About Us

2005 Faculty Publications

Wang, X., A. K. Dubey, K. Suzuki, C. S. Baker, P. Babitzke, and Tony Romeo. CsrA post-transcriptionally represses pgaABCD, responsible for the synthesis of a biofilm polysaccharide adhesion of Escherichia coli. Mol. Microbiol. 56:1648-1663.
 
Gollnick, P., P. Babitzke, A. Antson, and C. Yanofsky. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Ann. Rev. Genet. 39:47-68.
 
Dubey, A. K., C. S. Baker, T. Romeo, and P. Babitzke. RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA 11:1579-1587.
 
Bollinger, J. M. Jr., J. C. Price, L. M. Hoffart, E. W. Barr, and C. Krebs. Mechanism of taurine: a-ketoglutarate dioxygenase (TauD) from Escherichia coli. Eur. J. Inorg. Chem. 21:4245-4254.
 
Sommerhalter, M., L. Saleh, J. M. Bollinger, Jr., and A. C. Rosenzweig. Structure of Escherichia coli ribonucleotide reductase R2 in space group P6(1)22. Acta Cryst. D61:1649-1654.
 
Price, J. C., E. W. Barr, L. M. Hoffart, C. Krebs, and J. M. Bollinger, Jr. Kinetic dissection of the catalytic mechanism of taurine: a-ketoglutarate dioxygenase (TauD) from Escherichia coli. Biochemistry 44:8138-8147.
 
Krebs, C., J. C. Price, J. Baldwin, L. Saleh, M. T. Green, and J. M. Bollinger, Jr. Rapid freeze-quench57Fe-Mössbauer spectroscopy: Monitoring changes of an iron-containing active site during a biochemical reaction. Inorg. Chem. 44:742-757.
 
Shen, G., R. Balasubramanian, T. Wang, B. Tirupati, J. M. Bollinger, Jr., J. H. Golbeck, and D. A. Bryant. Functional genomics of genes for biogenesis of Fe-S proteins in cyanobacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 882-884, Allen Press, Lawrence, KA.
 
Iwig, D. F., A. Uchida, J. A. Stromberg, and S. J. Booker. The activity of Escherichia coli cyclopropane fatty acid synthase depends on the presence of bicarbonate. J. Am. Chem. Soc. 127:11612-11623.
 
Cicchillo, R. M., L. Tu, J. A. Stromberg, L. M. Hoffart, C. Krebs, and S. J. Booker. Escherichia coli quinolinate synthetase does indeed harbor a [4Fe-4S] cluster. J. Am. Chem. Soc. 127:7310-7311.
 
Cicchillo, R. M. and S. J. Booker. Mechanistic investigations of lipoic acid biosynthesis in Escherichia coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl synthase polypeptide. J. Am. Chem. Soc. 127:2860-2861.
 
Nesbitt, N. M., C. Baleanu-Gogonea, R. M. Cicchillo, K. Goodson, D. F. Iwig, J. A. Broadwater, J. A. Haas, B. G. Fox, and S. J. Booker. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Exp. Purif. 39:269-282.
 
Booker, S. J. Enzymatic free radical reactions. In: Nature Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chischester. http://www.els.net/ [doi:10.1038/npg.els.0000620].
 
Shipkowski, S. and J. Brenchley. Characterization of an unusual cold-active ß-glucosidase belonging to family 3 of the glycoside hydrolases from the psychrophilic isolate Paenibacillus sp. strain C7. Appl. Environ. Microbiol. 71:4225-4232.
 
Miteva, V. and J. Brenchley. Detection and isolation of ultrasmall microorganisms from a 120,000 year old Greenland glacier ice core. Appl. Environ. Microbiol. 71:7806-7818.
 
Biddle, J. F., C. H. House, and J. E. Brenchley. Enrichment and cultivation of microorganisms from sediment from the slope of the Peru Trench (ODP Site 1230). In: Proc. ODP, Sci. Results, 201 (B. B. Jørgensen, S. L. D'Hondt, and D. J. Miller, eds.), http://www-odp.tamu.edu/ publications/201_SR/107/107.htm.
 
Zambelli, B., M. Stola, K. De Vriendt, B. Samyn, B. Devreese, J. Van Beeumen, P. Turano, A. Dikiy, D. A. Bryant, and S. Ciurli. UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. J. Biol. Chem. 280:4684-4695.
                 
