Dr Xuejun Liu
	Room 228 College of Information Science & Technology Building A12, 29 Yudao Str. Nanjing University of Aeronautics & Astronautics Nanjing, 210016 Phone: +88 (0)25 84896490-12230 E-mail: xuejun.liu@nuaa.edu.cn

Research Interests

• Microarray data analysis
• Gene regulatory network
• Statistics and probabilistics

Teachings

• Programming language I & II (for undergraduates)
• The machining learning approaches in Bioinformatics (for graduates)
  

Graduate Students

• Zhang, Li
• Jin, Shenghua
• Shan, Zhihui
• Zhao, Zhilan
• Xu, Yafeng
  

Publications

• Pearson, R., Liu, X., Sanguinetti, G., Milo, M., Lawrence, N. D. and Rattray, M., puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis, BMC Bioinformatics, 2009 10:211. (featured article, Journal link )
  
• Liu, X., Lin, K. K., Andersen, B. and Rattray, M., Including probe-level uncertainty in model-based gene expression clustering, BMC Bioinformatics, 2007 8:98. (Journal link )
  
• Liu, X., Milo, M., Lawrence, N. D. and Rattray, M., Probe-level measurement error improves accuracy in detecting differential gene expression, Bioinformatics, 2006 22(17): 2107-2113. (Journal link )
  
• Rattray, M., Liu, X., Sanguinetti, G., Milo, M. and Lawrence, N. D., Propagating uncertainty in Microarray data analysis, Briefings in Bioinformatics, 2006 7(1):37-47. (Jounal link)
  
• Liu, X., Milo, M., Lawrence, N. D. and Rattray, M., A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips, Bioinformatics, 2005 21(18):3637-3644. (Jounal link)
  

Software

• pumaclustii: an R package to propagate probe-level measurement error in a robust t-mixture clustering model for replicated gene expression data. (Linux add-on package, Windows add-on package)

• mmgmos: an R package to estimate the expression levels and the confidence of measures for multiple arrays of the same type of Affymetrix GeneChips using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) and the modified gamma Model for Oligonucleotide Signal (mgMOS).

• pplr: an R package to include probe-level measurement error into the variance estimates of gene expression levels and to detect up-regulated genes by calculating probability of positive log-ratio (PPLR).

• pumaclust: an R package to propagate probe-level measurement error in the model-based clustering of gene expression data.