Jonathan Eisen’s Publications

Jonathan A. Eisen’s Publications

Below is a semi-regularly updated list of Jonathan Eisen’s publications. For alternative views see Eisen’s Mendeley Page,  Google Scholar “Citations” pagePintarest BoardImpactStory Collection w/ Alt Metrics Information.

2014


  1. Bik HM, Coil DA, Eisen JA. 2014. microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere. PLoS Biol 12(6): e1001884. doi:10.1371/journal.pbio.1001884

  1. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415. http://dx.doi.org/10.7717/peerj.415

  1. Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Faccioti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. 2014. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environmental Microbiology doi: 10.1111/1462-2920.12388.

  1. Eisen JA, Ganley E, MacCallum CJ. 2014. Open Science and Reporting Animal Studies: Who’s Accountable? PLOS Biology 12(1): e1001757. doi:10.1371/journal.pbio.1001757

  1. Darling AE; Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. http://dx.doi.org/10.7717/peerj.243.

  1. Kyrpides N, Woyke T, Eisen JA, Garrity G, Lilburn T, Beck B, Whitman W, Hugenholtz P, & Klenk HP. 2014. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9(3). doi:10.4056/506

2013



  1. Garrity G, Banfield J, Eisen JA, van der Lelie N, McMahon T, Rusch D, DeLong E, Moran MA, Currie C, Fuhrman J, Hallam S, Hugenholtz P, Moran NA, Nelson K, Roberts R,  Stepanauskas R. 2013. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences, 8(3). doi:10.4056/sigs.4638348 .

  1. Wu D, Jospin G, Eisen JA. 2013. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLOS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

  1. Eisen JA, MacCallum CJ, Neylon C. 2013. Expert Failure: Re-evaluating Research Assessment. PLOS Biology 11(10): e1001677. doi:10.1371/journal.pbio.1001677

  1. Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JS. 2013. The Impact of Helicobacter pylori Infection on the Gastric Microbiota of the Rhesus Macaque. PLOS ONE 8(10): e76375. doi:10.1371/journal.pone.0076375.

  1. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4:2120. doi: 10.1038/ncomms3120. PMID: 23979677.

  1. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459): 431-7. doi: 10.1038/nature12352.

  1. Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510. 

  1. Rands C, Darling AE, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. 2013. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequenceBMC Genomics 2013, 14:95 doi:10.1186/1471-2164-14-95.

  1. Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences USA. Ahead of print 12/31. PDF.

2012


  1. Eisen JA.  2012. Phylogenetic and phylogenomic approaches to analysis of microbial communities. In “The Social Biology of Microbial Communities – A Report from the National Academy of Sciences Forum on Microbial Threats.” PDF.

  1. Traag B, Pugliese A, Eisen JA, Losick R. 2012. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis  Journal of Bacteriology JB.01778-12 . PMID: 23123912. PDF.

  1. Kembel SW, Wu M, Eisen JA, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology 8(10): e1002743.  doi:10.1371/journal.pcbi.1002743. PMID: 23133348. PDF.

  1. Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KSEisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resourceBMC Bioinformatics 13: 264. doi:10.1186/1471-2105-13-264.  PMID: 23061897. PDF.
    • More information and data links available here.

  1. Jiang X, Langille MGI, Neches RY, Elliot MA, Levin SAEisen JA, Weitz JS, Dushoff J. 2012. Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scalesPLoS ONE 7(9): e43866. doi:10.1371/journal.pone.0043866. PMID: 23049741. PDF.

  1. Tritt A, Eisen JA, Facciotti M, Darling A. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7(9): e42304.  doi:10.1371/journal.pone.0042304. PMID: 23028432. PDF.

  1. Chandler JA, Eisen JA, Kopp A. 2012. Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts. Applied and Environmental Microbiology 78(20): 7327-7336. PMID: 22885750. PDF.

  1. Lynch EA, Langille MGI, Darling AE, Wilbanks EG, Haltiner C, Shao KSY, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389. PMID: 22848480. PDF.

  1. Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1:6. PDF.

  1. Langille MGI, Laird M, Hsiao W, Chiu T, Eisen JA, Brinkman F. 2012. MicrobeDB: a locally maintainable database of microbial genomic sequence. Bioinformatics doi: 10.1093/bioinformatics/bts273. PMID: 22576174. PDF.

  1. Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomicsPLoS ONE 7(1): e30288. PMID: 22272325. PDF.

  1. Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. 2012. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14(1): 162-76. PMID: 21914098. PDF

2011


  1. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K. 2011. Genome-scale analysis of programmed DNA elimination sites in Tetrahymena thermophila. G3 1(6): 515-522. PMID: 22384362. PDF.

  1. Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model systemPLoS Genetics 7(9): e1002272. PMID: 21966276. PDF. 

  1. Darling A, Tritt A, Eisen JA, Facciotti M. 2011. Mauve assembly metrics. Bioinformatics 10.1093/bioinformatics/btr451. PMID: 21810901. PDF.

  1. Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6(8): e23214. PMID: 21912589. PDF.

  1. Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. 2011. Aggregating, tagging and integrating biodiversity research. PLoS ONE 6(8): e19491. PMCID: PMC3148223. PDF.

  1. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proceedings of the National Academy of Sciences USA 108: 7850-7854. PMID: 21518859. PDF.

  1. Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees. PLoS ONE 6(3): e18011. PMID: 21437252. PDF.

  1. Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PhylOTU: A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology 7(1): e1001061.PMID: 21283775. PDF.

  1. Wu M, Eisen JA. 2011. Towards automated phylogenomic inference. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press. (NOTE – THIS IS A REPRINTING WITH ONLY SLIGHT MODIFICATIONS OF WU & EISEN 2008)

  1. Eisen JA. 2011. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches.  Wiley Press. (NOTE – THIS IS A REPRINTING WITH ONLY SLIGHT MODIFICATIONS OF EISEN 2007)

2010


  1. Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. The genome sequence of Methanohalophilus mahii SLP reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010: 690737. PMID: 21234345. PDF.

  1. Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. 2010. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics 11: 317. PMID: 20540779. PDF.

  1. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2010. Meeting Report. The Terabase Metagenomics workshop and the vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3): 243-248. PMID: 21304727. PDF.

  1. Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134. PDF.
    • Data available here.

  1. Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944. PDF.

  1. Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 5(3): e9605. PMID: 20333302. PDF.

2009


  1. 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, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462(7276): 1056-60. PMID: 20033048. PDF. Supplemental Information PDF.

  1. Hartman A, Lough D, Fiehn O, Barupal D, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proceedings of the National Academy of Sciences USA 106(40): 17187-17192. PMID: 19805153. PDF.

  1. Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biology 7(10): e1000224. PMID: 19855830. PDF.

