Dawei Huang, Ph.D.
Beijing Institute of Genomics, Chinese Academy of Sciences
NO.1-7 Beichen West Road, Chaoyang District
Email: huangdw(AT)big.ac.cn, daweimhuang(AT)gmail.com
- Ph.D. , Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China (2007-2012).
- B.S. in Agronomy, Collage of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China (2003-2007).
TITLE OF DOCTORAL DISSERTATION:
Molecular Mechanism and Function of Intron Expansion in Vertebrates
Dr. Jun Yu and Dr. Songnian Hu
2009-present: Ph.D. thesis: Molecular Mechanism and Function of Intron Expansion in Vertebrates. Supervised by Professor Jun Yu, the CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China:
My research interest is focused on the evolution of gene structure in animal and plant genomes, including several items such as intron insertion, exon arrangement and UTR expansion, etc. Through comparative genomic studies, we presently got several important conclusions as follows:
- Introns show more frequently inserted into 5’UTR of genes compared to other part of genes, CDS region and 3' UTR, which make a dominant contribution in gene expansion. We constructed a scenario of unbalanced intron expansion and proposed a hypothesis that introns frequently inserted into could be for releasing the transcription-associated mutational pressures.
- Based on the combining analysis between ortholo genes and RNA-seq-based gene expression profiles, we observed that the insertion of introns often occurred in housekeeping (HK) genes, which leads to the significant expansion of HK genes in evolution. Whereas, the size of TS genes show relatively evolutionary conservation. We here proposed introns expansion in HK genes should also be for balancing transcriptional-associated mutational pressures caused by frequently transcribed of HK genes.
- We further concluded that repeat element insertion is a main way of intron expansion. We described the fundamental routes of repeat elements expansion.
- We also described the co-evolution of exon in animal and plant genes for shortening the size to less than 200bp for releasing chromatin-associated mutational pressures.
2007-2010: laboratory rotations: Genome sequencing of Bifidobacterium longum BBMN68. Supervised by Professor Jun Yu and Songnian Hu, the CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China:
- In the laboratory rotations, I assembled and annotated a bacterial (Bifidobacterium longum BBMN68) genome. I firstly finished assembling based on about 80 M reads (average 300 bp in length) from the 1/4 run of Genome Sequencer FLX System form 454 sequencing, and used ABI 3700 reads close gaps. Finally, I got a 2.4M-size complete genome.
- After finishing genomes, I used some bioinformatic softwares (such as ORFHEUS, TRNASCAN, BLASTP AND HEMMER) to annotate the genomes. The genomes contain about 2000 protein-coding genes, 60tRNA and 12 ribosomal RNAs.
2006-2007: B.S. thesis: Molecular identification of a Gene (AvDH1) Encoding DEAD-box Helicase from Apocynum Venetum in transgenic cottons. Supervised by Professor FaFu Shen, Collage of Agronomy, Shandong Agricultural University, Tai’an, China: DNA helicase gene (AvDH1) of Folium Apocynum Venetum was introduced into cotton cultivar (lu613) growing in the field by the pollen tube pathway. The transformants were tested by PCR and PCR-Southern based on kanamycin selection. The results showed that DNA helicase gene of Apocynum Venetum had been integrated into cotton genomes.
- Zhu, J., He, F., Wang, D., Liu, K., Huang, D., Xiao, J., Wu, J., Hu, S. & Yu, J., 2010, A novel role for minimal introns: routing mRNAs to the cytosol, PloS one, 5(4), p. e10144.
- Hao, Y., Huang, D., Guo, H., Xiao, M., An, H., Zhao, L., Zuo, F., Zhang, B., Hu, S., Song, S., Chen, S. & Ren, F., 2011, Complete genome sequence of Bifidobacterium longum subsp. longum BBMN68, a new strain from a healthy Chinese centenarian, Journal of bacteriology, 193(3), pp. 787-8.
- Zhang, G., Pan, L., Yin, Y., Liu, W., Huang, D., Zhang, T., Wang, L., Xin, C., Lin, Q., Sun, G., Ba Abdullah, M.M., Zhang, X., Hu, S., Al-Mssallem, I.S. & Yu, J., 2012, Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.), Plant molecular biology, 79(6), pp. 521-36.
- Al-Mssallem, I.S., Hu, S., Zhang, X., Lin, Q., Liu, W., Tan, J., Yu, X., Liu, J., Pan, L., Zhang, T., Yin, Y., Xin, C., Wu, H., Zhang, G., Ba Abdullah, M.M., Huang, D., Fang, Y., Alnakhli, Y.O., Jia, S., Yin, A., Alhuzimi, E.M., Alsaihati, B.A., Al-Owayyed, S.A., Zhao, D., Zhang, S., Al-Otaibi, N.A., Sun, G., Majrashi, M.A., Li, F., Tala, Wang, J., Yun, Q., Alnassar, N.A., Wang, L., Yang, M., Al-Jelaify, R.F., Liu, K., Gao, S., Chen, K., Alkhaldi, S.R., Liu, G., Zhang, M., Guo, H. & Yu, J., 2013, Genome sequence of the date palm Phoenix dactylifera L, Nature communications, 4, p. 2274.
- Zhang, Z., Sang, J., Ma, L., Wu, G., Wu, H., Huang, D., Zou, D., Liu, S., Li, A., Hao, L., Tian, M., Xu, C., Wang, X., Wu, J., Xiao, J., Dai, L., Chen, L.L., Hu, S. & Yu, J., 2014, RiceWiki: a wiki-based database for community curation of rice genes, Nucleic acids research, 42(Database issue), pp. D1222-8.
- Ma, M., Huang, D. & Zhang, Z., 2014, Heterogeneity of translational selection in human tissues, In preparation.
- Perl script coding, R coding and using other bioinformatics software in UNIX/Mac OS X.
- Bioinformatics analysis: Bioinformatics analysis of EST data and high-throughput sequencing data, genome annotation, comparative genomic analysis and gene interaction network analysis.
- Sequencing technology: Bacteria genome de novel sequencing and assembling via next-generation Sequencing Technology (454 and Solid).
- daweih: https://github.com/daweih
- Cloud CAT: go to http://cat.big.ac.cn for a full functional version.to USE:
- Rice Database: We are current working on a new version of rice database. Click here to see a summary.
- InterMine:to see read more: