Modeling the dynamics of transcriptional gene regulatory networks for animal development

THE UBIQUITIN SYSTEM

Hershko, A., & Ciechanover, A. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.425 · Cited by 8,840 · see citing works

Untitled work

(2008) · doi:10.1038/nrg2290 · Cited by 5,199 · see citing works

Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice

McGhee, J. D., & von Hippel, P. H. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90031-x · Cited by 2,961 · see citing works

Modeling and Simulation of Genetic Regulatory Systems: A Literature Review

de Jong, H. (2002) · Journal of Computational Biology · doi:10.1089/10665270252833208 · Cited by 2,660 · see citing works

Structure and function of the feed-forward loop network motif

Mangan, S., & Alon, U. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133841100 · Cited by 1,827 · see citing works

Gene Activity in Early Development

Davidson, E. H. (1968) · Elsevier eBooks · doi:10.1016/c2013-0-12432-4 · Cited by 1,704 · see citing works

Controlling the double helix

Felsenfeld, G., & Groudine, M. T. (2003) · Nature · doi:10.1038/nature01411 · Cited by 1,153 · see citing works

Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell

Elf, J., Li, G., & Xie, X. (2007) · Science · doi:10.1126/science.1141967 · Cited by 1,063 · see citing works

The Regulatory Genome: Gene Regulatory Networks In Development And Evolution

Davidson, E. H. (2006) · Thammasat University Digital Collections · Cited by 1,055 · see citing works

Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome

Thanos, D., & Maniatis, T. (1995) · Cell · doi:10.1016/0092-8674(95)90136-1 · Cited by 1,014 · see citing works

Gene regulatory networks for development

Levine, M., & Davidson, E. H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408031102 · Cited by 796 · see citing works

Transcriptional regulation by the numbers: models

Bintu, L., Buchler, N. E. G., García, H. G., Gerland, U., Terence Hwa, B., Kondev, J., & Phillips, R. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.02.007 · Cited by 784 · see citing works

Oscillatory Expression of the bHLH Factor Hes1 Regulated by a Negative Feedback Loop

Hirata, H., Yoshiura, S., Ohtsuka, T., Bessho, Y., Harada, T., Yoshikawa, K., & Kageyama, R. (2002) · Science · doi:10.1126/science.1074560 · Cited by 765 · see citing works

The cap-to-tail guide to mRNA turnover

Wilusz, C. J., Wormington, M., & Peltz, S. W. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35067025 · Cited by 757 · see citing works

The lac represser-operator interaction

Riggs, A. D., Bourgeois, S., & Cohn, M. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90074-4 · Cited by 751 · see citing works

Genomic Regulatory Systems: Development and Evolution

Davidson, E. H. (2005) · Thammasat University Digital Collections · Cited by 690 · see citing works

Lac represser-operator interaction

Jobe, A. H., & Bourgeois, S. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90023-5 · Cited by 688 · see citing works

Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene

Yuh, C., Bolouri, H., & Davidson, E. H. (1998) · Science · doi:10.1126/science.279.5358.1896 · Cited by 682 · see citing works

On schemes of combinatorial transcription logic

Buchler, N. E. G., Gerland, U., & Terence Hwa, B. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0930314100 · Cited by 663 · see citing works

The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo

Driever, W., & Nüsslein‐Volhard, C. (1989) · Nature · doi:10.1038/337138a0 · Cited by 663 · see citing works

Multilineage Transcriptional Priming and Determination of Alternate Hematopoietic Cell Fates

Laslo, P., Spooner, C. J., Warmflash, A., Lancki, D. W., Lee, H.-J., Sciammas, R., Gantner, B. N., Dinner, A. R., & Singh, H. (2006) · Cell · doi:10.1016/j.cell.2006.06.052 · Cited by 632 · see citing works

Quantitative model for gene regulation by lambda phage repressor.

Ackers, G. K., Johnson, A. D., & Shea, M. A. (1982) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.79.4.1129 · Cited by 590 · see citing works

The Nonamer UUAUUUAUU Is the Key AU-Rich Sequence Motif That Mediates mRNA Degradation

Zubiaga, A. M., Belasco, J. G., & Greenberg, M. E. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.4.2219 · Cited by 543 · see citing works

Transcriptional repression of eukaryotic promoters

Levine, M., & Manley, J. L. (1989) · Cell · doi:10.1016/0092-8674(89)90024-x · Cited by 470 · see citing works

Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification

Dodd, I. B., Micheelsen, M. A., Sneppen, K., & Thon, G. (2007) · Cell · doi:10.1016/j.cell.2007.02.053 · Cited by 436 · see citing works

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

Pedraza, J. M., & Paulsson, J. (2008) · Science · doi:10.1126/science.1144331 · Cited by 404 · see citing works

Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulatorsPreprint

Pikaart, M. J., Targa, F. R., & Felsenfeld, G. (1998) · Genes & Development · doi:10.1101/gad.12.18.2852 · Cited by 398 · see citing works

Modeling transcriptional control in gene networks—methods, recent results, and future directions

Smolen, P., Baxter, D., & Byrne, J. (2000) · Bulletin of Mathematical Biology · doi:10.1006/bulm.1999.0155 · Cited by 386 · see citing works

Global regulatory logic for specification of an embryonic cell lineage

Oliveri, P., Tu, Q., & Davidson, E. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711220105 · Cited by 381 · see citing works