Maeda, H., Y. Sakuragi, D. A. Bryant, and D. DellaPenna. Tocopherols are essential in protecting Synechocystis sp. strain PCC 6803 from lipid peroxidation. Plant Physiol. 138:1422-1435.
 
Sakuragi, Y., B. Zybailov, G. Shen, D. A. Bryant, J. H. Golbeck, B. A. Diner, I. Karygina, Y. Pushkar, and D. Stehlik. Recruitment of a foreign quinone into the A1 site of Photosystem I. Characterization of a menB rubA double mutant in Synechococcus sp. PCC 7002 devoid of FX, FA and FB and containing plastoquinone or exchanged 9,10-anthraquinone. J. Biol. Chem. 280: 12371-12381.
                 
Frigaard, N.-U., H. Li, P. Martinsson, S. K. Das, H. A. Frank, T. J. Aartsma, and D. A. Bryant. Isolation and characterization of carotenosomes from a bacteriochlorophyll c-less mutant of Chlorobium tepidum. Photosynthesis Res. 86:101-111.
 
Shively, J. B., G. C. Cannon, D. A. Bryant, S. DasSarma, D. Bazylinski, J. Preiss, A. Steinbüchel, and R. Docampo. Bacterial Inclusions. In: Encyclopedia of Life Sciences, Nature Publishing Group, Macmillan Reference Ltd., London, United Kingdom. http://www.els.net/
 
Mimuro, M., T. Tsuchiya, Y. Itoh, H. Inoue, T. Gotoh, Y. Sakuragi, H. Miyashita, T. Yamashita, D. A. Bryant, and M. Kobayashi. The secondary electron acceptor of photosystem I in Gloeobacter violaceus PCC 7421 is menaquinone-4. FEBS Lett. 279:3493-3496.
 
Maresca, J. A., N.-U. Frigaard, and D. A. Bryant. Identification of a novel class of lycopene cyclases in photosynthetic bacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 884-886, Allen Press, Lawrence, KA.

Gomez Maqueo Chew, A., N.-U. Frigaard, and D. A. Bryant. Characterization of BchV, a C-31 hydratase specific for hypermethylated bacteriochlorophyll c in Chlorobium tepidum. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 875-877, Allen Press, Lawrence, KA.

Li, H., N.-U. Frigaard, and D. A. Bryant. Locations and interactions of chlorosome proteins on the chlorosome envelope in Chlorobium tepidum: Insights from cross-linking experiments. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 116-119, Allen Press, Lawrence, KA.

Shen, G., R. Balasubramanian, T. Wang, B. Tirupati, J. M. Bollinger, J. H. Golbeck, and D. A. Bryant. Functional genomics of genes for biogenesis of Fe-S proteins in cyanobacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 882-884, Allen Press, Lawrence, KA.

Balasubramanian, R., G. Shen, J. H. Golbeck, and D. A. Bryant. SufR is a [4Fe-4S] protein that functions as a negative transcriptional regulator of the suf regulon in cyanobacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 66-68, Allen Press, Lawrence, KA.

Stehlik, D., J. Pushkar, I. Karyagina, S. Brown, D. Bryant, and J. Golbeck. Control of function by protein-cofactor interaction in the electron transfer reactions of photosystem I. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 25-27, Allen Press, Lawrence, KA.

Bryant, D. A., N.-U. Frigaard, J. A. Maresca, A.Gomez Maqueo Chew, and T. Li. Chlorophyll and carotenoid biosynthesis in green sulfur bacteria: a genomic perspective. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 866-869, Allen Press, Lawrence, KA.
 
Tackett, A. J., Y. Chen, C. E. Cameron, and K. D. Raney. Multiple full-length NS3 molecules are required for optimal unwinding of oligonucleotide DNA in vitro. J. Biol. Chem. 280:10797-10806.
 
Castro, C., J. J. Arnold, and C. E. Cameron. Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Res. 107:141-149.
 
Belliot, G., S. V. Sosnovtsev, K.-O. Chang, V. Babu, U. Uche, J. Arnold, C. E. Cameron, and K. Green. The norovirus proteinase-polymerase and polymerase are both active forms of the RNA-dependent RNA polymerase. J. Virol. 79:2393-2403.
 
