Dr. Robert A. Edwards, B. Sc. D. Phil
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- R.A. Edwards
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Edwards, R.A. Olson, R., Disz, T., Pusch, G.D., Vonstein, V., Stevens, R., and R. Overbeek. 2012. Real Time Metagenomics: Using k-mers to annotate meta-genomes. Bioinformatics http://dx.doi.org/10.1093/bioinformatics/bts599 2014 journal impact factor 4.621. Cited by 14. 39.
Aziz, R.A., Devoid, S., Disz, T., Edwards, R.A., Henry, C.S., Olsen, G.J., Olson, R., Overbeek, R., Parrello, B., Pusch, G.D., Stevens, R.L., Vonstein, V., and F. Xia. 2012. SEED Servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 7:e48053. http://dx.doi.org/10.1371/journal.pone.0048053
2014 journal impact factor 3.534. Cited by 27. 40. Yue, M., Schmieder, R. g , Edwards, R.A., Rankin, S.C., and D.M. Schifferli. 2012 Microfluidic PCR combined with pyrosequencing identify allelic variants with phenotypic associations in targeted Salmonella genes. Appl. Env. Microbiol. 78:7480-7482 http://dx.doi.org/10.1128/AEM.01703-12 2014 journal impact factor 3.952. Cited by 3. 41. Bruce T., Meirelles P.M., Garcia G., Paranhos R., Rezende C.E., de Moura, R.L., Filho, R-F., Coni, E.O.C., Vasconcelos, A.T., Filho, G.A., Hatay, M., Schmieder, R., Edwards, R.A., Dinsdale, E.A., and F.L. Thompson 2012. Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data. PLoS ONE 7:e36687. http://dx.doi.org/10.1371/journal.pone.0036687 2014 journal impact factor 3.534. Cited by 28. 42.
Garza DR, Thompson CC, Loureiro ECB, Dutilh BE, Inada DT, Sousa, E.C. Jr., Cardoso, J.F., Nunes, M.R.T., Silva de Lima, C.P., Duarte Silvestre, R.V., Barbosa Nunes, K.N., Santos, E.C.O., Edwards, R.A., Vicente, A.C.P., and L.L. Canto de Sá Morais. 2012. Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic. PLoS ONE 7: e37283. http://dx.doi.org/10.1371/journal.pone.0037283
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Lynch, E.A. g , Langille, M.G.I., Darling, A., Wilbanks, E.G., Haltiner, C., Shao, K.S.Y., Starr, M.O., Teiling, C., Harkins, T.T., Edwards, R.A. Eisen, J.A., and M.T Facciotti. 2012. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS One. 7:e41389. http://dx.doi.org/10.1371/journal.pone.0041389 2014 journal impact factor 3.534. Cited by 10. 44. Yue, M., Rankin, S.C., Blanchet, R.T. u , Nulton, J.D., Edwards, R.A. and D.M. Schifferli. 2012. Diversification of the Salmonella Fimbriae: A Model of Macro-and Microevolution. PLoS One. 7:e38596. http://dx.doi.org/10.1371/journal.pone.0038596 2014 journal impact factor Page 8 of 30 Dr. Robert Edwards. Biosketch 3.534. Cited by 12. 45. Trindade-Silva A.E. g , Rua C.
g , Silva G.G.Z. u , Dutilh B.E., Moreira A.P.B., Edwards, R.A., Hajdu, E., Lobo-Hajdu, G., Vasconcelos, A.T., Berlinck, R.G.S., and F.L. Thompson. 2012. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis. PLoS ONE 7: e39905. http://dx.doi.org/10.1371/journal.pone.0039905 2014 journal impact factor 3.534. Cited by 13.
