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.

Buchko, G.W., Robinson, H., Ni, S., Pakrasi, H.B. and Kennedy, M.A. (2006) Cloning, expression, crystallization, and preliminary crystallographic analysis of a pentapeptide repeat protein (Rfr23) from the bacterium Cyanothece sp. 51142, Acta Crystallgr, 62: 1251-1254.

Buchko, G.W., Ni, S., Robinson, H., Welsh, E.A., Pakrasi, H.B. and Kennedy, M.A. (2006) Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142. Protein Science, 15: 2579-2595.

Kashino, Y., Inoue-Kashino, N., Roose, J. L., and Pakrasi, H. B. (2006) Absence of the PsbQ protein results in destabilization of the PsbV protein and decreased oxygen evolution activity in cyanobacterial photosystem II, J Biol Chem., 281:20834-41.

Koropatkin, N.M., Pakrasi, H.B., Smith, T.J. (2006). Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity, PNAS, 103(26):9820-0925

Liberton, M., Berg, H.R., et al. (2006) "Ultrastructure of the membrane systems in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803"Protoplasma 227:129-138

Bednarski, A., Elgin, S.C.R., Pakrasi, H.B. (2005). An Inquiry into Protein Structure and Genetic disease: Introducing Undergraduates to Bioinformatics in a Large Introductory Course, Cell Biology Education Vol 4 (Fall 2005): 207-220.

Inoue-Kashino, N., Kashino, Y., et al. (2005) PsbU Provides a Stable Architecture for the Oxygen-Evolving System in Cyanobacterial Photosystem II, Biochemistry, 44(36): 12214-12228.

Keren, N., Ohkawa, H., et al. (2005) Psb29, a Conserved 22-kD Protein, Functions in the Biogenesis of Photosystem II Complexes in Synechocystis and Arabidopsis, Plant Cell, 17:1768-2781.

Zhang, P., Battchikova N., et al. (2005) Isolation, subunit composition and interaction of the NDH-1 complexes from Thermosynechococcus elongatus BP-1, Biochem J., 390(Pt2):513-20.

Keren, N., Liberton, M. and Pakrasi, H. B. (2005) Photochemical competence of assembled photosystem II core complex in cyanobacterial plasma membrane. J. Biol. Chem., 280:6548-6553.

Thornton, L. E., Keren, N., Ohad, I. and Pakrasi, H. B. (2005) Physcomitrella patens and Ceratodon purpureus, mosses as model organisms in photosynthesis studies. Photosynthesis Res., 83:87-96.

Thornton, L. E., Roose, J. L., Ikeuchi, M. and Pakrasi, H. B. (2005) The Low Molecular Components: New Insights from Proteomics, Genomics, and Structural Studies. In Photosystem II: The Water/Plastoquinone Oxido-Reductase In Photosynthesisą (In Wydrzynski, T. and Satoh, K., eds.), Kluwer Academic Publ., Dordrecht, The Netherlands, In Press.

Roose, J. L. and Pakrasi, H. B. (2004) Evidence that D1 processing is required for manganese binding and extrinsic protein assembly into photosystem II. J. Biol. Chem., 279: 45417-45422.

Keren, N., Aurora, R. and Pakrasi, H. B. (2004) Critical roles of bacterioferritins in iron-storage and proliferation of cyanobacteria. Plant Physiol. 135:1666-1673.

Thornton, L. E., Ohkawa, H., Roose, J. L., Kashino, Y., Keren, N. and Pakrasi, H. B. (2004) Homologs of Plant PsbP and PsbQ Proteins are Necessary for Regulation of Photosystem II Activity in the Cyanobacterium, Synechocystis 6803. Plant Cell 16:2164-2175.

Kobayashi, M., Ishizuka, T., Katayama, M., Kanehisa, M., Bhattacharyya-Pakrasi, M, Pakrasi, H. B. and Ikeuchi, M. (2004) Response to Oxidative Stress Involves a Novel Peroxiredoxin Gene in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol., 45:290-299.

Banerjee, S., Wei, B., Bhattacharyya-Pakrasi, M., Pakrasi, H. B. and Smith, T. J. (2003) Structural determinants of metal specificity in the zinc transport protein ZnuA from Synechocystis 6803. J. Mol. Biol., 333: 1061-1069.

Chandler, L. E., Bartsevich, V. V. and Pakrasi, H. B. (2003) Regulation of manganese uptake in Synechocystis 6803 by RfrA, a member of a novel family of proteins containing a repeated five-residues domain. Biochemistry, 42: 5508-5514.

Swiatek, M., Regel, R. E., Meurer, J., Wanner, G., Pakrasi, H. B., Ohad, I. and Herrmann, R. G. (2003) Effects of selective inactivation of individual genes for low-molecular-mass subunits on the assembly of photosystem II, as revealed by chloroplast transformation: the psbEFLJ operon in Nicotiana tabacum. Mol. Genet. Genomics, 268: 699-710.

