Microbial Publications of Genomes
Microbial Program at JGI-Home

Publications of JGI Genomes

collage of microbial genomes

2012

  1. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta.. Abt, B., C. Han, et al. (2012) . Stand Genomic Sci. 6(2).
  2. Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria. Anderson, I., B. Abt, et al. (2012) PLoS One 7(6): e39331.
  3. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT). Anderson, I., O. Chertkov, et al. (2012) Stand Genomic Sci.6(3).
  4. Harnessing glycosylation to improve cellulase activity. Beckham, G. T., Z. Dai, et al. (2012) Curr Opin Biotechnol.23(3): 338-345.
  5. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4 T ). Anderson, I., B. Held, et al. (2012) Stand Genomic Sci 6(2).
  6. Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812 T ). Anderson, I., E. Saunders, et al. (2012) Stand Genomic Sci 6(2).
  7. Complete genome sequence of Halopiger xanaduensis type strain (SH-6 T ). Complete genome sequence of Halopiger xanaduensis type strain (SH-6 T ). (2012) Stand Genomic Sci 6(1).
  8. Bacterial genome annotation. Beckloff, N., S. Starkenburg, et al. (2012) Methods Mol Biol. 881: 471-503.
  9. The "most wanted" taxa from the human microbiome for whole genome sequencing. Fodor, A. A., T. Z. DeSantis, et al. (2012) PLoS One 7(7): e41294.
  10. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. . Blanc, G., I. Agarkova, et al. (2012) Genome Biol 13(5): R39.
  11. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Brumm, P. J., S. Lucas, et al. (2012) Stand Genomic Sci. 6(3).
  12. Complete genome sequence of Paenibacillus sp. strain JDR-2. Chow, V., G. Nong, et al. (2012) Stand Genomic Sci. 6(1).
  13. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1 T) from a deep-sea hydrothermal vent chimney. Copeland, A., W. Gu, et al. (2012) Stand Genomic Sci. 6(1).
  14. Exploring symbioses by single-cell genomics. Kamke, J., K. Bayer, et al.(2012) Biol Bull. 223(1): 30-43
  15. A vast collection of microbial genes that are toxic to bacteria. Kimelman, A., A. Levy, et al.(2012) Genome Res. 22(4): 802-809.
  16. A vast collection of microbial genes that are toxic to bacteria. Kimelman, A., A. Levy, et al.(2012) Genome Res. 22(4): 802-809.
  17. Elucidating Essential Role of Conserved Carboxysomal Protein CcmN Reveals Common Feature of Bacterial Microcompartment Assembly.. Kinney, J. N., A. Salmeen, et al. (2012) Kinney, J. N., A. Salmeen, et al. 287(21): 17729-17736.
  18. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP T). Copeland, A., A. Zaytun, et al. (2012) Stand Genomic Sci 6(2).
  19. Mobile genetic elements in the bacterial phylum Acidobacteria. Kuske, C. and J. Challacombe (2012) Mobile Genetic Elements 2(4): 179-183.
  20. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4 T ). LCopeland, A., X. Zhang, et al. (2012) Stand Genomic Sci 6(2).
  21. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Liolios, K., L. Schriml, et al. (2012) Stand Genomic Sci 6(3).
  22. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alphaproteobacterium Starkeya novella type strain (ATCC 8093T). Davenport, K., S. Benson, et al. (2012) Stand Genomic Sci 7(1).
  23. Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. Davis, J. R., L. A. Goodwin, et al. (2012) J Bacteriol 194(9): 2396-2397.
  24. Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191. Desiniotis, A., V. N. Kouvelis, et al. (2012) J Bacteriol 194(21): 5966-5967.
  25. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Mavromatis, K., O. Chertkov, et al. (2012) Stand Genomic Sci. 6(2).
  26. Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1 T ). Meincke, L., A. Copeland, et al. (2012) Stand Genomic Sci 6(1).
  27. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. Mason, O. U., T. C. Hazen, et al. (2012) . ISME J 6(9): 1715-1727.
  28. Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii. Penz, T., S. Schmitz-Esser, et al. (2012) ). PLoS Genet 8(10): e1003012.
  29. A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules. Queiroux, C., B. K. Washburn, et al. (2012) ). BMC Microbiol 12(1): 74.
  30. Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D. Roberts, E. W., F. Cai, et al.(2012) ). J Bacteriol 194(4): 787-795.
  31. Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans.Vandera, E., K. Kavakiotis, et al.(2012) ). Appl Environ Microbiol 78(3): 621-627
  32. The essential role of the N-terminal domain of the orange carotenoid protein in cyanobacterial photoprotection: importance of a positive charge for phycobilisome binding. Wilson, A., M. Gwizdala, et al. (2012) ). Plant Cell24(5): 1972-1983
  33. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. Siddaramappa, S., J. Challacombe, et al. (2012) BMC Genomics13(1): 165
  34. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. Park, J. I., E. J. Steen, et al. (2012) PLoS One7(5): e37010.
  35. Artificial polyploidy improves bacterial single cell genome recovery. Dichosa, A. E., M. S. Fitzsimons, et al. (2012) PLoS One 7(5): e37387
  36. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. Garcia, S. L., K. D. McMahon, et al. (2012) Stand Genomic Sci. ISME J.
  37. GComplete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent. Giovannelli, D., J. Ricci, et al. (2012) Stand Genomic Sci. Vol 7, No 1
  38. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314 T ). Göker, M., E. Sauders, et al. (2012) Stand Genomic Sci. 6(2).
  39. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1 T ). Han, C., O. Kotsyurbenko, et al. (2012) Stand Genomic Sci. 6(1).
  40. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1 T ). Huntemann, M., H. Teshima, et al. (2012) Stand Genomic Sci. 6(2).
  41. High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. Isanapong, J., L. Goodwin, et al. (2012) J Bacteriol. 194(10): 2744-2745.
  42. Complete Genome Sequence of Clostridium clariflavum DSM 19732. Izquierdo, J. A., L. Goodwin, et al. (2012) Stand Genomic Sci. 6(1).
  43. Complete genome sequence of Thauera aminoaromatica strain MZ1T. Jiang, K., J. Sanseverino, et al. (2012) Stand Genomic Sci. 6(3).
  44. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128 T). Klenk, H.-P., M. Lu, et al. (2012) Stand Genomic Sci. 6(2).
  45. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15 T ). Klenk, H.-P., M. Lu, et al. (2012) Stand Genomic Sci. 7(1).
  46. Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181T). Lucas-Elío, P., L. Goodwin, et al. (2012) Stand Genomic Sci. 7(1).
  47. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1 T ). Lucas-Elío, P., L. Goodwin, et al. (2012) Stand Genomic Sci. 6(1).
  48. Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil. Martinez, R. J., D. Bruce, et al. (2012) J Bacteriol. 194(8): 2113-2114.
  49. Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil. Martinez, R. J., D. Bruce, et al. (2012) J Bacteriol. 194(8): 2113-2114.
  50. Complete Genome Sequence of Rahnella aquatilis CIP 78.65. Martinez, R. J., D. Bruce, et al. (2012) J Bacteriol. 194(11): 3020-3021.
  51. Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia. Garcia, M., D. M. Brazel, et al. (2012) PLoS One 7(4): e35314.
  52. Complete genome sequences of six strains of the genus methylobacterium. Marx, C. J., F. Bringel, et al. (2012) J Bacteriol . 194(17): 4746-4748.
  53. Complete genome sequence of Serratia plymuthica strain AS12. Neupane, S., R. D. Finlay, et al. (2012) Standards in Genomic Sciences. 6(2).
  54. Complete genome sequence of the plant-associated Serratia plymuthica strain AS13. Neupane, S., R. D. Finlay, et al. (2012) Standards in Genomic Sciences. 7(1).
  55. Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9. Neupane, S., N. Högberg, et al. (2012) Standards in Genomic Sciences. 6(1).
  56. Complete genome sequence of Terriglobus saanensis strain SP1PR4 T , an Acidobacteria from tundra soil. Rawat, S. R., M. K. Männistö, et al. (2012) Standards in Genomic Sciences. 7(1).
  57. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T ). Riedel, T., B. Held, et al. (2012) Standards in Genomic Sciences. Vol 7, No 1.
  58. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9 T ) and comparison to "Dehalococcoides" strains.Siddaramappa, S., J. F. Challacombe, et al. (2012). Standards in Genomic Sciences. 6(2).
  59. Complete Genome Sequence of Francisella philomiragia ATCC 25017.Zeytun, A., S. A. Malfatti, et al. J Bacteriol. 194(12): 3266.
  60. Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date. Zhaxybayeva, O., K. S. Swithers, et al. Genome Biol Evol. 4(8): 700-708.
  61. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Pagani I, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D571-9. Epub 2011 Dec 1.
  62. IMG: the integrated microbial genomes database and comparative analysis system. Markowitz V et al. Nucleic Acids Res 2012 Jan;40(Database issue):D115-22.

