AIMC Topic: Saccharomyces cerevisiae
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Identifying term relations cross different gene ontology categories.
BMC bioinformatics
Dec 28, 2017
BACKGROUND: The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecu...
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems.
PLoS computational biology
Nov 17, 2017
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series ...
Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data.
Bio Systems
Nov 4, 2017
The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of t...
Reconstructing Genetic Regulatory Networks Using Two-Step Algorithms with the Differential Equation Models of Neural Networks.
Interdisciplinary sciences, computational life sciences
Jul 26, 2017
BACKGROUND: The identification of genetic regulatory networks (GRNs) provides insights into complex cellular processes. A class of recurrent neural networks (RNNs) captures the dynamics of GRN. Algorithms combining the RNN and machine learning scheme...
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...
A statistical framework for biomedical literature mining.
Statistics in medicine
Jul 4, 2017
In systems biology, it is of great interest to identify new genes that were not previously reported to be associated with biological pathways related to various functions and diseases. Identification of these new pathway-modulating genes does not onl...
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.
Journal of integrative bioinformatics
Jun 10, 2017
Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational int...
DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks.
Journal of chemical information and modeling
May 26, 2017
The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example,...
Identifying N-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine.
Scientific reports
Apr 25, 2017
N6-methyladenosine (mA) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear transl...
High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots.
PloS one
Mar 20, 2017
Saccharomyces cerevisiae (budding yeast) is a powerful eukaryotic model organism ideally suited to high-throughput genetic analyses, which time and again has yielded insights that further our understanding of cell biology processes conserved in human...
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