Article
Biology
Frida Lona-Durazo, Regina H. H. Reynolds, Sonja W. W. Scholz, Mina Ryten, Sarah A. Gagliano A. Taliun
Summary: Comprehensive analysis of GWAS summary statistic and gene expression data reveals significant regional correlations between different neurodegenerative diseases and single-cell immune-related eQTLs. This study systematically assesses the role of the immune system in five neurodegenerative diseases by estimating regional genetic correlations with immune-cell-derived single-cell expression quantitative trait loci (sc-eQTLs). The findings highlight potential risk genes and improve our understanding of the immune component of neurodegeneration, which could lead to the repurposing of existing immunotherapies.
COMMUNICATIONS BIOLOGY
(2023)
Article
Computer Science, Software Engineering
Ravi S. Arvapally, Xiaoqing Frank Liu, Fiona Fui-Hoon Nah, Wei Jiang
Summary: This paper presents a method for identifying stakeholders with outlier opinions in an argumentation process, based on individual stakeholder's opinions and collective opinions on them from other stakeholders. The experiments show that the method effectively detects outlier opinions in an online argumentation process.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2021)
Article
Microbiology
Hongping Guo, Tong Li, Haiyang Wen
Summary: This study identified shared genetic loci between COVID-19 and coronary artery disease, type 2 diabetes, obesity, and hypertension. These shared loci were enriched in signaling pathways and secretion pathways. Mendelian randomization analysis revealed significant causal effects of COVID-19 on coronary artery disease, obesity, and hypertension.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Qian Feng, Kathryn E. Tiedje, Shazia Ruybal-Pesantez, Gerry Tonkin-Hill, Michael F. Duffy, Karen P. Day, Heejung Shim, Yao-Ban Chan
Summary: This study introduces an algorithm to detect recent recombinant sequences without the need for multiple alignment. The algorithm is capable of handling a large number of gene sequences and remains effective in the presence of insertions and deletions. Applying the algorithm to analyze var genes of the malaria parasite, it is observed that sequences belonging to the same ups group or domain subclass recombine more frequently, and non-recombinant sequences are more conserved.
Article
Genetics & Heredity
David Bick, Sarah L. Bick, David P. Dimmock, Tom A. Fowler, Mark J. Caulfield, Richard H. Scott
Summary: Health care providers often turn to internet resources for information on rare genetic disorders, but finding treatment information can be challenging due to scattered details across multiple websites and journals. A website and mobile application mentioned in the article aim to provide a convenient starting point for accessing treatment information and continuously updating existing entries.
AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Xiaohua Guo, Edozie Samuel Okpara, Wanting Hu, Chuyun Yan, Yu Wang, Qionglin Liang, John Y. L. Chiang, Shuxin Han
Summary: The microbial community in the digestive tract and bile acids have a mutual relationship, which may be involved in the pathogenesis of various diseases such as inflammatory bowel disease, colorectal cancer, etc.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Horticulture
Guangxin Liu, Yue Lan, Lianwei Qu, Yilian Zhao, Haoyang Xin, Mengli Xi
Summary: Through our research on wild species and cultivars, we have clarified the genetic relationships between different sections of tulips, as well as the differences and variations in the 5S rDNA sequences. Our findings provide clearer and more stable evidence for the classification of tulips.
SCIENTIA HORTICULTURAE
(2022)
Article
Cardiac & Cardiovascular Systems
Brenda Xiao, Digna Velez R. Edwards, Anastasia Lucas, Theodore Drivas, Kathryn Gray, Brendan Keating, Chunhua Weng, Gail P. Jarvik, Hakon Hakonarson, Leah Kottyan, Noemie Elhadad, Wei-Qi Wei, Yuan Luo, Dokyoon Kim, Marylyn Ritchie, Shefali Setia Verma
Summary: This study aimed to investigate the genetic overlap and impact of cardiometabolic traits on female-specific health conditions. The results showed that there is a significant association between cardiometabolic polygenic scores and certain female-specific health conditions.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Genetics & Heredity
Cato Romero, Josefin Werme, Philip R. Jansen, Joel Gelernter, Murray B. Stein, Daniel Levey, Renato Polimanti, Christiaan de Leeuw, Danielle Posthuma, Mats Nagel, Sophie Van der Sluis
Summary: The comorbidity among psychiatric disorders is supported by genetic correlations, but finding shared biological mechanisms remains challenging due to variation in power and genetic architecture between disorders.
