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{"title"=>"Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux", "type"=>"journal", "authors"=>[{"first_name"=>"Erin A.", "last_name"=>"Lynch", "scopus_author_id"=>"55321407000"}, {"first_name"=>"Morgan G.I.", "last_name"=>"Langille", "scopus_author_id"=>"8693354000"}, {"first_name"=>"Aaron", "last_name"=>"Darling", "scopus_author_id"=>"8974024600"}, {"first_name"=>"Elizabeth G.", "last_name"=>"Wilbanks", "scopus_author_id"=>"36609303500"}, {"first_name"=>"Caitlin", "last_name"=>"Haltiner", "scopus_author_id"=>"55320637100"}, {"first_name"=>"Katie S.Y.", "last_name"=>"Shao", "scopus_author_id"=>"55319920300"}, {"first_name"=>"Michael O.", "last_name"=>"Starr", "scopus_author_id"=>"57197249738"}, {"first_name"=>"Clotilde", "last_name"=>"Teiling", "scopus_author_id"=>"6505630586"}, {"first_name"=>"Timothy T.", "last_name"=>"Harkins", "scopus_author_id"=>"35264029200"}, {"first_name"=>"Robert A.", "last_name"=>"Edwards", "scopus_author_id"=>"35560915600"}, {"first_name"=>"Jonathan A.", "last_name"=>"Eisen", "scopus_author_id"=>"35247902700"}, {"first_name"=>"Marc T.", "last_name"=>"Facciotti", "scopus_author_id"=>"6603705526"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22848480", "scopus"=>"2-s2.0-84864245183", "doi"=>"10.1371/journal.pone.0041389", "sgr"=>"84864245183", "pui"=>"365316861"}, "id"=>"2074b7de-c84d-3d68-94fd-2f65e35a2d1d", "abstract"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.", "link"=>"http://www.mendeley.com/research/sequencing-seven-haloarchaeal-genomes-reveals-patterns-genomic-flux", "reader_count"=>66, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>1, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>1, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>1, "Agricultural and Biological Sciences"=>47, "Medicine and Dentistry"=>1, "Chemistry"=>2, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>4, "Denmark"=>1, "Mexico"=>1, "Spain"=>2, "India"=>1}, "group_count"=>1}

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• http://doi.org/10.1007/s00792-013-0606-9
• http://doi.org/10.1371/journal.pone.0107863
• http://doi.org/10.4161/mge.22530
• http://doi.org/10.1038/srep34639
• http://doi.org/10.1016/j.margen.2015.03.012
• http://doi.org/10.1371/journal.pgen.1004784
• http://doi.org/10.1038/ncomms9321
• http://doi.org/10.1126/science.aaj1849
• http://doi.org/10.1128/genomeA.01001-13
• http://doi.org/10.1186/s12915-014-0103-3
• http://doi.org/10.1016/j.bbabio.2016.04.284
• http://doi.org/10.1080/01490451.2016.1179365
• http://doi.org/10.1371/journal.pcbi.1003373
• http://doi.org/10.3389/fmicb.2014.00143
• http://doi.org/10.1016/j.ympev.2013.03.024
• http://doi.org/10.1007/s00792-013-0561-5
• http://doi.org/10.1371/journal.pone.0215986
• http://doi.org/10.1128/AEM.01097-15
• http://doi.org/10.1093/gbe/evu219
• http://doi.org/10.1093/gbe/evs098
• http://doi.org/10.4161/rna.24045
• http://doi.org/10.1186/s12864-016-2920-y
• http://doi.org/10.1038/ismej.2014.18

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ae380ed1-11bd-4d87-ad6a-6aebfdb9e8b9", "title"=>"Corrected link.", "body"=>"http://img.jgi.doe.gov/cgi-bin/geba/main.cgi", "highlightedText"=>"''http://img.jgi.doe.gov/cgi-bin/geba/.''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0041389#article1.body1.sec3.sec3.p1", "isRemoved"=>false, "created"=>"2012-07-31T15:56:50Z", "lastModified"=>"2012-07-31T15:56:50Z", "creator"=>{"userId"=>"273299"}, "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0041389", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-07-31T15:56:50Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/fbd92a95-f137-407d-9d7f-3723e372d366", "title"=>"Supplemental Data Sets at Data Dryad", "body"=>"We have posted some of the supplemental data sets to Data Dryad. See http://datadryad.org/handle/10255/dryad.41404. ", "isRemoved"=>false, "created"=>"2012-08-24T18:54:18Z", "lastModified"=>"2012-08-24T18:54:18Z", "creator"=>{"userId"=>"162783"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I am an author on the paper. "}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0041389", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-08-24T18:54:18Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ae7d12a8-0504-44f2-9823-714554a9825e", "title"=>"Additional data sets", "body"=>"A full listing of data sets from this paper, and links to download sets (e.g., Data Dryad) is available here. \n\nhttp://phylogenomics.wordpress.com/phylogenomics-of-halophiles-data-from-lynch-et-al-2012/\n", "isRemoved"=>false, "created"=>"2012-12-03T00:56:42Z", "lastModified"=>"2012-12-03T00:56:42Z", "creator"=>{"userId"=>"162783"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I am an author of this paper"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0041389", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-12-03T00:56:42Z", "replies"=>[]}

