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Research Output 1995 2019

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Article
2019
2 Citations (Scopus)
Quinolones
Fluoroquinolones
DNA Topoisomerase IV
Mutation
Staphylococcus haemolyticus
2016
2 Citations (Scopus)

De novo characterization of genes that contribute to high-level ciprofloxacin resistance in Escherichia coli

Tran, T., Ran, Q., Ostrer, L. & Khodursky, A., Oct 2016, In : Antimicrobial agents and chemotherapy. 60, 10, p. 6353-6355 3 p.

Research output: Contribution to journalArticle

Ciprofloxacin
Escherichia coli
Anti-Bacterial Agents
Bacteria
Genes
2014
7 Citations (Scopus)
regulator genes
microRNA
promoter regions
gene
3' untranslated regions
2013
2 Citations (Scopus)

Transient growth arrest in Escherichia coli induced by chromosome condensation

Edwards, A. L., Sangurdekar, D. P., Jeong, K. S., Khodursky, A. B. & Rybenkov, V. V., Dec 23 2013, In : PloS one. 8, 12, e84027.

Research output: Contribution to journalArticle

Chromosomes
Escherichia coli
Condensation
chromosomes
Growth
2012
1 Citation (Scopus)

Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations

Wang, X., Chen, M., Khodursky, A. B. & Xiao, G., Nov 1 2012, In : Statistics in Biosciences. 4, 2, p. 300-318 19 p.

Research output: Contribution to journalArticle

Molecular Sequence Annotation
Bayes Theorem
Gene Expression Data
Gene expression
Annotation
2011
4 Citations (Scopus)

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

Zare, H., Kaveh, M. & Khodursky, A. B., Aug 18 2011, In : PloS one. 6, 8, e21969.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Regulator Genes
Gene expression
Genes
Gene Expression
12 Citations (Scopus)

Modeling three-dimensional chromosome structures using gene expression data

Xiao, G., Wang, X. & Khodursky, A. B., Mar 1 2011, In : Journal of the American Statistical Association. 106, 493, p. 61-72 12 p.

Research output: Contribution to journalArticle

Gene Expression Data
Chromosome
Three-dimensional
Modeling
Spatial Correlation
25 Citations (Scopus)

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

Sangurdekar, D. P., Zhang, Z. & Khodursky, A. B., Nov 28 2011, In : BMC Genomics. 12, 583.

Research output: Contribution to journalArticle

Trimethoprim
Starvation
Folic Acid
DNA Damage
Thymine
2010
6 Citations (Scopus)

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

Xie, Y., Pan, W., Jeong, K. S., Xiao, G. & Khodursky, A. B., Feb 20 2010, In : Statistics in Medicine. 29, 4, p. 489-503 15 p.

Research output: Contribution to journalArticle

DNA-binding Protein
Joint Modeling
Bayes Theorem
DNA-Binding Proteins
Bayesian Approach
32 Citations (Scopus)

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

Sangurdekar, D. P., Hamann, B. L., Smirnov, D., Srienc, F., Hanawalt, P. C. & Khodursky, A. B., Jan 1 2010, In : Molecular Microbiology. 75, 6, p. 1455-1467 13 p.

Research output: Contribution to journalArticle

Replication Origin
Thymine
Starvation
DNA Damage
Cause of Death
2009
12 Citations (Scopus)

Improved detection of differentially expressed genes through incorporation of gene locations

Xiao, G., Reilly, C. S. & Khodursky, A. B., Sep 1 2009, In : Biometrics. 65, 3, p. 805-814 10 p.

Research output: Contribution to journalArticle

Genes
Gene
Chromosomes
Chromosome
genes
38 Citations (Scopus)

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

Oppegard, L. M., Hamann, B. L., Streck, K. R., Ellis, K. C., Fiedler, H. P., Khodursky, A. B. & Hiasa, H., May 1 2009, In : Antimicrobial agents and chemotherapy. 53, 5, p. 2110-2119 10 p.

