-
3
-
-
84876271982
-
The African coelacanth genome provides insights into tetrapod evolution
-
Amemiya, C. T., J. Alfoldi, A. P. Lee, S. Fan, H. Philippe, I. MacCallum, I. Braasch et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311-316.
-
(2013)
Nature
, vol.496
, pp. 311-316
-
-
Amemiya, C.T.1
Alfoldi, J.2
Lee, A.P.3
Fan, S.4
Philippe, H.5
MacCallum, I.6
Braasch, I.7
-
4
-
-
84880569366
-
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
-
Auerbach, R. K., B. Chen, and A. J. Butte 2013. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics 29:1922-1924.
-
(2013)
Bioinformatics
, vol.29
, pp. 1922-1924
-
-
Auerbach, R.K.1
Chen, B.2
Butte, A.J.3
-
5
-
-
79959640102
-
Evaluation of next-generation sequencing software in mapping and assembly
-
Bao, S., R. Jiang, W. Kwan, B. Wang, X. Ma, and Y.-Q. Song 2011. Evaluation of next-generation sequencing software in mapping and assembly. Journal of Human Genetics 56:406-414.
-
(2011)
Journal of Human Genetics
, vol.56
, pp. 406-414
-
-
Bao, S.1
Jiang, R.2
Kwan, W.3
Wang, B.4
Ma, X.5
Song, Y.-Q.6
-
6
-
-
0036144823
-
ARACHNE: a whole-genome shotgun assembler
-
Batzoglou, S., D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger et al. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12:177-189.
-
(2002)
Genome Research
, vol.12
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.B.2
Stanley, K.3
Butler, J.4
Gnerre, S.5
Mauceli, E.6
Berger, B.7
-
7
-
-
84890116555
-
Unlocking the vault: next-generation museum population genomics
-
Bi, K., T. Linderoth, D. Vanderpool, J. M. Good, R. Nielsen, and C. Moritz 2013. Unlocking the vault: next-generation museum population genomics. Molecular Ecology 22:6018-6032.
-
(2013)
Molecular Ecology
, vol.22
, pp. 6018-6032
-
-
Bi, K.1
Linderoth, T.2
Vanderpool, D.3
Good, J.M.4
Nielsen, R.5
Moritz, C.6
-
8
-
-
84862591603
-
Toward almost closed genomes with GapFiller
-
Boetzer, M., and W. Pirovano 2012. Toward almost closed genomes with GapFiller. Genome Biology 13:R56.
-
(2012)
Genome Biology
, vol.13
, pp. R56
-
-
Boetzer, M.1
Pirovano, W.2
-
9
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer, M., C. V. Henkel, H. J. Jansen, D. Butler, and W. Pirovano 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578-579.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
10
-
-
78349238864
-
Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies
-
Boisvert, S., F. Laviolette, and J. Corbeil 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of Computational Biology 17:1519-1533.
-
(2010)
Journal of Computational Biology
, vol.17
, pp. 1519-1533
-
-
Boisvert, S.1
Laviolette, F.2
Corbeil, J.3
-
11
-
-
84991528460
-
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam, K., J. Fass, A. Alexandrov, P. Baranay, M. Bechner, I. Birol, S. Boisvert et al. 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2:10.
-
(2013)
GigaScience
, vol.2
, pp. 10
-
-
Bradnam, K.1
Fass, J.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
Birol, I.6
Boisvert, S.7
-
12
-
-
80053019891
-
Haplotype phasing: existing methods and new developments
-
Browning, S. R., and B. L. Browning 2011. Haplotype phasing: existing methods and new developments. Nature Reviews Genetics 12:703-714.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 703-714
-
-
Browning, S.R.1
Browning, B.L.2
-
13
-
-
38049057159
-
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes
-
Cantarel, B. L., I. Korf, S. M. C. Robb, G. Parra, E. Ross, B. Moore, C. Holt et al. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188-196.
