Philips Research, NV Organon, Radboud University Nijmegen
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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.
Benchmarking ortholog identification methods using functional genomics data
By combining the sensitivity and the selectivity into an overall score, it is shown that the InParanoid program is the best ortholog identification method in terms of identifying functionally equivalent proteins.
Identification of novel functional TBP‐binding sites and general factor repertoires
This study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TATA‐binding protein (TBP)‐binding sites in the human genome.
From Big Data to Precision Medicine
Both the opportunities and challenges posed to biomedical research by the increasing ability to tackle large datasets are discussed, including the need for standardization of data content, format, and clinical definitions.
Testing statistical significance scores of sequence comparison methods with structure similarity
- Tim Hulsen, J. de Vlieg, J. Leunissen, P. Groenen
- Computer Science, MedicineBMC Bioinformatics
- 12 October 2006
Two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith- waterman implementation with Z-score, and the compute intensive Z- score does not have a clear advantage over the e- value.
Evolution of closely linked gene pairs in vertebrate genomes.
- E. Franck, Tim Hulsen, M. Huynen, W. D. de Jong, N. Lubsen, O. Madsen
- BiologyMolecular biology and evolution
- 1 September 2008
It is shown here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception.
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
This work used a single linkage clustering algorithm to create 241 697 phylogenetic lineages, using all the orthologies provided by Ensembl v49, and described an updated version of PhyloPat which can be queried by an improved web server.
Heavier‐than‐air flying machines are impossible
Sharing Is Caring—Data Sharing Initiatives in Healthcare
- Tim Hulsen
- Medicine, Political ScienceInternational journal of environmental research…
- 27 April 2020
An analysis of the current literature around data sharing is shown, and five aspects of data sharing in the medical domain are discussed: publisher requirements, data ownership, growing support for data sharing, data sharing initiatives and how the use of federated data might be a solution.
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying and is presented, which allows the complete Ensembl gene database to be queried using phylogenetic patterns.