Publications

2017

Yu, F. B., Willis, L., Chau, R. M. W., Zambon, A., Horowitz, M., Bhaya, D., ... & Quake, S. R. (2017). Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing. BMC biology, 15(1), 1-14. https://doi.org/10.1186/s12915-016-0344-4

Bhaya, D. (2017). Cyanophages and Cyanobacteria in Extreme Environments (No. 503441). DOE Joint Genome Institute. https://doi.org/10.25585/1487481

Silas, S., Makarova, K. S., Shmakov, S., Páez-Espino, D., Mohr, G., Liu, Y., ... & Fire, A. Z. (2017). On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyperdiverse, enigmatic spacer repertoires. MBio, 8(4), e00897-17. https://doi.org/10.1128/mBio.00897-17

Chau, R. M. W., Bhaya, D., & Huang, K. C. (2017). Emergent phototactic responses of cyanobacteria under complex light regimes. MBio, 8(2). https://doi.org/10.1128/mBio.02330-16

Chandra, A., Joubert, L. M., & Bhaya, D. (2017). Modulation of Type IV pili phenotypic plasticity through a novel Chaperone-Usher system in Synechocystis sp. BioRxiv, 130278. https://doi.org/10.1101/130278

2016

Silas, S., Mohr, G., Sidote, D. J., Markham, L. M., Sanchez-Amat, A., Bhaya, D., Lambowitz, A. M., & Fire, A. Z. (2016). DIRECT CRISPR spacer acquisition from RNA by a natural reverse transcriptase–CAS1 fusion protein. Science, 351(6276). https://doi.org/10.1126/science.aad4234

Davison, M., Treangen, T. J., Koren, S., Pop, M., & Bhaya, D. (2016). Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers. PloS one, 11(9). https://doi.org/10.1371/journal.pone.0160574

Bhaya, D. (2016). In the limelight: Photoreceptors in cyanobacteria. Mbio, 7(3). https://doi.org/10.1128/mBio.00741-16

Grossman, A. R., & Bhaya, D. (2016). Gordon research conference on the dynamics and regulation of photosynthesis: from the origin of bio-catalysis to innovative solar conversion. Photosynthesis research, 127(3), 379-389. http://doi.org/10.1007/s11120-015-0187-9

2015

Bhaya, D., & Lindblad, P. (2015). Emerging technologies illuminate facets of photosynthesis in cyanobacteria. Photosynthesis research, 126(1), 1-2. https://doi.org/10.1007/s11120-015-0189-7

Davison, M., Hall, E., Zare, R., & Bhaya, D. (2015). Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. Photosynthesis research, 126(1), 135-146. https://doi.org/10.1007/s11120-014-0066-9

Rosen, M. J., Davison, M., Bhaya, D., & Fisher, D. S. (2015). Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science, 348(6238), 1019-1023. http://doi.org/10.1126/science.aaa4456

Chau, R. M. W., Ursell, T., Wang, S., Huang, K. C., & Bhaya, D. (2015). Maintenance of motility bias during cyanobacterial phototaxis. Biophysical journal, 108(7), 1623-1632. https://doi.org/10.1016/j.bpj.2015.01.042

Davison, M., & Bhaya, D. (2015). Creation and Analysis of a Virome: Using CRISPR Spacers. In CRISPR (pp. 307-316). Humana Press, New York, NY. http://doi.org/10.1007/978-1-4939-2687-9_20

2010 - 2014

Chau, R. M. W., Bhaya, D., & Huang, K. (2014). Motility Enhancement through Surface Modification is Sufficient for Emergent Behaviors During Phototaxis. Biophysical Journal, 106(2), 578a. https://doi.org/10.1371/journal.pcbi.1003205

Ursell, T., Chau, R. M. W., Wisen, S., Bhaya, D., & Huang, K. C. (2013). Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxis. PLoS computational biology, 9(9). https://doi.org/10.1371/journal.pcbi.1003205

Gomez-Garcia, M. R., Fazeli, F., Grote, A., Grossman, A. R., & Bhaya, D. (2013). Role of polyphosphate in thermophilic Synechococcus sp. from microbial mats. Journal of bacteriology, 195(15), 3309-3319. https://doi.org/10.1128/JB.00207-13

Brahamsha, B., & Bhaya, D. (2013). Motility in unicellular and filamentous Cyanobacteria. Cell Biology of Cyanobacteria.

