Publications table

 

Authors Year Title Citation and Web Link PMID PDF Links, press, data, etc.
Castelle C. Hug LA, Wrighton KC, Thgomas, BC, Williams KH, Wu D, Tringe SG, Singer S, Eisen JA, Banfield JF. 2013 Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4: 2120.      
Garrity G, Banfield J, Eisen JA, van der Lelie N, McMahon T, Rusch D, DeLong E, Moran M, Currie C, Fuhrman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, & Stepanauskas R.   Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2012. Standards in Genomic Sciences, 8(3): doi:10.4056/sigs.463.      
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. doi: 10.1038/nature12352.      
 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. In press     Preprint at arXiv.
Lang JM, Darling AE, Eisen JA. 2013 Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8(4): e62510.     Data and Figures available on Figshare.
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 sequence. BMC Genomics 14:95.     Data available at Figshare
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 U S A. 110(3): 1053-1058.   PDF.  
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.  
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 195(2): 253-260. 23123912 PDF.  
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. 23133348 PDF.  
Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KS, Eisen JA. 2012 Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics 13: 264. 23061897 PDF. More information and data links available here.
Jiang X, Langille MGI, Neches RY, Elliot MA, Levin SA, Eisen JA, Weitz JS, Dushoff J.

 

2012 Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scales. PLoS ONE 7(9): e43866. 23049741 PDF. Detailed blog post on the story behind the paper by Russell Neches
Tritt A, Eisen JA, Facciotti M, Darling A. 2012 An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7(9): e42304 . 23028432 PDF.

 

Software Page

 

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): 7327-36. 22885750 PDF. Data at Figshare.
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. 22848480 PDF. Links to data can be found here.
Eisen JA. 2012 Badomics words and the power and peril of the ome-meme. Gigascience 1:6.   PDF. Robert Lee Hotz story in the Wall Street Journal ”Here’s an Omical Tale: Scientists Discover Spreading Suffix.”

 

Other coverage: GigaScience launches: overseeing the transition from papers to “executable research objects” and Gigascience PR and ‘Big Data’ Journal GigaScience Makes Its Debut.

 

Also see blog post about paper: My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme

Langille MGI, Laird M, Hsiao W, Chiu T, Eisen JA, Brinkman F. 2012 MicrobeDB: a locally maintainable database of microbial genomic sequence. Bioinformatics 28(14): 1947-1948. 22576174 PDF. GitHub repository
Wu M, Chatterji S, Eisen JA. 2012 Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7(1): e30288. 22272325 PDF. Blog post with additional information. Zorro Software page.

 

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. 21914098  PDF  
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. 22384362 PDF.  
Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A 2011 Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe model system PLoS Genetics, 7(9): e1002272 21966276 PDF.  Data at Figshare.
Darling A, Tritt A, Eisen JA, Facciotti M 2011 Mauve assembly metrics Bioinformatics, 101093/bioinformatics/btr451 21810901 PDF.   Software Page.
Kembel S, Eisen JA, Pollard KS, Green JL 2011 The phylogenetic diversity of metagenomes PLoS One, 6(8): e23214 21912589 PDF. Blog post by Jonathan Eisen with more detail.
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.      
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.      
Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle R 2011 Aggregating, tagging and integrating biodiversity research PLoS One, 6(8): e19491 PMCID: PMC3148223 PDF.  
Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC 2011 Distributed globally, limited locally: drivers of beta-diversity depend on spatial scale Proc Natl Acad Sci USA 108: 7850-7854 21518859  PDF.  

 

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 21437252  PDF. Nature News article “The challenge of microbial diversity: Out on a limb.

 

Carl Zimmer Discover article “Glimpses of a fourth domain.“ Carl Zimmer Discover article #2 “Trouble in the fourth domain.

 

Newsy video post.

 

Economist Story PDF.

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 21283775 PDF. Blog post with additional detail. Software Page.
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 21234345 PDF.  

 

Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA 2010 Introducing WATERS: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences BMC Bioinformatics 11:317 20540779  PDF. WATERS Software page
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 21304727 PDF.  
Morgan JL, Darling A, Eisen JA 2010 Metagenomic sequencing of an in vitro-simulated microbial community PLoS ONE 5(4): e10209 20419134 PDF. Data available here.
Langille MGI, Eisen JA 2010 BioTorrents: a file sharing service for scientific data PLoS ONE 5(4): e10071 20418944 PDF. Website: Biotorrents.Net.

Jonathan Eisen Blog post with more detail.

 

Morgan Langille self interview Press Release.