Research output: Contribution to journalArticle

Streptomyces antibioticus
Anti-Bacterial Agents
Escherichia coli
DNA Topoisomerase IV
Gram-Negative Bacteria
18 Citations (Scopus)

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

Zare, H., Sangurdekar, D., Srivastava, P., Kaveh, M. & Khodursky, A. B., Apr 14 2009, In : BMC Systems Biology. 3, 39.

Research output: Contribution to journalArticle

Regulon
Gene Regulatory Networks
Regulatory Networks
Escherichia coli
Escherichia Coli
2008
2 Citations (Scopus)

A nonparametric empirical bayes approach to joint modeling of multiple sources of genomic data

Pan, W., Jeong, K. S., Xie, Y. & Khodursky, A., Apr 1 2008, In : Statistica Sinica. 18, 2, p. 709-729 21 p.

Research output: Contribution to journalArticle

Nonparametric Bayes
Joint Modeling
Empirical Bayes
Genomics
Protein
47 Citations (Scopus)

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

Zhang, Z., Pendse, N. D., Phillips, K. N., Cotner, J. B. & Khodursky, A., Jul 21 2008, In : BMC Genomics. 9, 344.

Research output: Contribution to journalArticle

Synechocystis
Starvation
Sulfur
Gene Expression
Genome
26 Citations (Scopus)

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

Lintner, R. E., Mishra, P. K., Srivastava, P., Martinez-Vaz, B. M., Khodursky, A. B. & Blumenthal, R. M., May 19 2008, In : BMC microbiology. 8, 60.

Research output: Contribution to journalArticle

Leucine-Responsive Regulatory Protein
Escherichia
Proteus
Vibrio
Proteus mirabilis
6 Citations (Scopus)

Overexpression of Phage HK022 Nun Protein Is Toxic for Escherichia coli

Uc-Mass, A., Khodursky, A., Brown, L. & Gottesman, M. E., Jul 25 2008, In : Journal of Molecular Biology. 380, 5, p. 812-819 8 p.

Research output: Contribution to journalArticle

Poisons
Escherichia coli
RNA Phages
Coliphages
Enterobacteria phage HK022 Nun protein
2007
5 Citations (Scopus)

Incorporating prior information via shrinkage: A combined analysis of genome-wide location data and gene expression data

Xie, Y., Pan, W., Jeong, K. S. & Khodursky, A. B., May 10 2007, In : Statistics in Medicine. 26, 10, p. 2258-2275 18 p.

Research output: Contribution to journalArticle

Prior Information
Shrinkage
Gene Expression Data
Genome
Gene Expression
11 Citations (Scopus)
Type I DNA Topoisomerase
DNA Topoisomerases
Chromosomes
Genome
Rec A Recombinases
2006
50 Citations (Scopus)

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

Sangurdekar, D. P., Srienc, F. & Khodursky, A. B., Apr 20 2006, In : Genome biology. 7, 4, R32.

Research output: Contribution to journalArticle

taxonomy
gene
Genes
perturbation
genes
30 Citations (Scopus)

Analysis of pleiotropic transcriptional profiles: A case study of DNA gyrase inhibition

Kyeong, S. J., Xie, Y., Hiasa, H. & Khodursky, A. B., Oct 10 2006, In : PLoS genetics. 2, 9, p. 1464-1476 13 p.

Research output: Contribution to journalArticle

DNA Gyrase
DNA topoisomerase (ATP-hydrolysing)
DNA replication
DNA Replication
case studies
8 Citations (Scopus)

Operon information improves gene expression estimation for cDNA microarrays

Xiao, G., Martinez-Vaz, B., Pan, W. & Khodursky, A. B., Apr 21 2006, In : BMC Genomics. 7, 87.

Research output: Contribution to journalArticle

Operon
Oligonucleotide Array Sequence Analysis
Gene Expression
Genes
Noise
192 Citations (Scopus)

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

Vemuri, G. N., Altman, E., Sangurdekar, D. P., Khodursky, A. B. & Eiteman, M. A., May 1 2006, In : Applied and environmental microbiology. 72, 5, p. 3653-3661 9 p.

