Article
Multidisciplinary Sciences
Kohei Fukuto, Tatsuya Takagi, Yu-Shi Tian
Summary: This study constructed a more accurate side effect prediction model using the logistic matrix factorization algorithm, addressing importance differences and cold-start problems through a weighting strategy and mapping method, improving prediction accuracy and potential applications in clinical warning systems.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Nina Lukashina, Elena Kartysheva, Ola Spjuth, Elizaveta Virko, Aleksei Shpilman
Summary: This paper investigates polypharmacy and its side effect prediction, proposing a new method called SimVec that enhances the knowledge graph (KG) structure and optimizes the learning process to improve the prediction. The experimental results show that the new method outperforms existing approaches in predicting polypharmacy side effects, and a cache-based approach is suggested for negative relations generation.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Ophthalmology
Blake Hugo Fortes, Harris Liou, Lauren A. Dalvin
Summary: Among 996 patients receiving immune checkpoint inhibitors, 28 (2.8%) experienced ophthalmic side effects requiring the attention of an eye care provider. PD-L1-targeted therapy was more likely to cause ocular surface adverse effects, but most ophthalmic events can be managed with targeted therapy without discontinuing life-prolonging immunotherapy.
BRITISH JOURNAL OF OPHTHALMOLOGY
(2021)
Article
Biochemical Research Methods
Xianyu Xu, Ling Yue, Bingchun Li, Ying Liu, Yuan Wang, Wenjuan Zhang, Lin Wang
Summary: In this study, a new method called DSGAT is proposed to predict the frequencies of drug side effects by using drug molecular graph instead of the conventional interaction graph. This method has the capability to learn embeddings for cold start drugs and addresses the sparsity issue with a novel loss function. Experimental results demonstrate significant improvement for cold start drugs and superior performance in the warm start scenario.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Junfeng Yao, Wen Sun, Zhongquan Jian, Qingqiang Wu, Xiaoli Wang
Summary: This paper proposes a novel model that incorporates complex relations of side effects into knowledge graph embeddings to predict the side effects of polypharmacy. Experimental results show that the model outperforms other methods in terms of performance.
Article
Biochemical Research Methods
Pietro Bongini, Franco Scarselli, Monica Bianchini, Giovanna Maria Dimitri, Niccolo Pancino, Pietro Lio
Summary: Drug side-effects have a significant impact on public health, care system costs, and drug discovery processes. Predicting the probability of side-effects before their occurrence is crucial to reduce this impact, especially in drug discovery. By integrating heterogeneous data into a graph dataset, this study successfully utilizes Graph Neural Networks (GNNs) to predict drug side-effects, showing promising results. The experimental results highlight the significance of utilizing relationships between data entities and suggest potential future developments in this field.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Environmental Sciences
Francesca Cappelli, Orietta Longoni, Jacopo Rigato, Michele Rusconi, Alberto Sala, Igor Fochi, Maria Teresa Palumbo, Stefano Polesello, Claudio Roscioli, Franco Salerno, Fabrizio Stefani, Roberta Bettinetti, Sara Valsecchi
Summary: During the SARS-CoV-2 pandemic, the provisional use of various drugs for COVID-19 treatment led to the release of pharmaceuticals into the environment through wastewater treatment plants. This study investigated the presence of COVID-19 treatment drugs in three WWTPs in Lombardy, Italy using suspect screening techniques. The results showed a positive correlation between the use of certain drugs and the number of COVID-19 cases and deaths. Additionally, the presence of compounds with ecological concerns was detected in the receiving water bodies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Immunology
Roshina Rabail, Waqar Ahmed, Madiha Ilyas, Muhammad Shahid Riaz Rajoka, Abdo Hassoun, Abdur Rauf Khalid, Moazzam Rafiq Khan, Rana Muhammad Aadil
Summary: COVID-19 vaccines play a vital role in protecting public health, but the acceptance is influenced by their efficacy and side effects. Research has shown that different types of vaccines have different safety profiles, with DNA and mRNA vaccines having more persistent side effects, while inactivated viral vaccines are associated with longer-lasting side effects. Women and younger individuals are more likely to experience side effects.