Held, N. L., Childs, L. M., Davison, M., Weitz, J. S., Whitaker, R. J., & Bhaya, D. (2013). CRISPR-Cas systems to probe ecological diversity and host–viral interactions. In CRISPR-Cas systems (pp. 221-250). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34657-6_9

Galante, A., Wisen, S., Bhaya, D., & Levy, D. (2012). Modeling local interactions during the motion of cyanobacteria. Journal of theoretical biology, 309, 147-158. https://doi.org/10.1016/j.jtbi.2012.06.013

Nelson, W. C., Bhaya, D., & Heidelberg, J. F. (2012). Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population. Journal of bacteriology, 194(14), 3636-3642. https://doi.org/10.1128/JB.00333-12

Chandra, A., Bhaya, D., & Huang, K. C. (2012, January). Elucidating phototaxis mechanism to engineer coordinated communities of cyanobacteria. In MOLECULAR BIOLOGY OF THE CELL (Vol. 23). 8120 WOODMONT AVE, STE 750, BETHESDA, MD 20814-2755 USA: AMER SOC CELL BIOLOGY.

Bhaya, D. (2012). Probing functional diversity of thermophilic cyanobacteria in microbial mats. In Functional genomics and evolution of photosynthetic systems (pp. 17-46). Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1533-2_2

Nelson, W. C., Wollerman, L., Bhaya, D., & Heidelberg, J. F. (2011). Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance. Applied and environmental microbiology, 77(15), 5458-5466. https://doi.org/10.1128/AEM.05090-11

Bhaya, D. (2011). Approaches to Understanding Population Level Functional Diversity in a Microbial Community. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, 341-354.

Chueh, B. H., Li, C. W., Wu, H., Davison, M., Wei, H., Bhaya, D., & Zare, R. N. (2011). Whole gene amplification and protein separation from a few cells. Analytical biochemistry, 411(1), 64-70. https://doi.org/10.1016/j.ab.2010.12.028

Jensen, S. I., Steunou, A. S., Bhaya, D., Kühl, M., & Grossman, A. R. (2011). In situ dynamics of O 2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS. The ISME journal, 5(2), 317-328. https://doi.org/10.1038/ismej.2010.131

Galante, A., Wisen, S., Bhaya, D., & Levy, D. (2011). Stochastic models and simulations of phototaxis. Unifying Themes in Complex Systems, 8, 105-119.

Gomez-Garcia, M. R., Davison, M., Blain-Hartnung, M., Grossman, A. R., & Bhaya, D. (2011). Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats. The ISME journal, 5(1), 141-149. https://doi.org/10.1038/ismej.2010.96

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-cas systems in bacteria and archaea: Versatile small RNAS for adaptive defense and regulation. Annual Review of Genetics, 45(1), 273–297. https://doi.org/10.1146/annurev-genet-110410-132430

Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., Kühl, M., Bryant, D. A., & Ward, D. M. (2011). Community ecology of hot spring cyanobacterial mats: Predominant populations and their functional potential. The ISME Journal, 5(8), 1262–1278. https://doi.org/10.1038/ismej.2011.73

Wisén, S., Levy, D., & Bhaya, D. (2010). Dissecting Phototaxis in the Cyanobacterium Synechocystis sp. Strain PCC6803: 249. Protein Science, 19.