  1. Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL. 2009. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS ONE 4(7): e6085. PMID: 19568419. PDF.

  1. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. 2009. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genetics 5(2): e1000362. PMID: 19197347. PDF.

  1. Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4(4): e5299. PMID: 19390573. PDF.

  1. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb FT Colman AS, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum PLoS ONE 4(1): e4207. PMID: 19148287. PDF.

  1. Eisen JA. 2009. Genomic Evolvability and the Origin of Novelty: Studying the Past, Interpreting the Present, and Predicting the Future. In Relman DA, Hamburg MA, Choffness ER, Mack A (ed), Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. The National Academies Press, Washington, DC. PDF.

  1. Eisen JA. 2009. What is so bad about brain doping? Apparently, NIH thinks something is. In Rohn J, (ed), The Open Laboratory 2008. Lulu.Com.

2008


  1. Eisen JA. 2008. PLoS Biology 2.0. PLoS Biology 6(2):e48. doi: 10.1371/journal.pbio.0060048. No abstract available. PMID: 18303952.

  1. Valdes J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9: 597. PMID: 19077236. PDF.

  1. Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methe BA. 2008. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics 9 (1): 562. PMID: 19036158. PDF.

  1. 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, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. 2008. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.  Genome Biology 9 (11): R158. PMID: 19000309. PDF.

  1. Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9(1): R151. PMID: 18851752. PDF.

  1. Wu D, Hartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3(7): e2566. PMID: 18596968. PDF.

  1. Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. Research in Computational Molecular Biology. Lecture Notes in Computer Science Volume 4955, 2008, pp 17-28PDF.

2007


  1. Hazen TH, Wu D, Eisen JA, Sobecky PA. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and Environmental Microbiology 73(23): 7703-7710. PMID: 17921277. PDF.

  1. Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. 2007. On the taxonomic status of the intracellular bacteria Wolbachia pipientis: should this species naming include the intracellular bacteria of filarial nematodes? International Journal of Systematic and Evolutionary Microbiology 57: 1677-8. PMID: 17684235. PDF.

  1. Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteria. Proceedings of the National Academy of Sciences USA 104: 11784-11789. PMID: 1760690. PDF.

  1. Norais C, Hawkins M, Eisen JA, Hartman A, Myllkallio H, Allers T. 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii.PLoS Genetics 3(5): e77. PMID: 17511521. PDF.

  1. Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82. PMID: 17355177. PDF.

  1. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. 2007. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families.  PLoS Biology 5(3): e16 . PMID: 17355171. PDF.

  1. 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 YH, Falcon 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(3): e77. PMID: 17355176. PDF.

  1. Newton ILG, 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, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000. PMID: 17303757. PDF. Supplement PDF.

2006


  1. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Lartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. 2006. Evolution of sensory complexity recorded in a myxobacterial genome. Proceedings of the National Academy of Sciences USA 103: 15200-5. PMID: 17015832. PDF.

  1. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology 4: e286. PMID: 16933976. PDF.

  1. Wu D, Daugherty SC, van Aken S, Pai G, Watkins K, Khouri H, Tallon L, Zaborsky J, Dunbar H, Tran P, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PLoS Biology 4: e188. PMID: 16729848. PDF.

  1. Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. 2006. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genetics 2: e21. PMID: 16482227. PDF.

  1. Leebens-Mac J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, DePamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin, EV, Mishler BD, Philippe H, Pirer JC, Qiu Y-L, Rheee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the first steps towards a phylogenetic reporting standard: minimal information about a phylogenetic analysis (MIAPA). OMICS 10(2): 231-238PDF.

  1. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. 2006. The use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics 88(4): 443-451PDF.

  1. Penn K, Wu D, Eisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72: 1680-1683. PMID: 16461727. PDF.

2005


  1. Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA. 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genetics 1: e65.  PMID: 16729848. PDF.

  1. Schmidt EW, Nelson JT, Rakso D, Sudek S, Eisen JA, Haygood MG, Ravel J. 2005. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the obligate cyanobacterial symbiont of Lissoclinum patella (ascidia). Proceedings of the National Academy of Sciences USA 102: 7315-7320.  PMID: 15883371. PDF.

  1. Badger JH, Eisen JA; Ward N. 2005. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA-based phylogenetic analysis; implications for the taxonomy of the orders Rhodobacterales and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology 55: 1021-1026. PMID: 15879228. PDF.

  1. Desjardins C, Eisen JA, Nene V. 2005. New evolutionary frontiers from unusual virus genomes. Genome Biology 6: 212-213. PMID: 15774035. PDF.

  1. Seshadri R, Adrian L, Fouts DE, Phillippy AM, Eisen JA, Methe BM, Deboy RT, Ward NL, Nelson WC, Khouri HM, Kang KH, Tran K, Forberger HA, Robinson JM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Fraser CM, Zinder SH, Heidelberg JF. 2005. Genome sequence of the anaerobic PCE-bioremediating bacterium, Dehalococcoides ethenogenes strain 195. Science 307: 105-108. PMID: 15637277. PDF.

  1. Robb FT, Gonzalez JM, Sokolova T, Chernyh N, Lebedinski A, Tallon LJ, Jones K, Wu MEisen JA. 2005.  Primary energy metabolism in geothermal environments: the role of carbon monoxide. In Inskeep WP, McDermott TR, (ed), Geothermal biology and geochemistry in Yellowstone National Park. Montana State University Thermal Biology Institute, Bozeman, MT. pp. 163-170. PDF.

  1. Eisen JA. 2005. Coordinating efforts to understand microbes in the environment. Letter to the Editor. Microbe, 71(4): 157.  PDF.

2004


  1. Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RB, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. 2004. Genome sequence of Silicibacter pomeroyi reveals unique adaptations to the marine environment. Nature 432: 910-913. PMID: 15602564. PDF.

  1. Tanaka M, Earl AM, Howell HA, Park M-J, Eisen JA, Peterson SN, Battista JR. 2004. Analysis of Deinococcus radiodurans’ transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 168: 21-33. PMID: 15454524. PDF.  Supplement.PDF

  1. Ward NM, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy R, Seshadria R, Salzberg SL, Jensen HB, Birkeland NK, Nelson W, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Feldblyum TV, Fraser CM, Lillehaug J, Eisen JA. 2004. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biology 2: 1616-1628. PMID: 15383840. PDF.

  1. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713. PDF.  Supplement.PDF.

  1. Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, Mohamoud Y, Lee P, Berry K, Khouri HM, Paulsen IT, Nelson KE, Martin W, Esser C, Ahmadinejad N, Wiegand C, Durkin AS, Nelson WC, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Gwinn M, Kolonay JF, Madupu R, Craven MB, Utterback T, Weidman J, Nierman WC, Aken SV, Tettelin H, O’Neill S, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements. PLoS Biology 2: 327-341. PMID: 15024419. PDF.

