Last week Salar presented his research on Giersch International Conference: From Multiscale Models to Digital Twins taking place in FIAS (Frankfurt Institute for Advanced Studies). The talk covered recent results from Salar’s PhD project on pattern formation under different active and passive forces acting on the tissue formation. The meeting was also great opportunity for networking with theorists, computational experts and data scientists. We look forward for next mtgs in FIAS!

Our group actively participated in this years Marian Smoluchowski Symposium, https://smoluchowski.if.uj.edu.pl/. I have presented recent results on tissue fluidization in developing spinal cord. The talk was followed by poster session including Salar’s work on pattern formation in tissues with passive and active forces, and Helder’s new developments on formation of Turing patterns in the presence of multiple diffusing species. The conference was great opportunity to discuss projects ranging from pure statistical physics to applications in biological systems. We look forward to next editions!

Ajay Subbaroyan from Areejit Samal’s group at IMSc in Chennai visited our group to give seminar on design principles in Boolean models of gene regulatory networks. Ajay focused on identifying properties of different logical functions that determine final state of the network. In his seminar in the Enigmas of Chance series he combined lot of biological case studies to validate against computational results.

In mid May we attended conference Physics of Cell Fate Decision (PCFD2024) at ISTA, https://pcfd2024.pages.ista.ac.at/. Salar presented poster about pattern formation in tissues with heterogenous motility and rigidity, and Helder had a poster on new classes of multimodal Turing patterns. I gave a talk on dynamics of source formation in growing tissues. The event was great opportunity for networking. We hope to get back there in the next editions!

I had a pleasure to give a series of invited talks about pattern formation and processing of biological information during development at the Workshop on Flags, Landscapes, Signaling: From gene regulatory dynamics to tissue patterning & morphogenesis, IMSc Chennai India, May 6-17, https://www.imsc.res.in/~sitabhra/meetings/wfls24/. The series included introduction, research and chalk-talk. The workshop was aimed for PhD students with physics and biology background. Lectures were followed up by informal discussions with many insightful comments.

On Monday Matt gave an invited talk on integrative modeling of glycoproteins on our weekly seminar of Enigmas of Chance. Matt is the head of newly established Dioscuri Centre for Modelling of Posttranslational Modifications, https://mcb.uj.edu.pl/en_GB/sikora-lab, at Małopolska Centre of Biotechnology of Jagiellonian University. The talked was followed by insightful discussion on applications of modeling to biological data.

We have opening for scholarship for one PhD student. The project goal is to understand to what extent growth, cellular dynamics, biomechanical feedbacks and global mechanical constraints limit patterning precision in the growing tissue. Details can be found at: https://zagorskigroup.com/open-positions/. If you are interested please contact me in advance. We wait for your applications till 1 October, but you already need to go through PhD recruitment at Doctoral School that takes place in June!

On Tue I had pleasure to give talk about formation of gene expression patterns in developing spinal cord at ALGORITMY 2024 conference in Slovakia (https://www.math.sk/alg2024/). The talk was part of minisymposium on Computational methods and algorithms for biomedical applications organized by Elfriede Friedmann (University of Kassel) and Jurjen Duintjer Tebbens (Charles University). It was great opportunity for networking!

Our latest work on the formation of Shh morphogen source (floor plate) in the growing spinal cord is now available at: https://www.biorxiv.org/content/10.1101/2024.03.01.582751v1. By supporting computational results with experiments @Kicheva Lab we showed that the floor plate is formed in two distinct phases: rapid formation through gene regulatory interactions, followed by passive expansion by tissue growth. This result might be of general relevance for pattern formation in growing organs.

Last week our commentary on assessing the precision of patterning in spinal cord appeared in Nature Communications. The text is open access: https://www.nature.com/articles/s41467-024-45148-8