The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes

Lin, S.-Y., & Riggs, A. D. (1975) · Cell · doi:10.1016/0092-8674(75)90116-6 · Cited by 338 · see citing works

Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9

Mutskov, V. J., & Felsenfeld, G. (2003) · The EMBO Journal · doi:10.1038/sj.emboj.7600013 · Cited by 297 · see citing works

Interaction of specific nuclear factors with the nuclease-hypersensitive region of the chicken adult β-globin gene: Nature of the binding domain

Emerson, B. M., Lewis, C. D., & Felsenfeld, G. (1985) · Cell · doi:10.1016/0092-8674(85)90057-1 · Cited by 256 · see citing works

Properties of developmental gene regulatory networks

Davidson, E. H., & Levine, M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806007105 · Cited by 247 · see citing works

Transcriptional Gene Silencing Promotes DNA Hypermethylation through a Sequential Change in Chromatin Modifications in Cancer Cells

Stirzaker, C., Song, J. Z., Davidson, B., & Clark, S. J. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3690 · Cited by 240 · see citing works

Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients*

Fujioka, M., Emi-Sarker, Y., Yusibova, G. L., Goto, T., & Jaynes, J. B. (1999) · Development · doi:10.1242/dev.126.11.2527 · Cited by 233 · see citing works

Heterochronic Genes and the Nature of Developmental Time

Moss, E. G. (2007) · Current Biology · doi:10.1016/j.cub.2007.03.043 · Cited by 228 · see citing works

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

Arnosti, D. N., Barolo, S., Levine, M., & Small, S. (1996) · Development · doi:10.1242/dev.122.1.205 · Cited by 226 · see citing works

Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics

Bolouri, H., & Davidson, E. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533293100 · Cited by 212 · see citing works

Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control

Yuh, C., Bolouri, H., & Davidson, E. H. (2001) · Development · doi:10.1242/dev.128.5.617 · Cited by 210 · see citing works

Biology by numbers: mathematical modelling in developmental biology

Tomlin, C. J., & Axelrod, J. D. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2098 · Cited by 199 · see citing works

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene

Janssens, H., Hou, S., Jaeger, J., Kim, A.-R., Марковна, М. Е., Sharp, D., & Reinitz, J. (2006) · Nature Genetics · doi:10.1038/ng1886 · Cited by 198 · see citing works

Epigenetic Mechanism of rRNA Gene Silencing: Temporal Order of NoRC-Mediated Histone Modification, Chromatin Remodeling, and DNA Methylation

Santoro, R., & Grummt, I. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.7.2539-2546.2005 · Cited by 188 · see citing works

Transcriptional repression in development

Gary, S., & Levin, M. (1996) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(96)80010-x · Cited by 184 · see citing works

Cooperative DNA‐binding by Bicoid provides a mechanism for threshold‐dependent gene activation in the Drosophila embryo

Burz, D. S., Rivera-Pomar, R. V., Jäckle, H., & Hanes, S. D. (1998) · The EMBO Journal · doi:10.1093/emboj/17.20.5998 · Cited by 178 · see citing works

Logic functions of the genomic cis-regulatory code

Istrail, S., & Davidson, E. H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409624102 · Cited by 170 · see citing works

Short-range repression permits multiple enhancers to function autonomously within a complex promoter.Preprint

Gray, S., Szymanski, P., & Levine, M. (1994) · Genes & Development · doi:10.1101/gad.8.15.1829 · Cited by 156 · see citing works

Gene Regulation: Gene Control Network in Development

de‐Leon, S. B., & Davidson, E. H. (2007) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.35.040405.102002 · Cited by 147 · see citing works

Repression of mesodermal fate by<i>foxa</i>, a key endoderm regulator of the sea urchin embryo

Oliveri, P., Walton, K. D., Davidson, E. H., & McClay, D. R. (2006) · Development · doi:10.1242/dev.02577 · Cited by 141 · see citing works

Interleukin-2 Transcription Is Regulated In Vivo at the Level of Coordinated Binding of Both Constitutive and Regulated Factors

Garrity, P., Chen, D. S., Rothenberg, E. V., & Wold, B. J. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.3.2159-2169.1994 · Cited by 139 · see citing works

Short-range transcriptional repressors mediate both quenching and direct repression within complex loci in Drosophila.Preprint

Gray, S., & Levine, M. (1996) · Genes & Development · doi:10.1101/gad.10.6.700 · Cited by 134 · see citing works

Transcriptional stochasticity in gene expression

Lipniacki, T., Paszek, P., Marciniak-Czochra, A. K., Brasier, A. R., & Kimmel, M. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.05.032 · Cited by 132 · see citing works

A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression

Smith, J., Theodoris, C. V., & Davidson, E. H. (2007) · Science · doi:10.1126/science.1146524 · Cited by 127 · see citing works

Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development

Ashby, M., Materna, S. C., Brown, C. T., Chen, L., Cameron, R. A., & Davidson, E. H. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.039 · Cited by 125 · see citing works

Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models

Zhu, R., Ribeiro, A. S., Salahub, D. R., & Kauffman, S. A. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.01.021 · Cited by 123 · see citing works

The Drosophila morphogenetic protein Bicoid binds DNA cooperatively

Ma, X., Yuan, D., Diepold, K., Scarborough, T., & Ma, J. (1996) · Development · doi:10.1242/dev.122.4.1195 · Cited by 122 · see citing works

Overlapping Positive and Negative Regulatory Elements Determine Lens-Specific Activity of the δ1-Crystallin Enhancer

Kamachi, Y., & Kondoh, H. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.9.5206-5215.1993 · Cited by 121 · see citing works

Developmental appearance of factors that bind specifically to cis-regulatory sequences of a gene expressed in the sea urchin embryo.Preprint

Calzone, F. J., Thézé, N., Thiébaud, P., Hill, R. L., Britten, R. J., & Davidson, E. H. (1988) · Genes & Development · doi:10.1101/gad.2.9.1074 · Cited by 112 · see citing works

Kinetic studies of sequence-specific binding of GCN4-bZIP peptides to DNA strands immobilized on a 27-MHz quartz-crystal microbalance.

