Developing a Logical Model of Yeast Metabolism PDF Download
Are you looking for read ebook online? Search for your book and save it on your Kindle device, PC, phones or tablets. Download Developing a Logical Model of Yeast Metabolism PDF full book. Access full book title Developing a Logical Model of Yeast Metabolism by Philip G. K. Reiser. Download full books in PDF and EPUB format.
Author: Philip G. K. Reiser
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
Get Book Here
Book Description
With the completion of the sequencing of genomes of an increasing number of organisms, the focus of biology is moving to determining the role of these genes (functional genomics). To this end it is useful to view the cell as a biochemical machine: it consumes simple molecules to manufacture more complex ones by chaining together biochemical reactions into long sequences referred to as metabolic pathways. Such metabolic pathways are not linear but often intersect to form a complex network. Genes play a fundamental role in this network by synthesising the enzymes that catalyse biochemical reactions. Although developing a complete model of metabolism is of fundamental importance to biology and medicine, the size and complexity of the network has proven beyond the capacity of human reasoning. This paper presents intermediate results in the Robot Scientist research programme that aims to discover the function of genes in the metabolism of the yeast Saccharomyces cerevisiae. Results include: (1) the first logical model of metabolism; (2) a method to predict phenotype by deductive inference; and (3) a method to infer reactions and gene function by abductive inference. We describe the in vivo experimental set-up which will allow these in silico inferences to be automatically tested by a laboratory robot.
Author: Philip G. K. Reiser
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
Get Book Here
Book Description
With the completion of the sequencing of genomes of an increasing number of organisms, the focus of biology is moving to determining the role of these genes (functional genomics). To this end it is useful to view the cell as a biochemical machine: it consumes simple molecules to manufacture more complex ones by chaining together biochemical reactions into long sequences referred to as metabolic pathways. Such metabolic pathways are not linear but often intersect to form a complex network. Genes play a fundamental role in this network by synthesising the enzymes that catalyse biochemical reactions. Although developing a complete model of metabolism is of fundamental importance to biology and medicine, the size and complexity of the network has proven beyond the capacity of human reasoning. This paper presents intermediate results in the Robot Scientist research programme that aims to discover the function of genes in the metabolism of the yeast Saccharomyces cerevisiae. Results include: (1) the first logical model of metabolism; (2) a method to predict phenotype by deductive inference; and (3) a method to infer reactions and gene function by abductive inference. We describe the in vivo experimental set-up which will allow these in silico inferences to be automatically tested by a laboratory robot.
Author: Luis Fariñas del Cerro
Publisher: John Wiley & Sons
ISBN: 1119015219
Category : Science
Languages : en
Pages : 328
Get Book Here
Book Description
Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.
Author: Stephen Muggleton
Publisher: Springer Science & Business Media
ISBN: 3540738460
Category : Computers
Languages : en
Pages : 466
Get Book Here
Book Description
This book constitutes the thoroughly refereed post-proceedings of the 16th International Conference on Inductive Logic Programming, ILP 2006, held in Santiago de Compostela, Spain, in August 2006. The papers address all current topics in inductive logic programming, ranging from theoretical and methodological issues to advanced applications.
Author: Paolo Frasconi
Publisher: Springer Science & Business Media
ISBN: 3642212948
Category : Computers
Languages : en
Pages : 289
Get Book Here
Book Description
This book constitutes the thoroughly refereed post-proceedings of the 20th International Conference on Inductive Logic Programming, ILP 2010, held in Florence, Italy in June 2010. The 11 revised full papers and 15 revised short papers presented together with abstracts of three invited talks were carefully reviewed and selected during two rounds of refereeing and revision. All current issues in inductive logic programming, i.e. in logic programming for machine learning are addressed, in particular statistical learning and other probabilistic approaches to machine learning are reflected.
Author: Luc De Raedt
Publisher: Springer Science & Business Media
ISBN: 364213839X
Category : Mathematics
Languages : en
Pages : 268
Get Book Here
Book Description
This book constitutes the proceedings of the 19th International Conference on Inductive Logic Programming, held in Leuven, Belgium, in July 2009.
