06-28-2023. The  24th Annual Computational Cell Biology (CCB) workshop took place at the Center for Cell Analysis and Modeling (CCAM) on June 26-28th. 11 participants from all over the US (from Maryland to Illinois) came to Farmington to work on developing their modeling projects using VCell and COPASI software tools, designed and maintained at CCAM. The students were helped by a CCAM team consisting of Michael Blinov, Ann Cowan, Leslie Loew, Pedro Mendes, Ion Moraru, Kelvin Peterson, Jim Schaff, Nathan Schaumburger, and Boris Slepchenko.

26 June 2023. Congratulations to Dr. Kshitiz and Dr. Afzal from UCSF that published Research Highlights in Nature on “CRISPRing the hypertrophic cardiomyopathy: correcting one pathogenic variant at a time”, https://www.nature.com/articles/s41392-023-01526-0

06-16-2023. Dr. Eran Agmon has published a pioneering paper that explores antibiotic resistance in E. coli by implementing a multiscale whole-cell model. Developed with Dr. Agmon‘s model integration software, Vivarium, the study encompasses single-cell dynamics and population-level heterogeneity to provide a mechanistic understanding of antibiotic resistance, furthering the fight against the rise of multidrug-resistant bacterial strains.

Skalnik, C. J., Cheah, S. Y., Yang, M. Y., Wolff, M. B., Spangler, R. K., … Agmon, E., & Covert, M. W. (2023). Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLOS Computational Biology, 19(6), e1011232.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011232

06-01-2023. Drs. Michael Blinov and Leslie Loew together with a former student Aniruddha Chattaraj (currently a PostDoc at Harvard) published a paper introducing a novel software, MolClustPy, to characterize and visualize the distribution of cluster sizes, molecular composition, and bonds across biomolecular clusters.

Chattaraj, A., Nalagandla, I., Loew, L. M., & Blinov, M. L. (2023). MolClustPy: a Python package to characterize multivalent biomolecular clusters. Bioinformatics, 39(6), btad385.

https://academic.oup.com/bioinformatics/article/39/6/btad385/7199581

Dr. Vera-Licona will be giving an invited talk on Model Checking during the thematic workshop on networks and biological model inference in the context of the CNRS Bioss working group on symbolic systems biology (https://www.bioss-cnrs.fr). The aim is to gather people working on this topic to present recent results and discuss challenges and perspectives. The workshop will take place on July 3-4 2023 at CIRM in Marseille, France