-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
3
-
-
33845630758
-
Harnessing the hypoxia-inducible factor in cancer and ischemic disease
-
Brahimi-Horn MC, Pouyssegur J (2007) Harnessing the hypoxia-inducible factor in cancer and ischemic disease. Biochem Pharmacol 73: 450-457.
-
(2007)
Biochem Pharmacol
, vol.73
, pp. 450-457
-
-
Brahimi-Horn, M.C.1
Pouyssegur, J.2
-
4
-
-
0032581277
-
Role of HIF-1alpha in hypoxia-mediated apoptosis, cell proliferation and tumour angiogenesis
-
Carmeliet P, Dor Y, Herbert JM et al (1998) Role of HIF-1alpha in hypoxia-mediated apoptosis, cell proliferation and tumour angiogenesis. Nature 394: 485-490.
-
(1998)
Nature
, vol.394
, pp. 485-490
-
-
Carmeliet, P.1
Dor, Y.2
Herbert, J.M.3
-
5
-
-
0035983324
-
Loss of HIF-2alpha and inhibition of VEGF impair fetal lung maturation, whereas treatment with VEGF prevents fatal respiratory distress in premature mice
-
Compernolle V, Brusselmans K, Acker T et al (2002) Loss of HIF-2alpha and inhibition of VEGF impair fetal lung maturation, whereas treatment with VEGF prevents fatal respiratory distress in premature mice. Nat Med 8: 702-710.
-
(2002)
Nat Med
, vol.8
, pp. 702-710
-
-
Compernolle, V.1
Brusselmans, K.2
Acker, T.3
-
6
-
-
27944461698
-
Hypoxia-inducible factors 1alpha and 2alpha regulate trophoblast differentiation
-
Cowden Dahl KD, Fryer BH, Mack FA et al (2005) Hypoxia-inducible factors 1alpha and 2alpha regulate trophoblast differentiation. Mol Cell Biol 25: 10479-10491.
-
(2005)
Mol Cell Biol
, vol.25
, pp. 10479-10491
-
-
Cowden Dahl, K.D.1
Fryer, B.H.2
Mack, F.A.3
-
7
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5: 113.
-
(2004)
BMC Bioinform
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
8
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB et al (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
-
9
-
-
0016436505
-
Darwinian evolution in the genealogy of haemoglobin
-
Goodman M, Moore GW, Matsuda G (1975) Darwinian evolution in the genealogy of haemoglobin. Nature 253: 603-608.
-
(1975)
Nature
, vol.253
, pp. 603-608
-
-
Goodman, M.1
Moore, G.W.2
Matsuda, G.3
-
10
-
-
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: 1664-1674.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1664-1674
-
-
Gu, X.1
-
11
-
-
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: 453-464.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 453-464
-
-
Gu, X.1
-
12
-
-
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 18: 500-501.
-
(2002)
Bioinformatics
, vol.18
, pp. 500-501
-
-
Gu, X.1
Vander Velden, K.2
-
13
-
-
0031733828
-
Molecular characterization and chromosomal localization of a third α-class hypoxia inducible factor subunit, HIF3α
-
Gu Y-Z, Moran SM, Hogenesch JB et al (1998) Molecular characterization and chromosomal localization of a third α-class hypoxia inducible factor subunit, HIF3α. Gene Expr 7: 205-213.
-
(1998)
Gene Expr
, vol.7
, pp. 205-213
-
-
Gu, Y.-Z.1
Moran, S.M.2
Hogenesch, J.B.3
-
14
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
-
(2003)
Syst Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
15
-
-
27644561755
-
Hypoxia requires notch signaling to maintain the undifferentiated cell state
-
Gustafsson MV, Zheng X, Pereira T et al (2005) Hypoxia requires notch signaling to maintain the undifferentiated cell state. Dev Cell 9: 617-628.
-
(2005)
Dev Cell
, vol.9
, pp. 617-628
-
-
Gustafsson, M.V.1
Zheng, X.2
Pereira, T.3
-
16
-
-
0042704727
-
Hypoxia rapidly activates HIF-3α mRNA expression
-
Heidbreder M, Frohlich F, Johren O et al (2003) Hypoxia rapidly activates HIF-3α mRNA expression. FASEB J 17: 1541-1543.
-
(2003)
FASEB J
, vol.17
, pp. 1541-1543
-
-
Heidbreder, M.1
Frohlich, F.2
Johren, O.3
-
17
-
-
0345491599
-
Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation
-
Hu CJ, Wang LY, Chodosh LA et al (2003) Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation. Mol Cell Biol 23: 9361-9374.
