Processes 2018, 6,38
8.
Zomorrodi, A.R.; Islam, M.M.; Maranas, C.D. d-OptCom: Dynamic multi-level and multi-objective metabolic
modeling of microbial communities. ACS Synth. Biol. 2014, 3, 247–257. [CrossRef][PubMed]
9.
Zomorrodi, A.R.; Maranas, C.D. OptCom: A multi-level optimization framework for the metabolic modeling
and analysis of microbial communities. PLoS Comput. Biol. 2012, 8, e1002363. [CrossRef][PubMed]
10. Orth, J.D.; Thiele, I.; Palsson, B.O. What is flux balance analysis? Nat. Biotechnol. 2010, 28, 245–248. [CrossRef]
[PubMed]
11. Cankorur-Cetinkaya, A.; Dikicioglu, D.; Oliver, S.G. Metabolic modeling to identify engineering targets for
Komagataella phaffii: The effect of biomass composition on gene target identification. Biotechnol. Bioeng. 2017,
114, 2605–2615. [CrossRef][PubMed]
12. Thiele, I.; Palsson, B.Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction.
Nat. Protoc. 2010, 5, 93–121. [CrossRef][PubMed]
13. Henry, C.S.; DeJongh, M.; Best, A.A.; Frybarger, P.M.; Linsay, B.; Stevens, R.L. High-throughput generation,
optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 2010, 28, 977–982. [CrossRef]
[PubMed]
14. Oberhardt, M.A.; Puchałka, J.; Fryer, K.E.; Dos Santos, V.A.M.; Papin, J.A. Genome-scale metabolic network
analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J. Bacteriol. 2008, 190, 2790–2803.
[CrossRef][PubMed]
15. Stolyar, S.; Van Dien, S.; Hillesland, K.L.; Pinel, N.; Lie, T.J.; Leigh, J.A.; Stahl, D.A. Metabolic modeling of a
mutualistic microbial community. Mol. Syst. Biol. 2007, 3, 92. [CrossRef][PubMed]
16. Lohman, E.J.; Gardner, R.D.; Halverson, L.; Macur, R.E.; Peyton, B.M.; Gerlach, R. An efficient and scalable
extraction and quantification method for algal derived biofuel. J. Microbiol. Methods 2013, 94, 235–244.
[CrossRef][PubMed]
17. Bremer, H.; Dennis, P.P. Modulation of chemical composition and other parameters of the cell by growth rate.
Escherichia coli Salmonella Cell. Mol. Biol. 1996, 2, 1553–1569.
18. Herbert, D.; Phipps, P.J.; Strange, R.E. Chemical analysis of microbial cells. In Methods in Microbiology;
Norris, J.R., Ribbons, D.W., Eds.; Academic Press: New York, NY, USA, 1971; Vol. 5, pp. 209–344.
19. Long, C.P.; Antoniewicz, M.R. Quantifying biomass composition by gas chromatography/mass spectrometry.
Anal. Chem. 2014, 86, 9423–9427. [CrossRef][PubMed]
20. Ausubel, F.M.; Brent, R.; Kingston, R.E.; Moore, D.D.; Seidman, J.G.; Smith, J.A.; Struhl, K. Short Protocols
in Molecular Biology, 2nd ed.; Greene Publishing Associates and John Wiley & Sons: New York, NY, USA,
1992; p. 834.
21. Bernstein, H.C.; Paulson, S.D.; Carlson, R.P. Synthetic Escherichia coli consortia engineered for syntrophy
demonstrate enhanced biomass productivity. J. Biotechnol. 2012, 157, 159–166. [CrossRef][PubMed]
22. Ludwig, M.; Bryant, D.A. Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC
7002 by next-gen (SOLiD (tm)) sequencing of cDNA. Front. Microbiol. 2011, 2, 41. [CrossRef][PubMed]
23. Stevens, S.E.; Patterson, C.O.; Myers, J. Production of hydrogen peroxide by blue-green algae—Survey.
J. Phycol. 1973, 9, 427–430. [CrossRef]
24. Farrand, S.G.; Linton, J.D.; Stephenson, R.J.; McCarthy, W.V. The use of response surface analysis to study
the growth of Bacillus acidocaldarius throughout the growth range of temperature and pH. Arch. Microbiol.
1983, 135, 272–275. [CrossRef]
25. Folsom, J.P.; Parker, A.E.; Carlson, R.P. Physiological and proteomic analysis of Escherichia coli iron-limited
chemostat growth. J. Bacteriol. 2014, 196, 2748–2761. [CrossRef][PubMed]
26. Klamt, S.; Saez-Rodriguez, J.; Gilles, E.D. Structural and functional analysis of cellular networks with
CellNetAnalyzer. BMC Syst. Biol. 2007, 1,2.[CrossRef][PubMed]
27. Klamt, S.; von Kamp, A. An application programming interface for CellNetAnalyzer. Biosystems 2011, 105,
162–168. [CrossRef][PubMed]
28. Mavromatis, K.; Sikorski, J.; Lapidus, A.; Del Rio, T.G.; Copeland, A.; Tice, H.; Cheng, J.-F.; Lucas, S.; Chen, F.;
Nolan, M. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Stand. Genom. Sci.
2010, 2,9.[CrossRef][PubMed]
29. Caspi, R.; Billington, R.; Ferrer, L.; Foerster, H.; Fulcher, C.A.; Keseler, I.M.; Kothari, A.; Krummenacker, M.;
Latendresse, M.; Mueller, L.A.; et al. The MetaCyc database of metabolic pathways and enzymes and
the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016, 44, D471–D480. [CrossRef]
[PubMed]
177
8.
