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For: Armit C, Venkataraman S, Richardson L, Stevenson P, Moss J, Graham L, Ross A, Yang Y, Burton N, Rao J, Hill B, Rannie D, Wicks M, Davidson D, Baldock R. eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome. Mamm Genome 2012;23:514-24. [PMID: 22847374 PMCID: PMC3463796 DOI: 10.1007/s00335-012-9407-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/22/2012] [Indexed: 01/10/2023]
Number Cited by Other Article(s)
1
Shi L, Li H, Huang X, Shu Z, Li J, Wang L, Yan H, Wang L. Integrated analysis of transcriptome and metabolome revealed biological basis of sows from estrus to lactation. iScience 2022;26:105825. [PMID: 36636351 PMCID: PMC9830223 DOI: 10.1016/j.isci.2022.105825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]  Open
2
Waites W, Davies JA. Emergence of structure in mouse embryos: Structural Entropy morphometry applied to digital models of embryonic anatomy. J Anat 2019;235:706-715. [PMID: 31276197 PMCID: PMC6742931 DOI: 10.1111/joa.13031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2019] [Indexed: 12/11/2022]  Open
3
Smit N, Bruckner S. Towards Advanced Interactive Visualization for Virtual Atlases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019;1156:85-96. [PMID: 31338779 DOI: 10.1007/978-3-030-19385-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
4
Survey of Human Chromosome 21 Gene Expression Effects on Early Development in Danio rerio. G3-GENES GENOMES GENETICS 2018;8:2215-2223. [PMID: 29760202 PMCID: PMC6027891 DOI: 10.1534/g3.118.200144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
5
Carlson JC, Taub MA, Feingold E, Beaty TH, Murray JC, Marazita ML, Leslie EJ. Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing. Birth Defects Res 2017;109:1030-1038. [PMID: 28762674 PMCID: PMC5549861 DOI: 10.1002/bdr2.23605] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
6
Li B, Qing T, Zhu J, Wen Z, Yu Y, Fukumura R, Zheng Y, Gondo Y, Shi L. A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq. Sci Rep 2017;7:4200. [PMID: 28646208 PMCID: PMC5482823 DOI: 10.1038/s41598-017-04520-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/16/2017] [Indexed: 02/07/2023]  Open
7
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods 2017;14:775-781. [PMID: 28775673 PMCID: PMC5536224 DOI: 10.1038/nmeth.4326] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
8
Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA. eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis. Dev Biol 2017;423:1-11. [PMID: 28161522 PMCID: PMC5442644 DOI: 10.1016/j.ydbio.2017.01.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/23/2022]
9
Armit C, Hill B, Venkataraman S, McLeod K, Burger A, Baldock R. The 'straight mouse': defining anatomical axes in 3D embryo models. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017;2017:3066360. [PMID: 28365728 PMCID: PMC5467569 DOI: 10.1093/database/bax010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/27/2017] [Indexed: 11/25/2022]
10
Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H. PhenoImageShare: an image annotation and query infrastructure. J Biomed Semantics 2016;7:35. [PMID: 27267125 PMCID: PMC4896029 DOI: 10.1186/s13326-016-0072-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/05/2016] [Indexed: 01/12/2023]  Open
11
Clarkson MD. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. BMC DEVELOPMENTAL BIOLOGY 2016;16:18. [PMID: 27206491 PMCID: PMC4875762 DOI: 10.1186/s12861-016-0116-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
12
Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks. Sci Rep 2016;6:20732. [PMID: 26864723 PMCID: PMC4749973 DOI: 10.1038/srep20732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/31/2015] [Indexed: 11/09/2022]  Open
13
Robert C, Kapetanovic R, Beraldi D, Watson M, Archibald AL, Hume DA. Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome. BMC Genomics 2015;16:970. [PMID: 26582032 PMCID: PMC4652390 DOI: 10.1186/s12864-015-2111-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/19/2015] [Indexed: 01/09/2023]  Open
14
