Peer reviewed journals (#: cofirst author, *: corresponding author)

• Y Qin#, W Zhang#, X Sun, S Nan, N Wei, HJ Wu, X Zheng*, Deconvolution of heterogeneous tumor samples using partial reference signals, PLoS Computational Biology, 2020, 16(11): e1008452.
• W Zhang#, Z Li#, N Wei, HJ Wu, X Zheng*, Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities, Bioinformatics, 2020, 36(7):2017-2024.
• T Xu, X Zheng, B Li, P Jin, Z Qin, H Wu*, A comprehensive review of computational prediction of genome-wide features, Briefings in Bioinformatics, 2020, 21(1):120-134.
• X Liu, T Liu, Y Shang, P Dai, W Zhang, BJ Lee, M Huang, D Yang, Q Wu, L Liu, X Zheng, BO Zhou, J Deng, LS Yeap, J Hu, T Xiao, S Zha, R Casellas, XS Liu, FL Meng*, ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells, Cell Research, 2020, 30:732-744.

• D Wei, C Liu, X Zheng*, Y Li*, Comprehensive anticancer drug response prediction based on a simple cell line-drug complex network model, BMC Bioinformatics, 2019, 20:44.
• Hu X, Zhang J, Wang J, Fu J, Li T, Zheng X, Wang B, Gu S, Jiang P, Fan J, Carroll, MC, Wucherpfennig K, Hacohen N, Zhang F, Zhang P, Liu JS*, Li B*, Liu XS*: Widespread B cell clonal expansions and related mechanism of immune evasion in human cancers, Nature Genetics, 2019, 51(3):560-567.

• H Dou, Y Fang, X Zheng*, Universal informative CpG sites for inferring tumor purity from DNA methylation microarray data, Journal of Bioinformatics and Computational Biology, 2018, 16(3):1750030.
• Y Qin, H Feng, M Chen, H Wu, X Zheng*, InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research, Genes & Diseases, 2018, 5:43e45.
• Fan H#, Lv P#, Huo X, Wu J, Wang Q, Cheng L, Liu Y, Tang Q, Zhang L, Zhang F, Zheng X, Wu H, Wen B*, The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes, Genome Research, 2018, 28:192–202.

• X Zheng*, N Zhang, HJ Wu, H Wu*, Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies, Genome Biology, 2017, 18:17.
• X Zheng*, S Zhong, From structure to function, how bioinformatics help to reveal functions of our genomes, Genome Biology, 2017, 18:183.
• Zhang W#, Feng H#, Wu H*, Zheng X*, Accounting for Tumor purity improves cancer subtype lassification from DNA methylation data, Bioinformatics, 2017, 33(17), 2651–2657.
• Niu B, Paulson JN, Zheng X, Koltera R*, Simplified and representative bacterial community of maize roots, Proceedings of the National Academy of Sciences of the United States of America, 2017 114 (12):E2450-E2459.

• Ni T, Li XY, Lu N, An T, Liu ZP, Fu R, Lv WC, Zhang YW, Xu XJ, Grant Rowe R, Lin YS, Scherer A, Feinberg T, Zheng XQ, Chen BA, Liu XS, Guo QL1, Wu ZQ, Weiss SJ*, Snail1-Dependent p53 Repression Regulates Expansion and Activity of Tumor-Initiating Cells in Breast Cancer, Nature Cell Biology, 2016, 18(11):1221-1232.
• X Liu, J Yang, Y Zhang, Y Fang, F Wang, J Wang, X Zheng* J Yang*: A systematic study on drug response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia, Scientific Reports, 2016, 6:22811.
• Y Li, Q Liu, X Zheng*: DUC-Curve, a Highly Compact 2D Graphical Representation of DNA Sequences and Its Application in Sequence Alignment , Physica A, 2016, 456:256-270.
• F Wang, N Zhang, J Wang, H Wu*, X Zheng*: Tumor purity and differential methylation in cancer epigenomics, Briefings in Functional Genomics, 2016, 15(6):408-419.

• N Zhang#, HJ Wu#, W Zhang, J Wang, H Wu*, X Zheng*: Predicting tumor purity from methylation microarray data Bioinformatics, 2015, 31(21):3401–3405.
  • Tumor purity data for TCGA samples with known 450k array by InfiniumPurify
• N Zhang#, H Wang#, Y Fang, J Wang*, X Zheng*, XS Liu*: Predicting anticancer drug responses using a duallayer integrated cell line-drug network model, PLoS Computational Biology, 2015, 11:e1004498.
• H Wang#, X Zheng#, T Fei, J Wang, X Li, Y Liu, F Zhang: Towards pathway-centric cancer therapies via pharmacogenomic profiling analysis of ERK signalling pathway. Clinical and translational medicine 2015, 4(1):1-9.
• Z Dong#, N Zhang#, C Li, H Wang, Y Fang, J Wang, X Zheng*: Anticancer drug sensitivity prediction in cell lines from baseline gene expression through recursive feature selection BMC cancer, 2015,15(1):489.
• Y Qin, M Chen, H Wang, X Zheng*: A Network Flow-Based Method to Predict Anticancer Drug Sensitivity, PloS one 2015, 10(5):e0127380.
• Y Fang, Y Qin, N Zhang, J Wang, H Wang, X Zheng*: DISIS: Prediction of Drug Response through an Iterative Sure Independence Screening PloS one 2015, 10(3):e0120408.

