Method for determining gene knockouts
Abstract
A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.
- Inventors:
- Issue Date:
- Research Org.:
- The Penn State Research Foundation (University Park, PA)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1084350
- Patent Number(s):
- 8457941
- Application Number:
- 13/210,484
- Assignee:
- The Penn State Research Foundation (University Park, PA)
- Patent Classifications (CPCs):
-
G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- DOE Contract Number:
- FG03-01ER25499
- Resource Type:
- Patent
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Maranas, Costa D, Burgard, Anthony R, and Pharkya, Priti. Method for determining gene knockouts. United States: N. p., 2013.
Web.
Maranas, Costa D, Burgard, Anthony R, & Pharkya, Priti. Method for determining gene knockouts. United States.
Maranas, Costa D, Burgard, Anthony R, and Pharkya, Priti. Tue .
"Method for determining gene knockouts". United States. https://www.osti.gov/servlets/purl/1084350.
@article{osti_1084350,
title = {Method for determining gene knockouts},
author = {Maranas, Costa D and Burgard, Anthony R and Pharkya, Priti},
abstractNote = {A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Jun 04 00:00:00 EDT 2013},
month = {Tue Jun 04 00:00:00 EDT 2013}
}
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Works referenced in this record:
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
journal, January 2000
- Overbeek, R.
- Nucleic Acids Research, Vol. 28, Issue 1
Metabolic pathways in the post-genome era
journal, May 2003
- Papin, Jason A.; Price, Nathan D.; Wiback, Sharon J.
- Trends in Biochemical Sciences, Vol. 28, Issue 5
Modeling DNA shuffling
conference, January 1998
- Sun, Fengzhu
- Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98
A minimal gene set for cellular life derived by comparison of complete bacterial genomes.
journal, September 1996
- Mushegian, A. R.; Koonin, E. V.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 19
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
journal, November 2002
- Ibarra, Rafael U.; Edwards, Jeremy S.; Palsson, Bernhard O.
- Nature, Vol. 420, Issue 6912
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
journal, February 2001
- Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O.
- Nature Biotechnology, Vol. 19, Issue 2
Applications of Multiobjective Optimization in Chemical Engineering
journal, January 2000
- Bhaskar, V.; Gupta, Santosh K.; Ray, Ajay K.
- Reviews in Chemical Engineering, Vol. 16, Issue 1
Glycerol Production in a Triose Phosphate Isomerase Deficient Mutant of Saccharomyces cerevisiae
journal, October 1996
- Compagno, C.; Boschi, F.; Ranzi, B. M.
- Biotechnology Progress, Vol. 12, Issue 5
Computer Program for Calculating the Melting Temperature of Degenerate Oligonucleotides Used in PCR or Hybridization
journal, June 1997
- Chen, Haoyuan; Zhu, Guan
- BioTechniques, Vol. 22, Issue 6
Analysis and design of metabolic reaction networks via mixed-integer linear optimization
journal, May 1996
- Hatzimanikatis, Vassily; Floudas, Christodoulos A.; Bailey, James E.
- AIChE Journal, Vol. 42, Issue 5
Hierarchical optimization: An introduction
journal, December 1992
- Anandalingam, G.; Friesz, T. L.
- Annals of Operations Research, Vol. 34, Issue 1
Regulation of Gene Expression in Flux Balance Models of Metabolism
journal, November 2001
- Covert, Markus W.; Schilling, Christophe H.; Palsson, Bernhard
- Journal of Theoretical Biology, Vol. 213, Issue 1
Eco Cyc: Encyclopedia of Escherichia coli genes and metabolism
journal, January 1999
- Karp, P. D.; Riley, M.; Paley, S. M.
- Nucleic Acids Research, Vol. 27, Issue 1
MetaCyc: a multiorganism database of metabolic pathways and enzymes
journal, January 2004
- Krieger, C. J.
- Nucleic Acids Research, Vol. 32, Issue 90001
Growth energetics and metabolic fluxes in continuous cultures of Penicillium chrysogenum
journal, February 1996
- Henriksen, C. M.; Christensen, L. H.; Nielsen, J.
- Journal of Biotechnology, Vol. 45, Issue 2
The KEGG resource for deciphering the genome
journal, January 2004
- Kanehisa, M.
- Nucleic Acids Research, Vol. 32, Issue 90001
Modification of central metabolic pathway inescherichia coli to reduce acetate accumulation by heterologous expression of thebacillus subtilis acetolactate synthase gene
journal, October 1994
- Aristidou, Aristos A.; San, Ka-Yiu; Bennett, George N.
- Biotechnology and Bioengineering, Vol. 44, Issue 8
MPW: the Metabolic Pathways Database
journal, January 1998
- Selkov, E.