Hall, E., Kim, S., Davis, M., Wei, H., Bhaya, D., & Zare, R. N. (2010). Amplification & Analysis of the Synechococcus Os-B'Crispr Region from Single Cells. Biophysical Journal, 98(3), 406a.

2005 - 2009

Heidelberg, J. F., Nelson, W. C., Schoenfeld, T., & Bhaya, D. (2009). Germ warfare in a Microbial Mat Community: Crisprs provide insights into the co-evolution of host and viral genomes. PLoS ONE, 4(1). https://doi.org/10.1371/journal.pone.0004169

Steunou, A.-S., Jensen, S. I., Brecht, E., Becraft, E. D., Bateson, M. M., Kilian, O., Bhaya, D., Ward, D. M., Peters, J. W., Grossman, A. R., & Kühl, M. (2008). Regulation of NIF gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. The ISME Journal, 2(4), 364–378. https://doi.org/10.1038/ismej.2007.117

Bhaya, D., Grossman, A. R., Steunou, A.-S., Khuri, N., Cohan, F. M., Hamamura, N., Melendrez, M. C., Bateson, M. M., Ward, D. M., & Heidelberg, J. F. (2007). Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. The ISME Journal, 1(8), 703–713. https://doi.org/10.1038/ismej.2007.46

Huang, B., Wu, H., Bhaya, D., Grossman, A., Granier, S., Kobilka, B. K., & Zare, R. N. (2007). Counting low-copy number proteins in a single cell. Science, 315(5808), 81–84. https://doi.org/10.1126/science.1133992

Ward, D. M., Cohan, F. M., Bhaya, D., Heidelberg, J. F., Kühl, M., & Grossman, A. (2007). Genomics, environmental genomics and the issue of microbial species. Heredity, 100(2), 207–219. https://doi.org/10.1038/sj.hdy.6801011

Kilian, O., Steunou, A. S., Fazeli, F., Bailey, S., Bhaya, D., & Grossman, A. R. (2007). Responses of a thermophilic Synechococcus isolate from the microbial mat of Octopus Spring to light. Applied and environmental microbiology, 73(13), 4268-4278. https://doi.org/10.1128/AEM.00201-07

Steunou, A.-S., Bhaya, D., Bateson, M. M., Melendrez, M. C., Ward, D. M., Brecht, E., Peters, J. W., Kühl, M., & Grossman, A. R. (2006). In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proceedings of the National Academy of Sciences, 103(7), 2398–2403. https://doi.org/10.1073/pnas.0507513103

Kappell, A. D., Bhaya, D., & van Waasbergen, L. G. (2006). Negative control of the high light-inducible hliA gene and implications for the activities of the NblS sensor kinase in the cyanobacterium Synechococcus elongatus strain PCC 7942. Archives of microbiology, 186(5), 403-413. https://doi.org/10.1007/s00203-006-0154-0

Bhaya, D., Nakasugi, K., Fazeli, F., & Burriesci, M. S. (2006). Phototaxis and impaired motility in adenylyl cyclase and cyclase receptor protein mutants of Synechocystis sp. strain PCC 6803. Journal of bacteriology, 188(20), 7306-7310. https://doi.org/10.1128/JB.00573-06

Zare, R. N., Huang, B., Wu, H., Bhaya, D., Grossman, A. R., & Kobilka, B. K. (2006, September). PHYS 338-Quantitating low-copy-number proteins in a single cell by direct counting. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY (Vol. 232). 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC.

Labiosa, R. G., Arrigo, K. R., Tu, C. J., Bhaya, D., Bay, S., Grossman, A. R., & Shrager, J. (2006). Examination of diel changes in global transcript accumulation in synechocystis (cyanobacteria) 1. Journal of phycology, 42(3), 622-636. https://doi.org/10.1111/j.1529-8817.2006.00217.x

Steunou, A. S., Bateson, M. M., Cohan, F. M., Grossman, A. R., Khuri, N., Ward, D. M., ... & Bhaya, D. (2005, July). THERMOPHILIC, MAT-DWELLING CYANOBACTERIAL STRAINS AND CONTROL OF METABOLISM. In PHYCOLOGIA (Vol. 44, No. 4, pp. 40-40). NEW BUSINESS OFFICE, PO BOX 1897, LAWRENCE, KS 66044-8897 USA: INT PHYCOLOGICAL SOC.

