Nathan LaPierre
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View article: Differing Genetics of Saline and Cocaine Self‐Administration in the Hybrid Mouse Diversity Panel
Differing Genetics of Saline and Cocaine Self‐Administration in the Hybrid Mouse Diversity Panel Open
To identify genes that regulate the response to the potentially addictive drug cocaine, we performed a control experiment using genome‐wide association studies (GWASs) and RNA‐Seq of a panel of inbred and recombinant inbred mice undergoing…
View article: Differing genetics of saline and cocaine self-administration in the hybrid mouse diversity panel
Differing genetics of saline and cocaine self-administration in the hybrid mouse diversity panel Open
To identify genes that regulate the response to the potentially addictive drug cocaine, we performed a control experiment using genome-wide association studies (GWASs) and RNA-Seq of a panel of inbred and recombinant inbred mice undergoing…
View article: Accounting for isoform expression increases power to identify genetic regulation of gene expression
Accounting for isoform expression increases power to identify genetic regulation of gene expression Open
A core problem in genetics is molecular quantitative trait locus (QTL) mapping, in which genetic variants associated with changes in the molecular phenotypes are identified. One of the most-studied molecular QTL mapping problems is express…
View article: Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior
Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior Open
Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here w…
View article: Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice
Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice Open
To identify addiction genes, we evaluate intravenous self-administration of cocaine or saline in 84 inbred and recombinant inbred mouse strains over 10 days. We integrate the behavior data with brain RNA-seq data from 41 strains. The self-…
View article: Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power
Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power Open
A core problem in genetics is eQTL mapping, in which genetic variants associated with changes in expression of genes are identified. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual…
View article: The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice
The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice Open
Tissue iron overload is a frequent pathologic finding in multiple disease states including non-alcoholic fatty liver disease (NAFLD), neurodegenerative disorders, cardiomyopathy, diabetes, and some forms of cancer. The role of iron, as a c…
View article: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
Leveraging family data to design Mendelian randomization that is provably robust to population stratification Open
Mendelian randomization (MR) has emerged as a powerful approach to leverage genetic instruments to infer causality between pairs of traits in observational studies. However, the results of such studies are susceptible to biases owing to we…
View article: Leveraging family data to design Mendelian Randomization that is provably robust to population stratification
Leveraging family data to design Mendelian Randomization that is provably robust to population stratification Open
Mendelian Randomization (MR) has emerged as a powerful approach to leverage genetic instruments to infer causality between pairs of traits in observational studies. However, the results of such studies are susceptible to biases due to weak…
View article: Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in inbred and recombinant inbred mice
Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in inbred and recombinant inbred mice Open
To identify genetic pathways for addiction, we analyzed intravenous self-administration of cocaine or saline in a panel of 84 inbred and recombinant inbred mouse strains over 10 days. We integrated the behavior data with RNA-Seq data from …
View article: Critical Assessment of Metagenome Interpretation: the second round of challenges
Critical Assessment of Metagenome Interpretation: the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on r…
View article: MiCoP_indices.zip
MiCoP_indices.zip Open
indices.zip file for the MiCoP program, re-uploaded after the google drive link stopped working.
View article: Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities Open
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation …
View article: MiCoP_indices.zip
MiCoP_indices.zip Open
indices.zip file for the MiCoP program, re-uploaded after the google drive link stopped working.
View article: Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy
Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy Open
Mendelian Randomization (MR) studies are threatened by population stratification, batch effects, and horizontal pleiotropy. Although a variety of methods have been proposed to mitigate those problems, residual biases may still remain, lead…
View article: Genetic pathways regulating the longitudinal acquisition of cocaine self administration in mice
Genetic pathways regulating the longitudinal acquisition of cocaine self administration in mice Open
To identify genetic pathways for addiction, we analyzed intravenous self-administration of cocaine or saline in a panel of 84 inbred and recombinant inbred mouse strains over 10 days. We integrated the behavior data with RNA-Seq data from …
View article: Identifying causal variants by fine mapping across multiple studies
Identifying causal variants by fine mapping across multiple studies Open
Increasingly large Genome-Wide Association Studies (GWAS) have yielded numerous variants associated with many complex traits, motivating the development of “fine mapping” methods to identify which of the associated variants are causal. Add…
View article: Critical Assessment of Metagenome Interpretation - the second round of challenges
Critical Assessment of Metagenome Interpretation - the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the communi…
View article: Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy
Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy Open
Mendelian Randomization (MR) exploits genetic variants as instrumental variables to estimate the causal effect of an “exposure” trait on an “outcome” trait from observational data. However, the validity of such studies is threatened by pop…
View article: Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing Open
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission 1, 2 . Frequent, widespread testing of the asymptomat…
View article: Metalign version 0.12.5 (Publication version)
Metalign version 0.12.5 (Publication version) Open
This is a tarball containing the source code of version 0.12.5 of the Metalign software. This is the version used in the published paper.
View article: Metalign: Efficient alignment-based metagenomic profiling via containment min hash
Metalign: Efficient alignment-based metagenomic profiling via containment min hash Open
Whole-genome shotgun sequencing enables the analysis of microbial communities in unprecedented detail, with major implications in medicine and ecology. Predicting the presence and relative abundances of microbes in a sample, known as “meta…
View article: Identifying Causal Variants by Fine Mapping Across Multiple Studies
Identifying Causal Variants by Fine Mapping Across Multiple Studies Open
Increasingly large Genome-Wide Association Studies (GWAS) have yielded numerous variants associated with many complex traits, motivating the development of “fine mapping” methods to identify which of the associated variants are causal. Add…
View article: Additional file 1 of Metalign: efficient alignment-based metagenomic profiling via containment min hash
Additional file 1 of Metalign: efficient alignment-based metagenomic profiling via containment min hash Open
Additional file 1. Supplementary text (including computing environments, information needed for replication, and performance metrics evaluated) and supplementary figures.
View article: Metalign:taxids_6789
Metalign:taxids_6789 Open
Organism files with taxids starting with 6, 7, 8, or 9 for Metalign
View article: Metalign:taxids_6789
Metalign:taxids_6789 Open
Organism files with taxids starting with 6, 7, 8, or 9 for Metalign
View article: Metalign:cmash_files
Metalign:cmash_files Open
CMash precomputed files needed for Metalign