-
(2003)
Mol Cell Biol
, vol.23
, pp. 9361-9374
-
-
Hu, C.J.1
Wang, L.Y.2
Chodosh, L.A.3
-
18
-
-
0032493368
-
Regulation of hypoxia-inducible factor 1α is mediated by an O2-dependent degradation domain via the ubiquitin-proteasome pathway
-
Huang LE, Gu J, Schau M et al (1998) Regulation of hypoxia-inducible factor 1α is mediated by an O2-dependent degradation domain via the ubiquitin-proteasome pathway. Proc Natl Acad Sci U S A 95: 7987-7992.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 7987-7992
-
-
Huang, L.E.1
Gu, J.2
Schau, M.3
-
19
-
-
56349123721
-
Evolutionary history of the UCP gene family: gene duplication and selection
-
Hughes J, Criscuolo F (2008) Evolutionary history of the UCP gene family: gene duplication and selection. BMC Evol Biol 8: 306.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 306
-
-
Hughes, J.1
Criscuolo, F.2
-
20
-
-
58249118050
-
Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis
-
Hughes DA, Jastroch M, Stoneking 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
Stoneking, M.3
-
21
-
-
15444342958
-
Cellular and developmental control of O2 homeostasis by hypoxia-inducible factor 1 alpha
-
Iyer NV, Kotch LE, Agani F et al (1998a) Cellular and developmental control of O2 homeostasis by hypoxia-inducible factor 1 alpha. Genes Dev 12: 149-162.
-
(1998)
Genes Dev
, vol.12
, pp. 149-162
-
-
Iyer, N.V.1
Kotch, L.E.2
Agani, F.3
-
22
-
-
0032167784
-
The human hypoxia-inducible factor 1alpha gene: HIF1A structure and evolutionary conservation
-
Iyer NV, Leung SW, Semenza GL (1998b) The human hypoxia-inducible factor 1alpha gene: HIF1A structure and evolutionary conservation. Genomics 52: 159-165.
-
(1998)
Genomics
, vol.52
, pp. 159-165
-
-
Iyer, N.V.1
Leung, S.W.2
Semenza, G.L.3
-
25
-
-
33751005278
-
Adaptive evolution of Hox-gene homeodomains after cluster duplications
-
Lynch VJ, Roth JJ, Wagner GP (2006) Adaptive evolution of Hox-gene homeodomains after cluster duplications. BMC Evol Biol 6: 86.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 86
-
-
Lynch, V.J.1
Roth, J.J.2
Wagner, G.P.3
-
26
-
-
0035969508
-
Inhibitory PAS domain protein is a negative regulator of hypoxia-inducible gene expression
-
Makino Y, Cao R, Svensson K et al (2001) Inhibitory PAS domain protein is a negative regulator of hypoxia-inducible gene expression. Nature 414: 550-554.
-
(2001)
Nature
, vol.414
, pp. 550-554
-
-
Makino, Y.1
Cao, R.2
Svensson, K.3
-
27
-
-
0345255239
-
Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny
-
Martinez-Castilla LP, Alvarez-Buylla ER (2003) Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny. Proc Natl Acad Sci U S A 100: 13407-13412.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 13407-13412
-
-
Martinez-Castilla, L.P.1
Alvarez-Buylla, E.R.2
-
28
-
-
0033587146
-
The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis
-
Maxwell PH, Wiesener MS, Chang GW et al (1999) The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature 399: 271-275.
-
(1999)
Nature
, vol.399
, pp. 271-275
-
-
Maxwell, P.H.1
Wiesener, M.S.2
Chang, G.W.3
-
29
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
31
-
-
43749106322
-
Origin of INSL3-mediated testicular descent in therian mammals
-
Park JI, Semyonov J, Chang CL et al (2008) Origin of INSL3-mediated testicular descent in therian mammals. Genome Res 18: 974-985.
-
(2008)
Genome Res
, vol.18
, pp. 974-985
-
-
Park, J.I.1
Semyonov, J.2
Chang, C.L.3
-
32
-
-
40949088476
-
Biology of hypoxia-inducible factor-2alpha in development and disease
-
Patel SA, Simon MC (2008) Biology of hypoxia-inducible factor-2alpha in development and disease. Cell Death Differ 15: 628-634.
-
(2008)
Cell Death Differ
, vol.15
, pp. 628-634
-
-
Patel, S.A.1
Simon, M.C.2
-
33
-
-
0034682513
-
The transcription factor EPAS-1/hypoxia-inducible factor 2alpha plays an important role in vascular remodeling
-
Peng J, Zhang L, Drysdale L et al (2000) The transcription factor EPAS-1/hypoxia-inducible factor 2alpha plays an important role in vascular remodeling. Proc Natl Acad Sci U S A 97: 8386-8391.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 8386-8391
-
-
Peng, J.1
Zhang, L.2
Drysdale, L.3
-
34
-
-
20744445650
-
Contrasting properties of hypoxia-inducible factor 1 (HIF-1) and HIF-2 in von Hippel-Lindau-associated renal cell carcinoma
-
Raval RR, Lau KW, Tran MG et al (2005) Contrasting properties of hypoxia-inducible factor 1 (HIF-1) and HIF-2 in von Hippel-Lindau-associated renal cell carcinoma. Mol Cell Biol 25: 5675-5686.
