Jingchu Luo

Jingchu Luo is a professor at the College for Life Sciences, Peking University. He is the China node manager of the European Molecular Biology Network (EMBnet). He spent one and half year at the University of Maryland as a visiting scholar in 1987-1989, and carried out part time collaborative research at the Cancer Research UK during 1991-1999. Together with the Late Professor Xiaocheng Gu, he started the Center for Bioinformatics (CBI) at Peking University in 1997. His main research focus is comparative plant genomics, tran1111ional regulation in plants, development of bioinformatics platforms and construction of bioinformatics databases. He is the editorial member of BMC Bioinformatics and Briefings of Bioinformatics. He was invited to give lectures at dozens international and domestic bioinformatics conferences, and is a program committee member of several international bioinformatics conferences. He has been running the Applied Bioinformatics Course (ABC) and organized several international and national workshops and training courses during the past 15 years. [Chinese]

Research

Development of the genome browse framework- ABrowse

Development of the rice genome database - RiceMap

Development of the bioinformatics platform - WebLab

Development of the Database of Plant Tran1111ion Factors - PlantTFDB

Development of the Database of Plant Leave Senescence - LSD

Investigation of genome duplication in plants

Investigation of the origion and evolution of seed related genes

Investigation of the zebrafish genome DNA methylation

Selected Publications (Full list collected in PubMed)

Jin J, Zhang H, Kong L, Gao G, Luo J. (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant tran1111ion factors. Nucleic Acids Res. 42:D1182-7. [PDF]

Li Z, Zhao Y, Liu X, Peng J, Guo H, Luo J. (2014) LSD 2.0: an update of the leaf senescence database. Nucleic Acids Res. 42:D1103-7. [PDF]

Luo J, Nijveen H, Attwood T, Judge D, Pongor S, Landsman D, Bishop M. (2013) Obituary: In memory of Jack Leunissen. Brief Bioinform. 14:261-2. [PDF]

Luo J. (2013) Teaching the ABCs of Bioinformatics: a brief introduction to the Applied Bioinformatics Course. Brief Bioinform. (in press) [PDF]

Wang J, Kong L, Gao G, Luo J. (2013) A brief introduction to web-based genome browsers. Brief Bioinform. 14:131-43. [PDF]

Kong L, Wang J, Zhao S, Gu X, Luo J, Gao G. (2012) ABrowse--a customizable next-generation genome browser framework. BMC Bioinformatics. 13:2.[PDF]

Wang J, Kong L, Zhao S, Zhang H, Tang L, Li Z, Gu X, Luo J, Gao G. (2011) Rice-Map: a new-generation rice genome browser. BMC Genomics. 12:165. [PDF]

Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant tran1111ion factor database. Nucleic Acids Res. 39:D1114-7. [PDF]

Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, Guo H, Luo J. (2011) LSD: a leaf senescence database. Nucleic Acids Res. 39:D1103-7.[PDF]

He K, Guo AY, Gao G, Zhu QH, Liu XC, Zhang H, Chen X, Gu X, Luo J. (2010) Computational identification of plant tran1111ion factors and the construction of the PlantTFDB database. Methods Mol Biol. 674:351-68. [PDF]

He K, Li X, Zhou J, Deng XW, Zhao H, Luo J. (2009) NTAP: for NimbleGen tiling array ChIP-chip data analysis. Bioinformatics. 25:1838-40. [PDF]

Liu X, Wu J, Wang J, Liu X, Zhao S, Li Z, Kong L, Gu X, Luo J, Gao G. (2009) WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Res. 37:W33-9. [PDF]

Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J. (2009) Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics. 10(Suppl 6):S8. [PDF]

Guo AY, Zhu QH, Gu X, Ge S, Yang J, Luo J. (2008) Genome-wide identification and evolutionary analysis of the plant specific SBP-box tran1111ion factor family. Gene. 418:1-8. [PDF]

Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. (2008) PlantTFDB: a comprehensive plant tran1111ion factor database. Nucleic Acids Res. 36:D966-9. [PDF]

Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang M, Luo J. (2007) DPTF: a database of poplar tran1111ion factors. Bioinformatics. 23:1307-8. [PDF]

Sun Y, Zhao S, Yu H, Gao G, Luo J. (2007) ABCGrid: Application for Bioinformatics Computing Grid. Bioinformatics. 23:1175-7. [PDF]

Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J. (2006) Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics. 7:447. [PDF]

Shi X, Wang X, Li Z, Zhu Q, Tang W, Ge S, Luo J. (2006) Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene. 376:199-206. [PDF]

Wu J, Mao X, Cai T, Luo J, Wei L. (2006) KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res. 34:W720-4. [PDF]

Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. (2006) DRTF: a database of rice tran1111ion factors. Bioinformatics. 22:1286-7. [PDF]

Wu X, Walker MG, Luo J, Wei L. (2005) GBA server: EST-based digital gene expression profiling. Nucleic Acids Res. 33:W673-6. [PDF]

Wang X, Shi X, Hao B, Ge S, Luo J. (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165:937-46. [PDF]

Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J. (2005) SPD--a web-based secreted protein database. Nucleic Acids Res. 33:D169-73. [PDF]

Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J. (2005) DATF: a database of Arabidopsis tran1111ion factors. Bioinformatics 21:2568-9. [PDF]