Jonathan Eisen Publications

Journal and Book Chapter Publications

2023

Rojas CA, Entrolezo Z, Jarett JK, Jospin G, Kingsbury DD, Martin A, Eisen JA, Ganz HH. 2023. Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues. Veterinary Sciences 10(9):561.DOI: 10.3390/vetsci10090561.
Yu L, Khachaturyan M, Matschiner M, Healey A, Bauer D, Cameron B, Cusson M, Emmett Duffy J, Joel Fodrie F, Gill D, Grimwood J, Hori M, Hovel K, Hughes AR, Jahnke M, Jenkins J, Keymanesh K, Kruschel C, Mamidi S, Menning DM, Moksnes PO, Nakaoka M, Pennacchio C, Reiss K, Rossi F, Ruesink JL, Schultz ST, Talbot S, Unsworth R, Ward DH, Dagan T, Schmutz J, Eisen JA, Stachowicz JJ, Van De Peer Y, Olsen JL, Reusch TBH. 2023. Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina). Nature Plants. 10.1038/s41477-023-01464-3
De León ME, Wilson HS, Jospin G, Eisen JA. 2023. Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein producing bacteria and non violacein producing close relatives. Microbial Genomes 9: 000971. DOI: 10.1099/mgen.0.000971.
Tran MT, Seuylemezian A, Wright A, Coil D, Eisen JA, Guan L. 2023. Draft genome sequences of spacecraft-associated microbes isolated from six NASA missions. Microbiology Resource Announcements 12: e01011-22. DOI: 10.1128/mra.01011-22.
Perry LM, Cruz SM, Kleber KT, Judge SJ, Darrow MA, Jones LB, Basmaci UN, Joshi N, Settles ML, Durbin-Johnson BP, Gingrich AA, Monjazeb AM, Carr-Ascher J, Thorpe SW, Murphy WJ, Eisen JA, Canter RJ. 2023. Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis. Journal for Immunotherapy of Cancer 11: e004285. DOI: 10.1136/jitc-2021-004285.
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O’Mahony L, O’Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. 2023. Questioning the fetal microbiome and pitfalls of low biomass microbial studies. Nature Microbiology 613: 639-649. DOI: 10.1038/s41586-022-05546-8.

2022

Kleber KT, Iranpur KR, Perry LM, Cruz SM, Razmara AM, Culp WTN, Kent MS, Eisen JA, Rebhun RB, Canter RJ. 2022. Using the canine microbiome to bridge translation of cancer immunotherapy from pre-clinical murine models to human clinical trials. Frontiers in Immunology 13: 983344. DOI: 10.3389/fimmu.2022.983344.
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T; MetaSUB Consortium. 2022. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environmental Research 207: 112183. DOI: 10.1016/j.envres.2021.112183.
Rojas CA, Holekamp KE, Viladomat MJ, Souza V, Eisen JA, Theis KR. 2022. Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study. mSystems 19: e0096522. DOI: 10.1128/msystems.00965-22.
Ganz HH, Jospin G, Rojas CA, Martin AL, Dahlhausen K, Kingsbury DD, Osborne CX, Entrolezo Z, Redner S, Ramirez B, Eisen JA, Leahy M, Keaton C, Wong J, Gardy J, Jarett JK. 2022. The Kitty Microbiome Project: Defining the Healthy Fecal “Core Microbiome” in Pet Domestic Cats. Veterinary Sciences 9: 635. DOI: 10.3390/vetsci9110635.
Coil DA, Pechacek R, Kaze M, Zuniga-Montanez R, Guerrero RG, Eisen JA, Shapiro K, Bischel HN. 2022. SARS-CoV-2 RNA is readily detectable at least 8 months after shedding in an isolation facility. mSphere 11: e0017722. DOI: 10.1128/msphere.00177-22.
Clever F, Sourisse JM, Preziosi RF, Eisen JA, Guerra ECR, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M. 2022. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Nature Communications Biology 17: 50. DOI: 10.1038/s42003-022-03679-0.
Wilbanks EG, Doré H, Ashby MH, Heiner C, Roberts RJ, Eisen JA. 2022. Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. ISME Journal 16: 1921-1931. DOI: 10.1038/s41396-022-01242-7.
Zuniga-Montanez R, Coil DA, Eisen JA, Pechacek R, Guerrero RG, Kim M, Shapiro K, Bischel H. 2022. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?. PLOS ONE 17: e0267212. DOI: 10.1371/journal.pone.0267212.
Aleman M, Sheldon SA, Jospin G, Coil DA, Stratton-Phelps M, Eisen JA. 2022. Cecal microbiota in horses with trigeminal-mediated headshaking. Veterinary Medicine and Science 2022: 1-7. DOI: 10.1002/vms3.735.
Price CA, Jospin G, Brownell K, Eisen JA, Laraia B, Epel ES. 2022. Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study. PLOS ONE 17: e0259889. DOI: 10.1371/journal.pone.0259889.

2021

De León ME, Wilson HS, Jospin G, Eisen JA. 2021. Draft genome sequences and genomic analysis for pigment production in bacteria isolated from blue discolored soymilk and tofu. Journal of Genomics 9: 55-67. DOI: 10.7150/jgen.65500.
Leray M, Wilkins LGE, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy JE, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan WO, O’Dea A, Pereira TJ, Petersen JM, Petticord DF, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. 2021. Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution. PLOS Biology 19: e3001322. DOI: 10.1371/journal.pbio.3001322.
Osvatic JT, Wilkins LGE, Leibrecht L, Leray M, Zauner S, Polzin J, Camacho Y, Gros O, van Gils JA, Eisen JA, Petersen JM, Yuen B. 2021. Global biogeography of chemosynthetic symbionts reveals both localized and globally-distributed symbiont groups. Proceedings of the National Academy of Sciences USA 118: e2104378118. DOI: 10.1073/pnas.2104378118.
Coil DA, Albertson T, Banerjee S, Brennan G, Campbell AJ, Cohen SH, Dandekar S, Díaz-Muñoz SL, Eisen JA, Goldstein T, Jose IR, Juarez M, Robinson BA, Rothenburg S, Sandrock C, Stoian AMM, Tompkins DG, Tremeau-Bravard A, Haczku A. 2021. SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. PLOS One 16: e0253578. DOI: 10.1371/journal.pone.0253578.
Ettinger CL, Vann LE, Eisen JA. 2021. Global diversity and biogeography of the Zostera marina mycobiome. Applied and Environmental Microbiology 87: e02795-20. DOI: 10.1128/AEM.02795-20.
Grettenberger C, Sumner DY, Eisen JA, Jungblut AD, Mackey TJ. 2021. Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria. Genes 12: 929. DOI: 10.3390/genes12060929.
Furrow RE, Kim HG, Abdelrazek SMR, Dahlhausen K, Yao AI, Eisen JA, Goldman MS, Albeck JG, Facciotti MT. 2021. Combining microbial culturing with mathematical modeling in an introductory course-based undergraduate research experience. Fronteirs in Microbiology 11:581903. DOI: 10.3389/fmicb.2020.581903.
Belk AD, Duarte T, Quinn C, Coil DA, Belk KE, Eisen JA, Quinn JC, Martin JN, Yang X, Metcalf JL. 2021. Air versus water chilling of chicken: a pilot study of quality, shelf-life, microbial ecology, and economics. mSystems 6: e00912-20. DOI: 10.1128/mSystems.00912-20.
Altamia MA, Shipway JR, Stein D, Betcher MA, Fung JM, Jospin G, Eisen JA, Haygood MG, Distel DL. 2021. Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter. International Journal of Systematic and Evolutionary Microbiology 71: 004627. DOI: 10.1099/ijsem.0.004627.
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE; International MetaSUB Consortium. 2021. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184: 3376-3393. DOI: 10.1016/j.cell.2021.05.002.

2020

Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LGE. 2020. Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ 8: e10177. DOI: 10.7717/peerj.10177.
Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology5: 987–994. DOI: 10.1038/s41564-020-0733-x.
Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. 2020. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology 11: 1848. DOI: 10.3389/fmicb.2020.01848.
Ettinger CL, Eisen JA. 2020. Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina. PLOS One 15: e0236135. DOI: 10.1371/journal.pone.0236135.
Grettenberger CL, Sumner D, Wall K, Brown CT, Eisen JA, Mackey T, Hawes I, Jungblut A. 2020. A phylogenetically novel cyanobacterium most closely related to Gloeobacter. ISME 14: 2142–2152. DOI: 10.1038/s41396-020-0668-5.
Rosado P, Varona N, Eisen JA, Peixoto R. 2020. An incredible invisible world – How probiotics could take care of corals in difficult times. Frontiers for Young Minds 8: 65. DOI: 10.3389/frym.2020.00065.
Coil DA, Neches R, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. 2020. Bacterial communities associated with cell phones and shoes. PeerJ 8: e9235. DOI: 10.7717/peerj.9235.
Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. 2020. Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PLOS One 14: e0231053. DOI: 10.1371/journal.pone.0231053.
Dietz L, Horve PF, Coil DA, Fretz M, Eisen JA, Van Den Wymelenberg K. 2020. Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission. mSystems 5: e00245-20. DOI: 10.1128/mSystems.00245-20.
Coil DA, Jospin G, Eisen JA. 2020. Draft Genome Analysis of Christensenella minuta DSM 22607, exhibiting an unusual expansion of transporter homologs of unknown function. Journal of Genomics 8: 25-29. DOI: 10.7150/jgen.43162.
Brown CL, Garner E, Jospin G, Coil DA, Schwake DO, Eisen JA, Mukhopadhayay B, Pruden A. 2020. Whole genome sequence analysis reveals broad distribution of the RtxA type 1 secretion system and four novel type 1 secretion systems throughout the Legionella genus. PLOS One 15: e0223033. DOI: 10.1371/journal.pone.0223033.
Dillon M, Hawes I, Jungblut A, Mackey T, Eisen JA, Doran P, Sumner DY. 2020. Energetic and environmental constraints on the community structure of benthic microbial mats in Lake Fryxell, Antarctica. FEMS Microbiology Ecology 96: fiz207. DOI: 10.1093/femsec/fiz207.
Shipway JR, Altamia MA, Betcher MA, Stein D, Fung JM, Jospin G, Eisen JA, Haygood MG, Distel DL. 2020. Teredinibacter waterburyi sp. nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae). International Journal of Systematic and Evolutionary Microbiolology 70: 2388–2394. DOI: 10.1093/femsec/fiz207.
Martiny JBH, Whiteson K, Bohannan B, David L, Hynson N, McFall-Ngai M, Rawls J, Schmidt T, Abdo Z, Blaser M, Bordenstein S, Bréchot C, Bull C, Dorrestein P, Eisen JA, Garcia-Pichel E, Gilbert J, Hofmockel K, Holtz M, Knight R, Welch DM, McDonald D, Methe B, Mouncey N, Mueller N, Pfister C, Proctor L, Sachs J. 2020. The emergence of microbiome centers. Nature Microbiology 5: 2-3. DOI: 10.1038/s41564-019-0644-x.

2019

Villela HDM, Vilela CLS, Assis JM, Varona N, Burke C, Coil DA, Eisen JA, Peixoto R. 2019. Prospecting contaminant-degrading microbial strains presenting putative beneficial characteristics for corals. Journal of Visualized Experiments 152: e60238. DOI: 10.3791/60238.
Wilkins LGE, Leray M, Yuen B, Peixoto R, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios H, Lucey N, Mejia LC, O’Dea A, Rasher DB, Sharp K, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. 2019. Host-associated microbiomes and their roles in marine ecosystem functions. PLOS Biology 17: e3000533. DOI: 10.1371/journal.pbio.3000533.
Ettinger CL, Eisen JA. 2019. Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids. Frontiers in Microbiology 10: 2476. DOI: 10.3389/fmicb.2019.02476.
Garner E, Brown C, Schwake DO, Rhoads WJ, Arango-Argoty G, Zhang L, Jospin G, Coil DA, Eisen JA, Edwards MA, Pruden A. 2019. Comparison of whole-genome sequences of Legionella pneumophila in tap water and in clinical strains, Flint, Michigan, USA, 2016. Emerging Infectious Diseases 25: 2013-2020. DOI: 10.3201/eid2511.181032.
Yamaguchi MS, Ganz HH, Cho AW, Zaw TH, Jospin G, McCartney MM, Davis CE, Eisen JA, Coil DA. 2019. Bacteria isolated from bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds associated with animal signaling. PLOS One 14: e0216846. DOI: 10.1371/journal.pone.0216846.
Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. 2019. Early-career scientists shaping the world. mSystems 4: e00196-19. DOI: 10.1128/mSystems.00196-19.
Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O’Flynn C. 2019. Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. PLOS One 14: e0214354. DOI: 10.1371/journal.pone.0214354.
Hicks DJ, Coil DA, Stahmer CG, Eisen JA. 2019. Network analysis to evaluate the impact of research funding on research community consolidation. PLOS One 14: e0218273. DOI: 10.1371/journal.pone.0218273.
Bik HM, Alexiev A, Aulakh SK, Bharadwaj L, Flanagan J, Haggerty JM, Hird SM, Jospin G, Lang JM, Sauder LA, Neufeld JD, Shaver A, Sethi A, Eisen JA, Coil DA. 2019. Microbial community succession and nutrient cycling responses following perturbations of experimental salt water aquaria. mSphere 4: e00043-19. DOI: 10.1128/mSphere.00043-19.
Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. 2019. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Nature Communications 9: 3059. DOI: 10.1038/s41598-019-39576-6.

2018

Ettinger C, Wilkins L, Dahlhausen K, Ghose S, Oberbauer D, Eisen JA, Coil D. 2018. Even superheroes need help sometimes: three incredible tales of microbial symbiosis. Frontiers in Young Minds 6: 50. DOI: 10.3389/frym.2018.00050.
Rosado PM, Leite DCA, Duarte GAS, Chaloub RM, Jospin G, Nunes da Rocha U, P Saraiva J, Dini-Andreote F,Eisen JA, Bourne DG, Peixoto RS. 2018. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME Journal 13: 921-926. DOI: 10.1038/s41396-018-0323-6.
Hird SM, Ganz H, Eisen JA, Boyce WM. 2018. The cloacal microbiome of five wild duck species varies by species and influenza A virus infection status. mSphere 3: e00382-18. DOI: 10.1128/mSphere.00382-18.
Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology 16: e2006352. DOI: 10.1371/journal.pbio.2006352.
Horng KR, Ganz HH, Eisen JA, Marks SL. 2018. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6: e4827. DOI: 10.7717/peerj.4827.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, The American Gut Consortium, Knight R. 2018. American Gut: an open platform for citizen science microbiome research. mSystems 3: e00031-18. DOI: 10.1128/mSystems.00031-18.
Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. 2018. Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ 6: e4452. DOI: 10.7717/peerj.4452.

2017

Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. 2017. A microbial survey of the International Space Station (ISS). PeerJ 5: e4029. DOI: 10.7717/peerj.4029.
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. 2017. Rokubacteria: genomic giants among the uncultured bacterial phyla. Frontiers in Microbiology 8: 2264. DOI: 10.3389/fmicb.2017.02264.
Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH, Zinder SH. 2017. The green berry consortia of the Sippewissett Salt Marsh: millimeter-sized aggregates of diazotrophic unicellular cyanobacteria. Frontiers in Microbiology 8: 1623. DOI: 10.3389/fmicb.2017.01623.
Ettinger CL, Williams SL, Abbott JM, Stachowicz JJ, Eisen JA. 2017. Microbiome succession during ammonification in eelgrass bed sediments. PeerJ 5: e3674. DOI: 10.7717/peerj.3674.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35: 725-731. DOI: 10.1038/nbt.3893.
Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35: 676-683. DOI: 10.1038/nbt.3886.
Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. 2017. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 5: e3246. DOI: 10.7717/peerj.3246.
Coil DA, Ettinger CL, Eisen JA. 2017. Gut Check: The evolution of an educational board game. PLOS Biology15: e2001984. DOI: 10.1371/journal.pbio.2001984.
Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. 2017. Global-scale structure of the eelgrass microbiome. Applied and Environmental Microbiology 83: e03391-16. DOI: 10.1128/AEM.03391-16.
Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL.2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLOS Biology 15: e2001793. DOI: 10.1371/journal.pbio.2001793.
Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM. 2017. Community-level differences in the microbiome of healthy wild mallards and those infected by influenza a viruses. mSystems 2: e00188-16. DOI: 10.1128/mSystems.00188-16.
Tokajian S, Salloum T, Eisen JA, Jospin G, Farra A, Mokhbat JE, Coil DA. 2017. Genomic attributes of extended-spectrum β-lactamase-producing Escherichia coli isolated from patients in Lebanon. Future Microbiology 12: 213-226. DOI: 10.2217/fmb-2017-0171.
Steussy EE, Eisen JA, Imwinkelried EJ, Vandamme A-M. 2017. Microbial forensics: the biggest thing since DNA? . Forensic Science Seminar 7: 1-16. DOI: n/a.

2016

Adams RI, Bhangar S, Dannemiller KC, Eisen JA, Fierer N, Gilbert JA, Green JL, Marr LC, Miller SL, Siegel JA, Stephens B. 2016. Ten questions concerning the microbiomes of buildings. Buildings and and Environment 109: 224-234. DOI: 10.1016/j.buildenv.2016.09.001.
Kozyreva VK, Jospin G, Greninger AL, Watt JP, Eisen JA, Chaturvedi V. 2016. Recent outbreaks of shigellosis in California caused by two distinct populations of Shigella sonnei with either increased virulence or fluoroquinolone resistance. mSphere 1: e00344-16. DOI: 10.1128/mSphere.00344-16.
Ibrahim J, Eisen JA, Jospin G, Coil DA, Khazen G, Tokajian S. 2016. Genome analysis of Streptococcus pyogenes associated with pharyngitis and skin infections. PLOS One 11: e0168177. DOI: 10.1371/journal.pone.0168177.
Shehata HR, Ettinger CL, Eisen JA, Raizada MN. 2016. Genes required for the anti-fungal activity of a bacterial endophyte isolated from a corn landrace grown continuously by subsistence farmers since 1000 BC. Frontiers in Microbiology 7: 1548. DOI: 10.3389/fmicb.2016.01548.
Mousa WK, Shearer C, Limay-Rios V, Ettinger CL, Eisen JA, Raizada MN. 2016. Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nature Microbiology 26: 16167. DOI: 10.1038/nmicrobiol.2016.167.
Coil DA, Neches RY, Lang JM, Brown WE, Severance M, Cavalier D, Eisen JA. 2016. Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ 4: e1842. DOI: 10.7717/peerj.1842.