Author: Luc Raedt
Publisher: Springer
ISBN: 3642138403
Category : Mathematics
Languages : en
Pages : 268
Get Book Here
Book Description
This book constitutes the proceedings of the 19th International Conference on Inductive Logic Programming, held in Leuven, Belgium, in July 2009.
Author: Albert Bifet
Publisher: Springer Nature
ISBN: 3031452755
Category : Computers
Languages : en
Pages : 725
Get Book Here
Book Description
This book constitutes the proceedings of the 26th International Conference on Discovery Science, DS 2023, which took place in Porto, Portugal, in October 2023. The 37 full papers and 10 short papers presented in this volume were carefully reviewed and selected from 133 submissions. They were organized in topical sections as follows: Machine learning methods and applications; natural language processing and social media analysis; interpretability and explainability in AI; data analysis and optimization; fairness, privacy and security in AI; control and spatio-temporal modeling; graph theory and network analysis; time series and forecasting; healthcare and biological data analysis; anomaly, outlier and novelty detection.
Author: Benjamin Douglas Heavner
Publisher:
ISBN:
Category :
Languages : en
Pages : 388
Get Book Here
Book Description
This document presents the results of efforts to apply the Yeast Consensus Reconstruction model of the Saccharomyces cerevisiae metabolic network to develop a metabolic engineering strategy for industrial strain improvement. Following a review of the development of mathematical models of metabolism, it describes an evaluation of the Consensus Reconstruction. We find that the computational reconstruction of this portion of metabolism differs from the biochemistry of this pathway as described in the literature. Our efforts to correct these discrepancies are described in Chapter 4. The updated model improves both the accuracy of the metabolic reconstruction and the prediction of viability and auxotrophy phenotypes, thus demonstrating that literature-based curation is a technique which can be successfully applied to improve the model. Chapter 5 describes an in silico screen for formate-producing yeast mutants. By working to reproduce an in silico screen previously conducted using the iND750 model, we found that the computational prediction of formate-producing yeast mutants is sensitive to implementation details and reaction constraints when using either the iND750 or the Yeast model. Our results suggest that comparative analysis of constraint based models is a useful tool for improving models of the yeast metabolic network. The main text concludes with a summary and discussion of future research opportunities in Chapter 6. MATLAB scripts which enable evaluation of model predictive accuracy and demonstrate model applications such growth simulation and mutant library screening are included as appendices. This work contributes to the ongoing effort to develop systems biotechnology tools which will enable the rational design of new microbial strains, and which may enable broader industrial-scale application of biotechnology. The fields of computational biology and systems biotechnology are young, and abundant opportunity remains to develop and apply this technology to meet human needs.
Author: Achim Hoffmann
Publisher: Springer
ISBN: 3540316981
Category : Science
Languages : en
Pages : 415
Get Book Here
Book Description
This book constitutes the refereed proceedings of the 8th International Conference on Discovery Science, DS 2005, held in Singapore in October 2005, co-located with the International Conference on Algorithmic Learning Theory (ALT 2005). The 21 revised long papers and the 6 revised regular papers presented together with 9 project reports and 5 invited papers were carefully reviewed and selected from 112 submissions. The papers cover all issues in the area of automating scientific discovery or working on tools for supporting the human process of discovery in science.
Author: Matteo Baldoni
Publisher: Springer
ISBN: 331903524X
Category : Computers
Languages : en
Pages : 555
Get Book Here
Book Description
This book constitutes the refereed proceedings of the 13th International Conference of the Italian Association for Artificial Intelligence, AI*IA 2013, held in Turin, Italy, in December 2013. The 45 revised full papers were carefully reviewed and selected from 86 submissions. The conference covers broadly the many aspects of theoretical and applied Artificial Intelligence as follows: knowledge representation and reasoning, machine learning, natural language processing, planning, distributed AI: robotics and MAS, recommender systems and semantic Web and AI applications.
