Bingshan Li
A5028708641- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- BRCA gene mutations in cancer
- Ovarian cancer diagnosis and treatment
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Nutrition, Genetics, and Disease
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
- RNA Research and Splicing
- Magnetic Properties of Alloys
- Computational Drug Discovery Methods
- Genomic variations and chromosomal abnormalities
- Genetic Mapping and Diversity in Plants and Animals
- Molecular Biology Techniques and Applications
- Cancer Cells and Metastasis
- RNA modifications and cancer
- Gene expression and cancer classification
- Ferroptosis and cancer prognosis
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Chromosomal and Genetic Variations
- Magnetic properties of thin films
Vanderbilt University Medical Center
2015-2025
Vanderbilt University
2016-2025
Beijing General Research Institute of Mining and Metallurgy
2020-2023
Jiangsu University
2023
Nashville Oncology Associates
2021
Circadian (United States)
2020
Beth Israel Deaconess Medical Center
2020
Harvard University
2020
Brigham and Women's Hospital
2020
Center for Human Genetics
2012-2018
Abstract Motivation: Next-generation sequencing technologies have enabled the large-scale assessment of impact rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze variants, where multiple in a gene region analyzed jointly. Applying gene-level sequence data requires integrating heterogeneous sources information (e.g. annotations, functional prediction scores, allele frequencies, genotypes phenotypes) determine optimal...
Abstract It remains elusive whether some of the associations identified in genome-wide association studies prostate cancer (PrCa) may be due to regulatory effects genetic variants on CpG sites, which further influence expression PrCa target genes. To search for sites associated with risk, here we establish models predict methylation (N = 1,595) and conduct analyses risk (79,194 cases 61,112 controls). We identify 759 showing an association, including 15 located at novel loci. Among those 42...
Although analysis pipelines have been developed to use RNA-seq identify long non-coding RNAs (lncRNAs), inference of their biological and pathological relevance remains a challenge. As result, most transcriptome studies autoimmune disease only assessed protein-coding transcripts.We used data from 99 lesional psoriatic, 27 uninvolved 90 normal skin biopsies, applied computational approaches characterize expressed lncRNAs. We detect 2,942 previously annotated 1,080 novel lncRNAs which are...
Abstract Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis human diseases. Variant functional annotations play critical role in WGS analysis, result interpretation, prioritization disease- or trait-associated causal Existing annotation databases have limited scope to perform online queries functionally annotate genotype data large studies....
Genome-wide association studies (GWAS) have identified numerous susceptibility loci for Alzheimer's disease (AD). However, utilizing GWAS and multi-omics data to identify high-confidence AD risk genes (ARGs) druggable targets that can guide development of new therapeutics patients suffering from has heretofore not been successful.
Drug repurposing represents an attractive alternative to the costly and time-consuming process of new drug development, particularly for serious, widespread conditions with limited effective treatments, such as Alzheimer's disease (AD). Emerging generative artificial intelligence (GAI) technologies like ChatGPT offer promise expediting review summary scientific knowledge. To examine feasibility using GAI identifying candidates, we iteratively tasked proposing twenty most promising drugs in...
Complex trait genome-wide association studies (GWAS) provide an efficient strategy for evaluating large numbers of common variants in individuals and identifying trait-associated variants. Nevertheless, GWAS often leave much the heritability unexplained. We hypothesized that some this unexplained might be due to rare reside identified loci but lack appropriate proxies modern genotyping arrays. To assess hypothesis, we re-examined 7 genes (APOE, APOC1, APOC2, SORT1, LDLR, APOB, PCSK9) 5...
Genetic variation within the male-specific portion of Y chromosome (MSY) can clarify origins contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 which have not previously been observed. We constructed a phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters each haplogroup. The was...
There is strong evidence that rare variants are involved in complex disease etiology. The first step implicating etiology their identification through sequencing both randomly ascertained samples (e.g., the 1,000 Genomes Project) and according to status. We investigated what extent will be observed across genome candidate genes samples, magnitude of variant enrichment diseased individuals, biases can occur due how discovered. Although cases enrich for casual variants, when a gene or not...
Mitochondrial DNA (mtDNA) variation can affect phenotypic variation; therefore, knowing its distribution within and among individuals is of importance to understanding many human diseases. Intra-individual mtDNA (heteroplasmy) has been generally assumed be random. We used massively parallel sequencing assess heteroplasmy across ten tissues demonstrate that in unrelated there are tissue-specific, recurrent mutations. Certain tissues, notably kidney, liver skeletal muscle, displayed the...
Genome-wide association studies have identified common genetic risk variants in many loci associated with multiple cancers. We sought to systematically evaluate the utility of these identifying high-risk individuals for eight cancers.We constructed polygenic scores (PRS) using genome-wide studies-identified each cancer. Using data from 400 812 participants European descent a population-based cohort study, UK Biobank, we estimated hazard ratios PRS Cox proportional models and evaluated...
Abstract Motivation: Spontaneous (de novo) mutations play an important role in the disease etiology of a range complex diseases. Identifying de novo (DNMs) sporadic cases provides effective strategy to find genes or genomic regions implicated genetics disease. High-throughput next-generation sequencing enables genome- exome-wide detection DNMs by parents-proband trios. It is challenging sift true through massive amount noise due error and alignment artifacts. One critical limitations...