Dapeng Wang: Difference between revisions
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*Dapeng Wang | *Dapeng Wang | ||
* | *Department of Plant Sciences, University of Oxford | ||
*Address: | *Address: S Parks Rd, Oxford OX1 3RB | ||
*Email: wangdp123@gmail.com | *Email: wangdp123@gmail.com | ||
==Position== | ==Position== | ||
* Mar. 2014- | * 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 | * 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 | * Jul. 2011-Dec. 2013, Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences | ||
Line 14: | Line 15: | ||
==Education== | ==Education== | ||
<!--Include info about your educational background--> | <!--Include info about your educational background--> | ||
* Sep. 2006-Jul. 2011, PhD, Genomics and Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences | * 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 | * Sep. 2002-Jul. 2006, BS, Information and Computing Science, School of Mathematics and System Sciences, Shandong University | ||
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<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed --> | <!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed --> | ||
== | ==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. [http://www.ncbi.nlm.nih.gov/pubmed/26697753 PMID: 26697753] | |||
* 2015 | * 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. [http://www.ncbi.nlm.nih.gov/pubmed/26376976 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. [http://www.ncbi.nlm.nih.gov/pubmed/26258441 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. [http://www.ncbi.nlm.nih.gov/pubmed/25378306 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. [http://www.ncbi.nlm.nih.gov/pubmed/26051941 PMID: 26051941] | |||
* 2013 | * 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. [http://www.ncbi.nlm.nih.gov/pubmed/24205343 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. [http://www.ncbi.nlm.nih.gov/pubmed/23451178 PMID: 23451178] '''Highlighted in [http://www.genomeweb.com/blog/week-plos-227 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. [http://www.ncbi.nlm.nih.gov/pubmed/23193278 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. [http://www.ncbi.nlm.nih.gov/pubmed/23955844 PMID: 23955844] | |||
* 2012 | * 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. [http://www.ncbi.nlm.nih.gov/pubmed/22807622 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. [http://www.ncbi.nlm.nih.gov/pubmed/22267903 PMID: 22267903] | |||
* 2011 | * 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. [http://www.ncbi.nlm.nih.gov/pubmed/21437290 PMID: 21437290] '''Highlighted in [http://www.genomeweb.com/blog/week-plos-129 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. [http://www.ncbi.nlm.nih.gov/pubmed/21342519 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. [http://www.ncbi.nlm.nih.gov/pubmed/21219437 PMID: 21219437] | |||
* 2010 | * 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. [http://www.ncbi.nlm.nih.gov/pubmed/20403773 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. [http://www.ncbi.nlm.nih.gov/pubmed/20451164 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. [http://www.ncbi.nlm.nih.gov/pubmed/20419085 PMID: 20419085] | |||
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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. [http://www.ncbi.nlm.nih.gov/pubmed/19531225 PMID: 19531225] | 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. [http://www.ncbi.nlm.nih.gov/pubmed/19531225 PMID: 19531225] | ||
==Tools and Databases== | ==Tools and Databases== |
Latest revision as of 14:00, 11 April 2016
Contact Info
- 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