- Faculty
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Fuyi Li
Author： Source： Date：2024-03-14
Fuyi Li
PhD, MEng, BEng
Mobile: (+61) 426681614 / (+86) 15229251614
Email: Fuyi.Li@unimelb.edu.au
Affiliation: Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia (QS World University Ranked 37th)
Google Scholar: https://scholar.google.com/citations?hl=en&user=vrADwVUAAAAJ
ResearchGate: https://www.researchgate.net/profile/Fuyi_Li
Education Background
Doctor of Philosophy, Bioinformatics, Monash Biomedicine Discovery Institute, Monash University, Australia (QS World University Ranked 58th)
Supervisors: Prof Trevor Lithgow (Academician of the Australian Academy of Science)
A/Prof Jiangning Song (Monash Bioinformatics theme leader) (2017.03-2020.05)
Master of Engineering, Software engineering, College of Information Engineering of Northwest A&F University, China (985&211Engineering University) (2013-2016)
Bachelor of Engineering, Software engineering, College of Information Engineering of Northwest A&F University, China (985 & 211Engineering University) (2009-2013)
Work Experiences
Professor, Northwest A&F University (2022.06-)
Bioinformatics Research Officer (level B), The University of Melbourne (2020-2022)
Data science Teaching Assistant, Monash University (2020.08-2020.12)
Postdoctoral researcher, Monash University (2020.05-2020.09)
Bioinformatics Research Assistant, Monash University (2018.10-2020.05)
Bioinformatics Teaching Assistant, Monash University (2017.07-2018.07)
Honours& Awards
FAOBMB Young Scientist Programme Award (2021)
Postgraduate Publications Award, Monash University (2020)
Best Presentation Award of ICBBB 2020 (2020)
2019 National Outstanding Scholarship for self-financed Overseas Students (Global 500), Scholarship Committee of the Ministry of Education (2020)
Monash Graduate Travel Grant, Monash University (2018)
Full Ph.D. Scholarship by Monash University, Monash University (2016)
Excellent Thesis at School-level, Northwest A&F University (2016)
Outstanding Graduate, Northwest A&F University (2016)
National Scholarship for Postgraduates, Ministry of Education (2015)
Outstanding Graduate Student (Ranked No.1 in College), Northwest A&F University (2014)
Outstanding Undergraduate Thesis at School-level, Northwest A&F University (2013)
Exempted from admission to the College of Information Engineering, Northwest A&F University (2012)
Second-Class Scholarship for Undergraduates, Northwest A&F University (2011)
First-Class Scholarship for Undergraduates, Northwest A&F University (2010)
Research Interests
My research interests focus on large-scale Data Mining, Artificial Intelligence, Machine Learning, Bioinformatics and Computational Systems Biology. More specifically, my research concentrates on Machine Learning, Sequence Analysis, Structural Analysis, Biomolecular Modification Informatics, and Phenotyping of Drug Resistance in Human Pathogenic Bacteria.
I have extensive expertise, skills and experience in Sequence Analysis, Structural Bioinformatics, Machine Learning-based Modelling and Biomedical Data Analysis.
I have published 51 SCI papers (26 in large category Zone1 and 35 in small category Zone1 of CAS) and 1 EI paper in Internationally Renowned Journals: Bioinformatics, Briefings in Bioinformatics, Nature communications, Genomics Proteomics & Bioinformatics, Molecular Microbiology, BMC Bio-informatics, IEEE/ACM TCBB, Molecular Therapy-Nucleic Acids, etc.
I have published 13 papers(6 in large category Zone1 of CAS) as the first author, 9 papers as the corresponding author (3 in large category Zone1 of CAS)，7 papers as the co-first author (4 in large category Zone1 of CAS). Among them, 11 articles are rated as highly cited by Clarivate, 2 are hot articles, and the total number of Google Scholar citations reached 2237. （H-index 35, i10-index 23, May 2022.）
I am one of the few young scholars who have published papers simultaneously in the four major bioinformatics journals of Bioinformatics, Briefings in Bioinformatics，Genomics Proteomics & Bioinformatics和BMC Bioinformatics as the first author.