Franco, D., H. B. Pathak, C. E. Cameron, B. Rombaut, E. Wimmer, and A. V. Paul. Stimulation of poliovirus synthesis in a HeLa cell-free in vitro translation-RNA replication system by viral protein 3CDpro. J. Virol. 79:6358-6367.
 
Arnold, J. J., M. Vignuzzi, J. Stone, R. Andino, and C. E. Cameron. Remote-site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase. J. Biol. Chem. 280:25706-25716.
 
Huang, L., J. Hwang, S. D. Sharma, M. R. Hargittai, Y. Chen, S. Reynolds, J. J. Arnold, K. D. Raney, and C. E. Cameron. Hepatitis C virus non-structural protein 5A (NS5A) is a RNA-binding protein. J. Biol. Chem. 280:36417-36428.
 
Franco, D., H. B. Pathak, C. E. Cameron, B. Rombaut, E. Wimmer, and A. V. Paul. Stimulation of poliovirus RNA synthesis and virus maturation in a HeLa cell-free in vitro translation-RNA replication system by viral protein 3CDpro. Virol. J. 2:86.
 
Graci, J. D. and C. E. Cameron. Lethal mutagenesis: Exploiting error-prone replication of riboviruses for antiviral therapy. In: Antiviral Drug Discovery for Emerging Diseases and Bioterrorism Threats. (P. F. Torrence, ed.), pp. 203-220, John Wiley & Sons, Hoboken, NJ.
 
Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. The proteome of Methanosarcina acetivorans. Part I, an expanded view of the biology of the cell. J. Proteome Res. 4:112-128.
 
Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. The proteome of Methanosarcina acetivorans. Part II, comparison of protein levels in acetate- and methanol-grown cells. J. Proteome Res. 4:129-136.
 
Gorrell, A., S. H. Lawrence, and J. G. Ferry. Structural and kinetic analyses of arginine residues in the active-site of the acetate kinase from Methanosarcina thermophila. J. Biol. Chem. 80:10731-10742.
 
Ingram-Smith, C., A. Gorrell, S. H. Lawrence, P. Iyer, K. Smith, and J. G. Ferry. Identification of the acetate binding site in the Methanosarcina thermophila acetate kinase. J. Bacteriol. 187:2386-2394.
 
Moran, J. J., C. H. House, K. H. Freeman, and J. G. Ferry. Trace methane oxidation studied in several Euryarchaeota under diverse conditions. Archaea 1:303-309.
 
Andrade, S. L. A, F. Cruz, C. L. Drennan, V. Ramakrishnan, D. C. Rees, J. G. Ferry, and O. Einsle. Structures of the iron-sulfur flavoproteins from Methanosarcina thermophila and Archaeoglobus fulgidus. J. Bacteriol. 187:3848-3854.
 
Rasche, M. E. and J. G. Ferry. Molecular biology of methanogens and the archaebacteria. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine. (R. A. Meyers, ed.), pp. 237-261, Wiley-VCH Verlag GmbH & Co., Weinheim.
 
Iyer, P. and J. G. Ferry. Acetate kinase from Methanosarcina thermophila, a key enzyme for methanogenesis In: Microbial Enzymes and Biotransformations. (J. L. Barredo, ed.), pp. 239-246, Humana Press Inc., Totowa, NJ.
 
Gay, C. V. The Osteoclast. In: Bone Tissue Engineering. (J. O. Hollinger, T. A. Einhorn, B. A. Doll, and C. Sfeir, eds.), pp. 55-87, CRC Press, Boca Raton, FL.
 
Zhang, Z., J. Fu, and D. S. Gilmour. CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3’ end processing factor, Pcf11. Genes & Dev. 19:1572-1580.
 
Wang, Y. V., H. Tang, and D. S. Gilmour. Identification in vivo of different rate-limiting steps associated with transcriptional activators in the presence and absence of a GAGA element. Mol. Cell. Biol. 25:3543–3552.
 
Wu, C-H., C. Lee, R. Fan, M. J. Smith, Y. Yamaguchi, H. Handa, and D. S. Gilmour. Molecular characterization of Drosophila NELF. Nucl. Acids Res. 33:1269–1279.
 
Dashdorj, N., W. Xu, R. O. Cohen, J. H. Golbeck, and S. Savikhin. Asymmetric electron transfer in cyanobacterial Photosystem I: Charge separation and secondary electron transfer dynamics of mutations near the primary electron acceptor A0. Biophys. J. 88:1238-1249.
 
