-
1
-
-
0016355478
-
A new look at the statistical model identifcation
-
Akaike H. 1974. A new look at the statistical model identifcation. IEEE Trans. Automat. Contr. 19:716-723.
-
(1974)
IEEE Trans. Automat. Contr.
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
2
-
-
77954762633
-
Annotating non-coding regions of the genome
-
Alexander R.P., Fang G., Rozowsky J., Snyder M., Gerstein M.B. 2010. Annotating non-coding regions of the genome. Nat. Rev. Genet. 11:559-571.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 559-571
-
-
Alexander, R.P.1
Fang, G.2
Rozowsky, J.3
Snyder, M.4
Gerstein, M.B.5
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. 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
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W., Mattick J., Haussler D. 2004. Ultraconserved elements in the human genome. Science. 304:1321.
-
(2004)
Science
, vol.304
, pp. 1321
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.5
Mattick, J.6
Haussler, D.7
-
6
-
-
85041357609
-
GLMULTI: An R package for easy automated model selection with (generalized) linear models
-
Calcagno V., de Mazancount C. 2010. GLMULTI: An R package for easy automated model selection with (generalized) linear models. J. Stat. Softw. 34:1-29.
-
(2010)
J. Stat. Softw.
, vol.34
, pp. 1-29
-
-
Calcagno, V.1
De Mazancount, C.2
-
7
-
-
0035130163
-
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
-
Chen F.C., Li W.H. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
-
(2001)
Am. J. Hum. Genet.
, vol.68
, pp. 444-456
-
-
Chen, F.C.1
Li, W.H.2
-
8
-
-
79959435199
-
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
-
Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499-510.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 499-510
-
-
Davey, J.W.1
Hohenlohe, P.A.2
Etter, P.D.3
Boone, J.Q.4
Catchen, J.M.5
Blaxter, M.L.6
-
9
-
-
13144295005
-
Conserved non-genic sequences-an unexpected feature of mammalian genomes
-
Dermitzakis E.T., Reymond A., Antonarakis S.E. 2005. Conserved non-genic sequences-an unexpected feature of mammalian genomes. Nat. Rev. Genet. 6:151-157.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 151-157
-
-
Dermitzakis, E.T.1
Reymond, A.2
Antonarakis, S.E.3
-
10
-
-
33749122708
-
Mammalian ultracon-served elements are strongly depleted among segmental duplications and copy number variants
-
Derti A., Roth F.P., Church G.M., Wu C.-T. 2006. Mammalian ultracon-served elements are strongly depleted among segmental duplications and copy number variants. Nat. Genet. 38:1216-1220.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1216-1220
-
-
Derti, A.1
Roth, F.P.2
Church, G.M.3
Wu, C.-T.4
-
11
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
12
-
-
58249100073
-
Is a new and general theory of molecular system-atics emerging?
-
Edwards S.V. 2008. Is a new and general theory of molecular system-atics emerging? Evolution. 63:1-19.
-
(2008)
Evolution.
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
14
-
-
59849113821
-
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
-
Gnirke A., Melnikov A., Maguire J., Rogov P., LeProust E.M., Brockman W., Fennell T., Giannoukos G., Fisher S., Russ C. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27:182-189.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 182-189
-
-
Gnirke, A.1
Melnikov, A.2
Maguire, J.3
Rogov, P.4
Leproust, E.M.5
Brockman, W.6
Fennell, T.7
Giannoukos, G.8
Fisher, S.9
Russ, C.10
-
15
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
-
(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
-
16
-
-
46449135061
-
A phyloge-nomic study of birds reveals their evolutionary history
-
Hackett S., Kimball R., Reddy S., Bowie R., Braun E., Braun M., Chojnowski J., Cox W., Han K., Harshman J. 2008. A phyloge-nomic study of birds reveals their evolutionary history. Science. 320:1763.
-
(2008)
Science.
