Complete List of Publications


  • Qiu, H., Dai, H., Jain, K., Shah, R., Hong, C., Pain, J., Tian, B., Vatner, D.E., Vatner, S.F., and Depre, C. (2008). Characterization of a novel cardiac isoform of the cell cycle-related kinase that is regulated during heart failure. J. Biol. Chem. In press.
  • Khaladkar, M., Liu, J., Wen, D., Wang, J.T. L., and Tian, B. (2008). Mining Structural Elements in Human and Mouse Untranslated Regions of mRNAs using Structure-based Alignment. BMC Genomics 9:189.
  • Lee, J. Y., Park, J. Y., and Tian, B. (2008). Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags and Trace. Methods Mol. Biol. 419:23-37.

  • Dass, B., Tardif, S., Park, J.Y., Tian, B., Weitlauf, H.M., Hess, R.A., Carnes, K., Griswold, M.D., Small, C.L., and Macdonald, C.C. (2007) Loss of polyadenylation protein tCstF-64 causes spermatogenic defects and male infertility. Proc. Natl. Acad. Sci. U.S.A. 104:20374-9
  • Terskiy, A., Wannemacher, K.M., Yadav, P.N., Tsai, M., Tian, B., and Howells, R.D. (2007). Search of the human proteome for endomorphin-1 and endomorphin-2 precursor proteins. Life Sciences. 81:1593-601.
  • Young, T.M., Tsai, M., Tian, B., Mathews, M.B., and Pe'ery, T. (2007). Cellular mRNA Activates Transcription Elongation by Displacing 7SK RNA. PLoS ONE. 2(10):e1010.
  • Kirchner, S., McDaniel, N.K., Sugiura, S.H., Soteropoulos, P., Tian, B., Fletcher, J.W., and Ferraris, R.P. (2007). Salmonid microarrays identify intestinal genes that reliably monitor P-deficiency in rainbow trout aquaculture. Anim. Genet. 38:319-31.
  • Khaladkar, M., Bellofatto, V., Wang, J.T.L., Tian, B., and Shapiro, B.A. (2007). RADAR: A Web Server for RNA Data Analysis and Research. Nucleic Acids Res. 35 (Web Server issue): W300-4.
  • Alcendor, R.R., Gao, S., Zhai, P., Zablocki, D., Holle, E., Yu, X., Tian, B., Wagner, T., Vatner, S.F., and Sadoshima, J. (2007). Sirt1 Regulates Aging and Resistance to Oxidative Stress in the Heart. Circ. Res. 100:1512-21.
  • Qiu, H., Tian, B., Resuello, R.G., Natividad, F.F., Peppas, A., Shen, Y.-T., Vatner, D.E., Vatner, S.F. and Depre, C. (2007). Gender-specific regulation of gene expression in the aging monkey aorta. Physiol. Genomics. 29:169-80.
  • Lu, B., Yadav, S., Shah, P.G., Liu, T., Tian, B., Pukszta, S., Villaluna, N., Kutejova, E., Newlon, C.S., Herzog, J.H., Suzuki, C.K. (2007). Roles for the human ATP-dependent Lon protease in mitochondrial DNA maintenance. J. Biol. Chem. 282:17363-74.
  • Tian, B., Pan, Z., and Lee, J.Y. (2007). Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res. 17:156-65.
  • Lee, J.Y., Yeh, I., Park, J.Y., and Tian, B. (2007). PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. D116-20.

  • D'mello, V., Lee, J.Y., Macdonald, C.C., and Tian, B. (2006). Alternative mRNA Polyadenylation Can Potentially Affect Detection of Gene Expression by Affymetrix GeneChip((R)) Arrays. Appl. Bioinformatics 5:249-53.
  • Ago, T., Yeh, I., Yamamoto, M., Schinke-Braun, M., Brown, J.A., Tian, B., and Sadoshima, J. (2006). Thioredoxin1 Upregulates Mitochondrial Proteins Related to Oxidative Phosphorylation and TCA Cycle in the Heart. Antioxid. Redox. Signal. 8:1635-50.
  • Cheng, Y., Miura, R.M., and Tian, B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5.
  • Usui, S., Yeh, I., Tian, B., and Sadoshima, J. (2006). Global changes in gene expression during cardiac hypertrophy: A new direction of cardiac signaling research. J. Mol. Cell. Cardiol. 41:219-22.
  • Lasfar, A., Lewis-Antes, A., Smirnov, S.V., Anantha, S., Abushahba, W., Tian, B., Reuhl, K., Dickensheets, H., Sheikh, F., Donnelly, R.P., Raveche, E., and Kotenko, S.V. (2006). Characterization of the Mouse IFN-lambda Ligand-Receptor System: IFN-lambdas Exhibit Antitumor Activity against B16 Melanoma. Cancer Res. 66:4468-77.
  • Pan, Z., Zhang, H., Hague, L.K., Lee, J.Y., Lutz, C.S., and Tian, B. (2006). An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene 366:325-334.

