Gregory ST, Dahlberg AE. “Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA.” RNA. Feb;15(2):215-23.(2009)

Ingleby, I., Maloney, R., Jepson, J., Horn, R. and Reenan, R. “ Regulated RNA editing and functional epistasis in Shaker potassium channels.” J. Gen. Phys. 133(1):17-27.(2009)

A. Ritz, G. Shakhnarovich, A. Salomon, B. Raphael "Discovery of phosphorylation motif mixtures in phosphoproteomics data." Bioinformatics. 25 (1) 14-21.(2009)

Paul E, Cronan R, Weston PJ, Boekelheide K, Sedivy JM, Lee SY, Wiest DL, Resnick MB, Klysik JE. “Disruption of Supv3L1 damages the skin and causes sarcopenia, loss of fat, and death.” Mamm Genome. (2009)

J. Pezza, S. Langseth, R. Yamamoto, S. Dorris, S. Ulin, A. Salomon, T. Serio "The NatA acetyltransferase couples Sup35 prion complexes to the [PSI+] phenotype." Molec. Biol. Cell. in press.(2009)

I. Lee, A. Salomon, K. Yu, L. Samavati, P. Pecina, A. Pecinova, M. Huttemann "Isolation of regulatory-competent, phosphorylated cytochrome c oxidase." Methods Enzymol. 457, in press.(2009)

Coleman, A.W. “Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide.” Molecular Phylogenet. and Evol. 50: 197-203.(2009)

Gregory ST, Carr JF, Dahlberg AE. ”A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA.” RNA. Feb;15(2):208-14. (2009)

Manley, K., O'Hara, B.A., and W.J. Atwood. “Nuclear factor of activated T-cells (NFAT) plays a role in SV40 infection.” Virology 372:48-55.(2008)

O'Hara, B.A., and W.J. Atwood. “Interferon ?1a and selective anti-5HT2a receptor antagonists inhibit infection of human glial cells by JC virus.” Virus Research 132:97-103(2008)

Dugan, A.S., Gasparovic, M.L., and W.J. Atwood. “Direct correlation between sialic acid binding and infection of cells by human polyomaviruses.” J. Virol 82:2560-2564.(2008)

Beale, S. I. "Photosynthetic pigments: perplexing persistent prevalence of ‘superfluous’ pigment production (Dispatch)." Current Biology 18, R342-R343. (2008)

Beale, S. I. "Biosynthesis of chlorophylls and hemes." In: Harris, L., Stern, D. B., and Witman, G., eds. The Chlamydomonas Sourcebook, 2nd. ed., Vol. 1, Elsevier, Dordrecht, pp. 731- 798. (2008)

Rodriguez-Correa D, Dahlberg AE. ”Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.” RNA. 2008 Nov;14(11):2314-8. Epub 2008 Sep 29.

Blakeslee, J.J., H.-W. Zhou, J.T. Heath, K.R. Skottke, J.A. Rodriguez Barrios, S.-Y. Liu and A. DeLong (2008) Specificity of RCN1-mediated protein phosphatase 2A regulation in meristem organization and stress response in roots. Plant Physiology 146:539 – 53.

Gregory ST, Dahlberg AE. “Transposition of an insertion sequence, ISTth7, in the genome of the extreme thermophile Thermus thermophilus HB8.” FEMS Microbiol Lett. 2008 Dec;289(2):187-92. Epub 2008 Oct 28.

Fairbrother W, Lipscombe D. "Repressing the neuron within." Bioessays. 2008 Jan; 30(1):1-4.(2008)

Tantin D, Gemberling M, Callister C, Fairbrother W. "High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes." Genome Research 2008 Mar 13.(2008)

Helfand, S. L., Bauer, J. H. and Wood, J. G. “Calorie Restriction in lower organisms in Molecular Biology of Aging” edited by L. Guarente, L. Partridge, and D. Wallace. Cold Spring Harbor Laboratory Press, New York.(2008)

Bauer JH, Chang C, Morris SNS, Hozier S, Andersen S, Waitzman JS, Helfand S.L. “Expression of dominant-negative Dmp53 in the adult fly brain inhibits insulin signaling.” Proc. Natl. Acad. Sci. (USA), 14; 104(33):13355-60Aug 8

Demirci H, Gregory S, Dahlberg AE, Jogl G; “Multiple site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.” Structure, 16, 1059-1066 (2008).

Demirci H, Gregory S, Dahlberg AE, Jogl G; “Crystal structure of the Thermus thermophilus 16S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine.” J. Biol. Chem. epub ahead of print (2008).

