Difference between revisions of "Papers that use the SEED"

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=2008=
 
=2008=
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# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]
+
# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]
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# Dinsdale, E.A., Edwards, R.A., Hall, D., Angly, F., Breitbart, M., Brulc, J., Chau, B., Furlan, M., Desnues, C.G., Haynes, M., Li, L., McDaniel, L., Moran, M.A., Nelson, K.E., Nilsson, C., Olson, R., Paul, J., Rodriguez-Brito, B., Swan, B., Stevens, R., Valentine, D., Vega-Thurber, R., Wegley, L., White, B., and F. Rohwer. 2008. Functional Metagenomic Profiling of Nine Biomes. Nature 452:629-632. [http://www.ncbi.nlm.nih.gov/pubmed/18337718 Pubmed] [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature06810.html Nature]
 +
# Krause, L., Diaz, N., Edwards, R.A., Rohwer, F., Kelley, S., and J. Stoye. 2008 Taxonomic Classification of Short Environmental DNA Fragments. 2008 NAR Online Feb 19th.  [http://www.ncbi.nlm.nih.gov/pubmed/18285365 Pubmed]    [http://nar.oxfordjournals.org/cgi/content/full/36/7/2230 NAR]
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# Dinsdale, E. A., O. Pantos, S. Smriga, R. A. Edwards, F. Angly, L. Wegley, M. Hatay, D. Hall, E. Brown, M. Haynes, L. Krause, E. Sala, S. A. Sandin, R. V. Thurber, B. L. Willis, F. Azam, N. Knowlton, and F. Rohwer. 2008. Microbial ecology of four coral atolls in the northern line islands. PLoS ONE 3:e1584. [http://www.plosone.org/doi/pone.0001584 PLoS One]
 +
# Desnues, C.G., Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Hall, D., Angly, F.E., Edwards, R.A., Vega, R., Breitbart, M., Siefert, J., Souza, V., Reid, P., Rohwer, F. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 20;452(7185):340-343. [http://www.ncbi.nlm.nih.gov/pubmed/18311127 PubMed] [http://www.nature.com/nature/journal/v452/n7185/abs/nature06735.html Nature]
 +
# Mou, X., 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://www.ncbi.nlm.nih.gov/pubmed/18223640 Pubmed] [http://www.nature.com/nature/journal/v451/n7179/abs/nature06513.html Nature]
 +
# 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. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology, 26:541-547. [http://www.ncbi.nlm.nih.gov/pubmed/18464787 Pubmed] [http://www.nature.com/nbt/journal/v26/n5/abs/nbt1360.html Nature Biotech]
 +
# Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol. 2008 Apr;74(8):2461-70. [http://www.ncbi.nlm.nih.gov/pubmed/18296538 PubMed] [http://aem.asm.org/cgi/content/full/74/8/2461?view=long&pmid=18296538 AEM]
  
 
=In press=
 
=In press=
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# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.
+
 
−
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.
 
 
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.
 
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.

Latest revision as of 14:59, 14 May 2008

2005

  1. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. PubMed NAR Supplemental Online Material

2006

  1. Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. PubMed PLoS Biology
  2. DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. PubMed
  3. Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. PubMed BioMed Central
  4. Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. PubMed Science Direct
  5. Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. PubMed J. Bact
  6. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. PubMed JBact
  7. Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. PubMed NAR
  8. Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
  9. El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. PubMed JBC# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. PubMed AEM
  10. Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. PubMed JBC

2007

  1. de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. PubMed Trends
  2. de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.PubMed Biomed Central
  3. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. PubMed Genome Research
  4. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 PubMed NAR
  5. Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. PubMed
  6. Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. PubMed PNAS
  7. Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. PubMed Environ Microbiol
  8. Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; PubMed JBact
  9. JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. ACS
  10. DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 Pubmed BMC Bioinformatics

2008

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics Pubmed BMC Genomics
  2. Dinsdale, E.A., Edwards, R.A., Hall, D., Angly, F., Breitbart, M., Brulc, J., Chau, B., Furlan, M., Desnues, C.G., Haynes, M., Li, L., McDaniel, L., Moran, M.A., Nelson, K.E., Nilsson, C., Olson, R., Paul, J., Rodriguez-Brito, B., Swan, B., Stevens, R., Valentine, D., Vega-Thurber, R., Wegley, L., White, B., and F. Rohwer. 2008. Functional Metagenomic Profiling of Nine Biomes. Nature 452:629-632. Pubmed Nature
  3. Krause, L., Diaz, N., Edwards, R.A., Rohwer, F., Kelley, S., and J. Stoye. 2008 Taxonomic Classification of Short Environmental DNA Fragments. 2008 NAR Online Feb 19th. Pubmed NAR
  4. Dinsdale, E. A., O. Pantos, S. Smriga, R. A. Edwards, F. Angly, L. Wegley, M. Hatay, D. Hall, E. Brown, M. Haynes, L. Krause, E. Sala, S. A. Sandin, R. V. Thurber, B. L. Willis, F. Azam, N. Knowlton, and F. Rohwer. 2008. Microbial ecology of four coral atolls in the northern line islands. PLoS ONE 3:e1584. PLoS One
  5. Desnues, C.G., Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Hall, D., Angly, F.E., Edwards, R.A., Vega, R., Breitbart, M., Siefert, J., Souza, V., Reid, P., Rohwer, F. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 20;452(7185):340-343. PubMed Nature
  6. Mou, X., 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. Pubmed Nature
  7. 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. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology, 26:541-547. Pubmed Nature Biotech
  8. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol. 2008 Apr;74(8):2461-70. PubMed AEM

In press

  1. Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.
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