  • Tian, B., Mukhopadhyay, R. and Mathews, M.B. (2005). Polymorphic CUG repeats in human mRNAs and their effects on gene expression. RNA Biol. 2:149-156.
  • Zhang, H., Lee, J.Y., and Tian, B. (2005). Biased alternative polyadenylation in human tissues. Genome Biol. 6:R100.
  • Hu, J., Lutz, C.S., Wilusz, J., and Tian, B. (2005). Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11:1485-1493.
  • Duttagupta1, R., Tian, B., Wilusz, C.J., Khounh, D.T., Soteropoulos, P., Ouyang, M., Dougherty, J.P., and Peltz, S.W. (2005). Global Analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol. Cell. Biol. 25:5499-5513.
  • Ondrovicova, G., Liu, T., Singh, K., Tian, B., Li, H., Gakh, O., Perecko, D., Janata, J., Granoti, Z., Orlyi, J., Kutejova., E., and Suzuki, C.K. (2005). Cleavage site selection within a folded substrate by the ATP-dependent LON protease. J. Biol. Chem. 280:25103-25110.
  • Hall-Pogar, T., Zhang, H., Tian, B., and Lutz, C.S. (2005). Alternative polyadenylation of COX-2: a mechanism for gene regulation. Nucleic Acids Res. 33:2565-2579.
  • Liu, J., Wang, T.L., Hu, J., and Tian, B. (2005). A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 6:89.
  • Hoque, M., Tian, B., Mathews, M.B., and Pe'ery, T. (2005). Granulin and granulin repeats interact with the Tat:P-TEFb complexand inhibit tat transactivation. J. Biol. Chem. 280:13648-13657.
  • Netterwald, J., Yang, S., Wang, W., Ghanny, S., Cody, M., Soteropoulos, P., Tian, B., Dunn, W., Liu, F., and Hua, Z. (2005). Two VRS Elements in the Human Cytomegalovirus Major Immediate-Early Promoter/Enhancer Are Important for Viral Replication. J. Virol. 79:5035-5046.
  • Tian, B., Hu, J., Zhang, H., and Lutz, C.S. (2005). A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33:201-212.
  • Zhang, H., Hu, J., Recce, M., and Tian, B. (2005). PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. D116-20.

  • Tian, B., Bevilacqua, P.C., Diegelman-Parente, A., and Mathews, M.B. (2004). The double-stranded RNA-binding motif: Interference and much more. Nat. Rev. Mol. Cell Biol. 5:1013-1023.
  • Toruner, G.A., Ulger, C., Alkan, M., Galante, A.T., Rinaggio, J., Wilk, R., Tian, B., Soteropoulos, P., Hameed, M.R., Schwalb, M.N., and Dermody, J.J. (2004). Association between gene expression profile and tumor invasion in oral squamous cell carcinoma. Cancer Genet. and Cytogenet. 154:27-35.
  • Lo, J.F., Hayashi, M., Kim, S.W., Tian, B., Huang, J.F. Fearns, C., Takayama, S., Zapata, J.M., Yang, Y. and Lee, J.D. (2004). Tid1, a cochaperone of the heat shock 70 protein and the mammalian counterpart of the Drosophila tumor suppressor l(2)tid, is critical for early embryonic development and cell survival. Mol. Cell. Biol. 24:2226-2236.
  • Dai, H., Tian, B., Zhao, D., Leung, A., Smith, S., Wan, J., and Yao, X . (2004). Dynamic integration of gene annotation and its application to microarray analysis. J. Bioinform. Comput. Biol. 1:627-645.
  • Tian, B., and Mathews, M.B. (2003). Phylogenetics and functions of the double-stranded RNA-binding motif: a genomic survey. Prog. Nucleic Acid Res. Mol. Biol. 74:123-158.

  • Bonaventure P., Guo H., Tian B., Liu X., Bittner A., Roland B., Salunga R., Ma X.J., Kamme F., Meurers B., Bakker M., Jurzak M., Leysen J.E., Erlander M.G. (2002). Nuclei and subnuclei gene expression profiling in mammalian brain. Brain Res. 943:38-47.
  • Zhang F., Romano P.R., Nagamura-Inoue T., Tian B., Dever T.E., Mathews M.B., Ozato K., Hinnebusch A.G. (2001). Binding of double-stranded RNA to protein kinase PKR is required for dimerization and promotes critical autophosphorylation events in the activation loop. J. Biol. Chem. 276:24946-24958.
  • Tian, B. and Mathews, M.B. (2001). Functional characterization of and cooperation between the double-stranded RNA-binding motifs of the protein kinase PKR. J. Biol. Chem. 276:9936-9944.
  • Taylor, D.R., Tian, B., Romano, P.R., Hinnebusch, A.G., Lai, M.M.C. and Mathews, M.B. (2001). Hepatitis C virus envelope protein E2 does not inhibit PKR by simple competition with autophosphorylation sites in the RNA-binding domain. J. Virol. 75:1265-1273.
  • Tian, B., White, R.J., Xia, T., Welle, S., Turner, D.H., Mathews, M.B., and Thornton, C.A. (2000). Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR. RNA 6:79-87.

 
Last updated: 6/3/2008
Tian Lab, UMDNJ-New Jersey Medical School