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.
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.
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.
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.
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.