The hardwiring of development: organization and function of genomic regulatory systems

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J. Biol. Chem., November 10, 2006; 281(45): 34406 - 34420.
[Abstract] [Full Text] [PDF]

X. Yu, K. Suzuki, Y. Wang, A. Gupta, R. Jin, M.-C. Orgebin-Crist, and R. Matusik
The Role of Forkhead Box A2 to Restrict Androgen-Regulated Gene Expression of Lipocalin 5 in the Mouse Epididymis
Mol. Endocrinol., October 1, 2006; 20(10): 2418 - 2431.
[Abstract] [Full Text] [PDF]

G. K. McEwen, A. Woolfe, D. Goode, T. Vavouri, H. Callaway, and G. Elgar
Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
Genome Res., April 1, 2006; 16(4): 451 - 465.
[Abstract] [Full Text] [PDF]

X. Gan, A. W.-C. Liew, and H. Yan
Microarray missing data imputation based on a set theoretic framework and biological knowledge
Nucleic Acids Res., March 20, 2006; 34(5): 1608 - 1619.
[Abstract] [Full Text] [PDF]

I. Abnizova and W. R. Gilks
Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes
Brief Bioinform, March 1, 2006; 7(1): 48 - 54.
[Abstract] [Full Text] [PDF]

F. M. Harold
Molecules into Cells: Specifying Spatial Architecture
Microbiol. Mol. Biol. Rev., December 1, 2005; 69(4): 544 - 564.
[Abstract] [Full Text] [PDF]

R. A. Cameron, S. H. Chow, K. Berney, T.-Y. Chiu, Q.-A. Yuan, A. Kramer, A. Helguero, A. Ransick, M. Yun, and E. H. Davidson
An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules
PNAS, August 16, 2005; 102(33): 11769 - 11774.
[Abstract] [Full Text] [PDF]

G. M. Cooper, E. A. Stone, G. Asimenos, NISC Comparative Sequencing Program, E. D. Green, S. Batzoglou, and A. Sidow
Distribution and intensity of constraint in mammalian genomic sequence
Genome Res., July 1, 2005; 15(7): 901 - 913.
[Abstract] [Full Text] [PDF]

A. G. Jegga, A. Gupta, S. Gowrisankar, M. A. Deshmukh, S. Connolly, K. Finley, and B. J. Aronow
CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W408 - W411.
[Abstract] [Full Text] [PDF]

J. P. Balhoff and G. A. Wray
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites
PNAS, June 14, 2005; 102(24): 8591 - 8596.
[Abstract] [Full Text] [PDF]

Z. Zhu, J. Shendure, and G. M. Church
Discovering functional transcription-factor combinations in the human cell cycle
Genome Res., June 1, 2005; 15(6): 848 - 855.
[Abstract] [Full Text] [PDF]

S. Istrail and E. H. Davidson
Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code
PNAS, April 5, 2005; 102(14): 4954 - 4959.
[Abstract] [Full Text] [PDF]

T. A. Down and T. J. P. Hubbard
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
Nucleic Acids Res., March 10, 2005; 33(5): 1445 - 1453.
[Abstract] [Full Text] [PDF]

S. Hooshangi, S. Thiberge, and R. Weiss
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
PNAS, March 8, 2005; 102(10): 3581 - 3586.
[Abstract] [Full Text] [PDF]

B. Pulendran
Variegation of the Immune Response with Dendritic Cells and Pathogen Recognition Receptors
J. Immunol., March 1, 2005; 174(5): 2457 - 2465.
[Abstract] [Full Text] [PDF]

J.-Y. Lee, S. F. Baum, J. Alvarez, A. Patel, D. H. Chitwood, and J. L. Bowman
Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis
PLANT CELL, January 1, 2005; 17(1): 25 - 36.
[Abstract] [Full Text] [PDF]

G. P. Wagner, C. Fried, S. J. Prohaska, and P. F. Stadler
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests
Mol. Biol. Evol., November 1, 2004; 21(11): 2116 - 2121.
[Abstract] [Full Text] [PDF]

