-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mo Biol. 215:403-410.
-
(1990)
J Mo Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0030986188
-
The hardwiring of development: Organization and function of genomic regulatory systems
-
Arnone MI, Davidson EH. 1997. The hardwiring of development: organization and function of genomic regulatory systems. Dev Camb Engl. 124:1851-1864.
-
(1997)
Dev Camb Engl.
, vol.124
, pp. 1851-1864
-
-
Arnone, M.I.1
Davidson, E.H.2
-
3
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. 2009. Diversity and complexity in DNA recognition by transcription factors. Science 324: 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
4
-
-
79956293316
-
Extensive DNA-binding specificity divergence of a conserved transcription regulator
-
Baker CR, Tuch BB, Johnson AD. 2011. Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc Natl Acad Sci U S A. 108:7493-7498.
-
(2011)
Proc Natl Acad Sci U S A.
, vol.108
, pp. 7493-7498
-
-
Baker, C.R.1
Tuch, B.B.2
Johnson, A.D.3
-
5
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger MF, Badis G, Gehrke AR, et al. 2008. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-1276.
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
-
6
-
-
59949083631
-
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
-
Berger MF, Bulyk ML. 2009. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc. 4:393-411.
-
(2009)
Nat Protoc.
, vol.4
, pp. 393-411
-
-
Berger, M.F.1
Bulyk, M.L.2
-
7
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. 2006. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol. 24:1429-1435.
-
(2006)
Nat Biotechnol.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep, P.W.5
Bulyk, M.L.6
-
8
-
-
80051991355
-
Evolution of a derived proteinprotein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation
-
Brayer KJ, Lynch VJ, Wagner GP. 2011. Evolution of a derived proteinprotein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation. Proc Natl Acad Sci U S A. 108:E414-E420.
-
(2011)
Proc Natl Acad Sci U S A.
, vol.108
, pp. E414-E420
-
-
Brayer, K.J.1
Lynch, V.J.2
Wagner, G.P.3
-
9
-
-
0015070886
-
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty
-
Britten RJ, Davidson EH. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q Rev Biol. 46:111-138.
-
(1971)
Q Rev Biol.
, vol.46
, pp. 111-138
-
-
Britten, R.J.1
Davidson, E.H.2
-
10
-
-
84857321577
-
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity
-
Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM. 2012. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Dev Camb Engl. 139: 1164-1174.
-
(2012)
Dev Camb Engl.
, vol.139
, pp. 1164-1174
-
-
Busser, B.W.1
Shokri, L.2
Jaeger, S.A.3
Gisselbrecht, S.S.4
Singhania, A.5
Berger, M.F.6
Zhou, B.7
Bulyk, M.L.8
Michelson, A.M.9
-
11
-
-
58149199570
-
SpBase: The sea urchin genome database and web site
-
Cameron RA, Samanta M, Yuan A, He D, Davidson E. 2009. SpBase: the sea urchin genome database and web site. Nucleic Acids Res. 37: D750-D754.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D750-D754
-
-
Cameron, R.A.1
Samanta, M.2
Yuan, A.3
He, D.4
Davidson, E.5
-
13
-
-
84908282773
-
A method for microinjection of Patiria minata Zygotes
-
Cheatle Jarvela AM, Hinman V. 2014. A method for microinjection of Patiria minata Zygotes. J Vis Exp. doi:10. 3791/51913.
-
(2014)
J Vis Exp.
-
-
Cheatle Jarvela, A.M.1
Hinman, V.2
-
14
-
-
77953751851
-
Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function
-
Chen L, Zhao P, Wells L, Amemiya CT, Condie BG, Manley NR. 2010. Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function. Proc Natl Acad Sci U S A. 107:10555-10560.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 10555-10560
-
-
Chen, L.1
Zhao, P.2
Wells, L.3
Amemiya, C.T.4
Condie, B.G.5
Manley, N.R.6
-
15
-
-
0034778407
-
Determinants of T box protein specificity
-
Conlon FL, Fairclough L, Price BM, Casey ES, Smith JC. 2001. Determinants of T box protein specificity. Dev Camb Engl. 128: 3749-3758.
-
(2001)
Dev Camb Engl
, vol.128
, pp. 3749-3758
-
-
Conlon, F.L.1
Fairclough, L.2
Price, B.M.3
Casey, E.S.4
Smith, J.C.5
-
16
-
-
0034888362
-
Ske-T, a T-box gene expressed in the skeletogenic mesenchyme lineage of the sea urchin embryo
-
Croce J, Lhomond G, Lozano JC, Gache C. 2001. ske-T, a T-box gene expressed in the skeletogenic mesenchyme lineage of the sea urchin embryo. Mech Dev. 107:159-162.