  1. Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen JA, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg SL, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM. 2004. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology 134: 183-191. PMID: 15003838. PDF.

  1. Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. 2004. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences USA 101: 5646-5651. PMID: 15064399. PDF.

  1. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotechnology 22: 554-559. PMID: 15077118. PDF

2003


  1. Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri, H Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. 2003. The genome of Geobacter sulfurreducens: insights into metal reduction in subsurface environments. Science 302: 1967-1969. PMID: 14671304. PDF.

  1. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. 2003. Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. Journal of Bacteriology 185: 5591-5601. PMID: 12949112. PDF.

  1. Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM. 2003. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. Journal of Bacteriology 185: 5220-5233. PMID: 12923095. PDF.

  1. Yang R-Z, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, Gong D-W. 2003. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochemical and Biophysical Research Communications 310: 927–935. PMID: 14550293. PDF.

  1. Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of Bacteriology 185: 3392-3399. PMID: 12754238. PDF.

  1. Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF. 2003. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proceedings of the National Academy of Sciences USA 100: 5455-5460. PMID: 12704232. PDF.

  1. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538. PDF.
  1. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071-2074. PMID: 12663927. PDF.

  1. Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. 2003. The age of the Arabidopsis thaliana genome duplication. Plant Molecular Biology 51: 859-866. PMID: 12777046. PDF.

  1. Shank T, Fornari D, Yoerger S, Humphries S, Bradley A, Hammond S, Lupton J, Schierer D, Collier R, Reysenbach A-L, Ding K, Seyfried W, Butterfield D, Olson E, Lilley M, Ward N, Eisen JA. 2003. Deep submergence synergy:Alvin and ABE explore the Galápagos Rift at 86°W. EOS 84: 425, 432-433. PDF.

  1. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM. 2003. The complete genome sequence of Bacillus anthracis Ames and comparison to closely-related B. cereus group bacteria. Nature 423: 81-86. PMID: 12721629. PDF.

2002


  1. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology 4: 799-808. PMID: 12534463. PDF.

  1. Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical and Population Biology 61: 481-487. PMID: 12167367. PDF.

  1. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature Biotechnology 20: 1118-1123. PMID: 12368813. PDF.

  1. Van Houten B, Eisen JA, Hanawalt PC. 2002. A cut above: discovery of an alternative excision repair pathway in bacteria. Proceedings of the National Academy of Sciences USA 99: 2581-2583. PMID: 11880612. PDF.

  1. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum.Nature 419: 498-511. PMID: 12368864. PDF.

  1. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proceedings of the National Academy of Sciences USA 99: 13148-13153. PMID: 12271122. PDF.

  1. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. 2002. The value of complete microbial genome sequencing (You get what you pay for). Journal of Bacteriology 184: 6403-6405. PMID: 12426324. PDF.

  1. Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. Journal of Bacteriology 184: 5479-5490. PMID: 12218036. PDF.

  1. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. 2002. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proceedings of the National Academy of Sciences USA 99: 12391-12396. PMID: 12200547. PDF.

  1. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF.2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633. PMID: 11832943. PDF.

  1. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Venter JC, Gruber TM, Ketchum KA, Tettelin H, Bryant DA, Fraser CM. 2002. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences USA 99: 9509-9514. PMID: 12093901. PDF.

  1. DasSarma S, Kennedy SP, Berquist B, Ng WV, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L. 2002. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynthesis Research 70: 3-17. PMID: 16228359. DOI: 10.1023/A:1013879706863. PDF.

  1. Eisen JA. 2002. Brouhaha over the other yeast. Nature 415: 845-848. PMID: 11859347. PDF.

  1. Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen JA, Slatko B. 2002. Sequencing and analysis of a 63 kb BAC from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi. International Journal of Parasitology 32: 159-166. PMID: 11812492. PDF.

2001


  1. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida Jr NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee Sr D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li M-J, McClelland R, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao Z-Y, Dolan M, Chumley F, Tingey SC, Tomb J-F, Gordon MP, Olson MV, Nester EW. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323. PMID: 11743193. PDF.

  1. Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology 2: interactions1004.1-1004.4. PDF.

  1. Tettelin H, Nelson KE, Paulsen I, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin S, Gwinn M, Kolonoay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CK, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293: 498-506. PMID: 11463916. PDF.

  1. Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527. PDF.

  1. Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM. 2001. Complete genome sequence of Caulobacter crescentus. Proceedings of the National Academy of Sciences USA 98: 4136-4141. PMID: 11259647. PDF.

  1. Salzberg SL, Eisen JA. 2001. Lateral gene transfer or viral colonization? Science 293: 1048. PMID: 11503638. PDF.

  1. Salzberg SL, White O, Peterson J, Eisen JA. 2001. Microbial genes in the human genome: lateral transfer or gene loss? Science 292: 1903-1906. PMID: 11358996.  PDF.

  1. Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes H-W. 2001. Sequence and analysis of the Arabidopsis genomeCurrent Opinion in Plant Biology 4: 105-110. PMID: 11228431. PDF.

  1. Nelson KE, Eisen JA, Fraser CM. 2001. The genome of Thermotoga maritima MSB8. Methods in Enzymology 330: 169-180. PMID: 11210497. PDF.

  1. Eisen JA. 2001. Gastrogenomics. Nature 409: 463-465. PMID: 11206526. PDF.

  1. Haft DH, Loftus, BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Research 29: 41-43. PMID: 11125044. PDF.

2000


  1. Eisen JA. 2000. Microbial and plant genomics. J Biolaw and Business, Spec Supp 21-24. PDF.

  1. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen JA, Fraser CM. 2000. Genome sequences of Chlamydia trachomatis MoPn and C. pneumoniae AR39. Nucleic Acids Research 28: 1397-1406. PMID: 10684935. PDF.

  1. Quetier F, Brennicke A, Eisen JA. 2000. Integration of the three genomes in the plant cell: the extent of protein and nucleic acid traffic between nucleus, plastids and mitochondria, In ‘Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.’ Nature 408: 796-815. PMID: 11130711. PDF.

  1. Britt AB, Eisen JA. 2000. DNA repair and recombination, In ‘Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. PMID: 11130711.  PDF.

  1. Nierman W, Eisen JA, Fleischmann RD, Fraser CM. 2000. Genome data: what do we learn? Current Opinion in Structural Biology 10: 343-348. PMID: 10851186. PDF.

  1. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287: 1809-1815. PMID: 10710307. PDF.

