Artificial intelligence publications
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Revisiting the y-ome of Escherichia coli
EcoCyc.org, the most comprehensive curated genome database for the model microorganism E. coli K-12, has implemented a new categorization schema that indicates the degree to which a gene has been…
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Visual Analysis of Multi-Omics Data
Abstract We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based…
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The Comparative Genome Dashboard
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.
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The Genome Explorer Genome Browser
In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily…
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Automating the Derivation of Unification Algorithms. A Case Study in Deductive Program Synthesis
The unification algorithm has long been a target for program synthesis research, but a fully automatic derivation remains a research goal.
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An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.
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CyanoCyc Cyanobacterial Web Portal
CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools.
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The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets.
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Human Body Model Based ID using Shape and Pose Parameters
We present a Human Body model-based IDentification system (HMID) system that is jointly trained for shape, pose, and biometric identification.
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SynRoute: A Retrosynthetic Planning Software
SynRoute is a new retrosynthetic planning software tool that uses a relatively small number of general reaction templates, currently 263, along with a literature-based reaction database to find short, practical…
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IxDRL: A Novel Explainable Deep Reinforcement Learning Toolkit based on Analyses of Interestingness
Our tool provides various measures of RL agent competence stemming from interestingness analysis and is applicable to a wide range of RL algorithms, natively supporting the popular RLLib toolkit.
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The EcoCyc Database (2023)
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to…