Difference between revisions of "Papers that use the SEED"

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# 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. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html SOM]  
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# 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. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material]  
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]

Revision as of 14:30, 31 December 2007

  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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
  7. 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
  8. 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
  9. 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

In press

  1. 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.
  2. 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.
  3. 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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