  1. Coleman MA, Eisen JA, Mohrenweiser HW. 2000. Cloning and characterization of HARP: A prokaryotic HepA related SNF2 helicase protein from human and mouse. Genomics 65: 274-282. PMID: 10857751. PDF.

  1. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. 2000. The genome sequence of Vibrio cholerae, the etiologic agent of cholera. Nature 406: 477-483. PMID: 10952301. PDF.

  1. Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1: research 0011.1-0011.9. PMID: 11178265. PDF.

  1. Pollock DD, Eisen JA, Doggett NA, Cummings MP. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular Biology and Evolution 7: 1776-1788. PMID: 11110893. PDF.

  1. Eisen JA. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Current Opinion in Genetics and Development 10: 606-611. PMID: 11088009. PDF.

  1. Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole genome analysis. Current Opinion in Microbiology 3: 475-480. PMID: 11050445. PDF.

  1. Fraser CM, Eisen JA, Fleischmann RD, Ketchum KA, Peterson S. 2000. Comparative genomics and understanding of microbial biology. Emerging Infectious Diseases 6: 505-512. PMID: 10998382. PDF.

  1. Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencing. Nature 406: 799-803. PMID: 10963611. PDF.

  1. Nierman W, Eisen JA, Fraser CM. 2000. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Research in Microbiology 151: 79-84.. PMID: 10865951. PDF.

1999


  1. Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Aken SV, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761-768. PMID: 10617197. PDF.

  1. Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation Research 435: 171-213. PMID: 10606811. PDF.

  1. Eisen JA. 1999. Going to extremes. Trends in Genetics 15: 218-219. PMID: 10419407. PDF.

  1. Eisen JA. 1999. Mechanistic basis of microsatellite instability. In Microsatellites: Evolution and Applications(DB Goldstein and C Schlotterer, eds). Oxford University Press, Oxford. PDF.

  1. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571-1577. PMID: 10567266. PDF.

  1. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329. PMID: 10360571. PDF.

1998


  1. Eisen JA. 1998. Evolution of DNA repair genes, proteins and processes.  PhD Thesis. Stanford University Department of Biology. PDF.

  1. Wei M-H, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, Lerman MI. 1998. In-silico initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Human Genetics 103: 355-364. PMID: 9799093. PDF.

  1. Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Research 26: 4291-4300. PMID: 9722651. PDF.

  1. Gruber TM, Eisen JA, Gish K, Bryant DA. 1998. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiology Letters 162: 53-60. PMID: 9595663. PDF.

  1. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8: 163-167. PMID: 9521918. PDF.

  1. White RB, Eisen JA, Kasten TW, Fernald RD. 1998. Second gene for gonadotropin-releasing hormone in humans. Proceedings of the National Academy of Sciences USA 95: 305-309. PMID: 941937. PDF.

1997


  1. Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078. PMID: 9334711. PDF.

  1. Eisen JA. 1997. The genetic data environment: a user modifiable and expandable multiple sequence analysis package, In Methods in Molecular Biology vol 70: Sequence Data Analysis Guidebook  (SR Swindell, ed), Humana, Totowa, NJ, pp. 13-38. PMID: 90896. PDF.

  1. Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. 1997. Sequence and drug susceptibility of subtype C reverse transcriptase from HIV-1-seroconverters in Zimbabwe. Journal of Virology 71: 5441-5448. PMID: 9188616. PDF.

1992-1996


  1. Eisen JA. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. Journal of Molecular Evolution 41: 1105-1123. PMID: 8587109. PDF.

  1. Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723. PMID: 7651832. PDF.

  1. Eisen JA, Benito M-I, Walbot V. 1994. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Research 22: 2634-2636. PMID: 8041625. PDF.

  1. Liu SK, Eisen JA, Hanawalt PC, Tessman IW. 1993. recA mutations that reduce the constitutive coprotease activity of the RecA1202(PrtC) protein: possible involvement of interfilament association in proteolytic and recombination activitiesJournal of Bacteriology 175: 6518-6529. PMID: 8407828. PDF.

  1. Eisen JA, Smith SW, Cavanaugh CM. 1992. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum Say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. Journal of Bacteriology 174: 3416-3421. PMID: 1577710. PDF.

Genome report publications. We have now begun publishing “report” papers for each genome we are sequencing. I am listing them separately because of the large number of reports.


2014


  1. Göker M, Spring S, Scheuner C, Anderson I, Zeytun A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2014. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci. 9(3): 1105-17. doi: 10.4056/sigs.3016383.

  1. Göker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2014. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences 9(3): 1076-88. doi: 10.4056/sigs.5138968.

  1. Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. 2014. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1. Genome Announcements 2(4). pii: e00833-14

  1. Lee RD, Jospin G, Coil DA, Eisen JA. 2014. Draft Genome Sequence of the Endosymbiont “Candidatus Ruthia magnifica” UCD-CM (Phylum Proteobacteria). Genome Announcements 2(4). pii: e00717-14

  1. Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. 2014. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announcements 2(3). pii: e00470-14. doi: 10.1128/genomeA.00470-14.

  1. Dunitz MI, James PM, Jospin G, Eisen JA, Coil DA, Chandler JA. 2014. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae. Genome Announc. 2014 Apr 24;2(2). pii: e00349-14. doi: 10.1128/genomeA.00349-14. PMID: 24762940

  1. Tokajian S, Eisen JA, Jospin G, Coil DA. 2014. Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon. Genome Announc. 2014 May 15;2(3). pii: e00358-14. doi: 10.1128/genomeA.00358-14. PMID: 24831139

  1. Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. 2014. Draft Genome Sequences of Extended-Spectrum β-Lactamase-Producing Escherchia coli Strains Isolated from Patients in Lebanon. Genome Announc. 2(1). pii: e00123-14. doi: 10.1128/genomeA.00123-14. PMID: 24558252.

  1. Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. 2014. Draft Genome Sequence of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon. Genome Announc. 2(1). pii: e00121-14. doi: 10.1128/genomeA.00121-14. PMID: 24558251

  1. Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. 2014. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12Genome Announc. 2(1). pii: e00109-14. doi: 10.1128/genomeA.00109-14. PMID: 24558247.
  1. Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen JA. 2013. Draft Genome Sequence of the arsenate respiring bacterium Chrysiogenes arsenatis DSM11915. Genome Announcements 1(6): e00953-13. doi:10.1128/genomeA.00953-13.

2013

  1. Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). Genome Announcements 1.3 (2013).  (Note – part of our Undergraduate Genome Sequencing project).

  1. Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1(3). doi:pii: e00172-13. 10.1128/genomeA.00172-13.  (Note – part of our Undergraduate Genome Sequencing project).

  1. Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1(3). doi:pii: e00244-13. 10.1128/genomeA.00244-13. (Note – part of our Undergraduate Genome Sequencing project).

