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.
Development of Biocomputing resources
I collaborate in the development of Biocomputing algorithms and databases. Most of them are publicly available through web servers.
|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]|
|Visualization of amino acid biased regions in protein alignments.
|Sequence similarity search against our collection of protein sequence clusters.
|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]|
|Candidate genes to inherited diseases derived by data mining.|
|HIPPIE||Study and filter the network of human protein-protein interaction data. [About]|
|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]|
|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]|
|Representation and linking of HMMer output.|
|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]|
|Colour a phylogenetic tree according to taxonomy.
|Obtain extended GO annotations for Affymetrix probe sets.|
|QiSampler evaluates alternative scoring schemes of a list of items based on a very small set of positives. [About]|
|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]|
|Analysis of queries in MEDLINE.|
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.|
Max Delbrück Center for Molecular Medicine
13125 Berlin, Germany