Jonathan Somer

jonathan.somer@gmail.com

I’m a Hacker-Scientist working on the next generation of Cancer treatments.

While the challenge should always dictate the approach, my skills and areas of interest include:

Machine Learning & Statistics
Dynamical Systems
Modern Control Theory & Reinforcement Learning
Molecular Biology
High-throuput omics analysis

My vision of precision cancer therapy builds upon principles from control theory and dynamical systems. The first step I’ve taken along this path is developing One-Shot Tissue Dynamics Reconsruction (OSDR) an approach for inferring a dynamical model of a tumor, using just a single biopsy. More to come soon!

Education

2016-2019 - B.Sc Summa cum laude Computer Science @ Tel-Aviv University

2020-2022 - B.Med.Sc Summa cum laude (rank #1) Medicine @ Technion Israel Institute of Technology

2023-present - PhD Electrical & Computer Engineering @ Technion Israel Institute of Technology, advised by Prof. Shie Mannor

** co-advised by Prof. Uri Alon, Molecular Cell Biology @ Weizmann Institute of Science,

selected publications

Temporal tissue dynamics from a single snapshot

Jonathan Somer , Shie Mannor , and Uri Alon

bioRxiv, 2024

abstract Cite paper

Physiological and pathological processes such as inflammation or cancer emerge from the interactions between cells over time. However, methods to follow cell populations over time within the native context of a human tissue are lacking, since tissue biopsy offers only a single snapshot. Here we present one-shot tissue dynamics reconstruction (OSDR), an approach to estimate a dynamical model of cell populations based on a single tissue sample. OSDR uses spatial proteomics data to learn how the composition of cellular neighborhoods influences division rate, providing a dynamical model of cell population change over time. We apply OSDR to human breast cancer data, and reconstruct two fixed points of fibroblasts and macrophage interactions. These fixed points correspond to hot and cold fibrosis, in agreement with co-culture experiments that measured dynamics directly. We then use OSDR to discover a pulse-generating excitable circuit of T and B cells in the tumor microenvironment, suggesting temporal flares of adaptive anti-cancer responses. OSDR can be applied to a wide range of spatial transcriptomic or proteomic assays to enable analysis of tissue dynamics based on patient biopsies.
@article{somer2024temporal, title = {Temporal tissue dynamics from a single snapshot}, author = {Somer, Jonathan and Mannor, Shie and Alon, Uri}, journal = {bioRxiv}, pages = {2024--04}, year = {2024}, publisher = {Cold Spring Harbor Laboratory}, eprint = {https://www.biorxiv.org/content/10.1101/2024.04.22.590503v1}, google_scholar_id = {LkGwnXOMwfcC}, }