

PMID:
21493819
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Data standards for Omics data: the basis of data sharing and reuse.

Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.

Methods Mol Biol. 2011;719:31-69. doi: 10.1007/978-1-61779-027-0_2. Review.

PMID:
21370078
[PubMed - indexed for MEDLINE]
18.

Discovery approaches to UPR in athero-susceptible endothelium in vivo.

Civelek M, Manduchi E, Grant GR, Stoeckert CJ Jr, Davies PF.

Methods Enzymol. 2011;489:109-26. doi: 10.1016/B978-0-12-385116-1.00007-8.

PMID:
21266227
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Treatman C, Wang H.

Nucleic Acids Res. 2011 Jan;39(Database issue):D612-9. doi: 10.1093/nar/gkq1006. Epub 2010 Oct 24.

PMID:
20974635
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.

Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.

Bioinformatics. 2010 Oct 1;26(19):2470-1. doi: 10.1093/bioinformatics/btq462. Epub 2010 Aug 23.

PMID:
20733062
[PubMed - indexed for MEDLINE]
Free PMC Article

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