2015

Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM, Eisen JA. 2015. Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ 3: e1400. DOI: 10.7717/peerj.1400.
O’Flynn C, Deusch O, Darling AE, Eisen JA, Wallis C, Davis IJ, Harris SJ. 2015. Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis. Genome Biology and Evolution 7: 3397-413. DOI: 10.1093/gbe/evv220.
Jungblut AD, Hawes I, Mackey TJ, Krusor M, Doran PT, Sumner DY, Eisen JA, Hillman C, Goroncy AK. 2015. Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic Lake. Applied and Environmental Microbiology 82: 620-30. DOI: 10.1128/AEM.02699-15.
Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. 2015. Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLOS Computational Biology 11: e1004573. DOI: 10.1371/journal.pcbi.1004573.
Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC. 2015. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences 10: 26. DOI: 10.1186/s40793-015-0017-x.
Boundy-Mills K, Hess M, Bennett AR, Ryan M, Kang S, Nobles D, Eisen JA, Inderbitzin P, Sitepu IR, Torok T, Brown DR, Cho J, Wertz JE, Mukherjee S, Cady SL, McCluskey K. 2015. The United States Culture Collection Network (USCCN): enhancing microbial genomics research through living microbe culture collections. Applied and Environmental Microbiology 81: 5671-5674. DOI: 10.1128/AEM.01176-15.
Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. Swabs to genomes: a comprehensive workflow. PeerJ 3: e960. DOI: 10.7717/peerj.960.
Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome 3: 21. DOI: 10.1186/s40168-015-0082-9.
Hasan NA, Grim CJ, Lipp EK, Rivera IN, Chun J, Haley BJ, Taviani E, Choi SY, Hoq M, Munk AC, Brettin TS, Bruce D, Challacombe JF, Detter JC, Han CS, Eisen JA, Huq A, Colwell RR. 2015. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proceedings of the National Academy of Sciences USA 112: E2813-9. DOI: 10.1073/pnas.1503928112.
Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. 2015. Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon. Frontiers in Cellular and Infection Microbiology 5: 32. DOI: 10.3389/fcimb.2015.00032.
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences USA 112: E911-20. DOI: 10.1073/pnas.1414592112.

2014

Lang JM, Eisen JA, Zivkovic AM. 2014. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ 2: e659. DOI: 10.7717/peerj.659.
Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. 2014. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLOS Genetics 10: e1004784. DOI: 10.1371/journal.pgen.1004784.
Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15: 924. DOI: 10.1186/1471-2164-15-924.
Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholtz P, Klenk HP. 2014. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences 9: 1278-1284. DOI: 10.4056/sigs.5068949.
Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS Biology 12: e1001920. DOI: 10.1371/journal.pbio.1001920.
Bik HM, Coil DA, Eisen JA. 2014. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. PLOS Biology 12: e1001884. DOI: 10.1371/journal.pbio.1001884.
Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2: e415. DOI: 10.7717/peerj.415.

2013

Wu D, Doroud L, Eisen JA. 2013. TreeOTU: operational taxonomic unit classification based on phylogenetic trees. arXiv . DOI: 10.48550/arXiv.1308.6333.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. 2013. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243. DOI: 10.7717/peerj.243.
Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. 2013. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environmental Microbiology 16: 3398-415. DOI: 10.1111/1462-2920.12388.
Eisen JA, Ganley E, MacCallum CJ. 2013. Open science and reporting animal studies: who’s accountable?. PLOS Biology 12: e1001757. DOI: 10.1371/journal.pbio.1001757.
Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. 2013. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME Journal 8: 1-3. DOI: 10.1038/ismej.2013.176.
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. 2013. Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences 8: 561-570. DOI: 10.4056/sigs.4638348.
Wu D, Jospin G, Eisen JA. 2013. Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLOS One 8: e77033. DOI: 10.1371/journal.pone.0077033.
Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JV. 2013. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLOS One 8: e76375. DOI: 10.1371/journal.pone.0076375.
Eisen JA, Maccallum CJ, Neylon C. 2013. Expert failure: re-evaluating research assessment. PLOS Biology 11: e1001677. DOI: 10.1371/journal.pbio.1001677.
Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4: 2120. DOI: 10.1038/ncomms3120.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437. DOI: 10.1038/nature12352.
Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLOS One 8: e62510. DOI: 10.1371/journal.pone.0062510.

2012

Rands CM, Darling A, 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. 2012. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14: 95. DOI: 10.1186/1471-2164-14-95.
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. 2012. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences USA 110: 1053-1058. DOI: 10.1073/pnas.1217107110.
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.” . DOI: 10.17226/13500.
Kembel SW, Wu M, Eisen JA, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLOS Computational Biology 8(10): e1002743. DOI: 10.1371/journal.pcbi.1002743.
Traag BA, Pugliese A, Eisen JA, Losick R. 2012. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis. Journal of Bacteriology 8(10): e1002743. DOI: 10.1128/JB.01778-12.
Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics 13: 264. DOI: 10.1186/1471-2105-13-264.
Jiang X, Langille MG, Neches RY, Elliot M, Levin SA, Eisen JA, Weitz JS, Dushoff J. 2012. Functional biogeography of ocean microbes revealed through non-negative matrix factorization. PLOS One 7: e43866. DOI: 10.1371/journal.pone.0043866.
Tritt A, Eisen JA, Facciotti MT, Darling AE. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLOS One 7: e42304. DOI: 10.1371/journal.pone.0042304.
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: 7327-7336. DOI: 10.1128/AEM.01741-12.
Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLOS One 7: e41389. DOI: 10.1371/journal.pone.0041389.
Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS. 2012. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics 28: 1947-1948. DOI: 10.1093/bioinformatics/bts273.
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. 2012. Genome-scale analysis of programmed DNA elimination sites in Tetrahymena thermophila. G3 1: 515-522. DOI: 10.1534/g3.111.000927.
Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomics. PLOS One 7: e30288. DOI: 10.1371/journal.pone.0030288.
Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1: 6. DOI: 10.1186/2047-217X-1-6.

2011

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: e1002272. DOI: 10.1371/journal.pgen.1002272.
Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. 2011. Aggregating, tagging and integrating biodiversity research. PLOS One 6: e19491. DOI: 10.1371/journal.pone.0019491.
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. 2011. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14: 162-76. DOI: 10.1111/j.1462-2920.2011.02576.x.
Kembel SW, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLOS One 6: e23214. DOI: 10.1371/journal.pone.0023214.
Darling AE, Tritt A, Eisen JA, Facciotti MT. 2011. Mauve assembly metrics. Bioinformatics 27: 2756-2757. DOI: 10.1093/bioinformatics/btr451.
Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial beta-diversity depend on spatial scale. Proceedings of the National Academy of Sciences USA 108: 7850-7854. DOI: 10.1073/pnas.1016308108.
Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLOS One 6: e18011. DOI: 10.1371/journal.pone.0018011.

2010

Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O’Dwyer JP, Green JL, Eisen JA, Pollard KS. 2010. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLOS Computational Biology 7: e1001061. DOI: 10.1371/journal.pcbi.1001061.
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(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010: 690737. DOI: 10.1155/2010/690737.
Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. 2010. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics 11: 317. DOI: 10.1186/1471-2105-11-317.
Morgan JL, Darling AE, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community.PLOS One 5: e10209. DOI: 10.1371/journal.pone.0010209.
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: 243-8. DOI: 10.4056/sigs.1433550.
Langille MG, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLOS One 5: e10071. DOI: 10.1371/journal.pone.0010071.

2009

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: e9605. DOI: 10.1371/journal.pone.0009605.
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: 1056-1060. DOI: 10.1038/nature08656.
Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLOS Biology 7: e1000224. DOI: 10.1371/journal.pbio.1000224.
Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proceedings of the National Academy of Sciences USA 106: 17187-17192. DOI: 10.1073/pnas.0904847106.
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: e6085. DOI: 10.1371/journal.pone.0006085.
Eisen JA. 2009. Genomic evolvability and the origin of novelty: studying the past, interpreting the present, and predicting the future. In Relman DA, Hamburg MA, Choffness ER, Mack A (ed), Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. The National Academies Press, Washington, DC. . DOI: 10.17226/12586.
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. . DOI: n/a.
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: e5299. DOI: 10.1371/journal.pone.0005299.
Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. 2009. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLOS Genetics 5: e1000362. DOI: 10.1371/journal.pgen.1000362.
Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, 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: e4207. DOI: 10.1371/journal.pone.0004207.

2008

Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R 2nd, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9: 597. DOI: 10.1186/1471-2164-9-597.
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: 562. DOI: 10.1186/1471-2164-9-562.
Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. 2008. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biology 9: R158. DOI: 10.1186/gb-2008-9-11-r158.
Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9: R151. DOI: 10.1186/gb-2008-9-10-r151.
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: e2566. DOI: 10.1371/journal.pone.0002566.
Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. Research in Computational Molecular Biology 2008: 17-28. DOI: 10.1007/978-3-540-78839-3_3.
Eisen JA. 2008. PLoS Biology 2.0. PLOS Biology 6: e48. DOI: 10.1371/journal.pbio.0060048.

2007

Hazen TH, Wu D, Eisen JA, Sobecky PA. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and Environmental Microbiology 73: 7703-7710. DOI: 10.1128/AEM.01577-07.
Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. 2007. On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes?. International Journal of Systematic and Evolutionary Microbiology 57(Pt 8): 1677-1678. DOI: 10.1099/ijs.0.65248-0.
Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. 2007. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proceedings of the National Academy of Sciences USA 104: 11784-11789. DOI: 10.1073/pnas.0702984104.
Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T. 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLOS Genetics 3: e77. DOI: 10.1371/journal.pgen.0030077.
Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLOS Biology 5: e82. DOI: 10.1371/journal.pbio.0050082.
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: e77. DOI: 10.1371/journal.pbio.0050077.
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: e16. DOI: 10.1371/journal.pbio.0050016.
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. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000. DOI: 10.1126/science.1138438.