A number of personal one-authored articles have been recognized by leading experts in the field, including Professor Trevor Lithgow, Academician of the Australian Academy of Sciences, Professor Geoff Webb (IEEE fellow), Director of Monash Data Future Research Institute, and Professor Tatsuya Akutsu, Kyoto University Bioinformatics Center.
In recent years, more than 20 bioinformatics databases, software and analysis platforms have been developed. These tools have been used more than 100000 times by international users in more than 80 countries and regions in the past five years. This bioinformatics software have been cited more than 1000 times in international high-level journals, including Cell, PNAS, Nature Chemical Biology and Nucleic Acids Research, and have produced extensive influence.
Publications
Papers published as the First author:
1. Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J. “GlycoMine: a machine learning-based approach for predicting N-, C-, and O-linked glycosylation in the human proteome”. Bioinformatics. 2015, 31(9), 1411-1419. (IF=6.937, CAS Large Category Zone2(Small Category Zone1), Top, JCR Q1, CCF-B) (140 Citations).
2. Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Smith AI, Lithgow T, Daly RJ, Song J, Chou KC. “Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome”. Bioinformatics. 2018, 34(24), 4223-4231. (IF=6.937, CAS Large category Zone2(Small Category Zone1), Top, JCR Q1, CCF-B) (124 Citations, Clarivate Highly Indexed Paper).
3. Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Smith AI, Lithgow T, Daly RJ, Whisstock JC, Song J. “Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods”. Briefings in Bioinformatics. 2019, 20(6), 2150-2166. (IF=11.622, CAS Large category Zone1, Top, JCR Q1, CCF-B) (68 Citations).
4. Li F, Chen J, Leier A, Marquez-Lago TT, Liu Q, Wang Y, Revote J, Smith AI, Akutsu T, Webb GI, Kurgan L, Song J. “DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites”. Bioinformatics. 2020, 36(4), 1057-1065. (IF=6.937, CAS Large Category Zone2(Small Category Zone1), Top, JCR Q1, CCF-B) (66 Citations, Clarivate Highly Indexed Paper)
5. Li F, Fan C, Marquez-Lago TT, Leier A, Revote J, Jia C, Zhu Y, Smith AI, Webb GI, Liu Q, Wei L, Li J, Song J. “PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact”. Briefings in Bioinformatics. 2020, 21(3), 1069-1079. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (24 Citations)
6. Li F, Leier A, Liu Q, Wang Y, Xiang D, Akutsu T, Webb GI, Smith AI, Marquez-Lago TT, Li J, Song J. “Procleave: Predicting Protease-Specific Substrate Cleavage Sites by Combining Sequence and Structural Information”. Genomics, Proteomics & Bioinformatics. 2020, 18(1), 52-64. (IF=7.691, CAS Large Category Zone1, Top, JCR Q1) (36 Citations)
7. Li F, Chen J, Ge Z, Wen Y, Yue Y, Hayashida M, Baggag A, Bensmail H, Song J. “Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework”. Briefings in Bioinformatics. 2021, 22(2), 2126-2140. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (30 Citations, Clarivate Highly Indexed Paper)
8. Li F, Guo X, Jin P, Chen J, Xiang D, Song J, Coin LJM. “Porpoise: a new approach for accurate prediction of RNA pseudouridine sites”. Briefings in Bioinformatics. 2021, 22(6), bbab245. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (14 Citations)
9. Li F, Dong S, Leier A, Han M, Guo X, Xu J, Wang X, Pan S, Jia C, Zhang Y, Webb GI, Coin LJM, Li C, Song J. “Positive-unlabeled learning in bioinformatics and computational biology: a brief review”. Briefings in Bioinformatics. 2021, 23(1), bbab461. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (1 Citation)
10. Li F, Guo X, Xiang D, Pitt EM, Bainomugisa A, Coin LJM. “Computational analysis and prediction of PE_PGRS proteins using machine learning”. Computational and Structural Biotechnology Journal. 2022. 20, 662-674. (IF=7.271, CAS Large Category Zone2, JCR Q1) (1 Citation)
11. Li F, Zhang Y, Purcell AW, Webb GI, Chou KC, Lithgow T, Li C, Song J. “Positive-unlabelled learning of glycosylation sites in the human proteome”. BMC Bioinformatics. 2019, 20, 112. (IF=3.169, CAS Large Category Zone3(Small Category Zone2), JCR Q1, CCF-C) (55 Citations).
