Nature Reviews Genetics, ISSN 1471-0056, 08/2012, Volume 13, Issue 8, pp. 523 - 536
At different stages of any research project, molecular biologists need to choose - often somewhat arbitrarily, even after careful statistical data analysis -...
PROTEIN | GENETICS & HEREDITY | LINKING GENES | INTERACTION NETWORKS | HETEROGENEOUS DATA SOURCES | INFORMATION EXTRACTION | ENRICHMENT ANALYSIS | EXPRESSION | WEB-SERVER | GENOME | PREDICTION | Haploinsufficiency - genetics | Computational Biology - methods | Genetic Predisposition to Disease | Animals | Genetic Association Studies - statistics & numerical data | Humans | Databases, Genetic | Genetic Association Studies - methods | Mice | Models, Genetic | Genetic research | Technology application | Usage | Applications software
PROTEIN | GENETICS & HEREDITY | LINKING GENES | INTERACTION NETWORKS | HETEROGENEOUS DATA SOURCES | INFORMATION EXTRACTION | ENRICHMENT ANALYSIS | EXPRESSION | WEB-SERVER | GENOME | PREDICTION | Haploinsufficiency - genetics | Computational Biology - methods | Genetic Predisposition to Disease | Animals | Genetic Association Studies - statistics & numerical data | Humans | Databases, Genetic | Genetic Association Studies - methods | Mice | Models, Genetic | Genetic research | Technology application | Usage | Applications software
Journal Article
Biology Direct, ISSN 1745-6150, 06/2018, Volume 13, Issue 1, pp. 12 - 13
Background: One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are...
Network-based methods | Biological networks | Network topology | GENES | BIOLOGY | Computational Biology - methods | Algorithms | Gene Regulatory Networks - genetics | Humans | Neuroblastoma - genetics | Gene Regulatory Networks - physiology | Genomics - methods | Medical research | Care and treatment | Innovations | Medicine, Experimental | Development and progression | Neuroblastoma | Computational biology | Networks | Computational neuroscience | Genomes | Metastasis | Gene expression | Patients | Molecular chains | Clinical outcomes | Datasets | Proteins | Classification | Computer applications | Cell cycle | Mathematical models | Computer networks | Bioinformatics | Methods | Cancer
Network-based methods | Biological networks | Network topology | GENES | BIOLOGY | Computational Biology - methods | Algorithms | Gene Regulatory Networks - genetics | Humans | Neuroblastoma - genetics | Gene Regulatory Networks - physiology | Genomics - methods | Medical research | Care and treatment | Innovations | Medicine, Experimental | Development and progression | Neuroblastoma | Computational biology | Networks | Computational neuroscience | Genomes | Metastasis | Gene expression | Patients | Molecular chains | Clinical outcomes | Datasets | Proteins | Classification | Computer applications | Cell cycle | Mathematical models | Computer networks | Bioinformatics | Methods | Cancer
Journal Article
Nucleic acids research, ISSN 0305-1048, 07/2016, Volume 44, Issue 1, pp. W117 - W121
Genomic studies and high-throughput experiments often produce large lists of candidate genes among which only a small fraction are truly relevant to the...
BIOCHEMISTRY & MOLECULAR BIOLOGY | Genetic Predisposition to Disease | Phenotype | Algorithms | Animals | Genetic Association Studies | Humans | Benchmarking | Genotype | Software | Internet | Web Server issue
BIOCHEMISTRY & MOLECULAR BIOLOGY | Genetic Predisposition to Disease | Phenotype | Algorithms | Animals | Genetic Association Studies | Humans | Benchmarking | Genotype | Software | Internet | Web Server issue
Journal Article
Nature Methods, ISSN 1548-7091, 11/2013, Volume 10, Issue 11, pp. 1083 - 1086
Massively parallel sequencing greatly facilitates the discovery of novel disease genes causing Mendelian and oligogenic disorders. However, many mutations are...
MUTATIONS | EXOMES | DISEASE | BIOCHEMICAL RESEARCH METHODS | Genetic Predisposition to Disease | Phenotype | Humans | Databases, Genetic | Polymorphism, Single Nucleotide | Mutation | Genome, Human | Gene mutations | Analysis | Exome sequencing | Genotype & phenotype | Fusion | Genomics
MUTATIONS | EXOMES | DISEASE | BIOCHEMICAL RESEARCH METHODS | Genetic Predisposition to Disease | Phenotype | Humans | Databases, Genetic | Polymorphism, Single Nucleotide | Mutation | Genome, Human | Gene mutations | Analysis | Exome sequencing | Genotype & phenotype | Fusion | Genomics
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 7/2008, Volume 36, Issue suppl_2, pp. W377 - W384
Endeavour (http://www.esat.kuleuven.be/endeavourweb; this web site is free and open to all users and there is no login requirement) is a web resource for the...
