Sriram Lab:Publications

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(Selected publications)
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(Articles in peer-reviewed journals)
 
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==Selected publications==
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==Articles in peer-reviewed journals==
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Nargund S, Sriram G (2013) Designer labels for plant metabolism: Statistical design of isotope labeling experiments for improved quantification of flux in complex plant metabolic networks. Molecular BioSystems 9: 99-112. DOI: 10.1039/C2MB25253H. [http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb25253h Link]
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Nargund S<sup>§</sup>, Misra A<sup>§</sup>, Zhang X<sup>§</sup>, Coleman GD, Sriram G (accepted) Flux and reflux: metabolite back-mixing in plant suspension cells and its implications on isotope-assisted metabolic flux analysis. Molecular BioSystems, doi: 10.1039/C3MB70348G. (<sup>§</sup>Equal contributors listed in the order in which they joined the project.) [http://pubs.rsc.org/en/content/articlelanding/2013/mb/c3mb70348g View at publisher]
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Zheng Y, Sriram G (2010) Mathematical modeling: bridging the gap between concept and realization in synthetic biology. Journal of Biomedicine and Biotechnology article ID 541609, 16 pages. [http://dx.doi.org/10.1155/2010/541609 Link]
+
Zheng Y<sup>§</sup>, Quinn AH<sup>§</sup>, Sriram G (2013) Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom <i>Phaeodactylum tricornutum</i>. Microbial Cell Factories 12: 109. (<sup>§</sup>Equal contributors listed in the order in which they joined the project.) [http://www.microbialcellfactories.com/content/12/1/109 View at publisher (OPEN ACCESS)]
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Sriram G, Rahib L, Parr LS, Liao JC, Dipple KM (2010) Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells. Metabolic Engineering 12:332-340. [http://dx.doi.org/10.1016/j.ymben.2010.04.001 Link]
+
Misra A, Sriram G (2013) Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. BMC Systems Biology 7: 126. [http://www.biomedcentral.com/1752-0509/7/126/abstract View at publisher (OPEN ACCESS)] <b>(Highly accessed)</b>
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Rahib L, Sriram G, Harada MK, Liao JC, Dipple KM (2009) Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency. Molecular Genetics and Metabolism 96:106-112. [http://dx.doi.org/10.1016/j.ymgme.2008.11.163 Link]
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Misra A, Conway MF, Johnnie J, Qureshi TM, Derrick AM, Agbo EC, Sriram G (2013) Metabolic analyses elucidate nontrivial gene targets for amplifying dihydroartemisinic acid production in yeast. Frontiers in Microbiology, 4: 200. [http://www.frontiersin.org/Journal/Abstract.aspx?s=679&name=microbiotechnology,%20ecotoxicology%20and%20bioremediation&ART_DOI=10.3389/fmicb.2013.00200 View at publisher (OPEN ACCESS)]
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Iyer VV, Sriram G, Fulton DB, Zhou R, Westgate ME, Shanks JV (2008) Metabolic flux maps: An effective tool for studying the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons. Plant, Cell, and Environment 31:506-517. [http://dx.doi.org/10.1111/j.1365-3040.2008.01781.x Link]
+
Nargund S, Sriram G (2013) Designer labels for plant metabolism: Statistical design of isotope labeling experiments for improved quantification of flux in complex plant metabolic networks. Molecular BioSystems 9: 99-112. [http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb25253h View at publisher]
