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Article
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics
Advances in artificial intelligence have paved the way for leveraging hematoxylin and eosin-stained tumor slides for precision oncology. We present ENLIGHT–DeepPT, an indirect two-step approach consisting of (...
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Article
Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning
Precision in the diagnosis of diverse central nervous system (CNS) tumor types is crucial for optimal treatment. DNA methylation profiles, which capture the methylation status of thousands of individual CpG si...
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Proximity to Precarity: Confronting the COVID-19 Pandemic as Graduate Apprentices in Physical Cultural Studies
The precarity of the graduate student experience has been exacerbated by the COVID 19 pandemic while illuminating new challenges and opportunities for considering how we interact with the neoliberal university...
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Article
Open AccessPhysical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data
Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust ...
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Article
Open AccessThe stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation
Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms o...
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Article
Open AccessFunctional rare and low frequency variants in BLK and BANK1 contribute to human lupus
Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. It is thought that many common variant gene loci of weak effect act additively to predispose to common autoimmune diseases, whi...
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Article
Predictor performance with stratified data and imbalanced classes
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Article
Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits
Most organisms exhibit senescence; a decline in physiological function with age. In nature, rates of senescence vary extensively among individuals and this variation has a significant genetic component; howeve...
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Article
Open AccessThe Drosophila melanogaster Genetic Reference Panel
A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict p...
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Article
Open AccessIdentification of RNA binding motif proteins essential for cardiovascular development
We recently identified Rbm24 as a novel gene expressed during mouse cardiac development. Due to its tightly restricted and persistent expression from formation of the cardiac crescent onwards and later in forming...
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Article
Open AccessThe non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate
Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues part...
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Article
The genetics of quantitative traits: challenges and prospects
Most phenotypic variation in natural populations is attributable to multiple interacting loci, with allelic effects that are sensitive to the exact environment...
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Article
Open AccessA transcriptional network associated with natural variation in Drosophilaaggressive behavior
Aggressive behavior is an important component of fitness in most animals. Aggressive behavior is genetically complex, with natural variation attributable to multiple segregating loci with allelic effects that ...
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Article
Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep
Trudy Mackay and colleagues measure sleep phenotypes in 40 wild-derived Drosophila lines, and report candidate genes and transcriptional networks associated with sleep regulation.
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Article
Systems genetics of complex traits in Drosophila melanogaster
Trudy Mackay and colleagues present a resource of 40 Drosophila melanogaster wild-derived inbred lines. The authors quantify genome-wide variation in transcript abundance for six ecologically relevant traits, cha...
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Article
Open AccessConstructing a meaningful evolutionary average at the phylogenetic center of mass
As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on va...
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Article
Open AccessMixture modeling of transcript abundance classes in natural populations
Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of t...
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Article
Role of α1-Adrenoceptors of the Locus Coeruleus in Self-Stimulation of the Medial Forebrain Bundle
The present experiments were undertaken to clarify the role of central α1-adrenoceptors in reward processes. Rats, trained to self-stimulate via electrodes in the medial forebrain bundle of the lateral hypothalam...
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Article
α1-Adrenergic and α2-adrenergic balance in the dorsal pons and gross behavioral activity of mice in a novel environment
Central α1- and α2-adrenoceptors in a number of different brain regions are known to have opposing actions on gross behavioral activity, with the former stimulating and the latter inhibiting activity. Therefore, ...
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Article
Rate-dependent behavioral effects of stimulation of central motoric α1-adrenoceptors: hypothesized relation to depolarization blockade
The purpose of this review is to clarify how central α1-adrenoceptors control behavioral activity under varying conditions of activity and stress.
