Michael I. Love
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View article: Supplementary Data from Molecular and Clinical Characterization of Postpartum-Associated Breast Cancer in the Carolina Breast Cancer Study Phase I–III, 1993–2013
Supplementary Data from Molecular and Clinical Characterization of Postpartum-Associated Breast Cancer in the Carolina Breast Cancer Study Phase I–III, 1993–2013 Open
Supplementary Data from Molecular and Clinical Characterization of Postpartum-Associated Breast Cancer in the Carolina Breast Cancer Study Phase I–III, 1993–2013
View article: Supplementary Tables S1-S12 from Gene-Level Germline Contributions to Clinical Risk of Recurrence Scores in Black and White Patients with Breast Cancer
Supplementary Tables S1-S12 from Gene-Level Germline Contributions to Clinical Risk of Recurrence Scores in Black and White Patients with Breast Cancer Open
Supplementary Tables S1-S12
View article: Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci Open
Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential ac…
View article: CNS1-induced Peripheral Regulatory T cells in the Resolution of Acute Lung Injury 2115
CNS1-induced Peripheral Regulatory T cells in the Resolution of Acute Lung Injury 2115 Open
Description RATIONALE Regulatory T cells (Tregs) perform essential functions during the resolution of acute lung injury. Tregs regulate immune cell trafficking into the lung, suppress excessive immune responses in late injury, and contribu…
View article: Taming the reference genome jungle: the refget sequence collection standard
Taming the reference genome jungle: the refget sequence collection standard Open
Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison. To address this, we introduce the G…
View article: Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow
Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow Open
As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains chall…
View article: Tree-based differential testing using inferential uncertainty for RNA-seq
Tree-based differential testing using inferential uncertainty for RNA-seq Open
Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exagg…
View article: Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish
Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish Open
CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restrict…
View article: Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish
Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish Open
CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restrict…
View article: Higher eQTL power reveals signals that boost GWAS colocalization
Higher eQTL power reveals signals that boost GWAS colocalization Open
Expression quantitative trait locus (eQTL) studies in human cohorts typically detect at least one regulatory signal per gene, and have been proposed as a way to explain mechanisms of genetic liability for other traits, as discovered in gen…
View article: Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function
Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function Open
The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale genomic initiatives, with most analyses …
View article: Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish
Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish Open
CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restrict…
View article: Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies Open
View article: Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes
Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes Open
Genetic variation can modulate response to treatment (G×T) or environmental stimuli (G×E), both of which can be highly consequential in biomedicine. An effective approach to identifying G×T signals and gaining insight into molecular mechan…
View article: Supplementary Figure 3 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Figure 3 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Oncogenic pathway level alterations and associations with subtype
View article: Supplementary Table 6 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 6 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Association between RNA-based TP53 pathway dysfunction and DNA-based TP53 defects
View article: Supplementary Figure 2 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Figure 2 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Arm level amplification and deletion prevalence differences by age at diagnosis
View article: Supplementary Figure 1 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Figure 1 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Enrichments for arm-level alterations by self reported race
View article: Data from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Data from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Cancer genomics consortia have identified somatic drivers of breast cancer subtypes. However, these studies have predominantly included older, non-Black women, and the related socioeconomic status (SES) data are limited. Increased represen…
View article: Supplementary Figure 4 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Figure 4 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Oncogenic pathway dysfunction differences by race and age at diagnosis
View article: Supplementary Table 1 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 1 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Differences in proportions of samples with detected mutations to each gene of target panel by pipeline [paired tumor/normal or tumor only].
View article: Supplementary Table 7 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 7 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Association between socioeconomic variables in CBCS and mutations or copy number alterations. All estimates are stratified by self reported race
View article: Supplementary Table 4 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 4 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Differences in arm-level copy number gains and losses by source data set (CBCS vs TCGA)
View article: Supplementary Table 5 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 5 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Differences in recurrent copy number alterations of mutations by self-reported race or age after stratifying on estrogen receptor (ER) status
View article: Supplementary Table 2 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 2 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Differences in proportions of samples with detected mutations by stage at diagnosis (Stage I/II vs. Stage III/IV)
View article: Supplementary Table 3 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors
Supplementary Table 3 from Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors Open
Complete tabulation of mutational frequency and proportion by self-reported race [either Black vs non-Black or Non-Hispanic white vs Non-Hispanic Black only] and age at diagnosis.
View article: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines Open
The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify. T…
View article: GA4GH Phenopacket-Driven Characterization of Genotype-Phenotype Correlations in Mendelian Disorders
GA4GH Phenopacket-Driven Characterization of Genotype-Phenotype Correlations in Mendelian Disorders Open
Comprehensively characterizing genotype-phenotype correlations (GPCs) in Mendelian disease would create new opportunities for improving clinical management and understanding disease biology. However, heterogeneous approaches to data sharin…
View article: Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories
Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories Open
Summary Human induced pluripotent stem cell (iPSC) derived cortical organoids (hCOs) model neurogenesis on an individual’s genetic background. The degree to which hCO phenotypes recapitulate the brain growth of the participants from which …
View article: Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data
Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data Open
We present Consenrich, a simple but principled technique for genome-wide estimation of signals hidden in noisy multi-sample sequencing-based functional genomics datasets. Consenrich appeals to a sequential prediction-correction framework a…