CellBio

Cell adaptation

How do cells get their fitnesses?

How do the behaviors of cells and populations arise from their underlying molecules, biochemical pathways, and cycles? How are homeostatic and evolutionary adaptations encoded?

We focus on principles of evolution crossing scales from molecular, to 4D genome, to intermediate between the small (molecules) and the large (cells); on establishing principled mechanisms of fitness; on how gene expressions as well as epigenetics are regulated; and on how biological systems live with noise and variation -- either to their advantage, or by mitigating it; or changing under it, as cancer cells do in the face of hundreds of mutations, or host cells do when infected -- how decisions are made about action, fueled by energy; how cells and cell populations determine their sizes and growth rates; and how cells age, causing changes in metabolism, hormone (e.g. insulin) production, immunity, and sleep.

First insights into 4D genome

Our chromosomes are the same in all our cells, but they encode different levels of proteins depending on the type of the cell. What is the physical basis of cell-specific differential gene expression patterns?

Data from Hi-C experiments, analyzed by the Bahar lab, using elastic network models showed that the 3D topology of gene-gene contacts uniquely defines their chromosomal dynamics. Gene loci subject to large fluctuations in their spatial positions tend to express higher levels of genes.

For details see: Banerjee, Zhang,  and Bahar (2024) Genome structural dynamics: insights from Gaussian network analysis of Hi-C data . Briefings in Funct Genomics, elae014; Zhang, Chen and  Bahar (2020) Differences in the Intrinsic Spatial Dynamics of the Chromatin Contribute to Cell Differentiation Nucleic Acids Res 48, 1131-1145. 

What is the role of protein folding in the biophysical origins of life?

Some Darwinian-evolution-like process must have preceded the origin of life (C. Kocher and K. Dill, PNAS 2022). We explore the roles of cooperativity in physical dynamics and of protein collapse and folding as the origins of the first bio-like functions.

Dr. Dima Kozakov and the Kozakov Group have been modeling the molecular interactions in the cell

Differential PPI network in Breast Cancer

Havugimana, P.C., Goel, R.K., Phanse, S. et al. Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. Nat Commun 13, 4043 (2022). https://doi.org/10.1038/s41467-022-31809-z