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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.

 

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]

BiasViz

 Visualization of amino acid biased regions in protein alignments.
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

Personal page

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