Yu Y, Fuscoe JC, Zhao C, Guo C, Jia M, Qing T, Bannon DI, Lancashire L, Bao W, Du T, Luo H, Su Z, Jones WD, Moland CL, Branham WS, Qian F, Ning B, Li Y, Hong H, Guo L, Mei N, Shi T, Wang KY, Wolfinger RD, Nikolsky Y, Walker SJ, Duerksen-Hughes P, Mason CE, Tong W, Thierry-Mieg J, Thierry-Mieg D, Shi L, Wang C. A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat Commun 2015;5:3230. [PMID: 24510058 PMCID: PMC3926002 DOI: 10.1038/ncomms4230] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 01/10/2014] [Indexed: 02/07/2023]  Open
15
Richardson L, Graham L, Moss J, Burton N, Roochun Y, Armit C, Baldock RA. Developing the eHistology Atlas. Database (Oxford) 2015;2015:bav105. [PMID: 26500249 PMCID: PMC4618478 DOI: 10.1093/database/bav105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/17/2015] [Accepted: 09/30/2015] [Indexed: 01/03/2023]
16
Armit C, Richardson L, Hill B, Yang Y, Baldock RA. eMouseAtlas informatics: embryo atlas and gene expression database. Mamm Genome 2015;26:431-40. [PMID: 26296321 PMCID: PMC4602050 DOI: 10.1007/s00335-015-9596-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/20/2015] [Indexed: 12/19/2022]
17
Papatheodorou I, Oellrich A, Smedley D. Linking gene expression to phenotypes via pathway information. J Biomed Semantics 2015;6:17. [PMID: 25901272 PMCID: PMC4404592 DOI: 10.1186/s13326-015-0013-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/19/2015] [Indexed: 11/10/2022]  Open
18
Liddelow SA, Dzięgielewska KM, Møllgård K, Whish SC, Noor NM, Wheaton BJ, Gehwolf R, Wagner A, Traweger A, Bauer H, Bauer HC, Saunders NR. Cellular specificity of the blood-CSF barrier for albumin transfer across the choroid plexus epithelium. PLoS One 2014;9:e106592. [PMID: 25211495 PMCID: PMC4161337 DOI: 10.1371/journal.pone.0106592] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 08/01/2014] [Indexed: 01/29/2023]  Open
19
Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M. The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn 2014;243:1176-86. [PMID: 24958384 DOI: 10.1002/dvdy.24155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/16/2014] [Accepted: 06/17/2014] [Indexed: 12/15/2022]  Open
20
Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK. DFLAT: functional annotation for human development. BMC Bioinformatics 2014;15:45. [PMID: 24507166 PMCID: PMC3928322 DOI: 10.1186/1471-2105-15-45] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 01/28/2014] [Indexed: 11/25/2022]  Open
21
Leslie EJ, Marazita ML. Genetics of cleft lip and cleft palate. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013;163C:246-58. [PMID: 24124047 DOI: 10.1002/ajmg.c.31381] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
22
Brinkley JF, Borromeo C, Clarkson M, Cox TC, Cunningham MJ, Detwiler LT, Heike CL, Hochheiser H, Mejino JLV, Travillian RS, Shapiro LG. The ontology of craniofacial development and malformation for translational craniofacial research. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013;163C:232-45. [PMID: 24124010 DOI: 10.1002/ajmg.c.31377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
23
Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics 2013;14:632. [PMID: 24053356 PMCID: PMC3849585 DOI: 10.1186/1471-2164-14-632] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/25/2013] [Indexed: 01/17/2023]  Open
24
Norris FC, Wong MD, Greene NDE, Scambler PJ, Weaver T, Weninger WJ, Mohun TJ, Henkelman RM, Lythgoe MF. A coming of age: advanced imaging technologies for characterising the developing mouse. Trends Genet 2013;29:700-11. [PMID: 24035368 DOI: 10.1016/j.tig.2013.08.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/17/2013] [Accepted: 08/12/2013] [Indexed: 12/21/2022]
25
Harmston N, Lenhard B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res 2013;41:7185-99. [PMID: 23766291 PMCID: PMC3753629 DOI: 10.1093/nar/gkt499] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
26
Wong F, Welten MCM, Anderson C, Bain AA, Liu J, Wicks MN, Pavlovska G, Davey MG, Murphy P, Davidson D, Tickle CA, Stern CD, Baldock RA, Burt DW. eChickAtlas: an introduction to the database. Genesis 2013;51:365-71. [PMID: 23355415 DOI: 10.1002/dvg.22374] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 12/21/2012] [Accepted: 01/17/2013] [Indexed: 11/12/2022]
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