 

Examples of news stories: Cheap option for file transfers launched and BioTorrents: An OA File Sharing Service and Review: BioTorrents. – Medpedia News and Nature News and GenomeWeb and BioTorrents: A BitTorrent Tracker Site for Scientists

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 20333302   PDF.Genome Page at UCSC Genome Browser
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 20033048   PDF. Supplemental Information PDF. New York Times article by Carl Zimmer. ARS Technica article by John Timmer. Addition information on Eisen’s Tree of Life Blog. Background Story on Eisen’s Tree of Life Blog. JGI GEBA Web Page

 

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 Proc Natl Acad Sci USA, 106(40): 17187-92 19805153   PDF. UC Davis Press Release. UPI Story. GenomeWeb Article. Nature News Story.

 

Eisen JA, MacCallum CJ 2009 Genomics of emerging infectious disease: A PLoS collection PLoS Biol, 7(10): e1000224 19855830   . PDF. PLoS Collection we edited. Podcast with Dr. Kiki. PLoS Blog Post. Press Release from PLoS.
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   19568419 PDF. Genome entry at NCBI
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 Genet, 5(2): e1000362     PMID: 19197347. PDF. Genome available in NCBI.
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.
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 19148287 PDF. .
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.       Link to original blog post. Blog post by Bora about the collection.
Eisen JA 2009 Genomic Evolvability and the Origin of Novelty: Studying the Past, Interpreting the Present, and Predicting the Future In “Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg”, THE NATIONAL ACADEMIES PRESS, Washington, DC    PDF.  
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 19077236 PDF.  
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 19036158 PDF.  
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 hospitalisNanoarchaeum equitans  Genome Biol 9(11): R158 19000309 PDF.  
Eisen JA. 2008 PLoS Biology 2.0. PLoS Biology 6(2):e48. 18303952    
Wu M, Eisen JA 2008 A simple, fast, and accurate method of phylogenomic inference Genome Biology 2008, 9:R151 18851752   PDF. AMPHORA software page. Faculty of 1000 reviews. Blogged about by Larry Moran.
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 18596968 PDF.  

STAP Software page. Blog post by Mike the Mad Biologist. Blogged about by Genome Technology and Jonathan Eisen and Bora Zivcovic.

Chatterji S, Yamazaki I, Bai Z, Eisen JA 2008 CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads RECOMB 2008   PDF.

 

 CompostBin Software page.
Hazen TH, Wu D, Eisen JA, Sobecky PA 2007 Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp  Appl Environ Microbiol 2007 73(23):7703-10 17921277 PDF.  
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? Int J Syst Evol Microbiol 57: 1677-8 17684235 PDF.

 

 
Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA 2007 Identification of a new family of lycopene cyclases in photosynthetic bacteria Proc Natl Acad Sci U S A 104: 11784-9 1760690 PDF.  
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 17511521 PDF.  
Eisen JA 2007 Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes PLoS Biology 5(3): e82 17355177 PDF.  
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 17355171 PDF.  
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 17355176  PDF.  
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 17303757    PDF. Supplement PDF.
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 Proc Natl Acad Sci U S A 103:15200-5 17015832 PDF.  
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 16933976   PDF. Press Releases: NIGMS, TIGR, PLoS, Grant Award. Ars Technica News Story by John Timmer. Tetrahymena Genome Database. Jonathan Eisen blog post
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 2006 Metabolic complementarity and genomics of the dual symbiosis of sharpshooters PLoS Biology 4: e188 16729848   PDF. Synopsis from PLoS Biology. Science Now “Dinner for Three” Story.News: Central Valley Business “Sharpshooter’s secret solved” UC Davis Press Release “Sharpshooter’s Secret Is Three-Way Symbiosis“. JCVI Press Release. Sequence traces
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 16482227 . PDF.

 