-
(2005)
Mol Cell Biol
, vol.25
, pp. 5675-5686
-
-
Raval, R.R.1
Lau, K.W.2
Tran, M.G.3
-
35
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
36
-
-
0032100732
-
HIF-1 alpha is required for solid tumor formation and embryonic vascularization
-
Ryan HE, Lo J, Johnson RS (1998) HIF-1 alpha is required for solid tumor formation and embryonic vascularization. EMBO J 17: 3005-3015.
-
(1998)
EMBO J
, vol.17
, pp. 3005-3015
-
-
Ryan, H.E.1
Lo, J.2
Johnson, R.S.3
-
37
-
-
46149099779
-
Variable patterns in the molecular evolution of the hypoxia-inducible factor-1 alpha (HIF-1alpha) gene in teleost fishes and mammals
-
Rytkonen KT, Ryynanen HJ, Nikinmaa M et al (2008) Variable patterns in the molecular evolution of the hypoxia-inducible factor-1 alpha (HIF-1alpha) gene in teleost fishes and mammals. Gene 420: 1-10.
-
(2008)
Gene
, vol.420
, pp. 1-10
-
-
Rytkonen, K.T.1
Ryynanen, H.J.2
Nikinmaa, M.3
-
38
-
-
11344292626
-
Binding of natively unfolded HIF-1alpha ODD domain to p53
-
Sanchez-Puig N, Veprintsev DB, Fersht AR (2005) Binding of natively unfolded HIF-1alpha ODD domain to p53. Mol Cell 17: 11-21.
-
(2005)
Mol Cell
, vol.17
, pp. 11-21
-
-
Sanchez-Puig, N.1
Veprintsev, D.B.2
Fersht, A.R.3
-
39
-
-
33747847779
-
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
40
-
-
0035968908
-
Comparative genomics provides evidence for an ancient genome duplication event in fish
-
Taylor JS, van de Peer Y, Braasch I et al (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356: 1661-1679.
-
(2001)
Philos Trans R Soc Lond B Biol Sci
, vol.356
, pp. 1661-1679
-
-
Taylor, J.S.1
van de Peer, Y.2
Braasch, I.3
-
41
-
-
0037351989
-
Genome duplication, a trait shared by 22000 species of ray-finned fish
-
Taylor JS, Braasch I, Frickey T et al (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13: 382-390.
-
(2003)
Genome Res
, vol.13
, pp. 382-390
-
-
Taylor, J.S.1
Braasch, I.2
Frickey, T.3
-
42
-
-
34249331345
-
Sequence and structural aspects of the functional diversification of plant alcohol dehydrogenases
-
Thompson CE, Salzano FM, de Souza ON et al (2007) Sequence and structural aspects of the functional diversification of plant alcohol dehydrogenases. Gene 396: 108-115.
-
(2007)
Gene
, vol.396
, pp. 108-115
-
-
Thompson, C.E.1
Salzano, F.M.2
de Souza, O.N.3
-
43
-
-
0032213236
-
The hypoxia-responsive transcription factor EPAS1 is essential for catecholamine homeostasis and protection against heart failure during embryonic development
-
Tian H, Hammer RE, Matsumoto AM et al (1998) The hypoxia-responsive transcription factor EPAS1 is essential for catecholamine homeostasis and protection against heart failure during embryonic development. Genes Dev 12: 3320-3324.
-
(1998)
Genes Dev
, vol.12
, pp. 3320-3324
-
-
Tian, H.1
Hammer, R.E.2
Matsumoto, A.M.3
-
44
-
-
56549087988
-
Neutralism and selectionism: a network-based reconciliation
-
Wagner A (2008) Neutralism and selectionism: a network-based reconciliation. Nat Rev Genet 9: 965-974.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 965-974
-
-
Wagner, A.1
-
45
-
-
0028816847
-
Purification and characterization of hypoxia-inducible factor 1
-
Wang GL, Semenza GL (1995) Purification and characterization of hypoxia-inducible factor 1. J Biol Chem 270: 1230-1237.
-
(1995)
J Biol Chem
, vol.270
, pp. 1230-1237
-
-
Wang, G.L.1
Semenza, G.L.2
-
46
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
Wong WS, Yang Z, Goldman N et al (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168: 1041-1051.
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.1
Yang, Z.2
Goldman, N.3
-
47
-
-
0036961518
-
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
-
Yang Z (2002) Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
-
(2002)
Genetics
, vol.162
, pp. 1811-1823
-
-
Yang, Z.1
-
48
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
49
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19: 908-917.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
50
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22: 2472-2479.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
|