2000 - 2004

Bhaya, D. (2004). Light matters: Phototaxis and signal transduction in unicellular cyanobacteria. Molecular Microbiology, 53(3), 745–754. https://doi.org/10.1111/j.1365-2958.2004.04160.x

Ng, W. O., Grossman, A. R., & Bhaya, D. (2003). Multiple light inputs control phototaxis in Synechocystis sp. strain PCC6803. Journal of Bacteriology, 185(5), 1599-1607. https://doi.org/10.1128/JB.185.5.1599-1607.2003

Bhaya, D., Dufresne, A., Vaulot, D., & Grossman, A. (2002). Analysis of the hli gene family in marine and freshwater cyanobacteria. FEMS Microbiology Letters, 215(2), 209-219. https://doi.org/10.1111/j.1574-6968.2002.tb11393.x

Bhaya, D., Takahashi, A., & Grossman, A. R. (2001). Light regulation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803. Proceedings of the National Academy of Sciences, 98(13), 7540–7545. https://doi.org/10.1073/pnas.131201098

Grossman, A. R., Bhaya, D., & He, Q. (2001). Tracking the light environment by cyanobacteria and the dynamic nature of light harvesting. Journal of Biological Chemistry, 276(15), 11449–11452. https://doi.org/10.1074/jbc.r100003200

Huala, E., Dickerman, A., Garcia-Hernandez, M., Weems, D., Reiser, L., LaFond, F., Hanley, D., Kiphart, D., Zhuang, M., Huang, W., Beavis, W., Sobral, B., Bhaya, D., Bhattacharyya, D., & Mueller, L. (2001). The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Research, 29(1), 102–105. https://doi.org/10.1093/nar/29.1.102

Bhaya, D., Takahashi, A., Shahi, P., & Grossman, A. R. (2001). Novel motility mutants of Synechocystis strain PCC 6803 generated by in vitro transposon mutagenesis. Journal of Bacteriology, 183(20), 6140-6143. https://doi.org/10.1128/JB.183.20.6140-6143.2001

Mrázek, J., Bhaya, D., Grossman, A. R., & Karlin, S. (2001). Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Research, 29(7), 1590-1601. https://doi.org/10.1093/nar/29.7.1590

Bhaya, D., Bianco, N. R., Bryant, D., & Grossman, A. (2000). Type IV pilus biogenesis and motility in the cyanobacterium synechocystis sp. PCC6803. Molecular Microbiology, 37(4), 941–951. https://doi.org/10.1046/j.1365-2958.2000.02068.x

Bhaya, D., Schwarz, R., & Grossman, A. R. (2000). Molecular responses to environmental stress. The Ecology of Cyanobacteria, 397–442. https://doi.org/10.1007/0-306-46855-7_15

Bhaya, D., Vaulot, D., Amin, P., Takahashi, A. W., & Grossman, A. R. (2000). Isolation of regulated genes of the cyanobacterium Synechocystis sp. strain PCC 6803 by differential display. Journal of bacteriology, 182(20), 5692-5699. https://doi.org/10.1128/JB.182.20.5692-5699.2000

1995-1999

Bhaya, D., Watanabe, N., Ogawa, T., & Grossman, A. R. (1999). The role of an alternative sigma factor in motility and pilus formation in the cyanobacterium synechocystis sp. strain PCC6803. Proceedings of the National Academy of Sciences, 96(6), 3188–3193. https://doi.org/10.1073/pnas.96.6.3188

Grossman, A. R., Schwarz, R., Bhaya, D., & Dolganov, N. (1998). Phycobilisome degradation and responses of cyanobacteria to nutrient limitation and high light. In Photosynthesis: Mechanisms and effects (pp. 2853-2858). Springer, Dordrecht. https://doi.org/10.1007/978-94-011-3953-3_669

Ward, D., Cohan, F., Bhaya, D., Heidelberg, J., & Grossman, A. (1998). Short Review.