46. Luckwu de Lucena, B.T. g , Silva, G.G. u , Manoel Dos Santos, B., Dias, G.M., Amaral, G.R. g ,
Thompson, C.C., and Thompson, F.L. 2012. Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9. J. Bacteriol. 194:3018. http://dx.doi.org/10.1128/JB.00446-12
47. Amaral G.R. g , Silva B.S. g , Santos, E.O., Dias, G.M., Lopes, R.M., Edwards, R.A., Thompson, C.C., and Thompson, F.L.. 2012. Genome sequence of the bacterioplanktonic mixotrophic
http://dx.doi.org/10.1128/JB.00377-12
48. Espinoza-Valles, I. g , Soto-Rodríguez, S., Edwards, R.A., Wang, Z., Vora, G., and B. Gomez- Gil. 2012. Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792. J. Bacteriol. 194:2104. http://dx.doi.org/10.1128/JB.00079-12
2014 journal impact factor 2.688. Cited by 5. 49. Akhter, S. g , Aziz, R., and Edwards, R.A. 2012. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. http://dx.doi.org/10.1093/nar/gks406
2014 journal impact factor 8.808. Cited by 27. 50. Farris-Hanna, L. g , Matthews, T.D., Dinsdale, E.A., Hasty, D., and Edwards, R.A. 2012 Characterization of the ELPhiS Prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl. Environ. Microbiol. http://dx.doi.org/10.1128/AEM.07241-11
2014 journal impact factor 3.952. Cited by 7. 51. McNair, K. g , Bailey, B., and Edwards, R.A. 2012. PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics. 28:614-8. http://dx.doi.org/10.1093/bioinformatics/bts014 2014 journal impact factor 4.621. Cited by 18.
52. Miller, M.E. g , Yeoman, C.J., Chia, N., Tringe, S.G., Angly, F.E., Edwards, R.A., Flint, H.J., Lamed, R., Bayer, E.A., and B.A. White. 2012. Phage-Bacteria Relationships and CRISPR Elements Revealed by a Metagenomic Survey of the Rumen Microbiome. Environmental Microbiology. 14:207–227. http://dx.doi.org/10.1111/j.1462-2920.2011.02593.x 2014 journal impact factor 6.24. Cited by 34. 53. Bolser, D.M., Chibon, P.Y., Palopoli, N., Gong, S., Jacob, D., Del Angel, V.D., Swan, D., Bassi, S., González, V., Suravajhala, P., Hwang, S., Romano, P., Edwards, R.A., Bishop, B., Eargle, J., Shtatland, T., Provart, N.J., Clements, D., Renfro, D.P., Bhak, D., and Bhak J. 2012 MetaBase: A community database of biological databases. Nucleic Acids Res. 40(Database issue):D1250-4. http://dx.doi.org/10.1093/nar/gkr1099 2014 journal impact factor 8.808. Cited by 17. 54.
Dwivedi, B., Schmieder, R., Goldsmith, D.B. g , Edwards, R.A., and Breitbart, M. 2012. PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for Page 9 of 30 Dr. Robert Edwards. Biosketch examining phage diversity. BMC Bioinformatics. BMC Bioinformatics 13:37 http://dx.doi.org/10.1186/1471-2105-13-37
2014 journal impact factor 4.621. Cited by 9. 55.
Schmieder, R, g Lim Y.W. g and Edwards, R.A. 2011. Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 2011; http://dx.doi.org/10.1093/bioinformatics/btr669
20. 56.
Schmieder, R. g , and Edwards, R.A. 2011. Insights into antibiotic resistance through metagenomic approaches. Future Microbiology. 7:73-89 http://dx.doi.org/10.2217/fmb.11.135
factor 3.819. Cited by 51. Ranked as one of the top 50 highest read pieces in 2015 across all the Future Medicine journal titles. 57. Thompson, C.C., Marin, M.A., Dias, G.M., Dutilh, B.E., Edwards, R.A., Iida, T. Thompson, F.L. and Vicente, A.C.P. 2011. Genome sequence of the human pathogen Vibrio cholerae Amazonia. J. Bacteriol. 193:5877-5878 http://dx.doi.org/10.1128/JB.05643-11
2014 journal impact factor 2.688. Cited by 4. 58. Schmieder, R, g and Edwards, R.A. 2011. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One. 6:e17288. http://dx.doi.org/10.1371/journal.pone.0017288
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66. 59.