  1. Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1(3). doi:pii: e00197-13. 10.1128/genomeA.00197-13. (Note – part of our Undergraduate Genome Sequencing project).

  1. Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13. (Note – part of our Undergraduate Genome Sequencing project).

  1.  Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13. (Note – part of our Undergraduate Genome Sequencing project).

  1. Anderson I, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Lang E, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences 2;9(1):83-92. doi: 10.4056/sigs.4338002. PMID: 24501647.

  1. Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Rohde M, Mayilraj S, Spring S, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences 9(1):57-70. doi: 10.4056/sigs.4237901. PMID: 24501645

  1. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides NC, Klenk HP. 2013. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Standards in Genomic Sciences 8(2):228-38. doi: 10.4056/sigs.3617113. PMID: 23991255.

  1. Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2013. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences. 8(2):177-87. doi: 10.4056/sigs.3637201. PMID: 23991250.

  1. Liolos K, Abt B, Scheuner C, Teshima H, Held B, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk HP, Kyrpides NC. 2013. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692T) from the alkaline Lake Magadi in the East African RiftStandards in Genomic Sciences, 8(2). doi:10.4056/sigs.3607108

  1. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides NC, Klenk HP. 2013. Complete genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT)Standards in Genomic Sciences, 8(2). doi:10.4056/sigs.3617113

  1. Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A 2013. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T). Standards in Genomic Sciences, 8(2). doi:10.4056/sigs.3637201

  1. Stackebrandt, E., Chertkov, O., Lapidus, A., Nolan, M., Lucas, S., Han, C., Cheng, J., Tapia, R., Goodwin, L., Bruce, D., Pitluck, S., Liolios, K., Mavromatis, K., Pagani, I., Ivanova, N., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Rohde, M., Tindall, B., Göker, M., Woyke, T., Detter, J., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H., & Kyrpides, N. 2013. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T). Standards in Genomic Sciences, 8(1). doi:10.4056/sigs.3537045

  1. Mavromatis, K., Stackebrandt, E., Held, B., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Land, M., Rohde, M., Spring, S., Göker, M., Woyke, T., Detter, J., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H., & Kyrpides, N. 2013. Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT). Standards in Genomic Sciences, 8(1). doi:10.4056/sigs.3547050

  1. Stackebrandt, E., Munk, C., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Rohde, M., Gronow, S., Göker, M., Detter, J., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N., Klenk, H., & Woyke, T. 2013. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T)Standards in Genomic Sciences, 8(1). doi:10.4056/sigs.3527032

  1. Stackebrandt, E., Zeytun, A., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Chang, Y., Land, M., Hauser, L., Rohde, M., Pukall, R., Göker, M., Detter, J., Woyke, T., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N., & Klenk, H. (2013). Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)Standards in Genomic Sciences, 8(1). doi:10.4056/sigs.3507020

2012


  1. Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. 2012. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8 T). Standards in Genomic Sciences, 7(2): 210-220.

  1. Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea. Standards in Genomic Sciences 7(1): 107-119.

  1. Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2012. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T). Standards in Genomic Sciences 7(1): 120-130.

  1. Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. 2012. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT). Standards in Genomic Sciences 6(3): 1-13.  doi: 10.4056/sigs.2736042.

  1. Copeland A, Zeytun A, Yassawong M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Mavromatis K, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Sikorski J, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2012. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Standards in Genomic Sciences 6(2):240-50. PMID: 22768367.

  1. Göker M, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2012.  Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences 6(2): 230-9. PMID: 22768366.

  1. Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Standards in Genomic Sciences 6(2):210-9. PMID: 22768364.

  1. Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Gronow S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2012.  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. Standards in Genomic Sciences 6(2): 194-209. PMID: 22768363

  1. Huntemann M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012.  Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences 6(2): 185-93. PMID: 22768362

  1. Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2012.  Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences 6(2): 174-84. PMID: 22768361.

  1. Anderson I, Saunders E, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Chang YJ, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2012. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences 6(2): 155-64. PMID: 22768359.

  1. Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. 2012. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences 6(2): 145-54. PMID: 22768358.

  1. Han C, Kotsyurbenko O, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2012. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1T). Standards in Genomic Sciences 6(1): 94-103. PDF. PMID: 22675602

  1. Copeland A, Gu W, Yasawong M, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng JF, Goodwin LA, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Pan C, Brambilla EM, Rohde M, Tindall BJ, Sikorski J, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Scieinces 6(1): 21-30. PMID: 22675595.

2011


  1. Göker M, Daligault H, Mwirichia R, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng J, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Han C, Land M, Hauser L, Pan C, Brambilla E, Rohde M, Spring S, Sikorski J, Wirth R, Detter J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P. 2011. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent. Standards in Genomic Sciences 5(3): 407-415.

  1. Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng J, Tapia R, Han C, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla E, Rohde M, Abt B, Verbag S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P, & Woyke T. 2011. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T). Standards in Genomic Sciences 5(3): 398-406.

  1. Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Göker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA. 2011. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) 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.  Standards in Genomic Sciences 5(1): 121-34.

  1. Chang YJ, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Standards in Genomic Sciences, 5(1): 97-111.

  1. Lapidus A, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Abt B, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2011. Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10). Standards in Genomic Sciences, 5(1): 86-96.

  1. Pati A, Gronow S, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Mikhailova N, Huntemann M, Chen A, Palaniappan K, Land M, Hauser L, Detter JC, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. 2011. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20). Standards in Genomic Sciences 5(1): 41-9.

  1. Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kotsyurbenko O, Rohde M, Tindall BJ, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.  2011. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113). Standards in Genomic Sciences 5(1): 30-40.

  1. Woyke T, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Mwirichia R, Sikorski J, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). Standards in Genomic Sciences 5(1): 21-9.

  1. Göker M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2). Standards in Genomic Sciences 4(3): 393-401.

  1. Anderson I, Göker M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Huber H, Yasawong M, Rohde M, Spring S, Abt B, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Standards in Genomic Sciences 4(3): 381-92.

  1. Han C, Mwirichia R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2011. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Standards in Genomic Sciences 4(3): 371-80.

  1. Han C, Gronow S, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Zeytun A, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC.  2011. Complete genome sequence of Treponema succinifaciens type strain (6091). Standards in genomic Sciences 4(3): 361-70.

  1. Daligault H, Lapidus A, Zeytun A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2011. Complete genome sequence of Haliscomenobacter hydrossis type strain (O). Standards in Genomic Sciences 4(3): 352-60.

  1. Munk AC, Lapidus A, Lucas S, Nolan M, Tice H, Cheng JF, Del Rio TG, Goodwin L, Pitluck S, Liolios K, Huntemann M, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Tapia R, Han C, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Yasawong M, Brambilla EM, Rohde M, Sikorski J, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33). Standards in Genomic Sciences 4(3): 342-51.