-
(2008)
Genome Research
, vol.18
, pp. 188-196
-
-
Cantarel, B.L.1
Korf, I.2
Robb, S.M.C.3
Parra, G.4
Ross, E.5
Moore, B.6
Holt, C.7
-
14
-
-
84890812848
-
The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
-
Castoe, T. A., A. P. J. de Koning, K. T. Hall, D. C. Card, D. R. Schield, M. K. Fujita, R. P. Ruggiero et al. 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences 110:20645-20650.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. 20645-20650
-
-
Castoe, T.A.1
de Koning, A.P.J.2
Hall, K.T.3
Card, D.C.4
Schield, D.R.5
Fujita, M.K.6
Ruggiero, R.P.7
-
15
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
The Chimpanzee Sequencing and Analysis Consortium
-
The Chimpanzee Sequencing and Analysis Consortium 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
16
-
-
84892877574
-
The tiger genome and comparative analysis with lion and snow leopard genomes
-
Article number
-
Cho, Y. S., L. Hu, H. Hou, H. Lee, J. Xu, S. Kwon, S. Oh et al. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications 4:Article number: 2433.
-
(2013)
Nature Communications
, vol.4
, pp. 2433
-
-
Cho, Y.S.1
Hu, L.2
Hou, H.3
Lee, H.4
Xu, J.5
Kwon, S.6
Oh, S.7
-
17
-
-
84883326440
-
Assembler for de novo assembly of large genomes
-
Chu, T.-C., C.-H. Lu, T. Liu, G. C. Lee, W.-H. Li, and A. C.-C. Shih 2013. Assembler for de novo assembly of large genomes. Proceedings of the National Academy of Sciences 110:E3417-E3424.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. E3417-E3424
-
-
Chu, T.-C.1
Lu, C.-H.2
Liu, T.3
Lee, G.C.4
Li, W.-H.5
Shih, A.C.-C.6
-
18
-
-
0034237782
-
Considering evolutionary processes in conservation biology
-
Crandall, K. A., O. R. P. Bininda-Emonds, G. M. Mace, and R. K. Wayne 2000. Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution 15:290-295.
-
(2000)
Trends in Ecology & Evolution
, vol.15
, pp. 290-295
-
-
Crandall, K.A.1
Bininda-Emonds, O.R.P.2
Mace, G.M.3
Wayne, R.K.4
-
19
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, M. A. DePristo, R. E. Handsaker et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156-2158.
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
DePristo, M.A.6
Handsaker, R.E.7
-
20
-
-
41949131367
-
Consensus generation and variant detection by Celera Assembler
-
Denisov, G., B. Walenz, A. L. Halpern, J. Miller, N. Axelrod, S. Levy, and G. Sutton 2008. Consensus generation and variant detection by Celera Assembler. Bioinformatics 24:1035-1040.
-
(2008)
Bioinformatics
, vol.24
, pp. 1035-1040
-
-
Denisov, G.1
Walenz, B.2
Halpern, A.L.3
Miller, J.4
Axelrod, N.5
Levy, S.6
Sutton, G.7
-
21
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire, C. Hartl, A. A. Philippakis et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43:491-498.
-
(2011)
Nature Genetics
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
-
22
-
-
83055181941
-
Assemblathon 1: a competitive assessment of de novo short read assembly methods
-
Earl, D., K. Bradnam, J. St. John, A. Darling, D. Lin, J. Fass, H. O. K. Yu et al. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research 21:2224-2241.
-
(2011)
Genome Research
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St. John, J.3
Darling, A.4
Lin, D.5
Fass, J.6
Yu, H.O.K.7
-
23
-
-
79959300621
-
Applications of next generation sequencing in molecular ecology of non-model organisms
-
Ekblom, R., and J. Galindo 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1-15.
-
(2011)
Heredity
, vol.107
, pp. 1-15
-
-
Ekblom, R.1
Galindo, J.2
-
24
-
-
84888274008
-
Genome sequencing and population genomics in non-model organisms
-
Ellegren, H. 2014. Genome sequencing and population genomics in non-model organisms. Trends in Ecology & Evolution 29:51-63.