2011

  1. Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Zhang T et al. Green Chem 2011, 13, 2083-2090
  2. Heterologous expression and characterization of two 1-hydroxy-2-naphtoic acid dioxygenases from Arthrobacter phenanthrenivorans. Kavakiotis K et al. Appl Environ Microbiol. In press.
  3. Novel Structural Elements within the Non-Proteolytic Clostridium botulinum type F Toxin Gene Cluster. Dover N et al. Appl Environ Microbiol. 2011 Mar;77(5):1904-6. Epub 2010 Dec 23.
  4. Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea. Swithers KS et al. J Bacteriol. 2011 Oct;193(19):5566-7.
  5. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7. Suen G et al. J Bacteriol. 2011 Oct;193(19):5574-5.
  6. Decontamination of MDA Reagents for Single Cell Whole Genome Amplification. Woyke T et al. PLoS One 2011;6(10):e26161. Epub 2011 Oct 20.
  7. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Klenk HP et al. Stand Genomic Sci 2011 Sep 23;5(1). doi:10.4056/sigs.2144922
  8. Engineering E. coli for biodiesel production utilizing a bacterial fatty acid methyltransferase. Nawabi P et al. Appl Environ Microbiol. 2011 Sep 16. [Epub ahead of print]
  9. Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076. Challacombe JF et al. PLoS One. 2011;6(9):e24882. Epub 2011 Sep 15.
  10. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Monier A et al. Environ Microbiol. 2011 Sep 14. doi: 10.1111/j.1462-2920.2011.02576.x. [Epub ahead of print]
  11. Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia. Yuichi S et al. J Bacteriol. 2011 Sep 1;193(18)5047-5048.
  12. Genome Sequences of Alicycliphilus denitrificans Strains BC and K601T. Oosterkamp MJ et al. J Bacteriol. 2011 Sep;193(18):5028-9. Epub 2011 Jul 8.
  13. Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype ATCC 29192. Kouvelis VN et al. J Bacteriol. 2011 Jul 8. [Epub ahead of print]
  14. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A) . Anderson I et al. Stand Genomic Sci. 2011 Jul 1;4(3):381-92
  15. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1) . Anderson I et al. Stand Genomic Sci. 2011 Jul 1;4(3):322-30.
  16. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Han C et al. Stand Genomic Sci. 2011 Jul 1;4(3):371-80.
  17. Complete Genome Sequences of Krokinobactersp. Strain 4H-3-7-5 and Lacinutrixsp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family Flavobacteriaceae. Klippel B et al. J Bacteriol. 2011 Sep;193(17):4545-6. Epub 2011 Jul 1.
  18. Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96. Svenning MM et al. J Bacteriol. 2011 Jul 1. [Epub ahead of print]
  19. Genome sequence of 1,4-dioxane degrading Pseudonocardia dioxanivorans strain CB1190. Sales CM et al. J Bacteriol. 2011 Jul 1. [Epub ahead of print]
  20. Complete genome sequence of Mahella australiensis type strain (50-1 BON). Sikorski J et al. Stand Genomic Sci. 2011 Jul 1;4(3):331-41. Epub 2011 Jun 30
  21. Complete genome sequence of Treponema succinifaciens type strain (6091). Han C et al. Stand Genomic Sci. 2011 Jul 1;4(3):361-70. Epub 2011 Jun 30.
  22. Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype ATCC 10988. Pappas KM et al. J Bacteriol. 2011 Jul 1. [Epub ahead of print]
  23. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33). Munk AC et al. Stand Genomic Sci. 2011 Jul 1;4(3):342-51. Epub 2011 Jun 30.
  24. Complete genome sequence of Rhodospirillum rubrum type strain (S1). Munk AC et al. Stand Genomic Sci. 2011 Jul 1;4(3):293-302. Epub 2011 Jun 30.
  25. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2). Göker M et al. Stand Genomic Sci. 2011 Jul 1;4(3):393-401. Epub 2011 Jun 30.
  26. Complete genome sequence of Haliscomenobacter hydrossis type strain (O). Daligault H et al. Stand Genomic Sci. 2011 Jul 1;4(3):352-60. Epub 2011 Jun 30.
  27. Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL). Ivanova N et al. Stand Genomic Sci. 2011 Jul 1;4(3):312-21. Epub 2011 Jun 30.
  28. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Huntemann M et al. Stand Genomic Sci. 2011 Jul 1;4(3):303-11. Epub 2011 Jun 30.
  29. Complete genome sequence of Mahella australiensis type strain (50-1 BON). Sikorski J et al. Stand Genomic Sci. 2011 Jul 1;4(3):331-41. Epub 2011 Jun 30.
  30. Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus. Tang KH et al. J Bacteriol. 2011 Jun 29;12(1):334. [Epub ahead of print]
  31. Complete Genome Sequence of the Marine Cellulose- and Xylan-Degrading Bacterium Glaciecolasp. Strain 4H-3-7+YE-5. Klippel B et al. J Bacteriol. 2011 Sep;193(17):4547-8. Epub 2011 Jun 24.
  32. Genome of the Cyanobacterium Microcoleus vaginatus FGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide. Starkenburg SR et al. J Bacteriol. 2011 Sep;193(17):4569-70. Epub 2011 Jun 24.
  33. The genomic standards consortium. Field D et al. PLoS Biol. 2011 Jun;9(6):e1001088. Epub 2011 Jun 21.
  34. The Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20. Hauser LJ et al. J Bacteriol. 2011 Aug;193(16):4274-5. Epub 2011 Jun 17 [Epub ahead of print].
  35. Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. Chain PS et al. J Bacteriol. 2011 Aug;193(16):4274-5. Epub 2011 Jun 17.
  36. Draft Genome Sequence of Thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. Kalamorz F et al. J Bacteriol. 2011 Jun 17. [Epub ahead of print]
  37. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. Rodionov DA et al. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3
  38. Comparative Genomic Analyses of Francisella novicida-like Isolates from North America and Australia Reveal Common Ancestry and Novel Genetic Traits. Siddaramappa S et al. Appl Environ Microbiol. 2011 Jun 10. [Epub ahead of print]
  39. Complete Genome Sequence of the Anaerobic Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT. Zhao B et al. J Bacteriol. 2011 Jun 3. [Epub ahead of print]
  40. Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems. van Passel MW et al. J Bacteriol. 2011 May; 193(9): 2367-2368.
  41. Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum. Miller DA et al. J Bacteriol. 2011 May; 193(9): 2357-2358.
  42. Complete genome sequence of Lactobacillus buchneri NRRL B-30929, a novel strain from a commercial ethanol plant. Liu S et al. J Bacteriol. 2011 Aug;193(15):4019-20. Epub 2011 May 27.
  43. Genomes of three methylotrophs from a single niche uncover genetic and metabolic divergence of Methylophilaceae. Lapidus A et al. J Bacteriol. 2011 May 27.