Sakuragi, Y., B. Zybailov, G. Shen, D. A. Bryant, J. H. Golbeck, B. A. Diner, I. Karygina, Y. Pushkar, and D. Stehlik. Recruitment of a foreign quinone into the A1 site of Photosystem I. Characterization of a menB rubA double mutant in Synechococcus sp. PCC 7002 devoid of FX, FA and FB and containing plastoquinone or exchanged 9,10-anthraquinone. J. Biol. Chem. 280:12371-12381.
 
Bautista, J. A., F. Rappaport, M. Guergova-Kuras, R. Cohen, J. H. Golbeck, J. Wang, D. Béal, and B. Diner. Biochemical and biophysical characterization of photosystem I from phytoene desaturase and zeta-carotene desaturase deletion mutants of Synechocystis sp. PCC 6803: Evidence for PsaA- and PsaB-side electron transport in cyanobacteria. J. Biol. Chem. 280:20030-20041.
 
Heinnickel, M., G. Shen, R. Agalarov, and J. H. Golbeck. Resolution and reconstitution of a bound Fe/S protein from the photosynthetic reaction center of Heliobacterium modesticaldum. Biochemistry 44:9950-9960.
 
Shen, G., R. Balasubramanian, T. Wang, B. Tirupati, J. M. Bollinger, J. H. Golbeck, and D. A. Bryant. Functional genomics of genes for biogenesis of Fe-S proteins in cyanobacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 882-884, Allen Press, Lawrence, KA.

Balasubramanian, R., G. Shen, J. H. Golbeck, and D. A. Bryant. SufR is a [4Fe-4S] protein that functions as a negative transcriptional regulator of the suf regulon in cyanobacteria. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 66-68, Allen Press, Lawrence, KA.

Stehlik, D., J. Pushkar, I. Karyagina, S. Brown, D. Bryant, and J. Golbeck. Control of function by protein-cofactor interaction in the electron transfer reactions of photosystem I. In: Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the XIIIth International Congress on Photosynthesis, Montreal. (A. van der Est and D. Bruce, eds.), pp. 25-27, Allen Press, Lawrence, KA.
 
Elnitski, L., B. Giardine, P. Shah, Y. Zhang, C. Riemer, M. Weirauch, R. Burhans, W. Miller, and R. C. Hardison. Improvements to GALA and dbERGEII: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res. 33:D466-470.
 
Ovcharenko, I., G. G. Loots, M. A. Nobrega, R. C. Hardison, W. Miller, and L. Stubbs. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15:137-145.
 
Ovcharenko, I., G. G. Loots, B. M. Giardine, M. Hou, J. Ma, R. C. Hardison, L. Stubbs, and W. Miller. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15:184-194.
 
King, D. C., J. Taylor, L. Elnitski, F. Chiaromonte, W. Miller, and R. C. Hardison. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 15:1051-1060.
 
Giardine, B., C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, W. Miller, W. J. Kent, and A. Nekrutenko. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15:1451-1455.
 
Tsukamoto, T., T. Ando, H. Watanabe, E. Marchesi, and T-h. Kao. Duplication of the S-locus F-box gene is associated with breakdown of pollen function in an S-haplotype identified in a natural population of self-incompatible Petunia axillaris. Plant Mol. Biol. 57:141-153.
 
Hong, S.-J., Q.-A. Tran, and K. C. Keiler. Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB. Mol. Microbiol. 57:565-575.
 
Turpin, E., K. Luke, J. Jones, T. Tumpey, K. Konan, and S. Schultz-Cherry. Influenza virus infection increases p53 activity: role of p53 in cell death and viral replication. J. Virol. 79:8802-8811.
 
Torres-Larios, A., K. K. Swinger, A. S. Krasilnikov, T. Pan, and A. Mondragon. Crystal structure of the RNA component of bacterial Ribonuclease P. Nature 437:584-587.
 
Bollinger, J. M. Jr., J. C. Price, L. M. Hoffart, E. W. Barr, and C. Krebs. Mechanism of taurine: a-ketoglutarate dioxygenase (TauD) from Escherichia coli. Eur. J. Inorg. Chem. 21:4245-4254.
 
