Daphne Koller
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View article: TDP-43 loss induces cryptic polyadenylation in ALS/FTD
TDP-43 loss induces cryptic polyadenylation in ALS/FTD Open
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 are cellular hallmarks of amyotrophic lateral sclerosis (ALS). TDP-43 nuclear loss causes de-repression of cryptic exons, yet cryptic alternative polyadenylati…
View article: EmbedGEM: a framework to evaluate the utility of embeddings for genetic discovery
EmbedGEM: a framework to evaluate the utility of embeddings for genetic discovery Open
Summary Machine learning-derived embeddings are a compressed representation of high content data modalities. Embeddings can capture detailed information about disease states and have been qualitatively shown to be useful in genetic discove…
View article: EmbedGEM: A framework to evaluate the utility of embeddings for genetic discovery
EmbedGEM: A framework to evaluate the utility of embeddings for genetic discovery Open
Machine learning (ML)-derived embeddings are a compressed representation of high content data modalities. Embeddings can capture detailed information about disease states and have been qualitatively shown to be useful in genetic discovery.…
View article: An allelic-series rare-variant association test for candidate-gene discovery
An allelic-series rare-variant association test for candidate-gene discovery Open
View article: An allelic series rare variant association test for candidate gene discovery
An allelic series rare variant association test for candidate gene discovery Open
Allelic series are of candidate therapeutic interest due to the existence of a dose-response relationship between the functionality of a gene and the degree or severity of a phenotype. We define an allelic series as a gene in which increas…
View article: Convolutional neural networks of H&E-stained biopsy images accurately quantify histologic features of non-alcoholic steatohepatitis
Convolutional neural networks of H&E-stained biopsy images accurately quantify histologic features of non-alcoholic steatohepatitis Open
View article: Peptide-Spectra Matching from Weak Supervision
Peptide-Spectra Matching from Weak Supervision Open
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to obtai…
View article: Inferring Multidimensional Rates of Aging from Cross-Sectional Data
Inferring Multidimensional Rates of Aging from Cross-Sectional Data Open
Modeling how individuals evolve over time is a fundamental problem in the natural and social sciences. However, existing datasets are often cross-sectional with each individual observed only once, making it impossible to apply traditional …
View article: Conservation and divergence in modules of the transcriptional programs of the human and mouse immune systems
Conservation and divergence in modules of the transcriptional programs of the human and mouse immune systems Open
Studies in mouse have shed important light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we compare previousl…
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View article: Correction: Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
Correction: Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases Open
Aging is one of the most important biological processes and is a known risk factor for many age-related diseases in human. Studying age-related transcriptomic changes in tissues across the whole body can provide valuable information for a …
View article: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases Open
View article: Sharing and Specificity of Co-expression Networks across 35 Human Tissues
Sharing and Specificity of Co-expression Networks across 35 Human Tissues Open
To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific g…
View article: Effect of predicted protein-truncating genetic variants on the human transcriptome
Effect of predicted protein-truncating genetic variants on the human transcriptome Open
Expression, genetic variation, and tissues Human genomes show extensive genetic variation across individuals, but we have only just started documenting the effects of this variation on the regulation of gene expression. Furthermore, only a…
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