  44. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes . Anderson I et al. PLoS One. 2011;6(5):e20237. Epub 2011 May 25.
  45. Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing Bacterium Halanaerobium hydrogeniformans. Brown SD et al. J Bacteriol. 2011 Jul;193(14):3682-3. Epub 2011 May 20.
  46. Comparative genomics of the dormancy regulons in mycobacteria. . Gerasimova A et al. J Bacteriol 2011 Jul;193(14):3446-52. Epub 2011 May 20.
  47. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. Galardini M et al. BMC Genomics 2011 May 12;12:235.
  48. Complete Genome Sequence of the Plant Growth-Promoting Endophyte Burkholderia phytofirmans Strain PsJN. Weilharter A et al. J Bacteriol. 2011 Jul;193(13):3383-4. Epub 2011 May 6.
  49. Genome sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614. Coleman NV et al. J Bacteriol. 2011 May 6. [Epub ahead of print]
  50. The Complete Genome Sequence of Streptomyces cf. griseus (XyelbKG-1), an Ambrosia Beetle-Associated Actinomycete. Grubbs KJ et al. J Bacteriol. 2011 Apr 1. [Epub ahead of print]
  51. Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium. Kant R et al. J Bacteriol. 2011 Apr 1. [Epub ahead of print]
  52. Genome sequence of Pedosphaera parvula Ellin514, an aerobic verrucomicrobial isolate from pasture soil. Kant R et al. J Bacteriol. 2011 Apr 1. [Epub ahead of print]
  53. Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313. Feinberg L et al. J Bacteriol. 2011 Apr 1. [Epub ahead of print]
  54. Complete genome sequence of Marivirga tractuosa type strain (H-43). Pagani I et al. Stand Genomic Sci. 2011 Apr 29;4(2):154-62.
  55. Complete genome sequence of Oceanithermus profundus type strain (506). Pati A et al. Stand Genomic Sci. 2011 Apr 29;4(2):210-20.
  56. Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Pati A et al. Stand Genomic Sci. 2011 Apr 29;4(2):221-32.
  57. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Land M et al. Stand Genomic Sci. 2011 Apr 29;4(2):233-43.
  58. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Mavromatis K et al. Stand Genomic Sci. 2011 Apr 29;4(2):144-53
  59. Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. Morrison N et al. Stand Genomic Sci. 2011 Apr 29;4(2):286-92
  60. Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3). Kallimanis A et al Stand Genomic Sci. 2011 Apr 29;4(2):123-30.
  61. Complete genome sequence of Bacteroides salanitronis type strain (BL78). Gronow S et al. Stand Genomic Sci. 2011 Apr 29;4(2):191-9.
  62. Complete genome sequence of Odoribacter splanchnicus type strain (1651/6). Göker M et al. Stand Genomic Sci. 2011 Apr 29;4(2):200-9.
  63. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans. Calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. Campbell MA et al. FEMS Microbiol Ecol. 2011 Apr;76(1):39-48
  64. Genome Sequence of Mercury-Methylating Desulfovibrio desulfuricans ND132. Brown SD et al. J Bacteriol. Apr;193(8):2078-9.
  65. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Wirth R et al. Stand Genomic Sci. 2011 Apr 29;4(2):173-82.
  66. Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Pukall R et al. Stand Genomic Sci. 2011 Apr 29;4(2):163-72. Epub 2011 Apr 25.
  67. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Zeytun A et al. Stand Genomic Sci. 2011 Apr 29;4(2):131-43
  68. The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist. Suen G et al. PLoS One. 2011 Apr 19;6(4):e18814
  69. The genomic potential of Marinobacter aquaeolei - A biogeochemical opportunitroph. Singer E et al. Appl Environ Microbiol. 2011 Apr; 77(8): 2763-2771
  70. Complete Genome Sequence of the Thermophilic Exiguobacterium sp. AT1b. Vishnivetskaya TA et al. J Bacteriol. 2011 Jun;193(11):2880-1. Epub 2011 Apr 1.
  71. Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242). Stein LY et al. J Bacteriol. 2011 May;193(10):2668-9. Epub 2011 Mar 25.
  72. Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant. Gibbons HS et al. PLoS One. 2011 Mar 25;6(3):e17836.]
  73. Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract. van Passel MW et al. J Bacteriol. 2011 Mar 11. [Epub ahead of print]
  74. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Abt B et al. Stand Genomic Sci. 2011 Mar 4;4(1):2-12.
  75. The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes. van Passel MW et al . PLoS One 2011 Mar 3;6(3):e16876.
  76. Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Sucgang R et al. Genome Biol. 2011 Feb 28;12(2):R20. [Epub ahead of print]
  77. Complete genome sequence of Cellulophaga algicola type strain (IC166). Abt B et al. Stand Genomic Sci. 2011 Feb 22;4(1):72-80.
  78. Complete genome sequence of Truepera radiovictrix type strain (RQ-24T). Ivanova N et al. Stand Genomic Sci. 2011 Feb 22;4(1):91-9.
  79. Complete genome sequence of Weeksella virosa type strain (9751T). Lang E et al. Stand Genomic Sci. 2011 Feb 22;4(1):81-90
  80. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Pati A et al. Stand Genomic Sci. 2011 Feb 22;4(1):45-53.
  81. Complete genome sequence of Isosphaera pallida type strain (IS1B). Goker M et al. Stand Genomic Sci. 2011 Feb 20;4(1):63-71.
  82. Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Gronow S et al. Stand Genomic Scit 2011 Feb 20;4(1):36-44.
  83. The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri. Frese SA et al. PLoS Genet. 2011 Feb;7(2):e1001314. Epub 2011 Feb 17
  84. Complete genome sequence of Thermomonospora curvata type strain (B9). Chertkov O et al. Stand Genomic Sci 2011 Feb 20;4(1):13-22.
  85. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Pitluck S et al. Stand Genomic Sci 2011 Feb 20;4(1):54-62..
  86. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3T). Pagani I et al. Stand Genomic Sci 2011 Feb 20;4(1):100-10.
  87. Complete genome sequence of Thioalkalivibrio sulfidophilus HL-EbGr7. Muyzer G et al. Stand Genomic Sci. 2011 Feb 14;4(1):23-35
  88. The ecoresponsive genome of Daphnia pulex. Colbourne JK et al. Science. 2011 Feb 4;331(6017):555-61.
  89. Using BLAST to Teach "E-value-tionary" Concepts. Kerfeld CA et al. PLoS Biol. 2011 Feb 1;9(2):e1001014.
  90. Comparative analysis of carboxysome shell proteins. Kinney JN et al. Photosynth Res2011 Jan 30. [Epub ahead of print]
  91. Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensenis, and Caldicellulosiruptor lactoaceticus. Blumer-Schuette SE et al. J Bacteriol. 2011 Mar;193(6):1483-4. Epub 2011 Jan 7.

