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Title: Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism

Abstract

Following publication of this article [1], it has come to our attention that an incomplete version of Fig. 7 was included in this article. The complete figure is shown below with the missing text included to the left of the chart.

Authors:
 [1];  [2];  [3];  [3];  [3];  [1];  [4];  [5];  [6]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); DOE Agile BioFoundry, Emeryville, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Indian Institute of Technology (IIT), Kharagpur (India)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Technical Univ. of Denmark, Horsholm (Denmark)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); DOE Agile BioFoundry, Emeryville, CA (United States); BCAM, Basque Center for Applied Mathematics, Bilbao (Spain)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1510743
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Bioinformatics
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2105
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., and Martín, Héctor García. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism. United States: N. p., 2017. Web. doi:10.1186/s12859-017-1631-y.
Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., & Martín, Héctor García. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism. United States. https://doi.org/10.1186/s12859-017-1631-y
Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., and Martín, Héctor García. Tue . "Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism". United States. https://doi.org/10.1186/s12859-017-1631-y. https://www.osti.gov/servlets/purl/1510743.
@article{osti_1510743,
title = {Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism},
author = {Birkel, Garrett W. and Ghosh, Amit and Kumar, Vinay S. and Weaver, Daniel and Ando, David and Backman, Tyler W. H. and Arkin, Adam P. and Keasling, Jay D. and Martín, Héctor García},
abstractNote = {Following publication of this article [1], it has come to our attention that an incomplete version of Fig. 7 was included in this article. The complete figure is shown below with the missing text included to the left of the chart.},
doi = {10.1186/s12859-017-1631-y},
journal = {BMC Bioinformatics},
number = 1,
volume = 18,
place = {United States},
year = {2017},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Fig. 7 Fig. 7 : Principal component analysis (PCA) of protein expression data

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Works referenced in this record:

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
journal, April 2017


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

  • George, Kevin W.; Chen, Amy; Jain, Aakriti
  • Biotechnology and Bioengineering, Vol. 111, Issue 8
  • DOI: 10.1002/bit.25226

13C Metabolic Flux Analysis
journal, July 2001


The compatibility of potential bioderived fuels with Jet A-1 aviation kerosene
journal, April 2014


Engineering Cellular Metabolism
journal, March 2016


High-throughput discovery metabolomics
journal, February 2015


Sustainable consumption within a sustainable economy – beyond green growth and green economies
journal, January 2014


Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate
journal, September 2011


Systems biotechnology for strain improvement
journal, July 2005


Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
journal, January 2007

  • Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
  • Metabolic Engineering, Vol. 9, Issue 1
  • DOI: 10.1016/j.ymben.2006.09.001

Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production
journal, September 2013


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


Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering
journal, March 2015


Addressing the Need for Alternative Transportation Fuels: The Joint BioEnergy Institute
journal, January 2008

  • Blanch, Harvey W.; Adams, Paul D.; Andrews-Cramer, Katherine M.
  • ACS Chemical Biology, Vol. 3, Issue 1
  • DOI: 10.1021/cb700267s

Systems metabolic engineering of Escherichia coli for L ‐threonine production
journal, January 2007

  • Lee, Kwang Ho; Park, Jin Hwan; Kim, Tae Yong
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100196

Engineering synergy in biotechnology
journal, April 2014

  • Nielsen, Jens; Fussenegger, Martin; Keasling, Jay
  • Nature Chemical Biology, Vol. 10, Issue 5
  • DOI: 10.1038/nchembio.1519

The challenges of integrating multi-omic data sets
journal, October 2010

  • Palsson, Bernhard; Zengler, Karsten
  • Nature Chemical Biology, Vol. 6, Issue 11
  • DOI: 10.1038/nchembio.462

Accelerated microbial turnover but constant growth efficiency with warming in soil
journal, September 2014

  • Hagerty, Shannon B.; van Groenigen, Kees Jan; Allison, Steven D.
  • Nature Climate Change, Vol. 4, Issue 10
  • DOI: 10.1038/nclimate2361

Improved reproducibility by assuring confidence in measurements in biomedical research
journal, August 2014

  • Plant, Anne L.; Locascio, Laurie E.; May, Willie E.
  • Nature Methods, Vol. 11, Issue 9
  • DOI: 10.1038/nmeth.3076

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

  • Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.
  • npj Systems Biology and Applications, Vol. 2, Issue 1
  • DOI: 10.1038/npjsba.2016.9

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
journal, March 2007

  • Becker, Scott A.; Feist, Adam M.; Mo, Monica L.
  • Nature Protocols, Vol. 2, Issue 3
  • DOI: 10.1038/nprot.2007.99

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

  • Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O.
  • Nature Reviews Microbiology, Vol. 10, Issue 4
  • DOI: 10.1038/nrmicro2737

Regulatory on/off minimization of metabolic flux changes after genetic perturbations
journal, May 2005

  • Shlomi, T.; Berkman, O.; Ruppin, E.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 21
  • DOI: 10.1073/pnas.0406346102

Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002

  • Segre, D.; Vitkup, D.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
  • DOI: 10.1073/pnas.232349399

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
journal, October 2012


INCA: a computational platform for isotopically non-stationary metabolic flux analysis
journal, January 2014


Proteome Analysis of Metabolically Engineered Escherichia coli Producing Poly(3-Hydroxybutyrate)
journal, January 2001


Metabolic remodeling of white adipose tissue in obesity
journal, August 2014

  • Cummins, Timothy D.; Holden, Candice R.; Sansbury, Brian E.
  • American Journal of Physiology-Endocrinology and Metabolism, Vol. 307, Issue 3
  • DOI: 10.1152/ajpendo.00271.2013

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis
journal, January 2009

  • Quek, Lake-Ee; Wittmann, Christoph; Nielsen, Lars K.
  • Microbial Cell Factories, Vol. 8, Issue 1
  • DOI: 10.1186/1475-2859-8-25

Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells
journal, January 2012

  • Crown, Scott B.; Ahn, Woo; Antoniewicz, Maciek R.
  • BMC Systems Biology, Vol. 6, Issue 1
  • DOI: 10.1186/1752-0509-6-43

COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013

  • Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O.
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-74

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
journal, August 2003

  • Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H.
  • Genome Biology, Vol. 4, Issue 9, p. R54
  • DOI: 10.1186/gb-2003-4-9-r54

Bon-EV: an improved multiple testing procedure for controlling false discovery rates
journal, January 2017


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

  • García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel
  • PLOS Computational Biology, Vol. 11, Issue 9
  • DOI: 10.1371/journal.pcbi.1004363

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