  1. Sikorski J, Teshima H, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Ngatchou-Djao OD, Rohde M, Pukall R, Spring S, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of Mahella australiensis type strain (50-1 BON). Standards in Genomic Sciences 4(3): 331-41.

  1. Anderson I, Sikorski J, Zeytun A, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Ngatchou-Djao OD, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1). Standards in Genomic Sciences 4(3): 322-30.

  1. Ivanova N, Sikorski J, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kannan KP, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL). Standards in Genomic Sciences 4(3): 312-21.

  1. Huntemann M, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. 2011. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Standards in Genomic Sciences 4(3): 303-11.

  1. Land M, Held B, Gronow S, Abt B, Lucas S, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Hauser L, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). Standards in Genomic Sciences 4(2): 233-43. PMID: 21677860

  1. Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. 2011. Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Standards in Genomic Sciences 4(2): 221-32. PMID: 21677859

  1. Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.  2011. Complete genome sequence of Oceanithermus profundus type strain (506).  Standards in Genomic Sciences 4(2): 210-20. PMID: 21677858

  1. Göker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Bacteroides salanitronis type strain (BL78).  Standards in Genomic Sciences 4(2): 200-9. PMID: 21677857

  1. Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA. 2011. Complete genome sequence of Bacteroides salanitronis type strain (BL78). Standards in Genomic Sciences 4(2): 191-9. PMID: 21677856

  1. Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).  Standards in Genomic Sciences 4(2): 173-82. PMID: 21677854

  1. Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011.  Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Standards in Genomic Science 4(2):163-72. PMID: 21677853

  1. Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Marivirga tractuosa type strain (H-43). Standards in Genomic Sciences 4(2): 154-62. PMID: 21677852

  1. Mavromatis K, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Göker M, Gronow S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Standards in Genomic Sciences 4(2): 144-53. PMID: 21677851

  1. Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Standards in Genomic Sciences 4(2): 131–143. PMCID: PMC3111988.

  1. Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Standards in Genomic Sciences 4(1): 100-10.

  1. Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Standards in Genomic Sciences 4(1): 91-9.

  1. Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.  2011. Complete genome sequence of Weeksella virosa type strain (9751). Standards in Genomic Sciences 4(1): 81-90.

  1. Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of Cellulophaga algicola type strain (IC166). Standards in Genomic Sciences 4(1): 72-80.

  1. Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Isosphaera pallida type strain (IS1B). Standards in Genomic Sciences 4(1): 63-71.

  1. Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. 2011. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Standards in Genomic Sciences 4(1): 54-62.

  1. Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. 2011. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Standards in Genomic Sciences 4(1): 45-53.

  1. Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Standards in Genomic Sciences 4(1): 36-44.

  1. Chertkov O, Sikorski J, Nolan M, Lapidus A, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Djao OD, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Detter JC, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Thermomonospora curvata type strain (B9). Standards in Genomic Sciences 4(1): 13-22.

  1. Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Standards in Genomic Sciences, 4(1): 2-12.

2010


  1. Han C, Gu W, Zhang X, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Schneider S, Rohde M, Göker M, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2010. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Standards in Genomic Sciences 3(3): 337-45.

  1. Sun H, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Djao OD, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509). Standards in Genomic Sciences 3(3): 325-36.

  1. Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010. Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences 3(3): 315-24.

  1. Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Standards in Genomic Sciences 3(3): 304-14.

  1. Del Rio TG, Chertkov O, Yasawong M, Lucas S, Deshpande S, Cheng JF, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Pukall R, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Complete genome sequence of Intrasporangium calvum type strain (7 KIP). Standards in Genomic Sciences 3(3): 294-303.

  1. Pitluck S, Yasawong M, Held B, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Chertkov O, Goodwin L, Tapia R, Han C, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Pukall R, Spring S, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). Standards in Genomic Sciences 3(3): 285-93.

  1. Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. 2010. Complete genome sequence of Desulfarculus baarsii type strain (2st14). Standards in Genomic Sciences 3(3): 276-84.

  1. Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1). Standards in Genomic Sciences 3(3): 268-75.

  1. Brambilla E, Djao OD, Daligault H, Lapidus A, Lucas S, Hammon N, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences 3(2): 203-11.

  1. Sikorski J, Munk C, Lapidus A, Ngatchou Djao OD, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Han C, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Sims D, Meincke L, Brettin T, Detter JC, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Lang E, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Standards in Genomic Sciences 3(2): 194-202.

  1. Nolan M, Sikorski J, Davenport K, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tapia R, Brettin T, Detter JC, Han C, Yasawong M, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Complete genome sequence of Ferrimonas balearica type strain (PAT). Standards in Genomic Sciences 3(2): 174-82.

  1. Roeselers G, 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, Cavanaugh CM. 2010.  Complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomic Sciences 3(2): 163-173.

  1. Kiss H, Cleland D, Lapidus A, Lucas S, Del Rio TG, Nolan M, Tice H, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Lu M, Brettin T, Detter JC, Göker M, Tindall BJ, Beck B, McDermott TR, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Cheng JF. 2010. Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1). Standards in Genomic Sciences 3(2): 153-162.

  1. Mavromatis K, Yasawong M, Chertkov O, Lapidus A, Lucas S, Nolan M, Del Rio TG, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Tapia R, Han C, Bruce D, Goodwin L, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Brambilla E, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010.  Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Standards in Genomic Sciences 3(2): 136-144.

  1. Yasawong M, Teshima H, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Standards in Genomic Sciences 3(2): 126-135.

  1. Mavromatis K, Sikorski J, Pabst E, Teshima H, Lapidus A, Lucas S, Nolan M, Glavina Del Rio T, Cheng JF, Bruce D, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Standards in Genomic Sciences 3(2): 117-125.

  1. Pitluck S, Yasawong M, Munk C, Nolan M, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT). Standards in Genomic Sciences 3: 108-116.

  1. Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Standards in Genomic Sciences 3(1): 85-92.

  1. Göker M, Held B, Lucas S, Nolan M, Yasawong M, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter JC, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Complete genome sequence of Olsenella uli type strain (VPI D76D-27C). Standards in Genomic Sciences 3(1): 76-84.

  1. Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010.  Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Standards in Genomic Sciences 3(1): 66-75.

  1. Sikorski J, Lapidus A, Chertkov O, Lucas S, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, Brambilla E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Bruce D, Detter C, Tapia R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Spring S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T). Standards in Genomic Sciences 3: 57-65.

  1. Labutti K, Sikorski J, Schneider S, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng J-F, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Tindall BJ, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T). Standards in Genomic Sciences 3: 47-56.

