CiteULike | Further Information

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• {"link"=>{"url"=>"http://www.citeulike.org/group/13036/article/12307578"}, "post_time"=>"2013-05-01 18:50:40", "tag"=>["conservation", "development", "duplication", "expression", "fish"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1003476"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636041/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/23637639"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=23637639"}], "group"=>"PollardWall", "group_id"=>"13036", "article_id"=>"12307578"}
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Mendeley | Further Information

{"title"=>"The Hourglass and the Early Conservation Models-Co-Existing Patterns of Developmental Constraints in Vertebrates", "type"=>"journal", "authors"=>[{"first_name"=>"Barbara", "last_name"=>"Piasecka", "scopus_author_id"=>"55139374800"}, {"first_name"=>"Paweł", "last_name"=>"Lichocki", "scopus_author_id"=>"27867897000"}, {"first_name"=>"Sébastien", "last_name"=>"Moretti", "scopus_author_id"=>"24484669300"}, {"first_name"=>"Sven", "last_name"=>"Bergmann", "scopus_author_id"=>"7101828386"}, {"first_name"=>"Marc", "last_name"=>"Robinson-Rechavi", "scopus_author_id"=>"6603739219"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"368819442", "sgr"=>"84876872011", "issn"=>"15537390", "arxiv"=>"arXiv:1210.6444v2", "pmid"=>"23637639", "scopus"=>"2-s2.0-84876872011", "doi"=>"10.1371/journal.pgen.1003476", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)"}, "id"=>"76bdb78d-3371-386a-9dd0-d6e633748689", "abstract"=>"Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early conservation model or the hourglass model, respectively. Conflicting results have been reported, but in recent studies of animal transcriptomes the hourglass model has been favored. Studies usually report descriptive statistics calculated for all genes over all developmental time points. This introduces dependencies between the sets of compared genes and may lead to biased results. Here we overcome this problem using an alternative modular analysis. We used the Iterative Signature Algorithm to identify distinct modules of genes co-expressed specifically in consecutive stages of zebrafish development. We then performed a detailed comparison of several gene properties between modules, allowing for a less biased and more powerful analysis. Notably, our analysis corroborated the hourglass pattern at the regulatory level, with sequences of regulatory regions being most conserved for genes expressed in mid-development but not at the level of gene sequence, age, or expression, in contrast to some previous studies. The early conservation model was supported with gene duplication and birth that were the most rare for genes expressed in early development. Finally, for all gene properties, we observed the least conservation for genes expressed in late development or adult, consistent with both models. Overall, with the modular approach, we showed that different levels of molecular evolution follow different patterns of developmental constraints. Thus both models are valid, but with respect to different genomic features.", "link"=>"http://www.mendeley.com/research/hourglass-early-conservation-modelscoexisting-patterns-developmental-constraints-vertebrates", "reader_count"=>90, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>2, "Student > Master"=>11, "Other"=>2, "Student > Bachelor"=>8, "Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>2, "Student > Master"=>11, "Other"=>2, "Student > Bachelor"=>8, "Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>67, "Neuroscience"=>1, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>67}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>4, "United Kingdom"=>3, "Switzerland"=>3, "Portugal"=>1, "Spain"=>2, "Netherlands"=>2, "South Korea"=>1, "Norway"=>1, "Italy"=>1, "Australia"=>1, "France"=>1, "Germany"=>1}, "group_count"=>5}

