| Year |
Citation |
Score |
| 2016 |
Tran T, Ran Q, Ostrer L, Khodursky A. De novo characterization of genes that contribute to high-level ciprofloxacin resistance in Escherichia coli. Antimicrobial Agents and Chemotherapy. PMID 27431218 DOI: 10.1128/Aac.00889-16 |
0.331 |
|
| 2015 |
Khodursky A, Guzmán EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annual Review of Microbiology. PMID 26253395 DOI: 10.1146/Annurev-Micro-092412-155749 |
0.44 |
|
| 2015 |
Ostrer L, Hamann BL, Khodursky A. Perturbed states of the bacterial chromosome: a thymineless death case study. Frontiers in Microbiology. 6: 363. PMID 25964781 DOI: 10.3389/Fmicb.2015.00363 |
0.655 |
|
| 2014 |
Zare H, Khodursky A, Sartorelli V. An evolutionarily biased distribution of miRNA sites toward regulatory genes with high promoter-driven intrinsic transcriptional noise. Bmc Evolutionary Biology. 14: 74. PMID 24707827 DOI: 10.1186/1471-2148-14-74 |
0.308 |
|
| 2013 |
Edwards AL, Sangurdekar DP, Jeong KS, Khodursky AB, Rybenkov VV. Transient growth arrest in Escherichia coli induced by chromosome condensation. Plos One. 8: e84027. PMID 24376785 DOI: 10.1371/Journal.Pone.0084027 |
0.672 |
|
| 2012 |
Wang X, Chen M, Khodursky AB, Xiao G. Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations Statistics in Biosciences. 4: 300-318. DOI: 10.1007/S12561-012-9065-6 |
0.58 |
|
| 2011 |
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. 12: 583. PMID 22122981 DOI: 10.1186/1471-2164-12-583 |
0.479 |
|
| 2011 |
Zare H, Kaveh M, Khodursky A. Inferring a transcriptional regulatory network from gene expression data using nonlinear manifold embedding. Plos One. 6: e21969. PMID 21857910 DOI: 10.1038/Npre.2010.5008.1 |
0.611 |
|
| 2011 |
Xiao G, Wang X, Khodursky AB. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data. Journal of the American Statistical Association. 106: 61-72. PMID 21760653 DOI: 10.1198/Jasa.2010.Ap09504 |
0.577 |
|
| 2010 |
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. Molecular Microbiology. 75: 1455-67. PMID 20132444 DOI: 10.1111/J.1365-2958.2010.07072.X |
0.628 |
|
| 2010 |
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. Statistics in Medicine. 29: 489-503. PMID 20049751 DOI: 10.1002/Sim.3815 |
0.717 |
|
| 2009 |
Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A. Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. Bmc Systems Biology. 3: 39. PMID 19366454 DOI: 10.1186/1752-0509-3-39 |
0.576 |
|
| 2009 |
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. Antimicrobial Agents and Chemotherapy. 53: 2110-9. PMID 19273673 DOI: 10.1128/Aac.01440-08 |
0.616 |
|
| 2009 |
Xiao G, Reilly C, Khodursky AB. Improved detection of differentially expressed genes through incorporation of gene locations. Biometrics. 65: 805-14. PMID 19173705 DOI: 10.1111/J.1541-0420.2008.01161.X |
0.626 |
|
| 2008 |
Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A. Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803. Bmc Genomics. 9: 344. PMID 18644144 DOI: 10.1186/1471-2164-9-344 |
0.478 |
|
| 2008 |
Uc-Mass A, Khodursky A, Brown L, Gottesman ME. Overexpression of phage HK022 Nun protein is toxic for Escherichia coli. Journal of Molecular Biology. 380: 812-9. PMID 18571198 DOI: 10.1016/J.Jmb.2008.05.030 |
0.431 |
|
| 2008 |
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 Microbiology. 8: 60. PMID 18405378 DOI: 10.1186/1471-2180-8-60 |
0.385 |
|
| 2008 |
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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 465-76. PMID 18229708 |
0.387 |
|
| 2007 |
Khodursky AB. Evolution, adaptation, and supercoiling. Journal of Bacteriology. 189: 5789-91. PMID 17573468 DOI: 10.1128/Jb.00669-07 |
0.41 |
|
| 2007 |
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 Research. 35: 79-86. PMID 17151069 DOI: 10.1093/Nar/Gkl981 |
0.65 |
|
| 2007 |
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. Statistics in Medicine. 26: 2258-75. PMID 16958153 DOI: 10.1002/Sim.2703 |
0.626 |
|
| 2006 |
Jeong KS, Xie Y, Hiasa H, Khodursky AB. Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition. Plos Genetics. 2: e152. PMID 17009874 DOI: 10.1371/Journal.Pgen.0020152 |
0.674 |
|
| 2006 |
Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K. Persisters: a distinct physiological state of E. coli. Bmc Microbiology. 6: 53. PMID 16768798 DOI: 10.1186/1471-2180-6-53 |
