DrOmer Karin

Overview
Biological systems (like our cells and tissues) are complex and made of many interacting components. Our goal is to understand how these systems achieve their remarkable functionality.

Our approach is based on developing predictive models to understand how biological mechanisms work, and developing mathematical and computational theories to understand the adaptive functionality and trade-offs of these mechanisms.

Biological Memory
Recording, using, and forgetting memories is a remarkable ability of biological systems. I am interested in how efficient memory retention and processing in biological systems emerge from genetic and cellular circuits in various systems, including epigenetic and immune memory.

Relevant papers:

Simons, Benjamin D., and Omer Karin. "Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence." Immunity (2024).

Karin, Omer, Eric A. Miska, and Benjamin D. Simons. "Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition." Cell systems 14.1 (2023): 24-40.

Systems Medicine and Human Physiology
A long-term goal of systems medicine is to develop mathematical reasoning to understand physiological circuits and their dysfunction in disease. There are many fascinating topics where ideas from engineering and applied mathematics can advance our understanding of important biomedical questions.

Some relevant papers:

Simons, Benjamin D., and Omer Karin. "Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence." Immunity (2024).

Karin, Omer, and Uri Alon. "Senescent cell accumulation mechanisms inferred from parabiosis." GeroScience 43.1 (2021): 329-341.

Tendler, Avichai, et al. "Hormone seasonality in medical records suggests circannual endocrine circuits." Proceedings of the National Academy of Sciences 118.7 (2021): e2003926118.

Karin, Omer, et al. "A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks." Molecular systems biology 16.7 (2020): e9510.

Karin, Omer, et al. "Senescent cell turnover slows with age providing an explanation for the Gompertz law." Nature communications 10.1 (2019): 5495.

Karin, Omer, et al. "Dynamical compensation in physiological circuits." Molecular systems biology 12.11 (2016): 886.

Cell Type Specification
Animals are made of many different cell types, sharing the same genetic code. We developed a mathematical theory on how many cell types are encoded by the genome and how they are retrieved during differentiation, revealing fundamental connections with models for associative memory in neural networks.

Karin, Omer. "A model for enhancer selection in dense regulatory networks captures the dynamics of cell type specification." bioRxiv (2024): 2024-02.

Cellular Circuits
Human physiology and development is essentially the study of the self-organization of cells, where the right cells need to emerge at the right location and time to achieve their appropriate functions. I am interested in understanding the feedback circuits that allow them to do this, specifically how they trade-off different functional requirements including robustness against mutations.

Relevant papers:

Simons, Benjamin D., and Omer Karin. "Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence." Immunity (2024).

Karin, Omer, and Uri Alon. "Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits." Molecular systems biology 13.6 (2017): 933.

Karin, Omer, et al. "Dynamical compensation in physiological circuits." Molecular systems biology 12.11 (2016): 886.

Movement regulation
We are interested in understanding the principles underlying biological circuits that control movement, drawing connections with reinforcement learning and sampling algorithms.

Relevant papers:

Karin, Omer, and Uri Alon. "The dopamine circuit as a reward-taxis navigation system." PLoS computational biology 18.7 (2022): e1010340.

Karin, Omer, and Uri Alon. "Temporal fluctuations in chemotaxis gain implement a simulated-tempering strategy for efficient navigation in complex environments." Iscience 24.7 (2021).