2010

  1. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Ayala-del-Rio HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, Murray A, Thomashow M and Tiedje JM. Appl Environ Microbiol. 2010 Apr; 76 (7): 2304-12
  2. Genome sequence of hybrid V. cholerae O1 MJ-1236, B-33 and CIRS101 and comparative genomics with V. cholerae. Grim CJ, Hasan NA, Taviani E, Haley B, Chun J, Brettin TS, Bruce DC, Detter JC, Han CS, Chertkov O, Challacombe J, Huq A, Nair GB and Colwell RR. J Bacteriol. 2010 Mar 26;
  3. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. Lykidis A, Perez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, Gonzalez B and Kyrpides NC. PLoS One. 2010 5 (3): e9729
  4. Prodigal: prokaryotic gene recognition and translation initiation site identification. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW and Hauser LJ. BMC Bioinformatics. 2010 11 119
  5. Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and Schu S4. Nalbantoglu U, Sayood K, Dempsey MP, Iwen PC, Francesconi SC, Barabote RD, Xie G, Brettin TS, Hinrichs SH and Fey PD. PLoS One. 2010 5 (2): e9007
  6. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. Young M, Artsatbanov V, Beller HR, Chandra G, Chater KF, Dover LG, Goh EB, Kahan T, Kaprelyants AS, Kyrpides N, Lapidus A, Lowry SR, Lykidis A, Mahillon J, Markowitz V, Mavromatis K, Mukamolova GV, Oren A, Rokem JS, Smith MC, Young DI and Greenblatt CL. J Bacteriol. 2010 Feb; 192 (3): 841-60
  7. The integrated microbial genomes system: an expanding comparative analysis resource. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Anderson I, Lykidis A, Mavromatis K, Ivanova NN and Kyrpides NC. Nucleic Acids Res. 2010 Jan; 38 (Database issue): D382-90
  8. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM and Kyrpides NC. Nucleic Acids Res. 2010 Jan; 38 (Database issue): D346-54
  9. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T). Foster, B., Pukall, R., Abt, B., Nolan, M., Glavina Del Rio, T., Chen, F., Lucas, S., Tice, H., Pitluck, S., Cheng, J., Chertkov, O., Brettin, T., Han, C., Detter, J., Bruce, D., Goodwin, L., Ivanova, N., Mavromatis, K., Pati, A., Mikhailova, N., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y., Jeffries, C., Chain, P., Rohde, M., Gker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N., Klenk, H., & Lapidus, A. Standards In Genomic Sciences. 2010; 2(1): 1-8.
  10. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT). Mavromatis, K., Sikorski, J., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y., Jeffries, C., Chain, P., Meincke, L., Sims, D., Chertkov, O., Han, C., Brettin, T., Detter, J., Wahrenburg, C., Rohde, M., Pukall, R., Gker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H., & Kyrpides, N. Standards In Genomic Sciences. 2010; 2(1): 9-18.
  11. Complete genome sequence of Gordonia bronchialis type strain (3410T). Ivanova, N., Sikorski, J., Jando, M., Lapidus, A., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, YJ., Jeffries, CD., Chain, P., Saunders, E., Han, C., Detter, JC., Brettin, T., Rohde, M., Gker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, HP., and Kyrpides, NC. Standards In Genomic Sciences. 2010; 2(1):19-28
  12. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T). Nolan, M., Sikorski, J., Jando, M., Lucas, S., Lapidus, A., Glavina Del Rio, T., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Chertkov, O., Sims, D., Meincke, L., Brettin, T., Han, C., Detter, JC., Bruce, D., Goodwin, L., Land, M., Hauser, L., Chang, YJ., Jeffries, CD., Ivanova, N., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Chain, P., , M., Gker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, HP. Standards In Genomic Sciences. 2010; 2(1):29-37.
  13. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T). Spring, S., Nolan, M., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., Lucas, S., Land, M., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Pati, A., Mikhailova, N., Chen, A., Palaniappan, K., Hauser, L., Chang, YJ., Jeffries, CD., Munk, C., Kiss2, H., Han, C., Brettin, T., Detter, JC., Schler, E., P., Rohde, M., Gker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, H-P. Standards In Genomic Sciences. 2010; 2(1):38-48.
  14. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T). Pati, A., LaButti, K., Pukall, R., Nolan, M., Glavina Del Rio, T., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Copeland, A., Ivanova, N., Mavrommatis, K., Mikhailova, N., Pitluck, S., Bruce, D., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, C-D., Chen, A., Palaniappan, K., Chain, P., Brettin, T., Rohde, M., Gker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.P., and Lapidus, A. Standards In Genomic Sciences. 2010; 2(1):49-56.
  15. Complete genome sequence of Veillonella parvula type strain (Te3T). Gronow, S., Welnitz, S., Lapidus, A., Nolan, M., Ivanova, N., Glavina Del Rio, T., Copeland, A., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Saunders, E., Brettin, T., Han, C., Detter, JC., Bruce, D., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Pati, A., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Chain, P., Rohde, M., Gker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP., and Lucas, S. Standards In Genomic Sciences. 2010; 2(1):57-65.
  16. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Reeve, W., O'Hara, G., Chain, P., Ardley, J., Bru, L., Nandesena, K., Tiwari, R., Malfatti, S., Kiss, H., Lapidus, A., Copeland, A., Nolan, M., Land, M., Ivanova, N., Mavromatis, K., Markowitz, V., Kyrpides, N., Melino, V., Denton, M., Yates, R., & Howieson, J. Standards In Genomic Sciences. 2010; 2(1): 66-76.
  17. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Reeve, W., Chain, P., O'Hara, G., Ardley, J., Nandesena, K., Bru, L., Tiwari, R., Malfatti, S., Kiss, H., Lapidus, A., Copeland, A., Nolan, M., Land, M., Hauser, L., Chang, Y., Ivanova, N., Mavromatis, K., Markowitz, V., Kyrpides, N., Gollagher, M., Yates, R., Dilworth, M., & Howieson, J.Standards In Genomic Sciences. 2010; 2(1): 77-86.
  18. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Glavina Del Rio, T., Abt, B., Spring, S., Lapidus, A., Nolan, M., Tice, H., Copeland, A., Cheng, J., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Mikhailova, N., Pait, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y., Jeffries, C., Chain, P., Saunders, E., Detter, J., Brettin, T., Rohde, M., Gker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N., Klenk, H., & Lucas, S. Standards In Genomic Sciences. 2010; 2(1): 87-95.
  19. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T). Ivanova, N., Daum, C., Lang, E., Abt, B., Kopitz, M., Saunders, E., Lapidus, A., Lucas, S., Glavina Del Rio, T., Nolan, M., Tice, H., Copeland, A., Cheng, J., Bruce, D., Goodwin, L., Pitluck, S., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y., Jeffries, C., Detter, J., Brettin, T., Rohde, M., Gker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N., Klenk, H. Standards In Genomic Sciences. 2010; 2(1):96-106.
  20. Complete genome sequence of Haloterrigena turkmenica type strain (4kT). Saunders, E., Tindall, B., Fhnrich, R., Lapidus, A., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Cheng, J., Han, C., Detter, J., Bruce, D., Goodwin, L., Chain, P., Pitluck, S., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y., Jeffries, C., Brettin, T., Rohde, M., Gker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H., & Kyrpides, N. Standards In Genomic Sciences. 2010; 2(1): 107-116.

