Identifying key multifunctional components shared by critical cancer and normal liver pathways via SparseGMM

Bakr, Shaimaa; Brennan, Kevin; Mukherjee, Pritam; Argemí, Josepmaria; Hernáez, Mikel; Gevaert, Olivier

doi:10.1016/j.crmeth.2022.100392

Cited by 2 publications

(2 citation statements)

References 90 publications

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“…Integration of single-cell data, for example, into CBMs of cell populations ( Damiani et al , 2019 , Wagner et al , 2021 ), has provided insights into the cellular heterogeneity of tumours, the tumour microenvironment, and the mechanisms of drug resistance in cancer therapy. Computational models that include single-cell data enhance our understanding of tumour evolution, the dynamics of cancer progression, and the biological processes in cancer ( Bakr et al , 2023 ), thereby informing more effective treatment strategies. Single-cell technologies have also revolutionized our understanding of the immune system’s complexity.…”

Section: Recent Developments In the Computational Modeling Of Biologi...mentioning

confidence: 99%

Perspectives on computational modeling of biological systems and the significance of the SysMod community

Puniya,

Verma,

Damiani

et al. 2024

Bioinformatics Advances

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Motivation In recent years, applying computational modeling to systems biology has caused a substantial surge in both discovery and practical applications and a significant shift in our understanding of the complexity inherent in biological systems. Results In this perspective article, we briefly overview computational modeling in biology, highlighting recent advancements such as multi-scale modeling due to the omics revolution, single-cell technology, and integration of artificial intelligence and machine learning approaches. We also discuss the primary challenges faced: integration, standardization, model complexity, scalability, and interdisciplinary collaboration. Lastly, we highlight the contribution made by the Computational Modeling of Biological Systems (SysMod) Community of Special Interest (COSI) associated with the International Society of Computational Biology (ISCB) in driving progress within this rapidly evolving field through community engagement (via both in person and virtual meetings, social media interactions), webinars, and conferences. Availability and implementation Additional information about SysMod is available at https://sysmod.info.

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Section: Recent Developments In the Computational Modeling Of Biologi...mentioning

confidence: 99%

Perspectives on computational modeling of biological systems and the significance of the SysMod community

Puniya,

Verma,

Damiani

et al. 2024

Bioinformatics Advances

Self Cite

View full text Add to dashboard Cite

show abstract

“…The next talk was from Qian Qin on the Pyro-Velocity, a framework that infers RNA velocity from single-cell ( Qin et al 2022 ). In the third talk, Shaimaa Bakr presented SparseGMM, a module network approach for gene regulatory network inference ( Bakr et al 2023 ), which was applied to healthy liver tissue and liver cancer samples to identify robust modules. Dr Joseph Wayman delivered the following presentation on building gene regulatory networks of Tfh10 cells using single-cell genomics to understand immune responses during ageing ( Wayman et al 2023 ).…”

Section: The Eventmentioning

confidence: 99%

Advancements in computational modelling of biological systems: seventh annual SysMod meeting

Puniya,

Dräger

2023

Bioinformatics

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Summary The Computational Modelling of Systems Biology (SysMod) Community of Special Interest (COSI) convenes annually at the Intelligent Systems for Molecular Biology (ISMB) conference to facilitate knowledge dissemination and exchange of research findings on systems modelling from interdisciplinary domains. The SysMod meeting 2022 was held in a hybrid mode in Madison, Wisconsin, spanning a 1-day duration centred on modelling techniques, applications, and single-cell technology implementations. The meeting showcased innovative approaches to modelling biological systems using cell-specific and multiscale modelling, multiomics data integration, and novel tools to develop systems models using single-cell and multiomics technology. The meeting also recognized outstanding research by awarding the three best posters. This report summarizes the key highlights and outcomes of the meeting. Availability and implementation: All resources and further information are freely accessible at https://sysmod.info.

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Identifying key multifunctional components shared by critical cancer and normal liver pathways via SparseGMM

Cited by 2 publications

References 90 publications

Perspectives on computational modeling of biological systems and the significance of the SysMod community

Perspectives on computational modeling of biological systems and the significance of the SysMod community

Advancements in computational modelling of biological systems: seventh annual SysMod meeting

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