S. MacArthur and J. F. Y. Brookfield
Expected Rates and Modes of Evolution of Enhancer Sequences
Mol. Biol. Evol., June 1, 2004; 21(6): 1064 - 1073.
[Abstract] [Full Text] [PDF]

G. Kreiman
Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
Nucleic Acids Res., May 20, 2004; 32(9): 2889 - 2900.
[Abstract] [Full Text] [PDF]

H. Wang, L. V. Caruso, A. B. Downie, and S. E. Perry
The Embryo MADS Domain Protein AGAMOUS-Like 15 Directly Regulates Expression of a Gene Encoding an Enzyme Involved in Gibberellin Metabolism
PLANT CELL, May 1, 2004; 16(5): 1206 - 1219.
[Abstract] [Full Text] [PDF]

J. Goutsias and S. Kim
A Nonlinear Discrete Dynamical Model for Transcriptional Regulation: Construction and Properties
Biophys. J., April 1, 2004; 86(4): 1922 - 1945.
[Abstract] [Full Text] [PDF]

R. E. Ward and J. B. German
Understanding Milk's Bioactive Components: A Goal for the Genomics Toolbox
J. Nutr., April 1, 2004; 134(4): 962S - 967S.
[Abstract] [Full Text] [PDF]

J.-A. Mas, E. Garcia-Zaragoza, and M. Cervera
Two Functionally Identical Modular Enhancers in Drosophila Troponin T Gene Establish the Correct Protein Levels in Different Muscle Types
Mol. Biol. Cell, April 1, 2004; 15(4): 1931 - 1945.
[Abstract] [Full Text] [PDF]

M.-C. Marin, J.-R. Rodriguez, and A. Ferrus
Transcription of Drosophila Troponin I Gene Is Regulated by Two Conserved, Functionally Identical, Synergistic Elements
Mol. Biol. Cell, March 1, 2004; 15(3): 1185 - 1196.
[Abstract] [Full Text] [PDF]

J. Phinchongsakuldit, S. MacArthur, and J. F. Y. Brookfield
Evolution of Developmental Genes: Molecular Microevolution of Enhancer Sequences at the Ubx Locus in Drosophila and Its Impact on Developmental Phenotypes
Mol. Biol. Evol., February 1, 2004; 21(2): 348 - 363.
[Abstract] [Full Text] [PDF]

R. J. P. van Berlo, E. P. van Someren, and M. J. T. Reinders
Studying the Conditions for Learning Dynamic Bayesian Networks to Discover Genetic Regulatory Networks
SIMULATION, December 1, 2003; 79(12): 689 - 702.
[Abstract] [PDF]

A. J. Poustka, D. Groth, S. Hennig, S. Thamm, A. Cameron, A. Beck, R. Reinhardt, R. Herwig, G. Panopoulou, and H. Lehrach
Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters
Genome Res., December 1, 2003; 13(12): 2736 - 2746.
[Abstract] [Full Text] [PDF]

D. E. Zak, G. E. Gonye, J. S. Schwaber, and F. J. Doyle III
Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network
Genome Res., November 1, 2003; 13(11): 2396 - 2405.
[Abstract] [Full Text] [PDF]

A. F. M. MOORMAN and V. M. CHRISTOFFELS
Cardiac Chamber Formation: Development, Genes, and Evolution
Physiol Rev, October 1, 2003; 83(4): 1223 - 1267.
[Abstract] [Full Text] [PDF]

I. Shmulevich, H. Lahdesmaki, E. R. Dougherty, J. Astola, and W. Zhang
The role of certain Post classes in Boolean network models of genetic networks
PNAS, September 16, 2003; 100(19): 10734 - 10739.
[Abstract] [Full Text] [PDF]

G. A. Wray, M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano
The Evolution of Transcriptional Regulation in Eukaryotes
Mol. Biol. Evol., September 1, 2003; 20(9): 1377 - 1419.
[Abstract] [Full Text] [PDF]

M. C. Frith, M. C. Li, and Z. Weng
Cluster-Buster: finding dense clusters of motifs in DNA sequences
Nucleic Acids Res., July 1, 2003; 31(13): 3666 - 3668.
[Abstract] [Full Text] [PDF]