2009

  1. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'Haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP and Eisen JA. Nature. 2009 Dec 24; 462 (7276): 1056-60
  2. Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM and Kyrpides NC. PLoS One. 2009 4 (11): e7979
  3. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. McMurdie PJ, Behrens SF, Muller JA, Goke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Loffler FE and Spormann AM. PLoS Genet. 2009 Nov; 5 (11): e1000714
  4. Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. Kouvelis VN, Saunders E, Brettin TS, Bruce D, Detter C, Han C, Typas MA and Pappas KM. J Bacteriol. 2009 Nov; 191 (22): 7140-1
  5. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ and Stein JL. Appl Environ Microbiol. 2009 Nov; 75 (21): 6864-75
  6. Genomics. Genome project standards in a new era of sequencing. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC. Science. 2009 Oct 9;326(5950):236-7
  7. Improved genome annotation for Zymomonas mobilis. Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, Klingeman DM, Chang YJ, Samatova NF, Brown SD. Nat Biotechnol. 2009 Oct;27(10):893-4.
  8. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS and Jensen PR. ISME J. 2009 Oct; 3 (10): 1193-203
  9. The genomic basis of trophic strategy in marine bacteria. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S and Cavicchioli R. Proc Natl Acad Sci U S A. 2009 Sep 15; 106 (37): 15527-33
  10. Prepublication data sharing. Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martin-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J and Yu J. Nature. 2009 Sep 10; 461 (7261): 168-70
  11. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Chun J, Grim CJ, Hasan NA, Lee JH, Choi SY, Haley BJ, Taviani E, Jeon YS, Kim DW, Brettin TS, Bruce DC, Challacombe JF, Detter JC, Han CS, Munk AC, Chertkov O, Meincke L, Saunders E, Walters RA, Huq A, Nair GB and Colwell RR. Proc Natl Acad Sci U S A. 2009 Sep 8; 106 (36): 15442-7
  12. IMG ER: a system for microbial genome annotation expert review and curation. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K and Kyrpides NC. Bioinformatics. 2009 Sep 1; 25 (17): 2271-8
  13. The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer. Yagi JM, Sims D, Brettin T, Bruce D and Madsen EL. Environ Microbiol. 2009 Sep; 11 (9): 2253-70
  14. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D, Chong KW, Pilak O, Chew HH, De Maere MZ, Ting L, Katrib M, Ng C, Sowers KR, Galperin MY, Anderson IJ, Ivanova N, Dalin E, Martinez M, Lapidus A, Hauser L, Land M, Thomas T and Cavicchioli R. ISME J. 2009 Sep; 3 (9): 1012-35
  15. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G and Lapidus A. BMC Genomics. 2009 10 351
  16. Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1. Schubbe S, Williams TJ, Xie G, Kiss HE, Brettin TS, Martinez D, Ross CA, Schuler D, Cox BL, Nealson KH and Bazylinski DA. Appl Environ Microbiol. 2009 Jul; 75 (14): 4835-52
  17. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Kyrpides NC. Nat Biotechnol. 2009 Jul; 27 (7): 627-32
  18. Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. Kataeva IA, Yang SJ, Dam P, Poole FL, 2nd, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J and Adams MW. J Bacteriol. 2009 Jun; 191 (11): 3760-1
  19. Focus: Synergistetes. Hugenholtz P, Hooper SD, Kyrpides NC. Environ Microbiol 2009 Jun;11(6):1327-9.
  20. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Medigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS and Berry AM. Genome Res. 2009 Jun; 19 (6): 1033-43
  21. Genomic characterization of methanomicrobiales reveals three classes of methanogens. Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J and Kyrpides N. PLoS One. 2009 4 (6): e5797
  22. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML and Lovley DR. BMC Microbiol. 2009 9 109
  23. Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P and Brune A. Appl Environ Microbiol. 2009 May; 75 (9): 2841-9
  24. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J and Kyrpides N. BMC Genomics. 2009 10 145
  25. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K and Kyrpides NC. Nucleic Acids Res. 2009 Apr; 37 (7): 2096-104
  26. Whole-genome-based phylogeny and divergence of the genus Brucella. Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T and Keim P. J Bacteriol. 2009 Apr; 191 (8): 2864-70
  27. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM and Sorek R. Proc Natl Acad Sci U S A. 2009 Mar 10; 106 (10): 3976-81
  28. A changing of the guard. Hugenholtz P, Kyrpides NC. Environ Microbiol. 2009 Mar;11(3):551-3.
  29. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. Wagner-Dbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk HP, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, von Jan M, Wanphrut N, Wichels A, Zech H, Simon M. The ISME journal 2010 Jan ;4(1):61-77.
  30. Assembling the marine metagenome, one cell at a time. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME and Stepanauskas R. PLoS One. 2009 4 (4): e5299
  31. Standard Operating Procedure for the Annotations of Microbial Genomes by the Production Genomic Facility of the DOE JGI. Mavromatis, K., Ivanova, N., Chen, I., Szeto, E., Markowitz, V., & Kyrpides, N. Standards In Genomic Sciences. 2009; 1(1):63-67.
  32. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB and Thomson NR. Genome Biol. 2009 10 (5): R51
  33. Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P, Patel B and Kyrpides NC. PLoS One. 2009 4 (1): e4192
  34. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Hooper SD, Mavromatis K and Kyrpides NC. Genome Biol. 2009 10 (4): R45
  35. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T). Lapidus, A., Pukall, R., LaButtii, K., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Rohde, M., Gker, M., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N. and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(1): 3-11.
  36. Complete genome sequence of Kytococcus sedentarius type strain (strain 541T). Sims, D., Brettin, T., Detter, JC., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Schneider , S., Goker, M., Pukall, R., Kyrpides, N.C. and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(1):12-20.
  37. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T). Land, M., Pukall, R., Abt, B., Rohde, M., Glavina Del Rio, T., Tice, T., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis ,K., Ovchinnikova, G., Pati, A., Chen, A., Hauser, L., Chang, Y-Y., Jeffries, C.D., Saunders, L., Brettin, T., Detter, J.C., Han, C., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A. Standards in Genomic Sciences. 2009; 1(1):21-28.
  38. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Copeland, A., Spring, S., Gker, M., Schneider, S., Lapidus, A., Glavina Del Rio, T., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Meincke ,L., Sims, D., Brettin, T., Detter, J.C., Han, C., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., Klenk, H-P., and Lucas, S. Standards in Genomic Sciences. 2009; 1(1):29-37.
  39. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Clum, A., Nolan, M., Lang, E., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis , K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Gker, M., Spring, S., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., Klenk, H-P., and Lapidus, A. Standards in Genomic Sciences. 2009; 1(1):38-45.
  40. Complete genome sequence of Actinosynnema mirum type strain (101T) . Land, M., Lapidus, A., Mayilraj, S., Chen, F., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Chertkov, O., Bruce, D., Goodwin, L., Pitluck, S., Rohde, M., Gker, M., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Hauser, L., Chang, Y.Y., Jeffries, C.D., Brettin, T., Detter, C.J., Han, C., Chain, P., Tindall, B.J., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(1):46-53.
  41. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Han, C., Spring, S., Lapidus, A., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N, Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Saunders, L., Chertkov, O., Brettin, T., Gker, M., Rohde, M., Bristow, J., J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Detter, J.C. Standards in Genomic Sciences. 2009; 1(1):54-62.
  42. Complete genome sequence of Cryptobacterium curtum type strain (12-3T). Mavromatis, K., Pukall, R., Rohde, C., Sims, D., Brettin, T., Kuske, C., Detter, J., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Chen, A., Palaniappan, K., Chain, P., D'haeseleer, P., Bristow, J., Eisen, J.A, Markowitz, V., Hugenholtz, P., Rohde, M., Klenk, H-P., and Kyrpides, N.C. Standards in Genomic Sciences. 2009; 1(2):93-100.
  43. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Mavromatis, K., Gronow, S., Saunders, E., Land, M., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Pati, A., Ivanova, N., Chen, A., Palaniappan, K., Chain, P., Hauser, L. Chang, Y.Y., Jeffries, C.D., Brettin, T., Detter, J.C., Han, C., Bristow, J., Gker, M., Rohde, M., Eisen, J.A., Markowitz, V., Kyrpides, N.C., Klenk, H-P., and Hugenholtz, P. Standards in Genomic Sciences. 2009; 1(2):101-109.
  44. Complete genome sequence of Sanguibacter keddieii type strain (ST-74T). Ivanova, N., Sikorski, J., Sims, D., Brettin, T., Detter, J.C., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Pati, A., Mavromatis, K., Chen, A., Palaniappan, K., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Gker, M., Pukall, R., Klenk, H-P., and Kyrpides, N.C. Standards in Genomic Sciences. 2009; 1(2):110-118.
