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- Liu H, Chen J, Huang RYC, Weisz D, Gross ML, Pakrasi HB (2013) "Mass spectrometry-based footprinting reveals structural dynamics of loop E of the chlorophyll-binding protein CP43 during photosystem II assembly in the cyanobacterium Synechocystis 6803" JBC doi:10.1074/jbc.M113.467613
- Landry BP, Stockel J, Pakrasi HB (2013) "Use of degradation tags to control protein levels in the cyanobacterium Synechocystis sp. PCC 6803" Appl Envinron Microbiol 79(8)2833-5.
- Stockel J, Elvitigala T, Liberton M, Pakrasi HB (2013) "Carbon availability affects diurnally controlled processes and cell morphology of Cyanothece 51142" PLoS ONE ; 8(2):e56887.
- Bandyopadhyay A, Elvitigala T, Liberton M, Pakrasi HB (2013) "Variations in the Rhythms of Respiration and Nitrogen Fixation in Members of the Unicellular Diazotrophic Cyanobacterial Genus Cyanothece" Plant Physiology Epub ahead of print, 2012DEC28.
- Musgrave WB, Yi H, Kline D, Cameron JC, Wignes J, Dey S, Pakrasi HB, Jez JM (2013) "Probing the origins of glutathione biosynthesis through biochemical analysis of glutamate-cysteine ligase and glutathione synthetase from a model photosynthetic prokaryote" Biochem J doi: 10.1042/BJ20121332.
- Memon D, Singh AK, Pakrasi HB, Wangikar PP (2013) "A global analysis of adaptive evolution of operons in cyanobacteria" Antonie van Leeuwenhoek doi:10.1007/s10482-012-9813-0.
- Liberton M, Page LE, O'Dell WB, O'Neill H, Mamontov E, Urban VS, Pakrasi HB (2013) "Organization and flexibility of cyanobacterial thylakoid membranes examined by neutron scattering" J Biol Chem doi: 10.1074/jbc.M112.416933.
- Page L, Liberton M, Pakrasi HB (2012) "Reduction of photoautotrophic productivity in the cyanobacterium Synechocystis sp. strain PCC 6803 by phycobilisome antenna truncation" Appl Environ Microbio doi: 10.1128/AEM.00499-12.
- Varman AM, Xiao Y, Pakrasi HB, Tang YJ (2012) "Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production" Appl Environ Microbiol doi: 10.1128/AEM.02827-12.
- Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, Maranas CD (2012) “Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803”, PloS ONE 7(10):e48285.
- Berla BM, Pakrasi HB (2012) "Up-regulation of plasmid-encoded genes during stationary phase in Synechocystis sp. PCC 6803, a cyanobacterium", Appl Environ Microbio, doi: 10.1128/AEM.01174-12.
- You L, Berla B, Feng X, Page L, Pakrasi H, Tang YJ (2012) "Metabolic pathway discovery and quantification via 13C-isotopomer analysis of proteinogenic amino acids", J Vis Exp. doi: 10.3791/3583.
- Aryal UK, Stockel J, Krovvidi R, Gritsenko MA, Monroe ME, Moore RJ, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM (2011) "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles", BMC Syst Biol, 5(1):194.
- Aryal UK, Stöckel J, Welsh EA, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM (2011) "Dynamic Proteome Analysis of Cyanothece sp. ATCC 51142 under Constant Light", J Proteome Res, 2011 Dec 1. [Epub ahead of print].
- Collins AM, Liberton M, Garcia OF, Jones HDT, Pakrasi HB, Timlin JA (2012) "Photosynthetic pigment localization and thylakoid membrane morphology are altered in Synechocystis 6803 phycobilisome mutants", Plant Physiol, 158: 1600-1609.
- Liu H, Huang RY, Chen J, Gross ML, Pakrasi HB (2011) "Psb27, a transiently associated protein, binds to the chlorophyll binding protein CP43 in photosystem II assembly intermediates", Proc Natl Acad Sci USA, 108(45):18536-4.