Schmieder, R, g and Edwards, R.A. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 27:863-864. http://dx.doi.org/10.1093/bioinformatics/btr026 2014 journal impact factor 4.621. Cited by 203. 60. Henry, C.S., Overbeek, R.A., Xia., F., Best, A.A., Glass, E. Gilbert, J.A., Larsen, P.E., Edwards, R.A., Disz, T., Meyer, F., Vonstein, V., DeJongh, M., Bartels, D., Desai, M., D'Souza, M., Devoid, S., Keegan, K.P., Olson, R., Wilke, A., Wilkening, J., Stevens, R.L. 2011. Connecting Genotype to Phenotype in the Era of High-throughput Sequencing. Biochem. Biophys. Acta. http://dx.doi.org/10.1016/j.bbagen.2011.03.010 2014 journal impact factor 3.829. Cited by 19. 61.
Desnues, C.G. p , Rodriguez-Brito, B. g , Rayhawk, S. g , Kelley, S., Tran, T. g , Haynes, M., Liu, H., Hall, D. g , Angly, F.E. g , Edwards, R.A., Vega, R. p , Breitbart, M., Siefert, J., Souza, V., Reid, P., Rohwer, F. 2011. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Pages 37-44. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Wiley-Blackwell, Hoboken, NJ. ISBN 978-0-470-64719-6. 62.
F.L. Thompson, Rodrigues, T.B., Gonzalez, A., Cardoso, A. Clementino, M., Costagliola, M., Hozbor, C., Otero, E., Paranhos, R., Piccini, C., Peressutti, S., Schmieder, R. g , Edwards, R., Smith, M., Takiyama, L.R., Vieira, R., Artigas, L.F. 2011. Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6-tag pyrosequencing. 2010. Arch. Microbiol. http://dx.doi.org/10.1007/s00203-010-0644-y 2014 journal impact factor 1.861. Cited by 10. 63. T. D. Matthews, R. Edwards, and S. Maloy. 2010. Chromosomal Rearrangements Formed by rrn Recombination Do Not Improve Replichore Balance in Host-specific Salmonella enterica Serovars. PLoS One. http://dx.doi.org/10.1371/journal.pone.0013503
2014 journal impact factor 3.534. Cited by 5. 64. Schmieder R. g , Lim Y.W. g , Rohwer F., Edwards R. 2010. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics Page 10 of 30 Dr. Robert Edwards. Biosketch 11:341-355. http://dx.doi.org/10.1186/1471-2105-11-341 2014 journal impact factor: 2.672. Cited by 45. 65.
Disz, T., Akhter, S. g , Cuevas, D. u , Olson, R., Overbeek, R., Vonstein, V., Stevens, R., and R.A. Edwards. 2010. Accessing the SEED genome databases via Web services API: Tools for Programmers. BMC Bioinformatics 11:319-330. http://dx.doi.org/10.1186/1471-2105-11- 319
2014 journal impact factor: 2.672. Cited by 45. 66.
Aziz, R. p , Breitbart, M., and Edwards, R. 2010. Transposases are the most abundant, most ubiquitous genes in nature. Nucl. Acids Research 38:4207-4217 http://dx.doi.org/10.1093/nar/gkq140 2014 journal impact factor 8.808. Cited by 98. 67.
Rodriguez-Brito, B. g , Li, L. g , Wegley, L. g , Furlan, M. g , Angly, F. g , Brietbart, M, Buchanan, J., Desnues, C. p , Dinsdale, E., Edwards, R.A., Felts, B., Wilner, D. g , Haynes, M., Liu, H., Lipson, D., Mahaffy, J., Martin-Cuadrado, A.B., Mira, A., Nulton, J., Pasic, L., Rayhawk, S. g , Rodriguez-Mueller, J., Rodriguez-Valera, F., Salamon, P., Srinagesh, S. g , Thingstad, T., Tran, T. g , Vega Thurber, R. p , Youle, M., Rohwer, F. 2010 Viral and microbial community dynamics in four aquatic environments. ISME J. 1-13. http://dx.doi.org/10.1038/ismej.2010.1 2014 journal impact factor 9.267. Cited by 135. 68.
Mobberley, J. g , Authement, R.N. g , Segall, A.M., Edwards, R.A., Slepecky, R.A., and Paul, J.H. 2010. Lysogeny and Sporulation in Bacillus Isolates from the Gulf of Mexico. Appl. Env. Microbiol. 76:829-842. http://dx.doi.org/10.1128/AEM.01710-09 2014 journal impact factor: 3.952. Cited by 3. 69.
