Affiliation: Center for Biological Sequence Analysis
- Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing readsLaurent Gautier
Center for Biological Sequence Analysis CBS, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark DTU Multiassay Core DMAC, Technical University of Denmark, Lyngby, Denmark
PLoS ONE 8:e83784. 2013..A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc...
- Bioconductor: open software development for computational biology and bioinformaticsRobert C Gentleman
Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
Genome Biol 5:R80. 2004..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
- affy--analysis of Affymetrix GeneChip data at the probe levelLaurent Gautier
Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
Bioinformatics 20:307-15. 2004..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
- Alternative mapping of probes to genes for Affymetrix chipsLaurent Gautier
Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
BMC Bioinformatics 5:111. 2004..However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available...
- An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translatorsLaurent Gautier
DMAC, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Matematiktorvet, 2100 Lyngby, Denmark
BMC Bioinformatics 11:S11. 2010..At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets...
- Implementation of a gene expression index calculation method based on the PDNN modelHenrik Bjørn Nielsen
Center for Biological Sequence Analysis, BioCentrum DTU Technical University of Denmark Building 208, DK 2800 Lyngby, Denmark
Bioinformatics 21:687-8. 2005..2003). Here we describe an open source implementation of the PDNN method for the statistical language R...
- The effect of network biology on drug toxicologyLaurent Gautier
Technical University of Denmark, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
Expert Opin Drug Metab Toxicol 9:1409-18. 2013..With this approach, the assessment of chemical safety can be done across multiple scales of complexity from molecular to cellular and system levels in human health. Network biology can be used at several levels of complexity...
- A new non-linear normalization method for reducing variability in DNA microarray experimentsChristopher Workman
Genedata AG, Basel, Switzerland
Genome Biol 3:research0048. 2002..Current normalization techniques are most often linear and therefore not capable of fully correcting for these effects...