Difference between revisions of "Papers that use the SEED"

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*2005
 
# 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]  
 
# 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]  
 +
*2006
 
# 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]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]
 
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
 
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]
 +
*2007
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]
 
# 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.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]
 
# 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.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]
 
# 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 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]
 
# 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 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]
 +
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]
 
+
# 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; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]
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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666
 
 
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394
 
 
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855.
 
 
 
 
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474
 
 
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515
 
 
 
 
 
# 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. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]
 
 
 
 
 
 
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]
 
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]
 
# 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; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]
 
 
 
 
 
 
 
  
  

Revision as of 21:54, 31 December 2007

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


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.