no code implementations • 5 Mar 2024 • Dong Chen, Gengzhuo Liu, Hongyan Du, JunJie Wee, Rui Wang, Jiahui Chen, Jana Shen, Guo-Wei Wei
As COVID-19 enters its fifth year, it continues to pose a significant global health threat, with the constantly mutating SARS-CoV-2 virus challenging drug effectiveness.
no code implementations • 14 Feb 2024 • Theodore Papamarkou, Tolga Birdal, Michael Bronstein, Gunnar Carlsson, Justin Curry, Yue Gao, Mustafa Hajij, Roland Kwitt, Pietro Liò, Paolo Di Lorenzo, Vasileios Maroulas, Nina Miolane, Farzana Nasrin, Karthikeyan Natesan Ramamurthy, Bastian Rieck, Simone Scardapane, Michael T. Schaub, Petar Veličković, Bei Wang, Yusu Wang, Guo-Wei Wei, Ghada Zamzmi
Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models.
1 code implementation • 15 Dec 2023 • Hongsong Feng, Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics.
no code implementations • 3 Dec 2023 • Hongyan Du, Guo-Wei Wei, Tingjun Hou
This study embarked on an innovative and rigorous strategy to unearth potential drug repurposing candidates for opioid and cocaine addiction treatment, bridging the gap between transcriptomic data analysis and drug discovery.
1 code implementation • 28 Oct 2023 • JunJie Wee, Jiahui Chen, Kelin Xia, Guo-Wei Wei
The Transformer, pretrained with hunderds of millions of protein sequences, embeds wild-type and mutant sequences, while persistent Laplacians track the topological invariant change and homotopic shape evolution induced by mutations in 3D protein structures, which are rendered from AlphaFold2.
1 code implementation • 24 Oct 2023 • Yuta Hozumi, Guo-Wei Wei
Single-cell RNA sequencing (scRNA-seq) is a relatively new technology that has stimulated enormous interest in statistics, data science, and computational biology due to the high dimensionality, complexity, and large scale associated with scRNA-seq data.
no code implementations • 23 Oct 2023 • Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
We further introduce a k-Nearest-Neighbor (kNN) persistent Laplacian technique to improve the robustness of our persistent Laplacian method.
1 code implementation • 11 Oct 2023 • Jian Liu, Li Shen, Guo-Wei Wei
This work serves as an initial step towards effectively transforming pure mathematical theories into practical computational tools, with the ultimate goal of enabling real applications across diverse fields.
no code implementations • 14 Aug 2023 • Rui Wang, Hongsong Feng, Guo-Wei Wei
This paper not only explores the integration of advanced AI in drug discovery but also reimagines the landscape by advocating for AI-powered chatbots as trailblazers in revolutionizing therapeutic innovation.
no code implementations • 27 Jul 2023 • Yuchi Qiu, Guo-Wei Wei
Protein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more.
1 code implementation • 11 Jul 2023 • Long Chen, Jian Jiang, Bozheng Dou, Hongsong Feng, Jie Liu, Yueying Zhu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei
Pain is a significant global health issue, and the current treatment options for pain management have limitations in terms of effectiveness, side effects, and potential for addiction.
no code implementations • 13 Jun 2023 • Hongsong Feng, Rui Wang, Chang-Guo Zhan, Guo-Wei Wei
Opioid Use Disorder (OUD) has emerged as a significant global public health issue, with complex multifaceted conditions.
no code implementations • 6 Jun 2023 • Yuchi Qiu, Guo-Wei Wei
Persistent Laplacians, an emerging technique in topological data analysis (TDA), have made structure-based embeddings a superb option in AIDE and AIPE.
no code implementations • 25 May 2023 • Gokul Bhusal, Ekaterina Merkurjev, Guo-Wei Wei
Overall, it is a very efficient procedure that requires much less labeled data to perform well compared to many ML techniques, and it can be adapted for both small and large datasets.
1 code implementation • 1 Mar 2023 • Hongsong Feng, Jian Jiang, Guo-Wei Wei
Using these predictors, we systematically analyzed the binding affinities of DrugBank compounds on four opioid receptors.
no code implementations • 25 Jan 2023 • Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei
Topological data analysis (TDA) is an emerging field in mathematics and data science.
1 code implementation • 12 Jan 2023 • Hongsong Feng, Rana Elladki, Jian Jiang, Guo-Wei Wei
Despite that a few pharmacological agents have been approved for OUD treatment, the efficacy of said agents for OUD requires further improvement in order to provide safer and more effective pharmacological and psychosocial treatments.
1 code implementation • 27 Dec 2022 • Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei
Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery.
1 code implementation • 12 Nov 2022 • Nicole Hayes, Ekaterina Merkurjev, Guo-Wei Wei
In molecular and biological sciences, experiments are expensive, time-consuming, and often subject to ethical constraints.
no code implementations • 18 Oct 2022 • Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei
Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections.
no code implementations • 7 Sep 2022 • Guo-Wei Wei
AI-based forecasting of Omicron's infectivity, vaccine breakthrough, and antibody resistance was later nearly perfectly confirmed by experiments.