12. Li F, Li C, Revote J, Zhang Y, Webb GI, Li J, Song J, Lithgow T. “G lycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features”. Scientific reports. 2016, 6, 34595. (IF=4.379, CAS Large Category Zone3, JCR Q1) (62 Citations).
13. Li F, Song J, Li C, Akutsu T, Zhang Y. “PAnDE: Averaged n-Dependence Estimators for Positive unlabeled learning”. ICIC express letters. Part B, Applications. 2017, 8(9), 1287-1297. (EI, 6 Citations).
Papers published as the Corresponding author:
14. Liu Q, Chen J, Wang Y, Li S, Jia C*, Song J*, Li F*. “DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites”. Briefings in Bioinformatics. 2021, 22(3), bbaa124. (IF=11.622, CAS Large Category Zone1, Top, CCF-B) (41 Citations, Clarivate Highly Indexed Paper).
15. Peng X, Wang X, Guo Y, Ge Z*, Li F*, Gao X*, Song J*. “RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins”. Briefings in Bioinformatics. 2022, bbac215. (IF=11.622, CAS Large Category Zone1, Top, CCF-B).
16. Wang X, Li F*, Xu J, Rong J, Webb GI, Ge Z*, Li J, Song J*. “ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning”. Briefings in Bioinformatics. 2022, 23(2), bbac031. (IF=11.622, CAS Large Category Zone1, Top, CCF-B).
17. Jia C, Bi Y, Chen J, Leier A, Li F*, Song J*. “PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs”. Bioinformatics. 2020, 36(15), 4276-4282. (IF=6.937, CAS Large Category Zone2 (Small Category Zone1), Top, JCR Q1, CCF-B) (31 Citations).
18. Chai D, Jia C*, Zheng J, Zou Q, Li F*. “Staem5: a novel computational approach for accurate prediction of m5C site”. Molecular Therapy-Nucleic Acids. 2021, 26, 1027-1034. (IF=8.886, CAS Large Category Zone2, JCR Q1) (4 Citations).
19. Bi Y, Xiang D, Ge Z, Li F*, Jia C*, Song J*. “An interpretable prediction model for identifying N7-methylguanosine sites based on XGBoost and SHAP”. Molecular Therapy-Nucleic Acids. 2020, 22, 362-372. (IF=8.886, CAS Large Category Zone2, JCR Q1) (33 Citations).
20. Jia C, Zhang M, Fan C, Li F*, Song J*. “Formator: predicting lysine formylation sites based on the most distant undersampling and safe-level synthetic minority oversampling”. IEEE/ACM transactions on computational biology and bioinformatics. 2021 18(5), 1937-1945. (IF=3.71, CAS Large Category Zone3(Small Category Zone2), JCR Q1, CCF-B) (19 Citations).
21. Li P, Zhang H, Zhao X, Li F*, Song J*. “Pippin: A Random Forest-based method for identifying presynaptic and postsynaptic neurotoxins”. Journal of Bioinformatics and Computational Biology. 2020, 18(2), 2050008. (IF=1.122, JCR Q3).
22. Zhu Y, Jia C, Li F*, Song J*. “Inspector: A lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling”. Analytical Biochemistry. 2020, 593, 113592. (IF=3.365, JCR Q2) (22 Citations).
Papers published as Co-first author:
23. Song J†, Li F†, Leier A, Marquez-Lago TT, Akutsu T, Haffari G, Chou KC, Webb GI, Pike RN. “PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy”. Bioinformatics. 2017, 34(4), 684-687. (IF=6.937, CAS Large Category Zone2(Small Category Zone1), Top, Co-first author, JCR Q1, CCF-B) (126 Citations, Clarivate Highly Indexed Paper).