 
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): 231-238   PDF.  
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): 443-451    PDF.  
Penn K, Wu D, Eisen JA, Ward N 2006 Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts Appl Environ Microbiol 72: 1680-1683 16461727 PDF  
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 16729848 PDF..  News: Slashdot story. Press release. Green Car Congress
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) Proc Natl Acad Sci USA 102: 7315-7320 15883371 PDF.  
Eisen JA 2005 Coordinating efforts to understand microbes in the environment Letter to the Editor Microbe, 71(4): 157   PDF.  
Robb FT, Gonzalez JM, Sokolova T, Chernyh N, Lebedinski A, Tallon LJ, Jones K, Wu M, Eisen 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 163-170    PDF.  
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  Int J System Evol Microbiol 55: 1021-1026 15879228 PDF.  
Desjardins C, Eisen JA, Nene V 2005 New evolutionary frontiers from unusual virus genomes Genome Biology 6: 212-213 15774035 PDF.  
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 15637277 . PDF.  
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 15602564  PDF.  
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 15454524 PDF. Supplement.PDF
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 15383840 PDF.  
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 15001713   PDF. Supplement.PDF. Commentary.
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 2004 Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements PLoS Biology 2: 327-341 15024419   PDF. Japan Times article
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 S, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM 2004 Gene synteny and evolution of genome architecture in trypanosomatids Mol Biochem Parasitol 134: 183-191 15003838 . PDF.  
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 Proc Natl Acad Sci USA 101: 5646-5651 15064399 . PDF.  
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 2004 The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough Nature Biotechnol 22: 554-559 15077118  PDF  
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 14671304 PDF.  
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  J Bacteriol 185: 5591-5601 12949112 PDF.  
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 J Bacteriol 185: 5220-5233 12923095 PDF.  
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 Bioch Biophys Res Commun 310: 927–935 14550293 PDF.  
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 J Bacteriol 185: 3392-3399 12754238 PDF.  
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 Proc Natl Acad Sci USA 100: 5455-5460 12704232  PDF.  
Eisen JA, Fraser CM 2003 Phylogenomics: intersection of evolution and genomics Science 300: 1706-1707 12805538  PDF.  
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 12663927 . PDF.  
Ermolaeva MD, Wu M, Eisen JA, Salzberg SL 2003 The age of the Arabidopsis thaliana genome duplication Plant Mol Biol 51: 859-866 12777046  PDF.  
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. Cruise Web Site
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 12721629 PDF.  
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 Environ Microbiol 4: 799-808 12534463 PDF.  
Eisen JA, Wu M 2002 Phylogenetic analysis and gene functional predictions: phylogenomics in action Theor Pop Biol 61: 481-487 12167367 PDF.  
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 Biotechnol 20: 1118-1123 12368813  PDF.  
Van Houten B, Eisen JA, Hanawalt PC 2002 A cut above: discovery of an alternative excision repair pathway in bacteria  Proc Natl Acad Sci USA 99: 2581-2583 11880612    PDF. Supplemental Figure on UvrC evolution
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 12368864    PDF. Google Scholar Page.
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 Proc Natl Acad Sci USA 99: 13148-13153 12271122  PDF.  
Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL 2002 The value of complete microbial genome sequencing (You get what you pay for) J Bacteriol 184: 6403-6405 12426324  PDF.  
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 J Bacteriol 184: 5479-5490 12218036 PDF.  
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 Proc Natl Acad Sci USA 99: 12391-12396 12200547 PDF.  
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 11832943  PDF. Commentary
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  Proc Natl Acad Sci USA 99: 9509-9514 12093901 PDF.  
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 Photosyn Res 70: 3-17 16228359 DOI: 101023/A:1013879706863 PDF.  
Eisen JA 2002 Brouhaha over the other yeast  Nature 415: 845-848 11859347 PDF.  
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  Int J Parasitol 32: 159-166 11812492  PDF.  
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 2001 The genome of the natural genetic engineer Agrobacterium tumefaciens C58 Science 294: 2317-2323 11743193   PDF. Commentary
Eisen JA 2001 Response to Mackiewicz et al Genome Biology 2: interactions10041-10044     PDF.
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 11463916   PDF. Commentary. Supplemental information
Ward N, Eisen JA, Fraser CM, Stackebrandt E 2001 Sequenced strains must be saved from extinction Nature 414: 148 11700527  PDF.  
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 Proc Natl Acad Sci USA 98: 4136-4141 11259647  PDF.  
Salzberg SL, Eisen JA 2001 Lateral gene transfer or viral colonization? Science 293:1048 11503638 PDF.  
Salzberg SL, White O, Peterson J, Eisen JA 2001 Microbial genes in the human genome: lateral transfer or gene loss? Science 292: 1903-1906 11358996   PDF. Enhanced version of the paper with detailed links. Genome News Network story. New York Times article by Nick Wade. Wired News article. Commentary
Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes H-W 2001 Sequence and analysis of the Arabidopsis genome  Curr Opin Plant Biol 4: 105-110 11228431  PDF.  
Nelson KE, Eisen JA, Fraser CM 2001 2001 The genome of Thermotoga maritima MSB8  Meth Enzymol 330: 169-180 11210497 PDF.  
Eisen JA 2001 Gastrogenomics Nature 409: 463-465 11206526  PDF.  
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 Nucl Acids Res 29: 41-43 11125044   PDF. TIGRFams web site.
Eisen JA 2000 Microbial and plant genomics J Biolaw and Business, Spec Supp 21-24   PDF.  
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 Nucl Acids Res 28: 1397-1406 10684935 PDF.