2006

Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. 2006. Evolution of sensory complexity recorded in a myxobacterial genome.Proceedings of the National Academy of Sciences USA 103: 15200-15205. DOI: 10.1073/pnas.0607335103.
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. DOI: 10.1371/journal.pbio.0040286.
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 standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 10: 231-237. DOI: 10.1089/omi.2006.10.231.
Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. 2006. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics 88: 443-451. DOI: 10.1016/j.ygeno.2006.05.002.
Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLOS Biology 4: e188. DOI: 10.1371/journal.pbio.0040188.
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. DOI: 10.1371/journal.pgen.0020021.
Penn K, Wu D, Eisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72: 1680-3. DOI: 10.1128/AEM.72.2.1680-1683.2006.

2005

Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, 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. DOI: 10.1371/journal.pgen.0010065.
Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J. 2005. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proceedings of the National Academy of Sciences USA 102: 7315-7320 . DOI: 10.1073/pnas.0501424102.
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. Inskeep WP, McDermott TR, (ed), Geothermal Biology and Geochemistry in Yellowstone National Park. Montana State University Thermal Biology Institute, Bozeman, MT. pp. 163-170. . DOI: .
Badger JH, Eisen JA, Ward NL. 2005. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders ‘Rhodobacterales’ and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology 55(Pt 3): 1021-1026. DOI: 10.1099/ijs.0.63510-0.
Desjardins C, Eisen JA, Nene V. 2005. New evolutionary frontiers from unusual virus genomes. Genome Biology 6: 212 . DOI: 10.1186/gb-2005-6-3-212.
Eisen JA. 2005. Coordinating efforts to understand microbes in the environment. Microbe 71: 157. DOI: .
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 PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307: 105-108. DOI: 10.1126/science.1102226.

2004

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 adaptations to the marine environment. Nature 432: 910-913. DOI: 10.1038/nature03170.
Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. 2004. Analysis of Deinococcus radiodurans’s transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 168: 21-33. DOI: 10.1534/genetics.104.029249.
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: e303. DOI: 10.1371/journal.pbio.0020303.
Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotechnology 22: 554-559. DOI: 10.1038/nbt959.
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, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea.Science 304: 66-74 . DOI: 10.1126/science.1093857.
Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT.2004. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences USA 101: 5646-51 . DOI: 10.1073/pnas.0307639101.
Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, Mohamoud Y, Lee P, Berry K, Khouri HM, Paulsen IT, Nelson KE, Martin W, Esser C, Ahmadinejad N, Wiegand C, Durkin AS, Nelson WC, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Gwinn M, Kolonay JF, Madupu R, Craven MB, Utterback T, Weidman J, Nierman WC, Aken SV, Tettelin H, O’Neill S, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLOS Biology 2: E69 . DOI: 10.1371/journal.pbio.0020069.
Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen JA, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg SL, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM. 2004. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology 134: 183-191. DOI: 10.1016/j.molbiopara.2003.11.012.

2003

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. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 302: 1967-1969. DOI: 10.1126/science.1088727.
Yang RZ, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, Gong DW. 2003. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochemical and Biophysical Research Communications 310: 927-935. DOI: 10.1016/j.bbrc.2003.09.093.
Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. 2003. Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83. Journal of Bacteriology 185: 5591-601. DOI: 10.1128/JB.185.18.5591-5601.2003.
Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM. 2003. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. Journal of Bacteriology 185: 5220-5233. DOI: 10.1128/JB.185.17.5220-5233.2003.
Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. DOI: 10.1126/science.1086292.
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. DOI: 10.1029/2003EO410001.
Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. 2003. The age of the Arabidopsis thaliana genome duplication. Plant Molecular Biology 51: 859-866. DOI: 10.1023/a:1023001130337.
Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of Bacteriology 185: 3392-3399. DOI: 10.1128/JB.185.11.3392-3399.2003.
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 genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 81-86. DOI: 10.1038/nature01586.
Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF. 2003. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proceedings of the National Academy of Sciences USA 100: 5455-5460 . DOI: 10.1073/pnas.0931379100.
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. DOI: 10.1126/science.1080613.

2002

Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology 4: 799-808. DOI: 10.1046/j.1462-2920.2002.00366.x.
Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. 2002. The value of complete microbial genome sequencing (you get what you pay for). Journal of Bacteriology 184: 6403-6405 . DOI: 10.1128/JB.184.23.6403-6405.2002.
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. DOI: 10.1038/nature01097.
Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature Biotechnology 20: 1118-1123. DOI: 10.1038/nbt749.
Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proceedings of the National Academy of Sciences USA 99: 13148-13153 . DOI: 10.1073/pnas.192319099.
Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. Journal of Bacteriology 184: 5479-5490. DOI: 10.1128/JB.184.19.5479-5490.2002.
Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. 2002. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proceedings of the National Academy of Sciences USA 99: 12391-12396. DOI: 10.1073/pnas.182380799.
Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical Population Biology 61: 481-487 . DOI: 10.1006/tpbi.2002.1594.
Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Venter JC, Gruber TM, Ketchum KA, Tettelin H, Bryant DA, Fraser CM. 2002. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences USA 99: 9509-9514. DOI: 10.1073/pnas.132181499.
Van Houten B, Eisen JA, Hanawalt PC. 2002. A cut above: discovery of an alternative excision repair pathway in bacteria. Proceedings of the National Academy of Sciences USA 99: 2581-2583. DOI: 10.1073/pnas.062062599.
Eisen JA. 2002. Brouhaha over the other yeast. Nature 415: 845-848. DOI: 10.1038/nature725.
Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen JA, Slatko B. 2002. Sequencing and analysis of a 63 kb BAC from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi.International Journal of Parasitology 32: 159-166. DOI: 10.1016/s0020-7519(01)00367-8.
DasSarma S, Kennedy SP, Berquist B, Ng WV, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L. 2002. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynthesis Research 70: 3-17. DOI: 10.1023/A:1013879706863.
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. DOI: 10.1038/415630a.

2001

Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida Jr NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee Sr D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li M-J, McClelland R, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao Z-Y, Dolan M, Chumley F, Tingey SC, Tomb J-F, Gordon MP, Olson MV, Nester EW.2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323. DOI: 10.1126/science.1066804.
Salzberg SL, Eisen JA. 2001. Lateral gene transfer or viral colonization?. Science 293: 1048. DOI: 10.1126/science.293.5532.1048b.
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. DOI: 10.1126/science.1061217.
Salzberg SL, White O, Peterson J, Eisen JA. 2001. Microbial genes in the human genome: lateral transfer or gene loss?. Science 292: 1903-1906. DOI: 10.1126/science.1061036.
Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM. 2001. Complete genome sequence of Caulobacter crescentus. Proceedings of the National Academy of Sciences USA 98: 4136-4141. DOI: 10.1073/pnas.061029298.
Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes HW. 2001. Sequence and analysis of the Arabidopsis genome. Current Opinion in Plant Biology 4: 105-110. DOI: 10.1016/s1369-5266(00)00144-8.
Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature414: 148. DOI: 10.1038/35102737.
Nelson KE, Eisen JA, Fraser CM. 2001. Genome of Thermotoga maritima MSB8. Methods in Enzymology 330: 169-180. DOI: 10.1016/S0076-6879(01)30374-9.
Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology 2: interactions1004.1-1004.4. DOI: 10.1186/gb-2001-2-12-interactions1004.
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Research 29: 41-43. DOI: 10.1093/nar/29.1.41.
Eisen JA. 2001. Gastrogenomics. Nature 409: 463-466. DOI: 10.1038/35054158.

2000

Arabidopsis Genome Intitiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. DOI: 10.1038/35048692.
Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1:RESEARCH0011. DOI: 10.1186/gb-2000-1-6-research0011.
Pollock DD, Eisen JA, Doggett NA, Cummings MP. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular Biology and Evolution 17: 1776-1788. DOI: 10.1093/oxfordjournals.molbev.a026278.
Eisen JA. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Current Opinion in Genetics and Development 10: 606-611. DOI: 10.1016/s0959-437x(00)00143-x.
Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole-genome analysis. Current Opinion in Microbiology 3: 475-480. DOI: 10.1016/s1369-5274(00)00125-9.
Fraser CM, Eisen JA, Fleischmann RD, Ketchum KA, Peterson S. 2000. Comparative genomics and understanding of microbial biology. Emerging Infectious Diseases 6: 505-512. DOI: 10.3201/eid0605.000510.
Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencing. Nature 406: 799-803. DOI: 10.1038/35021244.
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. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406: 477-483. DOI: 10.1038/35020000.
Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen JA, Fraser CM. 2000. Genome sequences of Chlamydia trachomatis MoPn and C. pneumoniae AR39. Nucleic Acids Research 28: 1397-1406. DOI: 10.1093/nar/28.6.1397.
Nierman W, Eisen JA, Fraser CM. 2000. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Research in Microbiology 151: 79-84. DOI: 10.1016/S0923-2508(00)00125-X.
Coleman MA, Eisen JA, Mohrenweiser HW. 2000. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse. Genomics 65: 274-282. DOI: 10.1006/geno.2000.6174.
Eisen JA. 2000. Microbial and plant genomics. Journal of Biolaw and Business Spec Supp 21-24. DOI: n/a.
Nierman WC, Eisen JA, Fleischmann RD, Fraser CM. 2000. Genome data: what do we learn?. Current Opinion in Structural Biology 10: 343-348. DOI: 10.1016/s0959-440x(00)00094-4.
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. DOI: 10.1126/science.287.5459.1809.

1999

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. DOI: 10.1038/45471.
Eisen JA. 1999. Mechanistic basis of microsatellite instability. In Microsatellites: Evolution and Applications (DB Goldstein and C Schlotterer, eds). Oxford University Press, Oxford. . DOI: n/a.
Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation Research 435: 171-213. DOI: 10.1016/s0921-8777(99)00050-6.
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. DOI: 10.1126/science.286.5444.1571.
Eisen JA. 1999. Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999. Trends in Genetics 15: 218-219. DOI: 10.1016/S0168-9525(99)01739-4.
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. DOI: 10.1038/20601.

