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1.
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Sangurdekar DP, Zhang Z, Khodursky AB. The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug Trimethoprim. BMC Genomics. 2011; 12:583.
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2.
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Zare H, Kaveh M, Khodursky A. Inferring a transcriptional regulatory network from gene expression data using nonlinear manifold embedding. PLoS One. 2011; 6(8):e21969.
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3.
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Xie Y, Pan W, Jeong KS, Xiao G, Khodursky AB. A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data. Stat Med. 2010 Feb 20; 29(4):489-503.
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4.
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Sangurdekar DP, Hamann BL, Smirnov D, Srienc F, Hanawalt PC, Khodursky AB. Thymineless death is associated with loss of essential genetic information from the replication origin. Mol Microbiol. 2010 Mar; 75(6):1455-67.
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5.
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Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A. Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. BMC Syst Biol. 2009; 3:39.
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6.
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Oppegard LM, Hamann BL, Streck KR, Ellis KC, Fiedler HP, Khodursky AB, Hiasa H. In vivo and in vitro patterns of the activity of simocyclinone D8, an angucyclinone antibiotic from Streptomyces antibioticus. Antimicrob Agents Chemother. 2009 May; 53(5):2110-9.
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7.
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Xiao G, Reilly C, Khodursky AB. Improved detection of differentially expressed genes through incorporation of gene locations. Biometrics. 2009 Sep; 65(3):805-14.
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8.
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Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A. Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803. BMC Genomics. 2008; 9:344.
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9.
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Uc-Mass A, Khodursky A, Brown L, Gottesman ME. Overexpression of phage HK022 Nun protein is toxic for Escherichia coli. J Mol Biol. 2008 Jul 25; 380(5):812-9.
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10.
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Lintner RE, Mishra PK, Srivastava P, Martinez-Vaz BM, Khodursky AB, Blumenthal RM. Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC Microbiol. 2008; 8:60.
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11.
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Pan W, Wei P, Khodursky A. A parametric joint model of DNA-protein binding, gene expression and DNA sequence data to detect target genes of a transcription factor. Pac Symp Biocomput. 2008; 465-76.
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12.
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Khodursky AB. Evolution, adaptation, and supercoiling. J Bacteriol. 2007 Aug; 189(16):5789-91.
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13.
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Xie Y, Pan W, Jeong KS, Khodursky A. Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data. Stat Med. 2007 May 10; 26(10):2258-75.
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14.
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Reckinger AR, Jeong KS, Khodursky AB, Hiasa H. RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli. Nucleic Acids Res. 2007; 35(1):79-86.
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15.
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Jeong KS, Xie Y, Hiasa H, Khodursky AB. Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition. PLoS Genet. 2006 Sep 29; 2(9):e152.
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16.
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Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 2006; 6:53.
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17.
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Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA. Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol. 2006 May; 72(5):3653-61.
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18.
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Xiao G, Martinez-Vaz B, Pan W, Khodursky AB. Operon information improves gene expression estimation for cDNA microarrays. BMC Genomics. 2006; 7:87.
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19.
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Sangurdekar DP, Srienc F, Khodursky AB. A classification based framework for quantitative description of large-scale microarray data. Genome Biol. 2006; 7(4):R32.
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20.
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Xie Y, Pan W, Khodursky AB. A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data. Bioinformatics. 2005 Dec 1; 21(23):4280-8.
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21.
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Martinez-Vaz BM, Xie Y, Pan W, Khodursky AB. Genome-wide localization of mobile elements: experimental, statistical and biological considerations. BMC Genomics. 2005; 6(1):81.
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22.
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Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 2004; 5(11):R87.
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23.
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Jeong KS, Ahn J, Khodursky AB. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol. 2004; 5(11):R86.
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24.
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Zhong S, Khodursky A, Dykhuizen DE, Dean AM. Evolutionary genomics of ecological specialization. Proc Natl Acad Sci U S A. 2004 Aug 10; 101(32):11719-24.
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25.
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Xie Y, Jeong KS, Pan W, Khodursky A, Carlin BP. A case study on choosing normalization methods and test statistics for two-channel microarray data. Comp Funct Genomics. 2004; 5(5):432-44.
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26.
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Khodursky AB, Bernstein JA. Life after transcription--revisiting the fate of messenger RNA. Trends Genet. 2003 Mar; 19(3):113-5.
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27.
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Khodursky AB, Bernstein JA, Peter BJ, Rhodius V, Wendisch VF, Zimmer DP. Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods Mol Biol. 2003; 224:61-78.
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28.
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Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Natl Acad Sci U S A. 2002 Oct 15; 99(21):13471-6.
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29.
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Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A. 2002 Jul 23; 99(15):9697-702.
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30.
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Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics. 2001 May; 158(1):41-64.
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31.
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Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Anal Biochem. 2001 Mar; 290(2):205-13.
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32.
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Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci U S A. 2000 Dec 19; 97(26):14674-9.
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33.
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Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):12170-5.
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34.
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Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc Natl Acad Sci U S A. 2000 Aug 15; 97(17):9419-24.
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35.
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Zechiedrich EL, Khodursky AB, Bachellier S, Schneider R, Chen D, Lilley DM, Cozzarelli NR. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem. 2000 Mar 17; 275(11):8103-13.
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36.
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Alexandrov AI, Cozzarelli NR, Holmes VF, Khodursky AB, Peter BJ, Postow L, Rybenkov V, Vologodskii AV. Mechanisms of separation of the complementary strands of DNA during replication. Genetica. 1999; 106(1-2):131-40.
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37.
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Khodursky AB, Cozzarelli NR. The mechanism of inhibition of topoisomerase IV by quinolone antibacterials. J Biol Chem. 1998 Oct 16; 273(42):27668-77.
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38.
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Zechiedrich EL, Khodursky AB, Cozzarelli NR. Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes Dev. 1997 Oct 1; 11(19):2580-92.
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39.
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Khodursky AB, Zechiedrich EL, Cozzarelli NR. Topoisomerase IV is a target of quinolones in Escherichia coli. Proc Natl Acad Sci U S A. 1995 Dec 5; 92(25):11801-5.
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