Article
Medicine, Research & Experimental
Vu Viet Hoang Pham, Lin Liu, Cameron Bracken, Gregory Goodall, Jiuyong Li, Thuc Duy Le
Summary: Researchers conducted a comprehensive review of computational methods for discovering cancer drivers, categorizing them into three groups and evaluating their performance in identifying biologically significant cancer drivers to provide readers with information.
Article
Biochemical Research Methods
Xiaohui Shi, Huajing Teng, Leisheng Shi, Wenjian Bi, Wenqing Wei, Fengbiao Mao, Zhongsheng Sun
Summary: This study evaluates and compares the performance of different algorithms based on network, function, and frequency in identifying mutation driver genes. The results show that the frequency-based driverMAPS and network-based HotNet2 methods perform the best. Network-based algorithms using protein-protein interaction networks outperform function- and frequency-based methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Pharmacology & Pharmacy
Martina Krusic, Gregor Jezernik, Uros Potocnik
Summary: The aim of this study was to examine the molecular mechanism of treatment responsiveness in psoriasis patients receiving biological drugs. By reviewing previous articles reporting genes associated with treatment response and performing gene ontology analysis, a significant association between NF-kappaB signaling, regulation of granulocyte macrophage colony-stimulating factor production, glial cell proliferation, and treatment response in psoriatic patients was identified. This study is the first to directly associate glial cells with treatment response and provides novel gene ontology terms implicated in the molecular pathway of psoriasis.
Article
Chemistry, Physical
Aimin Chen, Tianshou Zhou, Pamela Burrage, Tianhai Tian, Kevin Burrage
Summary: Stochastic differential equations (SDE) are a powerful tool for modeling biological regulatory processes, but numerical simulations of SDE models can be problematic when the noise terms are negative and large. To address this issue, the composite Patankar-Euler methods are proposed to obtain positive simulations of SDE models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Pharmacology & Pharmacy
Qiaoqiao Han, Hengtao Fu, Xiaoyue Chu, Ruixin Wen, Miao Zhang, Tao You, Peng Fu, Jian Qin, Tao Cui
Summary: With the increasing incidence of rare diseases, the global number of rare disease patients is nearing 400 million. Orphan medications, used to treat these diseases, are rare and expensive, leading to difficulties for patients to access them. However, due to substantial investments in the field of rare diseases, orphan drugs have become a focus for new drug research and development by pharmaceutical companies worldwide.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Sahil Ahlawat, Kaustubh R. Mote, Nils-Alexander Lakomek, Vipin Agarwal
Summary: In the past two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has evolved from investigating small molecules and industrial polymers to decrypting complex biological systems. This transformation is due to improvements in hardware design, sample preparation, and sensitivity. This review discusses state-of-the-art ssNMR methods and recent developments in signal filtering, proton methodologies, and data acquisition speed in fast magic-angle spinning (MAS) systems.
Review
Chemistry, Multidisciplinary
Sahil Ahlawat, Kaustubh R. Mote, Nils-Alexander Lakomek, Vipin Agarwal
Summary: In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has evolved from investigating small molecules and industrial polymers to decoding complex biological systems. Improvements in hardware design, sample preparation, and various techniques have increased the efficiency and accuracy of ssNMR in biological samples.
Review
Endocrinology & Metabolism
Eftaxia-Konstantina Valanti, Katerina Dalakoura-Karagkouni, Gerasimos Siasos, Dimitris Kardassis, Aristides G. Eliopoulos, Despina Sanoudou
Summary: Atherosclerosis is a multifactorial disease influenced by genetics, lifestyle, and environmental factors. Targeting genes involved in lipoprotein metabolism is considered a new approach for prevention and treatment. Multiple lipid lowering biological therapies have been approved by the FDA with impressive results in clinical trials.