, vol.320
, pp. 1763
-
-
Hackett, S.1
Kimball, R.2
Reddy, S.3
Bowie, R.4
Braun, E.5
Braun, M.6
Chojnowski, J.7
Cox, W.8
Han, K.9
Harshman, J.10
-
17
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
18
-
-
79955043502
-
Reptiles and mammals have differentially retained long conserved noncoding sequences from the Amniote ancestor
-
Janes D.E., Chapus C., Gondo Y., Clayton D.F., Sinha S., Blatti C.A., Organ C.L., Fujita M.K., Balakrishnan C.N., Edwards S.V. 2011. Reptiles and mammals have differentially retained long conserved noncoding sequences from the Amniote ancestor. Genome Biol. Evol. 3:102-113.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 102-113
-
-
Janes, D.E.1
Chapus, C.2
Gondo, Y.3
Clayton, D.F.4
Sinha, S.5
Blatti, C.A.6
Organ, C.L.7
Fujita, M.K.8
Balakrishnan, C.N.9
Edwards, S.V.10
-
19
-
-
79951827407
-
Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection
-
Kenny E.M., Cormican P., Gilks W.P., Gates A.S., O'Dushlaine C.T., Pinto C., Corvin A.P., Gill M., Morris D.W. 2011. Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. DNA Res. 18:31-38.
-
(2011)
DNA Res
, vol.18
, pp. 31-38
-
-
Kenny, E.M.1
Cormican, P.2
Gilks, W.P.3
Gates, A.S.4
O'Dushlaine, C.T.5
Pinto, C.6
Corvin, A.P.7
Gill, M.8
Morris, D.W.9
-
20
-
-
0024382879
-
Dynamics of mitochondrial DNA evolution in animals: Amplifcation and sequencing with conserved primers
-
Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., Wilson A.C. 1989. Dynamics of mitochondrial DNA evolution in animals: amplifcation and sequencing with conserved primers. Proc. Natl. Acad. Sci. U. S. A. 86:6196.
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 6196
-
-
Kocher, T.D.1
Thomas, W.K.2
Meyer, A.3
Edwards, S.V.4
Pääbo, S.5
Villablanca, F.X.6
Wilson, A.C.7
-
21
-
-
79952163548
-
Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fshes
-
Lee A.P., Kerk S.Y., Tan Y.Y., Brenner S., Venkatesh B. 2011. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fshes. Mol. Biol. Evol. 28:1205-1215.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 1205-1215
-
-
Lee, A.P.1
Kerk, S.Y.2
Tan, Y.Y.3
Brenner, S.4
Venkatesh, B.5
-
22
-
-
67449163699
-
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
-
Lemmon A.R., Brown J.M., Stanger-Hall K., Lemmon E.M. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 58:130.
-
(2009)
Syst. Biol.
, vol.58
, pp. 130
-
-
Lemmon, A.R.1
Brown, J.M.2
Stanger-Hall, K.3
Lemmon, E.M.4
-
23
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh K., Garber M., Zuk O., Lin MF., Parker B.J., Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., Ward L.D., Lowe C.B., Holloway A.K., Clamp M., Gnerre S., Alföldi J., Beal K., Chang J., Clawson H., Cuff J., Di Palma F., Fitzgerald S., Flicek P., Guttman M., Hubisz M.J., Jaffe D.B., Jungreis I., Kent W.J., Kostka D., Lara M., Martins A.L., Massingham T., Moltke I., Raney B.J., Rasmussen M.D., Robinson J., Stark A., Vilella A.J., Wen J., Xie X., Zody M.C., Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J., Bloom T., Chin C.W., Heiman D., Nicol R., Nusbaum C., Young S., Wilkinson J., Worley K.C., Kovar C.L., Muzny D.M., Gibbs R.A., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A., Dihn H.H., Fowler G., Jhangiani S., Joshi V., Lee S., Lewis L.R., Nazareth L.V., Okwuonu G., Santibanez J., Warren W.C., Mardis E.R., Weinstock G.M., Wilson R.K., Genome Institute at Washington University, Delehaunty K., Dooling D., Fronik C., Fulton L., Fulton B., Graves T., Minx P., Sodergren E., Birney E., Margulies E.H., Herrero J., Green E.D., Haussler D., Siepel A., Goldman N., Pollard K.S., Pedersen J.S., Lander E.S., Kellis M. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478:476-482.
