Istrail Lab

The Regulatory Genome, Gene Regulatory Networks and Transcriptomics

Research Summary

Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code

In this article, we discuss several computer science problems, inspired by our 15-year-long collaboration with Prof. Eric Davidson, focusing on computer science contributions to the study of the regulatory genome. Our joint study was inspired by his lifetime trailblazing research program rooted in causal gene regulatory networks (GRNs), system completeness, genomic Boolean logic, and genomically encoded regulatory information. We present first four inspiring questions that Eric Davidson asked, and the follow-up, namely, seven technical problems,

How Does the Regulatory Genome Work?

The regulatory genome controls genome activity throughout the life of an organism. This requires that complex information processing functions are encoded in, and operated by, the regulatory genome. Although much remains to be learned about how the regulatory genome works, we here discuss two cases where regulatory functions have been experimentally dissected in great detail and at the systems level, and formalized by computational logic models.

OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements

Images form a significant and useful source of information in published biomedical articles, which is still under-utilized in biomedical document classification and retrieval. Much current work on biomedical image retrieval and classification employs simple, standard image features such as gray scale histograms and edge direction to represent and classify images. We have used such features as well to classify images in our early work [5], where we used image-class-tags to represent and classify articles.

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