 

 
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 11130711 PDF.  
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 11130711 PDF.  
Nierman W, Eisen JA, Fleischmann RD, Fraser CM 2000 Genome data: what do we learn? Curr Opin Struct Biol 10: 343-348 10851186 PDF.  
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 10710307 PDF.  
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 10857751 PDF.  
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 10952301    PDF. Supplemental information.
Eisen JA, Heidelberg JF, White O, Salzberg SL 200 Evidence for symmetric chromosomal inversions around the replication origin in bacteria Genome Biol 1: research 00111-00119 11178265 PDF.  
Pollock DD, Eisen JA, Doggett NA, Cummings MP 2000 A case for evolutionary genomics and the comprehensive examination of sequence biodiversity Mol Biol Evol 7: 1776-1788 11110893  PDF.  
Eisen JA 2000 Horizontal gene transfer among microbial genomes: new insights from complete genome analysis Curr Opin Genetics Dev 10: 606-611 11088009 PDF.  
Eisen JA 2000 Assessing evolutionary relationships among microbes from whole genome analysis Curr Opin Microbiol 3: 475-480 11050445 PDF.  
Fraser CM, Eisen JA, Fleischmann RD, Ketchum KA, Peterson S 2000 Comparative genomics and understanding of microbial biology  Emerg Infect Dis 6: 505-512 10998382  PDF.  
Fraser CM, Eisen JA, Salzberg SL 2000 Microbial genome sequencing  Nature 406: 799-803 10963611 PDF.  
Nierman W, Eisen JA, Fraser CM 2000 Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis  Res Microbiol 151: 79-84 10865951  PDF.  
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 10617197 PDF.  
Eisen JA, Hanawalt PC 1999 A phylogenomic study of DNA repair genes, proteins, and processes Mut Res 435: 171-213 10606811  PDF.  
Eisen JA 1999 Going to extremes Trends Genet 15: 218-219 10419407 PDF  
Eisen JA 1999 Mechanistic basis of microsatellite instability In Microsatellites: Evolution and Applications (DB Goldstein and C Schlotterer, eds) Oxford University Press, Oxford     PDF. Paperback at Amazon. Hardback at Amazon.
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 10567266  PDF.  
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 10360571 PDF.  
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  Hum Genet 103: 355-364 9799093  PDF.  
Eisen JA 1998 Evolution of DNA repair genes, proteins and processes. PhD Thesis. Stanford University Department of Biology.    PDF.  
Eisen JA 1998 A phylogenomic study of the MutS family of proteins  Nucl Acids Res 26: 4291-4300 9722651 PDF.  
Gruber TM, Eisen JA, Gish K, Bryant DA 1998 The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences  FEMS Microbiol Lett 162: 53-60 9595663 PDF.  
Eisen JA 1998 Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res 8: 163-167 9521918 PDF.  
White RB, Eisen JA, Kasten TW, Fernald RD 1998 Second gene for gonadotropin-releasing hormone in humans Proc Natl Acad Sci USA 95: 305-309 941937  PDF.  
Eisen JA, Kaiser D, Myers RM 1997 Gastrogenomic delights: a movable feast Nature Medicine 3: 1076-1078 9334711  PDF.  
Eisen JA 1997 The genetic data environment: a user modifiable and expandable multiple sequence analysis package In Meth Mol Biol, vol 70: Sequence Data Analysis Guidebook  (SR Swindell, ed), Humana, Totowa, NJ, pp 13-38 90896 PDF.  
Shafer RW, Eisen JA, Merigan TC, Katzenstein DA 1997 Sequence and drug susceptibility of subtype C reverse transcriptase from HIV-1-seroconverters in Zimbabwe J Virol 71: 5441-5448 9188616  PDF.