-
(2001)
Mech Dev.
, vol.107
, pp. 159-162
-
-
Croce, J.1
Lhomond, G.2
Lozano, J.C.3
Gache, C.4
-
17
-
-
18744364157
-
T-brain homologue (HpTb) is involved in the archenteron induction signals of micromere descendant cells in the sea urchin embryo
-
Fuchikami T, Mitsunaga-Nakatsubo K, Amemiya S, Hosomi T, Watanabe T, Kurokawa D, Kataoka M, Harada Y, Satoh N, Kusunoki S, et al. 2002. T-brain homologue (HpTb) is involved in the archenteron induction signals of micromere descendant cells in the sea urchin embryo. Dev Camb Engl. 129:5205-5216.
-
(2002)
Dev Camb Engl.
, vol.129
, pp. 5205-5216
-
-
Fuchikami, T.1
Mitsunaga-Nakatsubo, K.2
Amemiya, S.3
Hosomi, T.4
Watanabe, T.5
Kurokawa, D.6
Kataoka, M.7
Harada, Y.8
Satoh, N.9
Kusunoki, S.10
-
18
-
-
0037148774
-
Evolution of a transcriptional repression domain in an insect Hox protein
-
Galant R, Carroll SB. 2002. Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415:910-913.
-
(2002)
Nature
, vol.415
, pp. 910-913
-
-
Galant, R.1
Carroll, S.B.2
-
19
-
-
83755196322
-
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
-
Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. 2011. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 12:R125.
-
(2011)
Genome Biol
, vol.12
, pp. R125
-
-
Gordân, R.1
Murphy, K.F.2
McCord, R.P.3
Zhu, C.4
Vedenko, A.5
Bulyk, M.L.6
-
20
-
-
0028944665
-
Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila
-
Halder G, Callaerts P, Gehring WJ. 1995. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267: 1788-1792.
-
(1995)
Science
, vol.267
, pp. 1788-1792
-
-
Halder, G.1
Callaerts, P.2
Gehring, W.J.3
-
21
-
-
0024320441
-
DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9
-
Hanes SD, Brent R. 1989. DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9. Cell 57: 1275-1283.
-
(1989)
Cell
, vol.57
, pp. 1275-1283
-
-
Hanes, S.D.1
Brent, R.2
-
22
-
-
0028206856
-
Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen
-
Hanes SD, Riddihough G, Ish-Horowicz D, Brent R. 1994. Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen. Mol Cell Biol. 14:3364-3375.
-
(1994)
Mol Cell Biol.
, vol.14
, pp. 3364-3375
-
-
Hanes, S.D.1
Riddihough, G.2
Ish-Horowicz, D.3
Brent, R.4
-
23
-
-
33751381461
-
TimeTree: A public knowledge-base of divergence times among organisms
-
Hedges SB, Dudley J, Kumar S. 2006. TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
24
-
-
37649014659
-
Evolutionary plasticity of developmental gene regulatory network architecture
-
Hinman VF, Davidson EH. 2007. Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A. 104:19404-19409.
-
(2007)
Proc Natl Acad Sci U S A.
, vol.104
, pp. 19404-19409
-
-
Hinman, V.F.1
Davidson, E.H.2
-
25
-
-
0344824373
-
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
-
Hinman VF, Nguyen AT, Cameron RA, Davidson EH. 2003. Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. Proc Natl Acad Sci U S A. 100:13356-13361.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 13356-13361
-
-
Hinman, V.F.1
Nguyen, A.T.2
Cameron, R.A.3
Davidson, E.H.4
-
26
-
-
0142026145
-
Expression and function of a starfish Otx ortholog, AmOtx: A conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa
-
Hinman VF, Nguyen AT, Davidson EH. 2003. Expression and function of a starfish Otx ortholog, AmOtx: A conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa. Mech Dev. 120:1165-1176.
-
(2003)
Mech Dev.
, vol.120
, pp. 1165-1176
-
-
Hinman, V.F.1
Nguyen, A.T.2
Davidson, E.H.3
-
27
-
-
36549025847
-
Caught in the evolutionary act: Precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins
-
Hinman VF, Nguyen A, Davidson EH. 2007. Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. Dev Biol. 312:584-595.
-
(2007)
Dev Biol.