  1. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Cheng J-F, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Complete genome sequence of Meiothermus silvanus type strain (VI-R2T). Standards in Genomic Sciences 3: 37-46.

  1. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng J-F, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Fähnrich R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Complete genome sequence of Meiothermus ruber type strain (21T). Standards in Genomic Sciences 3: 26-36.

  1. Abt B, Foster B, Lapidus A, Clum A, Sun H, Pukall R, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng J-F, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Cellulomonas flavigena type strain (134T). Standards in Genomic Sciences 3: 15-25.

  1. Chang Y-J, Pukall R, Saunders E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng J-F, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Acidaminococcus fermentans type strain (VR4T). Standards in Genomic Sciences 3: 1-14.

  1. von Jan M, Lapidus A, Del Rio TG, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Goodwin L, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Chertkov O, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Saunders E, Brettin T, Detter JC, Chain P, Eichinger K, Huber H, Spring S, Rohde M, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Standards in Genomic Sciences 2(3): 327-46.

  1. Liolios K, Sikorski J, Jando M, Lapidus A, Copeland A, Glavina T, Nolan M, Lucas S, Tice H, Cheng J-F, Han C, Woyke T, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Chertkov O, Kuske C, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Thermobispora bispora type strain (R51T). Standards in Genomic Sciences 2: 318-326.

  1. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, Han C, Chertkov O, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Arcobacter nitrofigilis type strain (CIT). Standards in Genomic Sciences 2: 300-308.

  1. Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng J-F, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T). Standards in Genomic Sciences 2: 290-299.

  1. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T). Standards in Genomic Sciences 2: 280-289.

  1. Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng J-F, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Detter JC, Brettin T, Spring S, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T). Standards in Genomic Sciences 2: 270-279.

  1. Pati A, Sikorski J, Gronow S, Munk C, Lapidus A, Copeland A, Glavina Del Tio T, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Brachyspira murdochii type strain (56-150T). Standards in Genomic Sciences 2: 260-269.

  1. Spring S, Rachel R, Lapidus A, Davenport K, 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 CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT). Standards in Genomic Sciences 2: 245-259.

  1. Harmon-Smith M, Celia L, Chertkov O, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Pati A, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Brettin T, Göker M, Beck B, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Chen F. 2010. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T). Standards in Genomic Sciences 2: 220-227.

  1. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. 2010. Complete genome sequence of Conexibacter woesei type strain (ID131577). Standards in Genomic Sciences 2(2): 212-9.

  1. Sikorski J, Lapidus A, Copeland A, Misra M, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, Jando M, Schneider S, Bruce D, Goodwin L, Pitluck S, Liolios K, Mikhailova N, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chertkov O, Land M, Hauser L, Chang Y-J, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T). Standards in Genomic Sciences 2: 203-211.

  1. Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, Han C, Detter JC, Tapia R, Bruce D, Goodwin L, Pitluck S, Pati A, Anderson I, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Bilek Y, Hader T, Land M, Hauser L, Chang Y-J, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Thermocrinis albus type strain (HI 11/12T). Standards in Genomic Sciences 2: 194-202.

  1. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, Lucas S, Chen F, Nolan M, LaButti K, Pati A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Brettin T. 2010. Complete genome sequence of Kribbella flavida type strain (IFO 14399T). Standards in Genomic Sciences 2: 186-193.

  1. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, Lucas S, 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 CD, Chain P, Brettin T, Detter JC, Schütze A, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Chen F. 2010. Complete genome sequence of Spirosoma linguale type strain (1T). Standards in Genomic Sciences 2: 176-185.

  1. Tice H, Mayilraj S, Sims D, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Copeland A, Cheng J-F, Meincke L, 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, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Chen F. 2010. Complete genome sequence of Nakamurella multipartita type strain (Y-104T). Standards in Genomic Sciences 2: 168-175.

  1. Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Meincke L, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Geodermatophilus obscurus type strain (G-20T). Standards in Genomic Sciences 2: 158.

  1. Sikorski 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, Ovchinnikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang Y-J, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Lang E, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T). Standards in Genomic Sciences 2: 149-157.

  1. Saunders E, Tindall BJ, Fähnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng J-F, Han C, Detter JC, Bruce D, Goodwin L, Chain P, Pitluck S, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Haloterrigena turkmenica type strain (4kT). Standards in Genomic Sciences 2: 107-116.

  1. 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 JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Markowitz V, Eisen JA, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T). Standards in Genomic Sciences 2(1): 96-106.

  1. Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng J-F, Chen F, 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, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lucas S. 2010. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Standards in Genomic Sciences 2: 87-95.

  1. 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, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lucas S. 2010. Complete genome sequence of Veillonella parvula type strain (Te3T). Standards in Genomic Sciences 2: 57-65.

  1. 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, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T). Standards in Genomic Sciences 2: 49-56.

  1. 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, Mikhailova N, Pati A, Chen A, Palaniappan K, Hauser L, Chang Y-J, Jeffries CD, Munk C, Kiss H, Chain P, Han C, Brettin T, Detter JC, Schüler E, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T). Standards in Genomic Sciences 2: 38-48.

  1. 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 Y-J, Jeffries CD, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC and Klenk H-P. 2010. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T). Standards in Genomic Sciences 2: 29-37.

  1. Ivanova N, Sikorski J, Jando M, Lapidus A, Nolan M, Lucas S, Del Rio TG, 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 Y-J, Jeffries CD, Chain P, Saunders E, Han C, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Gordonia bronchialis type strain (3410T). Standards in Genomic Sciences 2: 19-28.

  1. Mavromatis K, Sikorski J, 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, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Chain P, Meincke L, Sims D, Chertkov O, Han C, Brettin T, Detter JC, Wahrenburg C, Rohde M, Pukall R, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P and Kyrpides NC. 2010. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT). Standards in Genomic Sciences 2: 9-18.

  1. Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng J-F, Chertkov O, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T). Standards in Genomic Sciences 2: 1-8.

2009


  1. Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del Rio , Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, 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 JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Standards in Genomic Sciences 1(3): 308-316. See erratum in SIGS 2: 228

  1. Nolan M, Gronow S, Lapidus A, Ivanova N, Copeland A, Lucas S, Del Rio TG, Chen F, Tice H, Pitluck S, Cheng JF, 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 YJ, Jeffries CD, Rohde M, Spröer C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P. 2009. Complete genome sequence of Streptobacillus moniliformis type strain (9901T). Standards in Genomic Sciences 1: 300-307.

  1. Munk C, Lapidus A, Copeland A, Jando M, Mayilraj S, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Han C, Detter JC, 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 YJ, Jeffries CD, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T). Standards in Genomic Sciences 1: 292-299.

