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First author paper by ESR Lorenzo Signorini hosted at the Tel Aviv University in the Sharan group

Lorenzo Signorini has created an updated version of the ANAT Cytoscape plugin. ANAT3.0 is designed as a flexible graphical tool for scientists to explore and elucidate the protein–protein interaction pathways of a studied process in yeast and human.

Compared to previous versions, ANAT3.0 includes improved network reconstruction algorithms and more comprehensive protein–protein interaction networks. ANAT is available for download on the Cytoscape Appstore and at https://www.cs.tau.ac.il/~bnet/ANAT/.

Full open access text

First publication with SECRET ESR as first author published in BMC Bioinformatics in October 2021

SECRET-ITN ESRs seconding over the summer at partner organisations

So far, ESRs have seconded within the beneficiary network. The first two secondments at partner organisations have now also successfully been completed. ESR11, Juan Manuel García Illarramendi, hosted by Anaxomics in Barcelona, has performed his 3 month secondment at the Universitat Autònoma de Barcelona (UAB), in the group of Prof. Xavier Daura. Mario Macìa Guardado, ESR12, from the Medical University of Vienna, has spent 2 successful secondment months in the lab of Prof. Olivier de Wever at the University of Ghent.

Left: Photo of Ghent taken by Mario during his secondment.


SECRET-ITN seminar – June session (15.06.2021)

The SECRET-ITN seminar session in June brought two captivating talks from Roded Sharan from the School of Computer Science at the Tel Aviv University in Israel, and from Hesso Farhan, from the Institute of Pathophysiology at the Medical University of Innsbruck in Austria.

Prof. Dr. Roded Sharan gave insights into Using networks to decipher human disease. Research in the Sharan group focuses on modeling biological data using networks and applying graph algorithmic and machine learning techniques to mine these data and extract patterns of biological significance. Example projects include: (i) Inferring subnetworks that underlie a biological process of interest by integrating protein network data with gene expression or phenotypic information. (ii) Modelling mutational processes in cancer using machine learning techniques. (iii) Construction and analysis of Boolean network models using machine learning and integer programming techniques. (iv) Predicting drug properties and their applications in the clinical practice.

The talk of Prof. Dr. Hesso Farhan, titledRegulation of ER-export by mechanical signalling, focused on the regulation of proteostasis and membrane trafficking by signalling. Safeguarding the cellular proteome is of fundamental importance and thus nearly 70% of cellular energy is devoted to handle the proteome. The balance between protein synthesis, folding, trafficking and degradation is referred to as proteostasis. The Farhan group focuses on how proteostasis is regulated by signalling to and from endomembranes. Of particular interest is the regulation of membrane traffic, organelle dynamics and autophagy. A set of methods, such as live cell confocal microscopy, SRRF stream imaging, FRAP and high-content RNAi screening, are employed to study these processes. Knowledge gained from fundamental cell biology is further used to better understand human diseases or to develop new therapies. Two main areas of interest of the Farhan lab are the role of secretion in breast cancer migration and invasion as well as the role of proteostasis in multiple myeloma.

SECRET-ITN Seminar Series – June 2021

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