, vol.312
, pp. 584-595
-
-
Hinman, V.F.1
Nguyen, A.2
Davidson, E.H.3
-
28
-
-
0037103389
-
Evolution of developmental functions by the Eomesodermin, T-brain-1, Tbx21 subfamily of T-box genes: Insights from amphioxus
-
Horton AC, Gibson-Brown JJ. 2002. Evolution of developmental functions by the Eomesodermin, T-brain-1, Tbx21 subfamily of T-box genes: insights from amphioxus. J Exp Zool. 294:112-121.
-
(2002)
J Exp Zool.
, vol.294
, pp. 112-121
-
-
Horton, A.C.1
Gibson-Brown, J.J.2
-
29
-
-
33751550431
-
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus
-
Howard-Ashby M, Materna SC, Brown CT, Chen L, Cameron RA, Davidson EH. 2006. Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. Dev Biol. 300:90-107.
-
(2006)
Dev Biol.
, vol.300
, pp. 90-107
-
-
Howard-Ashby, M.1
Materna, S.C.2
Brown, C.T.3
Chen, L.4
Cameron, R.A.5
Davidson, E.H.6
-
30
-
-
70349918009
-
Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis
-
Jovelin R. 2009. Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis. Mol Biol Evol. 26: 2373-2386.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 2373-2386
-
-
Jovelin, R.1
-
31
-
-
63849246525
-
Protein structure prediction on theWeb: A case study using the Phyre server
-
Kelley LA, SternbergMJE. 2009. Protein structure prediction on theWeb: A case study using the Phyre server. Nat Protoc. 4:363-371.
-
(2009)
Nat Protoc.
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
32
-
-
84861434537
-
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
-
Kersting AR, Bornberg-Bauer E, Moore AD, Grath S. 2012. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol. 4: 316-329.
-
(2012)
Genome Biol Evol.
, vol.4
, pp. 316-329
-
-
Kersting, A.R.1
Bornberg-Bauer, E.2
Moore, A.D.3
Grath, S.4
-
33
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
34
-
-
81855211081
-
Gene duplication and loss in a MADS box gene transcription factor circuit
-
Lee H-L, Irish VF. 2011. Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol. 28:3367-3380.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 3367-3380
-
-
Lee, H.-L.1
Irish, V.F.2
-
35
-
-
67650497792
-
Nature of the protein universe
-
Levitt M. 2009. Nature of the protein universe. Proc Natl Acad Sci U S A. 106:11079-11084.
-
(2009)
Proc Natl Acad Sci U S A.
, vol.106
, pp. 11079-11084
-
-
Levitt, M.1
-
36
-
-
17144415299
-
Cofactor-interaction motifs and the cooption of a homeotic Hox protein into the segmentation pathway of Drosophila melanogaster
-
Lohr U, Pick L. 2005. Cofactor-interaction motifs and the cooption of a homeotic Hox protein into the segmentation pathway of Drosophila melanogaster. Curr Biol. 15:643-649.
-
(2005)
Curr Biol.
, vol.15
, pp. 643-649
-
-
Lohr, U.1
Pick, L.2
-
37
-
-
83555162573
-
Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB
-
Lynch VJ, May G, Wagner GP. 2011. Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature 480:383-386.
-
(2011)
Nature
, vol.480
, pp. 383-386
-
-
Lynch, V.J.1
May, G.2
Wagner, G.P.3
-
38
-
-
51549097146
-
Resurrecting the role of transcription factor change in developmental evolution
-
Lynch VJ, Wagner GP. 2008. Resurrecting the role of transcription factor change in developmental evolution. Evol Int J Org Evol. 62: 2131-2154.
-
(2008)
Evol Int J Org Evol.
, vol.62
, pp. 2131-2154
-
-
Lynch, V.J.1
Wagner, G.P.2
-
39
-
-
65649111564
-
Conformational stability and DNA binding specificity of the cardiac T-box transcription factor Tbx20
-
Macindoe I, Glockner L, Vukasin P, Stennard FA, Costa MW, Harvey RP, Mackay JP, Sunde M. 2009. Conformational stability and DNA binding specificity of the cardiac T-box transcription factor Tbx20. J Mol Biol. 389:606-618.
-
(2009)
J Mol Biol.
, vol.389
, pp. 606-618
-
-
Macindoe, I.1
Glockner, L.2
Vukasin, P.3
Stennard, F.A.4
Costa, M.W.5
Harvey, R.P.6
Mackay, J.P.7
Sunde, M.8
-
40
-
-
77951204771
-
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos
-
McCauley BS, Weideman EP, Hinman VF. 2010. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Dev Biol. 340:200-208.