F. J. Isaacs, J. Hasty, C. R. Cantor, and J. J. Collins
Prediction and measurement of an autoregulatory genetic module
PNAS, June 24, 2003; 100(13): 7714 - 7719.
[Abstract]

				G. Tuteja, S. T. Jensen, P. White, and K. H. Kaestner Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site Nucleic Acids Res., July 1, 2008; 36(12): 4149 - 4157. [Abstract] [Full Text] [PDF]

				T. H. Cheung, K. K. B. Barthel, Y. L. Kwan, and X. Liu Identifying pattern-defined regulatory islands in mammalian genomes PNAS, June 12, 2007; 104(24): 10116 - 10121. [Abstract] [Full Text] [PDF]

				J. S. Mattick A new paradigm for developmental biology J. Exp. Biol., May 1, 2007; 210(9): 1526 - 1547. [Abstract] [Full Text] [PDF]

				G. Zhao, L. A. Schriefer, and G. D. Stormo Identification of muscle-specific regulatory modules in Caenorhabditis elegans Genome Res., March 1, 2007; 17(3): 348 - 357. [Abstract] [Full Text] [PDF]

				C. W. Hay and K. Docherty Comparative Analysis of Insulin Gene Promoters: Implications for Diabetes Research Diabetes, December 1, 2006; 55(12): 3201 - 3213. [Abstract] [Full Text] [PDF]

				S. Pasquet, F. Naye, C. Faucheux, O. Bronchain, A. Chesneau, P. Thiebaud, and N. Theze Transcription Enhancer Factor-1-dependent Expression of the {alpha}-Tropomyosin Gene in the Three Muscle Cell Types J. Biol. Chem., November 10, 2006; 281(45): 34406 - 34420. [Abstract] [Full Text] [PDF]

				X. Yu, K. Suzuki, Y. Wang, A. Gupta, R. Jin, M.-C. Orgebin-Crist, and R. Matusik The Role of Forkhead Box A2 to Restrict Androgen-Regulated Gene Expression of Lipocalin 5 in the Mouse Epididymis Mol. Endocrinol., October 1, 2006; 20(10): 2418 - 2431. [Abstract] [Full Text] [PDF]

				G. K. McEwen, A. Woolfe, D. Goode, T. Vavouri, H. Callaway, and G. Elgar Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Genome Res., April 1, 2006; 16(4): 451 - 465. [Abstract] [Full Text] [PDF]

				X. Gan, A. W.-C. Liew, and H. Yan Microarray missing data imputation based on a set theoretic framework and biological knowledge Nucleic Acids Res., March 20, 2006; 34(5): 1608 - 1619. [Abstract] [Full Text] [PDF]

				I. Abnizova and W. R. Gilks Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes Brief Bioinform, March 1, 2006; 7(1): 48 - 54. [Abstract] [Full Text] [PDF]

				F. M. Harold Molecules into Cells: Specifying Spatial Architecture Microbiol. Mol. Biol. Rev., December 1, 2005; 69(4): 544 - 564. [Abstract] [Full Text] [PDF]

				R. A. Cameron, S. H. Chow, K. Berney, T.-Y. Chiu, Q.-A. Yuan, A. Kramer, A. Helguero, A. Ransick, M. Yun, and E. H. Davidson An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules PNAS, August 16, 2005; 102(33): 11769 - 11774. [Abstract] [Full Text] [PDF]

				G. M. Cooper, E. A. Stone, G. Asimenos, NISC Comparative Sequencing Program, E. D. Green, S. Batzoglou, and A. Sidow Distribution and intensity of constraint in mammalian genomic sequence Genome Res., July 1, 2005; 15(7): 901 - 913. [Abstract] [Full Text] [PDF]

				A. G. Jegga, A. Gupta, S. Gowrisankar, M. A. Deshmukh, S. Connolly, K. Finley, and B. J. Aronow CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes Nucleic Acids Res., July 1, 2005; 33(suppl_2): W408 - W411. [Abstract] [Full Text] [PDF]

