Publications

[Ordered by most recent]

Garcia-Pichel, F., et al. “What’s in a name? The case of cyanobacteria.” Journal of Phycology. (2019)

Weisz, D.A. and Johnson, V.M., et al., “A novel chlorophyll protein complex in the repair cycle of photosystem II.” PNAS. (2019).

Hendry, J.I., et al., “Metabolic model guided strain design of cyanobacteria.” Current Opinion in Biotechnology. (2019).

Nagarajan, A., et al., “Proteomic Insights into Phycobilisome Degradation, a Selective and Tightly Controlled Process in the Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973.” Biomolecules. (2019)

Knoot, C.J., et al., “Engineered production of hapalindole alkaloids in the cyanobacterium Synechococcus sp. UTEX 2973.” ACS Synthetic Biology. (2019).

Wendt, K.E. and Pakrasi, H.B. “Genomics Approaches to Deciphering Natural Transformation in Cyanobacteria.” Frontiers in Microbiology. (2019).

Liu, Haijun, et al. “Phycobilisomes Harbor FNRL in Cyanobacteria.” mBio. (2019).

Stingaciu, Laura-Roxana, et al. “Influence of Chemically Disrupted Photosynthesis on Cyanobacterial Thylakoid Dynamics in Synechocystis sp. PCC 6803.” Scientific Reports. 9.1 (2019): 5711.

Liberton, M., Bandyopadhyay,  A., and Pakrasi, H.B. “Enhanced nitrogen fixation in a glgX deficient strain of Cyanothece sp. ATCC 51142, a unicellular nitrogen-fixing cyanobacterium.” Appl. Environ. Microbiol. (2019).

Knoot, C.J. and Pakrasi, H.B. “Diverse hydrocarbon biosynthetic enzymes can substitute for olefin synthase in the cyanobacterium Synechococcus sp. PCC 7002.” Scientific Reports. (2019). 

Hendry, J.I., et al. “Genome-scale fluxome of Synechococcus elongatus UTEX 2973 using transient 13C-labeling data.” Plant Physiology (2019).

Sarkar, D., et al. “A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.” PLoS Computational Biology (2019).

Ungerer, J., et al. “Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions.” PNAS (2019).

Lin, P.C. and Pakrasi, H.B. “Engineering cyanobacteria for production of terpenoids.” Planta. (2018).

Jaiswal, D., et al. “Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC11801 Isolated from India.” Scientific Reports (2018).

Ungerer, J., et al. “Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973.” PNAS (2018).

Liu, D., et al. “Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph.” mBio (2018).

Sengupta, A., Pakrasi H.B., and Wangikar, P.P. “Recent advances in synthetic biology of cyanobacteria.” Applied Microbiology and Biotechnology (2018).

Liu, D., and Pakrasi, H.B. “Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803.” Microbial Cell Factories (2018).

Gopalakrishnan, S., Pakrasi, H. B. and Maranas, C. D. (2018) Elucidation of Photoautotrophic Carbon Flux Topology in Synechocystis PCC 6803 using Genome-scale Carbon Mapping Models. Metabolic Engineering, doi: 10.1016/j.ymben.2018.03.008

Singh, A., G. Kishore, and H.B. Pakrasi. “Emerging platforms for co-utilization of one-carbon substrates by photosynthetic organisms.” Current Opinion in Biotechnology (2018).

Ungerer, Justin, et al. “Adjustments to Photosystem Stoichiometry and Electron Transfer Proteins Are Key to the Remarkably Fast Growth of the Cyanobacterium Synechococcus elongatus UTEX 2973.” mBio (2018).

Chen, H.-Y.S., A. Bandyopadhyay, and H.B. Pakrasi. “Function, Regulation and Distribution of Isia, a Membrane-Bound Chlorophyll a-Antenna Protein in Cyanobacteria.” Photosynthetica (2018).

