-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
DOI 10.1093/bioinformatics/bti263
-
Abascal F, Zardoya R et al (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics (Oxford, England) 21(9):2104-2105 (Pubitemid 40668057)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
56549119570
-
Turning a hobby into a job: How duplicated genes find new functions
-
DOI 10.1038/nrg2482, PII NRG2482
-
Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9(12):938-950 (Pubitemid 352719432)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.12
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, K.H.2
-
3
-
-
4544254403
-
Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors
-
DOI 10.1073/pnas.0405310101
-
Erbel-Sieler C, Dudley C et al (2004) Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors. Proc Natl Acad Sci USA 101(37):13648-13653 (Pubitemid 39238457)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.37
, pp. 13648-13653
-
-
Erbel-Sieler, C.1
Dudley, C.2
Zhou, Y.3
Wu, X.4
Estill, S.J.5
Han, T.6
Diaz-Arrastia, R.7
Brunskill, E.W.8
Potter, S.S.9
McKnight, S.L.10
-
4
-
-
68949172534
-
The aryl hydrocarbon receptor in immunity
-
Esser C, Rannug A et al (2009) The aryl hydrocarbon receptor in immunity. Trends Immunol 30(9):447-454
-
(2009)
Trends Immunol
, vol.30
, Issue.9
, pp. 447-454
-
-
Esser, C.1
Rannug, A.2
-
5
-
-
0942298565
-
Signal transduction by heme-containing PAS-domain proteins
-
DOI 10.1152/japplphysiol.00941.2003
-
Gilles-Gonzalez MA, Gonzalez G (2004) Signal transduction by heme-containing PAS-domain proteins. J Appl Physiol 96(2):774-783 (Pubitemid 38140186)
-
(2004)
Journal of Applied Physiology
, vol.96
, Issue.2
, pp. 774-783
-
-
Gilles-Gonzalez, M.-A.1
Gonzalez, G.2
-
6
-
-
0041029974
-
Light-independent role of CRY1 and CRY2 in the mammalian circadian clock
-
New York, NY
-
Griffin EA Jr, Staknis D et al (1999) Light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Science (New York, NY) 286(5440):768-771
-
(1999)
Science
, vol.286
, Issue.5440
, pp. 768-771
-
-
Griffin Jr., E.A.1
Staknis, D.2
-
7
-
-
0032728408
-
Statistical methods for testing functional divergence after gene duplication
-
Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16(12):1664-1674
-
(1999)
Mol Biol Evol
, vol.16
, Issue.12
, pp. 1664-1674
-
-
Gu, X.1
-
8
-
-
0035061686
-
Maximum-likelihood approach for gene family evolution under functional divergence
-
Gu X (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 18(4):453-464
-
(2001)
Mol Biol Evol
, vol.18
, Issue.4
, pp. 453-464
-
-
Gu, X.1
-
9
-
-
0036205440
-
DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family
-
Gu X, Vander Velden K (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics (Oxford, England) 18(3):500-501 (Pubitemid 34284959)
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 500-501
-
-
Gu, X.1
Velden, K.V.2
-
10
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696-704 (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
11
-
-
66049128566
-
Distinguishing among evolutionary models for the maintenance of gene duplicates
-
Hahn MW (2009) Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered 100(5):605-617
-
(2009)
J Hered
, vol.100
, Issue.5
, pp. 605-617
-
-
Hahn, M.W.1
-
12
-
-
33748488877
-
Unexpected diversity of aryl hydrocarbon receptors in non-mammalian vertebrates: Insights from comparative genomics
-
DOI 10.1002/jez.323
-
Hahn ME, Karchner SI et al (2006) Unexpected diversity of aryl hydrocarbon receptors in non-mammalian vertebrates: insights from comparative genomics. J Exp Zool A Comp Exp Biol 305(9):693-706 (Pubitemid 44358297)
-
(2006)
Journal of Experimental Zoology Part A: Comparative Experimental Biology
, vol.305
, Issue.9
, pp. 693-706
-
-
Hahn, M.E.1
Karchner, S.I.2
Evans, B.R.3
Franks, D.G.4
Merson, R.R.5
Lapseritis, J.M.6
-
14
-
-
77949601825
-
CD-HIT Suite: A web server for clustering and comparing biological sequences
-
Oxford, England
-
Huang Y, Niu B et al (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics (Oxford, England) 26(5):680-682
-
(2010)
Bioinformatics
, vol.26
, Issue.5
