AIMC Topic: Genomics

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Logical Reasoning (Inferencing) on MicroRNA Data.

Methods in molecular biology (Clifton, N.J.)
Logical reasoning played an important role in artificial intelligence. Applying logical reasoning on microRNA data brings intelligence into data analysis. Here, we provide basic introduction about logic (especially propositional logic) and automated ...

Exploring Genome-Wide Expression Profiles Using Machine Learning Techniques.

Methods in molecular biology (Clifton, N.J.)
Although contemporary high-throughput -omics methods produce high-dimensional data, the resulting wealth of information is difficult to assess using traditional statistical procedures. Machine learning methods facilitate the detection of additional p...

DEEP MOTIF DASHBOARD: VISUALIZING AND UNDERSTANDING GENOMIC SEQUENCES USING DEEP NEURAL NETWORKS.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signa...

The Vision and Challenges of the Gene Ontology.

Methods in molecular biology (Clifton, N.J.)
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1...

The Gene Ontology and the Meaning of Biological Function.

Methods in molecular biology (Clifton, N.J.)
The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. It is specifically designed for supporting the computational representation of biological systems. A GO annotation is an...

GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

Journal of bioinformatics and computational biology
Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evol...

The Plant Ontology: A Tool for Plant Genomics.

Methods in molecular biology (Clifton, N.J.)
The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparat...

Networking Biology: The Origins of Sequence-Sharing Practices in Genomics.

Technology and culture
The wide sharing of biological data, especially nucleotide sequences, is now considered to be a key feature of genomics. Historians and sociologists have attempted to account for the rise of this sharing by pointing to precedents in model organism co...