Alyssa Morrow
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View article: ML-driven design of 3’ UTRs for mRNA stability
ML-driven design of 3’ UTRs for mRNA stability Open
Using mRNA as a therapeutic has received enormous attention in the last few years, but instability of the molecule remains a hurdle to achieving long-lasting therapeutic levels of protein expression. In this study, we describe our approach…
View article: RNAget: an API to securely retrieve RNA quantifications
RNAget: an API to securely retrieve RNA quantifications Open
Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in ma…
View article: Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning
Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning Open
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin acc…
View article: Epitome: Predicting epigenetic events in novel cell types with multi-cell deep ensemble learning
Epitome: Predicting epigenetic events in novel cell types with multi-cell deep ensemble learning Open
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin acc…
View article: Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets
Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets Open
The decreasing cost of DNA sequencing over the past decade has led to an explosion of sequencing datasets, leaving us with petabytes of data to analyze. However, current sequencing visualization tools are designed to run on single machines…
View article: Mango: Distributed Visualization for Genomic Analysis
Mango: Distributed Visualization for Genomic Analysis Open
Summary The decreasing cost of DNA sequencing over the past decade has led to an explosion of available sequencing datasets, leaving us with terabytes to petabytes of data to explore and analyze. It is critical for analysts in research and…
View article: Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction
Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction Open
We present a simple and efficient method for prediction of transcription factor binding sites from DNA sequence. Our method computes a random approximation of a convolutional kernel feature map from DNA sequence and then learns a linear mo…