Research output: Contribution to journalArticle

Oxidation-Reduction
acetate
metabolism
acetates
Escherichia coli
348 Citations (Scopus)

Persisters: A distinct physiological state of E. coli

Shah, D., Zhang, Z., Khodursky, A. B., Kaldalu, N., Kurg, K. & Lewis, K., Jun 12 2006, In : BMC microbiology. 6, 53.

Research output: Contribution to journalArticle

Escherichia coli
Bacterial Physiological Phenomena
Anti-Bacterial Agents
Antitoxins
Cell Separation
2005
68 Citations (Scopus)

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

Xie, Y., Pan, W. & Khodursky, A. B., Dec 1 2005, In : Bioinformatics. 21, 23, p. 4280-4288 9 p.

Research output: Contribution to journalArticle

Microarray Analysis
Microarrays
Microarray Data
Permutation
Statistics
4 Citations (Scopus)

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

Martinez-Vaz, B. M., Xie, Y., Pan, W. & Khodursky, A. B., Jun 1 2005, In : BMC Genomics. 6, 81.

Research output: Contribution to journalArticle

Genome
DNA Transposable Elements
Escherichia coli
Oligonucleotide Array Sequence Analysis
Genes
2004
14 Citations (Scopus)

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

Xie, Y., Jeong, K. S., Pan, W., Khodursky, A. B. & Carlin, B., Jul 1 2004, In : Comparative and Functional Genomics. 5, 5, p. 432-444 13 p.

Research output: Contribution to journalArticle

Microarray Analysis
Technology
Protein Array Analysis
Oligonucleotide Array Sequence Analysis
Genome
70 Citations (Scopus)

Evolutionary genomics of ecological specialization

Zhong, S., Khodursky, A., Dykhuizen, D. E. & Dean, A. M., Aug 10 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 32, p. 11719-11724 6 p.

Research output: Contribution to journalArticle

Genomics
Mutation
Lactulose
Galactosides
Insertional Mutagenesis
194 Citations (Scopus)

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

Peter, B. J., Arsuaga, J., Breier, A. M., Khodursky, A. B., Brown, P. O. & Cozzarelli, N. R., Jan 1 2004, In : Genome Biology. 5, 11

Research output: Contribution to journalArticle

genomics
Escherichia coli
chromosome
chromosomes
gene
117 Citations (Scopus)

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

Jeong, K. S., Ahn, J. & Khodursky, A. B., Jan 1 2004, In : Genome Biology. 5, 11

Research output: Contribution to journalArticle

Bacterial Chromosomes
chromosome
Chromosomes
Escherichia coli
chromosomes
2002
157 Citations (Scopus)

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

Tani, T. H., Khodursky, A. B., Blumenthal, R. M., Brown, P. O. & Matthews, R. G., Oct 15 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 21, p. 13471-13476 6 p.

Research output: Contribution to journalArticle

Microarray Analysis
Starvation
Genes
Leucine
Food
516 Citations (Scopus)

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

Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S. & Cohen, S. N., Jul 23 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 15, p. 9697-9702 6 p.

Research output: Contribution to journalArticle

RNA Stability
Oligonucleotide Array Sequence Analysis
Color
Escherichia coli
Messenger RNA
2001
567 Citations (Scopus)

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

Courcelle, J., Khodursky, A., Peter, B., Brown, P. O. & Hanawalt, P. C., Jan 1 2001, In : Genetics. 158, 1, p. 41-64 24 p.

Research output: Contribution to journalArticle

Transcriptome
Escherichia coli
Genes
Up-Regulation
Chromosomes
51 Citations (Scopus)

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

Wendisch, V. F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N. & Kustu, S., Mar 15 2001, In : Analytical Biochemistry. 290, 2, p. 205-213 9 p.