Okahata, Y., Niikura, K., Sugiura, Y., Sawada, M., & Morii, T. (1998) · Biochemistry · doi:10.1021/bi980037k · Cited by 111 · see citing works

Early B-Cell Factor, E2A, and Pax-5 Cooperate To Activate the Early B Cell-Specific mb-1 Promoter

Sigvardsson, M., Clark, D. R., Fitzsimmons, D., Doyle, M. J., Åkerblad, P., Breslin, T., Bilke, S., Li, R., Yeamans, C., Zhang, G., et al. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.24.8539-8551.2002 · Cited by 107 · see citing works

Analysis of the tissue-specific enhancer at the 3' end of the chicken adult beta-globin gene.

Emerson, B. M., Nickol, J. M., Jackson, P. D., & Felsenfeld, G. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.14.4786 · Cited by 104 · see citing works

hairy mediates dominant repression in the Drosophila embryo

Barolo, S., & Levine, M. (1997) · The EMBO Journal · doi:10.1093/emboj/16.10.2883 · Cited by 102 · see citing works

Gene regulatory factors of the sea urchin embryo: I. Purification by affinity chromatography and cloning of P3A2, a novel DNA-binding protein

Calzone, F. J., Höög, C., Teplow, D. B., Cutting, A. E., Zeller, R. W., Britten, R. J., & Davidson, E. H. (1991) · Development · doi:10.1242/dev.112.1.335 · Cited by 101 · see citing works

Role of poly (A) tail as an identity element for mRNA nuclear export

Fuke, H., & Ohno, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1120 · Cited by 99 · see citing works

Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations

Bernard, S., Čajavec, B., Pujo-Menjouet, L., Mackey, M. C., & Herzel, H. (2006) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2006.1761 · Cited by 97 · see citing works

The regulatory genome and the computer

Istrail, S., de‐Leon, S. B., & Davidson, E. H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.08.009 · Cited by 89 · see citing works

Protein synthesis, polyribosomes, and peptide elongation in early development of Strongylocentrotus purpuratus

Goustin, A. S., & Wilt, F. H. (1981) · Developmental Biology · doi:10.1016/0012-1606(81)90426-7 · Cited by 85 · see citing works

Oscillations, clocks and segmentation

Bessho, Y., & Kageyama, R. (2003) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(03)00083-2 · Cited by 84 · see citing works

Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network

Nam, J., Su, Y., Lee, P. Y., Robertson, A., Coffman, J. A., & Davidson, E. H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.03.033 · Cited by 82 · see citing works

Two mechanisms in the action of repressor δEF1: binding site competition with an activator and active repression

Sekido, R., Murai, K., Kamachi, Y., & Kondoh, H. (1997) · Genes to Cells · doi:10.1046/j.1365-2443.1997.1570355.x · Cited by 77 · see citing works

Concise Review: Role and Function of the Ubiquitin-Proteasome System in Mammalian Stem and Progenitor Cells

Naujokat, C., & Šarić, T. (2007) · Stem Cells · doi:10.1634/stemcells.2007-0255 · Cited by 77 · see citing works

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

Liberman, L. M., & Stathopoulos, A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.020 · Cited by 76 · see citing works

DNA methylation and histone modification regulate silencing of epithelial cell adhesion molecule for tumor invasion and progression

Tai, K.-Y., Shiah, S., Shieh, Y.-S., Kao, Y.-R., Chi, C.-Y., Huang, E., Lee, H.-S., Chang, L.-C., Yang, P.-C., & Wu, C.-W. (2007) · Oncogene · doi:10.1038/sj.onc.1210176 · Cited by 73 · see citing works

Whole-genome analysis of Drosophila gastrulation

Stathopoulos, A., & Levine, M. (2004) · Current Opinion in Genetics &amp; Development · doi:10.1016/j.gde.2004.07.004 · Cited by 71 · see citing works

Phosphorylation of Serine 239 of Groucho/TLE1 by Protein Kinase CK2 Is Important for Inhibition of Neuronal Differentiation

Nuthall, H. N., Joachim, K., & Stifani, S. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.19.8395-8407.2004 · Cited by 64 · see citing works

Epigenetic chromatin silencing: bistability and front propagation

Sedighi, M., & Sengupta, A. M. (2007) · Physical Biology · doi:10.1088/1478-3975/4/4/002 · Cited by 60 · see citing works

Collaboration between Smads and a Hox protein in target gene repression

Walsh, C. M., & Carroll, S. B. (2007) · Development · doi:10.1242/dev.009522 · Cited by 59 · see citing works

Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development

Giurumescu, C. A., Sternberg, P. W., & Asthagiri, A. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506476103 · Cited by 59 · see citing works

Role for Hes1-Induced Phosphorylation in Groucho-Mediated Transcriptional Repression

