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1

Isolation of Escherichia coli mRNA and Comparison of Expression Using mRNA and Total RNA on DNA Microarrays

Volker F Wendisch, Daniel P Zimmer, Arkady Khodursky, Brian Peter, Nicholas Cozzarelli, Sydney Kustu

Journal:

Analytical Biochemistry

Year:

2001

Language:

english

File:

PDF, 742 KB

english, 2001

2

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

Yang Xie, Wei Pan, Kyeong S. Jeong, Guanghua Xiao, Arkady B. Khodursky

Journal:

Statistics in Medicine

Year:

2010

Language:

english

File:

PDF, 507 KB

english, 2010

3

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

Yang Xie, Kyeong S. Jeong, Wei Pan, Arkady Khodursky, Bradley P. Carlin

Journal:

Comparative and Functional Genomics

Year:

2004

Language:

english

File:

PDF, 750 KB

english, 2004

4

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

Journal:

Year:

2011

Language:

english

File:

PDF, 307 KB

english, 2011

5

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

Yang Xie, Wei Pan, Kyeong S. Jeong, Arkady Khodursky

Journal:

Statistics in Medicine

Year:

2007

Language:

english

File:

PDF, 176 KB

english, 2007

6

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

Dipen P. Sangurdekar, Bree L. Hamann, Dmitri Smirnov, Friedrich Srienc, Philip C. Hanawalt, Arkady B. Khodursky

Journal:

Molecular Microbiology

Year:

2010

Language:

english

File:

PDF, 1.53 MB

english, 2010

7

Improved Detection of Differentially Expressed Genes Through Incorporation of Gene Locations

Guanghua Xiao, Cavan Reilly, Arkady B. Khodursky

Journal:

Year:

2009

Language:

english

File:

PDF, 225 KB

english, 2009

8

Life after transcription – revisiting the fate of messenger RNA

Arkady B. Khodursky, Jonathan A. Bernstein

Journal:

Trends in Genetics

Year:

2003

Language:

english

File:

PDF, 99 KB

english, 2003

9

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

Betsy M Martinez-Vaz, Yang Xie, Wei Pan, Arkady B Khodursky

Journal:

Year:

2005

Language:

english

File:

PDF, 458 KB

english, 2005

10

Operon information improves gene expression estimation for cDNA microarrays

Guanghua Xiao, Betsy Martinez-Vaz, Wei Pan, Arkady B Khodursky

Journal:

Year:

2006

Language:

english

File:

PDF, 358 KB

english, 2006

11

Gene expression patterns of sulfur starvation inSynechocystissp. PCC 6803

Zhigang Zhang, Ninad D Pendse, Katherine N Phillips, James B Cotner, Arkady Khodursky

Journal:

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

12

Persisters: a distinct physiological state ofE. coli

Devang Shah, Zhigang Zhang, Arkady B Khodursky, Niilo Kaldalu, Kristi Kurg, Kim Lewis

Journal:

BMC Microbiology

Year:

2006

Language:

english

File:

PDF, 524 KB

english, 2006

13

Limited functional conservation of a global regulator among related bacterial genera: Lrp inEscherichia,ProteusandVibrio

Robert E Lintner, Pankaj K Mishra, Poonam Srivastava, Betsy M Martinez-Vaz, Arkady B Khodursky, Robert M Blumenthal

Journal:

BMC Microbiology

Year:

2008

Language:

english

File:

PDF, 2.71 MB

english, 2008

14

Reconstruction ofEscherichia colitranscriptional regulatory networks via regulon-based associations

Hossein Zare, Dipen Sangurdekar, Poonam Srivastava, Mostafa Kaveh, Arkady Khodursky

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 345 KB

english, 2009

15

Overexpression of Phage HK022 Nun Protein Is Toxic for Escherichia coli

Augusto Uc-Mass, Arkady Khodursky, Lewis Brown, Max E. Gottesman

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 473 KB

english, 2008

16

Functional Genomics Volume 224 || Plastic Microarrays: A Novel Array Support Combining the Benefi ts of Macro- and Microarrays