Article
Multidisciplinary Sciences
Elham Jamshidi, Amirhossein Asgary, Ali Yazdizadeh Kharrazi, Nader Tavakoli, Alireza Zali, Maryam Mehrazi, Masoud Jamshidi, Babak Farrokhi, Ali Maher, Christophe von Garnier, Sahand Jamal Rahi, Nahal Mansouri
Summary: This study developed a novel machine learning approach to predict the most common adverse side effects of COVID-19 vaccines based on personal and health-related characteristics. The results showed that this method can accurately predict the occurrence of adverse side effects and can be used as a tool for vaccine selection and personalized information to alleviate concerns about vaccine adverse effects.
Article
Oncology
Su Zhang, Manqing Cao, Zhenyu Hou, Xiaoying Gu, Yongzi Chen, Lu Chen, Yi Luo, Liwei Chen, Dongming Liu, Hongyuan Zhou, Keyun Zhu, Zhiwei Wang, Xihao Zhang, Xiaolin Zhu, Yunlong Cui, Huikai Li, Hua Guo, Ti Zhang
Summary: ACE inhibitors are not effective in reducing proteinuria caused by anti-angiogenic drugs (AADs), and may even exacerbate AADs' anticancer effects. This finding highlights the importance of careful management of side effects in cancer patients undergoing anti-angiogenic therapy.
Article
Genetics & Heredity
Manon G. den Uil, Hannelotte W. Hut, Kay R. Wagelaar, Heshu Abdullah-Koolmees, Wiepke Cahn, Ingeborg Wilting, Vera H. M. Deneer
Summary: This study aims to investigate the influence of pharmacogenetic profile and phenoconversion on side effects experienced by psychiatric patients. The results show that phenoconversion is common for CYP2C19 and CYP2D6 when co-medication is used. Patients with an Intermediate metabolizer or Poor metabolizer phenotype of CYP2C19 had a higher incidence of nausea and vomiting, while those with an Intermediate metabolizer or Poor metabolizer phenotype of CYP2D6 had a higher incidence of depression.
FRONTIERS IN GENETICS
(2023)
Article
Immunology
Ma'mon M. Hatmal, Mohammad A. I. Al-Hatamleh, Amin N. Olaimat, Malik Hatmal, Dina M. Alhaj-Qasem, Tamadur M. Olaimat, Rohimah Mohamud
Summary: The study confirms the safety of authorized COVID-19 vaccines, with most side effects being mild to moderate, indicating the body's immune system is building protection. Many individuals feel more reassured after vaccination and recommend others to get vaccinated.
Article
Medicine, Research & Experimental
Dragica Bozic, Katarina Baralic, Katarina Zivancevic, Evica Antonijevic Miljakovic, Marijana Curcic, Biljana Antonijevic, Aleksandra Buha Djordjevic, Zorica Bulat, Yi Zhang, Li Yang, Danijela Dukic-Cosic
Summary: Colorectal cancer is a significant global health burden, with new therapeutic strategies such as sulforaphane being explored. However, its safety in CRC patients remains uncertain. The study identified several genes in CRC that could serve as predictive biomarkers, but there are still controversies regarding their safety.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemical Research Methods
Lin Wang, Chenhao Sun, Xianyu Xu, Jia Li, Wenjuan Zhang
Summary: In this study, a new method (NRFSE) is proposed to predict the frequency of drug side effects. By leveraging multiview data on drugs and side effects, this method can effectively guide randomized controlled trials and outperforms other approaches in terms of prediction performance.
Review
Nutrition & Dietetics
Matej Malik, Pavel Tlustos
Summary: This review provides an up-to-date overview of nootropics, discussing their classification, uses, dosage, side effects, and contraindications. It also briefly describes the plant extracts with nootropic effects and provides recommendations for the use of nootropics by both ill and healthy individuals.