1998

Eisen JA. 1998c. Evolution of DNA repair genes, proteins and processes. PhD Thesis.
Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, Lerman MI. 1998. In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Human Genetics 103: 355-364. DOI: 10.1007/s004390050829.
Eisen JA. 1998b. A phylogenomic study of the MutS family of proteins. Nucleic Acids Research 26: 4291-300. DOI: 10.1093/nar/26.18.4291.
Gruber TM, Eisen JA, Gish K, Bryant DA. 1998. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiology Letters 162: 53-60. DOI: 10.1111/j.1574-6968.1998.tb12978.x.
Eisen JA. 1998a. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8: 163-167. DOI: 10.1101/gr.8.3.163.
White RB, Eisen JA, Kasten TL, Fernald RD. 1998. Second gene for gonadotropin-releasing hormone in humans. Proceedings of the National Academy of Sciences USA 95: 305-309. DOI: 10.1073/pnas.95.1.305.

1997

Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078. DOI: 10.1038/nm1097-1076.
Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. 1997. Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. Journal of Virology 71: 5441-5448. DOI: 10.1128/JVI.71.7.5441-5448.1997.
Eisen JA. 1997. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. Methods in Molecular Biology 70: 13-38.

1992-1995

Eisen JA. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. Journal of Molecular Evolution 41: 1105-1123. DOI: 10.1007/BF00173192.
Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723. DOI: 10.1093/nar/23.14.2715.
Eisen JA, Benito MI, Walbot V. 1994. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Research 22: 2634-2636. DOI: 10.1093/nar/22.13.2634.
Liu SK, Eisen JA, Hanawalt PC, Tessman I. 1993. recA mutations that reduce the constitutive coprotease activity of the RecA1202(Prtc) protein: possible involvement of interfilament association in proteolytic and recombination activities. Journal of Bacteriology 175: 6518-6529. DOI: 10.1128/jb.175.20.6518-6529.1993.
Eisen JA, Smith SW, Cavanaugh CM. 1992. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. Journal of Bacteriology 174: 3416-3421. DOI: 10.1128/jb.174.10.3416-3421.1992.

Genome, Metagenome and Microbiome Data Reports. Listing these separately.

