-
1
-
-
66049128566
-
Distinguishing among evolutionary models for the maintenance of gene duplicates
-
10.1093/jhered/esp047, 19596713
-
Hahn MW. Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered 2009, 100:605-617. 10.1093/jhered/esp047, 19596713.
-
(2009)
J Hered
, vol.100
, pp. 605-617
-
-
Hahn, M.W.1
-
3
-
-
0031466095
-
Secor and CL: the role of hybridization and introgression In the diversification of animals
-
Dowling TE. Secor and CL: the role of hybridization and introgression In the diversification of animals. Annu Rev Ecol Evol Syst 1997, 28:593-619.
-
(1997)
Annu Rev Ecol Evol Syst
, vol.28
, pp. 593-619
-
-
Dowling, T.E.1
-
4
-
-
79952270485
-
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
-
10.1101/gr.114751.110, 3044849, 21270173
-
Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res 2011, 21:349-356. 10.1101/gr.114751.110, 3044849, 21270173.
-
(2011)
Genome Res
, vol.21
, pp. 349-356
-
-
Hobolth, A.1
Dutheil, J.Y.2
Hawks, J.3
Schierup, M.H.4
Mailund, T.5
-
5
-
-
73649129187
-
Fine-scale phylogenetic discordance across the house mouse genome
-
10.1371/journal.pgen.1000729, 2770633, 19936022
-
White MA, Ané C, Dewey CN, Larget BR, Payseur BA. Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genet 2009, 5:e1000729. 10.1371/journal.pgen.1000729, 2770633, 19936022.
-
(2009)
PLoS Genet
, vol.5
-
-
White, M.A.1
Ané, C.2
Dewey, C.N.3
Larget, B.R.4
Payseur, B.A.5
-
6
-
-
67651098662
-
Mechanisms of change in gene copy number
-
2864001, 19597530
-
Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009, 10:551-564. 2864001, 19597530.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 551-564
-
-
Hastings, P.J.1
Lupski, J.R.2
Rosenberg, S.M.3
Ira, G.4
-
7
-
-
84859462157
-
The genomic basis of adaptive evolution in threespine sticklebacks
-
10.1038/nature10944, 3322419, 22481358
-
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 2012, 484:55-61. 10.1038/nature10944, 3322419, 22481358.
-
(2012)
Nature
, vol.484
, pp. 55-61
-
-
Jones, F.C.1
Grabherr, M.G.2
Chan, Y.F.3
Russell, P.4
Mauceli, E.5
Johnson, J.6
Swofford, R.7
Pirun, M.8
Zody, M.C.9
White, S.10
Birney, E.11
Searle, S.12
Schmutz, J.13
Grimwood, J.14
Dickson, M.C.15
Myers, R.M.16
Miller, C.T.17
Summers, B.R.18
Knecht, A.K.19
Brady, S.D.20
Zhang, H.21
Pollen, A.A.22
Howes, T.23
Amemiya, C.24
Baldwin, J.25
Bloom, T.26
Jaffe, D.B.27
Nicol, R.28
Wilkinson, J.29
Lander, E.S.30
more..
-
8
-
-
0000342467
-
Statistical inference for probabilistic functions of finite state Markov chains
-
Baum LE, Petrie T. Statistical inference for probabilistic functions of finite state Markov chains. Ann Math Stat 1966, 37:1554-1563.
-
(1966)
Ann Math Stat
, vol.37
, pp. 1554-1563
-
-
Baum, L.E.1
Petrie, T.2
-
9
-
-
0025489075
-
The self-organizing map
-
Kohonen T. The self-organizing map. Proc IEEE 1990, 78:1464-1480.
-
(1990)
Proc IEEE
, vol.78
, pp. 1464-1480
-
-
Kohonen, T.1
-
10
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
10.1101/gr.3715005, 1182216, 16024819
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15:1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
Weinstock, G.M.11
Wilson, R.K.12
Gibbs, R.A.13
Kent, W.J.14
Miller, W.15
Haussler, D.16
-
11
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinf (Oxford, England) 2009, 25:54-62.
-
(2009)
Bioinf (Oxford, England)
, vol.25
, pp. 54-62
-
-
Garber, M.1
Guttman, M.2
Clamp, M.3
Zody, M.C.4
Friedman, N.5
Xie, X.6
-
12
-
-
84857687426
-
Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
-
Wu Y. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evol Int J Org Evol 2012, 66:763-775.
