The Bioinformatics Analysis Team, or BAT, was formed in September 2008 and is a small and agile research team combining usefully diverse expertise around horizontal mechanisms of immunity, or disease resistance, or stress response, in humans and plants.
Our main interest is the detailed characterization of immunoglobulin (IG) and T cell receptor (TR) genes in leukemias and lymphomas, the identification of sequence features of pathogenetic and/or clinical significance, a better understanding of the diseases and, eventually, the implementation of risk-adapted, personalized treatment. We have extensively published on subsets of stereotyped B cell receptors, somatic hypermutation patterns, and repertoire biases mainly in chronic lymphocytic leukemia (CLL). We are currently in the process of making key bioinformatics approaches available through our Antigen Receptors Research Tool / ARResT platform.
The biggest proportion of eukaryotic genomes, especially of plants, is occupied by transposable elements (TEs). Our plant-side research investigates the impact of their life dynamics on host genome evolution and, by focusing on plants, tries to unravel underlying TE-related mechanisms responsible for the plasticity and adaptive capacity of plant genomes, critical knowledge in a changing global environment. The last few years our team has delved into the lifestyle and history of the ancient Sirevirus genus of the Copia LTR retrotransposon superfamily, with a cascade of publications on methods, databases, and insights under the MASiVE (Mapping and Analysis of SIreVirus Elements) umbrella, e.g. MASiVEdb.
The different sections of our 'cave' should give you a better idea of the why, what, how, and with whom. Enjoy your stay.
March 2013 | Sirevirus phylogeny in Mobile DNAOur editorial 'Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world' has been published in Mobile DNA.
October 2012 | Antigen Receptors Research Tool / ARResTOur platform for analysis of antigen receptors is going public with ARResT/SeqCure, our antigen receptor sequence curation tool.
August 2012 | MASiVEdb updateOur database on Sireviruses has been updated and now covers a total of 37 host species (23 new).
August 2012 | Joint publication with our AlbaAlba Navarro, who visited us from Barcelona and the lab of Prof. Dr. Elias Campo for a few months a couple of years ago, has just published on mantle cell lymphoma with a few team members as co-authors.
August 2012 | Series of publications in CLL and SMZLWe just added another publication from a series of multi-institutional studies of immunoglobulins in chronic lymphocytic leukemia (CLL) and splenic marginal zone lymphoma (SMZL) patients. PLease check the links in our publications. Well done to everyone that made these possible.
May 2012 | MASiVEdb on BMC GenomicsThe database on Sireviruses from fully-sequenced plant genomes is now published in BMC Genomics.
March 2012 | Sireviruses go live on MaizeGDBOur data on maize Sireviruses from MASiVEdb have been integrated in the genome browser of MaizeGDB.
December 2011 | Sireviruses go to PAGXXWe are looking forward to presenting our work on Sireviruses in the Transposable Element workshop of PAGXX.
December 2011 | Sireviruses soon to appear on MaizeGDBWe are very happy to be able to contribute our Sireviruses to MaizeGDB.
October 2011 | Sireviruses in the maize genome"The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story." is now published in The Plant Journal.
July 2011 | MASiVEdb: Sireviruses in plant genomesMASiVEdb is a collective resource of Sirevirus populations in plant genome sequences, aiming to support research into their evolutionary dynamics and impact across the Plant kingdom. As the name suggests, MASiVE is involved.
June 2011 | MASiVE onlineThe MASiVE algorithm is now improved and ready to study plant DNA sequences for the presence of Sirevirus elements. As always, bare with us while we iron out any problems.
June 2011 | PuReD-MCL finally onlinePuReD-MCL, a tool for PubMed document clustering published in Bioinformatics in 2008, is now available online, hopefully working ok but still under observation.
May 2011 | MeSHy to be publishedMeSHy, the fruit of our collaboration with two Departments of the Aristotle University of Thessaloniki, has been accepted in the Journal of Biomedical Informatics.
March 2011 | site upgraded and updatedWe have done a lot of work on the site, including on the structure, function, and content.
January 2011 | ENosAI: collaborating on blood diseasesThe ENosAI collaborative research project between our team, the Hematology Department and HCT Unit of the G. Papanicolaou Hospital, the Department of Haematology of University of Crete School of Medicine, and Bioanalytica has officially started, funded through the GSRT. A website is planned, through which you will be able to follow the project.
August 2010 | Circoletto: visualising sequence similarityCircoletto, a tool based on Circos and able to beautifully visualise sequence similarity has been accepted in Bioinformatics and is now accessible to all (through tools as well).
August 2010 | MASiVE: the spotlight on SirevirusesMASiVE (Mapping and Analysis of SireVirus Elements), an algorithm able to identify with high accuracy and sensitivity Sirevirus LTR retrotransposons, is now published in Bioinformatics.
June 2010 | case report on acute lymphoblastic leukemia"Coexistence of different types of biallelic immunoglobulin heavy variable gene replacement events in a case of pediatric B precursor acute lymphoblastic leukemia." - in Leuk Lymphoma.
May 2010 | antigen-driven clonal evolution in CLL"Intraclonal diversification of immunoglobulin light chains in a subset of chronic lymphocytic leukemia alludes to antigen-driven clonal evolution." - in Leukemia.
April 2010 | MeSHy: unexpected knowledge from textWe have submitted MeSHy, and we are making it available through our tools page.
February 2010 | computational genomics workshop at INAInfo, poster, registration form.
February 2010 | highly conserved motifs in Sirevirus elements
"Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?" - in BMC Genomics.