- Bandyopadhyay A, Elvitigala T, Welsh E, Stöckel J, Liberton M, Min H, Sherman LA, Pakrasi HB (2011) "Novel metabolic attributes of the genus cyanothece, comprising a group of unicellular nitrogen-fixing cyanobacteria", MBio, 2(5). doi: 10.1128/mBio.00214-11.
- McDermott JE, Oehmen CS, McCue LA, Hill E, Choi DM, Stöckel J, Liberton M, Pakrasi HB, Sherman LA (2011) "A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142", Mol Biosyst, 7(8):2407-18.
- Wegener KM, Bennewitz S, Oelmüller R, Pakrasi HB (2011) "The Psb32 Protein Aids in Repairing Photodamaged Photosystem II in the Cyanobacterium Synechocystis 6803", Mol Plant, 4(6):1052-61 .
- Liu H, Roose JL, Cameron JC, Pakrasi HB (2011) "A genetically tagged Psb27 protein allows purification of two consecutive photosystem II (PSII) assembly intermediates in Synechocystis 6803, a cyanobacterium:", J Biol Chem, 286(28):24865-71.
- Cameron JC, Pakrasi HB (2011) "Glutathione facilitates antibiotic resistance and photosystem I stability during exposure to gentamicin in cyanobacteria", Appl Environ Microbiol, 77(10):3547-50.
- Liberton M, Austin JR 2nd, Berg RH, Pakrasi HB (2011) "Insights into the complex 3-D architecture of thylakoid membranes in unicellular cyanobacterium Cyanothece sp. ATCC 51142", Plant Signal Behav, 6(4):566-9.
- Stöckel J, Jacobs JM, Elvitigala TR, Liberton M, Welsh EA, Polpitiya AD, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB (2011) "Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142" PLoS One 6(2):e16680.
- Cameron JC, Pakrasi HB, (2011) "Glutathione in Synechocystis 6803: a closer look into the physiology of a ∆gshB mutant", Plant Signal Behav, 6(1):89-92.
- Feng X, Bandyopadhyay A, Berla B, Page L, Wu B, Pakrasi HB, Tang YJ (2010) "mixotrophic and photoheterotrophic metabolism in Cyanothece sp. PCC 51142 under continuous light", Microbiology 156(8):2566-2574.
- Feng X, Page L, Rubens J, Chircus L, Colletti P, Pakrasi HB, Tang YJ (2010) "Bridging the gap between fluxomics and industrial biotechnology", J Biomed Biotechnol, 2010:460717.
- Bandyopadhyay A, Stöckel J, Min H, Sherman LA, Pakrasi HB (2010) "High rates of photobiological H2 production by a cyanobacterium under aerobic conditions", Nat Commun 2010(1):139.
- Liberton M, Austin JR 2nd, Berg RH, Pakrasi HB (2011) "Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography", Plant Physiol, 155(4):1656-66.
- Inoue-Kashino N, Kashino Y, Orii H, Satoh K, Terashima I, Pakrasi HB (2011) "S4 Protein Sll1252 Is Necessary for Energy Balancing in Photosynthetic Electron Transport in Synechocystis sp. PCC 6803" Biochemistry, 50(3):329–39.
- Wang W, Ghosh BK, Pakrasi HB (2011) "Identification and modeling of genes with diurnal oscillations from microarray time series data", IEEE/ACM Trans Comput Biol Bioinform, 8(1):108-21.
- Cameron JC, Pakrasi HB (2010) "Essential role of glutathione in acclimation to environmental and redox perturbations in the cyanobacterium Synechocystis sp. PCC 6803", Plant Physiol, 154(4):1672-85.
- Elvitigala, T.R., Polpitiya, A.D., Wang, W., Stockel, J., Khandelwal, A., Quatrano, R.S., Pakrasi, H.B., and Ghosh, B.K (2010) "High-Throughput Biological Data Analysis: A step toward understanding cellular regulation", IEEE Control Systems Magazine, 30:81-100.
- Wegener, K.M., Singh, A.K., Jacobs, J.M., Elvitigala, T.R., Welsh, E.A., Keren, N., Gritsenko, M.A., Ghosh, B.K., Camp II, D.G., Smith, R.D., and Pakrasi, H.B. (2010), Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations, Mol Cell Proteomics, 9(12):2678-89.
