Home page for Miguel Andrade
I am the group leader of the Computational Biology and Data Mining group at the Max Delbrück Center for Molecular Medicine, and an affiliate investigator at the Ottawa Hospital Research Institute.
Contact information
| address: | Computational Biology and Data Mining group Max Delbrück Center for Molecular Medicine Robert-Rössle-Str. 10, 13125 Berlin, Germany |
| tel: | +49-30-9406-4250 |
| fax: | +49-30-9406-4240 |
| email: | Miguel.Andrade@mdc-berlin.de |
Publications
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Development of Biocomputing resources
I collaborate in the development of Biocomputing algorithms and databases. Most of them are publicly available through web servers.
NEW:
| ARD | Identification of alpha-rod repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. [About] |
| MLTrends | Graphs word and term usage trends in the Medline database of biomedical abstracts. [About] |
| Visualization of amino acid biased regions in protein alignments. |
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| Bluster | Sequence similarity search against our collection of protein sequence clusters. |
| Disease_KW | Get keywords associated to human disease from OMIM entries or from MEDLINE abstracts. |
| G2D | Candidate genes to inherited diseases derived by data mining. [About] |
| KAT | Keyword Annotation Tool: derive keywords from sets of references to the scientific literature. [About] |
| k2d | Prediction of protein secondary structure percentages from circular dichroism data. The program is also available. [About] |
| K2D2 | Predict protein secondary structure content from circular dichroism spectra. This is an update of k2d. |
| Marker Server | Detection of stem cell markers using gene expression data analysis. |
| Medline Ranker | Score abstracts from Medline according to a training set of abstracts or a MeSH term. [About] |
| NAIL | Representation and linking of HMMer output. [About] |
| PhyloView | Colour a phylogenetic tree according to taxonomy. [About] |
| Probe2GO |
Obtain extended GO annotations for Affymetrix probe sets. [About] |
| REP | Identification of protein repeats. [About] [Supplementary information] |
| StemBase | A database of stem cell gene expression data derived in our institute. [About] |
| Transcriptome Sailor | Examine a genomic region in mouse or human for 3' transcript ends according to EST evidence [About] |
| XplorMed | Analysis of queries in MEDLINE. [About] |
Some of these servers are dying (nothing is eternal!). If you are concerned about this please contact me. May be something can be done.
| AbXtract | 1998-2004 | Automatic Abstract eXtraction of keywords associated to protein function |
| GeneQuiz | 1998-2007 | Automatic large scale sequence analysis using a variety of DNA/protein databases and protein analysis methods. Analyses were performend during 1996-2003. Contact Christos Ouzounis for availability. The method was available at the EBI (1998-2004) and then at the Memorial Sloan-Kettering Cancer Center (2005-2007). |
Teaching
- Main page of the MDC/EMBL course on Computational Sequence Analysis and Supplementary material for Secondary structure prediction and threading.
- Supplementary material for Secondary structure prediction and threading. In Master in Molecular Medicine. Module VI: Functional Genomics, coordinator Hanspeter Herzel. April 2010. [Previous year: June 2009]
Contact
Max Delbrück Center for Molecular Medicine
Robert-Rössle-Str. 10
13125 Berlin, Germany
Tel: +49-30-9406-4250
Fax: +49-30-9406-4240
email: Miguel.Andrade@mdc-berlin.de
