AIMC Topic: Gene Expression Profiling

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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...
Gene Expression Profiling Gene Ontology Computational Biology Datasets as Topic Saccharomyces cerevisiae Protein Interaction Maps Gene Regulatory Networks
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Prediction of synergistic anti-cancer drug combinations based on drug target network and drug induced gene expression profiles.

Artificial intelligence in medicine Jun 3, 2017
OBJECTIVE: Synergistic drug combinations are promising therapies for cancer treatment. However, effective prediction of synergistic drug combinations is quite challenging as mechanisms of drug synergism are still unclear. Various features such as dru...
Pharmacogenetics Protein Interaction Maps Gene Regulatory Networks Gene Expression Profiling Transcriptome Antineoplastic Combined Chemotherapy Protocols Databases, Genetic Drug Synergism Computational Biology Gene Expression Regulation, Neoplastic Signal Transduction Humans Artificial Intelligence Computer Simulation Reproducibility of Results Neoplasms
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Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.

IEEE/ACM transactions on computational biology and bioinformatics Apr 5, 2017
Machine learning is an integral part of computational biology, and has already shown its use in various applications, such as prognostic tests. In the last few years in the non-biological machine learning community, ensembling techniques have shown t...
Databases, Genetic Data Mining Machine Learning Algorithms Female Breast Neoplasms Gene Expression Profiling Computational Biology Humans
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Optimization of Gene Set Annotations Using Robust Trace-Norm Multitask Learning.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2017
Gene set enrichment (GSE) is a useful tool for analyzing and interpreting large molecular datasets generated by modern biomedical science. The accuracy and reproducibility of GSE analysis are heavily affected by the quality and integrity of gene sets...
Humans Computer Simulation Neoplasms Supervised Machine Learning Molecular Sequence Annotation Gene Expression Profiling Computational Biology Databases, Genetic
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Reproducibility of computational workflows is automated using continuous analysis.

Nature biotechnology Mar 13, 2017
Replication, validation and extension of experiments are crucial for scientific progress. Computational experiments are scriptable and should be easy to reproduce. However, computational analyses are designed and run in a specific computing environme...
Computational Biology Workflow Gene Expression Profiling User-Computer Interface Machine Learning Software Reproducibility of Results Sensitivity and Specificity
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Development of a two-stage gene selection method that incorporates a novel hybrid approach using the cuckoo optimization algorithm and harmony search for cancer classification.

Journal of biomedical informatics Feb 3, 2017
For each cancer type, only a few genes are informative. Due to the so-called 'curse of dimensionality' problem, the gene selection task remains a challenge. To overcome this problem, we propose a two-stage gene selection method called MRMR-COA-HS. In...
Oligonucleotide Array Sequence Analysis Neoplasms Genetic Techniques Humans Gene Expression Profiling Algorithms Support Vector Machine
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Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

BMC genomics Jan 25, 2017
BACKGROUND: The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinfor...
Humans Gene Expression Profiling Sequence Analysis, RNA Neural Networks, Computer Computational Biology Models, Statistical Algorithms Bias
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Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles.

BMC genomics Jan 6, 2017
BACKGROUND: Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood is a useful way to study disease pathobiology and may help elucidate the molecular mechanisms of disease, or discovery of useful disease biomarker...
Humans Machine Learning Gene Expression Profiling Genomics Models, Statistical Blood Cells
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Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to .

Frontiers in cellular and infection microbiology Dec 26, 2016
() is problematic for lactating mammals and public health. Understanding of mechanisms by which the hosts respond to severe invasion of remains elusive. In this study, the genome-wide expression of mRNAs and miRNAs in bovine mammary gland cells wer...
Immunity, Innate Gene Expression Profiling MicroRNAs Humans Staphylococcal Infections Cattle Animals Mastitis, Bovine RNA, Messenger Mammary Glands, Human
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Grouping miRNAs of similar functions via weighted information content of gene ontology.

BMC bioinformatics Dec 22, 2016
BACKGROUND: Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regu...
Gene Expression Profiling Computational Biology Cluster Analysis Humans Algorithms MicroRNAs Models, Statistical Gene Ontology
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