First PhD to defend from the VOLUMINEX team
On the 2nd October, doctoral student and VOLUMINEX team member David Fernàndez Bonet will defend his thesis on spatial reconstruction of DNA barcode networks. David has been conducting his PhD at KTH and SciLifeLab where he has been supervised by Dr. Ian Hoffecker and Professor Afshin Adhmadian.
David’s thesis is about sequence-based microscopy, where DNA barcodes in a tissue sample interact with their neighbours, which after sequencing, creates a network that can be computationally reconstructed into an image of the sample without any optical imaging. Traditional imaging of the tissue sample is not needed, as a reconstruction algorithm recovers coordinates from the network of interactions between the DNA barcodes, providing the spatial information of the sample. The thesis contributes to four main achievements: (i) a reconstruction algorithm that is accurate, scaleable and robust, (ii) a computational way to validate the interaction network, (iii) applying the computation tools to real data, and (iv) a broader idea of what is “reconstructable”.
VOLUMINEX benefits from these tools and frameworks as they provide scaleable and robust reconstructions, a way to validate networks, and a theoretical result nudging the experimental design to have more “promiscuous” interactions.
David’s opponent for the defence will be Professor Nikolaus Rajewsky from the Max Delbrück Center for Molecular Medicine in Berlin. The thesis defence is public and can be joined either at person at SciLifeLab or online via zoom. For the video link, thesis abstract and further information visit this link to KTH’s website .