-
Sriram G, Rahib L, He J-S, Campos AE, Liao JC, Dipple KM (2008) Global metabolic changes due to glycerol kinase overexpression in rat liver cells. Molecular Genetics and Metabolism 93:145-159. [http://dx.doi.org/10.1016/j.ymgme.2007.09.008 Link]
+
Zheng Y, Sriram G (2010) Mathematical modeling: bridging the gap between concept and realization in synthetic biology. Journal of Biomedicine and Biotechnology (now BioMed Research International) article ID 541609, 16 pages. [http://dx.doi.org/10.1155/2010/541609 View at publisher (OPEN ACCESS)]
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Sriram G, Iyer VV, Fulton DB, Shanks JV (2007) Identification of hexose hydrolysis products in metabolic flux analytes: A case study of levulinic acid in plant protein hydrolysate. Metabolic Engineering 9: 442-451. [http://dx.doi.org/10.1016/j.ymben.2007.07.003 Link] (Cover article)
+
Sriram G, Rahib L, Parr LS, Liao JC, Dipple KM (2010) Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells. Metabolic Engineering 12:332-340. [http://dx.doi.org/10.1016/j.ymben.2010.04.001 View at publisher] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949272 View at PMC (OPEN ACCESS)]
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Sriram G, Fulton DB, Shanks JV (2007) Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing. Phytochemistry 68: 2243-2257. [http://dx.doi.org/10.1016/j.phytochem.2007.04.009 Link]
+
Rahib L, Sriram G, Harada MK, Liao JC, Dipple KM (2009) Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency. Molecular Genetics and Metabolism 96:106-112. [http://dx.doi.org/10.1016/j.ymgme.2008.11.163 View at publisher] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702540 View at PMC (OPEN ACCESS)]
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§Sriram G, §González-Rivera O, Shanks JV (2006) Determination of biomass composition of Catharanthus roseus hairy roots for metabolic flux analysis. Biotechnology Progress 22: 1659-1663. (§Contributed equally) [http://dx.doi.org/10.1021/bp060162k Link]
+
Iyer VV, Sriram G, Fulton DB, Zhou R, Westgate ME, Shanks JV (2008) Metabolic flux maps: An effective tool for studying the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons. Plant, Cell, and Environment 31:506-517. [http://dx.doi.org/10.1111/j.1365-3040.2008.01781.x View at publisher (OPEN ACCESS)]  
-
Sriram G, Martinez JA, McCabe ERB, Liao JC, Dipple KM (2005) Single-gene disorders: What role could moonlighting enzymes play? American Journal of Human Genetics 76: 911-924. [http://dx.doi.org/10.1086/430799 Link]
+
Sriram G, Rahib L, He J-S, Campos AE, Liao JC, Dipple KM (2008) Global metabolic changes due to glycerol kinase overexpression in rat liver cells. Molecular Genetics and Metabolism 93:145-159. [http://dx.doi.org/10.1016/j.ymgme.2007.09.008 View at publisher] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702542 View at PMC (OPEN ACCESS)]
-
Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV (2004) Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiology 136: 3043-3057. [http://dx.doi.org/10.1104/pp.104.050625 Link] [http://www.f1000biology.com/article/id/1021697 Featured in Faculty of 1000 Biology]
+
Sriram G, Iyer VV, Fulton DB, Shanks JV (2007) Identification of hexose hydrolysis products in metabolic flux analytes: A case study of levulinic acid in plant protein hydrolysate. Metabolic Engineering 9: 442-451. (Cover article) [http://dx.doi.org/10.1016/j.ymben.2007.07.003 View at publisher]
 +
 
