Dataset Information

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.

ABSTRACT: Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells' characteristics and regulatory programs, forecasting their evolution ultimately requires mathematical modeling. We develop a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This allows us to systematically integrate biological knowledge and multi-omics data to make them computable. We can then perform virtual "thought experiments" that challenge and extend our understanding of multicellular systems, and ultimately generate new testable hypotheses. In this paper, we motivate and describe the grammar, provide a reference implementation, and demonstrate its potential through a series of examples in tumor biology and immunotherapy. Altogether, this approach provides a bridge between biological, clinical, and systems biology researchers for mathematical modeling of biological systems at scale, allowing the community to extrapolate from single-cell characterization to emergent multicellular behavior.

SUBMITTER: Johnson JAI

PROVIDER: S-EPMC10516032 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.

Johnson Jeanette A I JAI Stein-O'Brien Genevieve L GL Booth Max M Heiland Randy R Kurtoglu Furkan F Bergman Daniel R DR Bucher Elmar E Deshpande Atul A Forjaz André A Getz Michael M Godet Ines I Lyman Melissa M Metzcar John J Mitchell Jacob J Raddatz Andrew A Rocha Heber H Solorzano Jacobo J Sundus Aneequa A Wang Yafei Y Gilkes Danielle D Kagohara Luciane T LT Kiemen Ashley L AL Thompson Elizabeth D ED Wirtz Denis D Wu Pei-Hsun PH Zaidi Neeha N Zheng Lei L Zimmerman Jacquelyn W JW Jaffee Elizabeth M EM Hwan Chang Young Y Coussens Lisa M LM Gray Joe W JW Heiser Laura M LM Fertig Elana J EJ Macklin Paul P

bioRxiv : the preprint server for biology 20231105

Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells' characteristics and regulatory programs, forecasting their evolution ultimately requires mathematical modeling. We develop a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This allows us to systematically integrate biological knowledge and multi-om ...[more]

PMID: 37745323

Similar Datasets

Project description:Autism is the fastest growing developmental disorder in the world today. The prevalence of autism in the US has risen from 1 in 2500 in 1970 to 1 in 88 children today. People with autism present with repetitive movements and with social and communication impairments. These impairments can range from mild to profound. The estimated total lifetime societal cost of caring for one individual with autism is $3.2 million US dollars. With the rapid growth in this disorder and the great expense of caring for those with autism, it is imperative for both individuals and society that techniques be developed to model and understand autism. There is increasing evidence that those individuals diagnosed with autism present with highly diverse set of abnormalities affecting multiple systems of the body. To this date, little to no work has been done using a whole body systems biology approach to model the characteristics of this disorder. Identification and modelling of these systems might lead to new and improved treatment protocols, better diagnosis and treatment of the affected systems, which might lead to improved quality of life by themselves, and, in addition, might also help the core symptoms of autism due to the potential interconnections between the brain and nervous system with all these other systems being modeled. This paper first reviews research which shows that autism impacts many systems in the body, including the metabolic, mitochondrial, immunological, gastrointestinal and the neurological. These systems interact in complex and highly interdependent ways. Many of these disturbances have effects in most of the systems of the body. In particular, clinical evidence exists for increased oxidative stress, inflammation, and immune and mitochondrial dysfunction which can affect almost every cell in the body. Three promising research areas are discussed, hierarchical, subgroup analysis and modeling over time. This paper reviews some of the systems disturbed in autism and suggests several systems biology research areas. Autism poses a rich test bed for systems biology modeling techniques.

Dataset Information

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.

Publications

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets