Simulating the metabolic pathway dynamics of an organism

Costello, Zachary; Martin, Hector Garcia

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Title: Simulating the metabolic pathway dynamics of an organism

Abstract

Disclosed herein are systems and methods for determining metabolic pathway dynamics using time series multiomics data. In one example, after receiving time series multiomics data comprising time-series metabolomics data associated a metabolic pathway and time-series proteomics data associated with the metabolic pathway, derivatives of the time series multiomics data can be determined. A machine learning model, representing a metabolic pathway dynamics model, can be trained using the time series multiomics data and the derivatives of the time series multiomics data, wherein the metabolic pathway dynamics model relates the time-series metabolomics data and time-series proteomics data to the derivatives of the time series multiomics data. The method can include simulating a virtual strain of the organism using the metabolic pathway dynamics model.

Inventors:: Costello, Zachary; Martin, Hector Garcia

Issue Date:: 2023-04-25

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1998332

Patent Number(s):: 11636917

Application Number:: 16/022,113

Assignee:: The Regents of the University of California (Oakland, CA)

DOE Contract Number:: AC02-05CH11231

Resource Type:: Patent

Resource Relation:: Patent File Date: 06/28/2018

Country of Publication:: United States

Language:: English

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                    Costello, Zachary, and Martin, Hector Garcia. Simulating the metabolic pathway dynamics of an organism.  United States: N. p., 2023. 
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@article{osti_1998332,

  title        = {Simulating the metabolic pathway dynamics of an organism},

  author       = {Costello, Zachary and Martin, Hector Garcia},

  abstractNote = {Disclosed herein are systems and methods for determining metabolic pathway dynamics using time series multiomics data. In one example, after receiving time series multiomics data comprising time-series metabolomics data associated a metabolic pathway and time-series proteomics data associated with the metabolic pathway, derivatives of the time series multiomics data can be determined. A machine learning model, representing a metabolic pathway dynamics model, can be trained using the time series multiomics data and the derivatives of the time series multiomics data, wherein the metabolic pathway dynamics model relates the time-series metabolomics data and time-series proteomics data to the derivatives of the time series multiomics data. The method can include simulating a virtual strain of the organism using the metabolic pathway dynamics model.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2023},

  month        = {4}

}

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Title: Simulating the metabolic pathway dynamics of an organism

Abstract

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A microfluidics-based in vitro model of the gastrointestinal human–microbe interface journal, May 2016

General mass action kinetics journal, January 1972

Mastering the game of Go with deep neural networks and tree search journal, January 2016

Systems-level analysis of mechanisms regulating yeast metabolic flux journal, October 2016

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data journal, September 2014

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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction journal, January 2013

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations journal, April 2007

Real-Time Digitization of Metabolomics Patterns from a Living System Using Mass Spectrometry journal, July 2014

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A Whole-Cell Computational Model Predicts Phenotype from Genotype journal, July 2012

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The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization journal, September 2017

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism journal, September 2016

Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress journal, January 2012

Metabolic ensemble modeling for strain engineers journal, October 2011

Interrogatory Cell-Based Assays and Uses Therof patent-application, October 2013

A Survey on Transfer Learning journal, October 2010

Synthetic and systems biology for microbial production of commodity chemicals journal, April 2016

Pathway Recognition Algorithm Using Data Integration on Genomic Models (Paradigm) patent-application, February 2012

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics journal, July 2012

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Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities: Integrated omics to discover microbial functions journal, February 2015

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods journal, February 2012

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Biofuel alternatives to ethanol: pumping the microbial well journal, July 2008

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The Regulation of Cellular Systems book, January 1996

The Elements of Statistical Learning book, January 2009

Thermodynamics-Based Metabolic Flux Analysis journal, March 2007

Synthetic biology: from hype to impact journal, March 2013

Ensemble Modeling for Aromatic Production in Escherichia coli journal, September 2009

Metabolic engineering of Saccharomyces cerevisiae for the production of triacetic acid lactone journal, September 2014

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA journal, September 2011

Acyl-CoA synthetases: fatty acid uptake and metabolic channeling journal, December 2008

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Promise of personalized omics to precision medicine journal, November 2012

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A Method to Constrain Genome-Scale Models with 13C Labeling Data journal, September 2015

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13C Metabolic Flux Analysis journal, July 2001

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels journal, September 2007

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data journal, October 2015

Big Data: Astronomical or Genomical? journal, July 2015

Granger causality in integrated GC–MS and LC–MS metabolomics data reveals the interface of primary and secondary metabolism journal, October 2012

High-throughput discovery metabolomics journal, February 2015

Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids journal, January 2015

Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli journal, June 2015

Reverse engineering and identification in systems biology: strategies, perspectives and challenges journal, February 2014

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis journal, May 2014

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains journal, December 2016

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning journal, July 2015

Dynamical effects of overparametrization in nonlinear models journal, January 1995

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
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Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism
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Protein Design Method and System
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Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model
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Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering
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Ensemble Modeling of Metabolic Networks
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Genetical Implications of the Structure of Deoxyribonucleic Acid
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Spectroscopic Systems and Methods for the Identification and Quantification of Pathogens
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Ensemble modeling for strain development of l-lysine-producing Escherichia coli
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The new frontier of genome engineering with CRISPR-Cas9
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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow
journal, May 2016

Private traits and attributes are predictable from digital records of human behavior
journal, March 2013

Integrated Proteomic and Metabolomic Analysis of an Artificial Microbial Community for Two-Step Production of Vitamin C
journal, October 2011

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
journal, May 2016

General mass action kinetics
journal, January 1972

Mastering the game of Go with deep neural networks and tree search
journal, January 2016

Systems-level analysis of mechanisms regulating yeast metabolic flux
journal, October 2016

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
journal, September 2014

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
journal, August 2013

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
journal, January 2013

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
journal, April 2007

Real-Time Digitization of Metabolomics Patterns from a Living System Using Mass Spectrometry
journal, July 2014

Biological discovery using gene regulatory networks generated from multiple-disruption expression libraries
patent, September 2008

Toward robotic cars
journal, April 2010

A Whole-Cell Computational Model Predicts Phenotype from Genotype
journal, July 2012

Systems metabolic engineering of microorganisms for natural and non-natural chemicals
journal, May 2012

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
journal, November 2014

Metabolic networks in motion: ¹³ C‐based flux analysis
journal, January 2006

Improving Fatty Acid Availability for Bio-Hydrocarbon Production in Escherichia coli by Metabolic Engineering
journal, October 2013

The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
journal, September 2017

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism
journal, September 2016

Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
journal, January 2012

Metabolic ensemble modeling for strain engineers
journal, October 2011

Interrogatory Cell-Based Assays and Uses Therof
patent-application, October 2013

A Survey on Transfer Learning
journal, October 2010

Synthetic and systems biology for microbial production of commodity chemicals
journal, April 2016

Pathway Recognition Algorithm Using Data Integration on Genomic Models (Paradigm)
patent-application, February 2012

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics
journal, July 2012

Channeling in native microbial pathways: Implications and challenges for metabolic engineering
journal, November 2017

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities: Integrated omics to discover microbial functions
journal, February 2015

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
journal, February 2014

Synthetic biology devices for in vitro and in vivo diagnostics
journal, November 2015

Dermatologist-level classification of skin cancer with deep neural networks
journal, January 2017

Smoothing and Differentiation of Data by Simplified Least Squares Procedures.
journal, July 1964

13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids
journal, October 2016

Biofuel alternatives to ethanol: pumping the microbial well
journal, July 2008

A wellness study of 108 individuals using personal, dense, dynamic data clouds
journal, July 2017

The Regulation of Cellular Systems
book, January 1996

The Elements of Statistical Learning
book, January 2009

Thermodynamics-Based Metabolic Flux Analysis
journal, March 2007

Synthetic biology: from hype to impact
journal, March 2013

Ensemble Modeling for Aromatic Production in Escherichia coli
journal, September 2009

Metabolic engineering of Saccharomyces cerevisiae for the production of triacetic acid lactone
journal, September 2014

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA
journal, September 2011

Acyl-CoA synthetases: fatty acid uptake and metabolic channeling
journal, December 2008

Generating a Virtual World to Assess Real-World Video Analysis Performance
patent-application, August 2017

Promise of personalized omics to precision medicine
journal, November 2012

A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins
journal, November 2014

A Method to Constrain Genome-Scale Models with 13C Labeling Data
journal, September 2015

The dynamic microbiome
journal, February 2014

13C Metabolic Flux Analysis
journal, July 2001

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels
journal, September 2007

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data
journal, October 2015

Big Data: Astronomical or Genomical?
journal, July 2015

Granger causality in integrated GC–MS and LC–MS metabolomics data reveals the interface of primary and secondary metabolism
journal, October 2012

High-throughput discovery metabolomics
journal, February 2015

Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids
journal, January 2015

Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli
journal, June 2015

Reverse engineering and identification in systems biology: strategies, perspectives and challenges
journal, February 2014

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis
journal, May 2014

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
journal, December 2016

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
journal, July 2015

Dynamical effects of overparametrization in nonlinear models
journal, January 1995

Circadian Metabolomics in Time and Space
journal, January 2017

Special Report: The birth of biotechnology
journal, January 2003

Real-time metabolome profiling of the metabolic switch between starvation and growth
journal, September 2015