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For: Garfield D, Haygood R, Nielsen WJ, Wray GA. Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus. Evol Dev 2013;14:152-67. [PMID: 23017024 DOI: 10.1111/j.1525-142x.2012.00532.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Number Cited by Other Article(s)
1
Tjeerdema E, Lee Y, Metry R, Hamdoun A. Semi-automated, high-content imaging of drug transporter knockout sea urchin (Lytechinus pictus) embryos. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024;342:313-329. [PMID: 38087422 DOI: 10.1002/jez.b.23231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/08/2023] [Accepted: 11/19/2023] [Indexed: 05/01/2024]
2
Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S. The Role of Chromatin Accessibility in cis-Regulatory Evolution. Genome Biol Evol 2020;11:1813-1828. [PMID: 31114856 PMCID: PMC6601868 DOI: 10.1093/gbe/evz103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 02/07/2023]  Open
3
Helmy M, Hatlen A, Marco A. The Impact of Population Variation in the Analysis of microRNA Target Sites. Noncoding RNA 2019;5:E42. [PMID: 31234531 PMCID: PMC6630466 DOI: 10.3390/ncrna5020042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023]  Open
4
Hodin J, Ferner MC, Ng G, Gaylord B. Sand Dollar Larvae Show Within-Population Variation in Their Settlement Induction by Turbulence. THE BIOLOGICAL BULLETIN 2018;235:152-166. [PMID: 30624118 DOI: 10.1086/699827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
5
Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. Proc Natl Acad Sci U S A 2018;114:5854-5861. [PMID: 28584099 DOI: 10.1073/pnas.1610611114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
6
Babbitt CC, Haygood R, Nielsen WJ, Wray GA. Gene expression and adaptive noncoding changes during human evolution. BMC Genomics 2017;18:435. [PMID: 28583075 PMCID: PMC5460488 DOI: 10.1186/s12864-017-3831-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/31/2017] [Indexed: 01/14/2023]  Open
7
Cary GA, Hinman VF. Echinoderm development and evolution in the post-genomic era. Dev Biol 2017;427:203-211. [PMID: 28185788 DOI: 10.1016/j.ydbio.2017.02.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 01/01/2023]
8
Koga H, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. PLoS One 2016;11:e0149067. [PMID: 26866800 PMCID: PMC4750990 DOI: 10.1371/journal.pone.0149067] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/27/2016] [Indexed: 11/19/2022]  Open
9
Payne JL, Wagner A. Mechanisms of mutational robustness in transcriptional regulation. Front Genet 2015;6:322. [PMID: 26579194 PMCID: PMC4621482 DOI: 10.3389/fgene.2015.00322] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/10/2015] [Indexed: 12/17/2022]  Open
10
A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. Dev Biol 2015;404:149-63. [PMID: 26025923 PMCID: PMC4528069 DOI: 10.1016/j.ydbio.2015.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/17/2022]
11
Evolutionary meandering of intermolecular interactions along the drift barrier. Proc Natl Acad Sci U S A 2014;112:E30-8. [PMID: 25535374 DOI: 10.1073/pnas.1421641112] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Horvath JE, Ramachandran GL, Fedrigo O, Nielsen WJ, Babbitt CC, St Clair EM, Pfefferle LW, Jernvall J, Wray GA, Wall CE. Genetic comparisons yield insight into the evolution of enamel thickness during human evolution. J Hum Evol 2014;73:75-87. [PMID: 24810709 DOI: 10.1016/j.jhevol.2014.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/29/2013] [Accepted: 01/09/2014] [Indexed: 12/29/2022]
13
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PLoS One 2014;9:e91924. [PMID: 24786295 PMCID: PMC4006794 DOI: 10.1371/journal.pone.0091924] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/18/2014] [Indexed: 11/23/2022]  Open
14
Koga H, Morino Y, Wada H. The echinoderm larval skeleton as a possible model system for experimental evolutionary biology. Genesis 2014;52:186-92. [PMID: 24549940 DOI: 10.1002/dvg.22758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 01/29/2023]
15
Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol 2013;11:e1001696. [PMID: 24204211 PMCID: PMC3812118 DOI: 10.1371/journal.pbio.1001696] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/16/2013] [Indexed: 11/18/2022]  Open
16
Pespeni MH, Chan F, Menge BA, Palumbi SR. Signs of adaptation to local pH conditions across an environmental mosaic in the California Current Ecosystem. Integr Comp Biol 2013;53:857-70. [PMID: 23980118 DOI: 10.1093/icb/ict094] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
17
Backström N, Shipilina D, Blom MPK, Edwards SV. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecol Evol 2013;3:655-66. [PMID: 23532859 PMCID: PMC3605853 DOI: 10.1002/ece3.484] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/17/2012] [Accepted: 12/24/2012] [Indexed: 01/19/2023]  Open
18
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EEM, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol 2012;13:R49. [PMID: 22950968 PMCID: PMC3491393 DOI: 10.1186/gb-2012-13-9-r49] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/23/2012] [Accepted: 06/08/2012] [Indexed: 12/31/2022]  Open
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