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, member of the Faculty of Biology of the Johannes Gutenberg University in Mainz, adjunct director of the Institute of Molecular Biology in Mainz and an affiliate investigator at the Ottawa Hospital Research Institute.

Bio

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:

FASTA Herder Clusters a set of protein sequences according to their similarity. [About]
Alkemio Ranks chemicals according to a topic. [About]
CAFE Detects chromosomal abnormalities from DNA microarray expression data. [About]
NYCE Predict subcellular location of eukaryotic proteins based on their sequence. [About]
CellFinder Browse and compare images, gene and protein expression data from mammalian cells. [About]

 

ARD Updated as ARD2. Identification of alpha-rod repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. [About]
ARD2 Identification of alpha-solenoid repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. This is an update of ARD. [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.
Génie Rank the genes of an organism according to a topic. [About]
G2D Candidate genes to inherited diseases derived by data mining. [About]
HIPPIE Study and filter the network of human protein-protein interaction data. [About]
K2D2 See also K2D3. Predict protein secondary structure content from circular dichroism spectra. This is an update of k2d. [About]
K2D3 See also K2D2. Predict protein secondary structure content from circular dichroism spectra using theoretical spectra. [About]
Marker Server Detection of stem cell markers using gene expression data analysis. [About]
Medline Ranker Score abstracts from Medline according to a training set of abstracts or a MeSH term. [About]
MLTrends Graphs word and term usage trends in the Medline database of biomedical abstracts. [About]
NAIL Representation and linking of HMMer output. [About]
PDBpaint Colour protein structures with sequence annotations. [About]
peer2ref Find referees for a manuscript using some of its text (e.g. abstract). [About]
PESCADOR Extract and analyse a network of gene and protein interactions from a set of Medline abstracts. [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]
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]
uORFdb Query the literature on upstream open reading frame (uORF) biology. [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.

KAT 2003-2011 Keyword Annotation Tool: derive keywords from sets of references to the scientific literature.
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).
k2d 2000-2014 Updated as K2D2. Prediction of protein secondary structure percentages from circular dichroism data.
REP 2000-2014 Identification of protein repeats.

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