Lin, Po-Cheng, Saha R, Zhang F, & Pakrasi HB. “Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocystis sp. PCC 6803.” Scientific Reports 7.1 (2017):17503.

Abernathy, Mary H., et al. “Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis.” Biotechnology for Biofuels 10.1 (2017): 273.

Weisz, Daniel A., Michael L. Gross, and Himadri B. Pakrasi. “Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II.” Science Advances 3.11 (2017): eaao3013.

Knoot, Cory J, et al. “Cyanobacteria: promising biocatalysts for sustainable chemical production.” JBC (2017). 

Murton, Jaclyn, et al. “Population-level coordination of pigment response in individual cyanobacterial cells under altered nitrogen levels.” Photosynthesis Research (2017): 1-10.

Liberton, Michelle, et al. “Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803.” PloS One 12.3 (2017): e0173251.

Weisz, Daniel A., et al. “Mass Spectrometry-Based Cross-Linking Study Shows That the Psb28 Protein Binds to Cytochrome B559 in Photosystem II.” Proceedings of the National Academy of Sciences (2017). 

Mueller, Thomas J., et al. “Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973.” Scientific Reports 7 (2017): 41569.

Chen, Hui-Yuan S., et al. “Reevaluating the mechanism of excitation energy regulation in iron-starved cyanobacteria.” Biochimica et Biophysica Acta (BBA)-Bioenergetics 1858.3 (2017): 249-258.

Nguyen, Amelia Y., et al. “The proteolysis adaptor, NblA, binds to the N-terminus of β-phycocyanin: implications for the mechanism of phycobilisome degradation.” Photosynthesis Research 132.1 (2017): 95-106.

Ungerer, Justin, and Himadri B. Pakrasi. “Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria.” Scientific Reports 6 (2016): 39681.

Zhu, Yuehui, Michelle Liberton, and Himadri B. Pakrasi. “A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I.” Journal of Biological Chemistry (2016): jbc-M116.

Liberton, M., Saha, R., Jacobs, J.M., Nguyen, A.Y., Gritsenko, M.A., Smith, R.D., Koppenaal, D.W. and Pakrasi, H.B. 2016 “Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium” Molecular & Cellular Proteomics 15.6 | DOI 10.1074/mcp.M115.057240

Wendt, K.E., Ungerer, J., Cobb, R.E., Zhao, H., and Pakrasi, H.B. 2016 “CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973″ Microb Cell Fact15:115 | DOI 10.1186/s12934-016-0514-7

Nagarajan, A., Pakrasi, H.P. June 2016 “Membrane-Bound Protein Complexes for Photosynthesis and Respiration in Cyanobacteria” eLS. John Wiley & Sons, Ltd:Chister. | DOI 10.1002/9780470015902.a0001670.pub2

Weisz, D.A., Gross, M.L., and Pakrasi, H.B. 2016 “The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II” Front. Plant Sci. 7:617 | DOI 10.3389/fpls2016.00617

Saha, R., Liu, D., Hoynes-O’Connor, A., Liberton, M., Yu, J., Bhattacharyya-Pakrasi, M., Balassy, A., Zhang, F., Moon, T.-S., Maranas, C.D., Pakrasi, H.B. 2016 “Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses” mBio 7(3):e00464-16 DOI 10.1128/mBio.00464-16.

Stingaciu, L.-R., O’Neill, H., Liberton, M., Urban, V.S., Pakrasi, H.B., and Ohl, M.  2016  “Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells” Scientific Reports 6:19627 | DOI 10.1038/srep19627

Gustafson, D., Hayes, M., Janssen, E., Lobell, D.B., Long, S. Nelson, G.C., Pakrasi, H.B., Raven, P., Robertson, G.P., Robertson, R. and Wuebbles, D.  2016 “Pharaoh’s Dream Revisited: An Integrated US Midwest Field Research Network for Climate Adaptation” BioScience 66:80-85 January 2016 | Vol. 66 No. 1 | DOI:10.1093/biosci/biv164