  45. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T). Copeland, A., Lapidus, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chertkov, O., Brettin, T., Detter, J.C., Han, C., Ali, Z., Tindall, B.J., Gker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(2):119-125.
  46. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT). Ivanova, N., Gronow, S., Lapidus, A., Copeland, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Saunders, L., Bruce, D., Goodwin, L., Brettin, T., Detter, J.C., Han, C., Pitluck, S., Mikhailova, N., Pati, A., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chain, P., Rohde, C., Gker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(2):126-132
  47. Complete genome sequence of Dyadobacter fermentans type strain (NS114T). Lang, E., Lapidus, A., Chertkov, O., Brettin, T., Detter, J.C., Han, C., Copeland, A., Glavina Del Rio, Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Land, M., Hauser, L., Chang, Y.Y., Jeffries, C.D., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Gker, M., Rohde, M., Kyrpides, N.C., and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(2): 133-140.
  48. Complete genome sequence of Saccharomonospora viridis type strain (P101T). Pati, A., Sikorski, J., Nolan, M., Lapidus, A., Copeland, A., Glavina Del Rio, Lucas, S., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Chertkov, O., Brettin, T., Han, C., Detter, J.C., Kuske, C., Bruce, D., Goodwin, L., Chain, P., D'haeseleer, P., Chen, A., Palaniappan, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Rohde, M., Tindall, B.J., Gker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(2):141-159.
  49. Complete genome sequence of Halogeometricum borinquense type strain (PR3T) . Malfatti, S., Tindall, B.J., Lapidus, A., LaButtii, K., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Anderson, I., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., D'haeseleer, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Chain, P. Standards in Genomic Sciences. 2009; 1(2):150-158.
  50. Complete genome sequence of Anaerococcus prevotii type strain (PC1T) . LaButti, K., Pukall, R., Steenblock, K., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Chain, P., Saunders, E., Brettin, T., Detter, J.C., Han, C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A. Standards in Genomic Sciences. 2009; 1(2):159-165.
  51. Complete genome sequence of Atopobium parvulum type strain (IPP 1246T) . Copeland, A., Sikorski, J., Lapidus, A., Nolan, M., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Pukall, R., Chertkov, O., Brettin, T., Han, C., Kuske, C., Bruce, D., Goodwin, L., Ivanova, N., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Chain, P., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Detter, C.J. Standards in Genomic Sciences. 2009; 1(2):166-173.
  52. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T). Saunders, E., Pukall, R., Abt, B., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, G., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-C., Jeffries, C.D., Chain, P., Meincke, L., Sims, D., Brettin, T., Detter, J.C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Han, C. Standards in Genomic Sciences. 2009; 1(2):174-182.
  53. Complete genome sequence of Methanoculleus marisnigri (Romesser et al. 1981) Maestrojuan et al. 1990 type strain JR1. Anderson, I.J., Sieprawska-Lupa, M., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Barry, K., Saunders, E., Han, C., Brettin, T., Detter, J.C., Bruce, D., Mikhailova, N., Pitluck, S., Hauser, L., Land, M., Lucas, S., Richardson, P., Whitman, W.B., and Kyrpides, N.C. Standards in Genomic Sciences. 2009; 1(2):183-188
  54. Complete genome sequence of Methanocorpusculum labreanum Zhao et al. 1989 type strain Z. Anderson, IJ., Sieprawska-Lupa, M., Goltsman, E., Lapidus, A., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Barry, K., Pitluck, S., Hauser, L., Land, M., Lucas, S., Richardson, P., Whitman, WB., and Kyrpides, N.C. Standards in Genomic Sciences. 2009; 1(2):189-196
  55. Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Anderson, IJ., Sun, H., Lapidus, A., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Lucas, S., Barry, K., Land, M., Richardson, P., Huber, H., and Kyrpides, N.C. Standards in Genomic Sciences. 2009; 1(2):197-203
  56. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T). Anderson, I., Tindall, B.J., Göker, M., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Chen, F., Tice, H., Cheng, J-F., Lucas, S., Chertkov, O., Bruce, D., Brettin, T., Detter, J.C., Han, C., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Pitluck, S., Pati, A., Mavromatis, K., Ivanova, N., Ovchinnikova, G., Chen, A., Palaniappan, K., Chain, P., Rohde, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P. Standards in Genomic Sciences. 2009; 1(3):218-225.
  57. Complete genome sequence of Kangiella koreensis type strain (SW-125T). Han, C., Sikorski, J., Lapidus, A., Nolan, M., Glavina Del Rio, T., Tice, H., Cheng, J-F., Lucas, D., Chen, F., Copeland, A., Ivanova, N., Mavrommatis, K., Ovchinnikova, G., Pati, A., Bruce, D., Goodwin, L., Pitluck, S., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Saunders, E., Brettin, T., Göker, M., Tindall, BJ., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Detter, CJ. Standards in Genomic Sciences. 2009; 1(3):226-233
  58. Complete genome sequence of Slackia heliotrinireducens type strain (RSH 1T). Pukall, R., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Chertkov, O., Bruce, D., Goodwin, L., Kuske, C., Brettin, T., Detter, JC., Han, C., Pitluck, S., Pati, A., Mavromatis, K., Ivanova, N., Ovchinnikova, G., Chen, A., Palaniappan, K., Schneider, S., Rohde, M., Chain, P., D'haeseleer, P., Göker, M., Bristow, J., Eisen, J., Markowitz, V, Kyrpides, NC., Klenk, HP., and Hugenholtz, P. Standards in Genomic Sciences. 2009; 1(3):234-241.
  59. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T). Spring, S., Lapidus, A., Schröder, M., Gleim, D., Sims, D., Meincke, L., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Saunders, E., Brettin, T., Detter, J.C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP., and Han, C. Standards in Genomic Sciences. 2009; 1(3):242-253
  60. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T). Chovatia, M., Sikorski, J., Schröder, M., Lapidus, A., Matt Nolan1, Hope Tice1, Glavina Del Rio, T., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Saunders, E., Detter, JC., Brettin, T., Rohde, M., Göker, M., Spring, S., Bristow, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP., and Eisen, JA. Standards in Genomic Sciences. 2009; 1(3):254-261
  61. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T). Pukall, R., Gehrich-Schröter, G., Lapidus, A., Nolan, M., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Pitluck, S., Jan-Fang Cheng, J-F., Copeland, A., Saunders, E., Brettin, T., Detter, JC., Bruce, D., Goodwin, L., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Han, C. Standards in Genomic Sciences. 2009; 1(3):262-269.
  62. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T). Tindall, B.J., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Saunders, E., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Brettin, T., Han, C., Rohde, M., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H-P., Kyrpides, NC., and Detter, JC. Standards in Genomic Sciences. 2009; 1(3):270-277.
  63. Complete genome sequence of Rhodothermus marinus type strain (R-10T). Nolan, M., Tindall, BJ., Pomrenke, H., Lapidus, A., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, Cheng, J-F., Saunders, E., Han, C., Bruce, D., Goodwin, L., Chain, P., Pitluck, S., Ovchinikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Brettin, T., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Detter, JC. Standards in Genomic Sciences. 2009; 1(3):283-291
  64. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T). Munk, C., Lapidus, A., Alex Copeland, A., Marlen Jando, M., Mayilraj, S., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Han, C., Detter, C.J., Bruce, D., Goodwin, L., Chain, P., Pitluck, S., Göker, M., Ovchinikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P. Standards in Genomic Sciences. 2009; 1(3):292-299.
  65. Complete genome sequence of Streptobacillus moniliformis type strain (9901T). Nolan, M., Gronow, S., Lapidus, A., Ivanova, N., Copeland, A., Lucas, S., Glavina Del Rio, T., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Sims, D., Meincke, L., Bruce, D., Goodwin, L., Brettin, T., Han, C., Detter, JC., Ovchinikova, G., Pati, A., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Rohde, M., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Chain, P. Standards in Genomic Sciences. 2009; 1(3):300-307.
  66. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T).Clum, A., Tindall, BJ., Johannes Sikorski, J., Natalia Ivanova, N., Mavromatis, K., Lucas, S., Glavina Del Rio, T., Nolan, M., Chen, F., Tice, H., Pitluck, S., Cheng, JF., Chertkov, O., Brettin, T., Han, C., Detter, J.C., Kuske, C., Bruce, D., Goodwin, L., Ovchinikova, G., Pati, A., Mikhailova, N., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, YJ., Jeffries, CD., Chain, P., Rohde, M., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Lapidus, A. Standards in Genomic Sciences. 2009; 1(3):308-316.