24. Zhang M†, Li F†, Marquez-Lago TT, Leier A, Fan C, Chou KC, Song J, Jia C. “MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters”. Bioinformatics. 2019, 35(17), 2957-2965. (IF=6.937, CAS Large Category Zone2 (Small Category Zone1), Top, JCR Q1, CCF-B) (80 Citations, Clarivate Highly Indexed Paper).
25. Yan Zhu†, Li F†, Xiang D, Akutsu T, Song J, Jia C. “Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks”. Briefings in Bioinformatics. 2021, 22(4), bbaa299. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (17 Citations).
26. Mei S†, Li F†, Xiang D, Ayala R, Faridi P, Webb GI, Illing PT, Rossjohn J, Akutsu T, Croft NP, Purcell AW, Song J. “Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules”. Briefings in Bioinformatics. 2021, 22(5), bbaa415. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (9 Citations).
27. Liang X†, Li F†, Chen J, Li J, Wu H, Li S, Song J, Liu Q. “Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification”. Briefings in Bioinformatics. 2021, 22(4), bbaa312. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (15 Citations).
28. Zhang M†, Jia C†, Li F†, Li C†, Zhu Y, Akutsu T, Webb GI, Zou Q, Coin JML, Song J. “Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction”. Briefings in Bioinformatics. 2022, bbab551. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (1 Citation).
29. Chen J†, Li F†, Wang M, Li J, Marquez-Lago TT, Leier A, Revote J, Li S, Liu Q, Song J. “BigFiRSt: a software program using big data technique for mining simple sequence repeats from large-scale sequencing data”. Frontiers in Big Data. 2022, 4, 727216.
30. Wang M†, Li F†, Wu H, Liu Q, Li S. “PredPromoter-MF (2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest”. Interdisciplinary Sciences: Computational Life Sciences. 2022, doi:10.1007/s12539-022-00520-4.
Mid-author papers:
31. Song J, Li F, Takemoto K, Haffari G, Akutsu T, Chou KC, Webb GI. “PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework”. Journal of Theoretical Biology. 2018, 443, 125-137. (IF=1.833, CAS Large Category Zone3, First author, JCR Q1) (116 Citations, Clarivate Hot Paper & Highly Indexed Paper).
32. Wang Y, Li F, Bharathwaj M, Rosas NC, Leier A, Akutsu T, Webb GI, Marquez-Lago TT, Li J, Lithgow T, Song J. “DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases”. Briefings in Bioinformatics. 2021, 22(4), bbaa301. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1) (3 Citations).
33. Chen H, Li F, Wang L, Jin Y, Chi CH, Lukasz K, Song J, Shen J. “Systematic evaluation of machine learning methods for identifying human–pathogen protein–protein interactions”. Briefings in Bioinformatics. 2021, 22(3), bbaa068. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (14 Citations).
34. Mei S, Li F, Leier A, Marquez-Lago TT, Giam K, Croft NP, Akutsu T, Smith AI, Li J, Rossjohn J, Purcell AW, Song J. “A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide binding prediction”. Briefings in Bioinformatics. 2020, 21(4), 1119-1135. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF- B) (69 Citations).
35. Iqbal S, Li F, Akutsu T, Ascher DB, Webb GI, Song J. “Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations”. Briefings in Bioinformatics. 2021, 22(6), bbab184. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (10 Citations).
36. Xu J, Li F, Leier A, Xiang D, Shen HH, Marquez-Lago TT, Li J, Yu DJ, Song J. “Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides”. Briefings in Bioinformatics. 2021, 22(5), bbab083. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (12 Citations).
37. Chen Z, Zhao P, Li C, Li F, Xiang D, Chen YZ, Akutsu T, Daly RJ, Webb GI, Zhao Q, Kurgan L, Song J. “iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization”. Nucleic Acids Research. 2021, 49(10), e60. (IF=16.971, CAS Large Category Zone1, Top, JCR Q1) (26 Citations).
38. Song J, Wang Y, Li F, Akutsu T, Rawlings ND, Webb GI, Chou KC. “iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites”. Briefings in Bioinformatics. 2018, 20(2), 638-658. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (184 Citations, Clarivate Hot Paper & Highly Indexed Paper).
