Hao Chi 迟浩

Associate Professor

pFind Team

Center for Advanced Computing Research

Institute of Computing Technology, Chinese Academy of Sciences



Research Interests

Computational Proteomics, e.g., algorithms and software tools for protein identification, de novo peptide sequencing and post-translational modification discovery


Employment Record

Associate Professor, Institute of Computing Technology, Chinese Academy of Sciences, 2016.9 --- present

Assistant Professor, Institute of Computing Technology, Chinese Academy of Sciences, 2013.7 --- 2016.9


Education

2002-2006 Bachelor of Engineering, Computer Science and Technology, Jilin University.

2006-2013 Doctor of Engineering, Institute of Computing Technology, Chinese Academy of Sciences. Supervisor: Si-Min He


Honors

2014 The Outstanding Researchers in ICT (计算所优秀科研人员)

2013 The Special Prize of President Scholarship (CAS 中科院院长特别奖) (<1%)

2010 The First Award of Excellent Paper in the Institute of Computing Technology (中科院计算所优秀论文一等奖)


Publications

Chi, H.#; Liu, C.; Yang, H.; Zeng, W. F.; Wu, L.; Zhou, W. J.; Wang, R. M.; Niu, X. N.; Ding, Y. H.; Zhang, Y.; Wang, Z. W.; Chen, Z. L.; Sun, R. X.; Liu, T.; Tan, G. M.; Dong, M. Q.; Xu, P.; Zhang, P. H.; He, S. M., Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. Nat Biotechnol 2018.

Chi, H.; He, K.; Yang, B.; Chen, Z.; Sun, R. X.; Fan, S. B.; Zhang, K.; Liu, C.; Yuan, Z. F.; Wang, Q. H.; Liu, S. Q.; Dong, M. Q.; He, S. M., pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data. J Proteomics 2015, 125, 89-97.

Chi, H.; Chen, H.; He, K.; Wu, L.; Yang, B.; Sun, R. X.; Liu, J.; Zeng, W. F.; Song, C. Q.; He, S. M.; Dong, M. Q., pNovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra. J Proteome Res 2013, 12 (2), 615-25.

Chi, H.; Sun, R. X.; Yang, B.; Song, C. Q.; Wang, L. H.; Liu, C.; Fu, Y.; Yuan, Z. F.; Wang, H. P.; He, S. M.; Dong, M. Q., pNovo: de novo peptide sequencing and identification using HCD spectra. J Proteome Res 2010, 9 (5), 2713-24.

Li, Y.; Chi, H.*; Wang, L. H.; Wang, H. P.; Fu, Y.; Yuan, Z. F.; Li, S. J.; Liu, Y. S.; Sun, R. X.; Zeng, R.; He, S. M., Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing. Rapid Commun Mass Spectrom 2010, 24 (6), 807-14.

Yang, H.; Chi, H.*; Zhou, W. J.; Zeng, W. F.; Liu, C.; Wang, R. M.; Wang, Z. W.; Niu, X. N.; Chen, Z. L.; He, S. M., pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization. J Proteome Res 2018, 17 (1), 119-128.

Yang, H.; Chi, H.#; Zhou, W. J.; Zeng, W. F.; He, K.; Liu, C.; Sun, R. X.; He, S. M., Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications. J Proteome Res 2017, 16 (2), 645-654.

Zhou, X. X.; Zeng, W. F.; Chi, H.; Luo, C.; Liu, C.; Zhan, J.; He, S. M.; Zhang, Z., pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning. Anal Chem 2017, 89 (23), 12690-12697.

Liu, M. Q.; Zeng, W. F.; Fang, P.; Cao, W. Q.; Liu, C.; Yan, G. Q.; Zhang, Y.; Peng, C.; Wu, J. Q.; Zhang, X. J.; Tu, H. J.; Chi, H.; Sun, R. X.; Cao, Y.; Dong, M. Q.; Jiang, B. Y.; Huang, J. M.; Shen, H. L.; Wong, C. C. L.; He, S. M.; Yang, P. Y., pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nat Commun 2017, 8 (1), 438.

Bu, S. L.; Liu, C.; Liu, N.; Zhao, J. L.; Ai, L. F.; Chi, H.; Li, K. L.; Chien, C. W.; Burlingame, A. L.; Zhang, S. W.; Wang, Z. Y., Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis. Mol Plant 2017, 10 (2), 345-348.

Zeng, W. F.; Liu, M. Q.; Zhang, Y.; Wu, J. Q.; Fang, P.; Peng, C.; Nie, A.; Yan, G.; Cao, W.; Liu, C.; Chi, H.; Sun, R. X.; Wong, C. C.; He, S. M.; Yang, P., pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3. Sci Rep 2016, 6, 25102.

Sun, R. X.; Luo, L.; Wu, L.; Wang, R. M.; Zeng, W. F.; Chi, H.; Liu, C.; He, S. M., pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification. Anal Chem 2016, 88 (6), 3082-90.