-
(2014)
Trends in Ecology & Evolution
, vol.29
, pp. 51-63
-
-
Ellegren, H.1
-
25
-
-
84870297139
-
The genomic landscape of species divergence in Ficedula flycatchers
-
Ellegren, H., L. Smeds, R. Burri, P. I. Olason, N. Backstrom, T. Kawakami, A. Kunstner et al. 2012. The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756-760.
-
(2012)
Nature
, vol.491
, pp. 756-760
-
-
Ellegren, H.1
Smeds, L.2
Burri, R.3
Olason, P.I.4
Backstrom, N.5
Kawakami, T.6
Kunstner, A.7
-
26
-
-
79955783956
-
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
-
Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto, E. S. Buckler, and S. E. Mitchell 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379.
-
(2011)
PLoS One
, vol.6
, pp. e19379
-
-
Elshire, R.J.1
Glaubitz, J.C.2
Sun, Q.3
Poland, J.A.4
Kawamoto, K.5
Buckler, E.S.6
Mitchell, S.E.7
-
27
-
-
84869814079
-
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology
-
English, A. C., S. Richards, Y. Han, M. Wang, V. Vee, J. Qu, X. Qin et al. 2012. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7:e47768.
-
(2012)
PLoS One
, vol.7
, pp. e47768
-
-
English, A.C.1
Richards, S.2
Han, Y.3
Wang, M.4
Vee, V.5
Qu, J.6
Qin, X.7
-
28
-
-
70449701942
-
Sense from sequence reads: methods for alignment and assembly
-
Flicek, P., and E. Birney 2009. Sense from sequence reads: methods for alignment and assembly. Nature Methods 6(11 Suppl):S6-S12.
-
(2009)
Nature Methods
, vol.6
, Issue.11 Suppl
, pp. S6-S12
-
-
Flicek, P.1
Birney, E.2
-
30
-
-
0003952541
-
-
2nd edn. Cambridge University Press, Cambridge, UK.
-
Frankham, R., J. D. Ballou, and D. A. Briscoe 2010. Introduction to Conservation Genetics, 2nd edn. Cambridge University Press, Cambridge, UK.
-
(2010)
Introduction to Conservation Genetics
-
-
Frankham, R.1
Ballou, J.D.2
Briscoe, D.A.3
-
31
-
-
0035544509
-
Adaptive evolutionary conservation: towards a unified concept for defining conservation units
-
Fraser, D. J., and L. Bernatchez 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology 10:2741-2752.
-
(2001)
Molecular Ecology
, vol.10
, pp. 2741-2752
-
-
Fraser, D.J.1
Bernatchez, L.2
-
32
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Gene Ontology Consortium
-
Gene Ontology Consortium 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 32(Suppl 1):D258-D261.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. D258-D261
-
-
-
33
-
-
71049176982
-
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species
-
Genome 10K Community of Scientists
-
Genome 10K Community of Scientists 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10, 000 vertebrate species. Journal of Heredity 100:659-674.
-
(2009)
Journal of Heredity
, vol.100
, pp. 659-674
-
-
-
34
-
-
70350012234
-
Assisted assembly: how to improve a de novo genome assembly by using related species
-
Gnerre, S., E. Lander, K. Lindblad-Toh, and D. Jaffe 2009. Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biology 10:R88.
-
(2009)
Genome Biology
, vol.10
, pp. R88
-
-
Gnerre, S.1
Lander, E.2
Lindblad-Toh, K.3
Jaffe, D.4
-
35
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre, S., I. MacCallum, D. Przybylski, F. J. Ribeiro, J. N. Burton, B. J. Walker, T. Sharpe et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences 108:1513-1518.
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
MacCallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
Walker, B.J.6
Sharpe, T.7
-
36
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas, B. J., A. L. Delcher, S. M. Mount, J. R. Wortman, R. K. Smith Jr, L. I. Hannick, R. Maiti et al. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research 31:5654-5666.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith Jr, R.K.5
Hannick, L.I.6
Maiti, R.7
-
37
-
-
84897978137
-
A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene
-
Halley, Y. A., S. E. Dowd, J. E. Decker, P. M. Seabury, E. Bhattarai, C. D. Johnson, D. Rollins et al. 2014. A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One 9:e90240.
