Skip to content

Latest commit

 

History

History

References

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
 
 
 
 

References

  1. Apprill A., McNally S., Parsons R., Weber L. 2015. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquatic microbial ecology: international journal 75:129–137. DOI: 10.3354/ame01753.
  2. Branton D., Deamer DW., Marziali A., Bayley H., Benner SA., Butler T., Di Ventra M., Garaj S., Hibbs A., Huang X., Jovanovich SB., Krstic PS., Lindsay S., Ling XS., Mastrangelo CH., Meller A., Oliver JS., Pershin YV., Ramsey JM., Riehn R., Soni GV., Tabard-Cossa V., Wanunu M., Wiggin M., Schloss JA. 2008. The potential and challenges of nanopore sequencing. Nature biotechnology 26:1146–1153. DOI: 10.1038/nbt.1495.
  3. Breitbart M., Hewson I., Felts B., Mahaffy JM., Nulton J., Salamon P., Rohwer F. 2003. Metagenomic analyses of an uncultured viral community from human feces. Journal of bacteriology 185:6220–6223.
  4. Breitbart M., Salamon P., Andresen B., Mahaffy JM., Segall AM., Mead D., Azam F., Rohwer F. 2002. Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences of the United States of America 99:14250–14255. DOI: 10.1073/pnas.202488399.
  5. Bult CJ., White O., Olsen GJ., Zhou L., Fleischmann RD., Sutton GG., Blake JA., FitzGerald LM., Clayton RA., Gocayne JD., Kerlavage AR., Dougherty BA., Tomb JF., Adams MD., Reich CI., Overbeek R., Kirkness EF., Weinstock KG., Merrick JM., Glodek A., Scott JL., Geoghagen NS., Venter JC. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073.
  6. Cammen KM., Andrews KR., Carroll EL., Foote AD., Humble E., Khudyakov JI., Louis M., McGowen MR., Olsen MT., Van Cise AM. 2016. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. The Journal of heredity 107:481–495. DOI: 10.1093/jhered/esw044.
  7. Caporaso JG., Lauber CL., Walters WA., Berg-Lyons D., Huntley J., Fierer N., Owens SM., Betley J., Fraser L., Bauer M., Gormley N., Gilbert JA., Smith G., Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal 6:1621–1624. DOI: 10.1038/ismej.2012.8.
  8. Chow C-ET., Suttle CA. 2015. Biogeography of Viruses in the Sea. Annual Review of Virology 2:41–66. DOI: 10.1146/annurev-virology-031413-085540.
  9. Cochrane G., Alako B., Amid C., Bower L., Cerdeño-Tárraga A., Cleland I., Gibson R., Goodgame N., Jang M., Kay S., Leinonen R., Lin X., Lopez R., McWilliam H., Oisel A., Pakseresht N., Pallreddy S., Park Y., Plaister S., Radhakrishnan R., Rivière S., Rossello M., Senf A., Silvester N., Smirnov D., Ten Hoopen P., Toribio A., Vaughan D., Zalunin V. 2013. Facing growth in the European Nucleotide Archive. Nucleic acids research 41:D30–35. DOI: 10.1093/nar/gks1175.
  10. Collins FS., Green ED., Guttmacher AE., Guyer MS., US National Human Genome Research Institute. 2003. A vision for the future of genomics research. Nature 422:835–847. DOI: 10.1038/nature01626.
  11. DeLong EF. 1992. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America 89:5685–5689.
  12. Dinsdale EA., Edwards RA., Hall D., Angly F., Breitbart M., Brulc JM., Furlan M., Desnues C., Haynes M., Li L., McDaniel L., Moran MA., Nelson KE., Nilsson C., Olson R., Paul J., Brito BR., Ruan Y., Swan BK., Stevens R., Valentine DL., Thurber RV., Wegley L., White BA., Rohwer F. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629–632. DOI: 10.1038/nature06810.
  13. Drake JW. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proceedings of the National Academy of Sciences of the United States of America 88:7160–7164. DOI: 10.1073/pnas.88.16.7160.
  14. Dutilh BE., Tompson C., Vicente AC., Marin MA., Lee CF., Silva GGZ., Schmieder R., Andrade BGN., Chimetto L., Cuevas D., Garza DR., Okeke IN., Aboderin O., Spangler J., Ross T., Dinsdale EA., Thompson FL., Harkins TT., Edwards RA. The genomic landscape of Vibrio cholerae connects genotype and phenotype across time, space, and habitat. BMC genomics In press.