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• {"id"=>"227976494071312384", "text"=>"Sequencing of Seven Haloarchaeal Genomes Reveals #Magnificent Patterns of Genomic Flux = #ComparativeGenomics @ http://t.co/ix7n3lUH", "created_at"=>"2012-07-25T04:00:06Z", "user"=>"SAGRudd", "user_name"=>"Stephen Rudd", "user_profile_image"=>"http://a0.twimg.com/profile_images/1387284629/n1350228140_30403185_7501029_normal.jpg"}
• {"id"=>"228555848815882240", "text"=>"Cool new paper from our groups #PLOS: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux http://t.co/JXovrjka", "created_at"=>"2012-07-26T18:22:15Z", "user"=>"saltyprof", "user_name"=>"Marc Facciotti", "user_profile_image"=>"http://a0.twimg.com/sticky/default_profile_images/default_profile_2_normal.png"}
• {"id"=>"228557496242016256", "text"=>"RT @saltyprof: Cool new paper from our groups Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux http://t.co/TMOukQgj", "created_at"=>"2012-07-26T18:28:48Z", "user"=>"FacciottiLabUCD", "user_name"=>"Facciotti Lab UCD", "user_profile_image"=>"http://a0.twimg.com/profile_images/1744679167/IMG_1944-150x150_normal.jpeg"}
• {"id"=>"229022881898700801", "text"=>"@BetaScience Congrats on the Haloarchaeal Genomes paper http://t.co/2PlQpBit", "created_at"=>"2012-07-28T01:18:04Z", "user"=>"donovan_parks", "user_name"=>"Donovan Parks", "user_profile_image"=>"http://a0.twimg.com/profile_images/1511947193/donovan_normal.jpg"}
• {"id"=>"229026910951309312", "text"=>"Nice work! I'm gearing up to analyze >60 biomass degrading bacteria at @jbei_. Might steal some ideas. RT @saltyprof http://t.co/1XL6Ybld", "created_at"=>"2012-07-28T01:34:05Z", "user"=>"PatrikD", "user_name"=>"Patrik D'haeseleer", "user_profile_image"=>"http://a0.twimg.com/profile_images/1931899668/d_haeseleer_square_normal.jpg"}
• {"id"=>"229066089047404547", "text"=>"RT @saltyprof Cool new #PLOS paper from UCD Genome Center (and ARC faves!) Prof. Marc Facciotti and Erin Lynch http://t.co/bD209h14", "created_at"=>"2012-07-28T04:09:46Z", "user"=>"kmkubo", "user_name"=>"Ken Kubo", "user_profile_image"=>"http://a0.twimg.com/profile_images/1774762680/arcbluedna_normal.jpg"}
• {"id"=>"229206916562296832", "text"=>"Read: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux http://t.co/vdVLhy3m", "created_at"=>"2012-07-28T13:29:22Z", "user"=>"fmartin1954", "user_name"=>"Francis Martin", "user_profile_image"=>"http://a0.twimg.com/profile_images/812287087/Francis_face_normal.jpg"}
• {"id"=>"229213060739526657", "text"=>"RT @fmartin1954: Read: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux http://t.co/vdVLhy3m", "created_at"=>"2012-07-28T13:53:46Z", "user"=>"philonotis", "user_name"=>"Sarah Watkinson", "user_profile_image"=>"http://a0.twimg.com/profile_images/2272054871/image_normal.jpg"}
• {"id"=>"229281134880628737", "text"=>"RT @fmartin1954: Read: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux http://t.co/vdVLhy3m", "created_at"=>"2012-07-28T18:24:17Z", "user"=>"prfpathogeno", "user_name"=>"prfpathogeno", "user_profile_image"=>"http://a0.twimg.com/profile_images/1643274999/image_normal.jpg"}
• {"id"=>"248581878460866560", "text"=>"Next up at #LAMG12 Tim Harkins who was co-author of mine on recent haloarchaeal genomics paper http://t.co/vEbRdZeN", "created_at"=>"2012-09-20T00:38:32Z", "user"=>"phylogenomics", "user_name"=>"Jonathan Eisen", "user_profile_image"=>"http://a0.twimg.com/profile_images/1628936304/20080408_eisen_jonathan_09b_normal.jpg"}
• {"id"=>"248606545863131137", "text"=>"RT @phylogenomics: Next up at #LAMG12 Tim Harkins who was co-author of mine on recent haloarchaeal genomics paper http://t.co/vEbRdZeN", "created_at"=>"2012-09-20T02:16:34Z", "user"=>"prfpathogeno", "user_name"=>"prfpathogeno", "user_profile_image"=>"http://a0.twimg.com/profile_images/1643274999/image_normal.jpg"}
• {"id"=>"248618834469212160", "text"=>"RT @phylogenomics: Next up at #LAMG12 Tim Harkins who was co-author of mine on recent haloarchaeal genomics paper http://t.co/vEbRdZeN", "created_at"=>"2012-09-20T03:05:23Z", "user"=>"JChrisPires", "user_name"=>"J. Chris Pires", "user_profile_image"=>"http://a0.twimg.com/profile_images/1416048607/jcp_2011_normal.jpg"}
