RNA World Informatics Phylogeny Database

RECENT PUBLICATIONS

PEER REVIEW PAPERS

    View the list of publications from PubMed at NCBI.

Añez ML, Putonti, C; Fox GE; Fofanov Y; Willson RC. “Exhaustive computational  identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers" J Biotechnol. 133: 267-76 (2008).  Sep 16,2007

Jackson GW, McNichols RM, Fox GE, & Willson RC. “Universal Bacterial Identification by Mass Spectrometry of Base-Specific 16S Ribosomal RNA Fragments,” Intn. J. Mass Spectrom. 261: 218-226 (2007).

Viswanath L, Lu Y, & Fox GE. “Genome Display Tool: Visualizing possible correlations   in complex data sets,”Source Code Biol Med 2:1 (2007).

Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, & Fox GE  “Characterization of Escherichia coli MG1655 Grown in a Low-Shear Modeled  Microgravity Environment”, BMC Microbiology 7:15 (2007).

Larios-Sanz M, Kourentzi KE, Warmflash D, Jones J, Willson RC, Pierson DL, & Fox GE, "16S rRNA Beacons for Bacterial Monitoring During Human Space    Missions,” Aviation, Space, & Environ. Med., 78:Supplement 1, A43-47(2007).

Warmflash D, Larios-Sanz M, Jones J, Fox GE, & McKay DS, “Biohazard Potential of Putative Martian Organisms for Exploration Class Human Space Missions,” Aviation, Space & Environ. Med., 78: Supplement 1, A79-88(2007).

Stepanov VG & Fox GE. "Stress-driven in vivo selection of a functional mini-gene from a  randomized library expressing combinatorial peptides in Escherichia coli”. Mol. Biol. Evol. Apr 9; [Epub ahead of print], 24:1480-91.(2007).

Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada Y, Fox GE, Haake SK, Weinstock GM & Highlander SK. “Genome sequence of Fusobacterium nucleatum subspecies polymorphum-a genetically tractable fusobacterium,” PLoS ONE,  2: e659 (2007).

Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazarath L, Blyth P, Holder M,  Buhay C, Tirumalai T, Liu Y, Dasgupta I,  Bokhetache L, Fujita M,   Karouia F, Moorthy PE, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Highlander SK,  Nicholson WL, Fox GE, Venkateswaran K, &   Weinstock GM. “Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus,” PLOS One, 2: e928 (2007).             

Zhu D, Fox GE, & Chakravarty S. “RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguishing among these viruses”,  BMC-Bioinformatics 8:39 (10 Oct 2007). 

Highlander SK, Hulten KG, Qin X, Jiang H, Yerrapragada Y, Mason EO Jr, Shang Y, Williams T, Fortunov RM, Liu Y, Igboeli O, Petrosino J, Tirumalai M, Uzman A, Fox GE, Cardenas AM, Muzny D, Hemphill L, Ding Y,  Dugan S, Blyth PR, Buhay CJ, Dinh HH, Hawes ACF, Holder MK, Kovar CL, Lee SL, Liu W, Nazareth LV, Wang Q, Zhou J, Kaplan SL, & Weinstock GM. “Subtle genetic changes enhance virulence of  methicillin resistant and  sensitive Staphylococcus aureus”, BMC-  Bioinformatics 7:99 2007. 

Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, & Fofanov Y. “Human-blind probes and primers for dengue virus identification: Exhaustive analysis of subsequences present in the human and 83 dengue genome sequences” FEBS J. 273: 398-408 (2006).

Potty AS, Fu JY, Balan S, Haymore BL, Hill DJ, Fox GE, & Willson, RC. “Neutral Additives Enhance the Metal-Chelate Affinity Adsorption of Nucleic Acids”, J. Chromatogr. A: 1115: 88-92 (2006).

Murphy JC, Cano, T. Fox GE, & Willson RC, “Compaction Agent Protection of  Nucleic Acids During  Mechanical Lysis”, Biotechnol. Prog. 22: 519-522 (2006). 

Forsman ZH, Hunter CL, Fox GE, & Wellington GM, “Is the ITS Region the Solution to the ‘Species Problem’ in Corals?: Intragenomic Variation and Alignment Permutation in Porites, Siderastrea and Outgroup Taxa”, Proc. 10Intn. Coral Reefs Symp.,Okinawa. 14-23(2006). 

Zhang, Z., Jackson, GW, Fox GE & Willson, RC. “Microbial Identification by Mass Cataloging”, BMC-Bioinformatics, 7: 117 [Epub ahead of print] (2006).

Zhu D, Fofanov Y, Willson RC, & Fox, GE, “A Parallel Computing Algorithm for 16S rRNA Probe Design”,Journal of Parallel and Distributed Computing,  66:1546-1551 (2006).

