Home page for Miguel Andrade

I am the group leader of the Computational Biology and Data Mining group, 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 (some at the Ottawa Hospital Research Institute).

NEW:

dAPE Annotates homorepeats (polyX) in protein sequence alignments.
CABRA Clusters and annotates the results of a BLAST search. [About]
FastaHerder2 Clustering for analysis of protein similarity. [About]
OrthoFind Obtains the orthologs and paralogs of a protein sequence. [About]
mBISON Finds enrichment of miRNA targets on lists of genes. [About]
FASTA Herder Clusters a set of protein sequences according to their similarity. [About]

 

Alkemio Ranks chemicals according to a topic. [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. [Code]
Bluster Sequence similarity search against our collection of protein sequence clusters.
CAFE Detects chromosomal abnormalities from DNA microarray expression data. [About]
CellFinder Browse and compare images, gene and protein expression data from mammalian cells. [About]
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]
NYCE Predict subcellular location of eukaryotic proteins based on their sequence. [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]
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 for data derived at the Ottawa Hospital Research Institute.
uORFdb Query the literature on upstream open reading frame (uORF) biology. [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.

Transcriptome Sailor 2006-2016 Examine a genomic region in mouse or human for 3' transcript ends according to EST evidence. Last active URL http://cbdm.mdc-berlin.de/tools/ts/
Probe2GO 2005-2016 Obtain extended GO annotations for Affymetrix probe sets. Last active URL http://cbdm.mdc-berlin.de/tools/p2g/
XplorMed 2001-2015 Analysis of queries in MEDLINE. Last active URL http://xplormed.ogic.ca/
Disease_KW 2000-2014 Get keywords associated to human disease from OMIM entries or from MEDLINE abstracts. Last active URL http://www.embl.de/%7Eandrade/papers/disease_kw
KAT 2003-2011 Keyword Annotation Tool: derive keywords from sets of references to the scientific literature. Last active URL href="http://www.bork.embl.de/kat/
AbXtract 1998-2004 Automatic Abstract eXtraction of keywords associated to protein function. Last active URL http://columba.ebi.ac.uk:8765/andrade/abx
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). Last active URL http://www.sander.ebi.ac.uk/genequiz/
k2d 2000-2014 Updated as K2D2. Prediction of protein secondary structure percentages from circular dichroism data. Last active URL http://www.bork.embl.de/%7Eandrade/k2d/
REP 2000-2014 Identification of protein repeats. Last active URL http://www.bork.embl.de/%7Eandrade/papers/rep/search.html
NAIL 2000-2014 Representation and linking of HMMer output. Last active URL http://www.bork.embl-heidelberg.de/NAIL/

 

Teaching

 

Contact
Tel: +49-6131-39-21582
Fax: +49-6131-39-21589
email: Andrade@uni-mainz.de