-
(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
Martins, A.L.31
Massingham, T.32
Moltke, I.33
Raney, B.J.34
Rasmussen, M.D.35
Robinson, J.36
Stark, A.37
Vilella, A.J.38
Wen, J.39
Xie, X.40
Zody, M.C.41
Baldwin, J.42
Bloom, T.43
Chin, C.W.44
Heiman, D.45
Nicol, R.46
Nusbaum, C.47
Young, S.48
Wilkinson, J.49
Worley, K.C.50
Kovar, C.L.51
Muzny, D.M.52
Gibbs, R.A.53
Cree, A.54
Dihn, H.H.55
Fowler, G.56
Jhangiani, S.57
Joshi, V.58
Lee, S.59
Lewis, L.R.60
Nazareth, L.V.61
Okwuonu, G.62
Santibanez, J.63
Warren, W.C.64
Mardis, E.R.65
Weinstock, G.M.66
Wilson, R.K.67
Delehaunty, K.68
Dooling, D.69
Fronik, C.70
Fulton, L.71
Fulton, B.72
Graves, T.73
Minx, P.74
Sodergren, E.75
Birney, E.76
Margulies, E.H.77
Herrero, J.78
Green, E.D.79
Haussler, D.80
Siepel, A.81
Goldman, N.82
Pollard, K.S.83
Pedersen, J.S.84
Lander, E.S.85
Kellis, M.86
more..
-
24
-
-
77951961553
-
PHYBASE: An R package for phylogenetic analysis
-
Liu L., Yu L. 2010. PHYBASE: an R package for phylogenetic analysis. Bioinformatics. 26:962-963.
-
(2010)
Bioinformatics
, vol.26
, pp. 962-963
-
-
Liu, L.1
Yu, L.2
-
25
-
-
70349425459
-
Estimating species phy-logenies using coalescence times among sequences
-
Liu L., Yu L., Pearl D.K., Edwards S.V. 2009. Estimating species phy-logenies using coalescence times among sequences. Syst. Biol. 58: 468-477.
-
(2009)
Syst. Biol.
, vol.58
, pp. 468-477
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
Edwards, S.V.4
-
26
-
-
77449121614
-
Target-enrichment strategies for next-generation sequencing
-
Mamanova L., Coffey A.J., Scott C.E., Kozarewa I., Turner E.H., Kumar A., Howard E., Shendure J., Turner D.J. 2009. Target-enrichment strategies for next-generation sequencing. Nat. Methods. 7:111-118.
-
(2009)
Nat. Methods.
, vol.7
, pp. 111-118
-
-
Mamanova, L.1
Coffey, A.J.2
Scott, C.E.3
Kozarewa, I.4
Turner, E.H.5
Kumar, A.6
Howard, E.7
Shendure, J.8
Turner, D.J.9
-
27
-
-
84859530730
-
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis
-
doi:10.1101/gr.125864.111
-
McCormack J.E., Faircloth B.C., Crawford N.G., Gowaty P.A., Brumfeld R.T., Glenn T.C. forthcoming 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Research. doi:10.1101/gr.125864.111.
-
(2012)
Genome Research.
-
-
McCormack, J.E.1
Faircloth, B.C.2
Crawford, N.G.3
Gowaty, P.A.4
Brumfeld, R.T.5
Glenn, T.C.6
-
28
-
-
83655201166
-
Next-generation sequencing reveals population genetic structure and a species tree for recent bird divergences
-
McCormack J.E., Maley J.M., Hird S.M., Derryberry E.P., Graves G.R., Brumfeld R.T. 2011. Next-generation sequencing reveals population genetic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution 62:397-406.
