Applied Bioinformatics Course [中文]


Jingchu Luo


I was a professor at the College for Life Sciences, Peking University. I am the China node manager of the European Molecular Biology Network (EMBnet). I was the editorial member of BMC Bioinformatics and Briefings in Bioinformatics.

I spent one and half year at the University of Maryland and two and half years in Michael Sternberg's Biomolecular Modeling Lab in Cancer Research UK during 1991-1999 (5 visits). Together with the Late Professor Xiaocheng Gu, I started the Center for Bioinformatics (CBI) at Peking University in 1997.

My main research interests were: I started to teach the Applied Bioinformatics Course (ABC) in 2001. After sending off my last PhD student in 2015, I focus on teaching ABC for PKU, CAAS and UCAS graduate students.

[Brief CV in Chinese]

Selected (first/last author since 2005) Publications (Full list collected in PubMed)

  1. Luo J. GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China. Genomics, proteomics and bioinformatics. 2017; 15(1):11-13. [PDF]
  2. Li Z, Zhao Y, Liu X, Jiang Z, Peng J, Jin J, Guo H, Luo J. Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes. Methods in molecular biology (Clifton, N.J.). 2017; 1533:315-333. [PDF]
  3. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017 Jan 4;45(D1):D1040-D1045. [PDF]
  4. Wu XY, Hu WJ, Luo H, Xia Y, Zhao Y, Wang LD, Zhang LM, Luo JC, Jing HC. Transcriptome profiling of developmental leaf senescence in sorghum (Sorghum bicolor). Plant molecular biology. 2016; 92(4-5):555-580. [PDF]
  5. Luo H, Zhao W, Wang Y, Xia Y, Wu X, Zhang L, Tang B, Zhu J, Fang L, Du Z, bekele WA, Tai S, Jordan DR, Godwin ID, Snowdon RJ, Mace ES, Luo J, Jing HC. (2016) SorGSD: a sorghum genome SNP database. Biotechnol Biofuels. 9:37. [PDF]
  6. Jin J, Zhang H, Kong L, Gao G, Luo J. (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 42:D1182-7. [PDF]
  7. 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]
  8. 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]
  9. Luo J. (2013) Teaching the ABCs of Bioinformatics: a brief introduction to the Applied Bioinformatics Course. Brief Bioinform. 15:1004-13. [PDF]
  10. Wang J, Kong L, Gao G, Luo J. (2013) A brief introduction to web-based genome browsers. Brief Bioinform. 14:131-43. [PDF]
  11. 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]
  12. 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]
  13. 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 transcription factor database. Nucleic Acids Res. 39:D1114-7. [PDF]
  14. 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].
  15. He K, Guo AY, Gao G, Zhu QH, Liu XC, Zhang H, Chen X, Gu X, Luo J. (2010) Computational identification of plant transcription factors and the construction of the PlantTFDB database. Methods Mol Biol. 674:351-68. [PDF].
  16. 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]
  17. 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]
  18. 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]
  19. 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 transcription factor family. Gene. 418:1-8. [PDF]
  20. 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 transcription factor database. Nucleic Acids Res. 36:D966-9. [PDF]
  21. Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang M, Luo J. (2007) DPTF: a database of poplar transcription factors. Bioinformatics. 23:1307-8. [PDF]
  22. Sun Y, Zhao S, Yu H, Gao G, Luo J. (2007) ABCGrid: Application for Bioinformatics Computing Grid. Bioinformatics. 23:1175-7. [PDF]
  23. 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]
  24. 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]
  25. 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]
  26. Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. (2006) DRTF: a database of rice transcription factors. Bioinformatics. 22:1286-7. [PDF]
  27. Wu X, Walker MG, Luo J, Wei L. (2005) GBA server: EST-based digital gene expression profiling. Nucleic Acids Res. 33:W673-6. [PDF]
  28. 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]
  29. 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]
  30. Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J. (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21:2568-9. [PDF]

Chinese papers

  1. Luo JC. (2023) Basics of pairwise sequence alignment and some application examples. Sheng Wu Xin Xi Xue (Chinese Journal of Bioinnformatics). 21:1-19. [Link]
  2. Luo JC. (2021) Application examples of EMBOSS sequence analysis program. Sheng Wu Xin Xi Xue (Chinese Journal of Bioinnformatics). 19:1-25. [Link]
  3. Luo JC. (2021) EMBOSS and EMBnet. Sheng Wu Xin Xi Xue (Chinese Journal of Bioinnformatics). 19:223-231. [Link]
  4. Luo JC. (2019) A Brief Introduction to UniProt. Sheng Wu Xin Xi Xue (Chinese Journal of Bioinnformatics). 17:131-144. [Link]
  5. Luo J. GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China. Genomics, proteomics & bioinformatics. 2017; 15(1):11-13. [PDF]
  6. Luo J. Teaching Examples of Applied Bioinformatics Course. Biotechnology Bulletin. 2015; 31(11. [PDF]
  7. Chen YJ, Gao G, Bao YM, Lopez R, Wu JM, Cai T, Ye ZQ, Gu XC, Luo JC. (2003) Initial analysis of complete genome sequences of SARS coronavirus. Yi Chuan Xue Bao. 30:493-500. [PDF]

Book chapters and scientific stories

  1. Luo JC. (2013) PKU Computing Center in My Eyes. [Link]
  2. Luo JC. (2003) Life Science and Bioinformatics Technology in the Internet Age. In "100 Interdesciplinary Science Puzzles of the 21 Century". Science Press, p.613-622. [PDF]
  3. Luo H and Luo JC (2003) In Memory of Rosalind Franklin. Hereditas, 25:247-248. [PDF]
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6 July 2024, J Luo, CBI, PKU, Beijing, China