JASPAR: an open-access database for eukaryotic transcription factor binding profiles
- A. Sandelin, W. Alkema, P. Engström, W. Wasserman, B. Lenhard
- BiologyNucleic Acids Res.
- 2004
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, Y. Hayashizaki
- BiologyNature 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
- Tim Hulsen, J. de Vlieg, W. Alkema
- Computer ScienceBMC Genomics
- 16 October 2008
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.
- E. Gabor, W. Alkema, D. Janssen
- BiologyEnvironmental Microbiology
- 1 September 2004
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, W. Alkema
- Economics, BiologyNucleic 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
- Ö. Johansson, W. Alkema, W. Wasserman, J. Lagergren
- BiologyIntelligent Systems in Molecular Biology
- 3 July 2003
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.
Diversity in Robustness of Lactococcus lactis Strains during Heat Stress, Oxidative Stress, and Spray Drying Stress
- A. Dijkstra, Meily C. Setyawati, J. Hugenholtz
- Biology, MedicineApplied 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.
Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling
- R. Smeets, W. Fleuren, W. Alkema
- BiologyBMC Immunology
- 14 March 2012
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.
The role of hydrophobic active-site residues in substrate specificity and acyl transfer activity of penicillin acylase.
- W. Alkema, A. Dijkhuis, E. de Vries, D. Janssen
- Biology, ChemistryEuropean Journal of Biochemistry
- 1 April 2002
The reduced specificity for the product and the high initial transferase/hydrolase ratio of betaF24A resulted in high yields in acyl transfer reactions and the role of hydrophobic residues in these reactions is studied.
MSCAN: identification of functional clusters of transcription factor binding sites
- W. Alkema, Ö. Johansson, J. Lagergren, W. Wasserman
- Biology, Computer ScienceNucleic Acids Res.
- 1 July 2004
MSCAN is a leading method for binding site cluster detection that determines the significance of observed sites while correcting for local compositional bias of sequences and is a web server that is intuitive to use.
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