Smith, A. D., G. N. L. Jameson, P. C. Dos Santos, J. N. Agar, S. Naik, C. Krebs, J. Frazzon, D. R. Dean, B. H. Huynh, and M. K. Johnson. NifS-mediated assembly of [4Fe-4S] clusters in the N- and C-terminal domains of the NifU scaffold protein.  Biochemistry 44:12955-12969.
 
Price, J. C., E. W. Barr, L. M. Hoffart, C. Krebs, and J. M. Bollinger, Jr. Kinetic dissection of the catalytic mechanism of taurine: a-ketoglutarate dioxygenase (TauD) from Escherichia coli. Biochemistry 44:8138-8147.
 
Cicchillo, R. M., L. Tu, J. A. Stromberg, L. M. Hoffart, C. Krebs, and S. J. Booker.  Escherichia coli quinolinate synthetase does indeed harbor a [4Fe-4S] cluster. J. Amer. Chem. Soc. 127:7310-7311.
 
Krebs, C., J. C. Price, J. Baldwin, L. Saleh, M. T. Green, and J. M. Bollinger, Jr. Rapid freeze-quench 57Fe-Mössbauer spectroscopy: Monitoring changes of an iron-containing active site during a biochemical reaction. Inorg. Chem. 44:742-757.
 
Lai, Z.-C., X. Wei, T. Shimizu, E. Ramos, M. Rohrbaugh, N. Nikolaidis, L.-L. Ho, and Y. Li. Control of cell proliferation and apoptosis by Mob as tumor suppressor, Mats. Cell 120:675-685.
 
Faux, N. G., S. P. Bottomley, A. M. Lesk, J. A. Irving, J. R. Morrison, M. Garcia de la Banda, and J. C. Whisstock. Functional insights from the distribution and role of simple polypeptide repeat-containing proteins. Genome Res. 25:537-555.
 
Fulton, K. F., A. M. Buckle, L. D. Cabrita, J. A. Irving, R. E. Butcher, I. Smith, S. Reeve, A. M. Lesk, S. P. Bottomley, J. Rossjohn, and J. C. Whisstock. The high resolution crystal structure of a native thermostable serpin reveals the complex mechanism underpinning the stressed to relaxed transition. J. Biol. Chem. 280:8435-8442.
 
Demirel, M. C. and A. M. Lesk. Molecular forces in antibody maturation. Phys. Rev. Lett. 95:208106.
 
Lecomte, J. T. J., D. A. Vuletich, and A. M. Lesk. Structural divergence and distant relationships in proteins: evolution of the globins. Curr. Opin. Struct. Biol. 15:290-301.
 
Lesk, A. M. Complexity in biological structures and systems. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. (L. B. Jorde, P. F. R. Little, M. J. Dunn, and S. Subramanian, eds.), vol. 7, pp. 3298-3321, John Wiley & Sons, Ltd., Chichester.
 
Lesk, A. M. Introduction to Bioinformatics, 2nd Edition. Oxford University Press.
 
Alldred, M. J., J. Mulder-Rosi, S. E. Lingenfelter, G. Chen, and B. Lüscher. Distinct gamma2 subunit domains mediate clustering and synaptic function of postsynaptic GABAA receptors and gephyrin. J. Neurosci. 25:594-603.
 
Hutnick, N. A., N. I. Williams, W. J. Kraemer, E. Orsega-Smith, R. H. Dixon, A. D. Bleznak, and A. M. Mastro. Exercise and lymphocyte activation following chemotherapy for breast cancer. Med. Sci. Sports Exerc. 37:1827-1835.
 
Mercer, R. M. and A. M. Mastro. Cytokines secreted by bone-metastatic breast cancer cells alter the expression pattern of f-actin and reduce focal adhesion plaques in osteoblasts through PI 3K. Exp. Cell Res. 310:270-281.
 
Molls, R. R., N. Ahluwalia, A. M. Mastro, H. Smiciklas-Wright, and G. C. Handte. Nutritional status predicts primary subclasses of T cells and lymphocyte proliferation response in healthy older women. J. Nutr. 135:2644-2650.
 
Mastro, A. M. and R. H. Bonneau. Exercise and Immunity. In: The Endocrine System in Sports and Exercise (IOC Encyclopedia). (W. J. Kraemer and A. D. Rogol, eds.), pp. 368-390, Blackwell Publishing, Oxford, UK.
 