-
(2012)
Evol Int J Org Evol
, vol.66
, pp. 763-775
-
-
Wu, Y.1
-
13
-
-
84873407500
-
Using self-organizing map (SOM) and support vector machine (SVM) for classification of selectivity of ACAT inhibitors
-
10.1007/s11030-012-9404-z, 23124952
-
Wang L, Wang M, Yan A, Dai B. Using self-organizing map (SOM) and support vector machine (SVM) for classification of selectivity of ACAT inhibitors. Mol Divers 2013, 17:85-96. 10.1007/s11030-012-9404-z, 23124952.
-
(2013)
Mol Divers
, vol.17
, pp. 85-96
-
-
Wang, L.1
Wang, M.2
Yan, A.3
Dai, B.4
-
14
-
-
84869078120
-
Use of self-organizing map to analyze images of fungi colonies grown from triticum aestivum seeds disinfected by ozone treatment
-
3479990, 23118753
-
Marique T, Allard O, Spanoghe M. Use of self-organizing map to analyze images of fungi colonies grown from triticum aestivum seeds disinfected by ozone treatment. Int J Microbiol 2012, 2012:865175. 3479990, 23118753.
-
(2012)
Int J Microbiol
, vol.2012
, pp. 865175
-
-
Marique, T.1
Allard, O.2
Spanoghe, M.3
-
15
-
-
18744388326
-
Transcription factor binding site identification using the self-organizing map
-
Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS. Transcription factor binding site identification using the self-organizing map. Bioinf (Oxford, England) 2005, 21:14-1807.
-
(2005)
Bioinf (Oxford, England)
, vol.21
, pp. 14-1807
-
-
Mahony, S.1
Hendrix, D.2
Golden, A.3
Smith, T.J.4
Rokhsar, D.S.5
-
17
-
-
82655187219
-
A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation
-
Schmidt DJ, Pickett BE, Camacho D, Comach G, Xhaja K, Lennon NJ, Rizzolo K, De Bosch N, Becerra A, Nogueira ML, Mondini A, Da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R, Gehrke L, Lefkowitz EJ, Birren BW, Henn MR, Bosch I. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation. Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis 2011, 11:2011-9.
-
(2011)
Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis
, vol.11
, pp. 2011-2019
-
-
Schmidt, D.J.1
Pickett, B.E.2
Camacho, D.3
Comach, G.4
Xhaja, K.5
Lennon, N.J.6
Rizzolo, K.7
De Bosch, N.8
Becerra, A.9
Nogueira, M.L.10
Mondini, A.11
Da Silva, E.V.12
Vasconcelos, P.F.13
Muñoz-Jordán, J.L.14
Santiago, G.A.15
Ocazionez, R.16
Gehrke, L.17
Lefkowitz, E.J.18
Birren, B.W.19
Henn, M.R.20
Bosch, I.21
more..
-
18
-
-
28944454501
-
DNA assembly with gaps (Dawg): simulating sequence evolution
-
Cartwright RA. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinf (Oxford, England) 2005, 21(3):8-31.
-
(2005)
Bioinf (Oxford, England)
, vol.21
, Issue.3
, pp. 8-31
-
-
Cartwright, R.A.1
-
19
-
-
34547844062
-
TOPD/FMTS: a new software to compare phylogenetic trees
-
Puigbò P, Garcia-Vallvé S, McInerney JO, Puigbò P, Garcia-Vallvé S, McInerney JO. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinf (Oxford, England) 2007, 23:8-1556.
-
(2007)
Bioinf (Oxford, England)
, vol.23
, pp. 8-1556
-
-
Puigbò, P.1
Garcia-Vallvé, S.2
McInerney, J.O.3
Puigbò, P.4
Garcia-Vallvé, S.5
McInerney, J.O.6
-
20
-
-
78649761558
-
-
Treatment, Prevention and Control. Geneva, WHO
-
WHO Dengue Guidelines for Diagnosis 2009, 3. Treatment, Prevention and Control. Geneva, WHO.
-
(2009)
Dengue Guidelines for Diagnosis
, pp. 3
-
-
-
21
-
-
48249102000
-
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
-
10.1093/nar/gkn180, 2447785, 18424797
-
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard J-F, Guindon S, Lefort V, Lescot M, Claverie J-M, Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008, 36:W465-9. 10.1093/nar/gkn180, 2447785, 18424797.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dereeper, A.1
Guignon, V.2
Blanc, G.3
Audic, S.4
Buffet, S.5
Chevenet, F.6
Dufayard, J.-F.7
Guindon, S.8
Lefort, V.9
Lescot, M.10
Claverie, J.-M.11
Gascuel, O.12
-
22
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340, 390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-7. 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
23
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
10.1080/10635150701472164, 17654362
-
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56:564-77. 10.1080/10635150701472164, 17654362.
