Zhang Y (2011) A Novel Bayesian Graphical Model for Genome-Wide Multi-SNP Association Mapping. Genet Epi, 36:36-37.
Software: BEAM3
Zhang Y, Zhang J, Liu JS (2011) Block-based Bayesian epistasis association mapping with application to WTCCC type 1 diabetes data. Ann Appl Stat, 5:2052-2077.
Software: BEAM2
Zhang Y and Liu JS (2011) Fast and accurate approximation to significance tests in genome-wide association studies. J Am Stat Assoc, 106:846-857.
Software: GPASS
Zhang Y (2011) Bayesian epistasis association mapping via SNP imputation, Biostatistics, 12:211-222.
Software: BEAMimpute
Chen KB and Zhang Y (2010) A varying threshold method for ChIP peak-calling using multiple sources of information, Bioinformatics, 26:i504-i510.
Software: PASS2 (32bit) (64bit) (Source)
Zhang Y, Song GT, Vinar T, Green ED, Siepel A, Miller W (2009) Evolutionary
history reconstruction for mammalian complex gene clusters, J Comp Biol, 16:1-20.
Zhang Y (2008) Poisson approximation for significance in genome-wide ChIP-chip tiling arrays, Bioinformatics.
Software: PASS
Zhang Y, Song GT, Vinar T, Green ED, Siepel A, Miller W (2008) Reconstructing the evolutionary history of complex human gene clusters. RECOMB08.
Zhang Y (2008) Tree-guided Bayesian inference of population structures. Bioinformatics 24:965-971.
Software: TIPS
Zhang Y, Liu J (2007) Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39:1167-1173.
Software: BEAM   source
Zhang Y, Niu T, Liu J (2006) A coalescence-guided hierarchical Bayesian method for haplotype inference. Am J Hum Genet 79:313-322.
Software: CHB
Valouev A*, Zhang Y*, Schwartz DC, Waterman MS (2006) Refinement of optical map assemblies. Bioinformatics 22:1217-1224.
(* equal contribution).
Zhang Y, Waterman MS (2005) An Eulerian path approach to local multiple alignment for DNA sequences. PNAS 102:1285-1290.
Software: EulerAlign