Review
Physiology
Mark J. Burish, Zheng Chen, Seung-Hee Yoo
Article
Biology
Syed Aun Muhammad, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, Jake Y. Chen
JOURNAL OF BIOLOGICAL RESEARCH-THESSALONIKI
(2019)
Article
Infectious Diseases
G. Clement Dobbins, Amit Patki, Dongquan Chen, Hemant K. Tiwari, Curtis Hendrickson, William J. Britt, Karen Fowler, Jake Y. Chen, Suresh B. Boppana, Shannon A. Ross
BMC INFECTIOUS DISEASES
(2019)
Correction
Infectious Diseases
G. Clement Dobbins, Amit Patki, Dongquan Chen, Hemant K. Tiwari, Curtis Hendrickson, William J. Britt, Karen Fowler, Jake Y. Chen, Suresh B. Boppana, Shannon A. Ross
BMC INFECTIOUS DISEASES
(2020)
Article
Cell Biology
Keshav K. Singh, Gyaneshwer Chaubey, Jake Y. Chen, Prashanth Suravajhala
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2020)
Article
Immunology
Huixian Hong, Min Gao, Qi Wu, Philomena Yang, Shanrun Liu, Hao Li, Peter D. Burrows, Daniel Cua, Jake Y. Chen, Hui-Chen Hsu, John D. Mountz
JOURNAL OF IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Eric Zhang, Thanh Nguyen, Meng Zhao, Son Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Article
Cell Biology
Syed Aun Muhammad, Hiba Ashfaq, Sidra Zafar, Fahad Munir, Muhammad Babar Jamshed, Jake Chen, Qiyu Zhang
BMC MOLECULAR AND CELL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Deng, James J. Cimino, Jake Y. Chen
Summary: PAGER-CoV is a new web-based database that assists biomedical researchers in interpreting coronavirus-related functional genomic study results using a vast collection of PAGs. By exploring relationships between PAGs, users can gain deeper insights into the research information. This database can help researchers find molecular biology mechanisms and tailored therapeutics for treating COVID-19 patients.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Medical Informatics
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen
Summary: This study demonstrated the use of clinical information and electronic medical records to support precision medicine research and clinical decision-making on complex diseases. Through integration of public omic databases and advanced machine learning techniques, the study successfully addressed issues such as patient stratification, significant associations between clinical information and diseases, and potential linkages between clinical information and genomic data.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2021)
Review
Neurosciences
Radomir M. Slominski, Chander Raman, Jake Y. Chen, Andrzej T. Slominski
Summary: During oncogenesis, tumors can affect local and systemic homeostasis by producing cytokines, immune mediators, neurotransmitters, and other substances. They can control the central neuroendocrine and immune systems to promote their own growth and expansion.
TRENDS IN NEUROSCIENCES
(2023)
Article
Genetics & Heredity
Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen
Summary: The Polar Gini Curve is a method for characterizing cluster markers by analyzing single-cell RNA sequencing data, which helps users understand the shape and density distribution of cells in a particular cluster. By combining gene expression and spatial information, it can detect uniformity patterns within clustered cells and identify biomarkers with consistent gene expression patterns across clusters.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John D. Osborne, Amy Y. Wang, S. Louis Bridges, Matt Wyatt, Jake Y. Chen
2020 IEEE 21ST INTERNATIONAL CONFERENCE ON INFORMATION REUSE AND INTEGRATION FOR DATA SCIENCE (IRI 2020)
(2020)
Article
Mathematical & Computational Biology
Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen
QUANTITATIVE BIOLOGY
(2019)
Article
Oncology
Xiaowen Liu, Zongliang Yue, Yimou Cao, Lauren Taylor, Qing Zhang, Sung W. Choi, Samir Hanash, Sawa Ito, Jake Y. Chen, Huanmei Wu, Sophie Paczesny
JCO PRECISION ONCOLOGY
(2019)