39. Chen Z, Zhao P, Li F, Leier A, Marquez-Lago TT, Wang Y, Webb GI, Smith AI, Daly RJ, Chou KC, Song J. “iFeature: a python package and web server for features extraction and selection from protein and peptide sequences”. Bioinformatics. 2018, 31(14), 2499-2502. (IF=6.937, CAS Large Category Zone2 (Small Category Zone1), Top, JCR Q1, CCF-B) (294 Citations, Clarivate Highly Indexed Paper).
40. Chen Z, Zhao P, Li F, Marquez-Lago TT, Leier A, Revote J, Zhu Y, Powell DR, Akutsu T, Webb GI, Chou KC, Smith AI, Daly RJ, Li J, Song J. “iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modelling of DNA, RNA and protein sequence data”. Briefings in Bioinformatics. 2020, 21(3), 1047-1057. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (175 Citations, Clarivate Highly Indexed Paper).
41. Chen Z, Liu X, Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Webb GI, Xu D, Smith AI, Li L, Chou KC, Song J. “Large-scale comparative assessment of computational predictors for lysine post-translational modification sites”. Briefings in Bioinformatics. 2019, 20(6), 2267-2290. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (79 Citations).
42. Wei L, Hu J, Li F, Song J, Su R, Zou Q. “Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms”. Briefings in Bioinformatics. 2020, 21(1), 106-119. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (83 Citations, Clarivate Highly Indexed Paper).
43. Chen Z, Zhao P, Li F, Wang Y, Smith AI, Webb GI, Akutsu T, Baggag A, Bensmail H, Song J. “Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences”. Briefings in Bioinformatics. 2020, 21(5), 1676-1696. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (59 Citations).
44. Ma X, Zhang L, Song J, Nguyen E, Lee SR, Rodgers SJ, Li F, Huang C, Schittenhelm RB, Chan H, Chheang C, Wu J, Brown KK, Mitchell CA, Simpson KJ, Daly RJ. “Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation”. Nature Communications. 2019, 10, 296. (IF=14.919, CAS Large Category Zone1, JCR Q1) (18 Citations).
45. Chen Z, Liu X, Zhao P, Li C, Wang Y, Li F, Akutsu T, Bain C, Gasser RB, Li J, Yang Z, Gao X, Kurgan L, Song J. “iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets”. Nucleic Acids Research. 2022, gkac351. (IF=16.971, CAS Large Category Zone1, Top, JCR Q1).
46. Zhu YH, Hu J, Ge Fang, Li F, Song J, Zhang Y, Yu DJ. “Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features”. Briefings in Bioinformatics. 2021, 22(3), bbaa076. (IF=11.622, CAS Large Category Zone1, Top, JCR Q1, CCF-B) (11 Citations).
47. Wang Y, Coudray N, Zhao Y, Li F, Hu C, Zhang YZ, Imoto S, Tsirigos A, Webb GI, Daly RJ, Song J. “HEAL: an automated deep learning framework for cancer histopathology image analysis”. Bioinformatics. 2021, 37(22), 4291-4295. (IF=6.937, CAS Large Category Zone2 (Small Category Zone1), Top, JCR Q1, CCF-B) (4 Citations).
48. Ozols M, Eckersley A, Platt CI, Stewart C, Hibbert SA, Revote J, Li F, Griffiths C, Watson R, Song J, Bell M, Sherratt MJ. “Predicting Proteolysis in Complex Proteomes Using Deep Learning”. International journal of molecular sciences. 2021, 22(6), 3071. (IF=5.923, CAS Large Category Zone2, JCR Q1) (5 Citations).
49. Wang X, Li C, Li F, Sharma VS, Song J, Webb GI. “SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in human proteome based on multi-stage ensemble-learning models”. BMC Bioinformatics. 2019, 20(1), 602. (IF=3.169, CAS Large Category Zone3 (Small Category Zone2), JCR Q1, CCF-C) (8 Citations).
