Experimental Bioinformatics Laboratory

2008 Publications

Pirooznia M, Habib T, Perkins EJ, Deng Y. GOfetcher: a database with complex searching facility for gene ontology. Bioinformatics. 2008;24:2561-2563. doi: 10.1093/bioinformatics/btn486. PMID: 18728045.

Deng Y, Zhang M, Riedel H. Mitogenic roles of Gab1 and Grb10 as direct cellular partners in the regulation of MAP kinase signaling. J Cell Biochem. 2008;104:105-118. doi: 10.1002/jcb.21606. PMID: 18985678.

Pirooznia M, Yang MQ, Deng Y. A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S13. PMID: 18366602.

Zhang M, Deng Y, Riedel H. PSM/SH2-B splice variants – critical role in Src catalytic activation and the STAT3-mediated mitogenic response. J Cell Biochem. 2008;104:105-118. doi: 10.1002/jcb.21605. PMID: 18247337.

Yang JY, Yang MQ, Zhu M, Arabnia HR, Deng Y. Promoting synergistic research and education in genomics and bioinformatics. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S1. PMID: 18366597.

Mao J, Habib T, Shenwu M, Kang B, Allen W, Robertson L, Deng Y. Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S14. PMID: 18366603.

Gong P, Guan X, Inouye L, Deng Y, Pirooznia M, Perkins EJ. Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S15. PMID: 18366604.

Yang JY, Yang MQ, Dunker KA, Deng Y, Huang X. Investigation of transmembrane proteins using a computational approach. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S7. PMID: 18366620.

Zhang M, Deng Y, Tandon R, Bai C, Riedel H. Essential role of PSM/SH2-B variants in insulin receptor catalytic activation and the resulting cellular responses. J Cell Biochem. 2008;103:162-181. doi: 10.1002/jcb.21497. PMID: 17615553.

Habib T, Zhang C, Yang MQ, Deng Y. Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S16. PMID: 18366605.

Yang JY, Li GZ, Meng HH, Yang MQ, Deng Y. Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S3. PMID: 18366616.

Yang JY, Yang QY, Luo Z, Ma Y, Li J, Deng Y, Huang X. A hybrid machine learning-based method for classifying the Cushing’s Syndrome with comorbid adrenocortical lesions. BMC Genomics. 2008;9(Suppl 1). doi: 10.1186/1471-2164-9-S1-S23. PMID: 18366613.

Rawat A, Deng Y. Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data. BMC Bioinformatics. 2008;9(Suppl 9). doi: 10.1186/1471-2105-9-S9-S7. PMID: 18793471.

Pirooznia M, Perkins E, Deng Y. Batch Blast Extractor: An automated blastx parser application. BMC Genomics. 2008;9(Suppl 2). doi: 10.1186/1471-2164-9-S2-S10. PMID: 18831775.

Pirooznia M, Yang MQ, Gong P, Edward J, Perkins J, Deng Y. ILOOP – A web application for two-channel microarray interwoven loop design. BMC Genomics. 2008;9(Suppl 2). doi: 10.1186/1471-2164-9-S2-S11. PMID: 18831776.

Yang JY, Yang MQ, Arabnia HR, Deng Y. Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research. BMC Genomics. 2008;9(Suppl 2). doi: 10.1186/1471-2164-9-S2-I1. PMID: 18831773.

Yang JY, Niemierko A, Yang MQ, Deng Y. Analyzing adjuvant radio therapy suggests a non-monotonic radio sensitivity over tumor volumes. BMC Genomics. 2008;9(Suppl 2). doi: 10.1186/1471-2164-9-S2-S9. PMID: 18831800.