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.
Publications
Development of Biocomputing resources
I collaborate in the development of Biocomputing algorithms and databases. Most of them are publicly available through web servers.
NEW:
| HIPPIE | Study and filter the network of human protein-protein interaction data. [About] |
| PESCADOR | Extract and analyse a network of gene and protein interactions from a set of Medline abstracts. [About] |
| K2D3 | Predict protein secondary structure content from circular dichroism spectra using theoretical spectra. [About] |
| PDBpaint | Colour protein structures with sequence annotations. [About] |
| QiSampler | Evaluate alternative scoring schemes of a list of items based on a very small set of positives. [About] |
| Génie | Rank the genes of an organism according to a topic. [About] |
| MLTrends | Graphs word and term usage trends in the Medline database of biomedical abstracts. [About] |
| ARD | Identification of alpha-rod repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. [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. [About] |
| 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] |
| QiSampler | QiSampler evaluates alternative scoring schemes of a list of items based on a very small set of positives. [About] |
| REP | Identification of protein repeats. [About] [Supplementary information] |
| StemBase | A database of stem cell gene expression data derived in our institute. |
| 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
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