-
(2014)
PLoS One
, vol.9
, pp. e90240
-
-
Halley, Y.A.1
Dowd, S.E.2
Decker, J.E.3
Seabury, P.M.4
Bhattarai, E.5
Johnson, C.D.6
Rollins, D.7
-
38
-
-
1842717960
-
The Atlas genome assembly system
-
Havlak, P., R. Chen, K. J. Durbin, A. Egan, Y. Ren, X.-Z. Song, G. M. Weinstock et al. 2004. The Atlas genome assembly system. Genome Research 14:721-732.
-
(2004)
Genome Research
, vol.14
, pp. 721-732
-
-
Havlak, P.1
Chen, R.2
Durbin, K.J.3
Egan, A.4
Ren, Y.5
Song, X.-Z.6
Weinstock, G.M.7
-
39
-
-
0032965634
-
Perspective: highly variable loci and their interpretation in evolution and conservation
-
Hedrick, P. W. 1999. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53:313-318.
-
(1999)
Evolution
, vol.53
, pp. 313-318
-
-
Hedrick, P.W.1
-
40
-
-
84893945338
-
A genetic atlas of human admixture history
-
Hellenthal, G., G. B. J. Busby, G. Band, J. F. Wilson, C. Capelli, D. Falush, and S. Myers 2014. A genetic atlas of human admixture history. Science 343:747-751.
-
(2014)
Science
, vol.343
, pp. 747-751
-
-
Hellenthal, G.1
Busby, G.B.J.2
Band, G.3
Wilson, J.F.4
Capelli, C.5
Falush, D.6
Myers, S.7
-
41
-
-
43149085041
-
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
-
Hernandez, D., P. François, L. Farinelli, M. Østerås, and J. Schrenzel 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Research 18:802-809.
-
(2008)
Genome Research
, vol.18
, pp. 802-809
-
-
Hernandez, D.1
François, P.2
Farinelli, L.3
Østerås, M.4
Schrenzel, J.5
-
42
-
-
79953778399
-
Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory
-
Herrera, C. M., and P. Bazaga 2011. Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Molecular Ecology 20:1675-1688.
-
(2011)
Molecular Ecology
, vol.20
, pp. 1675-1688
-
-
Herrera, C.M.1
Bazaga, P.2
-
44
-
-
78650164073
-
Using population genomics to detect selection in natural populations: key concepts and methodological considerations
-
Hohenlohe, P. A., P. C. Phillips, and W. A. Cresko 2010. Using population genomics to detect selection in natural populations: key concepts and methodological considerations. International Journal of Plant Sciences 171:1059-1071.
-
(2010)
International Journal of Plant Sciences
, vol.171
, pp. 1059-1071
-
-
Hohenlohe, P.A.1
Phillips, P.C.2
Cresko, W.A.3
-
45
-
-
0141853948
-
PCAP: a whole-genome assembly program
-
Huang, X., J. Wang, S. Aluru, S.-P. Yang, and L. Hillier 2003. PCAP: a whole-genome assembly program. Genome Research 13:2164-2170.
-
(2003)
Genome Research
, vol.13
, pp. 2164-2170
-
-
Huang, X.1
Wang, J.2
Aluru, S.3
Yang, S.-P.4
Hillier, L.5
-
46
-
-
84878076144
-
REAPR: a universal tool for genome assembly evaluation
-
Hunt, M., T. Kikuchi, M. Sanders, C. Newbold, M. Berriman, and T. Otto 2013. REAPR: a universal tool for genome assembly evaluation. Genome Biology 14:R47.
