AIMC Topic: Molecular Sequence Annotation
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Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling.
Database : the journal of biological databases and curation
Jan 1, 2018
We present a system for automatically identifying a multitude of biomedical entities from the literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID Assignment shared task in which our system demonstrated sta...
PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants.
Database : the journal of biological databases and curation
Jan 1, 2018
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although th...
ALE: automated label extraction from GEO metadata.
BMC bioinformatics
Dec 28, 2017
BACKGROUND: NCBI's Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experiment (metadata) is in the format...
A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.
BMC genomics
Oct 18, 2017
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed whe...
Semantic biclustering for finding local, interpretable and predictive expression patterns.
BMC genomics
Oct 16, 2017
BACKGROUND: One of the major challenges in the analysis of gene expression data is to identify local patterns composed of genes showing coherent expression across subsets of experimental conditions. Such patterns may provide an understanding of under...
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.
BMC bioinformatics
Oct 12, 2017
BACKGROUND: The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this c...
Investigations on factors influencing HPO-based semantic similarity calculation.
Journal of biomedical semantics
Sep 20, 2017
BACKGROUND: Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with complex phenotypes and high ge...
NoGOA: predicting noisy GO annotations using evidences and sparse representation.
BMC bioinformatics
Jul 21, 2017
BACKGROUND: Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of anno...
NewGOA: Predicting New GO Annotations of Proteins by Bi-Random Walks on a Hybrid Graph.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 15, 2017
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many ...
A disease similarity matrix based on the uniqueness of shared genes.
BMC medical genomics
May 24, 2017
BACKGROUND: Complex diseases involve many genes, and these genes are often associated with several different illnesses. Disease similarity measurement can be based on shared genotype or phenotype. Quantifying relationships between genes can reveal pr...
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