Zomorrodi, A.R.; Islam, M.M.; Maranas, C.D. d-OptCom: Dynamic multi-level and multi-objective metabolic
modeling of microbial communities. ACS Synth. Biol. 2014, 3, 247–257. [CrossRef][PubMed]
9.
Zomorrodi, A.R.; Maranas, C.D. OptCom: A multi-level optimization framework for the metabolic modeling
and analysis of microbial communities. PLoS Comput. Biol. 2012, 8, e1002363. [CrossRef][PubMed]
10. Orth, J.D.; Thiele, I.; Palsson, B.O. What is flux balance analysis? Nat. Biotechnol. 2010, 28, 245–248. [CrossRef]
[PubMed]
11. Cankorur-Cetinkaya, A.; Dikicioglu, D.; Oliver, S.G. Metabolic modeling to identify engineering targets for
Komagataella phaffii: The effect of biomass composition on gene target identification. Biotechnol. Bioeng. 2017,
114, 2605–2615. [CrossRef][PubMed]
12. Thiele, I.; Palsson, B.Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction.
Nat. Protoc. 2010, 5, 93–121. [CrossRef][PubMed]
13. Henry, C.S.; DeJongh, M.; Best, A.A.; Frybarger, P.M.; Linsay, B.; Stevens, R.L. High-throughput generation,
optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 2010, 28, 977–982. [CrossRef]
[PubMed]
14. Oberhardt, M.A.; Puchałka, J.; Fryer, K.E.; Dos Santos, V.A.M.; Papin, J.A. Genome-scale metabolic network
analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J. Bacteriol. 2008, 190, 2790–2803.
[CrossRef][PubMed]
15. Stolyar, S.; Van Dien, S.; Hillesland, K.L.; Pinel, N.; Lie, T.J.; Leigh, J.A.; Stahl, D.A. Metabolic modeling of a
mutualistic microbial community. Mol. Syst. Biol. 2007, 3, 92. [CrossRef][PubMed]
16. Lohman, E.J.; Gardner, R.D.; Halverson, L.; Macur, R.E.; Peyton, B.M.; Gerlach, R. An efficient and scalable
extraction and quantification method for algal derived biofuel. J. Microbiol. Methods 2013, 94, 235–244.
[CrossRef][PubMed]
17. Bremer, H.; Dennis, P.P. Modulation of chemical composition and other parameters of the cell by growth rate.
Escherichia coli Salmonella Cell. Mol. Biol. 1996, 2, 1553–1569.
18. Herbert, D.; Phipps, P.J.; Strange, R.E. Chemical analysis of microbial cells. In Methods in Microbiology;
Norris, J.R., Ribbons, D.W., Eds.; Academic Press: New York, NY, USA, 1971; Vol. 5, pp. 209–344.
19. Long, C.P.; Antoniewicz, M.R. Quantifying biomass composition by gas chromatography/mass spectrometry.
Anal. Chem. 2014, 86, 9423–9427. [CrossRef][PubMed]
20. Ausubel, F.M.; Brent, R.; Kingston, R.E.; Moore, D.D.; Seidman, J.G.; Smith, J.A.; Struhl, K. Short Protocols
in Molecular Biology, 2nd ed.; Greene Publishing Associates and John Wiley & Sons: New York, NY, USA,
1992; p. 834.
21. Bernstein, H.C.; Paulson, S.D.; Carlson, R.P. Synthetic Escherichia coli consortia engineered for syntrophy
demonstrate enhanced biomass productivity. J. Biotechnol. 2012, 157, 159–166. [CrossRef][PubMed]
22. Ludwig, M.; Bryant, D.A. Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC
7002 by next-gen (SOLiD (tm)) sequencing of cDNA. Front. Microbiol. 2011, 2, 41. [CrossRef][PubMed]
23. Stevens, S.E.; Patterson, C.O.; Myers, J. Production of hydrogen peroxide by blue-green algae—Survey.
J. Phycol. 1973, 9, 427–430. [CrossRef]
24. Farrand, S.G.; Linton, J.D.; Stephenson, R.J.; McCarthy, W.V. The use of response surface analysis to study
the growth of Bacillus acidocaldarius throughout the growth range of temperature and pH. Arch. Microbiol.
1983, 135, 272–275. [CrossRef]
25. Folsom, J.P.; Parker, A.E.; Carlson, R.P. Physiological and proteomic analysis of Escherichia coli iron-limited
chemostat growth. J. Bacteriol. 2014, 196, 2748–2761. [CrossRef][PubMed]
26. Klamt, S.; Saez-Rodriguez, J.; Gilles, E.D. Structural and functional analysis of cellular networks with
CellNetAnalyzer. BMC Syst. Biol. 2007, 1,2.[CrossRef][PubMed]
27. Klamt, S.; von Kamp, A. An application programming interface for CellNetAnalyzer. Biosystems 2011, 105,
162–168. [CrossRef][PubMed]
28. Mavromatis, K.; Sikorski, J.; Lapidus, A.; Del Rio, T.G.; Copeland, A.; Tice, H.; Cheng, J.-F.; Lucas, S.; Chen, F.;
Nolan, M. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Stand. Genom. Sci.
2010, 2,9.[CrossRef][PubMed]
29. Caspi, R.; Billington, R.; Ferrer, L.; Foerster, H.; Fulcher, C.A.; Keseler, I.M.; Kothari, A.; Krummenacker, M.;
Latendresse, M.; Mueller, L.A.; et al. The MetaCyc database of metabolic pathways and enzymes and
the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016, 44, D471–D480. [CrossRef]
[PubMed]
177