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Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability Journal article
Benjamin Tam, Philip Naderev P. Lagniton, Mariano da Luz, Bojin Zhao, Siddharth Sinha, Chon Lok Lei, San Ming Wang. Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability[J]. Briefings in Bioinformatics, 2024, 25(5), bbae400.
Authors:  Benjamin Tam;  Philip Naderev P. Lagniton;  Mariano da Luz;  Bojin Zhao;  Siddharth Sinha; et al.
Favorite | TC[WOS]:0 TC[Scopus]:0  IF:6.8/7.9 | Submit date：2024/08/07
Ramachandran Plot  Molecular Dynamics Simulations  Tp53  Somatic Missense Variants  
Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method Journal article
Tam, Benjamin, Qin, Zixin, Zhao, Bojin, Sinha, Siddharth, Lei, Chon Lok, Wang, San Ming. Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method[J]. International Journal of Molecular Sciences, 2024, 25(2), 850.
Authors:  Tam, Benjamin;  Qin, Zixin;  Zhao, Bojin;  Sinha, Siddharth;  Lei, Chon Lok; et al.
Favorite | TC[WOS]:3 TC[Scopus]:3  IF:4.9/5.6 | Submit date：2024/02/22
Autoencoder  Deep Learning  Mlh1  Molecular Dynamics Simulation  Neural Network  Ramachandran Plot  Vus  
Classification of PTEN missense VUS through exascale simulations Journal article
Sinha, Siddharth, Li, Jiaheng, Tam, Benjamin, Wang, San Ming. Classification of PTEN missense VUS through exascale simulations[J]. Briefings in Bioinformatics, 2023, 24(6), bbad361.
Authors:  Sinha, Siddharth;  Li, Jiaheng;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:1 TC[Scopus]:1  IF:6.8/7.9 | Submit date：2023/12/04
Evolution Selection  Lipid Phosphatase Activity  Md Simulations  Pten  Replica Exchange Molecular Dynamics (Remd) Simulations  Variants Of Uncertain Significance (Vus)  
TP53 germline pathogenic variants in modern humans were likely originated during recent human history Journal article
Si Hoi Kou, Jiaheng Li, Benjamin Tam,, Huijun Lei, Bojin Zhao, Fengxia Xiao, San Ming Wang. TP53 germline pathogenic variants in modern humans were likely originated during recent human history[J]. NAR Cancer, 2023, 5(3), zcad025.
Authors:  Si Hoi Kou;  Jiaheng Li;  Benjamin Tam,;  Huijun Lei;  Bojin Zhao; et al.
Favorite | TC[WOS]:7 TC[Scopus]:7  IF:3.4/4.1 | Submit date：2023/08/03
DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS Journal article
Lagniton,Philip Naderev P., Tam,Benjamin, Wang,San Ming. DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS[J]. Computer Methods and Programs in Biomedicine, 2023, 238, 107596.
Authors:  Lagniton,Philip Naderev P.;  Tam,Benjamin;  Wang,San Ming
Favorite | TC[WOS]:0 TC[Scopus]:0  IF:4.9/5.5 | Submit date：2023/08/03
Dihedral Angles  Human Muty Homolog (Mutyh)  Missense Variants  Molecular Dynamics Simulations (Md Simulations)  Protein Structure  Ramachandran Principle  Tumor Protein 53 (Tp53)  
Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification Journal article
Tam, Benjamin, Qin, Zixin, Zhao, Bojin, Wang, San Ming, Lei, Chon Lok. Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification[J]. ISCIENCE, 2023, 26(3), 106122.
Authors:  Tam, Benjamin;  Qin, Zixin;  Zhao, Bojin;  Wang, San Ming;  Lei, Chon Lok
Favorite | TC[WOS]:5 TC[Scopus]:5  IF:4.6/5.0 | Submit date：2023/04/03
Evolutionary Origin of MUTYH Germline Pathogenic Variations in Modern Humans Journal article
Xiao,Fengxia, Li,Jiaheng, Lagniton,Philip Naderev Panuringan, Kou,Si Hoi, Lei,Huijun, Tam,Benjamin, Wang,San Ming. Evolutionary Origin of MUTYH Germline Pathogenic Variations in Modern Humans[J]. Biomolecules, 2023, 13(3).
Authors:  Xiao,Fengxia;  Li,Jiaheng;  Lagniton,Philip Naderev Panuringan;  Kou,Si Hoi;  Lei,Huijun; et al.
Favorite | TC[WOS]:3 TC[Scopus]:3  IF:4.8/5.4 | Submit date：2023/08/03
Ancient Humans  Archaeological  Evolutionary Origin  Mutyh  Pathogenic Variant  Phylogenic  
Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population Journal article
Qin, Zixin, Li, Jiaheng, Tam, Benjamin, Sinha, Siddharth, Zhao, Bojin, Bhaskaran, Shanmuga Priya, Huang, Teng, Wu, Xiaobing, Chian, Jia Sheng, Guo, Maoni, Kou, Si Hoi, Lei, Huijun, Zhang, Li, Wang, Xiaoyu, Lagniton, Philip Naderev P., Xiao, Fengxia, Jiang, Xinyang, Wang, San Ming. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population[J]. International Journal of Cancer, 2022, 152(6), 1159-1173.
Authors:  Qin, Zixin;  Li, Jiaheng;  Tam, Benjamin;  Sinha, Siddharth;  Zhao, Bojin; et al.
Favorite | TC[WOS]:5 TC[Scopus]:6  IF:5.7/6.0 | Submit date：2023/01/30
Asian  Brca1  Brca2  Cancer  Database  Evolution  Germline Variation  Population  Structure  Variation  
Applications of Molecular Dynamics Simulation in Protein Study Review article
2022
Authors:  Sinha, Siddharth;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:32 TC[Scopus]:37  IF:3.3/3.6 | Submit date：2022/10/06
Molecular Dynamics Simulations  Enhanced Sampling Techniques  Membrane Dynamics  Gpcrs  Lipid-protein Interactions  Ace-2 Membrane Receptor  
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations Journal article
Sinha, Siddharth, Qin, Zixin, Tam, Benjamin, Wang, San Ming. Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations[J]. Briefings in functional genomics, 2022, 21(3), 202-215.
Authors:  Sinha, Siddharth;  Qin, Zixin;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:4 TC[Scopus]:4  IF:2.5/3.4 | Submit date：2022/06/10
Brca2 Brc4  Auc  Deleterious  Molecular Dynamics Simulations  Pca  Roc  Tolerated  Vus Classification