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JASPAR: an open-access database for eukaryotic transcription factor binding profiles
- A. Sandelin, W. Alkema, P. Engström, W. Wasserman, B. Lenhard
- Medicine, Computer ScienceNucleic Acids Res.
JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes that were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors.
Genome-wide analysis of mammalian promoter architecture and evolution
- Piero Carninci, A. Sandelin, +38 authors Y. Hayashizaki
- Biology, MedicineNature Genetics
- 28 April 2006
These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini.
BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers, which supports a wide range of identifiers from the most used biological databases currently available.
Quantifying the accessibility of the metagenome by random expression cloning techniques.
This study reveals significant differences in the predicted expression modes between distinct taxonomic groups of organisms and suggests that about 40% of the enzymatic activities may be readily recovered by random cloning in E. coli.
CoPub: a literature-based keyword enrichment tool for microarray data analysis
- Raoul Frijters, Bart Heupers, +5 authors W. Alkema
- Biology, Computer ScienceNucleic Acids Res.
- 28 April 2008
A publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs.
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
A novel method is presented, MSCAN, that circumvents the training data problem by measuring the statistical significance of any non-overlapping combination of TFBS in a window and returns putative regulatory regions.
Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling
This approach offers a robust and fast translational in vitro system for skewed T helper cell responses in Jurkat T cells, primary human CD4+ Tcells and in a more complex matrix such as human whole blood.
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
- Raoul Frijters, M. Vugt, R. Smeets, R. V. Schaik, J. D. Vlieg, W. Alkema
- Biology, Computer SciencePLoS Comput. Biol.
- 1 September 2010
The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid, making it a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to finding novel applications for existing drugs.
Diversity in Robustness of Lactococcus lactis Strains during Heat Stress, Oxidative Stress, and Spray Drying Stress
- A. Dijkstra, Meily C. Setyawati, +4 authors J. Hugenholtz
- Medicine, BiologyApplied and Environmental Microbiology
- 8 November 2013
The results demonstrate the relevance of screening culture collections for robustness under heat and oxidative stress on top of the typical screening for acidifying and flavor-forming properties, and reveal the absence or presence of specific genes was associated with heat or oxidative stress survival.
Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.
Regulogger is described, a novel computational method that uses comparative genomics to eliminate spurious members of predicted gene regulons and increases the specificity of predictions up to 25-fold over methods that use cis-element detection in isolation.