Jackson GW, McNichols RJ, Fox GE & Willson RC. “Bacterial Genotyping by 16S rRNA Mass Cataloging”, BMC-Bioinformatics 7: 321 (2006).      

Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D & Fofanov Y. “A Computational tool for the Genomic Identification of Regions of Unusual Compositional Properties and Its Utilization in the Detection of Horizontally Transferred Sequences”, Molec. Biol. Evol. 23: 1863-1868 (2006).

Fu J Y, Potty AS, Fox GE, & Willson RC. “Water-Elutability of Nucleic Acids from Metal-Chelate Affinity Asorbents: Enhancement by Control of Surface Charge Density”, J. Mol. Recognit. 19: 348-353 (2006).

Gioia J, Qin X, Jiang H, Clinkenbeard K, Lo R, Liu Y, Fox GE, McLeod MP, McNeil TZ, Hemphill L, Sodergren E, Weinstock GM, & Hightower SK. “The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence and Pasteurellaceae Phylogeny.” J. Bacteriol.  188: 7257-7266   (2006).

Hury J, Nagaswamy U, Larios-Sanz M, & Fox GE. “Ribosome Origins: The Relative Age of 23S rRNA Domains”,Origins Life & Evol. Biosphere 36: 421-429 (2006). 

Petrosino JF, Xiang Q, Karpathy SE, Jiang H, Yerrapragada S, Liu Y, Gioia J, Hemphill L, Gonzalez A, Raghaven  TM. Suman A, Fox GE, Highlander A, Reichard M, Morton RJ, Clinkenbeard KD, & Weinstock GM. “Chromosome Rearrangements  and Diversification of  Francisella tularensis revealed by the Type B  (OSU18)  Genome Sequence." J. Bacteriol. 188: 6977-6985 (2006). 

Huang H-C, Nagaswamy U, & Fox GE. “The Application of Cluster Analysis in the Inter-comparison of Loop Structures in RNA” RNA 11: 412-423 (2005).

Zhao Q., Nagaswamy U, Lee H, Xia Y, Huang HC, Gao,X & Fox, GE. “NMR Structure and Mg2+ Binding of an RNA Segment that Underlies the L7/L12 Stalk in the E. coli 50S Ribosomal Subunit”, Nucleic Acids Res. 33:3145-3153 (2005).

Tucker DL, Karouia F, Wang J, Luo Y, Li^, TB, Willson RC, Fofanov Y, & Fox, GE “The Effect of an Artificial RNA Marker on Gene Expression in Escherichia coli Applied Environ Microbiol., 71: 4156-4159 (2005).

Forsman, ZH, Guzman, H, Chen, CA, Fox, GE & Wellington, GM, “An ITS Region Phylogeny of the Coral Genus Siderastrea (Cnidaria:Anthrozoa): is S. glynni.” Endangered or introduced? Coral Reefs, 24: 343-347 (2005).

Cano T, Murphy JC, Fox GE, & Willson RC, "Separation of Genomic DNA from Plasmid DNA by Selective Renaturation with Imobilized Metal Affinity Capture", Biotechnol. Prog. 21: 1472-1477 (2005).

Chumakova S, Bepapurkara C, Putonti C, Li, T-B, Pettitt N, Fox GE, Willson RC, & Fofanov Y. “Theoretical Basis for Universal Identification Systems for Bacteria and Viruses”, J. Biol. Phys & Chem., 5: 121-128 (2005).

McLeod M. P., Karpathy S. E., Gioia J., Qin X., Highlander S.K., Fox G.E., McNeil T.Z., Jiang H., Muzny D., Jacob L.S., Hawes A.C., Sodergren E., Gill R., Hume J., Morgan M., Hong C., Yu X., Walker D.H., & Weinstock G.M., "The Complete Genome of Rickettsia typhi and Comparison with R. prowazekii and R. conorii," J. Bacteriol, 186: 5842-5855 (2004)

Forsman, Z. H., Lednickey J. A., Fox G. E., Willson R. C., White Z., Halvorson S., Wong C., Lewis A. M., & Butel J. S., "Phylogenetic Analysis of Polyomavirus Simian Virus 40 from Monkeys and Humans Reveals Genetic Variation," J. Virology., 78: 9306-9316 (2004).

Balan S., Murphy J. C., Galaev I., Kumar A., Fox G. E., Mattiasson B., & Willson R. C., "Metal Chelate Affinity  Precipitation of RNA and Purification of Plasmid DNA," Biotechnol. Lett., 25: 1111-1116 (2003).