0.307 |
|
| 2006 |
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 Applied and Environmental Microbiology. 72: 3653-3661. PMID 16672514 DOI: 10.1128/Aem.72.5.3653-3661.2006 |
0.409 |
|
| 2006 |
Xiao G, Martinez-Vaz B, Pan W, Khodursky AB. Operon information improves gene expression estimation for cDNA microarrays. Bmc Genomics. 7: 87. PMID 16630355 DOI: 10.1186/1471-2164-7-87 |
0.585 |
|
| 2006 |
Sangurdekar DP, Srienc F, Khodursky AB. A classification based framework for quantitative description of large-scale microarray data. Genome Biology. 7: R32. PMID 16626502 DOI: 10.1186/Gb-2006-7-4-R32 |
0.428 |
|
| 2005 |
Martinez-Vaz BM, Xie Y, Pan W, Khodursky AB. Genome-wide localization of mobile elements: experimental, statistical and biological considerations. Bmc Genomics. 6: 81. PMID 15929794 DOI: 10.1186/1471-2164-6-81 |
0.303 |
|
| 2004 |
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. Comparative and Functional Genomics. 5: 432-44. PMID 18629172 DOI: 10.1002/Cfg.416 |
0.585 |
|
| 2004 |
Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biology. 5: R87. PMID 15535863 DOI: 10.1186/Gb-2004-5-11-R87 |
0.745 |
|
| 2004 |
Jeong KS, Ahn J, Khodursky AB. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biology. 5: R86. PMID 15535862 DOI: 10.1186/Gb-2004-5-11-R86 |
0.649 |
|
| 2004 |
Zhong S, Khodursky A, Dykhuizen DE, Dean AM. Evolutionary genomics of ecological specialization. Proceedings of the National Academy of Sciences of the United States of America. 101: 11719-24. PMID 15289609 DOI: 10.1073/Pnas.0404397101 |
0.349 |
|
| 2004 |
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: Research Articles Comparative and Functional Genomics. 5: 432-444. DOI: 10.1002/Cfg.V5:5 |
0.591 |
|
| 2003 |
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 in Molecular Biology (Clifton, N.J.). 224: 61-78. PMID 12710666 DOI: 10.1385/1-59259-364-X:61 |
0.721 |
|
| 2003 |
Khodursky AB, Bernstein JA. Life after transcription--revisiting the fate of messenger RNA. Trends in Genetics : Tig. 19: 113-5. PMID 12615000 DOI: 10.1016/S0168-9525(02)00047-1 |
0.37 |
|
| 2002 |
Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 13471-6. PMID 12374860 DOI: 10.1073/Pnas.212510999 |
0.564 |
|
| 2002 |
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. Proceedings of the National Academy of Sciences of the United States of America. 99: 9697-702. PMID 12119387 DOI: 10.1073/Pnas.112318199 |
0.406 |
|
| 2001 |
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 Analytical Biochemistry. 290: 205-213. PMID 11237321 DOI: 10.1006/Abio.2000.4982 |
0.751 |
|
| 2000 |
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. Proceedings of the National Academy of Sciences of the United States of America. 97: 14674-9. PMID 11121068 DOI: 10.1073/Pnas.97.26.14674 |
0.748 |
|
| 2000 |
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. Proceedings of the National Academy of Sciences of the United States of America. 97: 12170-5. PMID 11027315 DOI: 10.1073/Pnas.220414297 |
0.781 |
|
| 2000 |
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. Proceedings of the National Academy of Sciences of the United States of America. 97: 9419-24. PMID 10944214 DOI: 10.1073/Pnas.97.17.9419 |
0.796 |
|
| 2000 |
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. The Journal of Biological Chemistry. 275: 8103-13. PMID 10713132 DOI: 10.1074/Jbc.275.11.8103 |
0.67 |
|
| 1999 |
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. 106: 131-40. PMID 10710719 DOI: 10.1023/A:1003749416449 |
0.761 |
|
| 1998 |
Khodursky AB, Cozzarelli NR. The mechanism of inhibition of topoisomerase IV by quinolone antibacterials. The Journal of Biological Chemistry. 273: 27668-77. PMID 9765303 DOI: 10.1074/Jbc.273.42.27668 |
0.663 |
|
| 1997 |
Zechiedrich EL, Khodursky AB, Cozzarelli NR. Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes & Development. 11: 2580-92. PMID 9334322 |
0.622 |
|
| 1995 |
Khodursky AB, Zechiedrich EL, Cozzarelli NR. Topoisomerase IV is a target of quinolones in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 92: 11801-5. PMID 8524852 DOI: 10.1073/Pnas.92.25.11801 |
0.556 |
|
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