Review
Endocrinology & Metabolism
Tongtong Ye, Guangdong Zhang, Hangyu Liu, Junfeng Shi, Hongyan Qiu, Yongping Liu, Fang Han, Ningning Hou
Summary: PVAT plays a critical role in the development of AAAs and may serve as a therapeutic target.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Luigi Nibali, Abish S. Stephen, Robert P. Allaker, Antonino Di Pino, Valentina Terranova, Marcella Pisano, Salvatore Di Marca, Viviana Ferrara, Roberto Scicali, Francesco Purrello, Nikolaos Donos, Matteo Regolo, Lorenzo Malatino
Summary: Host genetic variants may influence the oral microbiome and play a role in the link between periodontitis and systemic diseases. This study investigated the associations between host genetic variants and subgingival microbiota in patients with metabolic syndrome. Specific SNPs within certain genes were found to be associated with microbial diversity, but no genome-wide associations were detected for periodontitis severity or metabolic syndrome components. Severe periodontitis was associated with pathogenic bacteria. Some SNPs were correlated with specific bacterial genera and taxa. This suggests that host genotypes may contribute to dysregulated immune responses in periodontitis and further interact with the oral microbiome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Psychology, Mathematical
Laura Wall, David Gunawan, Scott D. Brown, Minh-Ngoc Tran, Robert Kohn, Guy E. Hawkins
Summary: This study introduces a statistically principled method to estimate the correlation between latent components of cognitive processing across tasks, contexts, and time. By simultaneously estimating individual and group-level parameters, as well as across-task correlations, the approach shows potential for borrowing strength across testing occasions to increase parameter estimation precision. Examples and simulation studies demonstrate the practicality and reliability of the method in estimating the relatedness of cognitive processes across different conditions.
BEHAVIOR RESEARCH METHODS
(2021)
Article
Multidisciplinary Sciences
Khunanon Chanasongkhram, Kasikrit Damkliang, Unitsa Sangket
Summary: In this study, a novel R library called DisVar was developed to identify disease-associated genetic variants in large-scale individual genomic data. DisVar is capable of searching for over 100 million variants simultaneously and can overcome the limitations of existing tools.
Article
Biochemistry & Molecular Biology
Simon Haworth, Pik Fang Kho, Pernilla Lif Holgerson, Liang-Dar Hwang, Nicholas J. Timpson, Miguel E. Renteria, Ingegerd Johansson, Gabriel Cuellar-Partida
Summary: Hypothesis-free Mendelian randomization studies and the LCV approach provide methods for causal inference across the human phenome. Automated pipeline for phenome-wide tests using LCV approach shows that lipids and BMI contribute to multiple traits and conditions, while dental caries and periodontitis are downstream consequences of other traits and diseases. Causal architecture plots based on partial genetic causality estimates offer a new way to visualize the overall causal map of the human phenome.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Computer Science, Information Systems
Qianqiao Liang, Xiaolin Zheng, Yan Wang, Mengying Zhu
Summary: This study discusses explainable recommendation systems (ERSs) and the E-3 model in an online learning setting, overcoming the limitations of existing ERSs in offline settings and proposing an online setting to adapt to real-time feedback for improved recommendations and explanations. By immediately integrating online feedback into the model, the E-3 model remarkably enhances performance in online scenarios.
INFORMATION SCIENCES
(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)
Letter
Infectious Diseases
Shizheng Qiu, Donghua Wang, Yu Zhang, Yang Hu
JOURNAL OF INFECTION
(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)
Article
Biochemical Research Methods
Fuxu Wang, Haoyan Wang, Lizhuang Wang, Haoyu Lu, Shizheng Qiu, Tianyi Zang, Xinjun Zhang, Yang Hu
Summary: This study introduces the MHCRoBERTa method, which uses RoBERTa pre-training approach to predict the binding affinity between type I MHC and peptides. Experimental results show that MHCRoBERTa outperforms other prediction methods, with a significant improvement on IC50 value, demonstrating its potential in cancer immunotherapy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yang Hu, Yan Zhang, Haihua Zhang, Shan Gao, Longcai Wang, Tao Wang, Zhifa Han, Bao-Liang Sun, Guiyou Liu
Summary: This study used large-scale genome-wide association studies (GWAS) to investigate the causal relationship between educational attainment, cognitive performance, intelligence, and Alzheimer's disease (AD) through univariable and multivariable Mendelian-randomization (MR) analyses. The findings highlight the protective role of cognitive performance in AD, independently of educational attainment and intelligence.
MOLECULAR PSYCHIATRY
(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.
Letter
Infectious Diseases
Yu Guo, Ying Zhang, Yang Hu
JOURNAL OF INFECTION
(2023)
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)
