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A literature review of gene function prediction by modeling gene ontology
Annotating the functional properties of gene products, ie, RNAs and proteins, is a
fundamental task in biology. The Gene Ontology database (GO) was developed to …
fundamental task in biology. The Gene Ontology database (GO) was developed to …
ProteInfer, deep neural networks for protein functional inference
Predicting the function of a protein from its amino acid sequence is a long-standing
challenge in bioinformatics. Traditional approaches use sequence alignment to compare a …
challenge in bioinformatics. Traditional approaches use sequence alignment to compare a …
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an
ongoing, global, community-driven effort to evaluate and improve the computational …
ongoing, global, community-driven effort to evaluate and improve the computational …
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq–based resource for pain and sensory neuroscience research
2. Methods We performed RNA-seq for hDRG and integratively analyzed the transcriptome
by comparing it with publicly available human and mouse RNA-seq data sets (sources …
by comparing it with publicly available human and mouse RNA-seq data sets (sources …
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …
is the assignment of function to proteins. While molecular experiments provide the most …
Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor
JP Coppé, CK Patil, F Rodier, YU Sun, DP Muñoz… - PLoS …, 2008 - journals.plos.org
Cellular senescence suppresses cancer by arresting cell proliferation, essentially
permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the …
permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the …
Automatic gene function prediction in the 2020's
The current rate at which new DNA and protein sequences are being generated is too fast to
experimentally discover the functions of those sequences, emphasizing the need for …
experimentally discover the functions of those sequences, emphasizing the need for …
Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high
throughput molecular data and generating hypotheses about underlying biological …
throughput molecular data and generating hypotheses about underlying biological …
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank
Abstract Motivation Gene Ontology (GO) has been widely used to annotate functions of
proteins and understand their biological roles. Currently only< 1% of> 70 million proteins in …
proteins and understand their biological roles. Currently only< 1% of> 70 million proteins in …
[PDF][PDF] Gene ontology: pitfalls, biases, and remedies
Abstract The Gene Ontology (GO) is a formidable resource, but there are several
considerations about it that are essential to understand the data and interpret it correctly …
considerations about it that are essential to understand the data and interpret it correctly …