Nuthall, H. N., Husain, J., McLarren, K. W., & Stifani, S. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.2.389-399.2002 · Cited by 59 · see citing works

Dependence of BSAP Repressor and Activator Functions on BSAP Concentration

Wallin, J. J., Gackstetter, E. R., & Koshland, M. E. (1998) · Science · doi:10.1126/science.279.5358.1961 · Cited by 57 · see citing works

Monomeric and Dimeric bZIP Transcription Factor GCN4 Bind at the Same Rate to Their Target DNA Site

Cranz, S., Berger, C. E. M., Baici, A., Jelesarov, I., & Bosshard, H. R. (2003) · Biochemistry · doi:10.1021/bi0355793 · Cited by 56 · see citing works

A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo

Smith, J., Kraemer, E., Liu, P. H., Theodoris, C. V., & Davidson, E. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.10.042 · Cited by 56 · see citing works

cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo

Amore, G., & Davidson, E. H. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.02.024 · Cited by 55 · see citing works

Intracellular delay limits cyclic changes in gene expression

Rateitschak, K., & Wolkenhauer, O. (2006) · Mathematical Biosciences · doi:10.1016/j.mbs.2006.08.010 · Cited by 55 · see citing works

Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II

Shuman, S. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.24.12758 · Cited by 52 · see citing works

Regulation of cytoplasmic mRNA prevalence in sea urchin embryos

Cabrera, C. V., Lee, J. J., Ellison, J. W., Britten, R. J., & Davidson, E. H. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90366-8 · Cited by 51 · see citing works

Dynamic changes in the functions of Odd-skipped during early Drosophila embryogenesis

Dréan, B. S.-L., Nasiadka, A., Dong, J., & Krause, H. M. (1998) · Development · doi:10.1242/dev.125.23.4851 · Cited by 42 · see citing works

Gene regulatory factors of the sea urchin embryo: II. Two dissimilar proteins, P3A1 and P3A2, bind to the same target sites that are required for early territorial gene expression

Höög, C., Calzone, F. J., Cutting, A. E., Britten, R. J., & Davidson, E. H. (1991) · Development · doi:10.1242/dev.112.1.351 · Cited by 41 · see citing works

Built to Run, Not Fail

Oliveri, P., & Davidson, E. H. (2007) · Science · doi:10.1126/science.1140979 · Cited by 41 · see citing works

Degradation of unstable interleukin-1 alpha mRNA in a rabbit reticulocyte cell-free system. Localization of an instability determinant to a cluster of AUUUA motifs.

Gorospe, M., & Baglioni, C. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)32650-9 · Cited by 37 · see citing works

Kinetic analysis of segmentation gene interactions in Drosophila embryos

Nasiadka, A., & Krause, H. M. (1999) · Development · doi:10.1242/dev.126.7.1515 · Cited by 35 · see citing works

CtBP-Independent Repression in the Drosophila Embryo

Nibu, Y., Senger, K., & Levine, M. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.11.3990-3999.2003 · Cited by 29 · see citing works

Polysome structure in sea urchin eggs and embryos: An electron microscopic analysis

Martin, K., & Miller, O. L. (1983) · Developmental Biology · doi:10.1016/0012-1606(83)90364-0 · Cited by 27 · see citing works

Rates of RNA chain growth in developing sea urchin embryos

Aronson, A. I., & Chen, K. (1977) · Developmental Biology · doi:10.1016/0012-1606(77)90238-x · Cited by 22 · see citing works

Modulation of sea urchin actin mRNA prevalence during embryogenesis: Nuclear synthesis and decay rate measurements of transcripts from five different genes

Lee, J. J., Calzone, F. J., & Davidson, E. H. (1992) · Developmental Biology · doi:10.1016/0012-1606(92)90296-s · Cited by 21 · see citing works

Energy requirement and kineties of transport of poly(A)‐free histone mRNA compared to poly(A)‐rich mRNA from isolated L‐cell nuclei

Schröder, H. C., Friese, U., Bachmann, M. P., Zaubitzer, T., & Müller, W. E. G. (1989) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1989.tb14706.x · Cited by 20 · see citing works

Constitutive Promoter Occupancy by the MBF-1 Activator and Chromatin Modification of the Developmental Regulated Sea Urchin α-H2A Histone Gene

Caro, V. D., Cavalieri, V., Melfi, R., & Spinelli, G. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.10.098 · Cited by 18 · see citing works

Loading of DNA-Binding Factors to an Erythroid Enhancer

Wen, S.-C., Roder, K., Hu, K.-Y., Rombel, I., Gavva, N. R., Daftari, P., Kuo, Y., Wang, C., & Shen, C. ‐. J. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.6.1993-2003.2000 · Cited by 18 · see citing works

Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks

Ribeiro, A. S. (2007) · Physical Review E · doi:10.1103/physreve.76.051915 · Cited by 15 · see citing works

Stochastic transcription initiation: Time dependent transcription rates

Murugan, R. (2006) · Biophysical Chemistry · doi:10.1016/j.bpc.2005.12.010 · Cited by 10 · see citing works

Repressors

Ptashne, M. (2007) · Current Biology · doi:10.1016/j.cub.2007.06.053 · Cited by 9 · see citing works

Cooperativity between the J and S elements of class II major histocompatibility complex genes as enhancers in normal and class II-negative patient and mutant B cell lines.

