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Items: 1 to 20 of 34

1.

Xtalk: a path-based approach for identifying crosstalk between signaling pathways.

Tegge AN, Sharp N, Murali TM.

Bioinformatics. 2016 Jan 15;32(2):242-51. doi: 10.1093/bioinformatics/btv549. Epub 2015 Sep 23.

PMID:
26400040
2.

Experimental testing of a new integrated model of the budding yeast Start transition.

Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J.

Mol Biol Cell. 2015 Nov 5;26(22):3966-84. doi: 10.1091/mbc.E15-06-0358. Epub 2015 Aug 26.

3.

Signaling hypergraphs.

Ritz A, Tegge AN, Kim H, Poirel CL, Murali TM.

Trends Biotechnol. 2014 Jul;32(7):356-62. doi: 10.1016/j.tibtech.2014.04.007. Epub 2014 May 22.

4.

Reverse engineering molecular hypergraphs.

Rahman A, Poirel CL, Badger DJ, Estep C, Murali TM.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1113-24. doi: 10.1109/TCBB.2013.71.

5.
6.

Summarizing cellular responses as biological process networks.

Lasher CD, Rajagopalan P, Murali TM.

BMC Syst Biol. 2013 Jul 29;7:68. doi: 10.1186/1752-0509-7-68.

7.

Systems biology characterization of engineered tissues.

Rajagopalan P, Kasif S, Murali TM.

Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. Review.

PMID:
23862675
8.

Top-down network analysis to drive bottom-up modeling of physiological processes.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM.

J Comput Biol. 2013 May;20(5):409-18. doi: 10.1089/cmb.2012.0274.

9.

Designing a multicellular organotypic 3D liver model with a detachable, nanoscale polymeric Space of Disse.

Larkin AL, Rodrigues RR, Murali TM, Rajagopalan P.

Tissue Eng Part C Methods. 2013 Nov;19(11):875-84. doi: 10.1089/ten.TEC.2012.0700. Epub 2013 Jun 22.

10.

The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets.

Kidane YH, Lawrence C, Murali TM.

PLoS One. 2013;8(3):e58553. doi: 10.1371/journal.pone.0058553. Epub 2013 Mar 13.

11.

Reconciling differential gene expression data with molecular interaction networks.

Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM.

Bioinformatics. 2013 Mar 1;29(5):622-9. doi: 10.1093/bioinformatics/btt007. Epub 2013 Jan 12.

12.

Sensitive detection of pathway perturbations in cancers.

Rivera CG, Tyler BM, Murali TM.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S9. doi: 10.1186/1471-2105-13-S3-S9.

13.

Network-based functional enrichment.

Poirel CL, Owens CC 3rd, Murali TM.

BMC Bioinformatics. 2011;12 Suppl 13:S14. Epub 2011 Nov 30.

14.

Computationally Driven Experimental Biology.

Murali TM.

Computer (Long Beach Calif). 2012 Mar;45(3):22-23.

15.

Network-based prediction and analysis of HIV dependency factors.

Murali TM, Dyer MD, Badger D, Tyler BM, Katze MG.

PLoS Comput Biol. 2011 Sep;7(9):e1002164. doi: 10.1371/journal.pcbi.1002164. Epub 2011 Sep 22.

16.

Supervised learning and prediction of physical interactions between human and HIV proteins.

Dyer MD, Murali TM, Sobral BW.

Infect Genet Evol. 2011 Jul;11(5):917-23. doi: 10.1016/j.meegid.2011.02.022. Epub 2011 Mar 5.

17.

Discovering networks of perturbed biological processes in hepatocyte cultures.

Lasher CD, Rajagopalan P, Murali TM.

PLoS One. 2011 Jan 5;6(1):e15247. doi: 10.1371/journal.pone.0015247.

18.

The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW.

PLoS One. 2010 Aug 9;5(8):e12089. doi: 10.1371/journal.pone.0012089.

19.

A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures.

Kim Y, Lasher CD, Milford LM, Murali TM, Rajagopalan P.

Tissue Eng Part C Methods. 2010 Dec;16(6):1449-60. doi: 10.1089/ten.TEC.2010.0012. Epub 2010 Jun 7.

20.

PIG--the pathogen interaction gateway.

Driscoll T, Dyer MD, Murali TM, Sobral BW.

Nucleic Acids Res. 2009 Jan;37(Database issue):D647-50. doi: 10.1093/nar/gkn799. Epub 2008 Nov 4.

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