Ettinger CL, Bryan J, Tokajian S, Jospin G, Coil D, Eisen JA. 2021. Reconstruction of metagenome-assembled genomes from aquaria. Microbiology Resource Announcements 10: e0055721. DOI: 10.1128/MRA.00557-21.
Alexiev A, Vann LE, Lang JM, Eisen JA. 2020. Bacterial community sequences of submerged aquatic vegetation in the Potomac River. Microbiology Resource Announcements 9: e01175-19. DOI: 10.1128/MRA.01175-19.
Mukhopadhyay R, Joaquin J, Hogue R, Fitzgerald S, Jospin G, Mars K, Eisen JA, Chaturvedi V. 2017. Complete genome sequence of Dolosigranulum pigrum from a patient with interstitial lung disease using single-molecule real-time sequencing technology. Genome Announcements 5(18): e00317-17. DOI: 10.1128/genomeA.00317-17.
Lujan KM, Eisen JA, Coil DA. 2017. Draft genome sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and Shewanella sp. Strain UCD-KL21, isolated from seagrass. Genome Announcements 5(13): e00023-17. DOI: 10.1128/genomeA.00023-17.
Klein BA, Lemon KP, Gajare P, Jospin G, Eisen JA, Coil DA. 2017. Draft genome sequences of Dermacoccus nishinomiyaensis strains UCD-KPL2534 and UCD-KPL2528 isolated from an indoor track facility. Genome Announcements 5(8): e01652-16. DOI: 10.1128/genomeA.01652-16.
Kincheloe GN, Eisen JA, Coil DA. 2017. Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria). Genome Announcements 5(6): e01599-16. DOI: 10.1128/genomeA.01599-16.
Jiao JY, Carro L, Liu L, Gao XY, Zhang XT, Hozzein WN, Lapidus A, Huntemann M, Reddy TBK, Varghese N, Hadjithomas M, Ivanova NN, Göker M, Pillay M, Eisen JA, Woyke T, Klenk HP, Kyrpides NC, Li WJ. 2017. Complete genome sequence of Jiangella gansuensis strain YIM 002(T) (DSM 44835(T)), the type species of the genus Jiangella and source of new antibiotic compounds. Standards in Genomic Sciences 12: 21. DOI: 10.1186/s40793-017-0226-6.
Lymperopoulou DS, Coil DA, Schichnes D, Lindow SE, Jospin G, Eisen JA, Adams RI. 2017. Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitisstrain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicumstrain H39, Plantibacter sp. strain H53, and Pseudomonas oryziha strain H72. Standards in Genomic Sciences 12: 17. DOI: 10.1186/s40793-017-0223-9.
Mukhopadhyay R, Joaquin J, Hogue R, Kilaru A, Jospin G, Mars K, Eisen JA, Chaturvedi V. 2017. Complete genome sequence of a Paenalcaligenes hominis strain isolated from a paraplegic patient with neurogenic bladder using single-molecule real-time sequencing technology. Genome Announcements 5(17): e00252-17. DOI: 10.1128/genomeA.00252-17.
Dahms PA, Martin AL, Ganz HH, Eisen JA, Coil DA. 2017. Draft genome sequence of Propionibacterium avidumStrain UCD-PD2 isolated from a feline anal sac. Genome Announcements 5(12): e00034-17. DOI: 10.1128/genomeA.00034-17.
De Vries DR, Martin AL, Ganz HH, Eisen JA, Coil DA. 2016. Draft genome sequence of Enterococcus faecalis Strain UCD-PD3. Genome Announcements 4(6): e01386-16. DOI: 10.1128/genomeA.01386-16.
Klein BA, Lemon KP, Faller LL, Jospin G, Eisen JA, Coil DA. 2016. Draft genome sequence of Curtobacterium sp. strain UCD-KPL2560 (Phylum Actinobacteria). Genome Announcements 4(5): e01040-16. DOI: 10.1128/genomeA.01040-16.
Koenigsaecker TM, Eisen JA, Coil DA. 2016. Draft genome sequence of Gordonia sp. strain UCD-TK1 (Phylum Actinobacteria). Genome Announcements 4(5): e01121-16. DOI: 10.1128/genomeA.01121-16.
Lujan KM, Eisen JA, Coil DA. 2016. Draft genome sequence of Tenacibaculum soleae UCD-KL19. Genome Announcements 4(5): e01120-16. DOI: 10.1128/genomeA.01120-16.
Nelson RL, Castro MA, Katti M, Eisen JA, Van Laar TA. 2016. Genome sequence of a multidrug-resistant strain of Bacillus pumilus, CB01, isolated from the feces of an american crow, Corvus brachyrhynchos. Genome Announcements 4(4): e00807-16. DOI: 10.1128/genomeA.00807-16.
Alexiev A, Coil DA, Jospin G, Eisen JA, Adams JY. 2016. Draft genome sequence of Klebsiella pneumoniaeUCD-JA29 isolated from a patient with sepsis. Genome Announcements 4(3): e00234-16. DOI: 10.1128/genomeA.00234-16.
Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. 2016. Draft genome sequences of two Pseudoalteromonas porphyrae strains isolated from seagrass sediment. Genome Announcements 4(2): e00092-16. DOI: 10.1128/genomeA.00092-16.
Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen JA, Coil DA. 2016. Draft genome sequence of Cobetia sp. UCD-24C, isolated from roots and leaves of the seagrass Zostera marina. Genome Announcements 4(2): e00116-16. DOI: 10.1128/genomeA.00116-16.
Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. 2016. Draft genome sequences of two Vibrio splendidusStrains, isolated from seagrass sediment. Genome Announcements 4(1): e01769-15. DOI: 10.1128/genomeA.01769-15.
Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen JA, Coil DA. 2016. Draft genome sequences of two Pseudoalteromonas strains isolated from roots and leaf blades of the seagrass Zostera marina. Genome Announcements 4(1): e00010-16. DOI: 10.1128/genomeA.00010-16.
Tokajian S, Eisen JA, Jospin G, Hamze M, Rafei R, Salloum T, Ibrahim J, Coil DA. 2016. Draft genome sequences of Acinetobacter baumannii strains harboring the blaNDM-1 gene isolated in Lebanon from civilians wounded during the Syrian Civil War. Genome Announcements 4(1): e01678-15. DOI: 10.1128/genomeA.01678-15.
Tokajian S, Eisen JA, Jospin G, Matar G, Araj GF, Coil DA. 2016. Draft genome sequence of Klebsiella pneumoniae KGM-IMP216 harboring blaCTX-M-15, blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, isolated from a patient in Lebanon. Genome Announcements 4(1): e01632-15. DOI: 10.1128/genomeA.01632-15.
Coil DA, Jospin G, Eisen JA, Adams JY. 2016. Additional draft genome sequences of Escherichia coli strains isolated from septic patients. Genome Announcements 4(1): e01614-15. DOI: 10.1128/genomeA.01614-15.
Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. 2015. Draft genome sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes). Genome Announcements 3(6): e01376-15. DOI: 10.1128/genomeA.01376-15.
Coil DA, Benardini JN, Eisen JA. 2015. Draft genome sequence of Bacillus safensis JPL-MERTA-8-2, isolated from a Mars-bound spacecraft. Genome Announcements 3(6): e01360-15. DOI: 10.1128/genomeA.01360-15.
Coil DA, Eisen JA. 2015. Draft genome sequence of Porphyrobacter mercurialis (sp. nov.) strain Coronado.Genome Announcements 3(6): e00856-15. DOI: 10.1128/genomeA.00856-15.
Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. 2015. Draft genome sequence of Pseudoalteromonas tetraodonis strain UCD-SED8 (Phylum Gammaproteobacteria). Genome Announcements 3(6): e01276-15. DOI: 10.1128/genomeA.01276-15.
Betts MN, Jospin G, Eisen JA, Coil DA. 2015. Draft genome sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes). Genome Announcements 3(5): e01209-15. DOI: 10.1128/genomeA.01209-15.
Coil DA, Alexiev A, Wallis C, O’Flynn C, Deusch O, Davis I, Horsfall A, Kirkwood N, Jospin G, Eisen JA, Harris S, Darling AE. 2015. Draft genome sequences of 26 Porphyromonas strains isolated from the canine oral microbiome. Genome Announcements 3(2): e00187-15. DOI: 10.1128/genomeA.00187-15.
Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. 2015. Genome sequence of a sulfate-reducing thermophilic bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). Genome Announcements 3(1): e01490-14. DOI: 10.1128/genomeA.01490-14.
Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. 2015. Genome sequence of the sulfate-reducing thermophilic bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). Genome Announcements 3(1): e01489-14. . DOI: 10.1128/genomeA.01489-14.
Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen JA. 2015. Draft genome sequence ofBurkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria). Genome Announcements 3(1): e01462-14. DOI: 10.1128/genomeA.01462-14.
Ettinger CL, Mousa WM, Raizada MN, Eisen JA. 2015. Draft genome sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria). Genome Announcements 3(1): e01461-14. DOI: 10.1128/genomeA.01461-14.
Dunitz MI, Coil DA, Jospin G, Eisen JA, Adams JY. 2014. Draft genome sequences of Escherichia coli strains isolated from septic patients. Genome Announcements 2(6): e01278-14. DOI: 10.1128/genomeA.01278-14.
Göker M, Spring S, Scheuner C, Anderson I, Zeytun A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2014. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Standards in Genomic Sciences 9(3): 1105-1117. DOI: 10.4056/sigs.3016383.
Göker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2014. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences 9(3): 1076-88. DOI: 10.4056/sigs.5138968.
Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. 2014. Draft genome sequence of the Pyridinediol-Fermenting bacterium Synergistes jonesii 78-1. Genome Announcements2(4): e00833-14. DOI: 10.1128/genomeA.00833-14.
Lee RD, Jospin G, Coil DA, Eisen JA. 2014. Draft genome sequence of the endosymbiont “Candidatus Ruthia magnifica” UCD-CM (Phylum Proteobacteria). Genome Announcements 2(4): e00717-14. DOI: 10.1128/genomeA.00717-14.
Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announcements 2(3): e00470-14. DOI: 10.1128/genomeA.00470-14.
Tokajian S, Eisen JA, Jospin G, Coil DA. 2014. Draft genome sequences of Streptococcus pyogenes strains associated with throat and skin infections in Lebanon. Genome Announcements 2(3): e00358-14. DOI: 10.1128/genomeA.00358-14.
Dunitz MI, James PM, Jospin G, Eisen JA, Coil DA, Chandler JA. 2014. Draft genome sequence of Tatumellasp. strain UCD-D_suzukii (Phylum Proteobacteria) isolated from Drosophila suzukii larvae. Genome Announcements 2(2): e00349-14. DOI: 10.1128/genomeA.00349-14.
Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. 2014. Draft genome sequences of extended-spectrum β-Lactamase-producing Escherichia coli strains isolated from patients in Lebanon. Genome Announcements 2(1): e00123-14. DOI: 10.1128/genomeA.00123-14.
Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. 2014. Draft genome sequence of extended-spectrum β-Lactamase-producing Klebsiella pneumoniae isolated from a patient in Lebanon. Genome Announcements 2(1): e00121-14. DOI: 10.1128/genomeA.00121-14.
Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of the extreme thermophile Dictyoglomus thermophilum H-6-12. Genome Announcements 2(1): e00109-14. DOI: 10.1128/genomeA.00109-14.
Anderson I, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Lang E, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.2013. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a Xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences 9(1): 83-92. DOI: 10.4056/sigs.4338002.
Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Rohde M, Mayilraj S, Spring S, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2013. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences 9(1): 57-70. DOI: 10.4056/sigs.4237901.
Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP.2013. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Standards in Genomic Sciences 9: 10. DOI: 10.1186/1944-3277-9-10.
Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen JA. 2013. Draft genome sequence of the arsenate-respiring bacterium Chrysiogenes arsenatis Strain DSM 11915. Genome Announcements 1(6): e00953-13. DOI: 10.1128/genomeA.00953-13.
Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides N, Klenk HP. 2013. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Standards in Genomic Sciences 8(2): 228-238. DOI: 10.4056/sigs.3617113.
Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Tapia L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Gronow S, Göker M, Detter J, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides N, Klenk HP, Lapidus A. 2013. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences 8(2): 177-187. DOI: 10.4056/sigs.3637201.
Liolios K, Abt B, Scheuner C, Chertkov O, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall B, Detter J, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk H, Klenk H-P, Kyrpides N. 2013. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences 8(2): 165-176. DOI: 10.4056/sigs.3607108.
Abt B, Göker M, Scheuner C, Han C, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Chang J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla E, Rohde M, Spring S, Gronow S, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Woyke T, Klenk H. 2013. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldariacomb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Standards in Genomic Sciences 8(1): 88-105. DOI: 10.4056/sigs.3096473.
Mavromatis K, Stackebrandt E, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Spring S, Göker M, Woyke T, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides N. 2013. Complete genome sequence of the moderate thermophile Anaerobaculum mobiletype strain (NGA(T)). Standards in Genomic Sciences 8(1): 47-57. DOI: 10.4056/sigs.3547050.
Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Han C, Cheng J, Tapia R, Goodwin L, Bruce D, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Rohde M, Tindall B, Göker M, Woyke T, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides N. 2013. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marinatype strain (En5(T)). Standards in Genomic Sciences 8(1): 37-46. DOI: 10.4056/sigs.3537045.
Mavromatis K, Stackebrandt E, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2013. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences 8(1): 26-36. DOI: 10.4056/sigs.3527032.
Stackebrandt E, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Chang Y, Land M, Hauser L, Rohde M, Pukall R, Göker M, Detter J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P. 2013. Complete genome sequence of Coriobacteriumglomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences 8(1): 15-25. DOI: 10.4056/sigs.3507020.
Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence ofLeucobacter sp. strain UCD-THU (Phylum Actinobacteria). Genome Announcements 1(3): e00325-13. DOI: 10.1128/genomeA.00325-13.
Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Curtobacteriumflaccumfaciens strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1(3): e00244-13. DOI: 10.1128/genomeA.00244-13.
Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1(3): e00197-13. DOI: 10.1128/genomeA.00197-13.
Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft genome sequence of Kocuria sp. strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1(3): e00172-13. DOI: 10.1128/genomeA.00172-13.
Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Microbacterium sp. strain UCD-TDU (Phylum Actinobacteria). Genome Announcements 1(2): e0012013. DOI: 10.1128/genomeA.00120-13.
Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announcements 1(2): e00086-13. DOI: 10.1128/genomeA.00086-13.
Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.2012. Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Standards in Genomic Sciences 7(1): 120-130. DOI: 10.4056/sigs.3296896.
Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Standards in Genomic Sciences 7(1): 107-119. DOI: 10.4056/sigs.3216895.
Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. 2012. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences 7(2): 210-220. DOI: 10.4056/sigs.3117229.
Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. 2012. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences6(3): 1-13. DOI: 10.4056/sigs.2736042.
Copeland A, Zeytun A, Yassawong M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Mavromatis K, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Sikorski J, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2012. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Standards in Genomic Sciences 6(2): 240-250. DOI: 10.4056/sigs.2756060.
Göker M, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2012. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences 6(2): 230-239. DOI: 10.4056/sigs.2726028.
Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Permanent draft genome sequence of the gliding predator Saprospiragrandis strain Sa g1 (= HR1). Standards in Genomic Sciences 6(2): 210-219. DOI: 10.4056/sigs.2816096.
Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Gronow S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. . 2012. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Standards in Genomic Sciences 6(2): 194-209. DOI: 10.4056/sigs.2796069.
Huntemann M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences 6(2): 185-193. DOI: 10.4056/sigs.2786069.
Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2012. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences 6(2): 174-184. DOI: 10.4056/sigs.2746047.
Anderson I, Saunders E, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Chang YJ, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2012. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences 6(2): 155-164. DOI: 10.4056/sigs.2665915.
Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. 2012. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences 6(2): 145-154. DOI: 10.4056/sigs.2475579.
Han C, Kotsyurbenko O, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2012. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences 6(1): 94-103. DOI: 10.4056/sigs.2456004.
Copeland A, Gu W, Yasawong M, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng JF, Goodwin LA, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Pan C, Brambilla EM, Rohde M, Tindall BJ, Sikorski J, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. 2012. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences6(1): 21-30. DOI: 10.4056/sigs.2435521.
Göker M, Daligault H, Mwirichia R, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng J, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Han C, Land M, Hauser L, Pan C, Brambilla E, Rohde M, Spring S, Sikorski J, Wirth R, Detter J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P. 2012. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Standards in Genomic Sciences 5(3): 407-415. DOI: 10.4056/sigs.2465574.
Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng J, Tapia R, Han C, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla E, Rohde M, Abt B, Verbag S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P, Woyke T. 2012. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). Standards in Genomic Sciences 5(3): 398-406. DOI: 10.4056/sigs.2344929.
Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Göker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA. 2011. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Standards in Genomic Sciences 5(1): 121-134. DOI: 10.4056/sigs.2144922.
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. DOI: 10.4056/sigs.2114901.
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. DOI: 10.4056/sigs.2235024.
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 Sciences5(1): 41-49. DOI: 10.4056/sigs.2164949.
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. DOI: 10.4056/sigs.2154937.
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): 21-29. DOI: 10.4056/sigs.2124912.
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. DOI: 10.4056/sigs.2064705.
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): 381-392. DOI: 10.4056/sigs.2014648.
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): 371-380. DOI: 10.4056/sigs.2004684.
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): 361-370. DOI: 10.4056/sigs.1984594.
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): 352-360. DOI: 10.4056/sigs.1964579.
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): 342-351. DOI: 10.4056/sigs.1894556.
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): 331-341. DOI: 10.4056/sigs.1864526.
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): 322-330. DOI: 10.4056/sigs.1844518.
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): 312-321. DOI: 10.4056/sigs.1824509.
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): 303-311. DOI: 10.4056/sigs.1814460.