Vega Thurber R. g , Willner-Hall D. g , Rodriguez-Mueller B. g , Desnues C. p , Edwards RA, Angly F. g
g , Rohwer F 2009. Metagenomic analysis of stressed coral holobionts. Environ Microbiol. 1:2148-63. http://dx.doi.org/10.1111/j.1462- 2920.2009.01935.x 2014 journal impact factor: 6.24. Cited by 147. 70. Wagner, C. u , Salamon, A. g , Edwards, R.A., Rohwer, F., and P. Salamon. 2009. Deviations from Ultrametricity in Phage Protein Distances. Open Systems & Information Dynamics 16:75– 84 .
http://dx.doi.org/10.1142/S1230161209000062 2014 journal impact factor: 0.808 71. Angly FE. g , Willner D. g , Prieto-Davó A. p , Edwards RA, Schmieder R. g , Vega-Thurber R. g , Antonopoulos DA, Barott K. g , Cottrell MT, Desnues C. p , Dinsdale EA, Furlan M. g , Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T. g , McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B. g , Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. 2009. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol 5:e1000593. http://dx.doi.org/10.1371/journal.pcbi.1000593 2014 journal impact factor: 4.829. Cited by 100. 72.
Brulc, J.M. g , Antonopoulos, D.A. p , Berg Miller, M.E., Wilson, M.K., Yannarell, A.C., Dinsdale, E.A., Edwards, R.A. Frank, E.D., Emerson, J.B., Wacklin, P., Coutinho, P.M., Henrissat, B., Nelson, K.E., and White, B.A.. 2009 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA. 106:1948 –1953. http://dx.doi.org/10.1073/pnas.0806191105 2014 journal impact factor: 9.809. Cited by 276. 73.
Edwards, R.A. 2009. Gaining New Insights into Microbial Communities. SciDac Review 13:43 74.
Breitbart, M., Hoare, A., Nitti, A., Siefert, J., Haynes, M., Dinsdale, E., Edwards, R., Souza, V., Rohwer, F., and Hollander, D. 2009. Metagenomic and Stable Isotopic Analyses of Modern Freshwater Microbialites in Cuatro Ciénegas, Mexico. Env. Microbiol.11:16-34.
Dr. Robert Edwards. Biosketch http://dx.doi.org/10.1111/j.1462-2920.2008.01725.x 2014 journal impact factor: 6.24. Cited by 78.
75. Dinsdale, E.A., Edwards, R.A., Hall, D. g , Angly, F. g , Breitbart, M., Brulc, J. g , Chau, B. g , Furlan, M. g , Desnues, C.G. p , Haynes, M., Li, L. g , McDaniel, L., Moran, M.A., Nelson, K.E., Nilsson, C., Olson, R., Paul, J., Rodriguez-Brito, B. g , Swan, B. g , Stevens, R., Valentine, D., Vega-Thurber, R. p , Wegley, L. g , White, B., and F. Rohwer. 2008. Functional Metagenomic Profiling of Nine Biomes. Nature 452:629-632. http://dx.doi.org/10.1038/nature06810
76. Dinsdale, E. A., Pantos O. p , Smriga, S. g , Edwards, R.A., Angly, F. g , Wegley, L. g , Hatay, M., Hall, D. g , Brown, E. g , Haynes, M., Krause, L. g , Sala, E., Sandin, S.A., Thurber, R. V., Willis, B.L., Azam, F., Knowlton, N., and Rohwer, F. 2008. Microbial ecology of four coral atolls in the northern line islands. PLoS ONE 3:e1584. http://dx.doi.org/10.1371/journal.pone.0001584 2014 journal impact factor 3.534. Cited by 197. 77.
Desnues, C.G. p , Rodriguez-Brito, B. g , Rayhawk, S. g , Kelley, S., Tran, T. g , Haynes, M., Liu, H., Hall, D. g , Angly, F.E. g , Edwards, R.A., Vega, R. p , Breitbart, M., Siefert, J., Souza, V., Reid, P., Rohwer, F. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343. http://dx.doi.org/10.1038/nature06735 2014 journal impact factor: 42.351. Cited by 148. 78.
Mou, X. p , Sun, S., Edwards, R., Hodson, R., and Moran, M.A. 2008. Bacterial Carbon Processing by Generalist Species in the Coastal Ocean. Nature. 451:709-711. http://dx.doi.org/10.1038/nature06513 2014 journal impact factor: 42.351. Cited by 158. 79.
