Dual ICA to extract interacting sets of genes and conditions from transcriptomic data

Author:

Choudhery Sanjeevani1ORCID,Ioerger Thomas R.2ORCID

Affiliation:

1. Department of Computer Science and Enginerering, Texas A&M University - College Station, College Station, TX, USA

2. Department of Computer Science and Enginerering, Texas A&M University - College Station, College Station, USA

Funder

NIH (National Institutes of Health)

Publisher

ACM

Reference41 articles.

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2. R. Yoo , K. Rychel , S. Poudel , T. Al-Bulushi , Y. Yuan , S. Chauhan , C. Lamoureux , B. O. Palsson , and A. Sastry , Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism , Stress Response, and Infection. mSphere , 2022 . 7(2): p. e0003322. R. Yoo, K. Rychel, S. Poudel, T. Al-Bulushi, Y. Yuan, S. Chauhan, C. Lamoureux, B. O. Palsson, and A. Sastry, Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. mSphere, 2022. 7(2): p. e0003322.

3. P. A. Jensen , Z. Zhu , and T. van Opijnen , Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Rep , 201 7. 20(7): p. 1705 -- 1716 . P. A. Jensen, Z. Zhu, and T. van Opijnen, Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Rep, 2017. 20(7): p. 1705--1716.

4. E. B. Goh , G. Yim , W. Tsui , J. McClure , M. G. Surette , and J. Davies , Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc Natl Acad Sci U S A , 200 2. 99(26): p. 17025 -- 17030 . E. B. Goh, G. Yim, W. Tsui, J. McClure, M. G. Surette, and J. Davies, Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc Natl Acad Sci U S A, 2002. 99(26): p. 17025--30.

5. S. C. Madeira and A. L. Oliveira , Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 200 4. 1(1): p. 24 -- 45 . S. C. Madeira and A. L. Oliveira, Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004. 1(1): p. 24--45.

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