Qiongshi Lu
A5083375749- Genetic Associations and Epidemiology
- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Birth, Development, and Health
- Epigenetics and DNA Methylation
- Dementia and Cognitive Impairment Research
- Metabolomics and Mass Spectrometry Studies
- Health, Environment, Cognitive Aging
- Nutrition, Genetics, and Disease
- Health Systems, Economic Evaluations, Quality of Life
- Genomics and Rare Diseases
- Intergenerational and Educational Inequality Studies
- Health disparities and outcomes
- Cognitive Abilities and Testing
- Genomic variations and chromosomal abnormalities
- Genetics and Neurodevelopmental Disorders
- Autism Spectrum Disorder Research
- Resilience and Mental Health
- RNA modifications and cancer
- Liver Disease Diagnosis and Treatment
- Diet and metabolism studies
- Folate and B Vitamins Research
- Nutritional Studies and Diet
University of Wisconsin–Madison
2017-2025
Yale University
2013-2023
National Bureau of Economic Research
2023
Oklahoma State University Center for Health Sciences
2020-2021
Nanfang Hospital
1999-2020
Zhujiang Hospital
2020
Oxford University Press (United Kingdom)
2018
West China Hospital of Sichuan University
2014
Sichuan University
2014
Tsinghua University
2013
Abstract Background Though most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies importance identifying binding proteins in understanding molecular mechanisms underlying functions lncRNAs. Only a few approaches available for predicting between and proteins. In this study, we introduce new method lncPro. Results By encoding RNA protein sequences into numeric vectors, used...
Premature fusion of the cranial sutures (craniosynostosis), affecting 1 in 2000 newborns, is treated surgically infancy to prevent adverse neurologic outcomes. To identify mutations contributing common non-syndromic midline (sagittal and metopic) craniosynostosis, we performed exome sequencing 132 parent-offspring trios 59 additional probands. Thirteen probands (7%) had damaging de novo or rare transmitted SMAD6, an inhibitor BMP - induced osteoblast differentiation (p<10-20). SMAD6...
Abstract Identifying functional regions in the human genome is a major goal genetics. Great efforts have been made to functionally annotate either through computational predictions, such as genomic conservation, or high-throughput experiments, ENCODE project. These resulted rich collection of annotation data diverse types that need be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, whole-genome method performs unsupervised statistical learning using...
Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate models will have great impacts on both disease prevention early treatment strategies. Despite the identification of thousands disease-associated genetic variants through genome wide association studies (GWAS), accuracy remains moderate for most diseases, which largely due to challenges identifying all functionally relevant accurately estimating their effect sizes presence linkage...
Local genetic correlation quantifies the similarity of complex traits in specific genomic regions. However, accurate estimation local remains challenging, due to linkage disequilibrium regions and sample overlap across studies. We introduce SUPERGNOVA, a statistical framework estimate correlations using summary statistics from genome-wide association demonstrate that SUPERGNOVA outperforms existing methods through simulations analyses 30 traits. In particular, we show positive yet...
Researchers often claim that sibling analysis can be used to separate causal genetic effects from the assortment of biases contaminate most downstream studies (e.g. polygenic score predictors). Indeed, typical results show large (>50%) attenuations in associations between scores and phenotypes compared non-sibling analysis, consistent with researchers’ expectations about bias reduction. This paper explores these by using family (quad) data simulations include indirect effect processes...
Abstract We conducted a genome-wide association study on income among individuals of European descent ( N = 668,288) to investigate the relationship between socio-economic status and health disparities. identified 162 genomic loci associated with common genetic factor underlying various measures, all small effect sizes (the Income Factor). Our polygenic index captures 1–5% variance, only one fourth due direct effects. A phenome-wide using this showed reduced risks for diseases including...
Abstract Approximately 30% of older adults exhibit the neuropathological features Alzheimer’s disease without signs cognitive impairment. Yet, little is known about genetic factors that allow these potentially resilient individuals to remain cognitively unimpaired in face substantial neuropathology. We performed a large, genome-wide association study (GWAS) two previously validated metrics resilience quantified using latent variable modelling approach and representing better-than-predicted...
Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell tissue types. However, synthesis these datasets into effective summary metrics to characterize the functional non-coding genome remains challenge. Here, we present GenoSkyline-Plus, an extension our previous work through integration expanded set annotations produce high-resolution, single annotations. After validating with catalog...
Extensive efforts have been made to understand genomic function through both experimental and computational approaches, yet proper annotation still remains challenging, especially in non-coding regions. In this manuscript, we introduce GenoSkyline, an unsupervised learning framework predict tissue-specific functional regions integrating high-throughput epigenetic annotations. GenoSkyline successfully identified a variety of regulatory machinery including enhancers, miRNA, hypomethylated...
Accurate prediction of disease risk based on genetic factors is an important goal in human genetics research and precision medicine. Advanced models will lead to more effective prevention treatment strategies. Despite the identification thousands disease-associated variants through genome-wide association studies (GWAS) past decade, accuracy remains moderate for most diseases, which largely due challenges both identifying all functionally relevant accurately estimating their effect sizes. In...
Abstract The study of metabolomics and disease has enabled the discovery new risk factors, diagnostic markers, drug targets. For neurological psychiatric phenotypes, cerebrospinal fluid (CSF) is particular importance. However, CSF metabolome difficult to on a large scale due relative complexity procedure needed collect fluid. Here, we present metabolome-wide association (MWAS), which uses genetic metabolomic data impute metabolites into samples with genome-wide summary statistics. We conduct...
Epigenetic clocks have been widely used to predict disease risk in multiple tissues or cells. Their success as a measure of biological ageing has prompted research on the connection between epigenetic pathways and socioeconomic gradient health mortality. However, studies examining social correlates yielded inconsistent results. We conducted comprehensive, comparative analysis associations various dimensions status (SES) (education, income, wealth, occupation, neighbourhood environment,...
Abstract Background Schizophrenia (SCZ) and bipolar disorder (BIP) are debilitating neuropsychiatric disorders, collectively affecting 2% of the world’s population. Recognizing major impact these psychiatric disorders on psychosocial function more than 200 000 US Veterans, Department Veterans Affairs (VA) recently completed genotyping 8000 veterans with SCZ BIP in Cooperative Studies Program (CSP) #572. Methods We performed genome-wide association studies (GWAS) CSP #572 benchmarked...
Abstract Approximately 30% of elderly adults are cognitively unimpaired at time death despite the presence Alzheimer’s disease neuropathology autopsy. Studying individuals who resilient to cognitive consequences may uncover novel therapeutic targets treat disease. It is well established that there sex differences in response pathology, and growing evidence suggests genetic factors contribute these differences. Taken together, we sought elucidate sex-specific drivers resilience. We extended...
Abstract Polygenic risk scores (PRS) calculated from genome-wide association studies (GWAS) of Europeans are known to have substantially reduced predictive accuracy in non-European populations, limiting their clinical utility and raising concerns about health disparities across ancestral populations. Here, we introduce a statistical framework named X-Wing improve performance ancestrally diverse quantifies local genetic correlations for complex traits between employs an annotation-dependent...