John C. Whittaker
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View article: Leveraging Large-Scale Biobanks for Therapeutic Target Discovery
Leveraging Large-Scale Biobanks for Therapeutic Target Discovery Open
Large biobanks, including the Million Veteran Program (MVP), the UK Biobank, and FinnGen, provide genetic association results for more than 1,000,000 individuals for hundreds of phenotypes. To select targets for pharmaceutical development,…
View article: Systematic comparison of colocalization methods using protein quantitative trait loci
Systematic comparison of colocalization methods using protein quantitative trait loci Open
Colocalization is frequently performed as a step to triage findings from genetic investigations linking molecular and disease data. However, the reliability and consistency of the various colocalization methods is not well understood. In p…
View article: A genomic-led strategy to anticipate drug safety effects
A genomic-led strategy to anticipate drug safety effects Open
Safety-related issues account for approximately 28% of failures in new drug discovery programs. On top of that, many are discovered during post-marketing surveillance, significantly limiting drug utility and application. To proactively add…
View article: Adaptive Bayesian computation for efficient biobank-scale genomic inference
Adaptive Bayesian computation for efficient biobank-scale genomic inference Open
Motivation: Modern biobanks, with unprecedented sample sizes and phenotypic diversity, have become foundational resources for genomic studies, enabling powerful cross-phenotype and population-scale analyses. As studies grow in complexity, …
View article: Whole-genome sequencing of 490,640 UK Biobank participants
Whole-genome sequencing of 490,640 UK Biobank participants Open
Whole-genome sequencing provides an unbiased and complete view of the human genome and enables the discovery of genetic variation without the technical limitations of other genotyping technologies. Here we report on whole-genome sequencing…
View article: A computational framework for defining and validating reproducible phenotyping algorithms of 313 diseases in the UK Biobank
A computational framework for defining and validating reproducible phenotyping algorithms of 313 diseases in the UK Biobank Open
Accurate and reproducible phenotyping is essential for large-scale biomedical research. However, developing robust phenotype definitions in biobanks is challenging due to diverse data sources and varying medical ontologies. As a result, th…
View article: Leveraging Large-Scale Biobanks for Therapeutic Target Discovery
Leveraging Large-Scale Biobanks for Therapeutic Target Discovery Open
Large biobanks, including the Million Veteran Program (MVP), the UK Biobank, and FinnGen, provide genetic association results for more than 1,000,000 individuals for hundreds of phenotypes. To select targets for pharmaceutical development,…
View article: No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology
No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Open
Despite substantial efforts, deep learning has not yet delivered a transformative impact on elucidating regulatory biology, particularly in the realm of predicting gene expression profiles. Here, we argue that genuine "foundation models" o…
View article: Testing and Reconsidering Atlatl Dart Ballistics: Implications for Recent Theories on Social Organization and Change
Testing and Reconsidering Atlatl Dart Ballistics: Implications for Recent Theories on Social Organization and Change Open
View article: Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments
Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments Open
Causal structure learning (CSL) refers to the task of learning causal relationships from data. Advances in CSL now allow learning of causal graphs in diverse application domains, which has the potential to facilitate data-driven causal dec…
View article: Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries
Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries Open
View article: Large-scale Mendelian randomization identifies novel pathways as therapeutic targets for heart failure with reduced ejection fraction and with preserved ejection fraction
Large-scale Mendelian randomization identifies novel pathways as therapeutic targets for heart failure with reduced ejection fraction and with preserved ejection fraction Open
We used expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) to conduct genome-wide Mendelian randomization (MR) using 27,799 cases of heart failure (HF) with reduced ejection fraction (HFrEF), 27,579 case…
View article: A frequentist test of proportional colocalization after selecting relevant genetic variants
A frequentist test of proportional colocalization after selecting relevant genetic variants Open
Colocalization analyses assess whether two traits are affected by the same or distinct causal genetic variants in a single gene region. A class of Bayesian colocalization tests are now routinely used in practice; for example, for genetic a…
View article: A Computational Framework for Defining and Validating Reproducible Phenotyping Algorithms of 313 Diseases in the UK Biobank
A Computational Framework for Defining and Validating Reproducible Phenotyping Algorithms of 313 Diseases in the UK Biobank Open
View article: Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure
Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure Open
View article: “Here come the anthropos”: what is an archeologist for ?
“Here come the anthropos”: what is an archeologist for ? Open
Pour une publication sur Épisciences. Whittaker John, 1997, “Here Come the Anthros. What Good is an Archaeologist?” in Andelson Jon (dir.), Anthropology Matters: Essays in Honor of Ralph A. Luebben, Grinnell College, Grinnell, p. 101-108. …
View article: Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer Open
Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
View article: Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer Open
Purpose: Patients with synchronous ovarian and endometrial cancers may represent cases of a single primary tumor with metastasis (SPM) or dual primary tumors (DP). The diagnosis given will influence the patient's treatment and progn…
View article: Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer Open
Supplementary Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
View article: Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer
Data from Predicting Clinical Outcome in Patients Diagnosed with Synchronous Ovarian and Endometrial Cancer Open
Purpose: Patients with synchronous ovarian and endometrial cancers may represent cases of a single primary tumor with metastasis (SPM) or dual primary tumors (DP). The diagnosis given will influence the patient's treatment and progn…
View article: Using genetic association data to guide drug discovery and development: Review of methods and applications
Using genetic association data to guide drug discovery and development: Review of methods and applications Open
View article: Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure
Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure Open
We conduct a large-scale meta-analysis of heart failure genome-wide association studies (GWAS) consisting of over 90,000 heart failure cases and more than 1 million control individuals of European ancestry to uncover novel genetic determin…
View article: Incidence, morbidity, mortality and disparities in dementia: A population linked electronic health records study of 4.3 million individuals
Incidence, morbidity, mortality and disparities in dementia: A population linked electronic health records study of 4.3 million individuals Open
Introduction We report dementia incidence, comorbidities, reasons for health‐care visits, mortality, causes of death, and examined dementia patterns by relative deprivation in the UK. Method A longitudinal cohort analysis of linked electro…
View article: Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes
Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes Open
Genotype imputation has the potential to assess human genetic variation at a lower cost than assaying the variants using laboratory techniques. The performance of imputation for rare variants has not been comprehensively studied. We utiliz…
View article: Exome sequencing and characterization of 49,960 individuals in the UK Biobank
Exome sequencing and characterization of 49,960 individuals in the UK Biobank Open
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world 1 . Here we describe the release of exome-sequence data for the first …
View article: High Density Lipoprotein pathway as a therapeutic target for coronary heart disease: individual participant meta-analysis in 28,597 individuals with 4197 coronary events
High Density Lipoprotein pathway as a therapeutic target for coronary heart disease: individual participant meta-analysis in 28,597 individuals with 4197 coronary events Open
Importance Cholesterol content in high-density lipoprotein particles (HDL-C) is associated inversely with coronary heart disease (CHD), but findings from Mendelian randomization studies and randomized trials of HDL-C raising drugs have que…
View article: An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people Open
Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individu…
View article: Editorial Reflections: Anthropology, the Fundamental Human Activity
Editorial Reflections: Anthropology, the Fundamental Human Activity Open
View article: Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries
Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries Open
View article: Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank
Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank Open
SUMMARY The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world. Here we describe the first tranche of large-scale exome seque…