With the rapid development of high-throughput sequencing technology, the avalanche of genomic data is coming towards us. How to mine biological knowledge from these massive data has become a pressing problem in bioinformatics. Based on high-throughput sequencing data, we employed bioinformatics, genomics, and molecular biology techniques to decode gene information, identify genomic dark matters, and discover the mechanism of regulation of gene expression.
We utilized next- and third-generation sequencing technologies to assemble complement animal and plant genomes, annotate complete gene information, and characterize gene expression profiles. We also identify non-coding RNAs and translatable non-coding RNAs from genomes, and explore the mechanisms by which these genomic dark matters regulate gene expression. In addition, we integrate multi-omics data to construct bioinformatics database, and develop pipeline and software to process high-throughput sequencing data.
Our research group employed high-throughput sequencing and multi-omics technologies to decode genomes
De novo assembly of genome, identification of gene variation, and genome-wide association study
Characterization of gene expression profile, identification of differentially expressed genes and alternative splicing
Estimation of genome-wide DNA methylation level and detection of differentially methylated regions
Understanding of protein expression abundance and identification of translated non-coding RNAs
Lianming Du, Qin Liu, Zhenxin Fan, Jie Tang, Xiuyue Zhang, Megan Price, Bisong Yue, Kelei Zhao. Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files. Briefings in Bioinformatics, 2021, 22(4)
Lianming Du, Qin Liu, Kelei Zhao, Jie Tang, Xiuyue Zhang, Bisong Yue, Zhenxin Fan. PSMD: An extensive database for pan-species microsatellite investigation and marker development. Molecular Ecology Resources, 2020, 20(1):283-291.
Lianming Du, Tao Guo, Qin Liu, Jing Li, Xiuyue Zhang, Jinchuan Xing, Bisong Yue, Jing Li, Zhenxin Fan. MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques. Database, 2020, 2020:baaa027.
Kelei Zhao, Ting Huang, Jiafu Lin, Chaochao Yan, Lianming Du, Tao Song, Jing Li, Yidong Guo, Yiwen Chu, Junfeng Deng, Xinrong Wang, Chaolan Liu, Yingshun Zhou. Genetic and Functional Diversity of Pseudomonas aeruginosa in Patients With Chronic Obstructive Pulmonary Disease. Frontiers in Microbiology, 2020, 11:598478.
Lianming Du, Qin Liu, Fujun Shen, Zhenxin Fan, Rong Hou, Bisong Yue, Xiuyue Zhang. Transcriptome analysis reveals immune-related gene expression changes with age in giant panda (Ailuropoda melanoleuca) blood. Aging, 2019, 11(1):249-262.