Meyer, F. Paarmann, D., D'Souza, M., Olson, R.D., Glass, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J. and R.A. Edwards. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. http://dx.doi.org/10.1186/1471-2105-9-386 2014 journal impact factor: 2.672. Cited by 837. 80. Breitbart M, Haynes M, Kelley S, Angly F g , Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S g , Rodriguez-Brito B g , Salamon P, Rohwer F. 2008. Viral diversity and dynamics in an infant gut. Res. Microbiol 159:367-373. http://dx.doi.org/10.1016/j.resmic.2008.04.006 2014 journal impact factor: 2.826. Cited by 111.
81. Gilbert, J.A., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., and I. Joint. 2008. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE 3(8): e3042. http://dx.doi.org/10.1371/journal.pone.0003042 2014 journal impact factor 3.534. Cited by 217. 82.
Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL. 2008. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc. Natl. Acad. Sci. USA 105:18413–18418. http://dx.doi.org/10.1073/pnas.0808985105 2014
journal impact factor: 9.809. Cited by 84. 83.
Qu, A. g , Brulc, J. M. g , Wilson, M.K., Law, B.F., Theoret, J.R., Joens, L.A., Konkel, M.A., Angly, F. g , Dinsdale, E.A., Edwards, R.A., Nelson, K.E., and White, B.A. 2008. Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Page 12 of 30 Dr. Robert Edwards. Biosketch Transfer Elements in the Chicken Cecum Microbiome. PLoS One, 3(8):e2945. http://dx.doi.org/10.1371/journal.pone.0002945 2014 journal impact factor 3.534. Cited by 101. 84.
Marhaver, K.L. g , Edwards, R.A., and F. Rohwer. Viral communities associated with healthy and bleaching corals. 2008. Env Microbiol. 10:2277-2286. http://dx.doi.org/10.1111/j.1462- 2920.2008.01652.x 2014 journal impact factor: 3.264. Cited by 58. 85. Krause, L. g , Diaz, N. N., Edwards, R.A., Gartemann, K-H., Krömeke, H., Neuweger, H., Pühler, A., Runte, K., Schlüter, A., Stoye, J., Szczepanowski, R., Tauch, A., and Goesmann, A. 2008. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Biotechnology, 136:91-101. http://dx.doi.org/10.1016/j.jbiotec.2008.06.003 2014 journal impact factor: 2.884. Cited by 96.
86. Krause L, g , Diaz NN, g , Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, and Stoye J. 2008. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36:2230-9. http://dx.doi.org/10.1093/nar/gkn038 2014 journal impact factor 8.808. Cited by 189. 87.
Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M.J., Ashburner, M., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., dePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Glockner, F-O., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kyrpides, N., Leebens-Mack, J., Lewis, S.E., Liste, A., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Moxon, R., Nelson, K., Parkhill, J., Sansone, S-A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T., Wilson, G., and Wipat, A., 2008. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnol. 26:541–547. http://dx.doi.org/10.1038/nbt1360 2014
journal impact factor: 39.08. Cited by 563. 88.
Aziz. R. K. p , Bartels. D., Best. A. A., DeJongh. M., Disz. T., Edwards. R. A., Formsma. K., Gerdes. S., Glass. E. M., Kubal. M., Meyer. F., Olsen. G. J., Olson. R., Osterman. A. L., Overbeek. R. A., McNeil. L. K., Paarmann. D., Paczian. T., Parrello. B., Pusch. G. D., Reich. C., Stevens. R., Vassieva. O., Vonstein. V., Wilke. A., Zagnitko. O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75 2014 journal impact factor 4.041. Cited by 1812. 89. Gupta, N., Tanner, S., Jaitly, N., Adkins, J., Lipton, M., Edwards, R., Romine, M., Osterman, A., Bafna, V., Smith, R.D., and Pevzner P. 2007. Whole proteome analysis of post- translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research. 17:1362-1377. http://dx.doi.org/10.1101/gr.6427907 2014 journal impact factor: 13.852. Cited by 131. 90. Yüklə 213,2 Kb. Dostları ilə paylaş:
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