Zhang, K.; Fu, Y.; Zeng, W. F.; He, K.; Chi, H.; Liu, C.; Li, Y. C.; Gao, Y.; Xu, P.; He, S. M., A note on the false discovery rate of novel peptides in proteogenomics. Bioinformatics 2015, 31 (20), 3249-53.

Fan, S. B.; Meng, J. M.; Lu, S.; Zhang, K.; Yang, H.; Chi, H.; Sun, R. X.; Dong, M. Q.; He, S. M., Using pLink to Analyze Cross-Linked Peptides. Curr Protoc Bioinformatics 2015, 49, 8 21 1-19.

Su, Z. D.; Sheng, Q. H.; Li, Q. R.; Chi, H.; Jiang, X.; Yan, Z.; Fu, N.; He, S. M.; Khaitovich, P.; Wu, J. R.; Zeng, R., De novo identification and quantification of single amino-acid variants in human brain. J Mol Cell Biol 2014, 6 (5), 421-33.

Liu, C.; Song, C. Q.; Yuan, Z. F.; Fu, Y.; Chi, H.; Wang, L. H.; Fan, S. B.; Zhang, K.; Zeng, W. F.; He, S. M.; Dong, M. Q.; Sun, R. X., pQuant improves quantitation by keeping out interfering signals and evaluating the accuracy of calculated ratios. Anal Chem 2014, 86 (11), 5286-94.

Zhao, Y.; Sun, W.; Zhang, P.; Chi, H.; Zhang, M. J.; Song, C. Q.; Ma, X.; Shang, Y.; Wang, B.; Hu, Y.; Hao, Z.; Huhmer, A. F.; Meng, F.; L'Hernault S, W.; He, S. M.; Dong, M. Q.; Miao, L., Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin). Proc Natl Acad Sci U S A 2012, 109 (5), 1542-7.

Yuan, Z. F.; Liu, C.; Wang, H. P.; Sun, R. X.; Fu, Y.; Zhang, J. F.; Wang, L. H.; Chi, H.; Li, Y.; Xiu, L. Y.; Wang, W. P.; He, S. M., pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics 2012, 12 (2), 226-35.

Yang, B.; Wu, Y. J.; Zhu, M.; Fan, S. B.; Lin, J.; Zhang, K.; Li, S.; Chi, H.; Li, Y. X.; Chen, H. F.; Luo, S. K.; Ding, Y. H.; Wang, L. H.; Hao, Z.; Xiu, L. Y.; Chen, S.; Ye, K.; He, S. M.; Dong, M. Q., Identification of cross-linked peptides from complex samples. Nat Methods 2012, 9 (9), 904-6.

Zhou, C.; Chi, H.; Wang, L. H.; Li, Y.; Wu, Y. J.; Fu, Y.; Sun, R. X.; He, S. M., Speeding up tandem mass spectrometry-based database searching by longest common prefix. BMC Bioinformatics 2010, 11, 577.

Ye, D.; Fu, Y.; Sun, R. X.; Wang, H. P.; Yuan, Z. F.; Chi, H.; He, S. M., Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 2010, 26 (12), i399-406.

Wang, L.; Wang, W.; Chi, H.; Wu, Y.; Li, Y.; Fu, Y.; Zhou, C.; Sun, R.; Wang, H.; Liu, C.; Yuan, Z.; Xiu, L.; He, S. M., An efficient parallelization of phosphorylated peptide and protein identification. Rapid Commun Mass Spectrom 2010, 24 (12), 1791-8.

Sun, R. X.; Dong, M. Q.; Song, C. Q.; Chi, H.; Yang, B.; Xiu, L. Y.; Tao, L.; Jing, Z. Y.; Liu, C.; Wang, L. H.; Fu, Y.; He, S. M., Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra. J Proteome Res 2010, 9 (12), 6354-67.

Jia, W.; Lu, Z.; Fu, Y.; Wang, H. P.; Wang, L. H.; Chi, H.; Yuan, Z. F.; Zheng, Z. B.; Song, L. N.; Han, H. H.; Liang, Y. M.; Wang, J. L.; Cai, Y.; Zhang, Y. K.; Deng, Y. L.; Ying, W. T.; He, S. M.; Qian, X. H., A strategy for precise and large scale identification of core fucosylated glycoproteins. Mol Cell Proteomics 2009, 8 (5), 913-23.

Fu, Y.; Jia, W.; Lu, Z.; Wang, H.; Yuan, Z.; Chi, H.; Li, Y.; Xiu, L.; Wang, W.; Liu, C.; Wang, L.; Sun, R.; Gao, W.; Qian, X.; He, S. M., Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences. BMC Bioinformatics 2009, 10 Suppl 1, S50.


Address

Bioinformatics Group

Institute of Computing Technology, Chinese Academy of Sciences

No.6 Zhongguancun South Road, Beijing, China, 100190

Phone: + 86 010-62600822

Email: chihao@ict.ac.cn


北京市海淀区科学院南路6号 中国科学院计算技术研究所 生物信息学研究组 迟浩

邮编:100190



Last update: Sep. 04, 2018