• {"id"=>"394584377533153280", "text"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula http://t.co/RmvILGSymu\"", "created_at"=>"2013-10-27T22:00:21Z", "user"=>"thebaybot", "user_name"=>"baybot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000263061007/bb2880bd6baf8e5298f42b156c5adebe_normal.jpeg"}
• {"id"=>"405803312177741824", "text"=>"@plosalm now showing links to @datacite, @EuropePMC, http://t.co/c2B4f8y8kw, e.g. this paper from @phylogenomics: http://t.co/8N0xWl1qyY", "created_at"=>"2013-11-27T21:00:23Z", "user"=>"mfenner", "user_name"=>"Martin Fenner", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1320249572/mfenner_normal.jpg"}
• {"id"=>"405803357664583680", "text"=>"5 new ALM on @PLOS journ- @EuropePMC_news cit. & DBcit, @datacite, @wordpressdotcom, @reddit. See @phylogenomics ex: http://t.co/YBnBYmicix", "created_at"=>"2013-11-27T21:00:34Z", "user"=>"PLOSALM", "user_name"=>"PLOS ALM", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2436224581/zmve3uo73uwm606l0d7i_normal.jpeg"}
• {"id"=>"418607652231344129", "text"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula http://t.co/CYyAkxl7L5\"", "created_at"=>"2014-01-02T05:00:16Z", "user"=>"thebaybot", "user_name"=>"baybot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000263061007/bb2880bd6baf8e5298f42b156c5adebe_normal.jpeg"}
• {"id"=>"439309026837659648", "text"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula http://t.co/JNZlwW2Xdx\"", "created_at"=>"2014-02-28T08:00:08Z", "user"=>"thebaybot", "user_name"=>"baybot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000263061007/bb2880bd6baf8e5298f42b156c5adebe_normal.jpeg"}
• {"id"=>"454106539000102912", "text"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula http://t.co/YHvo9TjDb5\"", "created_at"=>"2014-04-10T04:00:10Z", "user"=>"thebaybot", "user_name"=>"baybot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000263061007/bb2880bd6baf8e5298f42b156c5adebe_normal.jpeg"}
• {"id"=>"464736577194053632", "text"=>"We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula http://t.co/kfQNwNXQ0I\"", "created_at"=>"2014-05-09T12:00:09Z", "user"=>"thebaybot", "user_name"=>"baybot", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000263061007/bb2880bd6baf8e5298f42b156c5adebe_normal.jpeg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/315493", "https://ndownloader.figshare.com/files/315529", "https://ndownloader.figshare.com/files/315587", "https://ndownloader.figshare.com/files/315687", "https://ndownloader.figshare.com/files/315759", "https://ndownloader.figshare.com/files/315899", "https://ndownloader.figshare.com/files/315911", "https://ndownloader.figshare.com/files/315926", "https://ndownloader.figshare.com/files/315946", "https://ndownloader.figshare.com/files/315954", "https://ndownloader.figshare.com/files/315974", "https://ndownloader.figshare.com/files/315988", "https://ndownloader.figshare.com/files/316092"], "description"=>"<div><p>We report the sequencing of seven genomes from two haloarchaeal genera, <em>Haloferax</em> and <em>Haloarcula</em>. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds - 168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.</p> </div>", "links"=>[], "tags"=>["sequencing", "haloarchaeal", "genomes", "reveals", "patterns", "genomic", "flux"], "article_id"=>122272, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041389.s001", "https://dx.doi.org/10.1371/journal.pone.0041389.s002", "https://dx.doi.org/10.1371/journal.pone.0041389.s003", "https://dx.doi.org/10.1371/journal.pone.0041389.s004", "https://dx.doi.org/10.1371/journal.pone.0041389.s005", "https://dx.doi.org/10.1371/journal.pone.0041389.s006", "https://dx.doi.org/10.1371/journal.pone.0041389.s007", "https://dx.doi.org/10.1371/journal.pone.0041389.s008", "https://dx.doi.org/10.1371/journal.pone.0041389.s009", "https://dx.doi.org/10.1371/journal.pone.0041389.s010", "https://dx.doi.org/10.1371/journal.pone.0041389.s011", "https://dx.doi.org/10.1371/journal.pone.0041389.s012", "https://dx.doi.org/10.1371/journal.pone.0041389.s013"], "stats"=>{"downloads"=>38, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sequencing_of_Seven_Haloarchaeal_Genomes_Reveals_Patterns_of_Genomic_Flux/122272", "title"=>"Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-24 00:37:52"}
• {"files"=>["https://ndownloader.figshare.com/files/604660"], "description"=>"<p>Genomes included in this study.</p>", "links"=>[], "tags"=>["included"], "article_id"=>275149, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomes_included_in_this_study_/275149", "title"=>"Genomes included in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-24 01:25:49"}