Ivleva, N. B., Sidoruk, K.V., Pakrasi, H. B. and Shestakov S.V. (2002) Investigation of the functional role of Ctp proteins in Synechocystis sp. PCC 6803. Mikrobiologiia 71: 509-513.

Huang, F., Parmryd, I., Nilsson, F., Persson, A. L., Pakrasi, H. B., Andersson, B. and Norling, B. (2002) Proteomics of Synechocystis sp. strain PCC 6803: Identification of plasma membrane proteins. Mol. Cell. Proteomics, 1: 956-966.

Keren, N., Kidd, M. J., Penner-Hahn, J. E. and Pakrasi, H. B. (2002) A light dependent mechanism for massive accumulation of manganese in the photosynthetic bacterium, Synechocystis sp. PCC 6803. Biochemistry, 41: 15085-15092.

Kashino, Y., Koike, H., Yoshio, M., Egashira, H., Ikeuchi, M., Pakrasi, H. B. and Satoh, K. (2002) Low-molecular-mass polypeptide components of a photosystem II preparation from the thermophilic cyanobacterium Thermosynechococcus vulcanus. Plant Cell Physiol., 43: 1366-1373.

Ogawa, T., Bao, D. H., Katoh, H., Shibata, M., Pakrasi, H. B. and Bhattacharyya-Pakrasi, M. (2002) A two-component signal transduction pathway regulates manganese homeostasis in Synechocystis 6803, a photosynthetic organism. J. Biol. Chem., 277: 28981-28986.

Bhattacharyya-Pakrasi, M., Pakrasi, H. B., Ogawa, T. and Aurora, R. (2002) Manganese transport and its regulation in bacteria. Biochem. Soc. Trans, 30: 768-770.

Kashino, Y., Lauber, W. M., Carroll, J. A., Wang, Q., Whitmarsh, J., Satoh, K. and Pakrasi, H. B. (2002) Proteomic analysis of a highly active photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides. Biochemistry; 41: 8004-8012.

Ohkawa, H., Sonoda, M., Hagino, N., Shibata, M., Pakrasi, H. B. and Ogawa, T. (2002) Functionally distinct NAD(P)H dehydrogenases and their membrane localization in Synechocystis sp. PCC 6803. Funct. Plant Biol., 29: 195-­200

Zak, E., Norling, B., Maitra, R., Huang, F., Andersson, B. and Pakrasi, H.B. (2001) The initial steps of biogenesis of cyanobacterial photosystems occur in plasma membranes. Proc. Natl. Acad. Sci. USA; 98: 13443-13448.

Ng, W.-O. and Pakrasi, H.B. (2001) DNA photolyase homologues are the major UV resistance factors in Synechocystis sp. PCC 6803. Mol. Gen. Genet., 264: 924-930.

Pakrasi, H.B., Ogawa, T. and Bhattacharyya-Pakrasi, M. (2001) Transport of metals: a key process in oxygenic photosynthesis. In Regulatory Aspects of Photosynthesis (Aro, E.-M. and Andersson, B.A., eds.), pp. 253-264, Kluwer Academic Publ., Dordrecht, The Netherlands.

Inagaki, N., Maitra, R., Satoh, K. and Pakrasi, H. B. (2001) Amino acid residues that are critical for in vivo catalytic activity of CtpA, the carboxyl-terminal processing protease for the D1 Protein of Photosystem II. J. Biol. Chem., 276: 30099-30105.

Regel, R. E., Ivleva, N. B., Zer, H., Meurer, J., Shestakov, S. V., Herrmann, R. G., Pakrasi, H. B. and Ohad, I. (2001) Deregulation of electron flow within Photosystem II in the absence of the PsbJ protein. J. Biol. Chem., 276: 41473-41478.

Cho, Y.S., Pakrasi, H.B. and Whitmarsh, J. (2000) Cytochrome cM from Synechocystis 6803: detection in cells, expression in Escherichia coli, purification and physical characterization. Eur. J. Biochem., 267: 1067-1074.

Zak, E. and Pakrasi, H.B. (2000) The BtpA protein stabilizes the reaction center proteins of Photosystem I in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol., 123: 215-222.

Ng, W.-O., Zentella, R., Wang, Y., Taylor, J.-S. and Pakrasi, H.B. (2000) phrA, the major photoreactivating factor in the cyanobacterium Synechocystis sp. PCC 6803 codes for a cyclobutane pyrimidine dimer specific DNA photolyase. Arch. Microbiol., 173: 412-417.

Ohkawa, H., Pakrasi, H.B. and Ogawa, T. (2000) Two types of functionally distinct NAD(P)H dehydrogenases in Synechocystis sp. strain PCC6803. J. Biol. Chem., 275: 31630 - 31634.

Ivleva, N.B., Shestakov, S.V. and Pakrasi H.B. (2000) The carboxyl-terminal extension of the precursor D1 protein of Photosystem II is required for optimal photosynthetic performance of the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol., 124: 1403-1411.