Bhaya, D. (1996). Molecular Responses of Cyanobacteria in Macronutrient Limitation. Journal of scientific & industrial research, 55(8-9), 630-637.

Dolganov, N. A., Bhaya, D., & Grossman, A. R. (1995). Cyanobacterial protein with similarity to the chlorophyll a/b binding proteins of higher plants: Evolution and regulation. Proceedings of the National Academy of Sciences, 92(2), 636–640. https://doi.org/10.1073/pnas.92.2.636

Grossman, A. R., Bhaya, D., Apt, K. E., & Kehoe, D. M. (1995). Light-harvesting complexes in oxygenic photosynthesis: Diversity, control, and evolution. Annual Review of Genetics, 29(1), 231–288. https://doi.org/10.1146/annurev.ge.29.120195.001311

1984 - 1994

Srivastava, M., Bhaya, D., & Bose, S. (1994). Changes in the antenna size of Photosystem I and Photosystem II in Synechococcus sp. strain PCC 7942 grown in the presence of SANDOZ 9785—a Photosystem II inhibitor. Photosynthesis research, 41(2), 303-313. https://doi.org/10.1007/BF00019408

Apt, K. E., Bhaya, D., & Grossman, A. R. (1994). Characterization of genes encoding the light-harvesting proteins in diatoms: biogenesis of the fucoxanthin chlorophyll a/c protein complex. Journal of Applied Phycology, 6(2), 225-230. https://doi.org/10.1007/BF02186075

Bhaya, D., & Grossman, A. (1991). Targeting proteins to diatom plastids involves transport through an endoplasmic reticulum. Molecular and General Genetics MGG, 229(3), 400–404. https://doi.org/10.1007/bf00267462

Ray, J. M., Bhaya, D., Block, M. A., & Grossman, A. R. (1991). Isolation, transcription, and inactivation of the gene for an atypical alkaline phosphatase of Synechococcus sp. strain PCC 7942. Journal of Bacteriology, 173(14), 4297–4309. https://doi.org/10.1128/jb.173.14.4297-4309.1991

Bhaya, D., & Castelfranco, P. A. (1986). Synthesis of a Putative c-Type Cytochrome by Intact, Isolated Pea Chloroplast. Plant physiology, 81(4), 960-964. https://doi.org/10.1104/pp.81.4.960

Bhaya, D., & Castelfranco, P. A. (1985). Chlorophyll biosynthesis and assembly into chlorophyll-protein complexes in isolated developing chloroplasts. Proceedings of the National Academy of Sciences, 82(16), 5370-5374. https://doi.org/10.1073/pnas.82.16.5370

Bhaya, D., & Jagendorf, A. T. (1985). Synthesis of the α and β subunits of coupling factor 1 by polysomes from pea chloroplasts. Archives of biochemistry and biophysics, 237(1), 217-223. https://doi.org/10.1016/0003-9861(85)90272-3

Bhaya, D., & Jagendorf, A. T. (1984). Synthesis of subunit III of CF0 by thylakoid-bound polysomes from pea chloroplasts. Plant molecular biology, 3(5), 277-280. https://doi.org/10.1007/BF00017781

Bhaya, D., & Jagendorf, A. T. (1984). Optimal conditions for translation by thylakoid-bound polysomes from pea chloroplasts. Plant physiology, 75(3), 832-838. https://doi.org/10.1104/pp.75.3.832

Bhaya, D. (1984). THE FUNCTIONAL ROLE OF THYLAKOID-BOUND RIBOSOMES.