METABOLISM-CLINICAL AND EXPERIMENTAL
(2021)
Review
Pharmacology & Pharmacy
Yajie Zhang, Daniel A. Davis, Khaled AboulFotouh, Jieliang Wang, Donna Williams, Akhilesh Bhambhani, Michael Zakrewsky, Mohammed Maniruzzaman, Zhengrong Cui, Robert O. Williams
Summary: Recent advances in formulation sciences have expanded the design space for biological modalities, but new modalities like cellular and gene therapies pose challenges for scientists. To overcome these challenges, formulation scientists are developing novel formulations and drug delivery systems to improve patient compliance and stability.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Chemistry, Multidisciplinary
Viktoriya Sokolova, Matthias Epple
Summary: Calcium phosphate nanoparticles, due to their similarity to human hard tissue, have high biocompatibility and biodegradability, making them efficient carriers for various biomolecules. They can be functionalized with fluorescing dyes for imaging, and find applications in transfection, gene silencing, imaging, immunization, and bone substitution.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Jiaxi Peng, Calvin Chan, Shuailong Zhang, Alexandros A. Sklavounos, Maxwell E. Olson, Erica Y. Scott, Yechen Hu, Vigneshwar Rajesh, Bingyu B. Li, M. Dean Chamberlain, Shen Zhang, Hui Peng, Aaron R. Wheeler
Summary: This study reports the development of an All-in-One digital microfluidic (DMF) pipeline for proteomic sample analysis. The pipeline allows for automated sample reduction, alkylation, digestion, isotopic labeling, and analysis. The integration of dimethyl labeling enables relative quantification of trace samples at the nanogram level. The All-in-One pipeline shows potential for evaluating mass-limited samples and could be useful for proteomic cancer sub-typing.
Review
Microbiology
Liat Shenhav, Meghan B. Azad
Summary: Human milk is a complex and dynamic biological system that plays a crucial role in nourishing and protecting human infants. However, our current understanding of its composition and functions fails to fully recognize the importance of its chronobiology and systems biology. This knowledge gap can be attributed to the isolated study of each subsystem of the mother-milk-infant triad, limited consideration of temporal variability, and lack of computational methods to characterize and decipher the complex ecosystem. Longitudinal multiomics data collection and the integration of microbial community ecology and computational methods offer promising avenues for advancing the study of human milk as a comprehensive system.
Article
Engineering, Biomedical
Benjamin W. W. Streeter, Milton E. E. Brown, Preety Shakya, Hyun-Ji Park, Jichuan Qiu, Younan Xia, Michael E. E. Davis
Summary: Computational modeling was used to identify repair mechanisms in cardiac-derived c-Kit+ cells and design biomaterials to improve cardiac patch performance. Testing on CPCs from four donors showed that only patients with high ITGAV expression had improved anti-fibrotic and pro-angiogenic paracrine secretion on PCL + FN patches.
Article
Biochemical Research Methods
Dmytro Iurashev, Peter Anthony Jones, Nadejda Andreev, Yana Wang, Tomoko Iwata-Kajihara, Barbara Kraus, Juan A. Hernandez Bort
Summary: This article investigates the scale-up/-down of bioreactors in cell and gene therapy, focusing on the effect of shear stress on cell quality and yield. Computational fluid dynamics simulations are used to estimate the distribution of Kolmogorov length in different scales. The study provides experimental data and computational analysis to support the selection of appropriate bioreactors and operating conditions for various process steps in cell and gene therapy.
BIOTECHNOLOGY JOURNAL
(2023)
Review
Engineering, Marine
Michela Carlin, Marco Pelin, Cristina Ponti, Silvio Sosa, Aurelia Tubaro
Summary: Palytoxin and its analogues are marine polyethers that can cause adverse effects on humans. Various detection methods have been developed, including structural immunoassays and functional cell-based assays, which are sensitive and cost-effective. These methods play an important role in the rapid screening of Palytoxin.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Biochemical Research Methods
Liang Cheng, Xudong Han, Zijun Zhu, Changlu Qi, Ping Wang, Xue Zhang
Summary: Since the end of 2019, the COVID-19 pandemic has rapidly spread worldwide. Limited virus strains initially led to few mutations, but a steady mutation rate suggests an evolution towards increased infectivity and reduced virulence.
BRIEFINGS IN BIOINFORMATICS
(2021)
Letter
Multidisciplinary Sciences
Liang Cheng, Zijun Zhu, Chao Wang, Ping Wang, Yongqun Oliver He, Xue Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Feifei Cui, Liang Cheng, Quan Zou
BRIEFINGS IN FUNCTIONAL GENOMICS
(2021)
Article
Mathematical & Computational Biology
Yang Hu, Shizheng Qiu, Liang Cheng
Summary: This study analyzed population-specific genetic differences in coronary artery disease (CAD) between European and East Asian descents, identified novel susceptibility genes, evaluated variants, enriched risk genes, and explored population-specific differences. The integration of data from independent studies revealed population-specific pleiotropic/causal genes for CAD, highlighting the importance of elucidating genetic variations among different populations for a better understanding of pathogenic mechanisms and potential therapeutic targets for CAD.