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
-
15
-
-
58249118050
-
Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis
-
Hughes DA, Jastroch M et al (2009) Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis. BMC Evol Biol 9:4
-
(2009)
BMC Evol Biol
, vol.9
, pp. 4
-
-
Hughes, D.A.1
Jastroch, M.2
-
17
-
-
0033597904
-
mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop
-
DOI 10.1016/S0092-8674(00)81014-4
-
Kume K, Zylka MJ et al (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98(2):193-205 (Pubitemid 29344907)
-
(1999)
Cell
, vol.98
, Issue.2
, pp. 193-205
-
-
Kume, K.1
Zylka, M.J.2
Sriram, S.3
Shearman, L.P.4
Weaver, D.R.5
Jin, X.6
Maywood, E.S.7
Hastings, M.H.8
Reppert, S.M.9
-
18
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
DOI 10.1093/bioinformatics/btm404
-
Larkin MA, Blackshields G et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 23(21):2947-2948 (Pubitemid 350162903)
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
Mcgettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
19
-
-
84857506751
-
Single-minded and the evolution of the ventral midline in arthropods
-
Linne V, Eriksson BJ et al (2012) Single-minded and the evolution of the ventral midline in arthropods. Dev Biol 364(1):66-76
-
(2012)
Dev Biol
, vol.364
, Issue.1
, pp. 66-76
-
-
Linne, V.1
Eriksson, B.J.2
-
20
-
-
26244444380
-
From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD)
-
DOI 10.1002/bies.20293
-
Meyer A, Van de Peer Y (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27(9):937-945 (Pubitemid 41415948)
-
(2005)
BioEssays
, vol.27
, Issue.9
, pp. 937-945
-
-
Meyer, A.1
Van De, P.Y.2
-
21
-
-
77958051307
-
Evolution and functional divergence of the anoctamin family of membrane proteins
-
Milenkovic VM, Brockmann M et al (2010) Evolution and functional divergence of the anoctamin family of membrane proteins. BMC Evol Biol 10:319
-
(2010)
BMC Evol Biol
, vol.10
, pp. 319
-
-
Milenkovic, V.M.1
Brockmann, M.2
-
22
-
-
70349777587
-
Structure and signaling mechanism of Per-ARNT-Sim domains
-
Moglich A, Ayers RA et al (2009) Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17(10):1282-1294
-
(2009)
Structure
, vol.17
, Issue.10
, pp. 1282-1294
-
-
Moglich, A.1
Ayers, R.A.2
-
23
-
-
24644486449
-
Timing and mechanism of ancient vertebrate genome duplications - The adventure of a hypothesis
-
DOI 10.1016/j.tig.2005.08.004, PII S016895250500226X
-
Panopoulou G, Poustka AJ (2005) Timing and mechanism of ancient vertebrate genome duplications - the adventure of a hypothesis. Trends Genet 21(10):559-567 (Pubitemid 41278461)
-
(2005)
Trends in Genetics
, vol.21
, Issue.10
, pp. 559-567
-
-
Panopoulou, G.1
Poustka, A.J.2
-
24
-
-
21444461075
-
Disruption of a brain transcription factor, NPAS3, is associated with schizophrenia amid learning disability
-
DOI 10.1002/ajmg.b.30204
-
Pickard BS, Malloy MP et al (2005) Disruption of a brain transcription factor, NPAS3, is associated with schizophrenia and learning disability. Am J Med Genet B Neuropsychiatr Genet 136B(1):26-32 (Pubitemid 40917524)
-
(2005)
American Journal of Medical Genetics - Neuropsychiatric Genetics
, vol.136 B
, Issue.1
, pp. 26-32
-
-
Pickard, B.S.1
Malloy, M.P.2
Porteous, D.J.3
Blackwood, D.H.R.4
Muir, W.J.5
-
25
-
-
80051922481
-
The neuronal PAS domain protein 4 (Npas4) is required for new and reactivated fear memories
-
Ploski JE, Monsey MS et al (2011) The neuronal PAS domain protein 4 (Npas4) is required for new and reactivated fear memories. PLoS ONE 6(8):e23760
-
(2011)
PLoS ONE
, vol.6
, Issue.8
-
-
Ploski, J.E.1
Monsey, M.S.2
-
26
-
-
0037178787
-
The orphan nuclear receptor REV-ERBapha controls circadian transcription within the positive limb of the mammalian circadian oscillator
-
DOI 10.1016/S0092-8674(02)00825-5
-
Preitner N, Damiola F et al (2002) The orphan nuclear receptor REVERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110(2):251-260 (Pubitemid 34876552)
-
(2002)
Cell
, vol.110
, Issue.2
, pp. 251-260
-
-
Preitner, N.1
Damiola, F.2
Luis-Lopez-Molina3
Zakany, J.4
Duboule, D.5
Albrecht, U.6
Schibler, U.7
-
27
-
-
34447300950
-
Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
-
DOI 10.1126/science.1139158
-
Putnam NH, Srivastava M et al (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science (New York, NY) 317(5834):86-94 (Pubitemid 47056460)
-
(2007)
Science
, vol.317
, Issue.5834
, pp. 86-94
-
-
Putnam, N.H.1
Srivastava, M.2
Hellsten, U.3
Dirks, B.4
Chapman, J.5
Salamov, A.6
Terry, A.7
Shapiro, H.8
Lindquist, E.9
Kapitonov, V.V.10
Jurka, J.11
Genikhovich, G.12
Grigoriev, I.V.13
Lucas, S.M.14
Steele, R.E.15
Finnerty, J.R.16
Technau, U.17
Martindale, M.Q.18
Rokhsar, D.S.19
-
28
-
-
0035919618
-
NPAS2: An analog of clock operative in the mammalian forebrain
-
DOI 10.1126/science.1060699
-
Reick M, Garcia JA et al (2001) NPAS2: an analog of clock operative in the mammalian forebrain. Science (New York, NY) 293(5529):506-509 (Pubitemid 32679079)
-
(2001)
Science
, vol.293
, Issue.5529
, pp. 506-509
-
-
Reick, M.1
Garcia, J.A.2
Dudley, C.3
McKnight, S.L.4
-
29
-
-
77958463322
-
Light entrained rhythmic gene expression in the sea anemone Nematostella vectensis: The evolution of the animal circadian clock
-
Reitzel AM, Behrendt L et al (2010) Light entrained rhythmic gene expression in the sea anemone Nematostella vectensis: the evolution of the animal circadian clock. PLoS ONE 5(9):e12805
-
(2010)
PLoS ONE
, vol.5
, Issue.9
-
-
Reitzel, A.M.1
Behrendt, L.2
-
30
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England) 19(12):1572-1574 (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
31
-
-
79957440961
-
Molecular evolution of the metazoan PHD-HIF oxygen-sensing system
-
Rytkonen KT, Williams TA et al (2011) Molecular evolution of the metazoan PHD-HIF oxygen-sensing system. Mol Biol Evol 28(6):1913-1926
-
(2011)
Mol Biol Evol
, vol.28
, Issue.6
, pp. 1913-1926
-
-
Rytkonen, K.T.1
Williams, T.A.2
-
32
-
-
84865279751
-
Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites
-
Sailsbery JK, Dean RA (2012) Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites. BMC Evol Biol 12:154
-
(2012)
BMC Evol Biol
, vol.12
, pp. 154
-
-
Sailsbery, J.K.1
Dean, R.A.2
-
33
-
-
66549106623
-
The aryl hydrocarbon receptor: A perspective on potential roles in the immune system
-
Stevens EA, Mezrich JD et al (2009) The aryl hydrocarbon receptor: a perspective on potential roles in the immune system. Immunology 127(3):299-311
-
(2009)
Immunology
, vol.127
, Issue.3
, pp. 299-311
-
-
Stevens, E.A.1
Mezrich, J.D.2
-
34
-
-
33747847779
-
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama M, Torrents D et al (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34(Web Server issue):W609-W612
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.WEB SERVER ISSUE
-
-
Suyama, M.1
Torrents, D.2
-
35
-
-
34547781750
-
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
-
DOI 10.1093/molbev/msm092
-
Tamura KDJ, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
37
-
-
78149454649
-
Evolutionary mode and functional divergence of vertebrate NMDA receptor subunit 2 genes
-
Teng H, Cai W et al (2010) Evolutionary mode and functional divergence of vertebrate NMDA receptor subunit 2 genes. PLoS ONE 5(10):e13342
-
(2010)
PLoS ONE
, vol.5
, Issue.10
-
-
Teng, H.1
Cai, W.2
-
39
-
-
78650754129
-
Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (rayfinned fish)
-
Yan J, Cai Z (2010) Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (rayfinned fish). PLoS ONE 5(12):e14276
-
(2010)
PLoS ONE
, vol.5
, Issue.12
-
-
Yan, J.1
Cai, Z.2
-
40
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.1
-
41
-
-
78650502609
-
Molecular selection and functional divergence of HIF-alpha proteins in vertebrates
-
Zhang X, Wang M et al (2010) Molecular selection and functional divergence of HIF-alpha proteins in vertebrates. Genetica 138(11-12):1241-1250
-
(2010)
Genetica
, vol.138
, Issue.11-12
, pp. 1241-1250
-
-
Zhang, X.1
Wang, M.2
-
42
-
-
84863743043
-
Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events
-
Zhou M, Yan J et al (2012) Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events. PLoS ONE 7(7):e40649
-
(2012)
PLoS ONE
, vol.7
, Issue.7
-
-
Zhou, M.1
Yan, J.2
|