  15. Edwards RA., Rodriguez-Brito B., Wegley L., Haynes M., Breitbart M., Peterson DM., Saar MO., Alexander S., Alexander EC Jr., Rohwer F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC genomics 7:57. DOI: 10.1186/1471-2164-7-57.
  16. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians F., Cicero R., Clark S., Dalal R., Dewinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma C., Marks P., Maxham M., Murphy D., Park I., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong F., Korlach J., Turner S. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. DOI: 10.1126/science.1162986.
  17. Findley K., Oh J., Yang J., Conlan S., Deming C., Meyer JA., Schoenfeld D., Nomicos E., Park M., NIH Intramural Sequencing Center Comparative Sequencing Program., Kong HH., Segre JA. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature 498:367–370. DOI: 10.1038/nature12171.
  18. Frank JA., Reich CI., Sharma S., Weisbaum JS., Wilson BA., Olsen GJ. 2008. Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes. Applied and environmental microbiology 74:2461–2470. DOI: 10.1128/AEM.02272-07.
  19. Fuhrman JA., McCallum K., Davis AA. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148–149. DOI: 10.1038/356148a0.
  20. Haas AF., Knowles B., Lim YW., McDole Somera T., Kelly LW., Hatay M., Rohwer F. 2014. Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology. Journal of visualized experiments: JoVE:e52131. DOI: 10.3791/52131.
  21. Haggerty JM., Dinsdale EA. 2017. Distinct biogeographical patterns of marine bacterial taxonomy and functional genes. Global ecology and biogeography: a journal of macroecology 26:177–190. DOI: 10.1111/geb.12528.
  22. Handelsman J., Rondon MR., Brady SF., Clardy J., Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & biology 5:R245–249.
  23. Hollingsworth PM., Li D-Z., van der Bank M., Twyford AD. 2016. Telling plant species apart with DNA: from barcodes to genomes. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 371. DOI: 10.1098/rstb.2015.0338.
  24. Jiang X., Mu B., Huang Z., Zhang M., Wang X., Tao S. 2010. Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study. BMC evolutionary biology 10:298. DOI: 10.1186/1471-2148-10-298.
  25. Karl DM. 1979. Measurement of microbial activity and growth in the ocean by rates of stable ribonucleic Acid synthesis. Applied and environmental microbiology 38:850–860.
  26. Keightley PD. 1998. Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: a simulation study. Genetics 150:1283–1293.
  27. Kim K-H., Bae J-W. 2011. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Applied and environmental microbiology 77:7663–7668. DOI: 10.1128/AEM.00289-11.
  28. Kirchman DL. 2016. Growth Rates of Microbes in the Oceans. Annual review of marine science 8:285–309. DOI: 10.1146/annurev-marine-122414-033938.
  29. Klenk HP., Clayton RA., Tomb JF., White O., Nelson KE., Ketchum KA., Dodson RJ., Gwinn M., Hickey EK., Peterson JD., Richardson DL., Kerlavage AR., Graham DE., Kyrpides NC., Fleischmann RD., Quackenbush J., Lee NH., Sutton GG., Gill S., Kirkness EF., Dougherty BA., McKenney K., Adams MD., Loftus B., Peterson S., Reich CI., McNeil LK., Badger JH., Glodek A., Zhou L., Overbeek R., Gocayne JD., Weidman JF., McDonald L., Utterback T., Cotton MD., Spriggs T., Artiach P., Kaine BP., Sykes SM., Sadow PW., D’Andrea KP., Bowman C., Fujii C., Garland SA., Mason TM., Olsen GJ., Fraser CM., Smith HO., Woese CR., Venter JC. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370. DOI: 10.1038/37052.
  30. Labonté JM., Suttle CA. 2013. Previously unknown and highly divergent ssDNA viruses populate the oceans. The ISME journal 7:2169–2177. DOI: 10.1038/ismej.2013.110.
