Ling-Ling Chen-College of Informatics

Name

Ling-Ling Chen

Sex

Female

Title

Professor

Institute

College of Informatics, Huazhong Agricultural University

address

No. 1 Shizishan street, Hongshan District, Wuhan 430070, China

email

llchen@mail.hzau.edu.cn

Mobile phone

Fax

Research Interest

Bioinformatics, Plant genome and transcriptome analysis, System biology, NGS data analysis

Academic activities

Editor of Current Bioinformatics and JAEB

Education and research experience

Education

1991.9－1995.7 Institute of Qingdao Chemical Engineering Chemical Engineering, Bachelor

1996.9－1999.6 Institute of Qingdao Chemical Engineering Chemical Engineering, Master

2001.9－2004.6 Tianjin University Biophysics, PhD

Working Experience

1995.8-1996.8 Binzhou Dyeing Group Co., Ltd., Shandong, China

1999.8-2008.12 School of Life Sciences, Shandong University of Technology, Shandong, China

2008.12-2014.6 College of Life Science and Technology, Huazhong Agricultural University, Professor

2009.1-Present College of Informatics, Huazhong Agricultural University, Professor

Grants

§ 2019.01-2022.12 National Natural Science Foundation of China (31871269) 2018.07-2022.12 National Key Research and Development Program of China
(2016YFD0100904)

§ 2016.08-2020.12 National Key Research and Development Program of China
(2016YFD0100904)

§ 2016.01-2019.12 National Natural Science Foundation of China (31571351)

§ 2015.01-2017.12 National Science Foundation of Hubei Province (2015CFA044)

§ 2014.01-2016.12 New Century Excellent Talents in University (NCET-13-0807)

§ 2013.01-2016.12 National Natural Science Foundation of China (31271406)

§ 2012.01-2015.12 National High Technology Research and Development
Program (2012AA10A304)

§ 2011.01-2013.12 National Natural Science Foundation of China (31071659)

Representative publications（*for corresponding authors, # for first authors）

1. Song JM, Guan Z, Hu J,……, Liu K^*, Yang Q^*, ChenLL^*, Guo L^*. Eight high-quality reference genomes provide insights into pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants. accepted.

2. Sturtevant D, Lu S, Zhou ZW, Shen Y,……, ChenLL^*, ChapmanKD^*, Guo L^*. The genome of jojoba (Simmondsia chinensis): a taxonomically-isolated species that directs wax-ester accumulation in its seeds. Science Advances. accepted.

3. Tahir Ul Qamar M, Zhu X, Xing F, Chen LL*. ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline. Bioinformatics. 2019, 35(20): 4156-4158.

4. Chang JW, Ding Y, Tahir Ul Qamar M, Shen Y, Gao J*, Chen LL*. A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations. Carcinogenesis. 2019, pii: bgz044. doi: 10.1093/carcin/bgz044.

5. Feng JW, Huang S, Guo YX, Liu D, Song JM, Gao J, Li H*, Chen LL*. Plant ISOform sequencing database (PISO): a comprehensive repertory of full-length transcripts in plants. Plant Biotechnol J. 2019, 17(6): 1001-1003.

6. Sun J, Liu H, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu HJ*, Chen LL*. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics. 2019, 35(14): 2501-2503.

7. Song JM, Lei Y, Shu CC, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J, Chen LL*. Rice Information GateWay: a comprehensive boinformatics platform for indica rice genomes. Mol. Plant, 2018, 11(3):505-507.

8. Yang N, Xu XW, Wang RR, Peng WL, Cai L, Song JM, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, Pan Q, Liu F, Jackson D, Yang X, Chen LL*, Yan J*. Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nat. Commun., 2017, 8(1):1874.

9. Liu H, Ding Y, Zhou Y, Jin W, Xie K*, Chen LL*. CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants. Mol. Plant, 2017, 10: 530-532.

10. Zhang J^#, Chen LL^#, Xing F^#, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc. Natl. Acad. Sci. USA, 2016, 113: E5163-71.

11. Wang C, Deng ZL, Xie ZM, Chu XY, Chang JW, Kong DX, Li BJ, Zhang HY, Chen LL*. Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery. FEBS Lett., 2015, 589: 285-294.

12. Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y*, Chen LL*, Chen M*. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res., 2014, 42: 3028-43.

13. Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL*. CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants. Mol. Plant, 2014, 7(9): 1494-1496.

14. Xu Q,^#, Chen LL^#, Ruan X^#, et al. The draft genome of sweet orange (Citrus sinensis). Nat. Genetics, 2013, 45: 59-66.

15. Jiao WB, Huang D, Xing F, HuY, Deng XX, Xu Q*, Chen LL*. Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant J., 2013, 75: 954-964.

16. Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL*, Chen M*. PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res., 2012, 40: D1187-1193.