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 1.28 MB

english, 2003

17

Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations

Xinlei Wang, Min Chen, Arkady B. Khodursky, Guanghua Xiao

Journal:

Statistics in Biosciences

Year:

2012

Language:

english

File:

PDF, 814 KB

english, 2012

18

Functional Genomics Volume 224 || Statistical Issues in cDNA Microarray Data Analysis

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 500 KB

english, 2003

19

Functional Genomics Volume 224 || Statistical Methods for Identifying Differentially Expressed Genes in DNA Microarrays

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 178 KB

english, 2003

20

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

Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky

Journal:

Year:

2006

Language:

english

File:

PDF, 1.61 MB

english, 2006

21

Genomic transcriptional response to loss of chromosomal supercoiling inEscherichia coli

Brian J Peter, Javier Arsuaga, Adam M Breier, Arkady B Khodursky…

Journal:

Year:

2004

Language:

english

File:

PDF, 1.24 MB

english, 2004

22

Spatial patterns of transcriptional activity in the chromosome ofEscherichia coli

Kyeong Soo Jeong, Jaeyong Ahn, Arkady B Khodursky

Journal:

Year:

2004

Language:

english

File:

PDF, 2.05 MB

english, 2004

23

[IEEE 2009 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) - Minneapolis, MN, USA (2009.05.17-2009.05.21)] 2009 IEEE International Workshop on Genomic Signal Processing and Statistics - Entropy-based analysis of ChIP-Sequencing data

Zare, Hossein, Kaveh, Mostafa, Khodursky, Arkady B.

Year:

2009

Language:

english

File:

PDF, 3.27 MB

english, 2009

24

[IEEE 2006 IEEE International Workshop on Genomic Signal Processing and Statistics - College Station, TX, USA (2006.05.28-2006.05.30)] 2006 IEEE International Workshop on Genomic Signal Processing and Statistics - Gene clustering and gene function prediction using multiple sources of data

Zare, Hossein, Khodursky, Arkady, Kaveh, Mostafa

Year:

2006

Language:

english

File:

PDF, 120 KB

english, 2006

25

Functional Genomics Volume 224 || Isolation of Polysomal RNA for Microarray Analysis

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 283 KB

english, 2003

26

Functional Genomics Volume 224 ||

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 6.54 MB

english, 2003

27

Functional Genomics Volume 224 || Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 122 KB

english, 2003

28

[IEEE 2007 IEEE International Workshop on Genomic Signal Processing and Statistics - Tuusula, Finland (2007.06.10-2007.06.12)] 2007 IEEE International Workshop on Genomic Signal Processing and Statistics - Transcription Factor Discovery using Support Vector Machines and Heterogeneous Data

Barbe, Jose F., Tewfik, Ahmed H., Khodursky, Arkady B.

Year:

2007

Language:

english

File:

PDF, 1.96 MB

english, 2007

29

[IEEE ICASSP 2008 - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing - Las Vegas, NV, USA (2008.03.31-2008.04.4)] 2008 IEEE International Conference on Acoustics, Speech and Signal Processing - Modeling regulatory sites with higher order position-dependent weight matrices

Zare, Hossein, Kaveh, Mostafa, Khodursky, Arkady B.

Year:

2008

Language:

english

File:

PDF, 208 KB

english, 2008

30

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

Zare, Hossein, Khodursky, Arkady, Sartorelli, Vittorio

Journal:

BMC Evolutionary Biology

Year:

2014

Language:

english

File:

PDF, 869 KB

english, 2014

31

Analysis of Pleiotropic Transcriptional Profiles: A Case Study of DNA Gyrase Inhibition

Jeong, Kyeong Soo, Xie, Yang, Hiasa, Hiroshi, Khodursky, Arkady B.

