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diff --git a/gnqa/paper1_eval/src/data/queries/gpt4o-queries.json b/gnqa/paper1_eval/src/data/queries/gpt4o-queries.json new file mode 100644 index 0000000..74c18b0 --- /dev/null +++ b/gnqa/paper1_eval/src/data/queries/gpt4o-queries.json @@ -0,0 +1,159 @@ +[ + { + "level": "domainexpert", + "domain": "diabetes", + "query": [ + "How do recent advancements in multi-omics approaches, including proteomics and metabolomics, contribute to our understanding of Type 2 diabetes pathogenesis?", + "What novel diabetic loci have been identified through the latest meta-analyses of large-scale genome-wide association studies (GWAS)?", + "How do epigenetic modifications, such as DNA methylation and histone modification, influence the expression of diabetes-related genes?", + "Can you elaborate on the role of the gut microbiome in modulating host genetic predispositions to diabetes?", + "How effective are machine learning algorithms in integrating genomic data to predict individual risk and progression of diabetes?", + "What are the implications of recent findings on the role of long non-coding RNAs (lncRNAs) in the regulation of insulin secretion and sensitivity?", + "How do post-translational modifications of proteins affect key signaling pathways involved in glucose homeostasis?", + "What insights have been gained from studying the genetic basis of syndromic forms of diabetes, such as Wolfram Syndrome and Alström Syndrome?", + "How do genetic and epigenetic differences between monozygotic twins discordant for diabetes inform our understanding of its etiology?", + "What potential therapeutic targets have been identified through recent studies on the interaction between genetic variants and environmental factors in diabetes development?", + "How do rare variants identified through whole-genome sequencing contribute to the heritability of Type 2 diabetes?", + "What are the latest findings on the role of non-coding RNAs in the pathogenesis of diabetes?", + "How does the interaction between multiple polygenic risk scores (PRS) improve the prediction of Type 1 and Type 2 diabetes?", + "What are the mechanistic insights into the beta-cell failure pathways gleaned from recent single-cell RNA-sequencing studies?", + "How does the epigenetic landscape of key metabolic tissues change in diabetic versus non-diabetic individuals?", + "What recent advancements have been made in leveraging CRISPR-based approaches to correct monogenic forms of diabetes in vivo?", + "How do genome-wide association studies (GWAS) integrate with multi-omics data to elucidate the complex genetic architectures of diabetes?", + "What is the impact of genomic imprinting on the susceptibility and progression of diabetes?,", + "How do longitudinal genomics studies help in understanding gene-environment interactions in diabetes onset and management?", + "How have recent integrative genomics approaches, such as the use of single-cell RNA sequencing combined with epigenomic profiling, advanced our understanding of cellular heterogeneity and gene regulatory networks in pancreatic beta cells under diabetic conditions?" + ] + }, + { + "level": "citizenscientist", + "domain": "diabetes", + "query": [ + "How do genetic mutations in the insulin gene affect glucose metabolism?", + "What are the most common genetic loci associated with an increased risk of Type 2 diabetes?", + "How does genome-wide association studies (GWAS) help in identifying diabetes-related genes?", + "What is the role of the HLA region in the genetic predisposition to Type 1 diabetes?", + "How do genetic differences contribute to variations in diabetes prevalence among different populations?", + "What is the function of the PPAR-gamma gene in diabetes, and how do its variants impact the disease?", + "How can CRISPR/Cas9 technology be used to study or treat genetic forms of diabetes?", + "What is the significance of genetic polymorphisms in the GLUT4 gene for Type 2 diabetes?", + "How do microRNAs regulate gene expression related to diabetes?", + "What insights have been gained from studying the genetic basis of MODY (Maturity Onset Diabetes of the Young)?", + "What genes are most commonly associated with an increased risk of developing diabetes?", + "How can genetic testing help predict a person's risk for diabetes?", + "What role do family genetics play in the likelihood of getting diabetes?", + "Can lifestyle changes affect genetic risk factors for diabetes?", + "What recent breakthroughs have been made in understanding the genetic causes of diabetes?", + "How do genes influence how our bodies respond to sugar and insulin?", + "Are there specific genetic markers that can indicate a higher risk for Type 1 versus Type 2 diabetes?", + "How can new gene therapies potentially cure or treat diabetes?", + "What is the difference between monogenic and polygenic diabetes?", + "How does studying the DNA of people with diabetes help scientists find better treatments or cures?" + ] + }, + { + "level":"citizenscientist", + "domain": "aging", + "query": [ + "What are the main genetic factors that influence aging?", + "How do genes affect the aging process in humans?", + "What lifestyle choices can help slow down genetic aging?", + "How do scientists study the genetics of aging in animals?", + "Are there specific genes that have been linked to longer lifespans?", + "How do telomeres affect the aging process?", + "What role does DNA repair play in aging?", + "Can genetic research lead to treatments that slow down aging?", + "How does mitochondrial DNA influence aging?", + "Are there any known genetic mutations that cause premature aging?", + "What recent discoveries have been made about the genetics of aging?", + "How do epigenetic changes affect aging?", + "What is the role of the gene FOXO3 in longevity?", + "How does the environment interact with genes to influence aging?", + "What are senescent cells and how do they contribute to aging?", + "Are there any known lifestyle interventions that can positively impact genes related to aging?", + "What is the 'epigenetic clock,' and how is it used in aging research?", + "How do researchers use model organisms like yeast or worms to study human aging?", + "Are there any promising anti-aging therapies being developed based on genetic research?", + "How do caloric restriction and diet impact the genetics of aging?" + ] + }, + { + "level":"domainexpert", + "domain":"aging", + "query": [ + "How do recent single-cell transcriptomics studies enhance our understanding of cellular heterogeneity in aging tissues?", + "What are the latest findings on the role of senescence-associated