- Singh, A.K., Elvitigala, T.R., Cameron, J.C., Ghosh, B.K., Bhattacharyya-Pakrasi, M., and Pakrasi, H.B. (2010), Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium, BMC Systems Biology, 4:105.
- Wu, B., Zhang, B., Feng, X., Rubens, J.R., Huang, R., Hicks, L.M., Pakrasi, H.B., and Tang, Y.J. (2009) Alternate Isoleucine Synthesis Pathway in Cyanobacterial Species. Microbiology, doi:10.1099/mic.0.031799-0.
- Elvitigala T.R., Stöckel j., Ghosh B.K. and Pakrasi H.B. (2009) Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142, BMC Genomics, 10:226
- Singh, A.K., Bhattacharyya-Pakrasi, M., Elvitigala, T., Ghosh, B.K., Aurora,R. and Pakrasi, H.B. (2009) A systems level analysis of the effects of light quality on the metabolism of a cyanobacterium, Plant Physiol., 151:1596-1608.
- Elvitigala, T., Pakrasi, H.B. and Ghosh, B.K. (2009) Dynamic Network Modeling of Diurnal Genes in Cyanobacteria, In Emergent Problems in Nonlinear Systems and Control, Springer, 393: 21-41.
- Wang, W., Ghosh, B.K. and Pakrasi, H.B. (2009) Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE computer Society Digital Library. IEEE Computer Society, http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.37
- Welsh, E.A., Stöckel, J., and Pakrasi, H.B. (2009) Cycle detection in biological data sets. In Computational and Systems Biology, Methods and Applications, eds., Mazzarella, R. and Head, R., Research Signpost, Trivandrum, pp. 51-62.
- Elvitigala, T.R., Pakrasi, H.B., and Ghosh, B.K., Modeling and Simulation of Diurnal Biological Processes in Cyanobacteria, Proceedings of American Control Conference, 2009
- Elvitigala, T.R., Pakrasi, H.B., and Ghosh, B.K., Dynamical Systems Modeling Of Interactions In Cyanobacteria Diurnal Genes, Foundations of Systems Biology in Engineering, 2009.
- Elvitigala, T.R., Singh, A.K., Pakrasi, H.B., and Ghosh, B.K., Bayesian Network Approach to understand Regulation of Biological Processes in Cyanobacteria, Joint 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference, 2009.
- Xu, M., Bernat, G., Singh, A.K., Mi, H., Rogner, M., Pakrasi, H.B. and Ogawa, T. (2008) Properties of Mutants of Synechocystis sp. strain PCC 6803 Lacking Carbon Sequestration Systems. Plant Cell Physiol., 49: 1672-1677.
- Wegener, K.M., Welsh, E.A., Thornton, L.E., Jacobs, J.M., Hixson, K.K., Monroe, M.E., Camp II, D.G., Smith, R.D. and Pakrasi, H.B. (2008) High sensitivity proteomics assisted discovery of a novel operon involved in the assembly of photosystem II, a membrane protein complex, J. Biol. Chem., 283: 27829-27833.
- Nedbal, L., Trtilek, M., Cerveny, J., Komarek, O., and Pakrasi, H.B. (2008) A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high-content analysis of suspension dynamics, Biotechnology and Bioengineering, 100: 902-908.
- Buchko, G.W., Robinson, H., Pakrasi, H.B. and Kennedy, M.A. (2008) Insights into the structural variation between pentapeptide repeat proteins-Crystal structure of Rfr23 from Cyanothece 51142, J Struct Biol., 162: 184-192.
- Roose, J.L. and Pakrasi, H.B. (2008) The Psb27 Protein Facilitates Manganese Cluster Assembly in Photosystem II. J. Biol. Chem., 283: 4044-4050.
- Welsh E.A., Liberton M., Stöckel J., Loh T., Elvitigala T., Wang C., Wollam A., Fulton R.S., Clifton S.W., Jacobs J.M., Aurora R., Ghosh B.K., Sherman L.A., Smith R.D., Wilson R.K., and Pakrasi H.B. (2008) The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle, Proc Natl Acad Sci USA, 30;105(39):15094-9.
