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Items: 1 to 20 of 29


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.


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.


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.


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.


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.


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.


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.


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.


Evolution, adaptation, and supercoiling.

Khodursky AB.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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

Khodursky AB, Bernstein JA.

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


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