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Akademický článek

Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective

Autor: Wheaton L. Schroeder, Patrick F. Suthers, Thomas C. Willis, Eric J. Mooney, Costas D. Maranas

Publikováno v: Metabolites, Vol 14, Iss 7, p 365 (2024)

Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become l

Externí odkaz: https://doaj.org/article/bdd158b72ac54845b9b9b0058857c120

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Akademický článek

Using EuGeneCiD and EuGeneCiM computational tools for synthetic biology

Autor: Wheaton L. Schroeder, Anna S. Baber, Rajib Saha

Publikováno v: STAR Protocols, Vol 2, Iss 4, Pp 100820- (2021)

Summary: Synthetic biology often relies on the design of genetic circuits, utilizing “bioparts” (modular DNA pieces) to accomplish desired responses to external stimuli. While such designs are usually intuited, detailed here is a computational ap

Externí odkaz: https://doaj.org/article/ada0e65761ee482c8633abf7f5f080d0

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Akademický článek

Optimization-based Eukaryotic Genetic Circuit Design (EuGeneCiD) and modeling (EuGeneCiM) tools: Computational approach to synthetic biology

Autor: Wheaton L. Schroeder, Anna S. Baber, Rajib Saha

Publikováno v: iScience, Vol 24, Iss 9, Pp 103000- (2021)

Summary: Synthetic biology has the potential to revolutionize the biotech industry and our everyday lives and is already making an impact. Developing synthetic biology applications requires several steps including design and modeling efforts which ma

Externí odkaz: https://doaj.org/article/2abfa8d29f984588ae41c3524482ff36

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Akademický článek

Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis

Autor: Wheaton L. Schroeder, Rajib Saha

Publikováno v: STAR Protocols, Vol 1, Iss 2, Pp 100105- (2020)

Summary: Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used i

Externí odkaz: https://doaj.org/article/3c4d1074e3ae4d6c9dd9fac6f5fa594d

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Akademický článek

Computation-Driven Analysis of Model Polyextremo-tolerant Fungus Exophiala dermatitidis: Defensive Pigment Metabolic Costs and Human Applications

Autor: Wheaton L. Schroeder, Steven D. Harris, Rajib Saha

Publikováno v: iScience, Vol 23, Iss 4, Pp - (2020)

Summary: The polyextremotolerant black yeast Exophiala dermatitidis is a tractable model system for investigation of adaptations that support growth under extreme conditions. Foremost among these adaptations are melanogenesis and carotenogenesis. A p

Externí odkaz: https://doaj.org/article/ab6e7c2e1509426d9d24b1e4f601914e

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Akademický článek

OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models

Autor: Wheaton L. Schroeder, Rajib Saha

Publikováno v: iScience, Vol 23, Iss 1, Pp - (2020)

Summary: Stoichiometric metabolic modeling, particularly genome-scale models (GSMs), is now an indispensable tool for systems biology. The model reconstruction process typically involves collecting information from public databases; however, incomple

Externí odkaz: https://doaj.org/article/0e2e588c42ef44d1bd9e0c31fee0d31d

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