Journal:

Year:

2006

Language:

english

File:

PDF, 1.09 MB

english, 2006

32

Thymineless Death Lives On: New Insights into a Classic Phenomenon

Khodursky, Arkady, Guzmán, Elena C., Hanawalt, Philip C.

Journal:

Annual Review of Microbiology

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

33

Functional Genomics Volume 224 || Clustering in Life Sciences

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 627 KB

english, 2003

34

Functional Genomics Volume 224 || Escherichia coli Spotted Double-Strand DNA Microarrays: RNA Extraction, Labeling, Hybridization, Quality Control, and Data Management

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 151 KB

english, 2003

35

Functional Genomics Volume 224 || Preparing Fluorescent Probes for Microarray Studies

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 102 KB

english, 2003

36

Functional Genomics Volume 224 || Microarray Databases: Storage and Retrieval of Microarray Data

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 120 KB

english, 2003

37

Functional Genomics Volume 224 || Fabrication of cDNA Microarrays

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 103 KB

english, 2003

38

Functional Genomics Volume 224 || Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 235 KB

english, 2003

39

Functional Genomics Volume 224 || Nylon cDNA Expression Arrays

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 324 KB

english, 2003

40

Functional Genomics Volume 224 || A Primer on the Visualization of Microarray Data

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 331 KB

english, 2003

41

Functional Genomics Volume 224 || Experimental Design to Make the Most of Microarray Studies

Brownstein, Michael J., Khodursky, Arkady

Year:

2003

Language:

english

File:

PDF, 145 KB

english, 2003

42

Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data

Xiao, Guanghua, Wang, Xinlei, Khodursky, Arkady B.

Journal:

Journal of the American Statistical Association

Year:

2011

Language:

english

File:

PDF, 2.64 MB

english, 2011

43

Topoisomerase IV is a Target of Quinolones in Escherichia coli

Arkady B. Khodursky, E. Lynn Zechiedrich and Nicholas R. Cozzarelli

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 1.13 MB

english, 1995

44

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

Tran, Thu, Ran, Qinghong, Ostrer, Lev, Khodursky, Arkady

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2016

Language:

english

File:

PDF, 535 KB

english, 2016

45

Improved Detection of Differentially Expressed Genes through Incorporation of Gene Locations

Guanghua Xiao, Cavan Reilly and Arkady B. Khodursky

Journal:

Year:

2009

Language:

english

File:

PDF, 1.37 MB

english, 2009

46

Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis

Gharaibeh, Raad Z., Newton, Joshua M., Weller, Jennifer W., Gibas, Cynthia J., Khodursky, Arkady B.

Journal:

Year:

2010

Language:

english

File:

PDF, 347 KB

english, 2010

47

Self-Contained Gene-Set Analysis of Expression Data: An Evaluation of Existing and Novel Methods

Fridley, Brooke L., Jenkins, Gregory D., Biernacka, Joanna M., Khodursky, Arkady B.

Journal:

Year:

2010

Language:

english

File:

PDF, 2.42 MB

english, 2010

48

Cross-Platform Comparison of Microarray-Based Multiple-Class Prediction

Fan, Xiaohui, Shao, Li, Fang, Hong, Tong, Weida, Cheng, Yiyu, Khodursky, Arkady B.

Journal:

Year:

2011

Language:

english

File:

PDF, 617 KB

english, 2011

49

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions

Woodwark, Cara, Bateman, Alex, Khodursky, Arkady B.

Journal:

Year:

2011

Language:

english

File:

PDF, 274 KB

english, 2011

50

Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem

Bai, Xiaodong, Rivera-Vega, Loren, Mamidala, Praveen, Bonello, Pierluigi, Herms, Daniel A., Mittapalli, Omprakash, Khodursky, Arkady B.

Journal:

Year:

2011

Language:

english

File:

PDF, 796 KB

english, 2011

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