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A classification based framework for quantitative description of large-scale microarray data
Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky
Genome Biol. 2006; 7(4): R32. Published online 2006 April 20. doi: 10.1186/gb-2006-7-4-r32
PMCID:
PMC1557986
Abstract Full Text PDF–1.0M Supplementary Material

Is Cited by the Following 12 Articles in this Archive:

RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities
Amy K. Barczak, James E. Gomez, Benjamin B. Kaufmann, Ella R. Hinson, Lisa Cosimi, Mark L. Borowsky, Andrew B. Onderdonk, Sarah A. Stanley, Devinder Kaur, Kevin F. Bryant, David M. Knipe, Alexander Sloutsky, Deborah T. Hung
Proc Natl Acad Sci U S A. 2012 April 17; 109(16): 6217–6222. Published online 2012 April 2. doi: 10.1073/pnas.1119540109
PMCID:
PMC3341018
Free in PMC on 2012/10/17
The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug Trimethoprim
Dipen P Sangurdekar, Zhigang Zhang, Arkady B Khodursky
BMC Genomics. 2011; 12: 583. Published online 2011 November 28. doi: 10.1186/1471-2164-12-583
PMCID:
PMC3258297
Abstract Full Text PDF–557K Supplementary Material
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data
Guanghua Xiao, Xinlei Wang, Arkady B. Khodursky
J Am Stat Assoc. Author manuscript; available in PMC 2011 July 12.
Published in final edited form as: J Am Stat Assoc. 2011 March; 106(493): 61–72. doi: 10.1198/jasa.2010.ap0950
PMCID:
PMC3134274
Abstract Full Text PDF–6.1M
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
Elissa J Cosgrove, Timothy S Gardner, Eric D Kolaczyk
BMC Bioinformatics. 2010; 11: 454. Published online 2010 September 9. doi: 10.1186/1471-2105-11-454
PMCID:
PMC2949888
Abstract Full Text PDF–1.2M Supplementary Material
Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hütt
PLoS Comput Biol. 2010 July; 6(7): e1000836. Published online 2010 July 1. doi: 10.1371/journal.pcbi.1000836
PMCID:
PMC2895633
Abstract Full Text PDF–1.0M Supplementary Material
RNase R is a highly unstable protein regulated by growth phase and stress
Chenglu Chen, Murray P. Deutscher
RNA. 2010 April; 16(4): 667–672. doi: 10.1261/rna.1981010
PMCID:
PMC2844616
Abstract Full Text PDF–223K
Abasic sites and strand breaks in DNA cause transcriptional mutagenesis in Escherichia coli
Cheryl L. Clauson, Kenneth J. Oestreich, James W. Austin, Paul W. Doetsch
Proc Natl Acad Sci U S A. 2010 February 23; 107(8): 3657–3662. Published online 2010 February 8. doi: 10.1073/pnas.0913191107
PMCID:
PMC2840506
Abstract Full Text PDF–343K Supplementary Material
Quinolones: Action and Resistance Updated
Karl Drlica, Hiroshi Hiasa, Robert Kerns, Muhammad Malik, Arkady Mustaev, Xilin Zhao
Curr Top Med Chem. 2009 August; 9(11): 981–998. doi: 10.2174/156802609789630947
PMCID:
PMC3182077
Abstract Full Text PDF–468K
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations
Hossein Zare, Dipen Sangurdekar, Poonam Srivastava, Mostafa Kaveh, Arkady Khodursky
BMC Syst Biol. 2009; 3: 39. Published online 2009 April 14. doi: 10.1186/1752-0509-3-39
PMCID:
PMC2689187
Abstract Full Text PDF–345K Supplementary Material
In Vivo and In Vitro Patterns of the Activity of Simocyclinone D8, an Angucyclinone Antibiotic from Streptomyces antibioticus
Lisa M. Oppegard, Bree L. Hamann, Kathryn R. Streck, Keith C. Ellis, Hans-Peter Fiedler, Arkady B. Khodursky, Hiroshi Hiasa
Antimicrob Agents Chemother. 2009 May; 53(5): 2110–2119. Published online 2009 March 9. doi: 10.1128/AAC.01440-08
PMCID:
PMC2681514
Abstract Full Text PDF–1.0M Supplementary Material
Bioinformatics Resources for the Study of Gene Regulation in Bacteria
Julio Collado-Vides, Heladia Salgado, Enrique Morett, Socorro Gama-Castro, Verónica Jiménez-Jacinto, Irma Martínez-Flores, Alejandra Medina-Rivera, Luis Muñiz-Rascado, Martín Peralta-Gil, Alberto Santos-Zavaleta
J Bacteriol. 2009 January; 191(1): 23–31. Published online 2008 October 31. doi: 10.1128/JB.01017-08
PMCID:
PMC2612416
Full Text PDF–2.4M
Operon information improves gene expression estimation for cDNA microarrays
Guanghua Xiao, Betsy Martinez-Vaz, Wei Pan, Arkady B Khodursky
BMC Genomics. 2006; 7: 87. Published online 2006 April 21. doi: 10.1186/1471-2164-7-87
PMCID:
PMC1513396
Abstract Full Text PDF–358K Supplementary Material
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