Binglan Li
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View article: Association between carotid artery hemodynamics and neurovascular coupling in cerebral small vessel disease: an exploratory study
Association between carotid artery hemodynamics and neurovascular coupling in cerebral small vessel disease: an exploratory study Open
Background Recent studies have linked disrupted cerebral hemodynamics, including pulsatility index (PI) and wall shear stress (WSS), with neuroimaging features of cerebral small vessel disease (CSVD). Cerebral neurovascular coupling (NVC) …
View article: PGxQA: A Resource for Evaluating LLM Performance for Pharmacogenomic QA Tasks
PGxQA: A Resource for Evaluating LLM Performance for Pharmacogenomic QA Tasks Open
Pharmacogenetics represents one of the most promising areas of precision medicine, with several guidelines for genetics-guided treatment ready for clinical use. Despite this, implementation has been slow, with few health systems incorporat…
View article: Red Teaming Large Language Models in Medicine: Real-World Insights on Model Behavior
Red Teaming Large Language Models in Medicine: Real-World Insights on Model Behavior Open
0. Abstract Background The integration of large language models (LLMs) in healthcare offers immense opportunity to streamline healthcare tasks, but also carries risks such as response accuracy and bias perpetration. To address this, we con…
View article: Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms Open
Genes act in concert with each other in specific contexts to perform their functions. Determining how these genes influence complex traits requires a mechanistic understanding of expression regulation across different conditions. It has be…
View article: Gene burden analysis identifies genes associated with increased risk and severity of adult-onset hearing loss in a diverse hospital-based cohort
Gene burden analysis identifies genes associated with increased risk and severity of adult-onset hearing loss in a diverse hospital-based cohort Open
Loss or absence of hearing is common at both extremes of human lifespan, in the forms of congenital deafness and age-related hearing loss. While these are often studied separately, there is increasing evidence that their genetic basis is a…
View article: How to Run the Pharmacogenomics Clinical Annotation Tool (<scp>PharmCAT</scp>)
How to Run the Pharmacogenomics Clinical Annotation Tool (<span>PharmCAT</span>) Open
Pharmacogenomics (PGx) investigates the genetic influence on drug response and is an integral part of precision medicine. While PGx testing is becoming more common in clinical practice and may be reimbursed by Medicare/Medicaid and commerc…
View article: Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population
Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population Open
Background Pharmacogenomics (PGx) aims to utilize a patient’s genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong eviden…
View article: Polygenic risk vectors (PRV) improve genetic risk stratification for cardio-metabolic diseases
Polygenic risk vectors (PRV) improve genetic risk stratification for cardio-metabolic diseases Open
1. Abstract Accurate disease risk stratification can lead to more precise and personalized prevention and treatment of diseases. As an important component to disease risk, genetic risk factors can be utilized as an early and stable predict…
View article: Multi-ancestry Genome-wide Association Study of Varicose Veins Reveals Polygenic Architecture, Genetic Overlap with Arterial and Venous Disease, and Novel Therapeutic Opportunities
Multi-ancestry Genome-wide Association Study of Varicose Veins Reveals Polygenic Architecture, Genetic Overlap with Arterial and Venous Disease, and Novel Therapeutic Opportunities Open
Background Varicose veins represent a common cause of cardiovascular morbidity, with limited available medical therapies. Although varicose veins are heritable and epidemiologic studies have identified several candidate varicose veins risk…
View article: An Investigation of the Knowledge Overlap between Pharmacogenomics and Disease Genetics
An Investigation of the Knowledge Overlap between Pharmacogenomics and Disease Genetics Open
Precision medicine faces many challenges, including the gap of knowledge between disease genetics and pharmacogenomics (PGx). Disease genetics interprets the pathogenicity of genetic variants for diagnostic purposes, while PGx investigates…
View article: Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data
Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data Open
Understanding genetic factors of complex traits across ancestry groups holds a key to improve the overall health care quality for diverse populations in the United States. In recent years, multiple electronic health record-linked (EHR-link…
View article: From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries
From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries Open
Since their inception, genome-wide association studies (GWAS) have identified more than a hundred thousand single nucleotide polymorphism (SNP) loci that are associated with various complex human diseases or traits. The majority of GWAS di…
View article: Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms Open
Genes act in concert with each other in specific contexts to perform their functions. Determining how these genes influence complex traits requires a mechanistic understanding of expression regulation across different conditions. It has be…
View article: Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults
Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults Open
As a type of relatively new methodology, the transcriptome-wide association study (TWAS) has gained interest due to capacity for gene-level association testing. However, the development of TWAS has outpaced statistical evaluation of TWAS g…
View article: Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults
Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults Open
As a type of relatively new methodology, the transcriptome-wide association study (TWAS) has gained interest due to capacity for gene-level association testing. However, the development of TWAS has outpaced statistical evaluation of TWAS g…
View article: Influence of tissue context on gene prioritization for predicted transcriptome-wide association studies
Influence of tissue context on gene prioritization for predicted transcriptome-wide association studies Open
Transcriptome-wide association studies (TWAS) have recently gained great attention due to their ability to prioritize complex trait-associated genes and promote potential therapeutics development for complex human diseases. TWAS integrates…
View article: Collective feature selection to identify crucial epistatic variants
Collective feature selection to identify crucial epistatic variants Open
In this study, we were able to show that selecting variables using a collective feature selection approach could help in selecting true positive epistatic variables more frequently than applying any single method for feature selection via …
View article: Collective feature selection to identify crucial epistatic variants
Collective feature selection to identify crucial epistatic variants Open
Background Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remains a challenge due …
View article: Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression
Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression Open
Genome-wide association studies (GWAS) have been successful in facilitating the understanding of genetic architecture behind human diseases, but this approach faces many challenges. To identify disease-related loci with modest to weak effe…