- Singh, A.K., Elvitigala T., Bhattacharyya-Pakrasi, M., Aurora R., Ghosh B.K. and Pakrasi, H.B. (2008) Integration of Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the Cyanobacterium Synechocystis, Plant Physiology 148:467-478
- Xu, M., Ogawa, T., Pakrasi, H.B. and Mi, H. (2008) Identification and Localization of the CupB Protein Involved in Constitutive CO2-uptake in the Cyanobacterium, Synechocystis sp. Strain PCC 6803, Plant Cell Physiol., 49: 994-997.
- Singh, A.K., Bhattacharyya-Pakrasi, M., and Pakrasi, H.B. (2008) Identification of an atypical membrane protein involved in the formation of protein disulfide bonds in oxygenic photosynthetic organisms, J. Biol. Chem, 10.1074
- Stöckel J., Welsh E.A., Liberton M., Kunnvakkam R., Aurora R., Pakrasi H.B. (2008) Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes, Proc Natl Acad Sci USA, 105(16):6156-61.
- Toepel, J., Welsh, E.A., Summerfield, T., Pakrasi, H.B. and Sherman, L.A. (2008) Differential transcriptional analysis of the cyanobacterium Cyanothece sp. ATCC 51142 during light-dark and continuous-light Growth, J. Bacteriology, 190: 3904-3913.
- Ghosh B.K., Pakrasi, H.B. and Elvitigala T. (2008) Controlling diurnal rhythms by light, 10th International Conference on Control, Automation, Robotics and Vision, 2008.
- Koropatkin, N., Randich, A.M., Bhattacharyya-Pakrasi, M., Pakrasi, H.B., and Smith, T.J. (2007) The structure of the iron binding protein, FUTA1, from Synechocystis 6803. J. Biol. Chem., 282: 27468-27477.
- Wei, B., Randich, A.M., Bhattacharyya-Pakrasi, M., Pakrasi, H.B. and Smith, T.J. (2007) Possible Regulatory Role for the Histidine-Rich Loop in the Zinc Transport Protein, ZnuA, Biochemistry, 46: 8734-8743.
- Koropatkin, N.M., Koppenaal, D.W., Pakrasi, H.B. and Smith, T.J. (2007) The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA, J. Biol. Chem., 282: 2606-2614.
- Liberton, M. and Pakrasi, H.B. (2007) Membrane systems in cyanobacteria, The Cyanobacteria: Molecular Biology, Genomics and Evolution (Herrero, A. and Flores, E., eds.), pp. 271-287, Horizon Scientific Press, Norwich, UK.
- Aurora, R., Hihara, Y. and Pakrasi, H.B. (2007) A Network of Genes Regulated by Light in Cyanobacteria. OMICS, 11: 166-185.
- Kashino, Y., Harayama, T., Pakrasi, H.B. and Satoh, K. (2007) Preparation of membrane proteins for analysis by two-dimensional iso-electric focusing, J Chromatogr B Analyt Technol Biomed Life Sci., 849: 282-292.
- Roose, J. L., Wegener, K. M., and Pakrasi, H. B. (2007) The extrinsic proteins of Photosystem II. Photosynth Res., 92: 369-387.
- Roose, J. L., Kashino, Y., and Pakrasi, H. B. (2007) The PsbQ protein defines cyanobacterial Photosystem II complexes with highest activity and stability. Proc Natl Acad Sci U S A., 104:2548-2553.
- Elvitigala, T., Singh, A.K., Khandelwal, A., Bhattacharya-Pakrasi, M., Aurora, R., Pakrasi, H.B., Quatrano, R., and Ghosh, B.K., Computational Analysis of the Redox stress response in organisms, International Conference on Systems Biology, 2007.
- Wang, W., Elvitigala, T., Stöckel, J., Pakrasi, H.B., and Ghosh, B.K., Identi?cation and Modeling of Co-Rhythmic Genes from Micro-array Time Series Data, International Conference on Systems Biology, 2007.