• Zheng X#, Zhao Q#, Wu H-J#, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P*, Zhang Y*, Liu XS*: MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology 2014, 15:419. [Link]
• Li L, Yu S, Xiao W, Li Y, Huang L, Zheng X*, Zhou S*, Yang H*: Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM. BMC bioinformatics 2014, 15:340. [Link]
• Li Y, Liu Q, Zheng X*, He PA: UC‐Curve: A highly compact 2D graphical representation of protein sequences. International Journal of Quantum Chemistry 2014, 114:409-415.
• Li L, Yu S, Xiao W, Li Y, Hu W, Huang L, Zheng X*, Zhou S, Yang H: Protein submitochondria localization from integrated sequence repesentation and SVM-based backward feature extraction. Mol BioSyst 2014.
• Li L, Cui X, Yu S, Zhang Y, Luo Z, Yang H, Zhou Y, Zheng X*: PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations. PloS one 2014, 9:e92863.
• Yu X, Gao H, Zheng X, Li C, Wang J: A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. Computational biology and chemistry 2014, 51:36-41.

• Zhu J, Qin Y, Liu T, Wang J, Zheng X*: Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. BMC bioinformatics 2013, 14:S5.

• Yu X, Zheng X, Meng L, Li C, Wang J: A Support Vector Machine Based Method to Predict Success for Polymerase Chain Reactions. Combinatorial chemistry & high throughput screening 2012, 15:486-491.
• Yu X, Zheng X*, Liu T, Dou Y, Wang J: Predicting subcellular location of apoptosis proteins with pseudo amino acid composition: approach from amino acid substitution matrix and auto covariance transformation. Amino acids 2012, 42:1619-1625.
• Liu T, Geng X, Zheng X*, Li R, Wang J: Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles. Amino acids 2012, 42:2243-2249.
• Li Y, Qin Y, Zheng X*, Zhang Y: Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides. International Journal of Quantum Chemistry 2012, 112:2330-2335.
• Li L, Zhang Y, Zou L, Li C, Yu B, Zheng X*, Zhou Y: An ensemble classifier for eukaryotic protein subcellular location prediction using gene ontology categories and amino acid hydrophobicity. PloS one 2012, 7:e31057.

• Zheng X, Liu T, Yang Z, Wang J: Large cliques in Arabidopsis gene coexpression network and motif discovery. Journal of plant physiology 2011, 168:611-618.
• Yu X, Liu T, Zheng X*, Yang Z, Wang J: Prediction of regulatory interactions in Arabidopsis using gene-expression data and support vector machines. Plant Physiology and Biochemistry 2011, 49:280-283.
• Wang W, Geng X, Dou Y, Liu T, Zheng X*: Predicting protein subcellular localization by pseudo amino acid composition with a segment-weighted and features-combined approach. Protein and peptide letters 2011, 18:480-487.
• Li C, Ma H, Zhou Y, Wang X, Zheng X: Similarity analysis of DNA sequences based on the weighted pseudo‐entropy. Journal of computational chemistry 2011, 32:675-680.
• Dou Y, Geng X, Gao H, Yang J, Zheng X, Wang J: Sequence conservation in the prediction of catalytic sites. The protein journal 2011, 30:229-239.

• Zheng X, Li C, Wang J: An information‐theoretic approach to the prediction of protein structural class. Journal of computational chemistry 2010, 31:1201-1206.
• Liu T, Zheng X*, Wang J: Prediction of protein structural class for low-similarity sequences using support vector machine and PSI-BLAST profile. Biochimie 2010, 92:1330-1334.
• Liu T, Zheng X*, Wang J: Prediction of protein structural class using a complexity-based distance measure. Amino acids 2010, 38:721-728.
• Liu T, Zheng X*, Wang C, Wang J: Prediction of subcellular location of apoptosis proteins using pseudo amino acid composition: an approach from auto covariance transformation. Protein and peptide letters 2010, 17:1263-1269.
• Li C, Li Z, Zheng X, Ma H, Yu X: A generalization of Lempel-Ziv complexity and its application to the comparison of protein sequences. Journal of mathematical chemistry 2010, 48:330-338.
• Dou Y, Zheng X, Yang J, Wang J: Prediction of catalytic residues based on an overlapping amino acid classification. Amino acids 2010, 39:1353-1361.
• Dou Y, Zheng X, Wang J: Several appropriate background distributions for entropy-based protein sequence conservation measures. Journal of theoretical biology 2010, 262:317-322.

• Zheng X, Qin Y, Wang J: A Poisson model of sequence comparison and its application to coronavirus phylogeny. Mathematical biosciences 2009, 217:159-166.
• Zheng X, Liu T, Wang J: A complexity-based method for predicting protein subcellular location. Amino acids 2009, 37:427-433.
• Zheng X, Li C, Wang J: A complexity-based measure and its application to phylogenetic analysis. Journal of mathematical chemistry 2009, 46:1149-1157.
• Zheng X, Dou Y, Wang J: Phylogenetic inference from binary sequences reduced by primary DNA sequences. Journal of mathematical chemistry 2009, 46:1137-1148.
• Li C, Yu X, Yang L, Zheng X, Wang Z: 3-D maps and coupling numbers for protein sequences. Physica A: Statistical Mechanics and its Applications 2009, 388:1967-1972.
• Dou Y, Zheng X, Wang J: Prediction of catalytic residues using the variation of stereochemical properties. The protein journal 2009, 28:29-33.

• Wang J, Zheng X*: Comparison of protein secondary structures based on backbone dihedral angles. Journal of theoretical biology 2008, 250:382-387.
• Wang J, Zheng X*: WSE, a new sequence distance measure based on word frequencies. Mathematical biosciences 2008, 215:78-83.