 

 
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  J Mol Evol 41: 1105-1123 8587109 PDF.  
Eisen JA, Sweder KS, Hanawalt PC 1995 Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions Nucl Acids Res 23: 2715-2723 7651832 PDF.  
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 Nucl Acids Res 22: 2634-2636 8041625   PDF. Prosite motif
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 activities J Bacteriol 175: 6518-6529 8407828  PDF.  
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 J Bacteriol 174: 3416-3421 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

 

           
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      
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      
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      
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      
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      
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      
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      
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      
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      
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      
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      
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      
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      
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      
 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      
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) Stand Genomic Sci 4(2):233-43 21677860      
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) Stand Genomic Sci  4(2):221-32 21677859      
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) Stand Genomic Sci 4(2):210-20 21677858      
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) Stand Genomic Sci 29;4(2):200-9 21677857      
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) Stand Genomic Sci 29;4(2):191-9 21677856      
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) Stand Genomic Sci 29;4(2):173-82 21677854      
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) Stand Genomic Sci Apr 29;4(2):163-72 21677853      
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) Stand Genomic Sci 4(2):154-62 21677852      
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) Stand Genomic Sci 4(2):144-53 21677851      
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) Stand Genomic Sci April 29; 4(2): 131–143 PMCID: PMC3111988      
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) Stand Genomic Sci, 4(1): 100-10      
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) Stand Genomic Sci, 4(1): 91-9      
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) Stand Genomic Sci, 4(1): 81-90      
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) Stand Genomic Sci, 4(1): 72-80      
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) Stand Genomic Sci, 4(1): 63-71      
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) Stand Genomic Sci, 4(1): 54-62      
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) Stand Genomic Sci, 4(1): 45-53      
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) Stand Genomic Sci, 4(1): 36-44      
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) Stand Genomic Sci, 4(1): 13-22      
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) Stand Genomic Sci, 4(1): 2-12      
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   Complete genome sequence of Thermaerobacter marianensis type strain (7p75a) Stand Genomic Sci, 3(3): 337-45      
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) Stand Genomic Sci, 3(3): 325-36      
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   Complete genome sequence of Methanothermus fervidus type strain (V24S) Stand Genomic Sci, 3(3): 315-24      
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   Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1) Stand Genomic Sci, 3(3): 304-14      
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) Stand Genomic Sci, 3(3): 294-303      
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   Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3) Stand Genomic Sci, 3(3): 285-93,      
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   Complete genome sequence of Desulfarculus baarsii type strain (2st14) Stand Genomic Sci, 3(3): 276-84      
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   Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1) Stand Genomic Sci, 3(3): 268-75      
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) Stand Genomic Sci, 3(2): 203-11      
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) Stand Genomic Sci, 3(2): 194-202      
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) Stand Genomic Sci, 3(2): 174-82      
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 Stand Genomic Sci, 3(2): 163-73      
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) Stand Genomic Sci, 3(2): 153-62,      
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) Stand Genomic Sci, 3(2): 136-44      
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) Stand Genomic Sci, 3(2): 126-35      
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) Stand Genomic Sci, 3(2): 117-25      
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      
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) Stand Genomic Sci, 3(1): 85-92,      
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) Stand Genomic Sci, 3(1): 76-84,      
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 (AQ1S1) Stand Genomic Sci, 3(1): 66-75      
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      
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      
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      
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      
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      
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      
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) Stand Genomic Sci, 2(3): 327-46      
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      
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      
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      
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      
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      
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      
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      
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      
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) Stand Genomic Sci, 2(2): 212-9      
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      
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      
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      
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      
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      
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      
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      
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      
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) SIGS, 2(1): 96-106      
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      
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      
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      
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      
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      
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      
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      
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      
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) Stand Genomic Sci, 1(3): 308-16 See erratum in SIGS 2: 228      
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: 300-7      
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: 292-9      
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: 283-90      
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: 270-7      
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: 262-9      
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: 254-61      
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: 242-53      
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      
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      
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: 218-25      
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      
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: 166-73 Note erratum in Standards in Genomic Sciences 2: 361-362      
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: 159-65      
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: 150-9      
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) Stand Genomic Sci, 1(2): 141-9      
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      
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) Stand Genomic Sci, 1(2): 126-32      
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      
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      
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) Stand Genomic Sci, 1(2): 101-9      
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) Stand Genomic Sci, 1(2): 93-100      
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) Stand Genomic Sci, 1(1): 54-62      
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      
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) Stand Genomic Sci, 1(1): 38-45      
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) Stand Genomic Sci, 1(1): 29-37      
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: 21-8      
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) Stand Genomic Sci, 1(1): 12-20      
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) Stand Genomic Sci, 1(1): 3-11      
             
             
             
             
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      
Barton N, Briggs D, Eisen JA, Goldstein DB, Patel N 2007 Evolution  833 p, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY      
             

 

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