• {"files"=>["https://ndownloader.figshare.com/files/603954"], "description"=>"<p>COGs comprising a significantly different fraction of protein coding genes between <i>Haloarcula</i> and <i>Haloferax</i> species. Averages for each genus are signified by horizontal bars. Significance was determined with the non-parametric Wilcoxon ranksum test. For p-values and the portion of protein coding genes dedicated to these COGs in each species, see Table S2.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>274444, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_enrichment_/274444", "title"=>"COG enrichment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:14:04"}
• {"files"=>["https://ndownloader.figshare.com/files/604706"], "description"=>"<p>General transcription factor (GTF) counts.</p>", "links"=>[], "tags"=>["transcription"], "article_id"=>275194, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.t004", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_transcription_factor_GTF_counts_/275194", "title"=>"General transcription factor (GTF) counts.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-24 01:26:34"}
• {"files"=>["https://ndownloader.figshare.com/files/604485"], "description"=>"<p>A maximum likelihood tree of TATA-binding protein (TBP) homologs identified by RAST with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Successive duplications are shown in darkening shades of green (<i>Halobacterium</i>) or blue (<i>Haloferax</i>.)</p>", "links"=>[], "tags"=>["tata-binding", "haloarchaeal"], "article_id"=>274970, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g009", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Independent_expansion_of_the_TATA_binding_protein_family_in_two_haloarchaeal_genera_/274970", "title"=>"Independent expansion of the TATA-binding protein family in two haloarchaeal genera.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:22:50"}
• {"files"=>["https://ndownloader.figshare.com/files/604307"], "description"=>"<p>(A) Crystal structure of <i>Haloferax volcanii</i> PCNA <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041389#pone.0041389-Aziz1\" target=\"_blank\">[61]</a> with eukaryotic (light blue) and potential haloarchaeal DNA binding residues (green) shown. (B) Maximum likelihood tree of eukaryotic and archaeal PCNAs with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Branch colors: green – eukarya, purple – crenarchaeota, dark blue – euryarchaeota, red - haloarchaea. Duplicate haloarchaeal PCNAs are distinguished with colored leaves. (C) An alignment of eukaryotic and haloarchaeal PCNA homologs. Residues known to be involved in DNA binding in eukaryotes are shown in light blue, with suspected functionally homologous positions in haloarchaea shown in green.</p>", "links"=>[], "tags"=>["antigen"], "article_id"=>274797, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g007", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proliferating_cell_nuclear_antigen_PCNA_/274797", "title"=>"Proliferating cell nuclear antigen (PCNA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:19:57"}
• {"files"=>["https://ndownloader.figshare.com/files/604141"], "description"=>"<p>Gene counts of enzymes discussed in the text superimposed on <i>rpoB</i>′′ phylogeny. Methylaspartate ammonia-lyase (EC 4.3.1.2) – MA ammonia-lyase, methylaspartate mutase (EC 5.4.99.1) – MA mutase, succinyl-CoA:mesaconate CoA-transferase – SM-CoA transferase, polyhydroxyalkanoate synthase – PHA synthase, CRISPR associated sequences – CAS. Blue leaf labels indicate genomes sequenced in this study, black leaf labels indicate previously sequenced genomes. CRISPR and CAS data is represented as binary presence/ absence with abundance information provided in Table 3. MA mutase S subunit is also shown as binary although some species have two homologs of this gene, as only one homolog is present at the methylaspartate cycle locus.</p>", "links"=>[], "tags"=>["biotechnology"], "article_id"=>274632, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enzymes_of_interest_in_biotechnology_and_novel_metabolism_/274632", "title"=>"Enzymes of interest in biotechnology and novel metabolism.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:17:12"}