Mueller, T.J., Welsh, E.A., Pakrasi, H.B., and Maranas, C.D.  2015  “Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803” ACS Synth. Biol. | DOI: 10.1021/acssynbio.5b00202

Berla, Bertram M., Saha, Rajib, Maranas, Costas D. & Pakrasi, Himadri B. 2015 “Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress” Scientific Reports | 5:14894 | DOI: 10.1038/srep14894

Ng, Andrew H, Berla, Bertram, Pakrasi, Himadri B. 2015 “Fine-Tuning of Photoautotrophic Protein Production by Combining Promoters and Neutral Sites in the Cyanobacterium Synechocystis sp. Strain PCC 6803″ AEM 81:19.

Liu, H., Weisz, D.A., Pakrasi, H.B.  2015 “Multiple copies of the PsbQ protein in a cyanobacterial photosystem II assembly intermediate complex” Photosynth Res. | PMID:25800517 | DOI 10.1007/s11120-015-0123-z.

Yu, J., Liberton, M., Cliften, P. F., Head, R. D., Jacobs, J. M., Smith, R. D., Koppenaal, D. W., Brand, J. J. and Pakrasi, H. B. 2015 “Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2.” Scientific Rep., 5 : 8132 | DOI: 10.1038/srep08132.

Aryal, U. K., Callister, S. J., McMahon, B., McCue, L. A., Brown, J., Stöckel, J., Liberton, M., Mishra, S., Zhang, X., Nicora, C. D., Angel, T., Koppenaal, D. W., Smith, R. D., Pakrasi, H. B. and Sherman, L. A. 2014″Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece.” J. Proteome Res., 13: 3262-3276.

Wegener, K. M., Nagarajan, A. and Pakrasi, H. B. 2014 “An atypical psbA gene encodes a sentinel D1 protein to form a physiologically relevant inactive PSII complex in cyanobacteria.” J. Biol. Chem.,  jbc.M114.604124.

Nagarajan, A.; Page, L.E.; Liberton, M.; Pakrasi, H.B. “Consequences of Decreased Light Harvesting Capability on Photosystem II Function inSynechocystis sp. PCC 6803.” Life 2014, 4, 903-914.

Guo J, Nguyen AY, Dai Z, Su D, Gaffrey MJ, Moore RJ, Jacobs JM, Monroe ME, Smith RD, Koppenaal DW, Pakrasi HB, Qian WJ  “Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics” Mol Cell Proteomics 2014 Dec 13(12):3270-85 doi: 10.1074/mcp.M114.041160.

You L, Berla B, He L, Pakrasi HB and Tang YJ “13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions.” Biotechnol J, 2014 May 9(5):684-92 doi: 10.1002/biot.201300477.

Liu H, Zhang H, Weisz DA, Vidavsky I, Gross ML, Pakrasi HB “MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II” PNAS 2014 111(12): 4638-43.

Liberton M, Collins AM, Page LE, O’Dell WE, O’Neill H, Urban VS, Timlin JA and Pakrasi HB (2013) “Probing the consequences of antenna modification in cyanobacteria” Photosynth Res 118: 17-24.

Mueller TJ, Berla BM, Pakrasi HB and Maranas CD (2013) “Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow” BMC Systems Biology 7(1): 142.

Krishnakumar S, Gaudana SB, Viswanathan GA, Pakrasi HB and Wangikar PP (2013) Rhythm of carbon and nitrogen fixation in unicellular cyanobacteria under turbulent and highly aerobic conditions.Biotechnology and Bioengineering, 110: 2371-2379.

Berla BM, Saha R, Immethun CM, Moon TS, Maranas CD, Pakrasi HB (2013) “Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities” Frontiers in Microbiology 4:246 doi: 10.3389/fmicb.2013.00246

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” Frontiers in Microbiology 4:246 doi: 10.3389/fmicb.2013.00246

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. 

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. 

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].

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 Behav6(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.

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.

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.