Sugawara, M., Scholl, T., Mahanta, S. K., Ponath, P. D., & Strominger, J. L. (1995) · The Journal of Experimental Medicine · doi:10.1084/jem.182.1.175 · Cited by 7 · see citing works

Modification of octamer binding transcriptional factor is related to H2B histone gene repression during dimethyl sulfoxide-dependent differentiation of HL-60 cells

Lee, M., Son, M., Park, J., Park, C., Lee, Y., Son, C.-B., Kim, Y.-S., Paik, S., Yoon, W.-H., Park, S.-K., et al. (2001) · Cancer Letters · doi:10.1016/s0304-3835(01)00654-1 · Cited by 5 · see citing works

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works

On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development

Peshkin, L., Wühr, M., Pearl, E. J., Haas, W., Freeman, R. M., Gerhart, J. C., Klein, A. M., Horb, M. E., Gygi, S. P., & Kirschner, M. W. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.10.010 · Cited by 219 · see citing works

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Zhong, M., Niu, W., Lu, Z., Sarov, M., Murray, J. I., Janette, J., Raha, D., Sheaffer, K. L., Lam, H. Y. K., Preston, E., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000848 · Cited by 187 · see citing works

How subtle changes in 3D structure can create large changes in transcription

Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162 · see citing works

Systematic analysis of posttranscriptional gene expression

Morris, A. R., Mukherjee, N., & Keene, J. D. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.54 · Cited by 109 · see citing works

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

Su, Y., Li, E., Geiss, G. K., Longabaugh, W. J. R., Krämer, A., & Davidson, E. H. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.02.029 · Cited by 106 · see citing works

High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development

Materna, S. C., Nam, J., & Davidson, E. H. (2010) · Gene Expression Patterns · doi:10.1016/j.gep.2010.04.002 · Cited by 87 · see citing works

A spectrum of modularity in multi‐functional gene circuits

Jiménez, A., Cotterell, J., Munteanu, A., & Sharpe, J. A. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167347 · Cited by 80 · see citing works

Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus

García-Betancur, J. C., Goñi‐Moreno, Á., Horger, T., Schott, M., Sharan, M., Eikmeier, J., Wohlmuth, B. I., Zernecke, A., Ohlsen, K., Kuttler, C., et al. (2017) · eLife · doi:10.7554/elife.28023 · Cited by 73 · see citing works

Multicellular Computing Using Conjugation for Wiring

Goñi‐Moreno, Á., Amos, M., & de la Cruz, F. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065986 · Cited by 67 · see citing works

Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

Ríos‐Estepa, R., Lange, I., Lee, J. M., & Lange, B. M. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.152256 · Cited by 67 · see citing works

A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions

Peng, T., Liu, L., MacLean, A. L., Wong, C. W., Zhao, W., & Nie, Q. H. (2017) · BMC Systems Biology · doi:10.1186/s12918-017-0429-x · Cited by 63 · see citing works

Challenges for modeling global gene regulatory networks during development: Insights from Drosophila

Wilczyński, B., & Furlong, E. E. M. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.032 · Cited by 59 · see citing works

Information processing at the foxa node of the sea urchin endomesoderm specification network

de‐Leon, S. B., & Davidson, E. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004824107 · Cited by 59 · see citing works

Gene Regulatory Control in the Sea Urchin Aboral Ectoderm: Spatial Initiation, Signaling Inputs, and Cell Fate Lockdown

de-Leon, S., Su, Y.-H., Lin, K.-T., Li, E., & Davidson, E. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2012.11.013 · Cited by 66 · see citing works

Dynamics of the Interaction between Cotton Bollworm Helicoverpa armigera and Nucleopolyhedrovirus as Revealed by Integrated Transcriptomic and Proteomic Analyses

Xing, L., Yuan, C., Wang, M., Lin, Z., Shen, B.-C., Hú, Z., & Zou, Z. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.062547 · Cited by 46 · see citing works

Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics

Gildor, T., & de‐Leon, S. B. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005435 · Cited by 47 · see citing works

Analysis of early C2C12 myogenesis identifies stably and differentially expressed transcriptional regulators whose knock-down inhibits myoblast differentiation

Rajan, S., Dang, H. C. P., Djambazian, H. H. V., Zuzan, H., Fedyshyn, Y., Ketela, T., Moffat, J., Hudson, T. J., & SLADEK, R. M. (2011) · Physiological Genomics · doi:10.1152/physiolgenomics.00093.2011 · Cited by 41 · see citing works

Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus

Damle, S. S., & Davidson, E. H. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.06.016 · Cited by 40 · see citing works

Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor–Promoter Interplay

Goñi‐Moreno, Á., Benedetti, I., Kim, J., & de Lorenzo, V. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00397 · Cited by 40 · see citing works

Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms

Hinman, V. F., & Jarvela, A. M. C. (2014) · genesis · doi:10.1002/dvg.22757 · Cited by 40 · see citing works

Building developmental gene regulatory networks

Li, E., & Davidson, E. H. (2009) · Birth Defects Research Part C Embryo Today Reviews · doi:10.1002/bdrc.20152 · Cited by 36 · see citing works

Robust Gene Circuit Control Design for Time-Delayed Genetic Regulatory Networks Without SUM Regulatory Logic

Jiao, H., Zhang, L., Shen, Q., Zhu, J., & Shi, P. J. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2825445 · Cited by 36 · see citing works

Regulative deployment of the skeletogenic gene regulatory network during sea urchin development

Sharma, T., & Ettensohn, C. A. (2011) · Development · doi:10.1242/dev.065193 · Cited by 35 · see citing works

