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Results: 1 to 20 of 29

1.

Transient growth arrest in Escherichia coli induced by chromosome condensation.

Edwards AL, Sangurdekar DP, Jeong KS, Khodursky AB, Rybenkov VV.

PLoS One. 2013 Dec 23;8(12):e84027. doi: 10.1371/journal.pone.0084027. eCollection 2013.

PMID:
24376785
[PubMed - in process]
Free PMC Article
2.

The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim.

Sangurdekar DP, Zhang Z, Khodursky AB.

BMC Genomics. 2011 Nov 28;12:583. doi: 10.1186/1471-2164-12-583.

PMID:
22122981
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.

Xiao G, Wang X, Khodursky AB.

J Am Stat Assoc. 2011 Mar;106(493):61-72.

PMID:
21760653
[PubMed]
Free PMC Article
4.

Thymineless death is associated with loss of essential genetic information from the replication origin.

Sangurdekar DP, Hamann BL, Smirnov D, Srienc F, Hanawalt PC, Khodursky AB.

Mol Microbiol. 2010 Mar;75(6):1455-67. doi: 10.1111/j.1365-2958.2010.07072.x. Epub 2010 Feb 1.

PMID:
20132444
[PubMed - indexed for MEDLINE]
5.

A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data.

Xie Y, Pan W, Jeong KS, Xiao G, Khodursky AB.

Stat Med. 2010 Feb 20;29(4):489-503. doi: 10.1002/sim.3815.

PMID:
20049751
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

In vivo and in vitro patterns of the activity of simocyclinone D8, an angucyclinone antibiotic from Streptomyces antibioticus.

Oppegard LM, Hamann BL, Streck KR, Ellis KC, Fiedler HP, Khodursky AB, Hiasa H.

Antimicrob Agents Chemother. 2009 May;53(5):2110-9. doi: 10.1128/AAC.01440-08. Epub 2009 Mar 9.

PMID:
19273673
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Improved detection of differentially expressed genes through incorporation of gene locations.

Xiao G, Reilly C, Khodursky AB.

Biometrics. 2009 Sep;65(3):805-14. doi: 10.1111/j.1541-0420.2008.01161.x. Epub 2009 Jan 23.

PMID:
19173705
[PubMed - indexed for MEDLINE]
8.

Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio.

Lintner RE, Mishra PK, Srivastava P, Martinez-Vaz BM, Khodursky AB, Blumenthal RM.

BMC Microbiol. 2008 Apr 11;8:60. doi: 10.1186/1471-2180-8-60.

PMID:
18405378
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Evolution, adaptation, and supercoiling.

Khodursky AB.

J Bacteriol. 2007 Aug;189(16):5789-91. Epub 2007 Jun 15. No abstract available.

PMID:
17573468
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli.

Reckinger AR, Jeong KS, Khodursky AB, Hiasa H.

Nucleic Acids Res. 2007;35(1):79-86. Epub 2006 Dec 6.

PMID:
17151069
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition.

Jeong KS, Xie Y, Hiasa H, Khodursky AB.

PLoS Genet. 2006 Sep 29;2(9):e152. Epub 2006 Aug 2.

PMID:
17009874
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio.

Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA.

Appl Environ Microbiol. 2006 May;72(5):3653-61.

PMID:
16672514
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Operon information improves gene expression estimation for cDNA microarrays.

Xiao G, Martinez-Vaz B, Pan W, Khodursky AB.

BMC Genomics. 2006 Apr 21;7:87.

PMID:
16630355
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A classification based framework for quantitative description of large-scale microarray data.

Sangurdekar DP, Srienc F, Khodursky AB.

Genome Biol. 2006;7(4):R32. Epub 2006 Apr 20.

PMID:
16626502
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data.

Xie Y, Pan W, Khodursky AB.

Bioinformatics. 2005 Dec 1;21(23):4280-8. Epub 2005 Sep 27.

PMID:
16188930
[PubMed - indexed for MEDLINE]
Free Article
16.

Genome-wide localization of mobile elements: experimental, statistical and biological considerations.

Martinez-Vaz BM, Xie Y, Pan W, Khodursky AB.

BMC Genomics. 2005 Jun 1;6:81.

PMID:
15929794
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli.

Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR.

Genome Biol. 2004;5(11):R87. Epub 2004 Nov 1.

PMID:
15535863
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.

Jeong KS, Ahn J, Khodursky AB.

Genome Biol. 2004;5(11):R86. Epub 2004 Oct 27.

PMID:
15535862
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management.

Khodursky AB, Bernstein JA, Peter BJ, Rhodius V, Wendisch VF, Zimmer DP.

Methods Mol Biol. 2003;224:61-78. No abstract available.

PMID:
12710666
[PubMed - indexed for MEDLINE]
20.

Life after transcription--revisiting the fate of messenger RNA.

Khodursky AB, Bernstein JA.

Trends Genet. 2003 Mar;19(3):113-5.

PMID:
12615000
[PubMed - indexed for MEDLINE]

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