secretory phenotype (SASP) factors in age-related tissue dysfunction?", + "How do age-related changes in chromatin architecture contribute to the decline in cellular function?", + "What insights have been gained from studying the epigenetic reprogramming of aged cells to a more youthful state?", + "How do alterations in the mitochondrial genome and bioenergetics influence the aging process in humans?", + "What are the therapeutic potentials and challenges of targeting the insulin/IGF-1 signaling pathway for extending healthspan and lifespan?", + "How can the integration of proteomics and metabolomics data shed light on age-associated metabolic shifts?", + "What role do long non-coding RNAs (lncRNAs) play in the regulation of aging and age-related diseases?", + "How do recent advancements in CRISPR/Cas9 technology open new avenues for studying and potentially reversing aging?", + "What is the significance of the DNA damage response (DDR) in the context of both replicative and chronological aging?", + "How do age-dependent changes in the immune system, such as immunosenescence, contribute to increased susceptibility to diseases?", + "How do advancements in machine learning and artificial intelligence aid in the identification of biomarkers for biological aging?", + "What recent discoveries have been made regarding the impact of systemic factors, such as circulating microvesicles, on aging phenotypes?", + "How do changes in the gut microbiome composition correlate with aging and longevity?", + "What are the key molecular mechanisms through which caloric restriction exerts its lifespan-extending effects across different species?", + "How do oxidative stress and the subsequent accumulation of damaged macromolecules contribute to cellular aging?", + "How are extracellular matrix remodeling and tissue stiffness implicated in the aging process?", + "How do recent developments in autophagy research contribute to our understanding of its role in aging and longevity?", + "What are the implications of age-related shifts in stem cell niche composition and function for tissue regeneration capacity?", + "How do cross-links and advanced glycation end-products (AGEs) accumulation affect the structural integrity and function of aging tissues?" + ] + }, + { + "level": "domainexpert", + "domain": "gn", + "query": [ + "How do recent advancements in network-based integrative genomics alter our understanding of complex trait architectures?", + "What are the latest methodological improvements in evaluating gene-environment interactions using GeneNetwork.org?", + "How do multi-omics data integration techniques enhance the prediction accuracy of phenotypic traits in GeneNetwork datasets?", + "What are the computational challenges and solutions in analyzing large-scale transcriptomic data within GeneNetwork.org?", + "How has the inclusion of data from diverse populations impacted the generalizability of findings on GeneNetwork.org?", + "What novel insights have been obtained from GeneNetwork.org regarding the genetic basis of psychiatric disorders?", + "How do advancements in machine learning algorithms contribute to the deconvolution of gene expression data in complex tissues?", + "What role do enhancer-promoter interactions play in the regulation of gene networks uncovered through GeneNetwork.org?", + "How can the integration of ATAC-seq data with RNA-seq data on GeneNetwork.org inform about chromatin accessibility and gene regulation?", + "What are the latest strategies for inferring causal relationships within gene networks using data from GeneNetwork.org?", + "How do advancements in single-nucleus RNA sequencing provide more granular insights into cell-type-specific gene expression networks?", + "What impact have recent discoveries in non-coding RNA regulation had on refining gene interaction maps on GeneNetwork.org?", + "How are spatial transcriptomics approaches being integrated into GeneNetwork.org to enhance understanding of tissue architecture and function?", + "How do recent developments in quantitative trait locus (QTL) mapping refine our understanding of gene regulatory variants?", + "What are the implications of incorporating epigenomic data, such as histone modification maps, into the gene networks on GeneNetwork.org?", + "How do recent findings on 3D genome organization contribute to our understanding of functional genomic networks?", + "What are the potential applications of artificial intelligence in improving the annotation and interpretation of gene networks?", + "How has the study of genetic pleiotropy been advanced by data available on GeneNetwork.org?", + "What novel genetic pathways have been identified in GeneNetwork.org studies related to aging and lifespan?", + "How do polygenic risk scores (PRS) developed using GeneNetwork.org data enhance the prediction and prevention of complex diseases?" + ] + }, + { + "level": "citizenscientist", + "domain": "gn", + "query": [ + "What is GeneNetwork.org, and how does it help scientists understand genetics?", + "How do researchers use GeneNetwork.org to study diseases?", + "What can GeneNetwork.org tell us about how genes interact with each other?", + "How does GeneNetwork.org help in finding the genetic causes of common diseases?", + "Can GeneNetwork.org predict my risk of developing certain health conditions based on my genes?", + "How does GeneNetwork.org make use of data from different populations around the world?", + "What kinds of genetic data are available on GeneNetwork.org?", + "How do scientists use GeneNetwork.org to study differences in gene expression?", + "Can GeneNetwork.org be used to learn about genetic influences on behavior?", + "What role does GeneNetwork.org play in personalized medicine?", + "How does the information on GeneNetwork.org help in developing new treatments for diseases?", + "What is a gene network, and why is it important for understanding genetics?", + "How do researchers identify which genes are important for certain traits using GeneNetwork.org?", + "How can GeneNetwork.org help in understanding complex traits like height or intelligence?", + "Are there any known genetic mutations that cause premature aging?", + "What are the practical applications of the research done through GeneNetwork.org?", + "How can I access and use the data available on GeneNetwork.org?", + "What are some recent discoveries made using GeneNetwork.org?", + "How do scientists ensure the accuracy of the data on GeneNetwork.org?", + "What’s the difference between looking at one gene and studying a whole gene network?", + "How can GeneNetwork.org contribute to advancements in genetic engineering?" + ] + } +] |