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Items: 1 to 20 of 22

1.

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Oct;33(10):1109. doi: 10.1038/nbt1015-1109a. No abstract available.

PMID:
26448092
2.

Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. Erratum in: Nat Biotechnol. 2015 Oct;33(10):1109. Friend, Stephen; Dearry, Allen; Simeonov, Anton; Tice, Raymond R; Rusyn, Ivan; Wright, Fred A; Stolovitzky, Gustavo; Xie, Yang; and Saez-Rodriguez, Julio [Added].

3.

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC.

Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.

PMID:
25984700
4.

Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting.

Chaibub Neto E, Bare JC, Margolin AA.

PLoS One. 2014 Oct 7;9(10):e107957. doi: 10.1371/journal.pone.0107957. eCollection 2014.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.
17.

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.

18.

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
19.

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
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