 +
Sriram G, Fulton DB, Shanks JV (2007) Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing. Phytochemistry 68: 2243-2257. [http://dx.doi.org/10.1016/j.phytochem.2007.04.009 View at publisher]
 +
 
 +
§Sriram G, §González-Rivera O, Shanks JV (2006) Determination of biomass composition of Catharanthus roseus hairy roots for metabolic flux analysis. Biotechnology Progress 22: 1659-1663. §Equally contributing authors. [http://dx.doi.org/10.1021/bp060162k View at publisher]
 +
 
 +
Sriram G, Martinez JA, McCabe ERB, Liao JC, Dipple KM (2005) Single-gene disorders: What role could moonlighting enzymes play? American Journal of Human Genetics 76: 911-924. [http://dx.doi.org/10.1086/430799 View at publisher] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1196451 View at PMC (OPEN ACCESS)]
 +
 
 +
Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV (2004) Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiology 136: 3043-3057. [http://dx.doi.org/10.1104/pp.104.050625 View at publisher (OPEN ACCESS)] [http://www.f1000biology.com/article/id/1021697 Featured in Faculty of 1000 Biology]
 +
 
 +
Sriram G, Shanks JV (2004) Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. Metabolic Engineering 6: 116-132. [http://dx.doi.org/10.1016/j.ymben.2004.02.003 View at publisher]
 +
 
 +
==Books and chapters==
 +
 
 +
Sriram G, editor (2014) Plant Metabolism: Methods and Protocols. Methods in Molecular Biology, Vol. 1083, 300 pp. Humana Press, New York, NY. ISBN: [http://www.isbnsearch.org/isbn/9781627036603 978-1-62703-660-3] [http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-660-3 View at publisher] [http://link.springer.com/book/10.1007%2F978-1-62703-661-0 View chapters at publisher]
 +
 
 +
Simons M, Misra A, Sriram G (2014) Genome-scale models of plant metabolism. In: Sriram G, editor. Plant Metabolism. Methods in Molecular Biology. Humana Press. pp. 213–230. [http://link.springer.com/protocol/10.1007/978-1-62703-661-0_13 View at publisher]
 +
 
 +
Nargund S, Sriram G (2014) Mathematical modeling of isotope labeling experiments for metabolic flux analysis. In: Sriram G, editor. Plant Metabolism. Methods in Molecular Biology. Humana Press. pp. 109–131. [http://link.springer.com/protocol/10.1007/978-1-62703-661-0_8 View at publisher]
 +
 
 +
Zheng Y, Sriram G (2014) Steady-state and instationary modeling of proteinogenic and free amino acid isotopomers for flux quantification. In: Dieuaide-Noubhani M, Alonso AP, editors. Plant Metabolic Flux Analysis. Methods in Molecular Biology. Humana Press. pp. 155–179. [http://link.springer.com/protocol/10.1007/978-1-62703-688-7_11 View at publisher]
 +
 
 +
Nargund S§, Joffe ME§, Tran D, Tugarinov V, Sriram G (2013) Nuclear magnetic resonance methods for metabolic fluxomics. In: Alper HS, editor. Systems Metabolic Engineering. Methods in Molecular Biology, 985: 335–351, Humana Press, New York, NY. §Equally contributing authors. [http://dx.doi.org/10.1007/978-1-62703-299-5_16 View at publisher]
 +
 
 +
==Editorial==
 +
 
 +
Alper HS, Cirino PC, Nevoigt E, Sriram G (2010) Applications of synthetic biology in microbial biotechnology. Journal of Biomedicine and Biotechnology (now BioMed Research International), article ID 918391, 2 pages. Guest editorial (invited but not peer-reviewed). [http://dx.doi.org/10.1155/2010/918391 View at publisher (OPEN ACCESS)]  
-
Sriram G, Shanks JV (2004) Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. Metabolic Engineering 6: 116-132. [http://dx.doi.org/10.1016/j.ymben.2004.02.003 Link]
 
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Current revision

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Articles in peer-reviewed journals

Nargund S§, Misra A§, Zhang X§, Coleman GD, Sriram G (accepted) Flux and reflux: metabolite back-mixing in plant suspension cells and its implications on isotope-assisted metabolic flux analysis. Molecular BioSystems, doi: 10.1039/C3MB70348G. (§Equal contributors listed in the order in which they joined the project.) View at publisher

Zheng Y§, Quinn AH§, Sriram G (2013) Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom Phaeodactylum tricornutum. Microbial Cell Factories 12: 109. (§Equal contributors listed in the order in which they joined the project.) View at publisher (OPEN ACCESS)

Misra A, Sriram G (2013) Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. BMC Systems Biology 7: 126. View at publisher (OPEN ACCESS) (Highly accessed)

Misra A, Conway MF, Johnnie J, Qureshi TM, Derrick AM, Agbo EC, Sriram G (2013) Metabolic analyses elucidate nontrivial gene targets for amplifying dihydroartemisinic acid production in yeast. Frontiers in Microbiology, 4: 200. View at publisher (OPEN ACCESS)

Nargund S, Sriram G (2013) Designer labels for plant metabolism: Statistical design of isotope labeling experiments for improved quantification of flux in complex plant metabolic networks. Molecular BioSystems 9: 99-112. View at publisher

