AIMC Topic: Gene Expression Profiling
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De novo transcriptome assembly of pummelo and molecular marker development.
PloS one
Mar 23, 2015
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
High-Throughput Nucleotide Sequencing
Phenotype
Gene Frequency
Transcriptome
Reproducibility of Results
Citrus
Polymorphism, Single Nucleotide
Phylogeny
Cluster Analysis
Molecular Sequence Annotation
Gene Expression Profiling
Genetic Markers
Gene Ontology
Nucleotide Motifs
Gene Library
Microsatellite Repeats
Physical Chromosome Mapping
Integrating biological knowledge based on functional annotations for biclustering of gene expression data.
Computer methods and programs in biomedicine
Mar 18, 2015
Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect...
Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer--the INNODIAG study.
BMC medical genomics
Feb 7, 2015
BACKGROUND: Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data derived from tumor molecular...
Neoplasm Invasiveness
Decision Making
Neoplasm Recurrence, Local
Oligonucleotide Array Sequence Analysis
Cohort Studies
Humans
Computational Biology
Algorithms
Gene Expression Regulation, Neoplastic
Precision Medicine
Databases, Genetic
Reproducibility of Results
Fuzzy Logic
Prognosis
Sensitivity and Specificity
Female
Breast Neoplasms
Gene Expression Profiling
A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data.
BMC genomics
Jan 15, 2015
BACKGROUND: Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machin...
A fast gene selection method for multi-cancer classification using multiple support vector data description.
Journal of biomedical informatics
Dec 27, 2014
For cancer classification problems based on gene expression, the data usually has only a few dozen sizes but has thousands to tens of thousands of genes which could contain a large number of irrelevant genes. A robust feature selection algorithm is r...
Humans
Artificial Intelligence
Software
Algorithms
Neoplasms
Oligonucleotide Array Sequence Analysis
Models, Statistical
Gene Expression Regulation, Leukemic
Gene Expression Profiling
Bayes Theorem
Leukemia
Diagnosis, Computer-Assisted
Gene Expression
Gene Expression Regulation, Neoplastic
Colonic Neoplasms
Support Vector Machine
Pattern Recognition, Automated
LinkRbrain: multi-scale data integrator of the brain.
Journal of neuroscience methods
Dec 18, 2014
BACKGROUND: LinkRbrain is an open-access web platform for multi-scale data integration and visualization of human brain data. This platform integrates anatomical, functional, and genetic knowledge produced by the scientific community.
Molecular classification of amyotrophic lateral sclerosis by unsupervised clustering of gene expression in motor cortex.
Neurobiology of disease
Dec 10, 2014
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and ultimately fatal neurodegenerative disease, caused by the loss of motor neurons in the brain and spinal cord. Although 10% of ALS cases are familial (FALS), the majority are sporadic (S...
Inter-species pathway perturbation prediction via data-driven detection of functional homology.
Bioinformatics (Oxford, England)
Aug 22, 2014
MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER ...
Artificial Intelligence
Software
Algorithms
Cells, Cultured
Cytokines
Humans
Rats
Signal Transduction
Epithelial Cells
Phosphorylation
Translational Research, Biomedical
Databases, Factual
Animals
Gene Expression Profiling
Systems Biology
Oligonucleotide Array Sequence Analysis
Bronchi
Phosphoproteins
Gene Expression Regulation
Models, Animal
Species Specificity
Alpha-plane based automatic general type-2 fuzzy clustering based on simulated annealing meta-heuristic algorithm for analyzing gene expression data.
Computers in biology and medicine
Jul 2, 2014
This paper considers microarray gene expression data clustering using a novel two stage meta-heuristic algorithm based on the concept of α-planes in general type-2 fuzzy sets. The main aim of this research is to present a powerful data clustering app...
The limitations of simple gene set enrichment analysis assuming gene independence.
Statistical methods in medical research
Oct 14, 2012
Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess en...
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