Room 228 College of Computer 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
Liu, X., Gao, Z., Zhang, L. and Rattray, M.,
puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis,
BMC Bioinformatics,
2013 14:39. (Journal link )
Yan, G., Liu, X. and Lu, H.,
Fast airfoil design based on multi-output Gaussian process regression,
the 5nd Chinese Society of Aeronautics and Astronautics (CSAA) Science and Technique Youth Forum,
7-10 October 2012, Nanchang, China.(In Chinese)
Zhao, Z., Liu, X. and Zhang, L.,
A probabilsitic model for the analysis of RNA-Seq data,
CBME'2011,
30 Oct - 1 Nov 2011, Wuhan, China. (Third youth paper award, in Chinese)
Gao, Z., Liu, X., Zhang, L. and Rattray, M.,
A probabilistic model for probe-level analysis of Affymeterix exon arrays,
CBME'2011,
30 Oct - 1 Nov 2011, Wuhan, China. (in Chinese)
Xu, Y., Liu, X. and Lu, H.,
Fast airfoil design based on CST parameterization,
Aeronautical Computing Technique,
2011, 41(5): 25-33.(in Chinese)
Liu, X. and Rattray, M.,
Including probe-level measurement error in robust mixture clustering of replicated microarray gene expression,
Statistical Applications in Genetics and Molecular Biology:
2010 Vol. 9 : Iss. 1, Article 42.
(Journal
link )
Jin, S., Liu, X. and Zhang, L.,
The application of noise characteristics of primary Affymetrix GeneChip data,
Chinese Society of Biomedical Engineering (CSBME) Annual Meeting,
2-4 December 2010, Beijing, China. (Best youth paper award, in Chinese)
Shan, Z., Liu, X. and Lu, H.,
Gaussian process regression for fast evaluation of airfoil aerodynamic performance,
the 4nd Chinese Society of Aeronautics and Astronautics (CSAA) Science and Technique Youth Forum,
25-26 November 2010, Beijing, China.(In Chinese)
Zhang, L. and Liu, X.,
An improved probabilistic model for finding differential gene expression,
the 2nd International Conference on BioMedical Engineering and Informatics,
17-19 October 2009, Tianjin, China.(Download )
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.
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.
The above packages have been integrated in a large package puma
which is released by BioConductor.