INTERACTION NETWORK DATABASE | SEQUENCE-ANALYSIS | SYSTEMIC-LUPUS-ERYTHEMATOSUS | HUMAN-DISEASE GENES | VARIANTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | NEWLY IDENTIFIED LOCI | PROSTATE-CANCER | CANDIDATE GENES | SUSCEPTIBILITY | EXPRESSION | Genetic Predisposition to Disease | Animals | Caenorhabditis elegans - genetics | Genes | Humans | Rats | Models, Animal | Mice | Software | Internet | Drosophila melanogaster - genetics | Zebrafish - genetics
INTERACTION NETWORK DATABASE | SEQUENCE-ANALYSIS | SYSTEMIC-LUPUS-ERYTHEMATOSUS | HUMAN-DISEASE GENES | VARIANTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | NEWLY IDENTIFIED LOCI | PROSTATE-CANCER | CANDIDATE GENES | SUSCEPTIBILITY | EXPRESSION | Genetic Predisposition to Disease | Animals | Caenorhabditis elegans - genetics | Genes | Humans | Rats | Models, Animal | Mice | Software | Internet | Drosophila melanogaster - genetics | Zebrafish - genetics
Journal Article
PLoS ONE, ISSN 1932-6203, 03/2008, Volume 3, Issue 3, p. e1854
Background: Housekeeping genes are needed in every tissue as their expression is required for survival, integrity or duplication of every cell. Housekeeping...
BIOLOGY | Mice | Animals | Analysis of Variance | Oligonucleotide Array Sequence Analysis | Ribosomal Proteins - genetics | Mice, Inbred C57BL | Genetic research | Gene expression | Analysis | Genes | Cytochrome | Electrical engineering | Cell survival | Genomics | Genomes | Biology | Stability analysis | Group dynamics | Tissues | Statistics | Variance analysis | Proteins | DNA microarrays | Acids | Rodents | Stem cells | Localization | Arrays | Bioinformatics
BIOLOGY | Mice | Animals | Analysis of Variance | Oligonucleotide Array Sequence Analysis | Ribosomal Proteins - genetics | Mice, Inbred C57BL | Genetic research | Gene expression | Analysis | Genes | Cytochrome | Electrical engineering | Cell survival | Genomics | Genomes | Biology | Stability analysis | Group dynamics | Tissues | Statistics | Variance analysis | Proteins | DNA microarrays | Acids | Rodents | Stem cells | Localization | Arrays | Bioinformatics
Journal Article
Genome Biology, ISSN 1474-7596, 2016, Volume 17, Issue 1, p. 184
Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular...
Disease gene prioritization | Protein function prediction | ADAM | DISINTEGRIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | ONTOLOGY | Proteins - genetics | Algorithms | Databases, Protein | Humans | Molecular Sequence Annotation | Computational Biology | Software | Structure-Activity Relationship | Proteins - chemistry | Gene Ontology | Automation | Phenotypes | Ontology | Genes | Benchmarks | Experiments | Data bases | Proteins | Accuracy | Annotations | Computer applications | Bioinformatics | Methods | Quantitative Biology - Quantitative Methods
Disease gene prioritization | Protein function prediction | ADAM | DISINTEGRIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | ONTOLOGY | Proteins - genetics | Algorithms | Databases, Protein | Humans | Molecular Sequence Annotation | Computational Biology | Software | Structure-Activity Relationship | Proteins - chemistry | Gene Ontology | Automation | Phenotypes | Ontology | Genes | Benchmarks | Experiments | Data bases | Proteins | Accuracy | Annotations | Computer applications | Bioinformatics | Methods | Quantitative Biology - Quantitative Methods
Journal Article
IEEE Transactions on Pattern Analysis and Machine Intelligence, ISSN 0162-8828, 05/2012, Volume 34, Issue 5, pp. 1031 - 1039
This paper presents a novel optimized kernel k-means algorithm (OKKC) to combine multiple data sources for clustering analysis. The algorithm uses an...
