Author: Susan M Staurovsky

Ji Yu Publishes Article on Deep Learning

09-07-2023. Congratulations to the Yu lab on a new publication, Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing. The article describes a new deep learning algorithm for training convolutional neural nets (CNN) to perform the single-cell segmentation task using point-label or no human label. (Yu J. Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing. IEEE Trans Med Imaging. 2023 Sep 7;PP. doi: 10.1109/TMI.2023.3312988. Epub ahead of print. PMID: 37676808.)

Dr. Agmon’s pioneering paper on antibiotic resistance in E. coli

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 Biology19(6), e1011232.

Blinov & Loew publish new methods to analyze molecular clusters

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. Bioinformatics39(6), btad385.

Dr. Vera-Licona giving an invited talk on Model Checking in Marseille, France

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 ( 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

Dr. Agmon’s paper highlights dynamic 3D models (virtual cells)

04-11-2023. Dr. Eran Agmon, along with a diverse team of cell modelers from prestigious institutions including the Allen Institute for Cell Science, University of Washington, Stanford University, and University of Richmond, have collaboratively published a paper that advocates for the development of next-generation virtual cells. The paper highlights the potential of these dynamic 3D models in consolidating vast cellular information, facilitating a more comprehensive understanding of cellular behaviors, and fostering collaborative breakthroughs in cell science research.

 Johnson, G. T., Agmon, E., Akamatsu, M., Lundberg, E., Lyons, B., Ouyang, W., … & Horwitz, R. (2023). Building the next generation of virtual cells to understand cellular biology. Biophysical Journal.