• {"files"=>["https://ndownloader.figshare.com/files/604019"], "description"=>"<p>GenoPlast was used to infer rates of genomic gain (red) and loss (blue) in the Haloferax lineage, depicted by width of line along phylogeny branch. 95% confidence intervals are represented by bordering thin blue and red lines.</p>", "links"=>[], "tags"=>["flux"], "article_id"=>274502, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g003", "stats"=>{"downloads"=>0, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_segment_flux_in_Haloferax_/274502", "title"=>"Genomic segment flux in <i>Haloferax</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:15:02"}
• {"files"=>["https://ndownloader.figshare.com/files/604219"], "description"=>"<p>A maximum likelihood tree of the four previously described haloarchaeal opsin families along with the newly described sensory rhodopsin 3, with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Sensory rhodopsin - SR, halorhodopsin - HR, bacteriorhodopsin - BR.</p>", "links"=>[], "tags"=>["haloarchaeal"], "article_id"=>274705, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_haloarchaeal_opsins_/274705", "title"=>"Phylogeny of haloarchaeal opsins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:18:25"}
• {"files"=>["https://ndownloader.figshare.com/files/604092"], "description"=>"<p>Number of genes in each category differentially present between the <i>marismortui-mucosum</i> and the <i>denitrificans-sulfurifontis</i>-<i>volcanii</i> clades of <i>Haloferax</i>. For details on gene categories see Table S4.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>274576, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_gene_gain_loss_between_two_Haloferax_clades_/274576", "title"=>"Differential gene gain/loss between two <i>Haloferax</i> clades.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:16:16"}
• {"files"=>["https://ndownloader.figshare.com/files/604406"], "description"=>"<p>(A) Secondary structure of a sub-group of highlyconserved CRISPR direct repeats (DRs) predicted with RNAfold with percent conservation shown as heatmap. (B) Maximum likelihood tree of DRs with bootstrap support values above 0.50 shown for 500 bootstrap iterations.</p>", "links"=>[], "tags"=>["interspaced", "palindromic", "repeats"], "article_id"=>274894, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g008", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustered_Regularly_Interspaced_Short_Palindromic_Repeats_CRISPRs_/274894", "title"=>"Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:21:34"}
• {"files"=>["https://ndownloader.figshare.com/files/603894"], "description"=>"<p>Distribution of read-length in seven newlysequenced haloarchaeal genomes and one sequencing control (<i>Haloferax volcanii</i>). After quality-trimming, mean read-length for each genome was between 410 and 439 base pairs.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>274379, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.g001", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Read_length_/274379", "title"=>"Read length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-24 01:12:59"}
• {"files"=>["https://ndownloader.figshare.com/files/604627"], "description"=>"<p>Note: *Indicates results of mate-pair sequencing.</p><p>Note: The <i>Haloferax volcanii</i> control was not submitted to IMG for annotation and so some features are N/A.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>275109, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.t002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_characteristics_/275109", "title"=>"Genome characteristics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-24 01:25:09"}
• {"files"=>["https://ndownloader.figshare.com/files/604585"], "description"=>"<p>Note: Number of CRISPRs is the number of distinct CRISPR clusters.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology"], "article_id"=>275073, "categories"=>["Genetics", "Microbiology"], "users"=>["Erin A. Lynch", "Morgan G. I. Langille", "Aaron Darling", "Elizabeth G. Wilbanks", "Caitlin Haltiner", "Katie S. Y. Shao", "Michael O. Starr", "Clotilde Teiling", "Timothy T. Harkins", "Robert A. Edwards", "Jonathan A. Eisen", "Marc T. Facciotti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041389.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CRISPR_counts_/275073", "title"=>"CRISPR counts.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-24 01:24:33"}

PMC Usage Stats | Further Information

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• {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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Relative Metric

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F1000Prime