-
(2011)
Molecular Phylogenetics and Evolution
, vol.62
, pp. 397-406
-
-
McCormack, J.E.1
Maley, J.M.2
Hird, S.M.3
Derryberry, E.P.4
Graves, G.R.5
Brumfeld, R.T.6
-
29
-
-
39449089394
-
Parallel tagged sequencing on the 454 platform
-
Meyer M., Stenzel U., Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 3:267-278.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 267-278
-
-
Meyer, M.1
Stenzel, U.2
Hofreiter, M.3
-
31
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio L.A., Ahituv N., Moses A.M., Prabhakar S., Nobrega M.A., Shoukry M., Minovitsky S., Dubchak I., Holt A., Lewis K.D., Plajzer-Frick I., Akiyama J., De Val S., Afzal V., Black B.L., Couronne O., Eisen M.B., Visel A., Rubin E.M. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 444: 499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
Minovitsky, S.7
Dubchak, I.8
Holt, A.9
Lewis, K.D.10
Plajzer-Frick, I.11
Akiyama, J.12
De Val, S.13
Afzal, V.14
Black, B.L.15
Couronne, O.16
Eisen, M.B.17
Visel, A.18
Rubin, E.M.19
-
32
-
-
79961135005
-
-
R Development Core Team Vienna (Austria): R Foundation for Statistical Computing
-
R Development Core Team. 2011. R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
-
(2011)
R: A Language and Environment for Statistical Computing
-
-
-
33
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
Sandelin A., Bailey P., Bruce S., Engstrom P.G., Klos J.M., Wasserman W.W., Ericson J., Lenhard B. 2004. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics. 5: 99.
-
(2004)
BMC Genomics
, vol.5
, pp. 99
-
-
Sandelin, A.1
Bailey, P.2
Bruce, S.3
Engstrom, P.G.4
Klos, J.M.5
Wasserman, W.W.6
Ericson, J.7
Lenhard, B.8
-
34
-
-
50949129519
-
Calculating bootstrap probabilities of phy-logeny using multilocus sequence data
-
Seo T.K. 2008. Calculating bootstrap probabilities of phy-logeny using multilocus sequence data. Mol. Biol. Evol., 25: 960-971.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 960-971
-
-
Seo, T.K.1
-
35
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J., Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
36
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A., Bejerano G., Pedersen J.S., Hinrichs A.S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L.D.W., Richards S. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050.
-
(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.D.W.9
Richards, S.10
-
38
-
-
38949097100
-
Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
-
Stephen S., Pheasant M., Makunin I.V., Mattick J.S. 2008. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol. Biol. Evol. 25:402-408.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 402-408
-
-
Stephen, S.1
Pheasant, M.2
Makunin, I.V.3
Mattick, J.S.4
-
39
-
-
75349097525
-
Enrichment of sequencing targets from the human genome by solution hybridization
-
Tewhey R., Nakano M., Wang X., Pabón-Peña C., Novak B., Giuffre A., Lin E., Happe S., Roberts D.N., LeProust E.M. 2009. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 10:R116.
-
(2009)
Genome Biol.
, vol.10
-
-
Tewhey, R.1
Nakano, M.2
Wang, X.3
Pabón-Peña, C.4
Novak, B.5
Giuffre, A.6
Lin, E.7
Happe, S.8
Roberts, D.N.9
Leproust, E.M.10
-
40
-
-
80052006478
-
Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data
-
Wiens J.J., Morrill M.C. 2011. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst. Biol. 60:719-731.
-
(2011)
Syst. Biol.
, vol.60
, pp. 719-731
-
-
Wiens, J.J.1
Morrill, M.C.2
-
41
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe A., Goodson M., Goode D.K., Snell P., McEwen G.K., Vavouri T., Smith S.F., North P., Callaway H., Kelly K. 2004. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3: e7.
-
(2004)
PLoS Biol
, vol.3
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
Snell, P.4
McEwen, G.K.5
Vavouri, T.6
Smith, S.F.7
North, P.8
Callaway, H.9
Kelly, K.10
-
42
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D.R., Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821.
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(2008)
Genome Res.
, vol.18
, pp. 821
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Zerbino, D.R.1
Birney, E.2
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