W. Alkema

Publications56
h-index23
Citations3,870
Highly Influential Citations275
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JASPAR: an open-access database for eukaryotic transcription factor binding profiles
TLDR
JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. Expand
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BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
BackgroundIn many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly… Expand
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CoPub: a literature-based keyword enrichment tool for microarray data analysis
TLDR
We developed a publicly available bioinformatics tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. Expand
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Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
TLDR
We present a novel method, MSCAN, that circumvents the training data problem by measuring the statistical significance of any non-overlapping combination of TFBS in a window. Expand
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Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling
BackgroundT lymphocytes are orchestrators of adaptive immunity. Naïve T cells may differentiate into Th1, Th2, Th17 or iTreg phenotypes, depending on environmental co-stimulatory signals. To identify… Expand
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Diversity in Robustness of Lactococcus lactis Strains during Heat Stress, Oxidative Stress, and Spray Drying Stress
ABSTRACT In this study we tested 39 Lactococcus lactis strains isolated from diverse habitats for their robustness under heat and oxidative stress, demonstrating high diversity in survival (up to 4… Expand
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Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
TLDR
The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. Expand
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The use of chromogenic reference substrates for the kinetic analysis of penicillin acylases.
Determination of kinetic parameters of penicillin acylases for phenylacetylated compounds is complicated due to the low K(m) values for these substrates, the lack of a spectroscopic signal, and the… Expand
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The role of hydrophobic active-site residues in substrate specificity and acyl transfer activity of penicillin acylase.
Penicillin acylase of Escherichia coli catalyses the hydrolysis and synthesis of beta-lactam antibiotics. To study the role of hydrophobic residues in these reactions, we have mutated three… Expand
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High-throughput screening of a large collection of non-conventional yeasts reveals their potential for aroma formation in food fermentation.
Saccharomyces yeast species are currently the most important yeasts involved in industrial-scale food fermentations. However, there are hundreds of other yeast species poorly studied that are highly… Expand
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