01) Long Non-Coding RNAs and Complex Human Diseases, Int. J. Mol. Sci., 2013. ( invited review, corresponding author )
02) Systematic study of human long intergenic non-coding RNAs and their impact on cancer, Sci China Life Sci., 2013.
03) NONCODE v3.0: integrative annotation of long noncoding RNAs, Nucleic Acids Research, 2012.
04) CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing, Protein Cell, 2012. 05) ncFANs: a web server for functional annotation of long non-coding RNAs, Nucleic Acids Research, 2011. ( corresponding author ) 06) Large-scale prediction of long non-coding RNA functions in a coding non-coding gene co-expression network, Nucleic Acids Research, 2011. ( co-first author )
07) Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system, PLoS One, 2011.
08) dbDEMC: a database of differentially expressed miRNAs in human cancers, BMC Genomics InCoB2010 Supplement Issue, 2010.
09) Lex-SVM: exploring the potential of exon profiling for disease classification, CSB 2010. 10) Exploring hierarchical and overlapping modular structure in the yeast protein interaction network, BMC Genomics InCoB2010 Supplement Issue, 2010. (first author, corresponding author )
11) Postoperative adjuvant antiviral therapy for hepatitis B/C virus-related hepatocellular carcinoma: A meta-analysis, World J Gastroenterol., 2010. 12) Clustered microRNAs' coordination in regulating protein-protein interaction network, BMC Systems Biology, 2009. (co-first author) 13) MicroRNA-encoding long non-coding RNAs, BMC Genomics, 2008. (co-first author) 14) MicroRNA regulation of messenger-like non-coding RNAs -- a network of mutual microRNA control, Trends in Genetics, 2008. (co-first author)
15) Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass Spectra, Journal of Proteome Research, 2008. 16) NONCODE v2.0: decoding the non-coding, Nucleic Acids Research, 2008. (co-first author)
17) antiCODE: a natural sense-antisense transcripts database, BMC Bioinformatics, 2007. 18) Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors, PLoS Computational Biology, 2006. (co-first author)
19) The DNA sequence, annotation and analysis of human chromosome 3, Nature, 2006.
20) NPInter: the Noncoding RNAs and Protein related bio- macromolecules Interaction database, Nucleic Acids Research, 2006.
21) Integrated analysis of multiple data sources reveals modular structure of biological networks, Biochemical and Biophysical Research Communications, 2006.
22) HPtaa database - potential target genes for clinical diagnosis and immunotherapy of human carcinoma, Nucleic Acids Research, 2006.
23) Identifying Hfq-binding small RNA targets in Escherichia coli, Biochemical and Biophysical Research Communications, 2006.
24) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression, Genome Research, 2006. 25) NONCODE: an integrated knowledge database of non-coding RNAs, Nucleic Acids Research, 2005. (first author)