An integrative method to decode regulatory logics in gene transcription

Yan, B., Guan, D., Wang, C., Wang, J., He, B., Qin, J., Boheler, K. R., Lü, A., Zhang, G., & Zhu, H. (2017) · Nature Communications · doi:10.1038/s41467-017-01193-0 · Cited by 29 · see citing works

Bioinformatics and systems biology

Ram, P. T., Mendelsohn, J. M., & Mills, G. B. (2012) · Molecular Oncology · doi:10.1016/j.molonc.2012.01.008 · Cited by 27 · see citing works

Networks and pathways in pigmentation, health, and disease

Baxter, L. L., Loftus, S. K., & Pavan, W. J. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.20 · Cited by 26 · see citing works

p85α promotes nucleolin transcription and subsequently enhances EGFR mRNA stability and EGF-induced malignant cellular transformation

Xie, Q., Guo, X., Gu, J., Zhang, L., Jin, H., Huang, H., Li, J., & Huang, C. (2016) · Oncotarget · doi:10.18632/oncotarget.7674 · Cited by 24 · see citing works

Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins

Mandic, M., Ramon, M. L., Gracey, A. Y., & Richards, J. G. (2014) · Molecular Ecology · doi:10.1111/mec.12991 · Cited by 24 · see citing works

Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology

de‐Leon, S. B., & Davidson, E. H. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.24 · Cited by 23 · see citing works

Comparative transcriptome analysis of short-term responses to salt and glycerol hyperosmotic stress in the green alga Dunaliella salina

Lv, H., Kim, M., Park, S., Baek, K., Oh, H., Polle, J. E. W., & Jin, E. (2020) · Algal Research · doi:10.1016/j.algal.2020.102147 · Cited by 22 · see citing works

Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges

Rothenberg, E. V. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2019.0098 · Cited by 20 · see citing works

Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Genome biology · doi:10.1186/s13059-024-03305-8 · Cited by 21 · see citing works

Analytic Approaches to Stochastic Gene Expression in Multicellular Systems

Boettiger, A. N. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.10.033 · Cited by 20 · see citing works

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network

Kühn, C., Wierling, C., Kühn, A., Klipp, E., Panopoulou, G. V., Lehrach, H. R., & Poustka, A. J. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-83 · Cited by 20 · see citing works

Reconstructing transcriptional regulatory networks through genomics data

Sun, N., & Zhao, H. (2009) · Statistical Methods in Medical Research · doi:10.1177/0962280209351890 · Cited by 20 · see citing works

Regulatory states in the developmental control of gene expression

Peter, I. S. (2017) · Briefings in Functional Genomics · doi:10.1093/bfgp/elx009 · Cited by 17 · see citing works

Eric Davidson: Steps to a gene regulatory network for development

Rothenberg, E. V. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.01.020 · Cited by 17 · see citing works

Effect of temperature on Pi54-mediated leaf blast resistance in rice

Madhusudhan, P., Sinha, P., Rajput, L. S., Bhattacharya, M., Sharma, T., Bhuvaneshwari, V., Gaikwad, K., Krishnan, S. G., & SINGH, A. K. (2019) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-019-2724-8 · Cited by 16 · see citing works

A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks

Chen, T., Al-Radhawi, M. A., & Sontag, E. D. (2020) · Epigenetics · doi:10.1080/15592294.2020.1805686 · Cited by 15 · see citing works

Stepwise progression of embryonic patterning

Sandler, J. E., & Stathopoulos, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.04.004 · Cited by 17 · see citing works

Modularity of CHIP/LDB transcription complexes regulates cell differentiation

Bronstein, R., & Segal, D. (2011) · Fly · doi:10.4161/fly.5.3.14854 · Cited by 14 · see citing works

Placental transcriptomes in the common aneuploidies reveal critical regions on the trisomic chromosomes and genome‐wide effects

Bianco, K., Gormley, M. J., Farrell, J., Zhou, Y., Oliverio, O., Tilden, H., McMaster, M., & Fisher, S. J. (2016) · Prenatal Diagnosis · doi:10.1002/pd.4862 · Cited by 14 · see citing works

A kinetic model identifies phosphorylated estrogen receptor‐α (ERα) as a critical regulator of ERα dynamics in breast cancer

Tian, D., Solodin, N. M., Rajbhandari, P., Bjorklund, K., Alarid, E. T., & Kreeger, P. K. (2015) · The FASEB Journal · doi:10.1096/fj.14-265637 · Cited by 14 · see citing works

A single molecule view on Dbp5 and mRNA at the nuclear pore

Kaminski, T. P., Siebrasse, J. P., & Kubitscheck, U. (2013) · Nucleus · doi:10.4161/nucl.23386 · Cited by 13 · see citing works

Cell division curtails helper phenotype plasticity and expedites helper T‐cell differentiation

van den Ham, H., & de Boer, R. J. (2012) · Immunology and Cell Biology · doi:10.1038/icb.2012.23 · Cited by 13 · see citing works

Gene Regulatory Networks

Davidson, E. H., & Peter, I. S. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-404729-7.00002-2 · Cited by 13 · see citing works

Dynamical modeling of uncertain interaction-based genomic networks

Mohsenizadeh, D. N., Jianping Hua, A., Bittner, M. L., & Dougherty, E. R. (2015) · BMC Bioinformatics · doi:10.1186/1471-2105-16-s13-s3 · Cited by 11 · see citing works

Methods for the experimental and computational analysis of gene regulatory networks in sea urchins