Land M, Held B, Gronow S, Abt B, Lucas S, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Hauser L, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). Standards in Genomic Sciences 4(2): 233-243. DOI: 10.4056/sigs.1784330.
Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. 2011. Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Standards in Genomic Sciences 4(2): 221-232. DOI: 10.4056/sigs.1774329.
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. 2. 2011. Complete genome sequence of Oceanithermus profundus type strain (506). Standards in Genomic Sciences 4(2): 210-220. DOI: 10.4056/sigs.1734292.
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 Odoribacter splanchnicus type strain (1651/6). Standards in Genomic Sciences 4(2): 200-209. DOI: 10.4056/sigs.1714269.
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 salanitronistype strain (BL78). Standards in Genomic Sciences 4(2): 191-199. DOI: 10.4056/sigs.1704212.
Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Standards in Genomic Sciences 4(2): 173-182. DOI: 10.4056/sigs.1644004.
Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Standards in Genomic Sciences 4(2): 163-172. DOI: 10.4056/sigs.1633949.
Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Marivirga tractuosa type strain (H-43). Standards in Genomic Sciences 4(2): 154-162. DOI: 10.4056/sigs.1623941.
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 anatipestifertype strain (ATCC 11845). Standards in Genomic Sciences 4(2): 144-153. DOI: 10.4056/sigs.1553862.
Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Standards in Genomic Sciences 4(2): 131-143. DOI: 10.4056/sigs.1463589.
Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.2011. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Standards in Genomic Sciences 4(1): 100-110. DOI: 10.4056/sigs.1613929.
Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Standards in Genomic Sciences 4(1): 91-99. DOI: 10.4056/sigs.1563919.
Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Weeksella virosa type strain (9751). Standards in Genomic Sciences 4(1): 81-90. DOI: 10.4056/sigs.1603927.
Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2011. Complete genome sequence of Cellulophaga algicola type strain (IC166). Standards in Genomic Sciences 4(1): 72-80. DOI: 10.4056/sigs.1543845.
Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Isosphaera pallida type strain (IS1B). Standards in Genomic Sciences 4(1): 63-71. DOI: 10.4056/sigs.1533840.
Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. 2011. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Standards in Genomic Sciences 4(1): 54-62. DOI: 10.4056/sigs.1523807.
Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. 2011. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Standards in Genomic Sciences 4(1): 45-53. DOI: 10.4056/sigs.1513795.
Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Standards in Genomic Sciences 4(1): 36-44. DOI: 10.4056/sigs.1503846.
Chertkov O, Sikorski J, Nolan M, Lapidus A, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Djao OD, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Detter JC, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Thermomonospora curvata type strain (B9). Standards in Genomic Sciences 4(1): 13-22. DOI: 10.4056/sigs.1453580.
Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2011. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Standards in Genomic Sciences 4(1): 2-12. DOI: 10.4056/sigs.1413518.
Han C, Gu W, Zhang X, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Schneider S, Rohde M, Göker M, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. 2010. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Standards in Genomic Sciences 3(3): 337-345. DOI: 10.4056/sigs.1373474.
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. 2010. Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509). Standards in Genomic Sciences 3(3): 325-336. DOI: 10.4056/sigs.1363462.
Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010. Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences 3(3): 315-324. DOI: 10.4056/sigs.1283367.
Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Standards in Genomic Sciences 3(3): 304-314. DOI: 10.4056/sigs.1273360.
Del Rio TG, Chertkov O, Yasawong M, Lucas S, Deshpande S, Cheng JF, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Pukall R, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Complete genome sequence of Intrasporangium calvum type strain (7 KIP). Standards in Genomic Sciences 3(3): 294-303. DOI: 10.4056/sigs.1263355.
Pitluck S, Yasawong M, Held B, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Chertkov O, Goodwin L, Tapia R, Han C, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Pukall R, Spring S, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). Standards in Genomic Sciences 3(3): 285-293. DOI: 10.4056/sigs.1253298.
Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. 2010. Complete genome sequence of Desulfarculus baarsii type strain (2st14). Standards in Genomic Sciences 3(3): 276-284. DOI: 10.4056/sigs.1243258.
Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1). Standards in Genomic Sciences 3(3): 268-275. DOI: 10.4056/sigs.1233249.
Brambilla E, Djao OD, Daligault H, Lapidus A, Lucas S, Hammon N, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences 3(2): 203-211. DOI: 10.4056/sigs.1183143.
Sikorski J, Munk C, Lapidus A, Ngatchou Djao OD, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Han C, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Sims D, Meincke L, Brettin T, Detter JC, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Lang E, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Standards in Genomic Sciences 3(2): 194-202. DOI: 10.4056/sigs.1173118.
Nolan M, Sikorski J, Davenport K, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tapia R, Brettin T, Detter JC, Han C, Yasawong M, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Complete genome sequence of Ferrimonas balearica type strain (PAT). Standards in Genomic Sciences 3(2): 174-182. DOI: 10.4056/sigs.1161239.
Roeselers G, Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2010. Complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomic Sciences 3(2): 163-173. DOI: 10.4056/sigs.1103048.
Kiss H, Cleland D, Lapidus A, Lucas S, Del Rio TG, Nolan M, Tice H, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Lu M, Brettin T, Detter JC, Göker M, Tindall BJ, Beck B, McDermott TR, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Cheng JF. 2010. Complete genome sequence of ‘Thermobaculum terrenum‘ type strain (YNP1). Standards in Genomic Sciences 3(2): 153-162. DOI: 10.4056/sigs.1153107.
Mavromatis K, Yasawong M, Chertkov O, Lapidus A, Lucas S, Nolan M, Del Rio TG, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Tapia R, Han C, Bruce D, Goodwin L, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Brambilla E, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010. Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Standards in Genomic Sciences 3(2): 136-144. DOI: 10.4056/sigs.1143106.
Yasawong M, Teshima H, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Standards in Genomic Sciences 3(2): 126-135. DOI: 10.4056/sigs.1123072.
Mavromatis K, Sikorski J, Pabst E, Teshima H, Lapidus A, Lucas S, Nolan M, Glavina Del Rio T, Cheng JF, Bruce D, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. 2010. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Standards in Genomic Sciences 3(2): 117-125. DOI: 10.4056/sigs.1113067.
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-1228P). Standards in Genomic Sciences 3(2): 108-116. DOI: 10.4056/sigs.1133078.
Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2010. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Standards in Genomic Sciences 3(1): 85-92. DOI: 10.4056/sigs.1092865.
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 ulitype strain (VPI D76D-27C). Standards in Genomic Sciences 3(1): 76-84. DOI: 10.4056/sigs.1082860.
Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Standards in Genomic Sciences 3(1): 66-75. DOI: 10.4056/sigs.1072907.
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-7288). Standards in Genomic Sciences 3(1): 57-65. DOI: 10.4056/sigs.1062906.
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, Lapidus A. 2010. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290). Standards in Genomic Sciences 3(1): 47-56. DOI: 10.4056/sigs.1052813.
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, Lapidus A. 2010. Complete genome sequence of Meiothermus silvanus type strain (VI-R2). Standards in Genomic Sciences 3(1): 37-46. DOI: 10.4056/sigs.1042812.
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, Lapidus A. 2010. Complete genome sequence of Meiothermus ruber type strain (21). Standards in Genomic Sciences 3(1): 26-36. DOI: 10.4056/sigs.1032748.
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, Klenk H-P. 2010. Complete genome sequence of Cellulomonas flavigena type strain (134). Standards in Genomic Sciences 3(1): 15-25. DOI: 10.4056/sigs.1012662.
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, Klenk H-P. 2010. Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Standards in Genomic Sciences 3(1): 1-14. DOI: 10.4056/sigs.1002553.
von Jan M, Lapidus A, Del Rio TG, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Goodwin L, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Chertkov O, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Saunders E, Brettin T, Detter JC, Chain P, Eichinger K, Huber H, Spring S, Rohde M, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.2010. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Standards in Genomic Sciences 2(3): 327-346. DOI: 10.4056/sigs.942153.
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, Kyrpides NC. 2010. Complete genome sequence of Thermobispora bispora type strain (R51). Standards in Genomic Sciences 2(3): 318-326. DOI: 10.4056/sigs.962171.
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, Kyrpides NC. 2010. Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Standards in Genomic Sciences 2(3): 300-308. DOI: 10.4056/sigs.912121.
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, Kyrpides NC. 2010. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Standards in Genomic Sciences 2(3): 290-299. DOI: 10.4056/sigs.952166.
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, Klenk H-P. 2010. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Standards in Genomic Sciences 2(3): 280-289. DOI: 10.4056/sigs.902116.
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, Klenk H-P. 2010. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460). Standards in Genomic Sciences 2(3): 270-279. DOI: 10.4056/sigs.892105.
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, Klenk H-P. 2010. Complete genome sequence of Brachyspira murdochii type strain (56-150). Standards in Genomic Sciences 2(3): 260-269. DOI: 10.4056/sigs.831993.
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, Klenk H-P. 2010. Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Standards in Genomic Sciences 2(3): 245-259. DOI: 10.4056/sigs.821804.
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, Chen F. 2010. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300). Standards in Genomic Sciences 2(2): 220-227. DOI: 10.4056/sigs.811799.
Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. 2010. Complete genome sequence of Conexibacter woesei type strain (ID131577). Standards in Genomic Sciences 2(2): 212-219. DOI: 10.4056/sigs.751339.
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, Klenk H-P. 2010. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Standards in Genomic Sciences 2(2): 203-211. DOI: 10.4056/sigs.791633.
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, Klenk H-P. 2010. Complete genome sequence of Thermocrinis albus type strain (HI 11/12). Standards in Genomic Sciences 2(2): 194-202. DOI: 10.4056/sigs.761490.
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, Brettin T. 2010. Complete genome sequence of Kribbella flavida type strain (IFO 14399). Standards in Genomic Sciences 2(2): 186-193. DOI: 10.4056/sigs.731321.
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, Chen F. 2010. Complete genome sequence of Spirosoma linguale type strain (1). Standards in Genomic Sciences 2(2): 176-185. DOI: 10.4056/sigs.741334.
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, Chen F. 2010. Complete genome sequence of Nakamurella multipartitatype strain (Y-104). Standards in Genomic Sciences 2(2): 168-175. DOI: 10.4056/sigs.721316.
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-20). Standards in Genomic Sciences 2(2): 158-167. DOI: 10.4056/sigs.711311.
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, Klenk H-P. 2010. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Standards in Genomic Sciences 2(2): 149-157. DOI: 10.4056/sigs.671209.
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, Kyrpides NC. 2010. Complete genome sequence of Haloterrigena turkmenica type strain (4k). Standards in Genomic Sciences 2(1): 107-116. DOI: 10.4056/sigs.681272.
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-2). Standards in Genomic Sciences 2(1): 96-106. DOI: 10.4056/sigs.69.1277.
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, Lucas S. 2010. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Standards in Genomic Sciences 2(1): 87-95. DOI: 10.4056/sigs.661199.
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, Lucas S. 2010. Complete genome sequence of Veillonella parvula type strain (Te3). Standards in Genomic Sciences 2(1): 57-65. DOI: 10.4056/sigs.521107.
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, Lapidus A. 2010. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Standards in Genomic Sciences 2(1): 49-56. DOI: 10.4056/sigs.601105.
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, Klenk H-P. 2010. Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Standards in Genomic Sciences 2(1): 38-48. DOI: 10.4056/sigs.581048.
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, Klenk H-P. 2010. Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Standards in Genomic Sciences 2(1): 29-37. DOI: 10.4056/sigs.631049.
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, Kyrpides NC. 2010. Complete genome sequence of Gordonia bronchialis type strain (3410). Standards in Genomic Sciences 2(1): 19-28. DOI: 10.4056/sigs.611106.
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, Kyrpides NC. 2010. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Standards in Genomic Sciences 2(1): 9-18. DOI: 10.4056/sigs.591104.
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, Lapidus A. 2010. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Standards in Genomic Sciences 2(1): 1-8. DOI: 10.4056/sigs.571102.
Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del Rio , Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Standards in Genomic Sciences 1(3): 308-316. DOI: 10.4056/sigs.51657.
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 (9901). Standards in Genomic Sciences 1(3): 300-307. DOI: 10.4056/sigs.48727.
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-10). Standards in Genomic Sciences 1(3): 283-290. DOI: 10.4056/sigs.46736.
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-2). Standards in Genomic Sciences 1(3): 270-277. DOI: 10.4056/sigs.42644.
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 55134). Standards in Genomic Sciences 1(3): 262-269. DOI: 10.4056/sigs.41646.
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 (Su883). Standards in Genomic Sciences 1(3): 254-261. DOI: 10.4056/sigs.40645.
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 (5575). Standards in Genomic Sciences 1(3): 242-253. DOI: 10.4056/sigs.39508.
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, Hugenholtz P. 2009. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Standards in Genomic Sciences 1(3): 234-241. DOI: 10.4056/sigs.37633.
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-21). Standards in Genomic Sciences 1(3): 292-299. DOI: 10.4056/sigs.47643.
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, Detter JC. 2009. Complete genome sequence of Kangiella koreensis type strain (SW-125). Standards in Genomic Sciences 1(3): 226-233. DOI: 10.4056/sigs.36635.
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-2). Standards in Genomic Sciences 1(3): 218-225. DOI: 10.4056/sigs.31864.
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, Han C. 2009. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Standards in Genomic Sciences 1(2): 174-182. DOI: 10.4056/sigs.33592.
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, Detter JC. 2009. Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Standards in Genomic Sciences 1(2): 166-173. DOI: 10.4056/sigs.29547.
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 (PC1). Standards in Genomic Sciences 1(2): 159-165. DOI: 10.4056/sigs.24194.
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 (PR3). Standards in Genomic Sciences 1(2): 150-159. DOI: 10.4056/sigs.23264.
Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Chain P, D’haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Saccharomonospora viridis type strain (P101). Standards in Genomic Sciences 1(2): 141-149. DOI: 10.4056/sigs.20263.
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 (NS114). Standards in Genomic Sciences 1(2): 133-140. DOI: 10.4056/sigs.19262.
Ivanova N, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Brettin T, Detter JC, Han C, Pitluck S, Mikhailova N, Pati A, Mavrommatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Standards in Genomic Sciences 1(2): 126-132. DOI: 10.4056/sigs.1854.
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 139908). Standards in Genomic Sciences 1(2): 119-125. DOI: 10.4056/sigs.17259.
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-74). Standards in Genomic Sciences 1(2): 110-118. DOI: 10.4056/sigs.16197.
Mavrommatis K, Gronow S, Saunders E, Land M, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Bristow J, Göker M, Rohde M, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. 2009. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). Standards in Genomic Sciences 1(2): 101-109. DOI: 10.4056/sigs.15195.
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 curtumtype strain (12-3). Standards in Genomic Sciences 1(2): 93-100. DOI: 10.4056/sigs.12260.
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 heparinustype strain (HIM 762-3). Standards in Genomic Sciences 1(1): 54-62. DOI: 10.4056/sigs.22138.
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 (101). Standards in Genomic Sciences 1(1): 46-53. DOI: 10.4056/sigs.21137.
Clum A, Nolan M, Lang E, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Göker M, Spring S, Land M, Hauser L, Chang YJ, Jeffries CC, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. 2009. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). Standards in Genomic Sciences 1(1): 38-45. DOI: 10.4056/sigs.1463.
Copeland A, Spring S, Göker M, Schneider S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Meincke L, Sims D, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. 2009. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Standards in Genomic Sciences 1(1): 29-37. DOI: 10.4056/sigs.13134.
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 0122). Standards in Genomic Sciences 1(1): 21-28. DOI: 10.4056/sigs.1162.
Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Schneider S, Göker M, Pukall R, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Kytococcus sedentarius type strain (541). Standards in Genomic Sciences 1(1): 12-20. DOI: 10.4056/sigs.761.
Lapidus A, Pukall R, Labuttii K, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Rohde M, Göker M, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2009. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Standards in Genomic Sciences 1(1): 3-11. DOI: 10.4056/sigs.492.

