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At the CG2 we are currently looking for a young and motivated post-doc. Ideal candidates should hold a PhD in Bioinformatics or Computational Biology and combine a strong background in molecular biology and genetics with solid knowledge of statistics and (optimally) experience in scripting languages such as Python or Perl. The successful candidate will work on computational approaches of studying eukaryote genome architecture in one and three dimensions in close collaboration with experimental groups at the IMBB, FORTH in Heraklion, Crete. The expected starting date is January 2018 with an initial duration of one year.
Applicants are encouraged to contact us via email (cnikolaou [at] biology [dot] uoc [dot] gr). Our group was represented at the 12th annual meeting of the Hellenic Society of Computational Biology and Bioinformatics with two posters and a talk. One of our posters (by M. Malliarou et al) received an honourable mention. My talk was based on the two most recent papers of the group (see here and here) and was centered around patterns of yeast genome organization. You can see a video of the talk (starting around 03:58) in this link, while the rest of the talks are also available here.
Our lab's latest work is out in Current Genetics. The article, which comes as a continuation of our previous work, recently published in NAR (Tsochatzidou et al., 2017), describes a segmentation of the yeast genome in discrete territories with particular structural properties in terms of nucleosome positioning. Given our lab's love for Italo Calvino's "Invisible Cities" (all computers in CG2 are named after Calvino's cities) we are proud to have "squeezed" the book into the paper's title. You can read more on the "Invisible Cities. Segregated domains in the genome of S. cerevisiae with distinct structural and functional attributes" here.
We will be blogging more on this work (and hopefully others related to it) soon. Our lab's long-standing collaboration with the group of George Kollias at the Biomedical Sciences Research Center "Alexander Fleming" is bearing fresh fruit in our latest publication that came out last week at Arthritis and Rheumatology.
The paper titled "Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis" is the result of a couple of years of efforts with colleagues and friends Evangelos Ntougkos and Panagiotis Chouvardas to analyze the arthritogenic potential of synovial fibroblasts in a transgenic mouse model of Rheumatoid Arthritis. It is a work that took a long (perhaps too long) time to come out and which is (in my view) not over yet as a number of questions remain to be answered from the copious amounts of data we have gathered. For those of you who are too bored or too busy to go through the paper beforehand you can take a look at its editorial commentary, in which Ulf Muller-Lander and Elena Neumann give a concise but short summary of our findings and close with a rather intriguing comment on our bioinformatics work saying that: "Taken together, the paper shows nicely that the large scale puzzle RA cannot be solved by pouring millions of highly variable fragments into a high-end bioinformatics computer but only piece by piece by innovative scientists with careful evaluation of hypothesis-driven data sets." I will be covering this last comment and a number of questions that are cracked open by our work in an upcoming post on our CG2 blog. (For the time being I am off to grade some grad papers) Our lab's latest publication is a collaboration with the group of Niki Kretsovali at the IMBB, FORTH. Appearing in Stem Cell Reports, this work by lead author and friend Christiana Hadjimichael shows that Promyelocytic Leukemia Protein (PML) is a key factor in the maintenance of pluripotency in mouse ES cells, exhibiting its control on a number of pathways including that of TGF-β at an early stage. Antonis Klonizakis, an undergraduate student from our group, was involved in the analysis of public gene expression datasets to show that PML knockdown cells resemble a state of primed differentiation, lying intermediate between ES and epiblast cells. Besides the main finding behind it, this work was, from our part, a manifestation of the inherent difficulties in assessing published results in view of their heterogeneity, the lack of sufficient reporting and standardization, all of which are issues that need to be addressed yesterday in want of a more efficient way of accumulating knowledge instead of simply piling up information. Stay tuned for a blog post on this (and other matters).
At the CG2 we are currently looking for young students aiming for a PhD in Bioinformatics and Computational Genomics. Ideal candidates will combine a strong background in molecular biology and genetics and solid knowledge of statistics and (optimally) experience in scripting languages such as Python or Perl. We expect to have more than one openings in the first months of 2017 for people to work on topics related to the analysis of NGS data for the modeling of gene regulation and epigenetics in various contexts related to human disease and senescence. Applicants are encouraged to contact us via email (cnikolaou [at] biology [dot] uoc [dot] gr) or through our facebook page (inbox at: https://www.facebook.com/cg2uoc/).
Our group's latest paper is a bit out of the ordinary.
In a collaboration with the labs of George Kollias at BSRC "Fleming" and Georgios Theodoridis at the AUTH we have just published an analysis of the metabolic profile of an animal model of Rheumatoid Arthritis. Our paper, titled: "Targeted metabolic profiling of the Tg197 mouse model reveals itaconic acid as a marker of Rheumatoid Arthritis", published in the Journal of Proteome Research, has revealed the importance of new, only recently reported metabolite called itaconic acid. Our group was involved in both the overall analysis of metabolite profiles, their linking with gene expression profiles, while we also had the chance to remember our past in Biochemistry in establishing the link between itaconic acid production and the disruption of the TCA cycle. CG2 has a new paper out.
In collaboration with the group of Yannis Almirantis at NCSR "Demokritos" we return to the concept of Chargaff's 2nd parity rule of nucleotide composition and deviations thereof. In a novel and rather exhaustive analysis conducted by Konstantinos Apostolou-Karampelis as part of his PhD Thesis, we were able to show how a straight-forward analysis of nucleotide composition can reveal very significant aspects of genome evolution and the mutational mechanisms underlying it. Konstantinos started by analyzing more than 300 bacterial genomes, comparing the preference of specific dinucleotides occurring with different frequencies between the two DNA strands. Through a simple measure of this asymmetry, he showed that differences in these preferences can trace the phylogeny of bacteria in a way comparable to standard genome alignment methods. He then went on to show how these differences may be attributed to the different mutational biases towards different GC contents in bacteria. More importantly he showed that these bias are coupled to the structure of the genetic code and that the combination of a particular GC bias can lead to striking sequence composition through the constraints imposed by the genetic code. Last but not least, this work is the first to provide a mechanistic link between the observed genome composition patterns and molecular processes. By linking the pattern of each species to its employment of different DNA polymerase II-a subunit, we were able to associate specific pattern groups with different enzyme isoforms existing in diverse phyla. This is thus the first time the enzymatic activity of DNA polymerases is directly linked to the genome sequence in bacteria. For those brave enough to go into the details of the model and the analysis you can find the full paper here: http://dnaresearch.oxfordjournals.org/content/early/2016/06/22/dnares.dsw021.full We are very pleased to finally see our work on inferring gene regulatory networks in print. The work is based on Panagiotis Chouvardas' MSc thesis and is based on a new method aiming to define the most relevant regulatory network from a genome-wide expression profile. The paper was finally out (after a looooooong publication process) last Monday June 6th, hence we chose to call it the D-day paper :)
Currently working on human and mouse, our method, called RNEA has already been applied with success on collaborative works such as this one and this other one. You may find the full paper here. More info may be found in our Publications page. |
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