- Nucleic Acids Research, Vol. 26, Issue 1
Metabolic flux distributions in Penicillium chrysogenum during fed-batch cultivations: METABOLIC FLUX DISTRIBUTIONS IN PENICILLIUM CHRYSOGENUM
journal, April 1995
- Jørgensen, Henrik; Nielsen, Jens; Villadsen, John
- Biotechnology and Bioengineering, Vol. 46, Issue 2
Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments
journal, December 2003
- Methe, B. A.; Nelson, K. E.; Eisen, J. A.
- Science, Vol. 302, Issue 5652, p. 1967-1969
Synthesis of biochemical production routes
journal, June 1992
- Mavrovouniotis, M.; Stephanopoulos, G.; Stephanopoulos, G.
- Computers & Chemical Engineering, Vol. 16, Issue 6
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
journal, January 2003
- Ellis, L. B. M.
- Nucleic Acids Research, Vol. 31, Issue 1
Optimization in integrated biochemical systems
journal, August 1992
- Voit, Eberhard O.
- Biotechnology and Bioengineering, Vol. 40, Issue 5
Identifying rate-controlling enzymes in metabolic pathways without kinetic parameters
journal, January 1991
- Delgado, Javier P.; Liao, James C.
- Biotechnology Progress, Vol. 7, Issue 1
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
How will bioinformatics influence metabolic engineering?
journal, April 1998
- Edwards, Jeremy S.; Palsson, Bernhard O.
- Biotechnology and Bioengineering, Vol. 58, Issue 2-3, p. 162-169
Malonyl-Coenzyme A Reductase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO2 Fixation
journal, May 2002
- Hugler, M.; Menendez, C.; Schagger, H.
- Journal of Bacteriology, Vol. 184, Issue 9, p. 2404-2410
Mathematical models of metabolic pathways
journal, April 1999
- Varner, J.; Ramkrishna, D.
- Current Opinion in Biotechnology, Vol. 10, Issue 2
Metabolic Engineering of Propanediol Pathways
journal, February 1998
- Cameron, D. C.; Altaras, N. E.; Hoffman, M. L.
- Biotechnology Progress, Vol. 14, Issue 1
Spring clip safety IV catheter
patent, September 2000
- Woehr, Kevin; Orth, Manfred; Wynkoop, Mark
- US Patent Document 6,117,108
Predicting biological system objectives de novo from internal state measurements
journal, January 2008
- Gianchandani, Erwin P.; Oberhardt, Matthew A.; Burgard, Anthony P.
- BMC Bioinformatics, Vol. 9, Issue 1
The EcoCyc and MetaCyc databases
journal, January 2000
- Karp, P. D.
- Nucleic Acids Research, Vol. 28, Issue 1
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
journal, May 2000
- Edwards, J. S.; Palsson, B. O.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 10
Poly- -Hydroxybutyrate Biosynthesis in the Facultative Methylotroph Methylobacterium extorquens AM1: Identification and Mutation of gap11, gap20, and phaR
journal, November 2002
- Korotkova, N.; Chistoserdova, L.; Lidstrom, M. E.
- Journal of Bacteriology, Vol. 184, Issue 22
Electricity Production by Geobacter sulfurreducens Attached to Electrodes
journal, March 2003
- Bond, D. R.; Lovley, D. R.
- Applied and Environmental Microbiology, Vol. 69, Issue 3
Probing the performance limits of theEscherichia coli metabolic network subject to gene additions or deletions
journal, January 2001
- Burgard, Anthony P.; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 74, Issue 5
GENOME SEQUENCING: Laboratory Workhorse Decoded
journal, September 1997
- Pennisi, E.
- Science, Vol. 277, Issue 5331
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003
- Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 84, Issue 6
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
journal, January 2003
- Klamt, S.; Stelling, J.; Ginkel, M.
- Bioinformatics, Vol. 19, Issue 2
Multiple Formate Dehydrogenase Enzymes in the Facultative Methylotroph Methylobacterium extorquens AM1 Are Dispensable for Growth on Methanol
journal, December 2003
- Chistoserdova, L.; Laukel, M.; Portais, J. -C.
- Journal of Bacteriology, Vol. 186, Issue 1
Metabolic reconstruction using shortest paths
journal, April 2000
- Arita, Masanori
- Simulation Practice and Theory, Vol. 8, Issue 1-2
Reconstruction of the central carbon metabolism of Aspergillus niger: Reconstruction of Aspergillus niger metabolism
journal, October 2003
- David, Helga; Åkesson, Mats; Nielsen, Jens
- European Journal of Biochemistry, Vol. 270, Issue 21
Global Transposon Mutagenesis and a Minimal Mycoplasma Genome
journal, December 1999
- Hutchison III, C. A.
