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, and an affiliate investigator at the Ottawa Hospital Research Institute.
Publications
- ordered by subject
- ordered by year
- public professional profiles: [Google Scholar][ResearchGate][LinkedIn][ORCID][ScopusID][ResearcherID]
Development of Biocomputing resources
I collaborate in the development of Biocomputing algorithms and databases. Most of them are publicly available through web servers.
NEW:
| pSTR | identify duplications of protein short tandem repeats (pSTRs) in protein families. |
| polyXY | Search for regions of two amino acid types (polyXY) in datasets of protein sequences. |
| iOrME | Sequence clusters of insect odorant receptors. |
| seqQscorer | Automated quality control of NGS data using machine learning. |
| PolyX2 | Search for homorepeats in datasets of protein sequences. |
| AnABlast | Detect potential coding regions in DNA by sequence comparison. |
| 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. |
| CABRA | Clusters and annotates the results of a BLAST search. [About] |
| CAFE | Detects chromosomal abnormalities from DNA microarray expression data. [About] |
| CellFinder | Browse and compare images, gene and protein expression data from mammalian cells. [About] |
| DiseaseLinc | Associate lincRNAs with diseases. |
| dAPE | Annotates homorepeats (polyX) in protein sequence alignments. |
| FASTA Herder | Clusters a set of protein sequences according to their similarity. [About] |
| FastaHerder2 | Clustering for analysis of protein similarity. [About] |
| GAPI | Explores a hyperbolic mapping of the human potein interaction network. |
| Génie | Rank the genes of an organism according to a topic. [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] |
| LCT | Represent the distribution of repeatability versus compositional bias in a protein sequence. |
| LipiDisease | Associate lipids with diseases. |
| MAGA | Analyse amino acid conservation in user defined groups of proteins from a multiple sequence alignment. |
| mBISON | Finds enrichment of miRNA targets on lists of genes. [About] |
| Medline Ranker | Score abstracts from Medline according to a training set of abstracts or a MeSH term. [About] |
| MGFR | Detect markers segregating sample types in RNA-seq data. |
| MIPPIE | Study and filter the network of mouse protein-protein interaction data. |
| NYCE | Predict subcellular location of eukaryotic proteins based on their sequence. [About] |
| OrthoFind | Obtains the orthologs and paralogs of a protein sequence. [About] |
| PESCADOR | Extract and analyse a network of gene and protein interactions from a set of Medline abstracts. [About] |
| PlaToLoCo | Analyse low complexity regions in protein sequences. |
| ProteinPathTracker | Find selected orthologs to study the evolutionary path of a protein. |
| QiSampler | QiSampler evaluates alternative scoring schemes of a list of items based on a very small set of positives. |
| REP2 | Identification of protein repeats. |
| RES | Scan a protein sequence for its repeatability. |
| sQanner | Evaluate the distribution of polyQ stretches in a set of proteins. |
| Traitpedia | A collaborative database of species traits. |
| uORFdb | Query the literature on upstream open reading frame (uORF) biology. [About] |
Some of these tools are dying (nothing is eternal!). If you are concerned about this please contact me. May be something can be done.
| GS2D | 2016-2024 | Gene Set to Diseases identifies disease terms enriched in the bibliography of a set of genes. Last active URL http://cbdm-01.zdv.uni-mainz.de/~jfontain/ |
| StemBase | 2003-2008 | A database of stem cell gene expression for data derived at the Ottawa Hospital Research Institute. Last active URL http://www.stembase.ca/ |
| Alkemio | 2014-2022 | To rank chemical substances according to their relation to a biomedical topic. Last active URL http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/?page_id=319 |
| PhyloView | 2012-2014 | Colour a phylogenetic tree according to taxonomy. Last active URL http://www.ogic.ca/projects/phyloview/ |
| peer2ref | 2012-2014 | Find referees for a manuscript using some of its text (e.g. abstract). Last active URL http://peer2ref.ogic.ca/ |
| Marker Server | 2006-2014 | Detection of stem cell markers using gene expression data analysis. Last active URL https://cbdm.mdc-berlin.de/~markerserver/ |
| PDBpaint | 2010-2014 | Colour protein structures with sequence annotations. Last active URL http://cbdm.mdc-berlin.de/~pdbpaint |
| G2D | 2002-2014 | Candidate genes to inherited diseases derived by data mining. Last active URL http://www.ogic.ca/projects/g2d_2/ |
| ARD | 2008-2013 | Updated as ARD2. Identification of alpha-rod repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. |
| MLTrends | 2009-2018 | Graphs word and term usage trends in the Medline database of biomedical abstracts. Last active URL http://mltrends.ogic.ca/ |
| 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 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/ |
| NAIL | 2000-2014 | Representation and linking of HMMer output. Last active URL http://www.bork.embl-heidelberg.de/NAIL/ |
Contact
Tel: +49-6131-39-21582
Fax: +49-6131-39-21589
email: Andrade@uni-mainz.de