-
(2007)
Syst Biol
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
24
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
10.1093/sysbio/syq010, 20525638
-
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-21. 10.1093/sysbio/syq010, 20525638.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
25
-
-
0038386683
-
Emergence and global spread of a dengue serotype 3, subtype III virus
-
Messer WB, Gubler DJ, Harris E, Sivananthan K, De Silva AM. Emergence and global spread of a dengue serotype 3, subtype III virus. Emerging Infectious Dis 2003, 9:800-9.
-
(2003)
Emerging Infectious Dis
, vol.9
, pp. 800-809
-
-
Messer, W.B.1
Gubler, D.J.2
Harris, E.3
Sivananthan, K.4
De Silva, A.M.5
-
26
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
10.1038/nature10530, 3207357, 21993624
-
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011, 478:476-82. 10.1038/nature10530, 3207357, 21993624.
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
Kheradpour, P.7
Ernst, J.8
Jordan, G.9
Mauceli, E.10
Ward, L.D.11
Lowe, C.B.12
Holloway, A.K.13
Clamp, M.14
Gnerre, S.15
Alföldi, J.16
Beal, K.17
Chang, J.18
Clawson, H.19
Cuff, J.20
Di Palma, F.21
Fitzgerald, S.22
Flicek, P.23
Guttman, M.24
Hubisz, M.J.25
Jaffe, D.B.26
Jungreis, I.27
Kent, W.J.28
Kostka, D.29
Lara, M.30
more..
-
27
-
-
84863230553
-
Insights into hominid evolution from the gorilla genome sequence
-
10.1038/nature10842, 3303130, 22398555
-
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A. Insights into hominid evolution from the gorilla genome sequence. Nature 2012, 483:169-175. 10.1038/nature10842, 3303130, 22398555.
-
(2012)
Nature
, vol.483
, pp. 169-175
-
-
Scally, A.1
Dutheil, J.Y.2
Hillier, L.W.3
Jordan, G.E.4
Goodhead, I.5
Herrero, J.6
Hobolth, A.7
Lappalainen, T.8
Mailund, T.9
Marques-Bonet, T.10
McCarthy, S.11
Montgomery, S.H.12
Schwalie, P.C.13
Tang, Y.A.14
Ward, M.C.15
Xue, Y.16
Yngvadottir, B.17
Alkan, C.18
Andersen, L.N.19
Ayub, Q.20
Ball, E.V.21
Beal, K.22
Bradley, B.J.23
Chen, Y.24
Clee, C.M.25
Fitzgerald, S.26
Graves, T.A.27
Gu, Y.28
Heath, P.29
Heger, A.30
more..
-
28
-
-
1842536305
-
The DNA sequence and biology of human chromosome 19
-
10.1038/nature02399, 15057824
-
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D. The DNA sequence and biology of human chromosome 19. Nature 2004, 428:529-35. 10.1038/nature02399, 15057824.
-
(2004)
Nature
, vol.428
, pp. 529-535
-
-
Grimwood, J.1
Gordon, L.A.2
Olsen, A.3
Terry, A.4
Schmutz, J.5
Lamerdin, J.6
Hellsten, U.7
Goodstein, D.8
Couronne, O.9
Tran-Gyamfi, M.10
Aerts, A.11
Altherr, M.12
Ashworth, L.13
Bajorek, E.14
Black, S.15
Branscomb, E.16
Caenepeel, S.17
Carrano, A.18
Caoile, C.19
Chan, Y.M.20
Christensen, M.21
Cleland, C.A.22
Copeland, A.23
Dalin, E.24
Dehal, P.25
Denys, M.26
Detter, J.C.27
Escobar, J.28
Flowers, D.29
Fotopulos, D.30
more..
-
29
-
-
20744431725
-
Control of translation by the 5'- and 3'-terminal regions of the dengue virus genome
-
10.1128/JVI.79.13.8303-8315.2005, 1143759, 15956576
-
Chiu W-W, Kinney RM, Dreher TW. Control of translation by the 5'- and 3'-terminal regions of the dengue virus genome. J Virol 2005, 79:8303-15. 10.1128/JVI.79.13.8303-8315.2005, 1143759, 15956576.
-
(2005)
J Virol
, vol.79
, pp. 8303-8315
-
-
Chiu, W.-W.1
Kinney, R.M.2
Dreher, T.W.3
-
30
-
-
43549121020
-
Human MHC architecture and evolution: implications for disease association studies
-
Traherne JA. Human MHC architecture and evolution: implications for disease association studies. Int J Immunogenetics 2008, 35:179-92.
-
(2008)
Int J Immunogenetics
, vol.35
, pp. 179-192
-
-
Traherne, J.A.1
|