Research output: Contribution to journalArticle

Microarrays
Oligonucleotide Array Sequence Analysis
Escherichia coli
RNA
Messenger RNA
12 Citations (Scopus)

Role of DNA ligase in the illegitimate recombination that generates λbio-transducing phages in Escherichia coli

Courcelle, J., Khodursky, A., Peter, B., Brown, P. O. & Hanawalt, P. C., May 22 2001, In : Genetics. 158, 1, p. 29-39 11 p.

Research output: Contribution to journalArticle

Coliphages
DNA Ligases
Genetic Recombination
Sequence Homology
Bacteriophages
2000
137 Citations (Scopus)

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

Khodursky, A. B., Peter, B. J., Schmid, M. B., DeRisi, J., Botstein, D., Brown, P. O. & Cozzarelli, N. R., Aug 15 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 17, p. 9419-9424 6 p.

Research output: Contribution to journalArticle

DNA Topoisomerase IV
Oligonucleotide Array Sequence Analysis
DNA Gyrase
Plasmids
Genome
168 Citations (Scopus)

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

Khodursky, A. B., Peter, B. J., Cozzarelli, N. R., Botstein, D., Brown, P. O. & Yanofsky, C., Oct 24 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 22, p. 12170-12175 6 p.

Research output: Contribution to journalArticle

Microarray Analysis
Oligonucleotide Array Sequence Analysis
Tryptophan
Operon
Escherichia coli
247 Citations (Scopus)

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

Zimmer, D. P., Soupene, E., Lee, H. L., Wendisch, V. F., Khodursky, A. B., Peter, B. J., Bender, R. A. & Kustu, S., Dec 19 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 26, p. 14674-14679 6 p.

Research output: Contribution to journalArticle

PII Nitrogen Regulatory Proteins
Protein C
Nitrogen
Operon
Escherichia coli
213 Citations (Scopus)

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

Zechiedrich, E. L., Khodursky, A. B., Bachellier, S., Schneider, R., Chen, D., Lilley, D. M. J. & Cozzarelli, N. R., Mar 17 2000, In : Journal of Biological Chemistry. 275, 11, p. 8103-8113 11 p.

Research output: Contribution to journalArticle

DNA Topoisomerase IV
Type I DNA Topoisomerase
Escherichia coli
DNA
Integrases
1999
23 Citations (Scopus)

Mechanisms of separation of the complementary strands of DNA during replication

Alexandrov, A. I., Cozzarelli, N. R., Holmes, V. F., Khodursky, A. B., Peter, B. J., Postow, L., Rybenkov, V. & Vologodskii, A. V., Dec 1 1999, In : Genetica. 106, 1-2, p. 131-140 10 p.

Research output: Contribution to journalArticle

DNA replication
DNA Replication
Complementary DNA
DNA
Chromosomes
1998
133 Citations (Scopus)

The mechanism of inhibition of topoisomerase IV by quinolone antibacterials

Khodursky, A. B. & Cozzarelli, N. R., Oct 16 1998, In : Journal of Biological Chemistry. 273, 42, p. 27668-27677 10 p.

Research output: Contribution to journalArticle

DNA Topoisomerase IV
Quinolones
DNA
Norfloxacin
DNA Repair
1997
131 Citations (Scopus)

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

Zechiedrich, E. L., Khodursky, A. B. & Cozzarelli, N. R., Oct 1 1997, In : Genes and Development. 11, 19, p. 2580-2592 13 p.

Research output: Contribution to journalArticle

DNA Topoisomerase IV
Genetic Recombination
Escherichia coli
Norfloxacin
DNA
1995
275 Citations (Scopus)

Topoisomerase IV is a target of quinolones in Escherichia coli

Khodursky, A. B., Zechiedrich, E. L. & Cozzarelli, N. R., Dec 5 1995, In : Proceedings of the National Academy of Sciences of the United States of America. 92, 25, p. 11801-11805 5 p.

Research output: Contribution to journalArticle

DNA Topoisomerase IV
Quinolones
Escherichia coli
Catenanes
Pharmaceutical Preparations