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
(2021)
Article
Genetics & Heredity
Zijun Zhu, Xudong Han, Liang Cheng
Summary: This study integrates genetic mutation information and expression data to obtain a predictive signature for T2DM, which shows excellent performance and robustness.
CURRENT GENE THERAPY
(2022)
Review
Biochemistry & Molecular Biology
Haixiu Yang, Changlu Qi, Boyan Li, Liang Cheng
Summary: Recent studies have revealed the significant role of non-coding RNAs in regulating drug resistance in tumor cells. Understanding the relationship between ncRNAs and drug resistance can provide valuable insights into the mechanisms and biomarkers of chemoresistance, as well as facilitate personalized anticancer treatment regimens.
CURRENT MEDICINAL CHEMISTRY
(2022)
Letter
Infectious Diseases
Shizheng Qiu, Yang Hu, Liang Cheng
JOURNAL OF INFECTION
(2022)
Article
Biochemistry & Molecular Biology
Liang Cheng, Changlu Qi, Haixiu Yang, Minke Lu, Yiting Cai, Tongze Fu, Jialiang Ren, Qu Jin, Xue Zhang
Summary: gutMGene, a manually curated database, provides a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. The database documents curated relationships between gut microbes, microbial metabolites and genes in both species. The user-friendly interface allows browsing and retrieval of entries, and also offers the option to download all entries and submit new validated associations.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Zijun Zhu, Sainan Zhang, Ping Wang, Xinyu Chen, Jianxing Bi, Liang Cheng, Xue Zhang
Summary: This article reviews the advantages and limitations of integrating omics data for SARS-CoV-2 and COVID-19, and summarizes the existing data analysis methods and research results. It also proposes research directions for the integration of SARS-CoV-2 (COVID-19) multi-omics data and presents a case study for deeper exploration of the disease mechanisms of COVID-19.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Changlu Qi, Chao Wang, Lingling Zhao, Zijun Zhu, Ping Wang, Sainan Zhang, Liang Cheng, Xue Zhang
Summary: SCovid is a comprehensive resource of single-cell data to explore the molecular characteristics of COVID-19 in different human tissues. It collects 21 single-cell datasets and reveals the molecular features of COVID-19 through manual annotation.
NUCLEIC ACIDS RESEARCH
(2022)
Letter
Multidisciplinary Sciences
Zijun Zhu, Xinyu Chen, Chao Wang, Liang Cheng
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Junjie Wang, Jie Hu, Huiting Sun, MengDie Xu, Yun Yu, Yun Liu, Liang Cheng
Summary: In this study, we propose a multigranularity protein-ligand interaction model, which utilizes the Transformer model and convolutional neural network to accurately predict the binding affinity between drugs and protein targets.
Article
Biochemistry & Molecular Biology
Changlu Qi, Yiting Cai, Kai Qian, Xuefeng Li, Jialiang Ren, Ping Wang, Tongze Fu, Tianyi Zhao, Liang Cheng, Lei Shi, Xue Zhang
Summary: The gut microbiota plays a crucial role in maintaining health, and disruptions can lead to disorders. The gutMDisorder database provides a valuable resource for studying dysbiosis, and the latest version offers expanded data and improved features.
NUCLEIC ACIDS RESEARCH
(2023)
Letter
Gastroenterology & Hepatology
Zijun Zhu, Xinyu Chen, Chao Wang, Sainan Zhang, Liang Cheng
Article
Virology
Zijun Zhu, Xinyu Chen, Chao Wang, Sainan Zhang, Rui Yu, Yubin Xie, Shuofeng Yuan, Liang Cheng, Lei Shi, Xue Zhang
Summary: This study conducted a genome-wide association study (GWAS) to identify host genetic factors associated with COVID-19. The correlation between genetic variations and gene expression was assessed using expression quantitative trait locus (eQTL) analysis. The findings revealed 20 genes significantly associated with immunity and neurological disorders. Single-cell datasets were used to validate these findings and to explore the causal relationship between COVID-19 and neurological disorders. Cell experiments were conducted to investigate the effects of COVID-19-related protein-coding genes. This study provides important insights into the genetic architecture underlying the pathophysiology of COVID-19.
JOURNAL OF MEDICAL VIROLOGY
(2023)