-
(2013)
Genome Biology
, vol.14
, pp. R47
-
-
Hunt, M.1
Kikuchi, T.2
Sanders, M.3
Newbold, C.4
Berriman, M.5
Otto, T.6
-
47
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
-
48
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa, M., and S. Goto 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27-30.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
49
-
-
84873175933
-
Reference-assisted chromosome assembly
-
Kim, J., D. M. Larkin, Q. Cai, Asan, Y. Zhang, R.-L. Ge, L. Auvil et al. 2013. Reference-assisted chromosome assembly. Proceedings of the National Academy of Sciences 110:1785-1790.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. 1785-1790
-
-
Kim, J.1
Larkin, D.M.2
Cai, Q.3
Asan, .4
Zhang, Y.5
Ge, R.-L.6
Auvil, L.7
-
50
-
-
33749508096
-
Genomics and conservation genetics
-
Kohn, M. H., W. J. Murphy, E. A. Ostrander, and R. K. Wayne 2006. Genomics and conservation genetics. Trends in Ecology & Evolution 21:629-637.
-
(2006)
Trends in Ecology & Evolution
, vol.21
, pp. 629-637
-
-
Kohn, M.H.1
Murphy, W.J.2
Ostrander, E.A.3
Wayne, R.K.4
-
51
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren, S., M. C. Schatz, B. P. Walenz, J. Martin, J. T. Howard, G. Ganapathy, Z. Wang et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 30:693-700.
-
(2012)
Nature Biotechnology
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
Wang, Z.7
-
52
-
-
85006201950
-
Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
-
Lampa, S., M. Dahlo, P. Olason, J. Hagberg, and O. Spjuth 2013. Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. GigaScience 2:9.
-
(2013)
GigaScience
, vol.2
, pp. 9
-
-
Lampa, S.1
Dahlo, M.2
Olason, P.3
Hagberg, J.4
Spjuth, O.5
-
53
-
-
84857477622
-
Inference of population structure using dense haplotype data
-
Lawson, D. J., G. Hellenthal, S. Myers, and D. Falush 2012. Inference of population structure using dense haplotype data. PLoS Genetics 8:e1002453.
-
(2012)
PLoS Genetics
, vol.8
, pp. e1002453
-
-
Lawson, D.J.1
Hellenthal, G.2
Myers, S.3
Falush, D.4
-
54
-
-
84883204405
-
Web Apollo: a web-based genomic annotation editing platform
-
Lee, E., G. Helt, J. Reese, M. C. Munoz-Torres, C. Childers, R. M. Buels, L. Stein et al. 2013. Web Apollo: a web-based genomic annotation editing platform. Genome Biology 14:R93.
-
(2013)
Genome Biology
, vol.14
, pp. R93
-
-
Lee, E.1
Helt, G.2
Reese, J.3
Munoz-Torres, M.C.4
Childers, C.5
Buels, R.M.6
Stein, L.7
-
55
-
-
84864119729
-
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
-
Li, H. 2012. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28:1838-1844.
-
(2012)
Bioinformatics
, vol.28
, pp. 1838-1844
-
-
Li, H.1
-
56
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H., and R. Durbin 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
57
-
-
79960914105
-
Inference of human population history from individual whole-genome sequences
-
Li, H., and R. Durbin 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
-
(2011)
Nature
, vol.475
, pp. 493-496
-
-
Li, H.1
Durbin, R.2
-
58
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
-
59
-
-
75149155568
-
The sequence and de novo assembly of the giant panda genome
-
Li, R., W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463:311-317.
-
(2010)
Nature
, vol.463
, pp. 311-317
-
-
Li, R.1
Fan, W.2
Tian, G.3
Zhu, H.4
He, L.5
Cai, J.6
Huang, Q.7
-
60
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh, K., M. Garber, O. Zuk, M. F. Lin, B. J. Parker, S. Washietl, P. Kheradpour et al. 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
-
61
-
-
79251553493
-
Comparative and demographic analysis of orang-utan genomes
-
Locke, D. P., L. W. Hillier, W. C. Warren, K. C. Worley, L. V. Nazareth, D. M. Muzny, S.-P. Yang et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469:529-533.
