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Items: 46

1.

Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates.

Ostrer L, Khodursky RF, Johnson JR, Hiasa H, Khodursky A.

Int J Antimicrob Agents. 2019 Mar;53(3):318-324. doi: 10.1016/j.ijantimicag.2018.12.004. Epub 2018 Dec 21.

PMID:
30582984
2.

De Novo Characterization of Genes That Contribute to High-Level Ciprofloxacin Resistance in Escherichia coli.

Tran T, Ran Q, Ostrer L, Khodursky A.

Antimicrob Agents Chemother. 2016 Sep 23;60(10):6353-5. doi: 10.1128/AAC.00889-16. Print 2016 Oct.

3.

Thymineless Death Lives On: New Insights into a Classic Phenomenon.

Khodursky A, Guzmán EC, Hanawalt PC.

Annu Rev Microbiol. 2015;69:247-63. doi: 10.1146/annurev-micro-092412-155749. Epub 2015 Aug 7. Review.

PMID:
26253395
4.

Perturbed states of the bacterial chromosome: a thymineless death case study.

Ostrer L, Hamann BL, Khodursky A.

Front Microbiol. 2015 Apr 24;6:363. doi: 10.3389/fmicb.2015.00363. eCollection 2015. Review.

5.

An evolutionarily biased distribution of miRNA sites toward regulatory genes with high promoter-driven intrinsic transcriptional noise.

Zare H, Khodursky A, Sartorelli V.

BMC Evol Biol. 2014 Apr 4;14:74. doi: 10.1186/1471-2148-14-74.

6.

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.

7.

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.

8.

Inferring a transcriptional regulatory network from gene expression data using nonlinear manifold embedding.

Zare H, Kaveh M, Khodursky A.

PLoS One. 2011;6(8):e21969. doi: 10.1371/journal.pone.0021969. Epub 2011 Aug 12.

9.

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.

10.

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.

11.

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.

12.

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

BMC Syst Biol. 2009 Apr 14;3:39. doi: 10.1186/1752-0509-3-39.

13.

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.

14.

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
15.

Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803.

Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A.

BMC Genomics. 2008 Jul 21;9:344. doi: 10.1186/1471-2164-9-344.

16.

A case study on choosing normalization methods and test statistics for two-channel microarray data.

Xie Y, Jeong KS, Pan W, Khodursky A, Carlin BP.

Comp Funct Genomics. 2004;5(5):432-44. doi: 10.1002/cfg.416.

17.

Overexpression of phage HK022 Nun protein is toxic for Escherichia coli.

Uc-Mass A, Khodursky A, Brown L, Gottesman ME.

J Mol Biol. 2008 Jul 25;380(5):812-9. doi: 10.1016/j.jmb.2008.05.030. Epub 2008 May 17.

18.

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.

20.

Evolution, adaptation, and supercoiling.

Khodursky AB.

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

21.
22.

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.

23.
24.

Persisters: a distinct physiological state of E. coli.

Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K.

BMC Microbiol. 2006 Jun 12;6:53.

25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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.

32.

Evolutionary genomics of ecological specialization.

Zhong S, Khodursky A, Dykhuizen DE, Dean AM.

Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11719-24. Epub 2004 Aug 2.

33.

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
34.

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

Khodursky AB, Bernstein JA.

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

PMID:
12615000
35.

Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis.

Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG.

Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13471-6. Epub 2002 Oct 8.

36.

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays.

Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN.

Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9697-702. Epub 2002 Jul 15.

37.

Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli.

Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC.

Genetics. 2001 May;158(1):41-64.

38.

Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays.

Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S.

Anal Biochem. 2001 Mar;290(2):205-13.

PMID:
11237321
39.

Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation.

Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S.

Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14674-9.

40.

DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli.

Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C.

Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12170-5.

41.

Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays.

Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR.

Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9419-24.

42.

Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli.

Zechiedrich EL, Khodursky AB, Bachellier S, Schneider R, Chen D, Lilley DM, Cozzarelli NR.

J Biol Chem. 2000 Mar 17;275(11):8103-13.

43.

Mechanisms of separation of the complementary strands of DNA during replication.

Alexandrov AI, Cozzarelli NR, Holmes VF, Khodursky AB, Peter BJ, Postow L, Rybenkov V, Vologodskii AV.

Genetica. 1999;106(1-2):131-40. Review.

PMID:
10710719
44.

The mechanism of inhibition of topoisomerase IV by quinolone antibacterials.

Khodursky AB, Cozzarelli NR.

J Biol Chem. 1998 Oct 16;273(42):27668-77.

45.

Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli.

Zechiedrich EL, Khodursky AB, Cozzarelli NR.

Genes Dev. 1997 Oct 1;11(19):2580-92.

46.

Topoisomerase IV is a target of quinolones in Escherichia coli.

Khodursky AB, Zechiedrich EL, Cozzarelli NR.

Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11801-5.

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