The project, Computational methods to predict gene regulatory network dynamics and cell state transitions is funded by the NIGMS at the NIH. We will investigate fundamental processes underlying cell state transitions using theoretical modeling, statistical inference, and machine learning.
Our paper Modeling the competing effects of the immune system and EMT on tumor development is out now in Communications Biology. This large collaborative effort included multiscale evolutionary modeling led by Daniel Bergman and Bayesian data analysis led by Matt Karikomi. The paper was featured on the mathematical oncology blog with a write-up from Daniel.
Congratulations to Nikith, who received a Trudi Berwin Student Support Fellowship from the USC Bridge Institute to complete a BUGS summer research project in the lab. Nikith’s work on novel regulators of the Wnt signaling pathway paves the way for future research in the lab. Well done, Nikith!
Welcome to Ivy and Jesse who join the lab as postdoctoral researchers.
Ivy recently completed her PhD at the University of Oxford, studying the interplay between inherited and somatic genetic variants in cancer.
Jesse recently completed his PhD at the University of California, Irvine, modeling viral dynamics using various approaches including hybrid stochastic-deterministic methods.
Our editorial The diverse landscape of modeling in single-cell biology is out now in Physical Biology. This accompanies a special issue guest edited by Adam and Qing Nie, full of exciting recent advances in theoretical and biophysical modeling for single-cell biology.
This week at SMB 2021, Adam presented recent work led by Xiaojun on single-cell similarity-based parameter inference tools.
We (Adam and co-host Russell Rockne) also organized a mini-symposium on Dynamics and networks in single-cell biology. Thanks to all of the speakers in this two-part session for making it such a success!
Congratulations to all of the QBIO graduates of 2021. A uniquely challenging year, and you did it! Gina Yang and Jaclyn Ready both completed impressive undergraduate research projects this year in our lab. To you and to your classmates, congratulations!!
Our paper, led by Raktim, is out now in Bioinformatics.
Adam has written a perspective on the story behind our recent preprint and the connections to cancer. Thanks to the mathematical oncology blog for the invitation!
Megan Franke developed a multiscale hybrid model of cell-cell communication (with a deterministic cell-internal gene regulatory network and stochastic single-cell resolved signaling model). Through analysis of a large range of cell signaling topologies, we discovered that even subtle cell-cell communication can dramatically alter cell fate decision-making and result in heterogeneous distributions of hematopoietic cell types.
Our analysis also helps to resolve some controversies in the literature regarding myeloid cell fates controlled by the GATA1-PU.1 mutual inhibition loop. The preprint is available here.