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• http://doi.org/10.1093/gbe/evy177
• http://doi.org/10.1093/molbev/msv047
• http://doi.org/10.1371/journal.pone.0139463
• http://doi.org/10.1038/s41559-017-0318-0
• http://doi.org/10.7554/eLife.04775
• http://doi.org/10.12688/f1000research.6402.3
• http://doi.org/10.12688/f1000research.4583.1
• http://doi.org/10.1093/molbev/msv012
• http://doi.org/10.1093/molbev/msy175
• http://doi.org/10.1155/2015/316735
• http://doi.org/10.1155/2015/896176
• http://doi.org/10.12688/f1000research.6402.2
• http://doi.org/10.1002/jez.b.22595
• http://doi.org/10.1093/gbe/evt156
• http://doi.org/10.1002/jez.b.22569
• http://doi.org/10.1134/S0006297915130088
• http://doi.org/10.1371/journal.pone.0130413
• http://doi.org/10.1093/gbe/evw228
• http://doi.org/10.1016/j.celrep.2013.12.030
• http://doi.org/10.1093/gbe/evv200
• http://doi.org/10.1038/nrg3950
• http://doi.org/10.1093/molbev/msx266
• http://doi.org/10.1186/s12915-020-00842-z
• http://doi.org/10.1002/evl3.122
• http://doi.org/10.1146/annurev-ecolsys-110617-062339
• http://doi.org/10.1016/j.tplants.2014.07.003
• http://doi.org/10.12688/f1000research.4583.2
• http://doi.org/10.1093/gbe/evu183
• http://doi.org/10.1186/2041-9139-5-40
• http://doi.org/10.1038/ng.3522
• http://doi.org/10.1007/s10539-020-09762-2
• http://doi.org/10.1039/C8MO00111A
• http://doi.org/10.12688/f1000research.6402.1
• http://doi.org/10.1186/s13227-018-0111-4
• http://doi.org/10.1093/gbe/evz086
• http://doi.org/10.1016/j.gde.2017.03.003
• http://doi.org/10.1038/s41598-019-52577-9
• http://doi.org/10.1016/j.ydbio.2017.07.019
• http://doi.org/10.1134/S0006297916130137
• http://doi.org/10.1093/molbev/msw044
• http://doi.org/10.1186/s13059-017-1157-7
• http://doi.org/10.1093/molbev/msz065

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• 4523088
• 4489388
• 4625035
• 4408408
• 3845637
• 4202322
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• 4620428
• 4383337
• 4156030
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• 4530217

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/55c93473-9cea-4b0d-a299-15ac7e0e569f", "title"=>"Coelomata", "body"=>"A colleague has brought to our attention that we used an age group \"Coelomata+Chordata\", whereas this group no longer exists in Ensembl Compara. Indeed, the Coelomata grouping is no longer considered supported, and has been removed both from Ensembl and from NCBI Taxonomy. To reproduce our results, please use only Chordata.", "isRemoved"=>false, "created"=>"2013-07-09T11:25:50Z", "lastModified"=>"2013-07-09T11:25:50Z", "creator"=>{"userId"=>"352025"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I am an author of the paper."}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1003476", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2013-07-09T11:25:50Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/bdb9946c-3177-4059-b491-1ff08fa0250e", "title"=>"Story behind the paper", "body"=>"I wrote a blog post \"Story behind the paper\" here:\nhttp://people.unil.ch/marcrobinsonrechavi/2013/07/story-behind-the-paper-the-hourglass-and-the-early-conservation-models-co-existing-evolutionary-patterns-in-vertebrate-development/", "isRemoved"=>false, "created"=>"2013-09-13T14:04:22Z", "lastModified"=>"2013-09-13T14:04:22Z", "creator"=>{"userId"=>"352025"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I'm an author of the paper, and the author of the blog post."}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1003476", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2013-09-13T14:04:22Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/b8a12a04-280c-4922-be36-9197b9cc8fdf", "title"=>"Link to extra supplementary data", "body"=>"Gene ages, processed expression data, etc:\n\nhttp://bioinfo.unil.ch/supdata/Piasecka/datasets/", "highlightedText"=>"", "isRemoved"=>false, "created"=>"2016-05-31T07:23:43Z", "lastModified"=>"2016-05-31T07:23:43Z", "creator"=>{"userId"=>"66597"}, "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I am corresponding author."}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1003476", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2016-05-31T07:23:43Z", "replies"=>[]}

