Experimental Bioinformatics Laboratory

2011 Publications

Chaitankar V, Zhang C, Ghosh P, Gong P, Perkins EJ, Deng Y. Predictive Minimum Description Length Principle Approach to Inferring Gene Regulatory Networks. Adv Exp Med Biol. 2011;696:37-43. doi: 10.1007/978-1-4419-7046-6_5. PMID: 21082349.

Deng Y, Meyer SA, Guan X, Escalon BL, Ai J, Wilbanks MS, Welti R, Garcia-Reyero N, Perkins EJ. Analysis of common and specific mechanisms of liver function affected by nitrotoluene compounds. PLoS One. 2011;6(2). doi: 10.1371/journal.pone.0014662. PMID: 21386882; PMCID: PMC3040182.

Zhang K, Wang H, Bathke AC, Harrar SW, Piepho H, Deng Y. Gene set enrichment analysis for longitudinal gene expression data. BMC Bioinformatics. 2011;12:273. doi: 10.1186/1471-2105-12-273. PMID: 21726481; PMCID: PMC3155861.

Chen Z, Liu J, Ng TH, Nadarajah S, Howard KL, Yang YJ, Deng Y. Statistical methods on detecting differentially expressed genes for RNAseq data. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S1. PMID: 22280802; PMCID: PMC3266038.

Mao J, Ai J, Zhou X, Shenwu M, Ong M, Blue M, Washington JT, Wang XN, Deng Y. Transcriptomic profiles of peripheral white blood cells in type II diabetes and racial differences in expression profiles. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S12. PMID: 22369412; PMCID: PMC3308032.

Chang C, Wang J, Zhao C, Fostel J, Tong W, Bushel PR, Deng Y, Pusztai L, Symmans WF, Shi T. Maximizing biomarker discovery by minimizing gene signatures. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S6. PMID: 22369406; PMCID: PMC3308026.

Wu X, Li P, Wang N, Gong P, Perkins EJ, Deng Y, Zhang C. State Space Model with hidden variables for reconstruction of gene regulatory networks. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S3. PMID: 22280804; PMCID: PMC3266040.

Land WH, Qiao X, Margolis DE, Ford WS, Paquette CT, Perez-Rogers JF, Borgia JA, Yang YJ, Deng Y. Kernelized Partial Least Squares for feature reduction and classification of gene microarray data. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S13. PMID: 22280814; PMCID: PMC3266049.

Liu Q, Sung AH, Chen Z, Chen L, Liu J, Huang X, Qiao M, Wang Z, Deng Y. Gene selection and classification for cancer microarray data based on machine learning and similarity measures. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S1. PMID: 22369401; PMCID: PMC3308021.

Xu F, Zhao C, Li Y, Li J, Deng Y, Shi T. Exploring virus relationships based on virus-host protein-protein interaction network. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S11. PMID: 22280812; PMCID: PMC3266047.

Zhang K, Liu Y, Yang JY, Arabnia HR, Niemierko AJ, Ghafoor A, Li W, Deng Y. From genes to networks: in systematic points of view. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-I1. PMID: 22280822; PMCID: PMC3266053.

Chen Z, Liu Q, McGee M, Kong M, Huang X, Deng Y, Scheuermann RH. A gene selection method for GeneChip array data with small sample sizes. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S7. PMID: 22369407; PMCID: PMC3308027.

Zhang K, Yang Y, Devanarayan V, Xie L, Deng Y, Sens D. A hidden Markov model-based algorithm for identifying tumor subtype using array CGH data. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S1. PMID: 22369401; PMCID: PMC3308021.

Wang J, Qiu X, Li Y, Deng Y, Shi T. A transcriptional dynamic network during Arabidopsis thaliana pollen development. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S8. PMID: 22280809; PMCID: PMC3266044.

Liu X, Liu J, Xu X, Chun L, Tang J, Deng Y. A robust detail-preserving anisotropic diffusion for speckle reduction in ultrasound images. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S14. PMID: 22369413; PMCID: PMC3308033.

Liu J, Chen J, Liu X, Chun L, Tang J, Deng Y. Mass segmentation using a combined method for cancer detection. BMC Syst Biol. 2011;5(Suppl 3). doi: 10.1186/1752-0509-5-S3-S6. PMID: 22280807; PMCID: PMC3266042.

Zhang K, Pirooznia M, Arabnia HR, Yang JY, Wang L, Luo Z, Deng Y. Genomic signatures and gene networking: challenges and promises. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-I1. PMID: 22369415; PMCID: PMC3308035.

Zhao C, Shi L, Tong W, Shaughnessy JD Jr, Oberthuer A, Pusztai L, Deng Y, Symmans WF, Shi T. Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile. BMC Genomics. 2011;12(Suppl 5). doi: 10.1186/1471-2164-12-S5-S3. PMID: 22369403; PMCID: PMC3308023.