- Science, Vol. 286, Issue 5447
Biotechnology of succinic acid production and markets for derived industrial products
journal, May 1999
- Zeikus, J. G.; Jain, M. K.; Elankovan, P.
- Applied Microbiology and Biotechnology, Vol. 51, Issue 5
Metabolic engineering for the microbial production of 1,3-propanediol
journal, October 2003
- Nakamura, Charles E; Whited, Gregory M
- Current Opinion in Biotechnology, Vol. 14, Issue 5, p. 454-459
A genome-based approach for the identification of essential bacterial genes
journal, September 1998
- Arigoni, Fabrizio; Talabot, Francois; Peitsch, Manuel
- Nature Biotechnology, Vol. 16, Issue 9
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
journal, January 1994
- Varma, A.; Palsson, B. O.
- Applied and Environmental Microbiology, Vol. 60, Issue 10
From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting
journal, September 2003
- Segrè, Daniel; Zucker, Jeremy; Katz, Jeremy
- OMICS: A Journal of Integrative Biology, Vol. 7, Issue 3
Advances in flux balance analysis
journal, October 2003
- Kauffman, Kenneth J.; Prakash, Purusharth; Edwards, Jeremy S.
- Current Opinion in Biotechnology, Vol. 14, Issue 5
A hierarchical approach to protein molecular evolution
journal, March 1999
- Bogarad, L. D.; Deem, M. W.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 6
The Lagrangian Relaxation Method for Solving Integer Programming Problems
journal, January 1981
- Fisher, Marshall L.
- Management Science, Vol. 27, Issue 1
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
Method and system for modeling cellular metabolism
patent-application, November 2002
- Maranas, Costas D.; Burgard, Anthony P.
- US Patent Application 10/043440; 20020168654
Predicting crossover generation in DNA shuffling
journal, March 2001
- Moore, G. L.; Maranas, C. D.; Lutz, S.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 6
Study of two-stage processes for the microbial production of 1,3-propanediol from glucose
journal, October 2002
- M., Hartlep; W., Hussmann; N., Prayitno
- Applied Microbiology and Biotechnology, Vol. 60, Issue 1-2
E-CELL: software environment for whole-cell simulation
journal, January 1999
- Tomita, M.; Hashimoto, K.; Takahashi, K.
- Bioinformatics, Vol. 15, Issue 1
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
journal, February 1998
- SantaLucia, J.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 4
The Complete Genome Sequence of Escherichia coli K-12
journal, September 1997
- Blattner, F. R.
- Science, Vol. 277, Issue 5331
Metabolic modeling of microbial strains in silico
journal, March 2001
- Covert, Markus W.; Schilling, Christophe H.; Famili, Iman
- Trends in Biochemical Sciences, Vol. 26, Issue 3
The underlying pathway structure of biochemical reaction networks
journal, April 1998
- Schilling, C. H.; Palsson, B. O.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 8
Hydrogen production by biological processes: a survey of literature
journal, January 2001
- Das, D.
- International Journal of Hydrogen Energy, Vol. 26, Issue 1
Engineering Escherichia coli for efficient conversion of glucose to pyruvate
journal, February 2004
- Causey, T. B.; Shanmugam, K. T.; Yomano, L. P.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 8, p. 2235-2240
OptStrain: A computational framework for redesign of microbial production systems
journal, November 2004
- Pharkya, P.
- Genome Research, Vol. 14, Issue 11
Cleaning up with genomics: applying molecular biology to bioremediation
journal, October 2003
- Lovley, Derek R.
- Nature Reviews Microbiology, Vol. 1, Issue 1
An estimation of minimal genome size required for life
journal, April 1995
- Itaya, Mitsuhiro
- FEBS Letters, Vol. 362, Issue 3
Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant.
journal, January 1997
- Stols, L.; Donnelly, M. I.
- Applied and environmental microbiology, Vol. 63, Issue 7
Gene Expression Profiling by DNA Microarrays and Metabolic Fluxes in Escherichia coli
journal, April 2000
- Oh, M. -K.; Liao, J. C.
