Pitkanen2014 - Metabolic reconstruction of Aspergillus clavatus using CoReCo

Pitkanen2014 - Metabolic reconstruction of Aspergillus clavatus using CoReCo

This model was reconstructed with the CoReCo method (Comparative ReConstruction of genome-scale metabolic networks) from protein sequence and phylogeny data.

This model is described in the article:

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
PLoS Comput Biol. 2014 Feb 6;10(2):e1003465
Abstract:

We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.

This model is hosted on BioModels Database
and identified by: MODEL1302010012
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.

Pitkanen2014——基于CoReCo方法（Comparative ReConstruction of genome-scale metabolic networks）的棒曲霉（Aspergillus clavatus）代谢网络重构

本模型依托蛋白质序列与系统发育数据，采用CoReCo方法完成重构。

本模型对应的发表文章如下：
《现生与祖先物种的无间隙基因组规模代谢网络比较重构（Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species）》
作者：Esa Pitkänen、Paula Jouhten、Jian Hou、Muhammad Fahad Syed、Peter Blomberg、Jana Kludas、Merja Oja、Liisa Holm、Merja Penttilä、Juho Rousu、Mikko Arvas
刊载于：《公共科学图书馆·计算生物学（PLoS Comput Biol）》，2014年2月6日，第10卷第2期，文章编号e1003465

摘要：
本研究提出了一种用于比较性代谢重构的新型计算方法CoReCo，并为49种重要真菌物种构建了基因组规模的代谢网络模型。随着测序基因组数据的爆发式增长，本方法通过在概率框架下整合序列数据，可同时为大量物种重构出无间隙的基因组规模代谢网络。通过与经过精心注释与审核的酿酒酵母（Saccharomyces cerevisiae）共识模型以及大规模基因敲除实验结果进行对比，验证了本重构方法的高准确性。我们的比较性重构方法在可用序列数据质量不佳，以及重构进化距离较远的物种时尤为适用。此外，重构得到的代谢网络已完成完整的碳元素映射，可用于13C通量分析。我们通过计算稳态生物质生成实验验证了所构建真菌模型的功能与可用性——这些真菌涵盖了工业生物技术领域部分最重要的生产菌种。与诸多现有重构技术不同，本方法仅需极少量人工操作即可将重构模型用于通量平衡实验。CoReCo工具的访问地址为：http://esaskar.github.io/CoReCo/。

本模型存储于BioModels数据库（BioModels Database），其编号为MODEL1302010012。
引用BioModels数据库时，请使用以下著录格式：《BioModels数据库：面向已发表定量动力学模型的增强型注释与审核资源（BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models）》。

在法律允许的最大范围内，本编码模型的全部著作权及相关邻接权利已全部奉献至全球公共领域。如需了解更多信息，请参阅CC0公共领域贡献协议（CC0 Public Domain Dedication）。