19952019

Research output per year

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Research Output

2019
2 Scopus citations
2016

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

2 Scopus citations
2015

Perturbed states of the bacterial chromosome: A thymineless death case study

Ostrer, L., Hamann, B. L. & Khodursky, A., Jan 1 2015, In : Frontiers in Microbiology. 6, APR, 363.

Research output: Contribution to journalShort survey

Open Access
3 Scopus citations

Thymineless Death Lives On: New Insights into a Classic Phenomenon

Khodursky, A., Guzmán, E. C. & Hanawalt, P. C., Oct 15 2015, In : Annual Review of Microbiology. 69, 1, p. 247-263 17 p.

Research output: Contribution to journalReview article

20 Scopus citations
2014
7 Scopus citations
2013

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

2 Scopus citations
2012

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

1 Scopus citations
2011

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

4 Scopus citations

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

12 Scopus citations

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

30 Scopus citations
2010

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

6 Scopus citations

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., Mar 2010, In : Molecular Microbiology. 75, 6, p. 1455-1467 13 p.

Research output: Contribution to journalArticle

32 Scopus citations
2009

Entropy-based analysis of chip-sequencing data

Zare, H., Kaveh, M. & Khodursky, A. B., Oct 2 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 5174339. (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Improved detection of differentially expressed genes through incorporation of gene locations

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

Research output: Contribution to journalArticle

12 Scopus citations

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

38 Scopus citations

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

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

Research output: Contribution to journalArticle

18 Scopus citations
2008

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

2 Scopus citations

A parametric joint model of dna-protein binding, gene expression and dna sequence data to detect target genes of a transcription factor

Pan, W., Wei, P. & Khodursky, A. B., Dec 1 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 465-476 12 p. (Pacific Symposium on Biocomputing 2008, PSB 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

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

49 Scopus citations

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

26 Scopus citations

Modeling regulatory sites with higher order position-dependent weight matrices

Zare, H., Kaveh, M. & Khodursky, A. B., Sep 16 2008, 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP. p. 629-632 4 p. 4517688. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

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

6 Scopus citations
2007

Evolution, adaptation, and supercoiling

Khodursky, A. B., Aug 1 2007, In : Journal of bacteriology. 189, 16, p. 5789-5791 3 p.

Research output: Contribution to journalComment/debate

2 Scopus citations

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

5 Scopus citations
11 Scopus citations

Transcription factor discovery using support vector machines and heterogeneous data

Barbe, J. F., Tewfik, A. H. & Khodursky, A. B., Dec 1 2007, 5th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'07. 4365812. (GENSIPS'07 - 5th IEEE International Workshop on Genomic Signal Processing and Statistics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2006

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

50 Scopus citations

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

30 Scopus citations

Gene clustering and gene function prediction using multiple sources of data

Zare, H., Khodursky, A. B. & Kaveh, M., Dec 1 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. p. 113-114 2 p. 4161803. (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

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

9 Scopus citations

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

198 Scopus citations

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

362 Scopus citations
2005

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

70 Scopus citations

Characterizing transcriptional responses by condition-specific profiling of functional classes

Sangurdekar, D., Srienc, F. & Khodursky, A., Dec 1 2005. 1 p.

Research output: Contribution to conferencePaper

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

4 Scopus citations
2004

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

14 Scopus citations

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

70 Scopus citations

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., 2004, In : Genome biology. 5, 11, p. R87

Research output: Contribution to journalArticle

199 Scopus citations

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

Jeong, K. S., Ahn, J. & Khodursky, A. B., 2004, In : Genome biology. 5, 11, p. R86

Research output: Contribution to journalArticle

118 Scopus citations
2003

Life after transcription - Revisiting the fate of messenger RNA

Khodursky, A. B. & Bernstein, J. A., Mar 1 2003, In : Trends in Genetics. 19, 3, p. 113-115 3 p.

Research output: Contribution to journalShort survey

34 Scopus citations
2002

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

Tani, T. H., Khodursky, A., 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

158 Scopus citations

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

522 Scopus citations
2001

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

574 Scopus citations

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

51 Scopus citations

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

12 Scopus citations
2000

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

139 Scopus citations

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

168 Scopus citations

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

250 Scopus citations

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

218 Scopus citations
1999

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

23 Scopus citations