Li H and Jogl G; “Structural and Biochemical Studies of TIGAR (TP53-Induced Glycolysis and Apoptosis Regulator).” J. Biol. Chem. in press.(2008)

Hazelbaker D, Azaro MA, & Landy A “A biotin interference assay highlights two different asymmetric interaction profiles for lambda integrase arm-type binding sites in integrative versus excisive recombination “J. Biol. Chem. 283(18):12402-12414. (2008)

Warren D, Laxmikanthan G, & Landy A “A Chimeric Cre Recombinase with Regulated Directionality.” Proc .Natl. Acad. Sci. USA 47:18278-18283. (2008)

Lewis, R.A., Gagnon, J.A. and Mowry, K.L. “ PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes.” Mol. Cell. Biol. 28:678-686.(2008)

Messitt, T.J., Gagnon, J.A., Kreiling, J.A., Pratt, C.A., Yoon, Y.J. and Mowry, K.L. “Multiple kinesin motors coordinate cytoplasmic RNA transport on a subpopulation of microtubules in Xenopus oocytes.” Dev. Cell 15:426-36(2008)

Jepson, J.E. and Reenan, R. “RNA editing in regulating gene expression in the brain.” Biochim Biophys Acta. 1779:459-470.(2008)

Reenan, R. and Rogina, B. “Acquired temperature-sensitive paralysis as a biomarker of declining neuronal function in aging Drosophila.” Aging Cell. 7(2):179-186.(2008)

Ryan, M.Y., Maloney, R., Reenan, R. and R. Horn. “Characterization of five RNA editing sites in Shab potassium channels.” Channels 2:3, 202-209.(2008)

H. Yu, I. Lee, A. Salomon, K. Yu, M. Huttmann "Mammalian liver cytochrome c is tyrosine-48 phosphorylated in vivo, inhibiting mitochondrial respiration." Biochim. Biophys. Acta. 1777(7-8) 1066-71.(2008)

Liu YC, Li F, Handler J, Huang CR, Xiang Y, Neretti N, Sedivy JM, Zeller KI, Dang CV. “Global regulation of nucleotide biosynthetic genes by c-Myc.”
PLoS ONE. 2008 Jul 16;3(7):e2722.

Jeyapalan JC, Sedivy JM. “Cellular senescence and organismal aging.” Mech Ageing Dev. 2008 Jul-Aug;129(7-8):467-74.

Sedivy JM, Banumathy G, Adams PD. “Aging by epigenetics--a consequence of chromatin damage?” Exp Cell Res. 2008 Jun 10;314(9):1909-17

Rath O, Park S, Tang HH, Banfield MJ, Brady RL, Lee YC, Dignam JD, Sedivy JM, Kolch W, Yeung KC. “The RKIP (Raf-1 Kinase Inhibitor Protein) conserved pocket binds to the phosphorylated N-region of Raf-1 and inhibits the Raf-1-mediated activated phosphorylation of MEK.” Cell Signal. 2008 May;20(5):935-41

Francesconi M, Remondini D, Neretti N, Sedivy JM, Cooper LN, Verondini E, Milanesi L, Castellani G. “Reconstructing networks of pathways via significance analysis of their intersections.” BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S9.

Morrish F, Neretti N, Sedivy JM, Hockenbery DM. “The oncogene c-Myc coordinates regulation of metabolic networks to enable rapid cell cycle entry.” Cell Cycle. 2008 Apr 15;7(8):1054-66.

Klysik J, Theroux SJ, Sedivy JM, Moffit JS, Boekelheide K. “Signaling crossroads: the function of Raf kinase inhibitory protein in cancer, the central nervous system and reproduction.” Cell Signal. 2008 Jan;20(1):1-9.

Yeh, J. I., and Beale, S. I. "Calorimetric approaches to characterizing effects of additives on protein crystallization." Crystal Growth Design 7, 2134-2139.(2007)

Beale, S. I. "Biosynthesis of hemes", Chapter 3.6.3.11. In: Böck, A., Curtiss, R., III, Kaper, J. B., Neidhardt, F. C., Nyström, T., Slauch, J. M., and Squires, C. L., eds., EcoSal—Escherichia coli and Salmonella: Cellular and Molecular Biology. http://www.ecosal.org. ASM Press, Washington, D. C. (2007)

Satpute-Krishnan P., Langseth S., and Serio T.R. “Hsp104-Dependent Remodeling of Prion Complexes Mediates Protein-Only Inheritance.” PLoS Biology 5:e24 (2007)

Pezza J.A. and Serio T.R. Prion Propagation, “The Role of Protein Dynamics.” Prion 1: 36-43 (2007)

Wong, J. and Wessel, G.M. “Renovation of the egg extracellular matrix at fertilization.” Int. J. Dev. Biol. in press.(2008)

Wong, J. and Wessel, G.M. “Free-Radical Crosslinking of Specific Proteins Alters the Function of the Egg Extracellular Matrix At Fertilization.” Development 135:431-440.(2008)

Voronina, E., Lopez, M., Juliano, C., Gustafson, E., Song, J., Extavour, C., George, S., Oliveri, P., McClay, D.R., and Wessel, G.M. “ Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development.” Dev. Biol.314: 276-286.(2008)

Davis LC, Morgan AJ, Ruas M, Wong JL, Graeff RM, Poustka AJ, Lee HC, Wessel GM, Parrington J, Galione A. “Ca(2+) signaling occurs via second messenger release from intraorganelle synthesis sites.” Curr Biol. 2008 Oct 28;18(20):1612-8.

