Research

(updated on Dec 19, 2024)

Research Interests

BioTech, Biomedical Engineering

Publications 

https://scholar.google.com/citations?user=SmQ5WHMAAAAJ&hl=en

Chen, Lingtao, Qiaomu Li, Kazi Fahim Ahmad Nasif, Ying Xie, Bobin Deng, Shuteng Niu, Seyedamin Pouriyeh, Zhiyu Dai, Jiawei Chen, and Chloe Yixin Xie. "AI-Driven Deep Learning Techniques in Protein Structure Prediction." International journal of molecular sciences 25, no. 15 (2024): 8426.

Chen, Jiawei, Lingtao Chen, Heng Quan, Soongoo Lee, Kaniz Fatama Khan, Ying Xie, Qiaomu Li, Maria Valero, Zhiyu Dai, and Yixin Xie. "A Comparative Analysis of SARS-CoV-2 Variants of Concern (VOC) Spike Proteins Interacting with hACE2 Enzyme." International journal of molecular sciences 25, no. 15 (2024): 8032.

Chen, Jiawei, Ravi Potlapalli, Heng Quan, Lingtao Chen, Ying Xie, Seyedamin Pouriyeh, Nazmus Sakib, Lichao Liu, and Yixin Xie. "Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights." BioTech 13, no. 1 (2024): 3.

Kamau, Toni, Kareigh Gammon, Johaan Kathilankal Jis, and Chloe Yixin Xie. "Understand the mechanisms of Uracil-DNA glycosylase using computational methods." (2024).

Deng, Bobin, Bhargava Nadendla, Kun Suo, Yixin Xie, and Dan Chia-Tien Lo. "Fixed-point Encoding and Architecture Exploration for Residue Number Systems." ACM Transactions on Architecture and Code Optimization (2024).

Addepalli, Durga Narayana Varma, Jiawei Chen, and Chloe Yixin Xie. "Molecular Dynamics Simulations on Coronavirus Variants of Concern (VOC)." ACM. The 24th Annual Conference on Information Technology Education, pp. 213-215. 2023.

Anik, Fahim Islam, Nazmus Sakib, Hossain Shahriar, Yixin Xie, Helal An Nahiyan, and Sheikh Iqbal Ahamed. "Unraveling a blockchain-based framework towards patient empowerment: A scoping review envisioning future smart health technologies." Smart Health 29 (2023): 100401.

Rodriguez, G., Martinez, G.S., Negrete, O.D., Sun, S., Guo, W., Xie, Y., Li, L., Xiao, C., Ross, J.A. and Kirken, R.A., 2023. “JAK3 Y841 Autophosphorylation Is Critical for STAT5B Activation, Kinase Domain Stability and Dimer Formation”. International Journal of Molecular Sciences, 24(15), p.11928.

Donkada, Sricharan, Seyedamin Pouriyeh, Reza M. Parizi, Chloe Yixin Xie, and Hossain Shahriar. "Early Heart Disease Detection Using Mel-Spectrograms and Deep Learning.” 2023 IEEE Symposium on Computers and Communications (ISCC), pp. 1-6. IEEE, 2023.

Sun, Shengjie, Georgialina Rodriguez, Yixin Xie, Wenhan Guo, Alan E. Lopez Hernandez, Jason E. Sanchez, Robert Arthur Kirken, and Lin Li. "Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation." Life 13, no. 4 (2023): 981.

Sun, Shengjie, Honglun Xu, Yixin Xie, Jason E. Sanchez, Wenhan Guo, Dongfang Liu, and Lin Li. "HIT-2: Implementing machine learning algorithms to treat bound ions in biomolecules." Computational and Structural Biotechnology Journal 21 (2023): 1383-1389.

Xie, Yixin, and Lin Li. "Computational Study on the Electrostatic Interactions between Uracil‐DNA Glycosylase (UDG) and DNA." The FASEB Journal 36 (2022).

Xie, Yixin, and Lin Li. "Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin." International Journal of Molecular Sciences 23, no. 4 (2022): 2035.

Xie, Yixin, Wenhan Guo, Alan Lopez-Hernadez, Shaolei Teng, and Lin Li. "The pH effects on SARS-CoV and SARS-CoV-2 spike proteins in the process of binding to hACE2." Pathogens 11, no. 2 (2022): 238.