-
(2011)
Nature
, vol.469
, pp. 529-533
-
-
Locke, D.P.1
Hillier, L.W.2
Warren, W.C.3
Worley, K.C.4
Nazareth, L.V.5
Muzny, D.M.6
Yang, S.-P.7
-
62
-
-
84942887758
-
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
-
Luo, R., B. Liu, Y. Xie, Z. Li, W. Huang, J. Yuan, G. He et al. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18.
-
(2012)
GigaScience
, vol.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
Yuan, J.6
He, G.7
-
63
-
-
79952592810
-
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-
Marçais, G., and C. Kingsford 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764-770.
-
(2011)
Bioinformatics
, vol.27
, pp. 764-770
-
-
Marçais, G.1
Kingsford, C.2
-
66
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 17:10-12.
-
(2011)
EMBnet Journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
67
-
-
80052960863
-
Next-generation transcriptome assembly
-
Martin, J. A., and Z. Wang 2011. Next-generation transcriptome assembly. Nature Reviews Genetics 12:671-682.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
68
-
-
84911885318
-
How and why should we implement genomics into conservation? Evolutionary Applications
-
McMahon, B. J., E. C. Teeling, and J. Höglund . 2014. How and why should we implement genomics into conservation? Evolutionary Applications 7:999-1007.
-
(2014)
, vol.7
, pp. 999-1007
-
-
McMahon, B.J.1
Teeling, E.C.2
Höglund, J.3
-
69
-
-
56749119854
-
Sequencing the nuclear genome of the extinct woolly mammoth
-
Miller, W., D. I. Drautz, A. Ratan, B. Pusey, J. Qi, A. M. Lesk, L. P. Tomsho et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-390.
-
(2008)
Nature
, vol.456
, pp. 387-390
-
-
Miller, W.1
Drautz, D.I.2
Ratan, A.3
Pusey, B.4
Qi, J.5
Lesk, A.M.6
Tomsho, L.P.7
-
70
-
-
77952886150
-
Assembly algorithms for next-generation sequencing data
-
Miller, J. R., S. Koren, and G. Sutton 2010. Assembly algorithms for next-generation sequencing data. Genomics 95:315-327.
-
(2010)
Genomics
, vol.95
, pp. 315-327
-
-
Miller, J.R.1
Koren, S.2
Sutton, G.3
-
71
-
-
79961044560
-
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)
-
Miller, W., V. M. Hayes, A. Ratan, D. C. Petersen, N. E. Wittekindt, J. Miller, B. Walenz et al. 2011. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences 108:12348-12353.
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 12348-12353
-
-
Miller, W.1
Hayes, V.M.2
Ratan, A.3
Petersen, D.C.4
Wittekindt, N.E.5
Miller, J.6
Walenz, B.7
-
72
-
-
84865964725
-
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change
-
Miller, W., S. C. Schuster, A. J. Welch, A. Ratan, O. C. Bedoya-Reina, F. Zhao, H. L. Kim et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences 109:E2382-E2390.
-
(2012)
Proceedings of the National Academy of Sciences
, vol.109
, pp. E2382-E2390
-
-
Miller, W.1
Schuster, S.C.2
Welch, A.J.3
Ratan, A.4
Bedoya-Reina, O.C.5
Zhao, F.6
Kim, H.L.7
-
73
-
-
84863115547
-
Genome sequencing and analysis of the tasmanian devil and its transmissible cancer
-
Murchison, E. P., O. B. Schulz-Trieglaff, Z. Ning, L. B. Alexandrov, M. J. Bauer, B. Fu, M. Hims et al. 2012. Genome sequencing and analysis of the tasmanian devil and its transmissible cancer. Cell 148:780-791.