50. Li M, Wang Y, Li F, Zhao Y, Liu M, Zhang S, Bin Y, Smith AI, Webb GI, Li J, Song J, Xia J. “A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction”. IEEE/ACM transactions on computational biology and bioinformatics. 2020, doi:10.1109/TCBB.2020.3017386. (IF=3.71, CAS Large Category Zone3 (Small Category Zone2), JCR Q1, CCF-C) (13 Citations).
51. Dunstan R, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T. “The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail-fibre”. Molecular Microbiology. 2019, 112(6), 1831-1846. (IF=3.816, CAS Large Category Zone2, JCR Q1) (11 Citations).
52. Chen Z, Zhao P, Li F, Leier A, Marquez-Lago TT, Webb IG, Baggag A, Bensmail H, Song J. “PROSPECT: a web server for predicting protein histidine phosphorylation sites”. Journal of Bioinformatics and Computational Biology. 2020, 18(4), 2050018. (IF=1.122, JCR Q3) (7 Citations).
1. 16th Congress of the Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB 2021), Virtual congress, New Zealand, 22-25 November 2021. Oral presentation: “Porpoise: a new approach for accurate prediction of RNA pseudouridine sites”.
2. 10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2020), Kyoto, Japan, 19-22 January 2020. Invited speech: “Leveraging the Power of Data-Driven Machine Learning Techniques to Address Significant Biomedical Classification Problems”.
3. 10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2020), Kyoto, Japan, 19-22 January 2020. Oral presentation: “Procleave: A Bioinformatic Approach for Protease-Specific Substrate Cleavage Site Prediction by Combining Sequence and Structural Information”.
4. Artificial Intelligence International Conference (A2IC 2018), Barcelona, Spain, 21-23 November 2018. Oral presentation: “Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome”.
5. 12th International Conference on Innovative Computing Information and Control (ICICIC2017), Kurume, Japan, 28-30 August 2017. Oral presentation: “PAnDE: Averaged n-Dependence Estimators for Positive Unlabelled Learning”.
Invited presentation
1. Bioinformatics Center of Kyoto University, 23 January, 2020. Oral presentation: “A data-driven bioinformatic investigation into protein post-translational modifications”.
2. Bioinformatics Center of Kyoto University, 1 September, 2017. Oral presentation: “PROSPERous: integrative high-throughput prediction of the substrate cleavage sites for 90 proteases with improved accuracy”.
Review Editor and Program Committee
Review Editor on the Editorial Board of Frontiers in Bioinformatics
Editor on the Editorial Board of BioMed Research International
Editor on the Editorial Board of Current Gene Therapy
PC member of the International Conference on Genome Informatics (GIW) 2019
PC member of the 13th International Conference on Knowledge Discovery and Information Retrieval (KDIR 2021)
Journal and Conference Reviewers
Journals
Bioinformatics (Oxford Academic)
Briefings in Bioinformatics (Oxford Academic)
BMC Bioinformatics (Springer)
PLOS Computational Biology (PLOS)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE)
PLOS One (PLOS)
IEEE Access (IEEE)
Frontiers in Genetics (Frontiers)
Frontiers in Bioinformatics (Frontiers)
Frontiers in Bioengineering and Biotechnology (Frontiers)
Frontiers in Cell and Developmental Biology (Frontiers)
Scientific Reports (Nature)
Pattern recognition (Elsevier)
Journal of Computational Chemistry (Wiley)
Journal of Chemical Information and Modeling (ACS)
Analytical Biochemistry (Elsevier)
Journal of Biomolecular Structure & Dynamics (Taylor & Francis)
Journal of Bioinformatics and Computational Biology (World Scientific)
Molecular Omics (Royal Society of Chemistry)
Evolutionary Bioinformatics (SAGE journals)
BioMed Research International (Hindawi)
Conferences
The 30th International Conference on Genome Informatics (GIW 2019)
The 29th International Conference on Genome Informatics (GIW 2018)
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018)
2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017)
2020 International Conference on Intelligent Computing (ICIC 2020)
2019 International Conference on Intelligent Computing (ICIC 2019)
2018 International Conference on Intelligent Computing (ICIC 2018)
The IEEE 13th International Conference on e-Science, 2017