Experimental Bioinformatics Laboratory

2014 Publications

Melson J, Li Y, Cassinotti E, Melnikov A, Boni L, Ai J, Greensland M, Mobarhan S, Levenson V, Deng Y. Commonality and differences of methylation signatures in the plasma of patients with pancreatic cancer and colorectal cancer. Int J Cancer. 2014;134(11):2656-2662. doi: 10.1002/ijc.28588. PMID: 24375810.

Guo N, Schwartz RS, Qian J, Jia P, Deng Y. Network and Pathway Analysis of Cancer Susceptibility. Cancer Inform. 2014;13(S5):125-127. doi: 10.4137/CIN.S14085. PMID: 25309708; PMCID: PMC4193549.

Guan D, Shao J, Deng Y, et al. CMGRN: a web server for constructing multi-level gene regulatory networks using ChIP-seq and gene expression data. Bioinformatics. 2014 Jan 2;30(8):119-121. doi: 10.1093/bioinformatics/btt698. PMID: 24389658.

The Sequencing Quality Control Consortium (Deng Y is one of co-authors). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014;32(9):903-914. doi: 10.1038/nbt.2957. PMID: 25150838.

Wei X, Ai J, Deng Y, Guan X, Johnson DR, Ang CY, Zhang C, Perkins EJ. Identification of biomarkers that distinguish chemical contaminants using a gradient feature selection method. BMC Genomics. 2014;15(1):248. doi: 10.1186/1471-2164-15-248. PMID: 24708768; PMCID: PMC3995665.

Stidd DA, Theessen H, Deng Y, Li Y, Scholz B, Rohkohl C, Jhaveri MD, Moftakhar R, Chen M, Lopes DK. Evaluation of a Metal Artifacts Reduction Algorithm Applied to Postinterventional Flat Panel Detector CT Imaging. AJNR Am J Neuroradiol. 2014;35(11):2164-2169. doi: 10.3174/ajnr.A4079. PMID: 25128191.

Gu J, Lu Y, Li F, Qiao L, Wang Q, Li N, Borgia JA, Deng Y, Lei G, Zheng Q. Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation. Cell Death Dis. 2014;5. doi: 10.1038/cddis.2014.444. PMID: 25341033; PMCID: PMC4237482.

Guan D, Shao J, Zhao Z, Wang P, Qin J, Deng Y, Boheler K, Wang J, Yan B. PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. Nucleic Acids Res. 2014;42. doi: 10.1093/nar/gku419. PMID: 24848006.

Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, ?abaj PP, Kreil DP, Megherbi D, Florian C, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach S, Tong W. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014;32(9):926-932. doi: 10.1038/nbt.3001. PMID: 25150838.

Liu C, Lu L, Kong Q, Li Y, Wu H, Xu S, Wu Q, Song X, Yang X, Deng Y. Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. BMC Bioinformatics. 2014;15(Suppl 17). doi: 10.1186/1471-2105-15-S17-S5. PMID: 25522214; PMCID: PMC4261745.

Zhou H, Chen JX, Yang CS, Deng Y, Wang H. Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer. BMC Genomics. 2014;15(Suppl 11). doi: 10.1186/1471-2164-15-S11-S3. PMID: 25373470; PMCID: PMC4287377.

Deng Y, Ai J, Guan X, Wang Z, Ang CY. MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity. BMC Genomics. 2014;15(Suppl 11). doi: 10.1186/1471-2164-15-S11-S1. PMID: 25373468; PMCID: PMC4287376.

Yang W, Yoshigoe K, Qin X, Liu JS, Yang JY, Niemierko A, Deng Y, Liu Y, Dunker A, Chen Z, Wang L, Xu D, Arabnia HR, Tong W, Yang M. Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics. 2014;15(Suppl 17). doi: 10.1186/1471-2105-15-S17-S2. PMID: 25522211; PMCID: PMC4261742.

Yang JY, Dunker A, Liu JS, Qin X, Arabnia HR, Yang W, Niemierko A, Chen Z, Luo Z, Wang L, Liu Y, Xu D, Deng Y, Tong W, Yang M. Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics. 2014;15(Suppl 17). doi: 10.1186/1471-2105-15-S17-I1. PMID: 25522210; PMCID: PMC4261741.