Basic Information
Name	Ling-Ling Chen		Sex	Female		Title	Professor
Institute		College of Informatics, Huazhong Agricultural University
address		No. 1 Shizishan street, Hongshan District, Wuhan 430070, China
email		llchen@mail.hzau.edu.cn
Mobile phone					Fax
Research Interest
Bioinformatics, Plant genome and transcriptome analysis, System biology, NGS data analysis
Academic activities
Editor of Current Bioinformatics and JAEB
Education and research experience
Education 1991.9－1995.7 Institute of Qingdao Chemical Engineering Chemical Engineering, Bachelor 1996.9－1999.6 Institute of Qingdao Chemical Engineering Chemical Engineering, Master 2001.9－2004.6 Tianjin University Biophysics, PhD Working Experience 1995.8-1996.8 Binzhou Dyeing Group Co., Ltd., Shandong, China 1999.8-2008.12 School of Life Sciences, Shandong University of Technology, Shandong, China 2008.12-2014.6 College of Life Science and Technology, Huazhong Agricultural University, Professor 2009.1-Present College of Informatics, Huazhong Agricultural University, Professor
Grants
§ 2019.01-2022.12 National Natural Science Foundation of China (31871269) 2018.07-2022.12 National Key Research and Development Program of China (2016YFD0100904) § 2016.08-2020.12 National Key Research and Development Program of China (2016YFD0100904) § 2016.01-2019.12 National Natural Science Foundation of China (31571351) § 2015.01-2017.12 National Science Foundation of Hubei Province (2015CFA044) § 2014.01-2016.12 New Century Excellent Talents in University (NCET-13-0807) § 2013.01-2016.12 National Natural Science Foundation of China (31271406) § 2012.01-2015.12 National High Technology Research and Development Program (2012AA10A304) § 2011.01-2013.12 National Natural Science Foundation of China (31071659)
Representative publications（*for corresponding authors, # for first authors）
1. Song JM, Guan Z, Hu J,……, Liu K^, Yang Q^, ChenLL^, Guo L^. Eight high-quality reference genomes provide insights into pan-genome architecture and ecotype differentiation of Brassica napus. *Nature Plants. accepted. 2. Sturtevant D, Lu S, Zhou ZW, Shen Y,……, ChenLL^, ChapmanKD^, Guo L^. The genome of jojoba (Simmondsia chinensis): a taxonomically-isolated species that directs wax-ester accumulation in its seeds. *Science Advances. accepted. 3. Tahir Ul Qamar M, Zhu X, Xing F, Chen LL. ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline. Bioinformatics*. 2019, 35(20): 4156-4158. 4. Chang JW, Ding Y, Tahir Ul Qamar M, Shen Y, Gao J, *Chen LL. A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations. Carcinogenesis*. 2019, pii: bgz044. doi: 10.1093/carcin/bgz044. 5. Feng JW, Huang S, Guo YX, Liu D, Song JM, Gao J, Li H, Chen LL. Plant ISOform sequencing database (PISO): a comprehensive repertory of full-length transcripts in plants. Plant Biotechnol J. 2019, 17(6): 1001-1003. 6. Sun J, Liu H, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu HJ, Chen LL. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics. 2019, 35(14): 2501-2503. 7. Song JM, Lei Y, Shu CC, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J, Chen* LL. Rice Information GateWay: a comprehensive boinformatics platform for indica rice genomes. Mol. Plant, 2018, 11(3):505-507. 8. Yang N, Xu XW, Wang RR, Peng WL, Cai L, Song JM, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, Pan Q, Liu F, Jackson D, Yang X, Chen LL*, Yan J. Contributions of Zea mays subspecies mexicana haplotypes to modern maize. *Nat. Commun., 2017, 8(1):1874. 9. Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL. CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants. Mol. Plant, 2017, 10: 530-532. 10. Zhang J^#, Chen LL^#, Xing F^#, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc. Natl. Acad. Sci. USA, 2016, 113: E5163-71. 11. Wang C, Deng ZL, Xie ZM, Chu XY, Chang JW, Kong DX, Li BJ, Zhang HY, Chen LL. Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery. *FEBS Lett., 2015, 589: 285-294. 12. Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y, Chen LL, Chen M. Dissecting the chromatin interactome of microRNA genes. *Nucleic Acids Res., 2014, 42: 3028-43. 13. Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants. Mol. Plant, 2014, 7(9): 1494-1496. 14. Xu Q,^#, Chen LL*^#, Ruan X^#, et al. The draft genome of sweet orange (Citrus sinensis). Nat. Genetics, 2013, 45: 59-66. 15. Jiao WB, Huang D, Xing F, HuY, Deng XX, Xu Q, Chen LL. Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant J., 2013, 75: 954-964. 16. Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL*, Chen M. PlantNATsDB: a comprehensive database of plant natural antisense transcripts. *Nucleic Acids Res.*, 2012, 40: D1187-1193.