Peter, I. S. (2018) · Methods in cell biology · doi:10.1016/bs.mcb.2018.10.003 · Cited by 9 · see citing works

Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin

Gildor, T., Malik, A., Sher, N., & de‐Leon, S. B. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.04.007 · Cited by 9 · see citing works

Computational Modeling and Simulation of Animal Early Embryogenesis with the MecaGen Platform

Delile, J., Doursat, R., & Peyriéras, N. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-405926-9.00016-2 · Cited by 8 · see citing works

A resource dependent protein synthesis model for evaluating synthetic circuits

Halter, W., Montenbruck, J. M., Tuza, Z. A., & Allgöwer, F. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.03.004 · Cited by 8 · see citing works

Cis-Regulatory Logic Produces Gene-Expression Noise Describing Phenotypic Heterogeneity in Bacteria

Chowdhury, D., Wang, C., Lü, A., & Zhu, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.698910 · Cited by 7 · see citing works

Linguistic modelling of gene regulation: Translation from the language of experiments to the language of modelling

Spirov, A. V., & Myasnikova, E. M. (2018) · ICT Express · doi:10.1016/j.icte.2018.10.008 · Cited by 7 · see citing works

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

Alexiou, A. T., Chatzichronis, S., Perveen, A., Hafeez, A., & Ashraf, G. M. (2019) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026619666190311125256 · Cited by 7 · see citing works

Positive effect of Mdm2 on p53 expression explains excitability of p53 in response to DNA damage

Eliaš, J. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.01.038 · Cited by 6 · see citing works

Identifying Transcription Factor Combinations to Modulate Circadian Rhythms by Leveraging Virtual Knockouts on Transcription Networks

Chowdhury, D., Wang, C., Lü, A., & Zhu, H. (2020) · iScience · doi:10.1016/j.isci.2020.101490 · Cited by 6 · see citing works

Division time-based amplifiers for stochastic gene expression

Wang, H., Yuan, Z., Liu, Y., & Zhou, T. (2015) · Molecular BioSystems · doi:10.1039/c5mb00391a · Cited by 6 · see citing works

Understanding molecular signaling cascades in neural disease using multi-resolution models

Viswan, N. A., & Bhalla, U. S. (2023) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2023.102808 · Cited by 5 · see citing works

Addressing Non-linear System Dynamics of Single-Strand RNA Virus–Host Interaction

Romano, A., Casazza, M., & Gonella, F. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.600254 · Cited by 7 · see citing works

Connecting the molecular function of microRNAs to cell differentiation dynamics

Posner, R., & Laubenbacher, R. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0437 · Cited by 5 · see citing works

Chlorella vulgaris heterotrophy-to-phototrophy conversion dynamics are mostly independent of light intensity.

Levasseur, W., & Pozzobon, V. (2025) · Bioresource Technology · doi:10.1016/j.biortech.2025.133262 · Cited by 4 · see citing works

Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics

Cotton, T. B., Nguyen, H., Said, J. I., Ouyang, Z., Zhang, J., & Song, M. J. (2015) · Scientific Reports · doi:10.1038/srep09634 · Cited by 4 · see citing works

Effects of β-HgS on cell viability and intracellular oxidative stress in PC-12 cells

Geng, L., Xia, Z., Lu, Y., Li, C., Zhang, M., Du, Y., Wei, L., & Bi, H. (2020) · Metallomics · doi:10.1039/d0mt00088d · Cited by 4 · see citing works

Differential sensitivity to longitudinal and transverse stretch mediates transcriptional responses in mouse neonatal ventricular myocytes

Cao, S., Buchholz, K. S., Tan, P. M., Stowe, J. C., Wang, A., Fowler, A., Knaus, K. R., Khalilimeybodi, A., Zambon, A. C., Omens, J. H., et al. (2023) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00562.2023 · Cited by 4 · see citing works

Perturbation analysis analyzed—mathematical modeling of intact and perturbed gene regulatory circuits for animal development

de‐Leon, S. B. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.06.020 · Cited by 4 · see citing works

Off-axis Neuromuscular Training for Knee Ligament Injury Prevention and Rehabilitation

Ren, Y., Park, H., Wu, Y., Geiger, F., & Zhang, L. (2010) · InTech eBooks · doi:10.5772/7606 · Cited by 3 · see citing works

Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators

Guo, Y., & Xiao, Z. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae542 · Cited by 3 · see citing works

Study on Membrane Protein Interaction Networks by Constructing Gene Regulatory Network Model

Ding, Y., Shen, Y., Cheng, L., & Xu, J. (2010) · Communications in computer and information science · doi:10.1007/978-3-642-15859-9_34 · Cited by 3 · see citing works

Is the Cell Nucleus a Necessary Component in Precise Temporal Patterning?

Albert, J., & Rooman, M. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134239 · Cited by 3 · see citing works

Encounters across networks: windows into principles of genomic regulation

Rothenberg, E. (2019) · Marine Genomics · doi:10.1016/j.margen.2019.01.003 · Cited by 3 · see citing works

Future prospects of transcriptomics

Pinhel, M. A. D. S., Watanabe, L. M., Fernandes-Ferreira, R., Noronha, N. Y., Rodrigues, G. D. S., Souza, D. R. S., & Nonino, C. B. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91810-7.00005-4 · Cited by 2 · see citing works

Deconvolution of gene expression noise into physical dynamics of cognate promotersPreprint

Goñi‐Moreno, Á., Benedetti, I., Kim, J., & de Lorenzo, V. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/019927 · Cited by 2 · see citing works

Comparative Identification of Differential Interactions from Trajectories of Dynamic Biological Networks.

