Publications

Zhang F, Lu Y, Yan S, Xing Q, Tian W: SPRINT: an SNP-free toolkit for identifying RNA editing sites. Bioinformatics 2017. Jul 24.

Yin T, Chen S, Wu X, Tian W: GenePANDA—a novel network-based gene prioritizing tool for complex diseasesScientific Reports 2017. Jan 23.

Dong X, Wang X, Zhang F, Tian W:  Genome-wide identification of regulatory sequences undergoing accelerated evolution in the human genome. Mol Biol Evol 2016. Jul 8.  

Chang BH, Tian W: GSA-Lightning: Ultra-fast Permutation-based Gene Set Analysis. Bioinformatics 2016. Jun 13.  

Chen J, Tian W: Explaining the disease phenotype of intergenic SNP through predicted long range regulation. Nucleic Acids Res 2016. Jun 8.  

Dong X, Hao Y, Wang X, Tian W: LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weightsScientific Reports 2016. Jan 11.

Gong Q, Ning W, Tian W. GoFDR: A sequence alignment based method for predicting protein functions. Methods 2015. 

Ni Q, Sun X, Chen J, Tian W: Predict metabolic gene biomarkers for neurodegenerative disease by an integrated network-based approach.BioMed research international 2015.

Zhou J, Dong X, Zhou Q, Wang H, Qian Y, Tian W, Ma D, Li X: microRNA expression profiling of heart tissue during fetal development. International journal of molecular medicine 2014, 33(5):1250-1260.

Yang C, Liu J, Dong X, Cai Z, Tian W, Wang X: Short-term and continuing stresses differentially interplay with multiple hormones to regulate plant survival and growth. Molecular plant 2014, 7(5):841-855.

Liang S, Zhou Y, Wang H, Qian Y, Ma D, Tian W, Persaud-Sharma V, Yu C, Ren Y, Zhou S et al: The effect of multiple single nucleotide polymorphisms in the folic acid pathway genes on homocysteine metabolism. BioMed research international 2014, 2014:560183.

 Wang S, Dong X, Zhu Y, Wang C, Sun G, Luo T, Tian W, Zheng H, Gao Q: Revealing of Mycobacterium marinum transcriptome by RNA-seq. PloS one2013, 8(9):e75828.

 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A et al: A large-scale evaluation of computational protein function prediction. Nature methods 2013, 10(3):221-227.

Lu Y, Zhou Y, Tian W: Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. Nucleic acids research 2013, 41(22):10391-10402.

Chen J, Ma M, Shen N, Xi JJ, Tian W: Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets. Journal of proteome research 2013, 12(6):2354-2364.

Chang B, Kustra R, Tian W: Functional-network-based gene set analysis using gene-ontology. PloS one 2013, 8(2):e55635.

Zhou Y, Lu Y, Tian W: Epigenetic features are significantly associated with alternative splicing. BMC genomics 2012, 13:123.

Zheng W, Wang X, Tian D, Zhang H, Tian W, Andersen ME, Zheng Y, Sun X, Jiang S, Cao Z et al: Pollution trees: identifying similarities among complex pollutant mixtures in water and correlating them to mutagenicity. Environmental science & technology 2012, 46(13):7274-7282.

Yang L, Wang H, Luo X, Mao P, Tian W, Shi Y, Huang G, Zhang J, Ma D: Virion protein 16 induces demethylation of DNA integrated within chromatin in a novel mammalian cell model. Acta biochimica et biophysica Sinica 2012, 44(2):154-161.

Sun Z, Tian W: SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery. PloS one2012, 7(8):e42887.

Sun S, Dong X, Fu Y, Tian W: An iterative network partition algorithm for accurate identification of dense network modules. Nucleic acids research2012, 40(3):e18.

Sun G, Luo T, Yang C, Dong X, Li J, Zhu Y, Zheng H, Tian W, Wang S, Barry CE, 3rd et al: Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients. The Journal of infectious diseases 2012, 206(11):1724-1733.

Ma H, Hao Y, Dong X, Gong Q, Chen J, Zhang J, Tian W: Molecular mechanisms and function prediction of long noncoding RNA.TheScientificWorldJournal 2012, 2012:541786.

Kang Y, Dong X, Zhou Q, Zhang Y, Cheng Y, Hu R, Su C, Jin H, Liu X, Ma D et al: Identification of novel candidate maternal serum protein markers for Down syndrome by integrated proteomic and bioinformatic analysis. Prenatal diagnosis 2012, 32(3):284-292.

Fang Z, Tian W, Ji H: A network-based gene-weighting approach for pathway analysis. Cell research 2012, 22(3):565-580.

Cai L, Tan D, Aibaidula G, Dong XR, Chen JC, Tian WD, Chen GQ: Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. Microbial cell factories2011, 10:88.

Sun Y, Ren Y, Fang Z, Li C, Fang R, Gao B, Han X, Tian W, Pao W, Chen H et al: Lung adenocarcinoma from East Asian never-smokers is a disease largely defined by targetable oncogenic mutant kinases. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2010,28(30):4616-4620.

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP: FuncBase: a resource for quantitative gene function annotation. Bioinformatics 2010,26(14):1806-1807.

Tian W, Zhang LV, Tasan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP: Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome biology 2008, 9 Suppl 1:S7.

Tasan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP: An en masse phenotype and function prediction system for Mus musculus. Genome biology2008, 9 Suppl 1:S8.

Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D et al: Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature methods 2008, 5(7):597-600.

Arakaki AK, Tian W, Skolnick J: High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC genomics 2006, 7:315.

Tian W, Arakaki AK, Skolnick J: EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic acids research2004, 32(21):6226-6239.

Tian W, Skolnick J: How well is enzyme function conserved as a function of pairwise sequence identity? Journal of molecular biology 2003,333(4):863-882.

Tian W, Hong K, Chen GQ, Wu Q, Zhang RQ, Huang W: Production of polyesters consisting of medium chain length 3-hydroxyalkanoic acids by Pseudomonas mendocina 0806 from various carbon sources. Antonie van Leeuwenhoek 2000, 77(1):31-36.