Gustafson EA, Wessel GM. “Polycomb group gene expression in the sea urchin.” Dev Dyn. 2008 Jul;237(7):1851-61.

Wong JL, Wessel GM. “FRAP analysis of secretory granule lipids and proteins in the sea urchin egg.” Methods Mol Biol. 2008;440:61-76.

Wong JL, Wessel GM. “Free-radical crosslinking of specific proteins alters the function of the egg extracellular matrix at fertilization.” Development. 2008 Feb;135(3):431-40. Epub 2007 Dec 19.

Kreiling J.A., Balantac Z.L, Crawford A., Ren Y., Toure J., Zchut S., Kochilas L., Creton R. “Suppression of the endoplasmic reticulum calcium pump during zebrafish gastrulation affects left-right asymmetry of the heart and brain.” Mech Dev 125, 396-410.(2008)

Monshupanee, T., Gregory, S.T., Douthwaite, S., Chungjatupornchai, W. and Dahlberg, A.E. “Mutations in the conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.” Journal of Bacteriology 190:7754-7761. (2008)

Haley, S.A., Zhao, T., Zou, L., Klysik, J.E., Padbury, J.F., Kochilas, L.K., “Forced Expression of the Cell Cycle Inhibitor p57Kip2 in Cardiomyocytes Attenuates Ischemia-Reperfusion Injury in the Mouse Heart.” BMC Physiology, 8:4.(2008)

DePaepe, M.E., Gundavarapu, S., Tantravahi, U., Pepperell, J.R., Haley, S.A., Luks, F.I., Mao, Q., “Fas-Ligand-Induced Apoptosis of Respiratory Epithelial Cells Causes Disruption of Postcanalicular Alveolar Development.” Am. J. Pathology, 173(1):42-56.(2008)

Coleman, A.W. and M.J.H. vanOppen. “Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in Acroporid corals.” J. Molec. Evol. 67:389-396.(2008)

Manley, K., Gee, G.V., Simkevich, C.P., Sedivy, J.M., and W.J. Atwood. “Microarray analysis of glial cells resistant to JCV infection suggests a correlation between viral infection and inflammatory cytokine gene expression.” Virology 366:394-404.(2007)

Dugan, A.S., Gasparovic, M.L., Tsomaia, N., Mierke, D.F., O'Hara, B.A., Manley, K., and W.J. Atwood. “Identification of amino acid residues in BK virus VP1 critical for viability and growth.” J. Virol. 81:11798-11808.(2007)

Demirci, H., Gregory, S., Dahlberg, A. and G. Jogl (2007) “Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA” . EMBO J. 26, 567-577.

Lizotte, D.L., J.J. Blakeslee, A. Siryaporn, J. Heath and A. DeLong. (2007)  A PP2A active site mutant impedes growth and causes misregulation of native catalytic subunit expression.  Journal of Cellular Biochemistry 103:1309 - 25.

Braun L, Fausto-Sterling A, Fullwiley D, Hammonds EM, Nelson A, Quivers W, Reverby SM, Shields AE. “Racial categories in medical practice: how useful are they?”PLoS Med. 2007 Sep;4(9):e271.

Voronina, E, Lovasco LA, Gyuris, A, Baumgartner, RA, Parlow, AF and RN Freiman “Ovarian Granulosa Cell Survival and Proliferation Requires the Gonad-Selective TFIID Subunit TAF4b.” Dev. Biol. 303:  715-726. (2007)

 Lewis, R.A. and Mowry, K.L. “RNP remodeling during RNA localization.” Differentiation 75:507-518.(2007)

 Lee, J., Page, R., Contreras, R.G., Palermino, J.M., Zhang, X.S., Doshi, O., Wood, T.K. and Peti, W. “Structure and function of the E. coli protein YMGB : a protein critical for biofilm formation and acid resistance,” J Mol Biol, 373, 11-26. (2007)

Peti, W. & Page, R. “Strategies to Maximize Heterologous Protein Expression in E. coli with Minimal Cost. “ Prot Exp Purif, 51, 1-10. (2007)

Song JL, Wessel GM. “Genes involved in the RNA interference pathway are differentially expressed during sea urchin development.” Dev Dyn. 2007 Nov;236(11):3180-90.