Coelho, D. J., D. J. Sims, P. J. Ruegg, I. Minn, A. R. Muench, and P. J. Mitchell. Cell type-specific and sexually dimorphic expression of transcription factor AP-2 in the adult mouse brain. Neuroscience 134:907-919.
 
Chlenov, M., S. Masuda, K. S. Murakami, V. Nikiforov, S. A. Darst, and A. Mustaev. Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta’ subunit. J. Mol. Biol. 353:138-154.
 
Nekrutenko, A., S. Wadhawan, P. Goetting-Minesky, and K. Makova. Oscillating evolution of a mammalian gene with overlapping reading frames: an XL-alpha-S/ALEX relay. PloS Genet. 1(2):e18.
 
Giardine, B., C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, W. Miller, J. Kent, and A. Nekrutenko. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15:1451-1455.
 
Nixon, B. T., H. P. Yennawar, M. Doucleff, J. G. Pelton, D. E. Wemmer, S. Krueger, and E. Kondrashkina. SAS solution structures of the Apo and Mg(2+)/BeF(3)(-)-bound receiver domain and DctD from Sinorhizobium meliloti. Biochemistry 44:13962-13969.
 
Doucleff, M., B. Chen, A. Maris, D. E. Wemmer, E. Kondrashkina, and B. T. Nixon. Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria. J. Mol. Biol. 353:242-255.
 
Ghosh, J. and K. Postle. Disulfide trapping of an in vivo energy-dependent conformation of Escherichia coli TonB protein. Mol. Microbiol. 55:276-288.
 
Zhang, A. and J. C. Reese. Molecular genetic analysis of the Yeast Repressor Rfx1/Crt1 reveals a novel two-step regulatory mechanism. Mol. Cell. Biol. 25:7399-7411.
 
Zhang, A., B. Li, and J. C. Reese. Isolation of yeast nuclei and micrococcal nuclease mapping of nucleosome positioning. Methods Mol. Biol. 313:245-256.
 
Ercan, S., J. C. Reese, J. L. Workman, and R. T. Simpson. Yeast recombination enhancer is stimulated by transcription activation. Mol. Cell. Biol. 25:7976-7987.
 
Santy, L. C., K. S. Ravichandran, and J. E. Casanova. The DOCK180/Elmo complex couples ARNO-mediated Arf6 activation to the downstream activation of Rac1. Curr. Biol. 15:1749-1754.
 
Schuster, S. C. and G. Gottschalk. Microbial genomics in its second decade. Curr. Opin. Microbiol. 8:561-563.
 
Thieme, F., R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Büttner, C. Caldana, L. Gaigalat, A.
Goesmann, S. Kay, O. Kirchner, B. Linke, A. McHardy, F. Meyer, G. Mittenhuber, D. Nies, U.
Niesbach-Klösgen, T. Patschkowski, C. Rückert, O. Rupp, S. Schneiker, C. Lanz, S. C.
Schuster, E. Vorhölter, A. Pühler, U. Bonas, D. Bartels, and O. Kaiser. Novel insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J. Bacteriol. 187:7254-7266.
 
Schuster, S. C. and S. Rendulic. Mikrobielle Jäger und Parasiten - Wie räuberische Bakterien Bakterien fressen. Naturw. Rdsch. 58:469-474.
 
Treusch, A. H., S. Leininger, A. Kletzin, S. C. Schuster, H.-P. Klenk, and C. Schleper. Role of mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 7:1985-1995.
 
Bartels, D., S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, O. Kaiser, A. Pühler, F. Pfeiffer, G.
Raddatz, J. Stoye, F. Meyer, and S. C. Schuster. BACCardI – A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21:853-859.
 
Henz, S. R., A. F. Auch, D. H. Huson, K. Nieselt-Struwe, and S. C. Schuster. Whole genome-based prokaryotic phylogeny. Bioinformatics 21:2329-2335.
 
Lichty, J. J., J. L. Malecki, H. D. Agnew, D. J. Michelson-Horowitz, and S. Tan. Comparison of affinity tags for protein purification. Protein Expr. Purif. 41:98-105.
 
Selleck, W., I. Fortin, D. Sermwittayawong, J. Cote, and S. Tan. The Saccharomyces cerevisiae Piccolo NuA4 histone acetyltransferase complex requires the enhancer of Polycomb A domain and chromodomain to acetylate nucleosomes. Mol. Cell. Biol. 25:5535-5542.
 
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