Other Publications

Books

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

Other Publications

Eisen JA. 2021. Legionella is scary disease that grows in contaminated water. Sacramento Bee.
Wu M, Eisen JA. 2011. Towards automated phylogenomic inference. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press. (Note – this is a slightly edited reprinting of a paper published in Genome Biology).
Eisen JA. 2011. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press. (Note – this is a slightly edited reprinting of a paper published in PLOS Biology).
Eisen JA, McConnell W. 2009. My View: UC Davis strike: Teaching is more than just about being paid. Sacramento Bee September 23, 2009.
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.

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

Improving Food Safety Through a One Health Approach: Workshop Summary. 2012. Institute of Medicine Forum on Microbial Threats (US). Washington (DC): National Academies Press (US).
The Social Biology of Microbial Communities: Workshop Summary. 2012. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
Antibiotic Resistance: Implications for Global Health and Novel Intervention Strategies: Workshop Summary. 2010. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
The Causes and Impacts of Neglected Tropical and Zoonotic Diseases: Opportunities for Integrated Intervention Strategies. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
Fungal Diseases: An Emerging Threat to Human, Animal, and Plant Health: Workshop Summary. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
The Science and Applications of Synthetic and Systems Biology: Workshop Summary. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
Sequence-Based Classification of Select Agents: A Brighter Line (2010). National Research Council (US) Committee on Scientific Milestones for the Development of a Gene Sequence-Based Classification System for the Oversight of Select Agents. Washington (DC): National Academies Press (US). (Report from Workshop in which I participated.)
A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. (2009). National Research Council (US) Committee on a New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. Washington (DC): National Academies Press (US). (Report from NAS Committee to which I contributed).

DiRuggiero J, Nandakumar R, Eisen JA, Schwartz M, Thomas R, Davila J, Ofman L, Robb FT. 2002. Genomic and physiological studies on extremophiles: model systems for exobiology. In “Frontiers of Astrobiology. Proceedings of the Astrobiology Workshop”, St Petersburg, Russia. Pavlov A. PDF. Report from Workshop to which I contributed:
MARS Sample Handling Protocol Workshops, NASA Technical Reports, 2000-2001. (Report from Workshops in which I participated.)

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