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• {"id"=>"328851915603603458", "text"=>"Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinformatics", "created_at"=>"2013-04-29T12:43:01Z", "user"=>"marc_rr", "user_name"=>"Marc RobinsonRechavi", "user_profile_image"=>"http://a0.twimg.com/profile_images/1751744306/mrr_caricature_normal.jpg"}
• {"id"=>"328852572398043137", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-04-29T12:45:37Z", "user"=>"lenovere", "user_name"=>"Nicolas Le Novere", "user_profile_image"=>"http://a0.twimg.com/profile_images/3574634932/7a05aa66fa9ac292842dbe303c76c141_normal.jpeg"}
• {"id"=>"328865167926501379", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-04-29T13:35:40Z", "user"=>"gawbul", "user_name"=>"Steve Moss", "user_profile_image"=>"http://a0.twimg.com/profile_images/3312426579/8f14296f0b9229c25e842c728bd86a2b_normal.jpeg"}
• {"id"=>"328878098399494145", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-04-29T14:27:03Z", "user"=>"PLOSGenetics", "user_name"=>"PLOS Genetics", "user_profile_image"=>"http://a0.twimg.com/profile_images/2435441933/pk712n4blw8kyf7yzqwc_normal.jpeg"}
• {"id"=>"328938798551547904", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-04-29T18:28:15Z", "user"=>"cdessimoz", "user_name"=>"Christophe Dessimoz", "user_profile_image"=>"http://a0.twimg.com/profile_images/1467970873/photo_normal.png"}
• {"id"=>"328939783529316353", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-04-29T18:32:10Z", "user"=>"caseybergman", "user_name"=>"Casey Bergman", "user_profile_image"=>"http://a0.twimg.com/profile_images/2092288245/Untitled-1_normal.png"}
• {"id"=>"330128495919374336", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-05-03T01:15:41Z", "user"=>"JChrisPires", "user_name"=>"J. Chris Pires", "user_profile_image"=>"http://a0.twimg.com/profile_images/1416048607/jcp_2011_normal.jpg"}
• {"id"=>"359548919975383040", "text"=>"RT @marc_rr: Our paper on the Hourglass and the Early Conservation Models is out in @PLOSGenetics: http://t.co/UzWMLSSb0S #evodevo #bioinfo…", "created_at"=>"2013-07-23T05:41:57Z", "user"=>"couchbandit", "user_name"=>"Daniel Lang", "user_profile_image"=>"http://a0.twimg.com/profile_images/272810060/BadBoyklein_normal.gif"}
• {"id"=>"369144330331512832", "text"=>"@AMartinezArias @briscoejames @benoitbruneau in that context they should reference @marc_rr http://t.co/HlSxsdL1Zs", "created_at"=>"2013-08-18T17:10:41Z", "user"=>"PavelTomancak", "user_name"=>"Pavel Tomancak", "user_profile_image"=>"http://a0.twimg.com/profile_images/2612422002/2jn1eaf2u5v2ampkzd0e_normal.png"}
• {"id"=>"620481336973901825", "text"=>"Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1SSK #smbe15", "created_at"=>"2015-07-13T06:34:13Z", "user"=>"marc_rr", "user_name"=>"Marc RobinsonRechavi", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1751744306/mrr_caricature_normal.jpg"}
• {"id"=>"620481980958920704", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T06:36:46Z", "user"=>"TwelveSharp", "user_name"=>"Yves Clement", "user_profile_image"=>"http://pbs.twimg.com/profile_images/555863011143864320/XevgBFwK_normal.jpeg"}
• {"id"=>"620482699199934464", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T06:39:38Z", "user"=>"jgschraiber", "user_name"=>"Joshua G. Schraiber", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000563181239/626fcb69854eedfbe60f66af22cc2d14_normal.jpeg"}
• {"id"=>"620483249505091588", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T06:41:49Z", "user"=>"yoshidamasaaki", "user_name"=>"Masa-aki Yoshida", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2557953204/____normal.jpg"}
• {"id"=>"620483887106551808", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T06:44:21Z", "user"=>"ljljolin", "user_name"=>"Jialin.Liu", "user_profile_image"=>"http://pbs.twimg.com/profile_images/583582528214278145/jaDkCrwm_normal.jpg"}
• {"id"=>"620506352058793984", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T08:13:37Z", "user"=>"monimunozto", "user_name"=>"Monica Munoz-Torres", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000601347599/ec14d09fb87f516d559566324b79cc87_normal.jpeg"}
• {"id"=>"620524229881110528", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T09:24:39Z", "user"=>"Bastounette", "user_name"=>"Bastien Boussau", "user_profile_image"=>"http://pbs.twimg.com/profile_images/330493460/FacebookPortrait_normal.jpg"}
• {"id"=>"620571848833503232", "text"=>"RT @marc_rr: Is it rude to point out that we found a few problems with TAI method studying age of genes in deveopment? http://t.co/DnLXeZ1S…", "created_at"=>"2015-07-13T12:33:53Z", "user"=>"JChrisPires", "user_name"=>"J. Chris Pires", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1416048607/jcp_2011_normal.jpg"}
• {"id"=>"722089088795480066", "text"=>"@michaelhoffman I would have done it if today, and regret not doing it then. Analysis is in subdata of https://t.co/DnLXeZ1SSK", "created_at"=>"2016-04-18T15:47:09Z", "user"=>"marc_rr", "user_name"=>"Marc RobinsonRechavi", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1751744306/mrr_caricature_normal.jpg"}