Algorithm design and analysis | Support vector machines | data fusion | multiple kernel learning | Clustering algorithms | Hilbert space | Complexity theory | Partitioning algorithms | Fisher discriminant analysis | least-squares support vector machine | Clustering | Kernel | DISCRIMINANT-ANALYSIS | CONSENSUS | COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE | ENGINEERING, ELECTRICAL & ELECTRONIC | Technology application | Electronic data processing | Usage | Kernel functions | Innovations | Least squares | Markov processes | Quadratic programming
Algorithm design and analysis | Support vector machines | data fusion | multiple kernel learning | Clustering algorithms | Hilbert space | Complexity theory | Partitioning algorithms | Fisher discriminant analysis | least-squares support vector machine | Clustering | Kernel | DISCRIMINANT-ANALYSIS | CONSENSUS | COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE | ENGINEERING, ELECTRICAL & ELECTRONIC | Technology application | Electronic data processing | Usage | Kernel functions | Innovations | Least squares | Markov processes | Quadratic programming
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2016, Volume 44, Issue 2, pp. e18 - e18
Disease-gene identification is a challenging process that has multiple applications within functional genomics and personalized medicine. Typically, this...
PRIORITIZATION | IDENTIFICATION | ASSOCIATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CANDIDATE GENES | Computational Biology - methods | Algorithms | Genetic Association Studies - statistics & numerical data | Humans | Probability | Search Engine | Data Mining | Software | Methods Online
PRIORITIZATION | IDENTIFICATION | ASSOCIATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CANDIDATE GENES | Computational Biology - methods | Algorithms | Genetic Association Studies - statistics & numerical data | Humans | Probability | Search Engine | Data Mining | Software | Methods Online
Journal Article
Bioinformatics, ISSN 1367-4803, 12/2012, Volume 28, Issue 23, pp. 3081 - 3088
Motivation: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates-so as to maximize the yield and...
DISEASE GENES | VARIANTS | CANDIDATE GENES | BIOCHEMICAL RESEARCH METHODS | CONGENITAL-ANOMALIES | HAPLOINSUFFICIENCY | IDENTIFIES SUSCEPTIBILITY LOCI | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | RECEPTOR GENE | DUPLICATION | MUTATIONS | GENOME-WIDE ASSOCIATION | Databases, Genetic | Internet | Genetic Association Studies | Humans
DISEASE GENES | VARIANTS | CANDIDATE GENES | BIOCHEMICAL RESEARCH METHODS | CONGENITAL-ANOMALIES | HAPLOINSUFFICIENCY | IDENTIFIES SUSCEPTIBILITY LOCI | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | RECEPTOR GENE | DUPLICATION | MUTATIONS | GENOME-WIDE ASSOCIATION | Databases, Genetic | Internet | Genetic Association Studies | Humans
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 7/2011, Volume 39, Issue suppl_2, pp. W334 - W338
PINTA (available at http://www.esat.kuleuven.be/pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for...
PHENOTYPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | CANDIDATE GENES | Animals | Disease - genetics | Genes | Humans | Rats | Gene Expression Profiling | Mice | Software | Internet | Protein Interaction Mapping
PHENOTYPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | CANDIDATE GENES | Animals | Disease - genetics | Genes | Humans | Rats | Gene Expression Profiling | Mice | Software | Internet | Protein Interaction Mapping
Journal Article
Genome Research, ISSN 1088-9051, 2014, Volume 24, Issue 3, pp. 511 - 521
Alternative splicing is the main mechanism of increasing the proteome diversity coded by a limited number of genes. It is well established that different...
NETWORK | TRANSCRIPTOME | MICROARRAY | LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ISOFORM REGULATION | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | REGULATORS | BINDING PROTEIN HUR | REVEALS | Human Umbilical Vein Endothelial Cells | User-Computer Interface | Epithelial Cells - metabolism | Alternative Splicing | Oligonucleotide Array Sequence Analysis | Exons | Humans | Gene Expression Profiling | Animals | MCF-7 Cells | Cell Line, Tumor | Mice | Software | Epithelial Cells - cytology | RNA-Binding Proteins - metabolism | Fibroblasts - metabolism | Fibroblasts | Genetic aspects | Research | Comparative analysis | Epithelial cells | RNA splicing | Genomics | Cellular Biology | Life Sciences | Fibroblasts/metabolism | Computer Science | Subcellular Processes | Bioinformatics | Epithelial Cells/metabolism | Epithelial Cells/cytology | Quantitative Methods | Biochemistry, Molecular Biology | RNA-Binding Proteins/metabolism | Cancer | Resource
NETWORK | TRANSCRIPTOME | MICROARRAY | LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ISOFORM REGULATION | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | REGULATORS | BINDING PROTEIN HUR | REVEALS | Human Umbilical Vein Endothelial Cells | User-Computer Interface | Epithelial Cells - metabolism | Alternative Splicing | Oligonucleotide Array Sequence Analysis | Exons | Humans | Gene Expression Profiling | Animals | MCF-7 Cells | Cell Line, Tumor | Mice | Software | Epithelial Cells - cytology | RNA-Binding Proteins - metabolism | Fibroblasts - metabolism | Fibroblasts | Genetic aspects | Research | Comparative analysis | Epithelial cells | RNA splicing | Genomics | Cellular Biology | Life Sciences | Fibroblasts/metabolism | Computer Science | Subcellular Processes | Bioinformatics | Epithelial Cells/metabolism | Epithelial Cells/cytology | Quantitative Methods | Biochemistry, Molecular Biology | RNA-Binding Proteins/metabolism | Cancer | Resource
Journal Article
Cell Reports, ISSN 2211-1247, 06/2014, Volume 7, Issue 6, pp. 1900 - 1913
The RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins that are involved in gene-expression regulation; however, their...