				J. P. Balhoff and G. A. Wray Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites PNAS, June 14, 2005; 102(24): 8591 - 8596. [Abstract] [Full Text] [PDF]

				Z. Zhu, J. Shendure, and G. M. Church Discovering functional transcription-factor combinations in the human cell cycle Genome Res., June 1, 2005; 15(6): 848 - 855. [Abstract] [Full Text] [PDF]

				S. Istrail and E. H. Davidson Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code PNAS, April 5, 2005; 102(14): 4954 - 4959. [Abstract] [Full Text] [PDF]

				T. A. Down and T. J. P. Hubbard NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence Nucleic Acids Res., March 10, 2005; 33(5): 1445 - 1453. [Abstract] [Full Text] [PDF]

				S. Hooshangi, S. Thiberge, and R. Weiss Ultrasensitivity and noise propagation in a synthetic transcriptional cascade PNAS, March 8, 2005; 102(10): 3581 - 3586. [Abstract] [Full Text] [PDF]

				B. Pulendran Variegation of the Immune Response with Dendritic Cells and Pathogen Recognition Receptors J. Immunol., March 1, 2005; 174(5): 2457 - 2465. [Abstract] [Full Text] [PDF]

				J.-Y. Lee, S. F. Baum, J. Alvarez, A. Patel, D. H. Chitwood, and J. L. Bowman Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis PLANT CELL, January 1, 2005; 17(1): 25 - 36. [Abstract] [Full Text] [PDF]

				G. P. Wagner, C. Fried, S. J. Prohaska, and P. F. Stadler Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests Mol. Biol. Evol., November 1, 2004; 21(11): 2116 - 2121. [Abstract] [Full Text] [PDF]

				S. MacArthur and J. F. Y. Brookfield Expected Rates and Modes of Evolution of Enhancer Sequences Mol. Biol. Evol., June 1, 2004; 21(6): 1064 - 1073. [Abstract] [Full Text] [PDF]

				G. Kreiman Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes Nucleic Acids Res., May 20, 2004; 32(9): 2889 - 2900. [Abstract] [Full Text] [PDF]

				H. Wang, L. V. Caruso, A. B. Downie, and S. E. Perry The Embryo MADS Domain Protein AGAMOUS-Like 15 Directly Regulates Expression of a Gene Encoding an Enzyme Involved in Gibberellin Metabolism PLANT CELL, May 1, 2004; 16(5): 1206 - 1219. [Abstract] [Full Text] [PDF]

				J. Goutsias and S. Kim A Nonlinear Discrete Dynamical Model for Transcriptional Regulation: Construction and Properties Biophys. J., April 1, 2004; 86(4): 1922 - 1945. [Abstract] [Full Text] [PDF]

				R. E. Ward and J. B. German Understanding Milk's Bioactive Components: A Goal for the Genomics Toolbox J. Nutr., April 1, 2004; 134(4): 962S - 967S. [Abstract] [Full Text] [PDF]

				J.-A. Mas, E. Garcia-Zaragoza, and M. Cervera Two Functionally Identical Modular Enhancers in Drosophila Troponin T Gene Establish the Correct Protein Levels in Different Muscle Types Mol. Biol. Cell, April 1, 2004; 15(4): 1931 - 1945. [Abstract] [Full Text] [PDF]

				M.-C. Marin, J.-R. Rodriguez, and A. Ferrus Transcription of Drosophila Troponin I Gene Is Regulated by Two Conserved, Functionally Identical, Synergistic Elements Mol. Biol. Cell, March 1, 2004; 15(3): 1185 - 1196. [Abstract] [Full Text] [PDF]

				J. Phinchongsakuldit, S. MacArthur, and J. F. Y. Brookfield Evolution of Developmental Genes: Molecular Microevolution of Enhancer Sequences at the Ubx Locus in Drosophila and Its Impact on Developmental Phenotypes Mol. Biol. Evol., February 1, 2004; 21(2): 348 - 363. [Abstract] [Full Text] [PDF]