-
(2010)
Dev Biol.
, vol.340
, pp. 200-208
-
-
McCauley, B.S.1
Weideman, E.P.2
Hinman, V.F.3
-
41
-
-
0025647969
-
Human Hox-4. 2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae
-
McGinnis N, Kuziora MA, McGinnis W. 1990. Human Hox-4. 2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae. Cell 63:969-976.
-
(1990)
Cell
, vol.63
, pp. 969-976
-
-
McGinnis, N.1
Kuziora, M.A.2
McGinnis, W.3
-
42
-
-
4444299144
-
TOPALi: Software for automatic identification of recombinant sequences within DNA multiple alignments
-
Milne I, Wright F, Rowe G, Marshall DF, Husmeier D, McGuire G. 2004. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20: 1806-1807.
-
(2004)
Bioinformatics
, vol.20
, pp. 1806-1807
-
-
Milne, I.1
Wright, F.2
Rowe, G.3
Marshall, D.F.4
Husmeier, D.5
McGuire, G.6
-
43
-
-
73049167504
-
Teleonomic mechanisms in cellular metabolism, growth, and differentiation
-
Monod J, Jacob F. 1961. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb Symp Quant Biol. 26: 389-401.
-
(1961)
Cold Spring Harb Symp Quant Biol.
, vol.26
, pp. 389-401
-
-
Monod, J.1
Jacob, F.2
-
44
-
-
33749389932
-
Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
-
Mortazavi A, Thompson ECL, Garcia ST, Myers RM, Wold B. 2006. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res. 16:1208-1221.
-
(2006)
Genome Res
, vol.16
, pp. 1208-1221
-
-
Mortazavi, A.1
Thompson, E.C.L.2
Garcia, S.T.3
Myers, R.M.4
Wold, B.5
-
45
-
-
0039706410
-
Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor
-
Muller CW, Herrmann BG. 1997. Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Nature 389:884-888.
-
(1997)
Nature
, vol.389
, pp. 884-888
-
-
Muller, C.W.1
Herrmann, B.G.2
-
46
-
-
84880681583
-
DNAbinding specificity changes in the evolution of forkhead transcription factors
-
Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML. 2013. DNAbinding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci U S A. 110(30):12349-12354.
-
(2013)
Proc Natl Acad Sci U S A.
, vol.110
, Issue.30
, pp. 12349-12354
-
-
Nakagawa, S.1
Gisselbrecht, S.S.2
Rogers, J.M.3
Hartl, D.L.4
Bulyk, M.L.5
-
47
-
-
33645768556
-
Binding-linked protonation of a DNA minor-groove agent
-
Nguyen B, Stanek J, Wilson WD. 2006. Binding-linked protonation of a DNA minor-groove agent. Biophys J. 90:1319-1328.
-
(2006)
Biophys J.
, vol.90
, pp. 1319-1328
-
-
Nguyen, B.1
Stanek, J.2
Wilson, W.D.3
-
48
-
-
0036607107
-
A regulatory gene network that directs micromere specification in the sea urchin embryo
-
Oliveri P, Carrick DM, Davidson EH. 2002. A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev Biol. 246:209-228.
-
(2002)
Dev Biol.
, vol.246
, pp. 209-228
-
-
Oliveri, P.1
Carrick, D.M.2
Davidson, E.H.3
-
50
-
-
79958204355
-
The cisregulatory logic of Hedgehog gradient responses: Key roles for gli binding affinity, competition, and cooperativity
-
Parker DS, White MA, Ramos AI, Cohen BA, Barolo S. 2011. The cisregulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity. Sci Signal. 4:ra38.
-
(2011)
Sci Signal.
, vol.4
, pp. ra38
-
-
Parker, D.S.1
White, M.A.2
Ramos, A.I.3
Cohen, B.A.4
Barolo, S.5
-
51
-
-
84871587536
-
Neuralspecific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
-
Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, et al. 2012. Neuralspecific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev. 26:2802-2816.
-
(2012)
Genes Dev.
, vol.26
, pp. 2802-2816
-
-
Peterson, K.A.1
Nishi, Y.2
Ma, W.3
Vedenko, A.4
Shokri, L.5
Zhang, X.6
McFarlane, M.7
Baizabal, J.M.8
Junker, J.P.9
Van Oudenaarden, A.10
-
52
-
-
83655163777
-
Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships
-
Pisani D, Feuda R, Peterson KJ, Smith AB. 2012. Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships. Mol Phylogenet Evol. 62: 27-34.