Kourentzi K. D., Fox G. E., & Willson R. C., "Hybridization-responsive Fluorescent DNA Probes Containing the Adenine Analog 2-AminoPurine," Anal. Biochem. 322: 124-126 (2003).

Nagaswamy U. & Fox G. E., "RNA Ligation and the Origin of tRNA," Origins Life & Evol. Biosphere. 33: 199-209 (2003).

Martin K. A., Siefert J. L., Yerrapragada Y., Lu Y., McNeil T. Z., Moreno P. A., Weinstock, G. M., Widger W. R., & Fox G. E., "Cyanobacterial Signature Genes," Photosynt. Res., 75: 211-221 (2003).

DeWalt B., Murphy J. C., Fox G. E., & Willson, R. C., "Compaction Agent Clarification of Microbial Lysates," Protein Exp. Purif., 28: 220-223 (2003).

Murphy J. C., Jewell D. L., White K. I., Fox G. E., & Willson R. C., "Nucleic Acid Separations Using Immobilized Metal Affinity Chromatography," Biotechnol. Progr., 19: 982-986 (2003).

D’Souza L. M., Larios-Sanz M., Setterquist R. A., Willson R. C., & Fox G. E., "Small RNA sequences are readily stabilized by inclusion in a carrier rRNA," Biotechno. Progr., 19: 734-738 (2003).

Zhang Z., D’Souza L. M., & Fox G. E., "Common 5S rRNA Variants are Likely to be Accepted in Many Sequence Contexts," J. Mol. Evol., 56: 69-76 (2003).

Murphy J. C., Fox G. E., & Willson R. C., "Enhancement of Anion-Exchange Chromatography of DNA Using Compaction Agents," J. Chromatogr., A 984: 215-221 (2003).

Starikov D., Boney C., Medelci N., Um J. W., Larios-Sanz M., Fox G. E., & Bensaoula A. N., "Experimental Simulation of Integrated Optoelectronic Sensors Based on III Nitrides," J. Vacuum Science & Technology, 20: 1815-2820 (2002).

 Nagaswamy U.& Fox, G. E., "Frequent Occurrence of the T-loop RNA Folding Motif in Ribosomal RNAs," RNA, 8: 1112-1119 (2002).

Larkin D. C., Williams A. M., Martinis S. A., & Fox, G. E., "Identification of Essential Domains for Escherichia coli tRNAleu Aminoacylation and Amino Acid Editing Using Minimalist RNA Molecules," Nucleic Acids Res., 30: 2103-2113 (2002).

Kourentzi K. D., Fox G. E., & Willson R. C., "Microbial Identification by Immunohybridization Assay of Artificial RNA Labels," J. Microbiol. Methods, 49: 301-306 (2002).

Zhang Z., Willson R. C., & Fox, G. E., "Identification of Characteristic Oligonucleotides in the 16S Ribosomal RNA Sequence Dataset," Bioinformatics, 18: 244-250 (2002).

Nagaswamy U., Larios-Sanz M., Hury J., Collins S., Zhang Z., Zhao Q., and Fox G. E., "NCIR: A Database of Non-Canonical Interactions in Known RNA Structures," Nucl. Acids Res., 29: 395-397 (2002).

 Nagaswamy U., Gao X., Martinis S. A., and Fox, G. E. "NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop," Nucl. Acids Res., 29: 5129-5139 (2001).

Larkin D. C., Martinis S. A., Roberts D. J., and Fox, G. E., "Ala-His Mediated Peptide Bond Formation Revisited," Origins Life & Evol. Biosphere, 31: 511-526 (2001).

Kourentzi K. D., Fox G. E., and Willson, R. C., "Microbial Detection with Low Molecular Weight RNA," Curr. Microbiol, 43: 444-447 (2001).

Murphy J. C., Fox G. E., and Willson R. C. "RNA Isolation and Fractionation with Compaction Agents," Anal. Biochem., 295: 143-148 (2001).

 

BOOK CHAPTERS

Larios-Sanz M., Kourentzi K. D., Murphy J. C., Maillard K. I., Pearson D. L., Willson R. C., & Fox G. E., "Estudio de las Poblaciones Microbiologicas en el Ambiente Espacial," in Dianostico Molecular, JGH Editors SA de CV, Mexico City, Mexico, pp 293-311 (2003).

Fox G. E. & Naik A. K. "The Evolutionary History of the Ribosome," in The Genetic Code and the Origin of Life, (L. Ribas de Poplana ed), Landes Bioscience, Chapter 6; pp 92-105 (2004).

Nagaswamy U., Larios-Sanz, M., Zhang, Z., Huang, H-C., & Fox, G. E., "Non-Canonical Interactions in RNA," in Recent  Developments in Nucleic Acids, Transworld Research Network, 1: 103-129 (2004).