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For: Cui M, Vielmas E, Davidson EH, Peter IS. Sequential Response to Multiple Developmental Network Circuits Encoded in an Intronic cis- Regulatory Module of Sea Urchin hox11/13b. Cell Rep 2017;19:364-74. [DOI: 10.1016/j.celrep.2017.03.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/27/2017] [Accepted: 03/13/2017] [Indexed: 01/13/2023]  Open
Number Cited by Other Article(s)
1
Voronov D, Paganos P, Magri MS, Cuomo C, Maeso I, Gómez-Skarmeta JL, Arnone MI. Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level. Development 2024;151:dev202278. [PMID: 39058236 DOI: 10.1242/dev.202278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
2
Russo R, Ragusa MA, Arancio W, Zito F. Gene, Protein, and in Silico Analyses of FoxO, an Evolutionary Conserved Transcription Factor in the Sea Urchin Paracentrotus lividus. Genes (Basel) 2024;15:1078. [PMID: 39202438 PMCID: PMC11353378 DOI: 10.3390/genes15081078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024]  Open
3
Valencia JE, Peter IS. Combinatorial regulatory states define cell fate diversity during embryogenesis. Nat Commun 2024;15:6841. [PMID: 39122679 PMCID: PMC11315938 DOI: 10.1038/s41467-024-50822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 07/22/2024] [Indexed: 08/12/2024]  Open
4
Glimm T, Kaźmierczak B, Newman SA, Bhat R. A two-galectin network establishes mesenchymal condensation phenotype in limb development. Math Biosci 2023;365:109054. [PMID: 37544500 DOI: 10.1016/j.mbs.2023.109054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/09/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
5
Arenas-Mena C, Akin S. Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 2023;225:iyad145. [PMID: 37551428 PMCID: PMC10789315 DOI: 10.1093/genetics/iyad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]  Open
6
Yamakawa S, Yamazaki A, Morino Y, Wada H. Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos. EvoDevo 2023;14:7. [PMID: 37101206 PMCID: PMC10131483 DOI: 10.1186/s13227-023-00210-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023]  Open
7
Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Wang Z, Ercan S, Danko CG. Identification and prediction of developmental enhancers in sea urchin embryos. BMC Genomics 2021;22:751. [PMID: 34666684 PMCID: PMC8527612 DOI: 10.1186/s12864-021-07936-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022]  Open
8
Sampilo NF, Stepicheva NA, Song JL. microRNA-31 regulates skeletogenesis by direct suppression of Eve and Wnt1. Dev Biol 2021;472:98-114. [PMID: 33484703 PMCID: PMC7956219 DOI: 10.1016/j.ydbio.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 11/22/2022]
9
Magri MS, Voronov D, Ranđelović J, Cuomo C, Gómez-Skarmeta JL, Arnone MI. ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos. Methods Mol Biol 2021;2219:253-265. [PMID: 33074546 DOI: 10.1007/978-1-0716-0974-3_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
10
Newman SA. Cell differentiation: What have we learned in 50 years? J Theor Biol 2020;485:110031. [DOI: 10.1016/j.jtbi.2019.110031] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
11
Rothenberg EV. Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges. J Comput Biol 2019;26:703-718. [PMID: 31063008 DOI: 10.1089/cmb.2019.0098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
12
Genomic resources for the study of echinoderm development and evolution. Methods Cell Biol 2019;151:65-88. [PMID: 30948032 DOI: 10.1016/bs.mcb.2018.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
13
Erkenbrack EM, Davidson EH, Peter IS. Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids. Development 2018;145:dev.167288. [PMID: 30470703 DOI: 10.1242/dev.167288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
14
Peter IS. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. Methods Cell Biol 2018;151:89-113. [PMID: 30948033 DOI: 10.1016/bs.mcb.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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