迟 浩

Hao CHI

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

Professor, Institute of Computing Technology, Chinese Academy of Sciences, 2021.9

Associate Professor, Institute of Computing Technology, Chinese Academy of Sciences, 2016.9 --- 2021.9

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


Education

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

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


Honors

2021 Academic revitalization award of China Human Proteome Organisation (中国人类蛋白质组组织学术振兴奖)

2019 First prize of technical invention of Chinese Computer Society (CCF) (中国计算机学会技术发明一等奖，本人为第二完成人)

2018 Ten progresses in bioinformatics in China (中国生物信息学十大进展)

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

Wen-Jing Zhou, Zhuo-Hong Wei, Si-Min He, Chi, H.#, pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power. J Proteomics 2022.

Shao Guangcan, Cao Yong#, Chen Zhenlin, Liu Chao, Li Shangtong, Chi Hao#, Dong Meng-Qiu#, How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data. Biophysics Reports 2021.

Hao Yang, Hao Chi#, Wen-Feng Zeng, Wen-Jing Zhou, Si-Min He#, pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework. Bioinformatics 2019.

Wen-Jing Zhou, Hao Yang, Wen-Feng Zeng, Kun Zhang, Hao Chi#, Si-Min He#, pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics. J Proteome Res 2019.

Wenxue Li, Hao Chi*, Barbora Salovska, Chongde Wu, Liangliang Sun, George Rosenberger, Yansheng Liu, Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. Journal of The American Society for Mass Spectrometry 2019.

Hao Yang*, Yanchang Li*, Mingzhi Zhao*, Feilin Wu, Xi Wang, Weidi Xiao, Yihao wang, Junling Zhang, Fuqiang Wang, Feng Xu, Wen-Feng Zeng, Christopher M. Overall, Si-Min He#, Hao Chi# and Ping Xu#., Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics. Molecular & cellular Proteomics 2019.

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

pFind Team

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 pFind团队 迟浩

邮编：100190



Last update: Jul. 11, 2022