Guo, Wenhan, Shengjie Sun, Jason E. Sanchez, Alan E. Lopez-Hernandez, Tolulope A. Ale, Jiawei Chen, Tanjina Afrin, Weihong Qiu, Yixin Xie, and Lin Li. "Using a comprehensive approach to investigate the interaction between Kinesin-5/Eg5 and the microtubule." Computational and structural biotechnology journal 20 (2022): 4305-4314.

Sun, Shengjie, Juan A. Lopez, Yixin Xie, Wenhan Guo, Dongfang Liu, and Lin Li. "HIT web server: A hybrid method to improve electrostatic calculations for biomolecules." Computational and Structural Biotechnology Journal 20 (2022): 1580-1583.

Cui, Yiming, Zhiwen Cao, Yixin Xie, Xingyu Jiang, Feng Tao, Yingjie Victor Chen, Lin Li, and Dongfang Liu. "Dg-labeler and dgl-mots dataset: Boost the autonomous driving perception." In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, pp. 58-67. 2022.

Sobitan, Adebiyi, Vidhyanand Mahase, Raina Rhoades, Dejaun Williams, Dongxiao Liu, Yixin Xie, Lin Li, Qiyi Tang, and Shaolei Teng. "Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2." Frontiers in Molecular Biosciences (2021): 1212.

Xie, Yixin, Chitra B. Karki, Jiawei Chen, Dongfang Liu, and Lin Li. "Computational study on DNA repair: The roles of electrostatic interactions between uracil-DNA glycosylase (UDG) and DNA." Frontiers in Molecular Biosciences 8 (2021): 718587.

Lopez-Hernandez, Alan E., Yixin Xie, Wenhan Guo, and Lin Li. "The electrostatic features of dengue virus capsid assembly." Journal of Computational Biophysics and Chemistry 20, no. 02 (2021): 201-207.

Guo, Wenhan, Yixin Xie, Alan E. Lopez-Hernandez, Shengjie Sun, and Lin Li. "Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2." Mathematical biosciences and engineering: MBE 18, no. 3 (2021): 2372.

Xian, Yuejiao, Yixin Xie, Sebastian Miki Silva, Chitra B. Karki, Weihong Qiu, and Lin Li. "StructureMan: A structure manipulation tool to study large scale biomolecular interactions." Frontiers in molecular biosciences 7 (2021): 627087.

Sun, Shengjie, Chitra Karki, Yixin Xie, Yuejiao Xian, Wenhan Guo, Bruce Z. Gao, and Lin Li. "Hybrid method for representing ions in implicit solvation calculations." Computational and Structural Biotechnology Journal 19 (2021): 801-811.

Xie, Yixin, Chitra B. Karki, Dan Du, Haotian Li, Jun Wang, Adebiyi Sobitan, Shaolei Teng, Qiyi Tang, and Lin Li. "Spike proteins of SARS-CoV and SARS-CoV-2 utilize different mechanisms to bind with human ACE2." Frontiers in molecular biosciences (2020): 392.

Mahase, Vidhyanand, Adebiyi Sobitan, Christina Johnson, Farion Cooper, Yixin Xie, Lin Li, and Shaolei Teng. "Computational analysis of hereditary spastic paraplegia mutations in the kinesin motor domains of KIF1A and KIF5A." Journal of Theoretical and Computational Chemistry 19, no. 06 (2020): 2041003.

Xie, Yixin, Dan Du, Chitra B. Karki, Wenhan Guo, Alan E. Lopez-Hernandez, Shengjie Sun, Brenda Y. Juarez, Haotian Li, Jun Wang, and Lin Li. "Revealing the mechanism of SARS-CoV-2 spike protein binding with ACE2." Computing in science & engineering 22, no. 6 (2020): 21-29.

Karki, Chitra, Yuejiao Xian, Yixin Xie, Shengjie Sun, Alan E. Lopez-Hernandez, Brenda Juarez, Jun Wang, Jianjun Sun, and Lin Li. "A computational model of ESAT-6 complex in membrane." Journal of Theoretical and Computational Chemistry 19, no. 03 (2020): 2040002.

Salas, Gicela G. Saucedo, Alan E. Lopez Hernandez, Jiadi He, Chitra Karki, Yixin Xie, Shengjie Sun, Yuejiao Xian, and Lin Li. "Using computational approaches to study dengue virus capsid assembly." Computational and Mathematical Biophysics 7, no. 1 (2019): 64-72.