Ouyang, Z., & Song, M. J. (2009) · PubMed · Cited by 2 · see citing works

Accurate prediction of genetic circuit behavior requires multidimensional characterization of partsPreprint

Dods, G., Gómez-Schiavon, M., El‐Samad, H., & Ng, A. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.30.122077 · Cited by 2 · see citing works

Transcriptional memory emerges from cooperative histone modificationsPreprint

Binder, H., Steiner, L., Rohlf, T., Prohaska, S. J., & Galle, J. (2011) · Nature Precedings · doi:10.1038/npre.2011.6507.1 · Cited by 2 · see citing works

Genetic, Epigenetic and Molecular Changes in Melanoma: A New Paradigm for Biological Classification

Staibano, S., Mascolo, M., Siano, M., Ilardi, G., & De, G. (2011) · InTech eBooks · doi:10.5772/19966 · Cited by 1 · see citing works

Dynamic and collective analysis of membrane protein interaction network based on gene regulatory network model

Ding, Y., Shen, Y., Ren, L., & Cheng, L. (2012) · Neurocomputing · doi:10.1016/j.neucom.2011.05.047 · Cited by 1 · see citing works

NNs-Based Adaptive Control for Genetic Regulatory Networks With Sensor Faults

Lu, B., & Shen, Q. (2021) · IEEE Access · doi:10.1109/access.2021.3113988 · Cited by 1 · see citing works

Gene Networks Driving Development, Conservation and Evolution of

Hinman, V. F. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00130-x · Cited by 1 · see citing works

Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing neuronsPreprint

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.04.556212 · Cited by 1 · see citing works

Régulation traductionnelle en réponse à la fécondation et en conditions perturbées dans l’embryon d’oursin

Costache, V. (2012) · HAL

Topology Analysis of a Metabolic Functional Gene Transcriptional Regulatory Network of Escherichia Coli

Zou, Q. Y., Liu, F., & Hou, T. (2013) · Applied Mechanics and Materials · doi:10.4028/www.scientific.net/amm.461.648

The developmental regulator Gon4-like functions within the transcriptional networks that control B lymphopoiesis and CD4+ T cell responses

Hankel, I. L. (2011) · doi:10.17077/etd.nabwtq56

Transcriptional variation among populations of salmon: The ge netic architecture of local adaptation

Ouellette, M. (2013) · Scholarship at UWindsor (University of Windsor)

whose knock-down inhibits myoblast differentiation and differentially expressed transcriptional regulators Analysis of early C2C12 myogenesis identifies stably

Fedyshyn, Y., Ketela, T., Moffat, J., Hudson, T. J., Rajan, S., Chu, H., Dang, P., Djambazian, H. H. V., Zuzan, H., Czech, M., et al. (2015)

A link partition approach for finding overlapping functional modules in the transcriptional regulatory network

Zou, Q., Liu, F., Hou, T., Jiang, Y., & Mo, R. (2014) · Bio-Medical Materials and Engineering · doi:10.3233/bme-141200

Predição computacional de sítios de ligação de fatores de transcrição baseada em gramáticas regulares estocásticas

Neto, A. F. P. P. (2018) · doi:10.11606/d.95.2018.tde-02012018-144349

Fuzzy Linguistic Modeling of the Regulation of Drosophila Segmentation Genes

Makashov, A., Myasnikova, E. M., & Spirov, A. V. (2021) · BIOPHYSICS · doi:10.1134/s0006350921010073

Mechanisms of How Random Input Controls Bursting Gene Expression

Xiao, S., Wang, Y., Wang, Z., & Wang, H. (2022) · Complexity · doi:10.1155/2022/5181333

Analysis and synthesis of cellular decision making: modeling epigenetic regulation in cell fate networks and designing a distributed synthetic counter circuit

Chen, T. (2022) · doi:10.17760/d20474742

Effect of Phosphorylation on the Circadian Clock of Drosophila by Analytical and Graph Theory Matrix Approach

Kirthiga, M., Geetha, N. K., & Vivekanandam, B. (2024) · Algorithms for intelligent systems · doi:10.1007/978-981-97-0180-3_10

Editorial: Women in evolutionary developmental biology 2023

de‐Leon, S. B., & Arnone, M. I. (2024) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2024.1464506

Additional file 14 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736747

Additional file 4 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736717

Additional file 9 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736732

Additional file 7 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736726

Additional file 8 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736729

Additional file 10 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736735

Additional file 6 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons

Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736723

Modeling DNA Sequence-Based cis-Regulatory Gene Networks

Bolouri, H., & Davidson, E. H. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0617 · Cited by 82 · see citing works

REVIEW Modeling DNA Sequence-Based cis-Regulatory Gene

Bolouri, H., & Davidson, E. H. (2008)

Perturbation analysis analyzed—mathematical modeling of intact and perturbed gene regulatory circuits for animal development

de‐Leon, S. B. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.06.020 · Cited by 4 · see citing works

Modeling and Dynamics of Gene Regulatory Networks

Sweigart, C. (2011) · doi:10.13016/m2obez-ha47

Modeling gene regulatory networks for cell fate specification

Warmflash, A., & Dinner, A. R. (2009) · Cambridge University Press eBooks · doi:10.1017/cbo9780511576768.006 · Cited by 5 · see citing works