2008

  1. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM and Mills DA. Proc Natl Acad Sci U S A. 2008 Dec 2; 105 (48): 18964-9
  2. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Oda Y, Larimer FW, Chain PS, Malfatti S, Shin MV, Vergez LM, Hauser L, Land ML, Braatsch S, Beatty JT, Pelletier DA, Schaefer AL and Harwood CS. Proc Natl Acad Sci U S A. 2008 Nov 25; 105 (47): 18543-8
  3. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J and Tiedje JM. BMC Genomics. 2008 9 547
  4. Divergence among genes encoding the elongation factor Tu of Yersinia Species. Isabel S, Leblanc E, Boissinot M, Boudreau DK, Grondin M, Picard FJ, Martel EA, Parham NJ, Chain PS, Bader DE, Mulvey MR, Bryden L, Roy PH, Ouellette M and Bergeron MG. J Bacteriol. 2008 Nov; 190 (22): 7548-58
  5. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG and Ragsdale SW. Environ Microbiol. 2008 Oct; 10 (10): 2550-73
  6. A korarchaeal genome reveals insights into the evolution of the Archaea. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M and Stetter KO. Proc Natl Acad Sci U S A. 2008 Jun 10; 105 (23): 8102-7
  7. Genomic sequencing of single microbial cells from environmental samples. Ishoey T, Woyke T, Stepanauskas R, Novotny M and Lasken RS. Curr Opin Microbiol. 2008 Jun; 11 (3): 198-204
  8. Habitat-Lite: a GSC case study based on free text terms for environmental metadata. Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, Schriml LM and Field D. OMICS. 2008 Jun; 12 (2): 129-36
  9. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N and White O. OMICS. 2008 Jun; 12 (2): 137-41
  10. Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glockner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D and Dawyndt P. OMICS. 2008 Jun; 12 (2): 123-7
  11. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW and Starkenburg SR. Appl Environ Microbiol. 2008 Jun; 74 (11): 3559-72
  12. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. Weiner RM, Taylor LE, 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I and Hutcheson S. PLoS Genet. 2008 May; 4 (5): e1000087
  13. Genomics of an extreme psychrophile, Psychromonas ingrahamii. Riley M, Staley JT, Danchin A, Wang TZ, Brettin TS, Hauser LJ, Land ML and Thompson LS. BMC Genomics. 2008 9 210
  14. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B and Bottomley PJ. Appl Environ Microbiol. 2008 May; 74 (9): 2852-63
  15. The minimum information about a genome sequence (MIGS) specification. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glockner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G and Wipat A. Nat Biotechnol. 2008 May; 26 (5): 541-7
  16. Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J and Kyrpides N. J Bacteriol. 2008 Apr; 190 (8): 2957-65
  17. The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains. Auger S, Galleron N, Bidnenko E, Ehrlich SD, Lapidus A and Sorokin A. Appl Environ Microbiol. 2008 Feb; 74 (4): 1276-80
  18. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hugler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q and Simon J. Appl Environ Microbiol. 2008 Feb; 74 (4): 1145-56
  19. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Lapidus A, Goltsman E, Auger S, Galleron N, Segurens B, Dossat C, Land ML, Broussolle V, Brillard J, Guinebretiere MH, Sanchis V, Nguen-The C, Lereclus D, Richardson P, Wincker P, Weissenbach J, Ehrlich SD and Sorokin A. Chem Biol Interact. 2008 Jan 30; 171 (2): 236-49
  20. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Liolios K, Mavromatis K, Tavernarakis N and Kyrpides NC. Nucleic Acids Res. 2008 Jan; 36 (Database issue): D475-9
  21. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN and Kyrpides NC. Nucleic Acids Res. 2008 Jan; 36 (Database issue): D528-33
  22. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Jr., Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M and Stetter KO. Genome Biol. 2008 9 (11): R158

