A literature review of gene function prediction by modeling gene ontology

Y Zhao, J Wang, J Chen, X Zhang, M Guo… - Frontiers in genetics, 2020 - frontiersin.org
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 …

ProteInfer, deep neural networks for protein functional inference

T Sanderson, ML Bileschi, D Belanger, LJ Colwell - Elife, 2023 - elifesciences.org
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 …

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh… - Genome biology, 2019 - Springer
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an
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

P Ray, A Torck, L Quigley, A Wangzhou, M Neiman… - Pain, 2018 - journals.lww.com
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 …

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Y Jiang, TR Oron, WT Clark, AR Bankapur, D D'Andrea… - Genome biology, 2016 - Springer
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 …

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 …

Automatic gene function prediction in the 2020's

S Makrodimitris, RCHJ Van Ham, MJT Reinders - Genes, 2020 - mdpi.com
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 …

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

A Tomczak, JM Mortensen, R Winnenburg, C Liu… - Scientific reports, 2018 - nature.com
Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high
throughput molecular data and generating hypotheses about underlying biological …

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank

R You, Z Zhang, Y **ong, F Sun, H Mamitsuka… - …, 2018 - academic.oup.com
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 …

[PDF][PDF] Gene ontology: pitfalls, biases, and remedies

P Gaudet, C Dessimoz - The gene ontology handbook, 2017 - library.oapen.org
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 …