Published in AAAI Fall Symposium: Artificial Intelligence for Synthetic Biology, 2018
This paper describes the application of a neural attention mechanism for studying the architecture of regulatory elements within the genome
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Published in International Workshop on Bio-Design Automation, 2018
This paper describes the application of a convolutional nerual network with an attention mechanism that can identify regulatory circuits in the genome with state-of-the-art performance. The attention mechanism of the neural network can also reveal the architecture of regulatory circuits within the genome
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Published in Scientific Reports, 2018
This study examines a gene expression signature in the circulating monocytes of Parkinson’s disease patients that can be used as a potential biomarker early in the disease course.
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Published in BioRxiv, 2018
This paper describes the application of a logistic regression model that uses a feature set, which is programmatically curated to reduce multiple collinearity, to identify combinations of sequence features targeted by transcription factors within the AP-1 transcription factor family.
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Published in Cell, 2018
Analyses of genetic variation in macrophages from inbred mouse strains reveal how a complex network of transcription factors influence cis- regulatory elements to impact differentiation and responses to environmental change.
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Published in Proceedings of the National Academy of Sciences, 2018
This paper describes novel cell-specific differences in LXR responses to natural and synthetic ligands in macrophages and liver cells that provide a conceptually new basis for future drug development.
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Published in Cell Metabolism, 2017
In this paper, the authors identify a biphasic macrophage gene expression program underlying anti-inflammatory fatty acid production following TLR4 activation. The late anti-inflammatory program is dependent on SREBP1. This is surprising given the known roles of SREBP1 in promoting IL1B production during the induction of inflammation and highlights its dual roles.
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Published in eLife, 2016
This paper investigates transcription factors that regulate the wound-healing response using genomics techniques
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Published in ACS Synthetic Biology, 2014
This paper describes RavenCAD, a dynamic programing algorithm for planing DNA synthesis protocols that is accessible as a web application.
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Published in Nature Methods, 2014
This paper describes RavenCAD, a dynamic programing algorithm for planing DNA synthesis protocols that is accessible as a web application.
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