Wikipedia | Further Information

• {"title"=>"Phylotypic stage", "url"=>"http://en.wikipedia.org/wiki/Phylotypic_stage", "timestamp"=>"2019-01-01T06:08:11Z"}

Wordpress.com | Further Information

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1036781"], "description"=>"<p>A higher TAI value implies that evolutionary younger genes are preferentially expressed at the corresponding time-point. The pink shaded area indicates the phylotypic stage. Colors of the curves reflect the main developmental periods and correspond to the colors used in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003476#pgen.1003476-DomazetLoo1\" target=\"_blank\">[11]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Genome evolution", "Genome expression analysis", "microarrays", "developmental biology", "Evolutionary developmental biology", "Evolutionary biology", "Genomic evolution", "log-transformed"], "article_id"=>692103, "categories"=>["Biological Sciences"], "users"=>["Barbara Piasecka", "Paweł Lichocki", "Sébastien Moretti", "Sven Bergmann", "Marc Robinson-Rechavi"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003476.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcriptome_age_index_TAI_using_raw_and_log_transformed_expression_signal_intensities_/692103", "title"=>"Transcriptome age index (TAI) using raw and log-transformed expression signal intensities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-25 00:35:03"}
• {"files"=>["https://ndownloader.figshare.com/files/1036782"], "description"=>"<p>A) Zebrafish ontogeny (drawings of the embryos are based upon sketches and photographs from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003476#pgen.1003476-Kimmel1\" target=\"_blank\">[49]</a>. B) Median, 25th and 75th percentiles of expression value of genes in modules. Red bars denote the condition scores assigned to developmental points by the ISA.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Genome evolution", "Genome expression analysis", "microarrays", "developmental biology", "Evolutionary developmental biology", "Evolutionary biology", "Genomic evolution", "genes", "time-specific", "zebrafish"], "article_id"=>692104, "categories"=>["Biological Sciences"], "users"=>["Barbara Piasecka", "Paweł Lichocki", "Sébastien Moretti", "Sven Bergmann", "Marc Robinson-Rechavi"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003476.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modules_of_genes_with_time_specific_expression_during_zebrafish_development_/692104", "title"=>"Modules of genes with time-specific expression during zebrafish development.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-25 00:35:04"}
• {"files"=>["https://ndownloader.figshare.com/files/1036783"], "description"=>"<p>A) Box and Whisker plot showing non-synonymous to synonymous substitution ratios () for genes in the modules. The dotted line denotes median for all genes. The dash-dotted lines denote confidence interval for the median. B) Observed minus expected frequencies of age of genes in modules. C) Observed minus expected frequencies of orthology type (between zebrafish and mouse) for genes in modules. D) Mean expression level of zebrafish genes in modules, and their one-to-one orthologs in mouse in six developmental metastages. The transition between the two mouse data sets is denoted with the vertical dashed line. The Pearson's correlation coefficients for zebrafish and mouse expression profiles are reported for every module. E) The number of transcription factors (TFs) in modules (whole bar) and their enrichment in highly conserved non-coding elements (HCNEs) and transposon-free regions (TFRs). The stars denote significant enrichment () of TFs in HCNEs (yellow) and in TFRs (red). The dash-dotted lines denote confidence interval for the expected number of TFs in modules.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Genome evolution", "Genome expression analysis", "microarrays", "developmental biology", "Evolutionary developmental biology", "Evolutionary biology", "Genomic evolution", "constraints"], "article_id"=>692105, "categories"=>["Biological Sciences"], "users"=>["Barbara Piasecka", "Paweł Lichocki", "Sébastien Moretti", "Sven Bergmann", "Marc Robinson-Rechavi"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003476.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Measures_of_developmental_constraints_for_various_gene_properties_/692105", "title"=>"Measures of developmental constraints for various gene properties.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-25 00:35:05"}