  31. Langille MGI., Zaneveld J., Caporaso JG., McDonald D., Knights D., Reyes JA., Clemente JC., Burkepile DE., Vega Thurber RL., Knight R., Beiko RG., Huttenhower C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology 31:814–821. DOI: 10.1038/nbt.2676.
  32. Lim YW., Cuevas DA., Silva GGZ., Aguinaldo K., Dinsdale EA., Haas AF., Hatay M., Sanchez SE., Wegley-Kelly L., Dutilh BE., Harkins TT., Lee CC., Tom W., Sandin SA., Smith JE., Zgliczynski B., Vermeij MJA., Rohwer F., Edwards RA. 2014. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ 2:e520. DOI: 10.7717/peerj.520.
  33. Merrick MJ., Edwards RA. 1995. Nitrogen control in bacteria. Microbiological reviews 59:604–622.
  34. Metzker ML. 2010. Sequencing technologies - the next generation. Nature reviews. Genetics 11:31–46. DOI: 10.1038/nrg2626.
  35. Mutreja A., Kim DW., Thomson NR., Connor TR., Lee JH., Kariuki S., Croucher NJ., Choi SY., Harris SR., Lebens M., Niyogi SK., Kim EJ., Ramamurthy T., Chun J., Wood JLN., Clemens JD., Czerkinsky C., Nair GB., Holmgren J., Parkhill J., Dougan G. 2011. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477:462–465. DOI: 10.1038/nature10392.
  36. Nyrén P. 1987. Enzymatic method for continuous monitoring of DNA polymerase activity. Analytical biochemistry 167:235–238.
  37. Okoro CK., Kingsley RA., Connor TR., Harris SR., Parry CM., Al-Mashhadani MN., Kariuki S., Msefula CL., Gordon MA., de Pinna E., Wain J., Heyderman RS., Obaro S., Alonso PL., Mandomando I., MacLennan CA., Tapia MD., Levine MM., Tennant SM., Parkhill J., Dougan G. 2012. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature genetics 44:1215–1221. DOI: 10.1038/ng.2423.
  38. Overbeek R., Begley T., Butler RM., Choudhuri JV., Chuang H-Y., 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. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic acids research 33:5691–5702. DOI: 10.1093/nar/gki866.
  39. Overbeek R., Disz T., Stevens R. 2004. The SEED: A Peer-to-peer Environment for Genome Annotation. Communications of the ACM 47:46–51. DOI: 10.1145/1029496.1029525.
  40. Overbeek R., Larsen N., Walunas T., D’Souza M., Pusch G., Selkov E Jr., Liolios K., Joukov V., Kaznadzey D., Anderson I., Bhattacharyya A., Burd H., Gardner W., Hanke P., Kapatral V., Mikhailova N., Vasieva O., Osterman A., Vonstein V., Fonstein M., Ivanova N., Kyrpides N. 2003. The ERGO genome analysis and discovery system. Nucleic acids research 31:164–171.
  41. Reuter JA., Spacek DV., Snyder MP. 2015. High-throughput sequencing technologies. Molecular cell 58:586–597. DOI: 10.1016/j.molcel.2015.05.004.
  42. Rodriguez-Brito B., Li L., Wegley L., Furlan M., Angly F., Breitbart M., Buchanan J., Desnues C., Dinsdale E., Edwards R., Felts B., Haynes M., Liu H., Lipson D., Mahaffy J., Martin-Cuadrado AB., Mira A., Nulton J., Pasić L., Rayhawk S., Rodriguez-Mueller J., Rodriguez-Valera F., Salamon P., Srinagesh S., Thingstad TF., Tran T., Thurber RV., Willner D., Youle M., Rohwer F. 2010. Viral and microbial community dynamics in four aquatic environments. The ISME journal 4:739–751. DOI: 10.1038/ismej.2010.1.
  43. Rodriguez-Brito B., Rohwer F., Edwards RA. 2006. An application of statistics to comparative metagenomics. BMC bioinformatics 7:162. DOI: 10.1186/1471-2105-7-162.
  44. Rohwer F., Edwards R. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. Journal of bacteriology 184:4529–4535.
  45. Ronaghi M., Karamohamed S., Pettersson B., Uhlén M., Nyrén P. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Analytical biochemistry 242:84–89. DOI: 10.1006/abio.1996.0432.
  46. Rosario K., Nilsson C., Lim YW., Ruan Y., Breitbart M. 2009. Metagenomic analysis of viruses in reclaimed water. Environmental microbiology 11:2806–2820. DOI: 10.1111/j.1462-2920.2009.01964.x.