Zheng Y, Sriram G (2010) Mathematical modeling: bridging the gap between concept and realization in synthetic biology. Journal of Biomedicine and Biotechnology (now BioMed Research International) article ID 541609, 16 pages. View at publisher (OPEN ACCESS)

Sriram G, Rahib L, Parr LS, Liao JC, Dipple KM (2010) Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells. Metabolic Engineering 12:332-340. View at publisher View at PMC (OPEN ACCESS)

Rahib L, Sriram G, Harada MK, Liao JC, Dipple KM (2009) Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency. Molecular Genetics and Metabolism 96:106-112. View at publisher View at PMC (OPEN ACCESS)

Iyer VV, Sriram G, Fulton DB, Zhou R, Westgate ME, Shanks JV (2008) Metabolic flux maps: An effective tool for studying the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons. Plant, Cell, and Environment 31:506-517. View at publisher (OPEN ACCESS)

Sriram G, Rahib L, He J-S, Campos AE, Liao JC, Dipple KM (2008) Global metabolic changes due to glycerol kinase overexpression in rat liver cells. Molecular Genetics and Metabolism 93:145-159. View at publisher View at PMC (OPEN ACCESS)

Sriram G, Iyer VV, Fulton DB, Shanks JV (2007) Identification of hexose hydrolysis products in metabolic flux analytes: A case study of levulinic acid in plant protein hydrolysate. Metabolic Engineering 9: 442-451. (Cover article) View at publisher

Sriram G, Fulton DB, Shanks JV (2007) Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing. Phytochemistry 68: 2243-2257. View at publisher

§Sriram G, §González-Rivera O, Shanks JV (2006) Determination of biomass composition of Catharanthus roseus hairy roots for metabolic flux analysis. Biotechnology Progress 22: 1659-1663. §Equally contributing authors. View at publisher

Sriram G, Martinez JA, McCabe ERB, Liao JC, Dipple KM (2005) Single-gene disorders: What role could moonlighting enzymes play? American Journal of Human Genetics 76: 911-924. View at publisher View at PMC (OPEN ACCESS)

Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV (2004) Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiology 136: 3043-3057. View at publisher (OPEN ACCESS) Featured in Faculty of 1000 Biology

Sriram G, Shanks JV (2004) Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. Metabolic Engineering 6: 116-132. View at publisher

Books and chapters

Sriram G, editor (2014) Plant Metabolism: Methods and Protocols. Methods in Molecular Biology, Vol. 1083, 300 pp. Humana Press, New York, NY. ISBN: 978-1-62703-660-3 View at publisher View chapters at publisher

Simons M, Misra A, Sriram G (2014) Genome-scale models of plant metabolism. In: Sriram G, editor. Plant Metabolism. Methods in Molecular Biology. Humana Press. pp. 213–230. View at publisher

Nargund S, Sriram G (2014) Mathematical modeling of isotope labeling experiments for metabolic flux analysis. In: Sriram G, editor. Plant Metabolism. Methods in Molecular Biology. Humana Press. pp. 109–131. View at publisher

Zheng Y, Sriram G (2014) Steady-state and instationary modeling of proteinogenic and free amino acid isotopomers for flux quantification. In: Dieuaide-Noubhani M, Alonso AP, editors. Plant Metabolic Flux Analysis. Methods in Molecular Biology. Humana Press. pp. 155–179. View at publisher

Nargund S§, Joffe ME§, Tran D, Tugarinov V, Sriram G (2013) Nuclear magnetic resonance methods for metabolic fluxomics. In: Alper HS, editor. Systems Metabolic Engineering. Methods in Molecular Biology, 985: 335–351, Humana Press, New York, NY. §Equally contributing authors. View at publisher

Editorial

Alper HS, Cirino PC, Nevoigt E, Sriram G (2010) Applications of synthetic biology in microbial biotechnology. Journal of Biomedicine and Biotechnology (now BioMed Research International), article ID 918391, 2 pages. Guest editorial (invited but not peer-reviewed). View at publisher (OPEN ACCESS)

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