2007

  1. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Tuanyok A, Auerbach RK, Brettin TS, Bruce DC, Munk AC, Detter JC, Pearson T, Hornstra H, Sermswan RW, Wuthiekanun V, Peacock SJ, Currie BJ, Keim P and Wagner DM. J Bacteriol. 2007 Dec; 189 (24): 9044-9
  2. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Stein LY, Arp DJ, Berube PM, Chain PS, Hauser L, Jetten MS, Klotz MG, Larimer FW, Norton JM, Op den Camp HJ, Shin M and Wei X. Environ Microbiol. 2007 Dec; 9 (12): 2993-3007
  3. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P and Chisholm SW. PLoS Genet. 2007 Dec; 3 (12): e231
  4. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM and Kane SR. Appl Environ Microbiol. 2007 Nov; 73 (22): 7347-57
  5. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavrommatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV and Daly MJ. PLoS One. 2007 2 (9): e955
  6. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR and Moore BS. Proc Natl Acad Sci U S A. 2007 Jun 19; 104 (25): 10376-81
  7. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC and Hugenholtz P. BMC Bioinformatics. 2007 8 209
  8. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM and Lidstrom ME. J Bacteriol. 2007 Jun; 189 (11): 4020-7
  9. Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Xie G, Bruce DC, Challacombe JF, Chertkov O, Detter JC, Gilna P, Han CS, Lucas S, Misra M, Myers GL, Richardson P, Tapia R, Thayer N, Thompson LS, Brettin TS, Henrissat B, Wilson DB and McBride MJ. Appl Environ Microbiol. 2007 Jun; 73 (11): 3536-46
  10. The positive role of the ecological community in the genomic revolution. Field D and Kyrpides N. Microb Ecol. 2007 Apr; 53 (3): 507-11
  11. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Kane SR, Chakicherla AY, Chain PS, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM and Hristova KR. J Bacteriol. 2007 Mar; 189 (5): 1931-45
  12. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB and Kyrpides N. J Bacteriol. 2007 Mar; 189 (6): 2477-86
  13. The Calyptogena magnifica chemoautotrophic symbiont genome. Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA and Cavanaugh CM. Science. 2007 Feb 16; 315 (5814): 998-1000
  14. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C and Benson DR. Genome Res. 2007 Jan; 17 (1): 7-15
  15. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Arp DJ, Chain PS and Klotz MG. Annu Rev Microbiol. 2007 61 503-28
  16. Comparative genome analysis in the integrated microbial genomes (IMG) system. Markowitz VM and Kyrpides NC. Methods Mol Biol. 2007 395 35-56

2006

  1. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hugler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Jr., Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE and Zeruth GT. PLoS Biol. 2006 Nov; 4 (12): e383
  2. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. Maeder DL, Anderson I, Brettin TS, Bruce DC, Gilna P, Han CS, Lapidus A, Metcalf WW, Saunders E, Tapia R and Sowers KR. J Bacteriol. 2006 Nov; 188 (22): 7922-31
  3. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB and Tiedje JM. Proc Natl Acad Sci U S A. 2006 Oct 17; 103 (42): 15280-7
  4. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM and Ward BB. Appl Environ Microbiol. 2006 Sep; 72 (9): 6299-315
  5. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC and Andersen GL. J Bacteriol. 2006 Jun; 188 (12): 4453-63
  6. The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Mavromatis K, Doyle CK, Lykidis A, Ivanova N, Francino MP, Chain P, Shin M, Malfatti S, Larimer F, Copeland A, Detter JC, Land M, Richardson PM, Yu XJ, Walker DH, McBride JW and Kyrpides NC. J Bacteriol. 2006 Jun; 188 (11): 4015-23
  7. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ and Hickey WJ. Appl Environ Microbiol. 2006 Mar; 72 (3): 2050-63
  8. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP and Kelly DP. J Bacteriol. 2006 Feb; 188 (4): 1473-88
  9. Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. Porat I, Kim W, Hendrickson EL, Xia Q, Zhang Y, Wang T, Taub F, Moore BC, Anderson IJ, Hackett M, Leigh JA and Whitman WB. J Bacteriol. 2006 Feb; 188 (4): 1373-80
  10. The integrated microbial genomes (IMG) system. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N and Kyrpides NC. Nucleic Acids Res. 2006 Jan 1; 34 (Database issue): D344-8
  11. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Liolios K, Tavernarakis N, Hugenholtz P and Kyrpides NC. Nucleic Acids Res. 2006 Jan 1; 34 (Database issue): D332-4

2005

  1. Whole-genome analyses of speciation events in pathogenic Brucellae. Chain PS, Comerci DJ, Tolmasky ME, Larimer FW, Malfatti SA, Vergez LM, Aguero F, Land ML, Ugalde RA and Garcia E. Infect Immun. 2005 Dec; 73 (12): 8353-61
  2. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, Land M, Richardson PM, Kyrpides NC, Ivanova N and Lindow SE. Proc Natl Acad Sci U S A. 2005 Aug 2; 102 (31): 11064-9

2004

  1. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JL, Peres C, Harrison FH, Gibson J and Harwood CS. Nat Biotechnol. 2004 Jan; 22 (1): 55-61

2003

  1. The genome of a motile marine Synechococcus. Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA and Waterbury J. Nature. 2003 Aug 28; 424 (6952): 1037-42
  2. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER and Chisholm SW. Nature. 2003 Aug 28; 424 (6952): 1042-7
  3. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M and Arp D. J Bacteriol. 2003 May; 185 (9): 2759-73