Fang Ge received her M.S. degree from Anhui University and Ph.D. degree from Nanjing University of Science and Technology.She is a member of the Pattern Recognition and Bioinformatics Group. Her current interests include bioinformatics, pattern recognition, machine learning, and data mining.

Published Papers ( >>Google Scholar Citation Profile)(x+y)(>> Web Servers)

• Ming Zhang, Chao Gong, Fang Ge, Dongjun Yu^#. FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework [J]. Journal of Chemical Information and Modeling, 2024,64(6):1394–1406. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.3c02025] [Github Link] (WOS: xxxxxx)

• Zihao Yan, Fang Ge,Yumeng Zhang, Fuyi Li, Jiangning Song^#, and Dongjun Yu^#. TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusio [J]. Journal of Chemical Information and Modeling, 2024,64(6):1407–1418. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.3c02019] [Github Link] (WOS: xxxxxx)

• Muhammad Arif，Fang Ge, Huma Fida, Saleh Musleh, Dongjun Yu, Tanvir Alam^#. iMRSAPred: Improved Prediction of Anti-MRSA Peptides Using Physicochemical and Pairwise Contact-Energy Properties of Amino Acids [J]. ACS Omega, 2024,9(2):2874–2883. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acsomega.3c08303] [Github Link] (WOS: xxxxxx)

• Fang Ge, Muhammad Arif, Zihao Yan, Apilak Worachartcheewan, Hanin Alahmadi, Dongjun Yu^#, and Watshara Shoombuatong^#. MMPatho: Interpretable Model with Multilevel Consensus and Evolutionary Information for Missense Mutation Pathogenic Prediction and Annotationl [J]. Sumbitted, 2023, *(*): ****. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.3c00950] [Web Server] (WOS: xxxxxx)

• Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song^#, and Dong-Jun Yu^#. Prediction of multiple types of RNA modifications via biological language model [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, *(*): ****. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2023.3283985] [Web Server] (WOS: xxxxxx)

• Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A.Thafar, Zi-Hao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song^#, and Dong-Jun Yu^#. VPatho: a deep learning-based two-step approach for accurate prediction of gain-of-function and loss-of-function variants [J]. Briefings in Bioinformatics, 2023, 24(1): bbab535. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbad019] [Web Server] (WOS: 000911247800001)

• Fang Ge,Ying Zhang, Jian Xu, Arif Muhammad, Jiangning Song^#, and Dong-Jun Yu^#. Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion [J]. Briefings in Bioinformatics, 2022, 23(1): bbab530. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbab530] [Web Server] (WOS: 000763000800043)

• Fang Ge^#, Yi-Heng Zhu, Jian Xu, Arif Muhammad, Jiangning Song, and Dong-Jun Yu^#. MutTMPredictor: robust and accurate cascade XGBoost classifier for prediction of disease-associated mutations in transmembrane proteins [J]. Computational and Structural Biotechnology Journal, 2021, 19:6400-6416. [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.csbj.2021.11.024] [Web Server] (WOS: 000731411300003)

• Fang Ge, Arif Muhammad, Dong-Jun Yu^#. DeepnsSNPs: Accurate Prediction of Non-synonymous Single-nucleotide Polymorphisms by Combining Multi-scale Convolutional Neural Network and Residue Environment Information [J]. Chemometrics and Intelligent Laboratory Systems, 2021, 215: 104326. [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.chemolab.2021.104326] [Github code link] (WOS: 000674505600013)

• Fang Ge, Jun Hu, Yi-Heng Zhu, Muhammad Arif, Wen-Wen Kan, and Dong-Jun Yu^#. TargetMM: Accurate Missense Mutation Prediction by Utilizing Local and Global Sequence Information with Classifier Ensemble [J]. Combinatorial Chemistry & High Throughput Screening, 2022, 25(1), 38-52. [Download Citation with Endnote or BibTex Format] [DOI:10.2174/1386207323666201204140438] [Github code link] (WOS: 000737601100006)

• Fang Ge, Jun Hu, Yi-heng Zhu, Dong-jun Yu^#. Review on pathogenicity prediction studies of non-synonymous single nucleotide variations. Journal of Nanjing University of Science and Technology. 2021, 45 (1): 1-17. [Download Citation with Endnote or BibTex Format] [Paper link]

• Iqbal Shahid, Fang Ge,Li Fuyi, Akutsu Tatsuya, Zheng Yuanting, Gasser Robin, Yu Dong-Jun^#, Webb Geoffery^#, Song Jiangning^#. PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations [J]. Journal of Chemical Information and Modeling, 2022, 62(17), 4270-4282. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.2c00799] [Web Server:https://prost.erc.monash.edu/seq] [Github code link] (PMID: 35973091)

• Yi-Heng Zhu, Jun Hu, Fang Ge,Fuyi Li, Jiangning Song^#, Yang Zhang^#, Dong-Jun Yu^#. Accurate Multi-Stage Prediction of Protein Crystallization Propensity Using Deep-Cascade Forest with Sequence-Based Features [J]. Briefings in Bioinformatics, 2021, 22 (3): bbaa076. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbaa076] [Web Server] (WOS: 000709461300028)

• Meng Zhang, Jian Zhao, Chen Li, Fang Ge,Jing Wu, Bin Jiang, Jiangning Song^#, and Xiaofeng Song^#. csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames [J]. Briefings in Bioinformatics, 2022, bbac392. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbac392] [Web Server] (WOS: XXXXX)

• Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, and Dong-Jun Yu^#. SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network [J]. Journal of Chemical Information and Modeling, 2020,60(6):3295-3303. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.9b01207] [Web Server] (WOS: 000543717300057)

• Muhammad Arif, Saeed Ahmed, Fang Ge, Muhammad Kabir, Yaser Daanial Khan, Dong-Jun Yu^#, Maha Thafar^#. Prediction of anticancer peptides by integrating optimized multiple feature descriptors with stacked ensemble approach [J]. Chemometrics and Intelligent Laboratory Systems, 2022, 220: 104458. [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.chemolab.2021.104458] (WOS: 000796888500002)

• Muhammad Arif, Muhammad Kabir, Saeed Ahmad, Fang Ge, Adel Khelifi, Dong-Jun Yu^#. DeepCPPred: a deep learning framework for the discrimination of cell-penetrating peptides and their uptake efficiencies [J]. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2021, 19(5): 2749-2759. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2021.3102133] (PMID: 34347603)

• Muhammad Arif, Saeed Ahmad, Farman Ali, Fang Ge, Min Li, and Dong-Jun Yu^#. TargetCPP: Accurate prediction of cell-penetrating peptides from optimized multi-scale feature using gradient boost decision tree [J]. Journal of Computer-Aided Molecular Design, 2020, 34 (8): 841-856. [Download Citation with Endnote or BibTex Format] [DOI:10.1007/s10822-020-00307-z] (WOS: 000520658300001)

• Fang Ge, Arif Muhammad. Missense variants in human ACE2 May influence its binding interaction with SARS-CoV-2 and infectivity of COVID-19[C]. Journal of Physics: Conference Series, 2021, 1828(1): 012179. [Download Citation with Endnote or BibTex Format] [DOI:10.1088/1742-6596/1828/1/012179] [Paper link]

• Fang Ge, Arif Muhammad. Functional variants in human ACE2 can decrease its protein stability and may influence the binding with SARS-CoV-2. Journal of Physics: Conference Series. 2021, 1828(1): 012180. [Download Citation with Endnote or BibTex Format] [DOI:10.1088/1742-6596/1828/1/012180] [Paper link]

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