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Results: 18

1.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-9. doi: 10.1038/ng.2932. No abstract available.

PMID:
24675517
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Network portal: a database for storage, analysis and visualization of biological networks.

Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.

Nucleic Acids Res. 2014 Jan;42(Database issue):D184-90. doi: 10.1093/nar/gkt1190. Epub 2013 Nov 23.

PMID:
24271392
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Architecture for interoperable software in biology.

Bare JC, Baliga NS.

Brief Bioinform. 2014 Jul;15(4):626-36. doi: 10.1093/bib/bbs074. Epub 2012 Dec 11.

PMID:
23235920
[PubMed - in process]
Free PMC Article
4.

Niche adaptation by expansion and reprogramming of general transcription factors.

Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.

Mol Syst Biol. 2011 Nov 22;7:554. doi: 10.1038/msb.2011.87.

PMID:
22108796
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Parallel evolution of transcriptome architecture during genome reorganization.

Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MW, Barnebey A, Yannone SM, Leigh JA, Baliga NS.

Genome Res. 2011 Nov;21(11):1892-904. doi: 10.1101/gr.122218.111. Epub 2011 Jul 12.

PMID:
21750103
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.

Plaisier CL, Bare JC, Baliga NS.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W125-31. doi: 10.1093/nar/gkr374. Epub 2011 May 20.

PMID:
21602264
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Integration and visualization of systems biology data in context of the genome.

Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.

BMC Bioinformatics. 2010 Jul 19;11:382. doi: 10.1186/1471-2105-11-382.

PMID:
20642854
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

GTC: A web server for integrating systems biology data with web tools and desktop applications.

Tenenbaum D, Bare JC, Baliga NS.

Source Code Biol Med. 2010 Jul 13;5:7. doi: 10.1186/1751-0473-5-7.

PMID:
20626906
[PubMed]
Free PMC Article
9.

Prevalence of transcription promoters within archaeal operons and coding sequences.

Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS.

Mol Syst Biol. 2009;5:285. doi: 10.1038/msb.2009.42. Epub 2009 Jun 16.

PMID:
19536208
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A predictive model for transcriptional control of physiology in a free living cell.

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS.

Cell. 2007 Dec 28;131(7):1354-65.

PMID:
18160043
[PubMed - indexed for MEDLINE]
Free Article
11.

Potent activity of the HIV-1 maturation inhibitor bevirimat in SCID-hu Thy/Liv mice.

Stoddart CA, Joshi P, Sloan B, Bare JC, Smith PC, Allaway GP, Wild CT, Martin DE.

PLoS One. 2007 Nov 28;2(11):e1251.

PMID:
18043758
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

Bare JC, Shannon PT, Schmid AK, Baliga NS.

BMC Bioinformatics. 2007 Nov 19;8:456.

PMID:
18021453
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Validation of the SCID-hu Thy/Liv mouse model with four classes of licensed antiretrovirals.

Stoddart CA, Bales CA, Bare JC, Chkhenkeli G, Galkina SA, Kinkade AN, Moreno ME, Rivera JM, Ronquillo RE, Sloan B, Black PL.

PLoS One. 2007 Aug 1;2(7):e655.

PMID:
17668043
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Critical analysis of the mathematical relationships and comprehensiveness of life cycle impact assessment approaches.

Bare JC, Gloria TP.

Environ Sci Technol. 2006 Feb 15;40(4):1104-13. Review.

PMID:
16572762
[PubMed - indexed for MEDLINE]
15.

Tools for comparative analysis of alternatives: competing or complementary perspectives?

Hofstetter P, Bare JC, Hammitt JK, Murphy PA, Rice GE.

Risk Anal. 2002 Oct;22(5):833-51. Review.

PMID:
12442983
[PubMed - indexed for MEDLINE]
16.

Comparison of chemical screening and ranking approaches: the waste minimization prioritization tool versus toxic equivalency potentials.

Pennington DW, Bare JC.

Risk Anal. 2001 Oct;21(5):897-912.

PMID:
11798125
[PubMed - indexed for MEDLINE]
17.

Developments in the application of impact assessment methodologies for pollution prevention.

Bare JC, Cicmanec J, Cabezas H.

Drug Chem Toxicol. 1997 Nov;20(4):411-7. Review.

PMID:
9433668
[PubMed - indexed for MEDLINE]
18.

Indoor air pollution source database.

Bare JC.

JAPCA. 1988 May;38(5):670-1. No abstract available.

PMID:
3411335
[PubMed - indexed for MEDLINE]

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