Kreiling J.A., Prabhat, Williams G., Creton R. “Analysis of Kupffer's vesicle in zebrafish embryos using a cave automated virtual environment.” Dev. Dyn. 236, 1963-1969.(2007)

Kreiling J.A., Creton R, Reinisch C. “Early embryonic exposure to polychlorinated biphenyls disrupts heat-shock protein 70 cognate expression in zebrafish.” J Toxicol Environ Health A. 70, 1005-1013.(2007)

Beale, S. I. "Biosynthesis of 5-aminolevulinic acid." In: Grimm, B., Porra, R., Rüdiger, W., and Scheer, H., eds., Chlorophylls and Bacteriochlorophylls: Biochemistry, Biophysics, Functions and Applications (Vo.l 25 of Advances in Photosynthesis and Respiration, Series Editor: Govindjee), Springer, Dordrecht, The Netherlands, pp. 147-158. (2006)

Ebbs, M. L. and Bender, J.  “Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. “Plant Cell 18, 1166-1176.(2006)

Swinburne, I, Meyer, C. A., Liu, X. S., Silver, P.A. and Brodsky, A.S., "Genomic Localization of RNA-binding Proteins Reveals Links Between pre-mRNA Processing and Transcription" Genome Research, Published Online June 12, 2006.

Muday, G.K., S. Brady, C. Argueso, J. Deruère, J. Kieber and A. DeLong (2006)  RCN1-regulated phosphatase activity and EIN2 modulate hypocotyl gravitropism by a mechanism that does not require ethylene signaling.  Plant Physiology 141:1617-1629.

Braun L, Fausto-Sterling A. “Science and technology studies: its relevance to medical education and the practice of medicine.” Med Health R I. 2006 Sep;89(9):316-8.

Geles, KG, Freiman, RN, Liu W-L, Zheng, S, Voronina, E and Tjian R. “Cell type-selective induction of c-jun by TAF4b directs ovarian-specific transcription networks.” PNAS 103(8): 2594-2599. (2006)

Johnson MA, and Lord, E. “Extracellular Guidance Cues and Intracellular Signaling Pathways that Direct Pollen Tube Growth. In, "The Pollen Tube: A Cellular and Molecular Perspective" Rui Malhó, editor. Plant Cell Monographs, Springer Berlin / Heidelberg pp. 223 – 242 (2006)

Laney, J.D., Mobley, E.F., and Hochstrasser, M. “The short-lived Matalpha2 transcriptional repressor is protected from degradation in vivo by interactions with its corepressors Tup1 and Ssn6.” Mol. Cell Biol 26, 371-380.(2006)

Wang, L., Rajan, H., Pitman, J.L., McKeown, M., Tsai, C.C. “Histone deacetylase-associating Atrophin proteins are nuclear receptor corepressors. “ Genes Dev. 20:525-530.(2006)

Shirangi, TR, Taylor, BJ, McKeown, M. “A double-switch system regulates male courtship behavior in male and female Drosophila melanogaster.” Nature Genetics DOI 10.1038/Ng1908.(2006)

Bangi E. and Wharton, K.A. “Dpp and Gbb exhibit different effective ranges in the establishment of the BMP activity gradient critical for Drosophila wing patterning.” Devel. Biol. 295, 178-193.(2006)

Bangi, E. and Wharton, K. “Dual function of the Drosophila Alk1/Alk1 ortholog Saxophone shapes the BMP activity gradient in the wing.” Development 133,3295-3303.(2006)

Joyner AJ, Zervas M “Genetic Inducible fate mapping in mouse: establishing genetic lineages and defining genetic neuroanatomy in the nervous system.” Dev. Dynamics 235:2376-2385.(2006)

Celenza, J. L., Quiel, J. A., Smolen, G. A., Merrikh, H., Silvestro, A. R., Normanly, J., and Bender, J.  “The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis.” Plant Physiol. 137, 253-262.(2005)

Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Szary, A. J., Shao, W., Meyer, C. A., Hestermann, E. V., Geistlinger, T. R., Fox, E. A., Silver, P. A., Brown, M. "Chromosome-wide Mapping of Estrogen Receptor Binding Reveals Long-range Combinatorial Regulation" Cell 122 33-43 (2005).

Brodsky, A. S., Meyer, C. A., Hall, G., Swinburne, I., Keenan, B. K., Liu, X., Fox, E. A., and Silver, P. A. "Genomic Mapping of RNA Polymerase II Reveals Sites of Co-Transcriptional Regulation in Human Cells" Genome Biology. 6(8):R64, (2005)

Borovjagin, A.V. and Gerbi, S.A. “An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA.” Nucleic Acids Res. 33: 4995-5005.(2005)

Gerbi, S.A. Mapping origins of DNA replication in eukaryotes. In "Methods in Molecular Biology, Cell Cycle Protocols". Humana Press, vol. 296: pp. 167-180.(2005)