Milda Stanislauskas from the Wu lab has successfully defended her PhD thesis, titled “Investigating Mechanical Signaling in Cells Through Live Cell Imaging of Genetically Encoded Tension Sensors.” Congratulations, Dr. Stanislauskas!
Author: Susan M Staurovsky
Dr. Sarabipour’s article cited on OSTP
June 28, 2024. Dr. Sarabipour’s article on the benefits of preprints for the academic enterprise has been cited on the White House Office of Science and Technology Policy (OSTP) report to the U.S. Congress on financial mechanisms for open access publishing of federally funded research. The report details developments in the open access publishing landscape including potential and anticipated impacts of a Memorandum to Executive Departments and Agencies titled, “Ensuring Free, Immediate, and Equitable Access to Federally Funded Research” on federal research investments, research integrity, and the peer review process.
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 Biology, 19(6), e1011232.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011232
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. Bioinformatics, 39(6), btad385.
https://academic.oup.com/bioinformatics/article/39/6/btad385/7199581