Dapeng Wang

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Contact Info

Dapeng Wang (an artistic interpretation)
  • Dapeng Wang
  • Department of Plant Sciences, University of Oxford
  • Address: S Parks Rd, Oxford OX1 3RB
  • Email: wangdp123@gmail.com

Position

  • Feb. 2016-Present, Postdoctoral Research Assistant, Department of Plant Sciences, University of Oxford, Oxford, UK (With Prof. John Mackay)
  • Mar. 2014-Jan. 2016, Research Associate, UCL Cancer Institute, University College London (With Prof. Enver Tariq and Dr. Javier Herrero)
  • Jan. 2014-Feb. 2014, Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences
  • Jul. 2011-Dec. 2013, Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences

Education

  • Sep. 2006-Jul. 2011, PhD, Genomics and Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences (With Prof. Jun Yu)
  • Sep. 2002-Jul. 2006, BS, Information and Computing Science, School of Mathematics and System Sciences, Shandong University

Research interests

  • Next generation sequencing
  • Molecular evolution
  • Bioinformatics
  • Database
  • Software


Publications

first/co-first author(#) and/or corresponding/co-corresponding author(*)

  • Under review or in preparation

22. Charlotta Böiers, Simon E. Richardson, Alya Zriwil, Virginia Turati, John Brown, Dapeng Wang, Javier Herrero, Stefan Karlsson, Andrew J. H. Smith, Sten Erik W Jacobsen and Tariq Enver. ETV6-RUNX1 Targets a Developmentally Restricted Embryonic Human B-myeloid Progenitor. In preparation.

21. Dapeng Wang*. ChIPwrapper: A highly-efficient wrapper for handling massive ChIP-Seq samples. In preparation.

20. Dapeng Wang*. hppRNA: A handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Under review.


  • 2016

19. Dapeng Wang*. DLGP: A database for lineage-conserved and lineage-specific gene pairs in animal and plant genomes. Biochemical and Biophysical Research Communications 469 (2016) 542-545. PMID: 26697753


  • 2015

18. Dapeng Wang*, Jiayue Xu and Jun Yu. KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation. Biology Direct 2015, 10:53. PMID: 26376976

17. Dapeng Wang* and Jun Yu. LCGserver: a webserver for exploring evolutionary trajectory of gene orders in a large number of genomes. OMICS: A Journal of Integrative Biology. 2015 Sep;19(9):574-7. PMID: 26258441

16. Dapeng Wang* and Jun Yu. Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Research. 2015 Jan;43(Database issue):D990-5. PMID: 25378306

15. Cristina Pina, Jose Teles, Cristina Fugazza, Gill May, Dapeng Wang, Yanping Guo, Shamit Soneji, John Brown, Patrik Eden, Mattias Ohlsson, Carsten Peterson and Tariq Enver. Single-cell network analysis identifies ddit3 as a nodal lineage regulator in hematopoiesis. Cell Reports 2015 Jun 16;11(10):1503-10. PMID: 26051941


  • 2013

14. Bin Xie, Dapeng Wang#, Yong Duan, Jun Yu, and Hongxing Lei. Functional networking of human divergently paired genes. PLoS ONE. 2013, 8(10): e78896. PMID: 24205343

13. Yunbo Li, Dapeng Wang#, Lei Wang, Jinhai Yu, Danhua Du, Ye Chen, Peng Gao, Duen-Mei Wang, Jun Yu, Feng Zhang, and Shuanglin Fu. Distinct genomic aberrations between low-grade and high-grade gliomas of Chinese patients. PLoS ONE. 2013, 8(2): e57168. PMID: 23451178 Highlighted in GenomeWeb Daily Scan

12. Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou and Jun Yu. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Research. 2013; 41: D1199-D1205. PMID: 23193278

11. Lei Wang, Xiaowei Zhang, Linlin Pan, Wanfei Liu, Dapeng Wang, Guangyu Zhang, Yuxin Yin, An Yin, ShangangJia, Xiaoguang Yu, Gaoyuan Sun, Songnian Hu, Ibrahim S. Al-Mssallem, and Jun Yu. A Large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae). Insect Science 2013, 20: 689–702. PMID: 23955844


  • 2012

10. Dapeng Wang, Yao Su, Xumin Wang, Hongxing Lei and Jun Yu. Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion. Evolutionary Bioinformatics 2012:8 301-319. PMID: 22807622

9. Dapeng Wang, Yubin Zhang, Zhonghua Fan, Guiming Liu and Jun Yu. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. Evolutionary Bioinformatics 2012:8 39-46. PMID: 22267903


  • 2011

8. Dapeng Wang and Jun Yu. Both size and GC-content of minimal introns are selected in human populations. PLoS ONE 2011, 6(3): e17945. PMID: 21437290 Highlighted in GenomeWeb Daily Scan

7. Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu. Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biology Direct 2011, 6:13. PMID: 21342519

6. Yan-Hui Zhao, Da-Peng Wang#, Li-Li Zhang, Feng Zhang, Duen-Mei Wang and Wei-Yuan Zhang. Genomic expression profiles of blood and placenta reveal significant immune-related pathways and categories in Chinese women with gestational diabetes mellitus. Diabetic Medicine 2011, 28: 237–246. PMID: 21219437


  • 2010

5. Feng Liu, Dapeng Wang#, Jianjun Fu, Gaoyuan Sun, Yubang Shen, Lingli Dong, Bing Zhang, Songnian Hu, and Jiale Li. Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 2010, 5(2):116-23. PMID: 20403773

4. Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, and Jun Yu. KaKs Calculator 2.0: a toolkit of incorperating gamma methods and sliding window strategies. Genomics Proteomics & Bioinformatics 2010, 8(1): 77-80. PMID: 20451164

3. Jiang Zhu, Fuhong He, Dapeng Wang, Kan Liu, Dawei Huang, Jingfa Xiao, Jiayan Wu, Songnian Hu, and Jun Yu. A novel role for minimal introns: routing mRNAs to the cytosol. PLoS ONE 2010, 5(4): e10144. PMID: 20419085


  • 2009

2. Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, and Jun Yu. How do variable substitution rates influence the calculations of Ka and Ks? Genomics Proteomics & Bioinformatics 2009, 7(3): 116-127. PMID: 19944384

1. Da-Peng Wang, Hao-Lei Wan, Song Zhang, and Jun Yu. Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biology Direct 2009, 4:20. PMID: 19531225

Tools and Databases

  1. LCGserver
  2. DLGP
  3. plastid-LCGbase
  4. KGCAK
  5. RGKbase
  6. KaKs_Calculator 2.0

Useful links