- Biotechnology Progress, Vol. 16, Issue 2
Equations and calculations for fermentations of butyric acid bacteria
journal, February 1984
- Papoutsakis, Eleftherios Terry
- Biotechnology and Bioengineering, Vol. 26, Issue 2
Creating multiple-crossover DNA libraries independent of sequence identity
journal, September 2001
- Lutz, S.; Ostermeier, M.; Moore, G. L.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 20
A modular minimal cell model: Purine and pyrimidine transport and metabolism
journal, April 2004
- Castellanos, M.; Wilson, D. B.; Shuler, M. L.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 17
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000
- Kanehisa, Minoru; Goto, Susumu
- Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
Methods for identifying drug targets based on genomic sequence data
patent-application, January 2002
- Palsson, Bernhard
- US Patent Application 09/923870; 20020012939
Microbial production of 1,3-propanediol
journal, September 1999
- Biebl, H.; Menzel, K.; Zeng, A. -P.
- Applied Microbiology and Biotechnology, Vol. 52, Issue 3
Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CoA Carboxylase in Autotrophic Crenarchaeota and Indication for Operation of a 3-Hydroxypropionate Cycle in Autotrophic Carbon Fixation
†
journal, January 1999
- Menendez, Castor; Bauer, Zsuzsa; Huber, Harald
- Journal of Bacteriology, Vol. 181, Issue 4
Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments
journal, October 2001
- Burgard, A. P.; Vaidyaraman, S.; Maranas, C. D.
- Biotechnology Progress, Vol. 17, Issue 5
Studies on hydrogen production by continuous culture system of hydrogen-producing anaerobic bacteria
journal, September 1997
- Kataoka, Naoaki; Miya, Akiko; Kiriyama, Koichi
- Water Science and Technology, Vol. 36, Issue 6-7
The challenges of in silico biology
journal, November 2000
- Palsson, Bernhard
- Nature Biotechnology, Vol. 18, Issue 11
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
journal, January 2001
- Quackenbush, J.
- Nucleic Acids Research, Vol. 29, Issue 1
Metabolic Flux Analysis ofEscherichia coliDeficient in the Acetate Production Pathway and Expressing theBacillus subtilisAcetolactate Synthase
journal, January 1999
- Yang, Yea-Tyng; Aristidou, Aristos A.; San, Ka-Yiu
- Metabolic Engineering, Vol. 1, Issue 1
Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances
journal, June 1999
- Schilling, C. H.; Edwards, J. S.; Palsson, B. O.
- Biotechnology Progress, Vol. 15, Issue 3
Integrated approaches to the design of media and feeding strategies for fed-batch cultures of animal cells
journal, March 1997
- Xie, Liangzhi; Wang, Daniel I. C.
- Trends in Biotechnology, Vol. 15, Issue 3
PathMiner: predicting metabolic pathways by heuristic search
journal, September 2003
- McShan, D. C.; Rao, S.; Shah, I.
- Bioinformatics, Vol. 19, Issue 13
Computer-aided synthesis of biochemical pathways
journal, December 1990
- Mavrovouniotis, Michael L.; Stephanopoulos, George; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 36, Issue 11
Modeling DNA Mutation and Recombination for Directed Evolution Experiments
journal, August 2000
- Moore, Gregory L.; Maranas, Costas D.
- Journal of Theoretical Biology, Vol. 205, Issue 3
GENETICS:Ethical Considerations in Synthesizing a Minimal Genome
journal, December 1999
- Cho, M. K.
- Science, Vol. 286, Issue 5447
The metabolic world of Escherichia coli is not small
journal, February 2004
- Arita, M.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 6
Genome-wide expression profiling in Escherichia coli K-12
journal, October 1999
- Richmond, C.
- Nucleic Acids Research, Vol. 27, Issue 19
Combining evidence using p-values: application to sequence homology searches
journal, February 1998
- Bailey, T. L.; Gribskov, M.
- Bioinformatics, Vol. 14, Issue 1
Stoichiometric analysis of animal cell growth and its application in medium design
journal, May 1994
- Xie, Liangzhi; Wang, Daniel I. C.
- Biotechnology and Bioengineering, Vol. 43, Issue 11
Metabolic Capabilities of Escherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors
journal, December 1993
- Varma, Amit; Palsson, Bernhard O.
- Journal of Theoretical Biology, Vol. 165, Issue 4
Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations
journal, January 1985
- Papoutsakis, Eleftherios Terry; Meyer, Charles L.
- Biotechnology and Bioengineering, Vol. 27, Issue 1
Optimization-based framework for inferring and testing hypothesized metabolic objective functions
journal, June 2003
- Burgard, Anthony P.; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 82, Issue 6
Metabolic flux distributions inCorynebacterium glutamicum during growth and lysine overproduction
journal, March 1993
- Vallino, Joseph J.; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 41, Issue 6
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock
journal, December 2003
- Pharkya, Priti; Burgard, Anthony P.; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 84, Issue 7
Biochemical systems analysis
journal, December 1969
- Savageau, Michael A.
- Journal of Theoretical Biology, Vol. 25, Issue 3