  1. Nolan M, Tindall BJ, Pomrenke H, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, 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 YJ, Jeffries CD, Brettin T, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2009. Complete genome sequence of Rhodothermus marinus type strain (R-10T). Standards in Genomic Sciences 1: 283-290.

  1. Tindall BJ, Schneider S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC, Detter JC. 2009. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T). Standards in Genomic Sciences 1: 270-277.

  1. Pukall R, Gehrich-Schröter G, Lapidus A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Copeland A, Saunders E, Brettin T, Detter JC, Bruce D, Goodwin L, Pati A, Ivanova N, Mavromatis K, Ovchinnikova G, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. 2009. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T). Standards in Genomic Sciences 1: 262-269.

  1. Chovatia M, Sikorski J, Schröder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, 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 YJ, 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, Eisen JA. 2009. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T). Standards in Genomic Sciences 1: 254-261.

  1. Spring S, Lapidus A, Schröder M, Gleim D, Sims D, Meincke L, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, 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 YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. 2009. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T). Standards in Genomic Sciences 1: 242-253.

  1. 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, Mavrommatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Schneider S, Rohde M, Chain P, D’haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk H-P and Hugenholtz P. 2009. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T). Standards in Genomic Sciences 1: 234-241.

  1. Han C, Sikorski J, Lapidus A, Nolan M, Glavina Del Rio T, Tice H, Cheng J-F, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis 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 JC. 2009. Complete genome sequence of Kangiella koreensis type strain (SW-125T). Standards in Genomic Sciences 1: 226-233.

  1. Anderson I, Tindall BJ, Pomrenke H, Göker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H, Cheng JF, Lucas S, Chertkov O, Bruce D, Brettin T, Detter JC, Han C, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Pitluck S, Pati A, Mavromatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Chain P, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T). Standards in Genomic Sciences 1: 218-225.

  1. 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 A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Han C. 2009. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T). Standards in Genomic Sciences 1: 174-182.

  1. Copeland A, Sikorski J, Lapidus A, Nolan M, Glavina 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, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Detter JC. 2009. Complete genome sequence of Atopobium parvulum type strain (IPP 1246T). Standards in Genomic Sciences 1: 166-173. Note erratum in Standards in Genomic Sciences 2: 361-362.

  1. Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, 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 YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Han C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Anaerococcus prevotii type strain (PC1T). Standards in Genomic Sciences 1: 159-165.

  1. Malfatti S, Tindall BJ, Schneider S, Fähnrich R, Lapidus A, Labuttii K, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Anderson I, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, D’haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P.  2009. Complete genome sequence of Halogeometricum borinquense type strain (PR3T). Standards in Genomic Sciences 1: 150-159.

  1. Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Chain P, D’haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Saccharomonospora viridis type strain (P101). Standards in Genomic Sciences 1(2): 141-149.

  1. Lang E, Lapidus A, Chertkov O, Brettin T, Detter JC, Han C, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Land M, Hauser L, Chang YJ, Jeffries CD, Kopitz M, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Rohde M, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Dyadobacter fermentans type strain (NS114T). Standards in Genomic Sciences 1: 133.

  1. Ivanova N, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Brettin T, Detter JC, Han C, Pitluck S, Mikhailova N, Pati A, Mavrommatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Standards in Genomic Sciences, 1(2): 126-132.

  1. Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Pati A, Ivanov N, Mavromatis K, Chen A, Palaniappan K, Chai P, Land M, Hauser L, Chang YJ, Jeffries CD, Chertkov O, Brettin T, Detter JC, Han C, Ali Z, Tindall BJ, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP 2009. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T). Standards in Genomic Sciences 1: 119-125.

  1. Ivanova N, 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 JF, Bruce D, Goodwin L, Pitluck S, Pati A, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Goker M, Pukall R, Klenk HP, Kyrpides NC 2009. Complete genome sequence of Sanguibacter keddieii type strain (ST-74T). Standards in Genomic Sciences 1: 110-118.

  1. Mavrommatis K, Gronow S, Saunders E, Land M, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Bristow J, Göker M, Rohde M, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. 2009. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). Standards in Genomic Sciences 1(2): 101-109.

  1. Mavrommatis K, Pukall R, Rohde C, Chen F, Sims D, Brettin T, Kuske C, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, D’haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Rohde M, Klenk HP, Kyrpides NC. 2009. Complete genome sequence of Cryptobacterium curtum type strain (12-3). Standards in Genomic Sciences 1(2): 93-100.

  1. Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, 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 YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2009. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Standards in Genomic Sciences 1(1): 54-62.

  1. Land M, Mayilraj S, Chen F, Copeland A, Glavina del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, Chertkov O, Bruce D, Goodwin L, Pitluck S, Rohde M, Goeker M, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Chang Y-J, Jeffries CC, Brettin T, Detter JC, Han C, Chain P, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, 2009. Complete genome sequence of Actinosynnema mirum type strain (101T).  Standards in Genomic Sciences 1: 46-53.

  1. Clum A, Nolan M, Lang E, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Göker M, Spring S, Land M, Hauser L, Chang YJ, Jeffries CC, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). Standards in Genomic Sciences 1(1): 38-45.

  1. Copeland A, Spring S, Göker M, Schneider S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Meincke L, Sims D, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. 2009. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Standards in Genomic Sciences 1(1): 29-37.

  1. Land M, Pukall R, Abt B, Göker M, Rohde M, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jefferies CC, Saunders E, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T). Standards in Genomic Sciences 1: 21-28.

  1. 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 JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Schneider S, Göker M, Pukall R, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Kytococcus sedentarius type strain (541). Standards in Genomic Sciences 1(1): 12-20.

  1. Lapidus A, Pukall R, Labuttii K, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Rohde M, Göker M, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Standards in Genomic Sciences 1(1): 3-11.

Books 


  • Barton N, Briggs D, Eisen JA, Goldstein DB, Patel N. Evolution, 833 p, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Other Publications 


  • Schlom DG, Gall KA, Eisen JA, Joseph AD, Murphy CJ. 2007. Passive and semi-passive nanomaterial-based sensors for multi-year remote detection. Defense Science Study Group 2004-2005 Papers.

  • Brodley C, Eisen JA. 2007. Tampering with DNA: National Security Needs for Detection and Design. Defense Science Study Group 2004-2005 Papers.

  • Eisen JA. 2007. Toward a global field guide for microorganisms. Defense Science Study Group 2004-2005 Papers.  Now available on Figshare.

  • Eisen JA; McConnell W. 2009 My View: UC Davis strike: Teaching is more than just about being paid. Sacramento Bee.

Meeting reports, white papers, and other documents in which I have played a role, helped write, etc.