• {"files"=>["https://ndownloader.figshare.com/files/1036786"], "description"=>"<p>Mean expression level of zebrafish genes in modules, and of their one-to-one orthologs in mouse. The same colors denote corresponding developmental metastages in zebrafish and mouse.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Genome evolution", "Genome expression analysis", "microarrays", "developmental biology", "Evolutionary developmental biology", "Evolutionary biology", "Genomic evolution"], "article_id"=>692107, "categories"=>["Biological Sciences"], "users"=>["Barbara Piasecka", "Paweł Lichocki", "Sébastien Moretti", "Sven Bergmann", "Marc Robinson-Rechavi"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003476.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Developmental_metastages_/692107", "title"=>"Developmental metastages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-25 00:35:07"}
• {"files"=>["https://ndownloader.figshare.com/files/1036788", "https://ndownloader.figshare.com/files/1036790", "https://ndownloader.figshare.com/files/1036791", "https://ndownloader.figshare.com/files/1036792", "https://ndownloader.figshare.com/files/1036793", "https://ndownloader.figshare.com/files/1036795", "https://ndownloader.figshare.com/files/1036796", "https://ndownloader.figshare.com/files/1036797", "https://ndownloader.figshare.com/files/1036798", "https://ndownloader.figshare.com/files/1036799", "https://ndownloader.figshare.com/files/1036801", "https://ndownloader.figshare.com/files/1036802", "https://ndownloader.figshare.com/files/1036803", "https://ndownloader.figshare.com/files/1036804", "https://ndownloader.figshare.com/files/1036805", "https://ndownloader.figshare.com/files/1036806"], "description"=>"<div><p>Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early conservation model or the hourglass model, respectively. Conflicting results have been reported, but in recent studies of animal transcriptomes the hourglass model has been favored. Studies usually report descriptive statistics calculated for all genes over all developmental time points. This introduces dependencies between the sets of compared genes and may lead to biased results. Here we overcome this problem using an alternative modular analysis. We used the Iterative Signature Algorithm to identify distinct modules of genes co-expressed specifically in consecutive stages of zebrafish development. We then performed a detailed comparison of several gene properties between modules, allowing for a less biased and more powerful analysis. Notably, our analysis corroborated the hourglass pattern at the regulatory level, with sequences of regulatory regions being most conserved for genes expressed in mid-development but not at the level of gene sequence, age, or expression, in contrast to some previous studies. The early conservation model was supported with gene duplication and birth that were the most rare for genes expressed in early development. Finally, for all gene properties, we observed the least conservation for genes expressed in late development or adult, consistent with both models. Overall, with the modular approach, we showed that different levels of molecular evolution follow different patterns of developmental constraints. Thus both models are valid, but with respect to different genomic features.</p> </div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Genome evolution", "Genome expression analysis", "microarrays", "developmental biology", "Evolutionary developmental biology", "Evolutionary biology", "Genomic evolution", "hourglass", "patterns", "constraints"], "article_id"=>692108, "categories"=>["Biological Sciences"], "users"=>["Barbara Piasecka", "Paweł Lichocki", "Sébastien Moretti", "Sven Bergmann", "Marc Robinson-Rechavi"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003476.s001", "https://dx.doi.org/10.1371/journal.pgen.1003476.s002", "https://dx.doi.org/10.1371/journal.pgen.1003476.s003", "https://dx.doi.org/10.1371/journal.pgen.1003476.s004", "https://dx.doi.org/10.1371/journal.pgen.1003476.s005", "https://dx.doi.org/10.1371/journal.pgen.1003476.s006", "https://dx.doi.org/10.1371/journal.pgen.1003476.s007", "https://dx.doi.org/10.1371/journal.pgen.1003476.s008", "https://dx.doi.org/10.1371/journal.pgen.1003476.s009", "https://dx.doi.org/10.1371/journal.pgen.1003476.s010", "https://dx.doi.org/10.1371/journal.pgen.1003476.s011", "https://dx.doi.org/10.1371/journal.pgen.1003476.s012", "https://dx.doi.org/10.1371/journal.pgen.1003476.s013", "https://dx.doi.org/10.1371/journal.pgen.1003476.s014", "https://dx.doi.org/10.1371/journal.pgen.1003476.s015", "https://dx.doi.org/10.1371/journal.pgen.1003476.s016"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Hourglass_and_the_Early_Conservation_Models_8212_Co_Existing_Patterns_of_Developmental_Constraints_in_Vertebrates_/692108", "title"=>"The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-25 00:35:08"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/People and places/Population groupings", "average_usage"=>[265, 456, 578, 682, 782, 881, 965, 1053, 1133, 1223, 1310, 1391, 1457]}]}

F1000Prime