flap to Circoletto | ARResT/SeqCure | ARResT/AssignSubsets | MASiVE | LTRharvester | MeSHy | PuReD-MCL

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 - recently, this has involved work on high-throughput data within the ESLHO::EuroClonality-NGS consortium.

Enjoy Prof. Kostas Stamatopoulos providing a great overview of his/their/our work on CLL: YouTube.

The largest proportion of most plants is occupied by transposable elements (TEs). Our research investigates the impact of their life dynamics on host genome evolution and 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.

Here is Dr. Alexandros Bousios gesticulating his way through plenty of material and ideas: YouTube.

The different sections of our 'cave' should give you a better idea of the why, what, how, and with whom. Enjoy your stay.


news

Sireviruses and their epigenetic 'war' on Genome Research

Enjoy.


A couple of talks on YouTube

Found them recently, both given end of Spring 2015 at IMBB in Crete, Greece. Enjoy Prof. Kostas Stamatopoulos providing a great overview of his/their/our work on CLL: YouTube, and Dr. Alexandros Bousios gesticulating his way through plenty of material and ideas: YouTube.


EuroClonality-NGS and new bioinformatics partner

Our work within the EuroClonality-NGS consortium on Next-Generation Sequencing for IG / TR immunogenetic analysis [PDF] is going strong. We also now have a new bioinformatics partner, the Bonsai Bioinformatics group from Lille, FR.


Circoletto update

Circoletto has been updated with plenty of new and hopefully useful features. A big thank you to all Circoletto users, especially the ones that take the time to contact us with feedback and ideas.


5th IgCLL Educational Workshop on Immunoglobulin Sequence Analysis in Chronic Lymphocytic Leukemia

The two-day educational workshop was held in Brno, beautifully hosted by Prof Sarka Pospisilova and her group, scientifically organised by the IgCLL group, and attended by many new and old colleagues, including the key speaker Nicholas Chiorazzi, MD, from the Albert Einstein College of Medicine of Yeshiva University, NY, USA. More at igcll.org


Moving servers to Brno, CZ

We have finally moved (most of) our compute and data infrastructure to our cave in Brno, CZ, along with a clean-up and many improvements. There's still plenty of things to do, but it's been a major step ahead. And thanks to all of you who find our tools and databases useful and share your thoughts with us.


ARResT/AssignSubsets

Our platform for analysis of antigen receptors is expanding with ARResT/AssignSubsets, assigning new members to existing subsets of stereotyped antigen receptor sequences, currently applicable to the 19 major subsets of stereotyped B-cell receptors in chronic lymphocytic leukemia (CLL).


Sirevirus phylogeny in Mobile DNA

Our editorial 'Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world' has been published in Mobile DNA.


Antigen Receptors Research Tool / ARResT

Our platform for analysis of antigen receptors is going public with ARResT/SeqCure, our antigen receptor sequence curation tool.


MASiVEdb update

Our database on Sireviruses has been updated and now covers a total of 37 host species (23 new).


Joint publication with our Alba

Alba 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.


Series of publications in CLL and SMZL

We 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.


MASiVEdb on BMC Genomics

The database on Sireviruses from fully-sequenced plant genomes is now published in BMC Genomics.


Sireviruses go live on MaizeGDB

Our data on maize Sireviruses from MASiVEdb have been integrated in the genome browser of MaizeGDB.


Sireviruses go to PAGXX

We are looking forward to presenting our work on Sireviruses in the Transposable Element workshop of PAGXX.


Sireviruses soon to appear on MaizeGDB

We are very happy to be able to contribute our Sireviruses to MaizeGDB.


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.


MASiVEdb: Sireviruses in plant genomes

MASiVEdb 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.


MASiVE online

The 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.


PuReD-MCL finally online

PuReD-MCL, a tool for PubMed document clustering published in Bioinformatics in 2008, is now available online, hopefully working ok but still under observation.


MeSHy to be published

MeSHy, the fruit of our collaboration with two Departments of the Aristotle University of Thessaloniki, has been accepted in the Journal of Biomedical Informatics.


site upgraded and updated

We have done a lot of work on the site, including on the structure, function, and content.


ENosAI: collaborating on blood diseases

The 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.


Circoletto: visualising sequence similarity

Circoletto, 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).


MASiVE: the spotlight on Sireviruses

MASiVE (Mapping and Analysis of SireVirus Elements), an algorithm able to identify with high accuracy and sensitivity Sirevirus LTR retrotransposons, is now published in Bioinformatics.


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.


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.


MeSHy: unexpected knowledge from text

We have submitted MeSHy, and we are making it available through our tools page.


computational genomics workshop at INA

Info, poster, registration form.


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.




a different ontogenesis for CLL

"A different ontogenesis for chronic lymphocytic leukemia cases carrying stereotyped antigen receptors: molecular and computational evidence." - in Leukemia.


site goes live

This is April 2009...