Yupeng Wang, Liang Liang, Bucong Han, Yu Quan, Xiao Wang, Tao Tao, Zhiliang Ji. (2006) GEPS: The Gene Expression Pattern Scanner. Nucleic Acids Res, 34: W492-W497.
 P. Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, and Y. Z. Chen. (2009) Update of KDBI: Kinetic Data of Bio-molecular Interaction database. Nucleic Acids Res, 37: D636-D641.
 Yupeng Wang and Romdhane Rekaya. (2009) A comprehensive analysis of gene expression evolution between humans and mice. Evol Bioinform Online, 5: 81-90.
 Wensheng Zhang, Kelly Robbins, Yupeng Wang , Keith Bertrand and Romdhane Rekaya. (2010) A jackknife-like method for classification and uncertainty assessment of multi-category tumor samples using gene expression information. BMC Genomics, 11: 273.
 Yupeng Wang, Xinyu Liu, Kelly Robbins and Romdhane Rekaya. (2010) AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. BMC Res Notes, 3: 117.
 Yupeng Wang and Romdhane Rekaya. (2010) LSOSS: detection of cancer outlier differential gene expression. Biomark Insights, 5:69-78.
 Yupeng Wang, Kelly Robbins and Romdhane Rekaya. (2010) Comparison of computational models for assessing conservation of gene expression across species. PLoS One, 5: e13239.
 Yupeng Wang, Xiyin Wang, Haibao Tang, Xu Tan, Stephen Ficklin, Alex Feltus and Andrew Paterson. (2011) Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One, 6: e28150.
 The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet, 43: 1035-1039.
 Yupeng Wang, Sandeep Joseph, Xinyu Liu, Michael Kelley and Romdhane Rekaya. (2012) SNPxGE2: a database for human SNP-coexpression associations. Bioinformatics, 28: 403-410.
 Yupeng Wang, Xiyin Wang and Andrew Paterson. (2012) Genome and gene duplications and gene expression divergence: a view from plants. Ann NY Acad Sci, 1256: 1-14.
 Yupeng Wang, Haibao Tang, Jeremy DeBarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo, Jessica Kissinger and Andrew Paterson. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40: e49.
 Xinyu Liu, Yupeng Wang, Romdhane Rekaya and T.N. Sriram. (2012) Sample size determination for classifiers based on single nucleotide polymorphisms. Biostatistics, 13: 217-227.
 Tomato Genome Consortium. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485: 635-641.
 Yupeng Wang, Xiyin Wang, Tae-Ho Lee, Shabid Mansoor and Andrew Paterson. (2013) Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice). New Phytologist, 198: 274-283.
 Yupeng Wang. (2013) Divergence between whole-genome duplication-derived duplicated genes can be enhanced by their local duplications in Arabidopsis and rice. Genome Biol Evol, 5: 362-369.
 Yupeng Wang, Jingping Li and Andrew Paterson. (2013) MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics, doi: 10.1093/bioinformatics/btt150.
 Yupeng Wang, Stephen Ficklin, Xiyin Wang, Alex Feltus and Andrew Paterson. Evolution of dispersed duplicated genes in Arabidopsis. Submitted.
 Xinyu Liu, Yupeng Wang and T.N. Sriram. Sample size determination for multi-class SNP classifier by a VUS-based approach. Submitted.
 Yupeng Wang, Xu Tan and Andrew Paterson. Transposed gene duplications are associated with dramatic and biased changes in gene structure in Arabidopsis. To be submitted.
 Shengyi Liu, …, Yupeng Wang, …. The genome evolution underlying speciation revealed in Brassica oleracea and B. rapa. Submitted.