2 code implementations • 8 Jun 2022 • Yuta Hozumi, Rui Wang, Guo-Wei Wei
Most dimensionality reduction methods employ frequency domain representations obtained from matrix diagonalization and may not be efficient for large datasets with relatively high intrinsic dimensions.
no code implementations • 1 May 2022 • Jiahui Chen, Yuchi Qiu, Rui Wang, Guo-Wei Wei
In particular, BA. 4 and BA. 5 are about 36\% more infectious than BA. 2 and are projected to become new dominating variants by natural selection.
no code implementations • 20 Apr 2022 • Jiahui Chen, Guo-Wei Wei
It is imperative to develop effective mutation-proof mAbs for treating COVID-19 patients infected by all emerging variants and/or the original SARS-CoV-2.
no code implementations • 10 Feb 2022 • Jiahui Chen, Guo-Wei Wei
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2 variant because of natural selection, which favors the variant with higher infectivity and stronger vaccine breakthrough ability.
1 code implementation • 1 Jan 2022 • Hongsong Feng, Kaifu Gao, Dong Chen, Alfred J Robison, Edmund Ellsworth, Guo-Wei Wei
Cocaine dependence is neurological and involves many interacting proteins in the interactome.
no code implementations • 1 Dec 2021 • Jiahui Chen, Rui Wang, Nancy Benovich Gilby, Guo-Wei Wei
The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B. 1. 1. 529) has ushered panic responses around the world due to its contagious and vaccine escape mutations.
no code implementations • 9 Oct 2021 • Rui Wang, Jiahui Chen, Guo-Wei Wei
The importance of understanding SARS-CoV-2 evolution cannot be overemphasized.
no code implementations • 24 Sep 2021 • Jiahui Chen, Weihua Geng, Guo-Wei Wei
Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions.
1 code implementation • 17 Sep 2021 • Kaifu Gao, Dong Chen, Alfred J Robison, Guo-Wei Wei
Cocaine addiction accounts for a large portion of substance use disorders and threatens millions of lives worldwide.
no code implementations • 15 Sep 2021 • Jiahui Chen, Rui Wang, Guo-Wei Wei
We anticipate that viral evolution will combine RBD co-mutations at these two sites, creating future variants that are tens of times more infectious than the original SARS-CoV-2.
no code implementations • 9 Sep 2021 • Rui Wang, Jiahui Chen, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
The molecular mechanism underlying such surge is elusive due to 4, 653 non-degenerate mutations on the spike protein, which is the target of most COVID-19 vaccines.
1 code implementation • 8 Sep 2021 • Ekaterina Merkurjev, Duc DUy Nguyen, Guo-Wei Wei
In particular, the performance of machine learning methods is often severely affected in case of diverse data, usually associated with smaller data sets or data related to areas of study where the size of the data sets is constrained by the complexity and/or high cost of experiments.
no code implementations • 14 Mar 2021 • Rui Wang, Jiahui Chen, Kaifu Gao, Guo-Wei Wei
We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants can potentially disrupt the binding between the RDB and many known antibodies.
no code implementations • 1 Feb 2021 • Kaifu Gao, Rui Wang, Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta Huzumi, Yuchi Qiu, Tom Schluckbier, Guo-Wei Wei
To provide the reader a quick update about the status of molecular modeling, simulation, and prediction of SARS-CoV-2, we present a comprehensive and systematic methodology-centered narrative in the nick of time.
no code implementations • 17 Aug 2020 • Rui Wang, Yuta Hozumi, Yong-Hui Zheng, Changchuan Yin, Guo-Wei Wei
Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 because of their overreacting to the viral infection.
no code implementations • 24 Jul 2020 • Rui Wang, Jiahui Chen, Kaifu Gao, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
Using genotyping, sequence-alignment, time-evolution, $k$-means clustering, protein-folding stability, algebraic topology, and network theory, we reveal that the US SARS-CoV-2 has four substrains and five top US SARS-CoV-2 mutations were first detected in China (2 cases), Singapore (2 cases), and the United Kingdom (1 case).
no code implementations • 2 Jul 2020 • Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2.
no code implementations • 28 May 2020 • Kaifu Gao, Duc D. Nguyen, Meihua Tu, Guo-Wei Wei
Current drug discovery is expensive and time-consuming.
Biomolecules Quantitative Methods
no code implementations • 5 May 2020 • Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
no code implementations • 29 Apr 2020 • Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
no code implementations • 6 Nov 2017 • Guo-Wei Wei
A century ago physicists and mathematicians worked in tandem and established quantum mechanism.
no code implementations • 31 Mar 2017 • Bao Wang, Zhixiong Zhao, Duc D. Nguyen, Guo-Wei Wei
The underpinning assumptions of FFT-BP are as follows: i) representability: there exists a microscopic feature vector that can uniquely characterize and distinguish one protein-ligand complex from another; ii) feature-function relationship: the macroscopic features, including binding free energy, of a complex is a functional of microscopic feature vectors; and iii) similarity: molecules with similar microscopic features have similar macroscopic features, such as binding affinity.
no code implementations • 31 Mar 2017 • Kedi Wu, Guo-Wei Wei
Toxicity analysis and prediction are of paramount importance to human health and environmental protection.
no code implementations • 4 Oct 2015 • Zixuan Cang, Lin Mu, Kedi Wu, Kristopher Opron, Kelin Xia, Guo-Wei Wei
However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology.
Biomolecules