-
(2012)
Mol Phylogenet Evol.
, vol.62
, pp. 27-34
-
-
Pisani, D.1
Feuda, R.2
Peterson, K.J.3
Smith, A.B.4
-
53
-
-
0038403827
-
Study of structure-function relationships in human glutamate dehydrogenases reveals novel molecular mechanisms for the regulation of the nerve tissue-specific (GLUD2) isoenzyme
-
Plaitakis A, Spanaki C, Mastorodemos V, Zaganas I. 2003. Study of structure-function relationships in human glutamate dehydrogenases reveals novel molecular mechanisms for the regulation of the nerve tissue-specific (GLUD2) isoenzyme. Neurochem Int. 43: 401-410.
-
(2003)
Neurochem Int.
, vol.43
, pp. 401-410
-
-
Plaitakis, A.1
Spanaki, C.2
Mastorodemos, V.3
Zaganas, I.4
-
55
-
-
84855462918
-
The genomic regulatory control of skeletal morphogenesis in the sea urchin
-
Rafiq K, Cheers MS, Ettensohn CA. 2012. The genomic regulatory control of skeletal morphogenesis in the sea urchin. Dev Camb Engl. 139: 579-590.
-
(2012)
Dev Camb Engl.
, vol.139
, pp. 579-590
-
-
Rafiq, K.1
Cheers, M.S.2
Ettensohn, C.A.3
-
56
-
-
84857230925
-
Experimental approaches to evaluate the contributions of candidate cis-regulatory mutations to phenotypic evolution
-
Rebeiz M, Williams TM. 2011. Experimental approaches to evaluate the contributions of candidate cis-regulatory mutations to phenotypic evolution. Methods Mol Biol. 772:351-375.
-
(2011)
Methods Mol Biol.
, vol.772
, pp. 351-375
-
-
Rebeiz, M.1
Williams, T.M.2
-
57
-
-
0037148839
-
Hox protein mutation and macroevolution of the insect body plan
-
Ronshaugen M, McGinnis N, McGinnis W. 2002. Hox protein mutation and macroevolution of the insect body plan. Nature 415:914-917.
-
(2002)
Nature
, vol.415
, pp. 914-917
-
-
Ronshaugen, M.1
McGinnis, N.2
McGinnis, W.3
-
58
-
-
77952352833
-
Precise temporal control of the eye regulatory gene Pax6 via enhancerbinding site affinity
-
Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL. 2010. Precise temporal control of the eye regulatory gene Pax6 via enhancerbinding site affinity. Genes Dev. 24:980-985.
-
(2010)
Genes Dev.
, vol.24
, pp. 980-985
-
-
Rowan, S.1
Siggers, T.2
Lachke, S.A.3
Yue, Y.4
Bulyk, M.L.5
Maas, R.L.6
-
60
-
-
0032123571
-
Xenopus eomesodermin is expressed in neural differentiation
-
Ryan K, Butler K, Bellefroid E, Gurdon JB. 1998. Xenopus eomesodermin is expressed in neural differentiation. Mech Dev. 75:155-158.
-
(1998)
Mech Dev.
, vol.75
, pp. 155-158
-
-
Ryan, K.1
Butler, K.2
Bellefroid, E.3
Gurdon, J.B.4
-
61
-
-
84860433173
-
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function
-
Sakabe NJ, Aneas I, Shen T, Shokri L, Park S-Y, Bulyk ML, Evans SM, Nobrega MA. 2012. Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Hum Mol Genet. 21:2194-2204.
-
(2012)
Hum Mol Genet.
, vol.21
, pp. 2194-2204
-
-
Sakabe, N.J.1
Aneas, I.2
Shen, T.3
Shokri, L.4
Park, S.-Y.5
Bulyk, M.L.6
Evans, S.M.7
Nobrega, M.A.8
-
63
-
-
80054078476
-
Fast, scalable generation of highquality protein multiple sequence alignments using Clustal Omega
-
Sievers F, Wilm A, Dineen D, et al. 2014. Fast, scalable generation of highquality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 7:539.
-
(2014)
Mol Syst Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
-
64
-
-
0034090257
-
A starfish homolog of mouse T-brain-1 is expressed in the archenteron of Asterina pectinifera embryos: Possible involvement of two T-box genes in starfish gastrulation
-
Shoguchi E, Satoh N, Maruyama YK. 2000. A starfish homolog of mouse T-brain-1 is expressed in the archenteron of Asterina pectinifera embryos: possible involvement of two T-box genes in starfish gastrulation. Dev Growth Differ. 42:61-68.