  47. Rusch DB., Halpern AL., Sutton G., Heidelberg KB., Williamson S., Yooseph S., Wu D., Eisen JA., Hoffman JM., Remington K., Beeson K., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter JE., Li K., Kravitz S., Heidelberg JF., Utterback T., Rogers Y-H., Falcón LI., Souza V., Bonilla-Rosso G., Eguiarte LE., Karl DM., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari MR., Strausberg RL., Nealson K., Friedman R., Frazier M., Venter JC. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS biology 5:e77. DOI: 10.1371/journal.pbio.0050077.
  48. Schmidt TM., DeLong EF., Pace NR. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Journal of bacteriology 173:4371–4378.
  49. Sogin SJ., Sogin ML., Woese CR. Phylogenetic measurement in procaryotes by primary structural characterization. Journal of molecular evolution 1:173–184. DOI: 10.1007/BF01659163.
  50. Steven B., Gallegos-Graves LV., Starkenburg SR., Chain PS., Kuske CR. 2012. Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environmental microbiology reports 4:248–256. DOI: 10.1111/j.1758-2229.2012.00328.x.
  51. Thompson CC., Amaral GR., Campeão M., Edwards RA., Polz MF., Dutilh BE., Ussery DW., Sawabe T., Swings J., Thompson FL. 2015. Microbial taxonomy in the post-genomic era: rebuilding from scratch? Archives of microbiology 197:359–370. DOI: 10.1007/s00203-014-1071-2.
  52. Torres PJ., Edwards RA., McNair KA. 2017. PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive. Bioinformatics . DOI: 10.1093/bioinformatics/btx184.
  53. Tringe SG., von Mering C., Kobayashi A., Salamov AA., Chen K., Chang HW., Podar M., Short JM., Mathur EJ., Detter JC., Bork P., Hugenholtz P., Rubin EM. 2005. Comparative metagenomics of microbial communities. Science 308:554–557. DOI: 10.1126/science.1107851.
  54. Tyson GW., Chapman J., Hugenholtz P., Allen EE., Ram RJ., Richardson PM., Solovyev VV., Rubin EM., Rokhsar DS., Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43. DOI: 10.1038/nature02340.
  55. Venter JC., Remington K., Heidelberg JF., Halpern AL., Rusch D., Eisen JA., Wu D., Paulsen I., Nelson KE., Nelson W., Fouts DE., Levy S., Knap AH., Lomas MW., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y-H., Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. DOI: 10.1126/science.1093857.
  56. Woese CR., Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 74:5088–5090. DOI: 10.1073/pnas.74.11.5088.
  57. Wong VK., Baker S., Pickard DJ., Parkhill J., Page AJ., Feasey NA., Kingsley RA., Thomson NR., Keane JA., Weill F-X., Edwards DJ., Hawkey J., Harris SR., Mather AE., Cain AK., Hadfield J., Hart PJ., Thieu NTV., Klemm EJ., Glinos DA., Breiman RF., Watson CH., Kariuki S., Gordon MA., Heyderman RS., Okoro C., Jacobs J., Lunguya O., Edmunds WJ., Msefula C., Chabalgoity JA., Kama M., Jenkins K., Dutta S., Marks F., Campos J., Thompson C., Obaro S., MacLennan CA., Dolecek C., Keddy KH., Smith AM., Parry CM., Karkey A., Mulholland EK., Campbell JI., Dongol S., Basnyat B., Dufour M., Bandaranayake D., Naseri TT., Singh SP., Hatta M., Newton P., Onsare RS., Isaia L., Dance D., Davong V., Thwaites G., Wijedoru L., Crump JA., De Pinna E., Nair S., Nilles EJ., Thanh DP., Turner P., Soeng S., Valcanis M., Powling J., Dimovski K., Hogg G., Farrar J., Holt KE., Dougan G. 2015. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature genetics 47:632–639. DOI: 10.1038/ng.3281.
  58. Zakrzewski M., Proietti C., Ellis JJ., Hasan S., Brion M-J., Berger B., Krause L. 2017. Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions. Bioinformatics 33:782–783. DOI: 10.1093/bioinformatics/btw725.
  59. Zhou Z., McCann A., Weill F-X., Blin C., Nair S., Wain J., Dougan G., Achtman M. 2014. Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proceedings of the National Academy of Sciences of the United States of America 111:12199–12204. DOI: 10.1073/pnas.1411012111.