ANALYSIS REVEALS | COMPLEX | P68 | EPITHELIAL-MESENCHYMAL TRANSITIONS | SMAD | PROTEINS | G-QUADRUPLEX | BINDING | EXPRESSION | SUBSET | CELL BIOLOGY | Epithelial Cells - metabolism | Alternative Splicing | Exons | Down-Regulation | Humans | Gene Expression Regulation | Heterogeneous-Nuclear Ribonucleoproteins - metabolism | MicroRNAs - biosynthesis | MicroRNAs - metabolism | Epithelial-Mesenchymal Transition - genetics | Heterogeneous-Nuclear Ribonucleoproteins - genetics | Cell Differentiation - genetics | DEAD-box RNA Helicases - genetics | Epithelial Cells - physiology | Myoblasts - metabolism | Animals | MCF-7 Cells | Epithelial Cells - enzymology | Transcription, Genetic | Mice | MicroRNAs - genetics | DEAD-box RNA Helicases - metabolism | Myoblasts - enzymology | Myoblasts - physiology
ANALYSIS REVEALS | COMPLEX | P68 | EPITHELIAL-MESENCHYMAL TRANSITIONS | SMAD | PROTEINS | G-QUADRUPLEX | BINDING | EXPRESSION | SUBSET | CELL BIOLOGY | Epithelial Cells - metabolism | Alternative Splicing | Exons | Down-Regulation | Humans | Gene Expression Regulation | Heterogeneous-Nuclear Ribonucleoproteins - metabolism | MicroRNAs - biosynthesis | MicroRNAs - metabolism | Epithelial-Mesenchymal Transition - genetics | Heterogeneous-Nuclear Ribonucleoproteins - genetics | Cell Differentiation - genetics | DEAD-box RNA Helicases - genetics | Epithelial Cells - physiology | Myoblasts - metabolism | Animals | MCF-7 Cells | Epithelial Cells - enzymology | Transcription, Genetic | Mice | MicroRNAs - genetics | DEAD-box RNA Helicases - metabolism | Myoblasts - enzymology | Myoblasts - physiology
Journal Article
Briefings in Bioinformatics, ISSN 1467-5463, 01/2011, Volume 12, Issue 1, pp. 22 - 32
Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem. It is a recurrent problem in...
Candidate gene | Review | Gene prioritization | In silico prediction | Disease gene | NETWORK | disease gene | COMPLEX HUMAN TRAITS | BIOCHEMICAL RESEARCH METHODS | gene prioritization | SEARCH TOOL | in silico prediction | IDENTIFICATION | DATA FUSION | INHERITED DISEASES | candidate gene | HUMAN GENOME | HUMAN-DISEASE GENES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | review | INTEGRATED APPROACH | TYPE-2 DIABETES-MELLITUS | Computational Biology - methods | Software | Internet | Genes | Humans | Bioinformatics
Candidate gene | Review | Gene prioritization | In silico prediction | Disease gene | NETWORK | disease gene | COMPLEX HUMAN TRAITS | BIOCHEMICAL RESEARCH METHODS | gene prioritization | SEARCH TOOL | in silico prediction | IDENTIFICATION | DATA FUSION | INHERITED DISEASES | candidate gene | HUMAN GENOME | HUMAN-DISEASE GENES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | review | INTEGRATED APPROACH | TYPE-2 DIABETES-MELLITUS | Computational Biology - methods | Software | Internet | Genes | Humans | Bioinformatics
Journal Article