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For: Busser BW, Bulyk ML, Michelson AM. Toward a systems-level understanding of developmental regulatory networks. Curr Opin Genet Dev 2008;18:521-9. [PMID: 18848887 DOI: 10.1016/j.gde.2008.09.003] [Citation(s) in RCA: 31] [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] [Received: 08/19/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 02/01/2023]
Number Cited by Other Article(s)
1
Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019;63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
2
Sandoval PC, Claxton JS, Lee JW, Saeed F, Hoffert JD, Knepper MA. Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin. Sci Rep 2016;6:34863. [PMID: 27725713 PMCID: PMC5057153 DOI: 10.1038/srep34863] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/16/2016] [Indexed: 11/09/2022]  Open
3
Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA. Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics 2015;48:154-66. [PMID: 26508704 DOI: 10.1152/physiolgenomics.00090.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022]  Open
4
Busser BW, Lin Y, Yang Y, Zhu J, Chen G, Michelson AM. An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis. PLoS One 2015;10:e0141066. [PMID: 26485529 PMCID: PMC4617299 DOI: 10.1371/journal.pone.0141066] [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: 07/29/2015] [Accepted: 10/05/2015] [Indexed: 01/18/2023]  Open
5
Li Y, Lin B, Yang L. Comparative transcriptomic analysis of multiple cardiovascular fates from embryonic stem cells predicts novel regulators in human cardiogenesis. Sci Rep 2015;5:9758. [PMID: 25997157 PMCID: PMC4440522 DOI: 10.1038/srep09758] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/13/2015] [Indexed: 12/28/2022]  Open
6
O’Malley MA, Soyer OS, Siegal ML. A Philosophical Perspective on Evolutionary Systems Biology. BIOLOGICAL THEORY 2015;10:6-17. [PMID: 26085823 PMCID: PMC4465572 DOI: 10.1007/s13752-015-0202-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
7
Busser BW, Haimovich J, Huang D, Ovcharenko I, Michelson AM. Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila. Nucleic Acids Res 2015;43:1726-39. [PMID: 25609699 PMCID: PMC4330375 DOI: 10.1093/nar/gkv011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
8
Waardenberg AJ, Ramialison M, Bouveret R, Harvey RP. Genetic networks governing heart development. Cold Spring Harb Perspect Med 2014;4:a013839. [PMID: 25280899 PMCID: PMC4208705 DOI: 10.1101/cshperspect.a013839] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
9
The transcription factors Tec1 and Ste12 interact with coregulators Msa1 and Msa2 to activate adhesion and multicellular development. Mol Cell Biol 2014;34:2283-93. [PMID: 24732795 DOI: 10.1128/mcb.01599-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
10
Ahmad SM, Busser BW, Huang D, Cozart EJ, Michaud S, Zhu X, Jeffries N, Aboukhalil A, Bulyk ML, Ovcharenko I, Michelson AM. Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification. Development 2014;141:878-88. [PMID: 24496624 PMCID: PMC3912831 DOI: 10.1242/dev.101709] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
11
Busser BW, Gisselbrecht SS, Shokri L, Tansey TR, Gamble CE, Bulyk ML, Michelson AM. Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs. PLoS One 2013;8:e69385. [PMID: 23922708 PMCID: PMC3724861 DOI: 10.1371/journal.pone.0069385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022]  Open
12
Clough E, Oliver B. Genomics of sex determination in Drosophila. Brief Funct Genomics 2013;11:387-94. [PMID: 23023665 DOI: 10.1093/bfgp/els019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
13
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network. Proc Natl Acad Sci U S A 2012. [PMID: 23184988 DOI: 10.1073/pnas.1210415109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
14
Busser BW, Taher L, Kim Y, Tansey T, Bloom MJ, Ovcharenko I, Michelson AM. A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet 2012;8:e1002531. [PMID: 22412381 PMCID: PMC3297574 DOI: 10.1371/journal.pgen.1002531] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 12/23/2011] [Indexed: 12/22/2022]  Open
15
Zhu X, Ahmad SM, Aboukhalil A, Busser BW, Kim Y, Tansey TR, Haimovich A, Jeffries N, Bulyk ML, Michelson AM. Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors. Development 2012;139:1457-66. [PMID: 22378636 PMCID: PMC3308180 DOI: 10.1242/dev.069005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
16
Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development 2012;139:1164-74. [PMID: 22296846 PMCID: PMC3283125 DOI: 10.1242/dev.077362] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
17
Biggin M. Animal Transcription Networks as Highly Connected, Quantitative Continua. Dev Cell 2011;21:611-26. [DOI: 10.1016/j.devcel.2011.09.008] [Citation(s) in RCA: 247] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
18
Rada-Iglesias A, Wysocka J. Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease. Genome Med 2011;3:36. [PMID: 21658297 PMCID: PMC3218810 DOI: 10.1186/gm252] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
19
Lachke SA, Maas RL. Building the developmental oculome: systems biology in vertebrate eye development and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011;2:305-323. [PMID: 20836031 DOI: 10.1002/wsbm.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
20
Li HY, Liao CY, Lee KH, Chang HC, Chen YJ, Chao KC, Chang SP, Cheng HY, Chang CM, Chang YL, Hung SC, Sung YJ, Chiou SH. Collagen IV significantly enhances migration and transplantation of embryonic stem cells: involvement of α2β1 integrin-mediated actin remodeling. Cell Transplant 2010;20:893-907. [PMID: 21176409 DOI: 10.3727/096368910x550206] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
21
Kaltman JR, Schramm C, Pearson GD. The National Heart, Lung, and Blood Institute bench to bassinet Program: a new paradigm for translational research. J Am Coll Cardiol 2010;55:1262-1265. [PMID: 20298934 DOI: 10.1016/j.jacc.2009.11.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 11/10/2009] [Indexed: 11/12/2022]
22
Pu L, Brady S. Systems biology update: cell type-specific transcriptional regulatory networks. PLANT PHYSIOLOGY 2010;152:411-9. [PMID: 19965967 PMCID: PMC2815853 DOI: 10.1104/pp.109.148668] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/30/2009] [Indexed: 05/23/2023]
23
Zeitlinger J, Stark A. Developmental gene regulation in the era of genomics. Dev Biol 2010;339:230-9. [PMID: 20045679 DOI: 10.1016/j.ydbio.2009.12.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 12/04/2009] [Accepted: 12/23/2009] [Indexed: 01/30/2023]
24
Degnan BM, Vervoort M, Larroux C, Richards GS. Early evolution of metazoan transcription factors. Curr Opin Genet Dev 2009;19:591-9. [PMID: 19880309 DOI: 10.1016/j.gde.2009.09.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/16/2009] [Accepted: 09/27/2009] [Indexed: 11/29/2022]
25
Aravind L, Anantharaman V, Venancio TM. Apprehending multicellularity: regulatory networks, genomics, and evolution. ACTA ACUST UNITED AC 2009;87:143-64. [PMID: 19530132 DOI: 10.1002/bdrc.20153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
26
Systems-level analysis of cell-specific AQP2 gene expression in renal collecting duct. Proc Natl Acad Sci U S A 2009;106:2441-6. [PMID: 19190182 DOI: 10.1073/pnas.0813002106] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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