-
(2000)
Dev Growth Differ.
, vol.42
, pp. 61-68
-
-
Shoguchi, E.1
Satoh, N.2
Maruyama, Y.K.3
-
65
-
-
0035544655
-
Molecular studies of hemichordate development: A key to understanding the evolution of bilateral animals and chordates
-
Tagawa K, Satoh N, Humphreys T. 2001. Molecular studies of hemichordate development: A key to understanding the evolution of bilateral animals and chordates. Evol Dev. 3:443-454.
-
(2001)
Evol Dev.
, vol.3
, pp. 443-454
-
-
Tagawa, K.1
Satoh, N.2
Humphreys, T.3
-
66
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD. 2008. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6:e38.
-
(2008)
PLoS Biol.
, vol.6
, pp. e38
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
67
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
Wang M, Caetano-Anolles G. 2009. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Struct Lond Engl. 1993 17:66-78.
-
(2009)
Struct Lond Engl. 1993
, vol.17
, pp. 66-78
-
-
Wang, M.1
Caetano-Anolles, G.2
-
68
-
-
0037125941
-
Drosophila atonal fully rescues the phenotype of Math1 null mice: New functions evolve in new cellular contexts
-
Wang VY, Hassan BA, Bellen HJ, Zoghbi HY. 2002. Drosophila atonal fully rescues the phenotype of Math1 null mice: new functions evolve in new cellular contexts. Curr Biol. 12:1611-1616.
-
(2002)
Curr Biol.
, vol.12
, pp. 1611-1616
-
-
Wang, V.Y.1
Hassan, B.A.2
Bellen, H.J.3
Zoghbi, H.Y.4
-
69
-
-
4544244485
-
Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx
-
Wang W, Grimmer JF, Van De Water TR, Lufkin T. 2004. Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx. Dev Cell. 7:439-453.
-
(2004)
Dev Cell.
, vol.7
, pp. 439-453
-
-
Wang, W.1
Grimmer, J.F.2
Van De Water, T.R.3
Lufkin, T.4
-
70
-
-
83855163414
-
Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence
-
Wittkopp PJ, Kalay G. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet. 13:59-69.
-
(2012)
Nat Rev Genet.
, vol.13
, pp. 59-69
-
-
Wittkopp, P.J.1
Kalay, G.2
-
71
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 8:206-216.
-
(2007)
Nat Rev Genet.
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
72
-
-
78650805779
-
Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms
-
Yankura KA, Martik ML, Jennings CK, Hinman VF. 2010. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biol. 8:143.
-
(2010)
BMC Biol.
, vol.8
, pp. 143
-
-
Yankura, K.A.1
Martik, M.L.2
Jennings, C.K.3
Hinman, V.F.4
-
73
-
-
9244247603
-
Evolving protein functional diversity in new genes of Drosophila
-
Zhang J, Dean AM, Brunet F, Long M. 2004. Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci U S A. 101: 16246-16250.
-
(2004)
Proc Natl Acad Sci U S A.
, vol.101
, pp. 16246-16250
-
-
Zhang, J.1
Dean, A.M.2
Brunet, F.3
Long, M.4
-
74
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu C, Byers KJRP, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, et al. 2009. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 19:556-566.
-
(2009)
Genome Res
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.R.P.2
McCord, R.P.3
Shi, Z.4
Berger, M.F.5
Newburger, D.E.6
Saulrieta, K.7
Smith, Z.8
Shah, M.V.9
Radhakrishnan, M.10
-
75
-
-
84863338247
-
Differential regulation of mesodermal gene expression by Drosophila cell type-specific forkhead transcription factors
-
Zhu X, Ahmad SM, Aboukhalil A, Busser BW, Kim Y, Tansey TR, Haimovich A, Jeffries N, Bulyk ML, Michelson AM. 2012. Differential regulation of mesodermal gene expression by Drosophila cell type-specific forkhead transcription factors. Dev Camb Engl. 139:1457-1466.
-
(2012)
Dev Camb Engl
, vol.139
, pp. 1457-1466
-
-
Zhu, X.1
Ahmad, S.M.2
Aboukhalil, A.3
Busser, B.W.4
Kim, Y.5
Tansey, T.R.6
Haimovich, A.7
Jeffries, N.8
Bulyk, M.L.9
Michelson, A.M.10
|