-
(2012)
Cell
, vol.148
, pp. 780-791
-
-
Murchison, E.P.1
Schulz-Trieglaff, O.B.2
Ning, Z.3
Alexandrov, L.B.4
Bauer, M.J.5
Fu, B.6
Hims, M.7
-
75
-
-
84879723871
-
Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna
-
Nakamura, Y., K. Mori, K. Saitoh, K. Oshima, M. Mekuchi, T. Sugaya, Y. Shigenobu et al. 2013. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proceedings of the National Academy of Sciences 110:11061-11066.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. 11061-11066
-
-
Nakamura, Y.1
Mori, K.2
Saitoh, K.3
Oshima, K.4
Mekuchi, M.5
Sugaya, T.6
Shigenobu, Y.7
-
76
-
-
84878427471
-
Genotyping-by-sequencing in ecological and conservation genomics
-
Narum, S. R., C. A. Buerkle, J. W. Davey, M. R. Miller, and P. A. Hohenlohe 2013. Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology 22:2841-2847.
-
(2013)
Molecular Ecology
, vol.22
, pp. 2841-2847
-
-
Narum, S.R.1
Buerkle, C.A.2
Davey, J.W.3
Miller, M.R.4
Hohenlohe, P.A.5
-
77
-
-
79955724657
-
Comparing de novo genome assembly: the long and short of it
-
Narzisi, G., and B. Mishra 2011. Comparing de novo genome assembly: the long and short of it. PLoS One 6:e19175.
-
(2011)
PLoS One
, vol.6
, pp. e19175
-
-
Narzisi, G.1
Mishra, B.2
-
78
-
-
79956314887
-
Genotype and SNP calling from next-generation sequencing data
-
Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song 2011. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12:443-451.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 443-451
-
-
Nielsen, R.1
Paul, J.S.2
Albrechtsen, A.3
Song, Y.S.4
-
79
-
-
84864643664
-
Gene-associated markers provide tools for tackling illegal fishing and false eco-certification
-
Nielsen, E. E., A. Cariani, E. M. Aoidh, G. E. Maes, I. Milano, R. Ogden, M. Taylor et al. 2012a. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nature Communications 3:851.
-
(2012)
Nature Communications
, vol.3
, pp. 851
-
-
Nielsen, E.E.1
Cariani, A.2
Aoidh, E.M.3
Maes, G.E.4
Milano, I.5
Ogden, R.6
Taylor, M.7
-
80
-
-
84864273210
-
SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data
-
Nielsen, R., T. Korneliussen, A. Albrechtsen, Y. Li, and J. Wang 2012b. SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7:e37558.
-
(2012)
PLoS One
, vol.7
, pp. e37558
-
-
Nielsen, R.1
Korneliussen, T.2
Albrechtsen, A.3
Li, Y.4
Wang, J.5
-
81
-
-
84875165671
-
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
-
Novák, P., P. Neumann, J. Pech, J. Steinhaisl, and J. Macas 2013. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793.
-
(2013)
Bioinformatics
, vol.29
, pp. 792-793
-
-
Novák, P.1
Neumann, P.2
Pech, J.3
Steinhaisl, J.4
Macas, J.5
-
82
-
-
84878420758
-
The Norway spruce genome sequence and conifer genome evolution
-
Nystedt, B., N. R. Street, A. Wetterbom, A. Zuccolo, Y.-C. Lin, D. G. Scofield, F. Vezzi et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature 497:579-584.
-
(2013)
Nature
, vol.497
, pp. 579-584
-
-
Nystedt, B.1
Street, N.R.2
Wetterbom, A.3
Zuccolo, A.4
Lin, Y.-C.5
Scofield, D.G.6
Vezzi, F.7
-
83
-
-
84877256024
-
A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education
-
Oleksyk, T., J.-F. Pombert, D. Siu, A. Mazo-Vargas, B. Ramos, W. Guiblet, Y. Afanador et al. 2012. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. GigaScience 1:14.
-
(2012)
GigaScience
, vol.1
, pp. 14
-
-
Oleksyk, T.1
Pombert, J.-F.2
Siu, D.3
Mazo-Vargas, A.4
Ramos, B.5
Guiblet, W.6
Afanador, Y.7
-
84
-
-
77949915021
-
Conservation genetics in transition to conservation genomics
-
Ouborg, N. J., C. Pertoldi, V. Loeschcke, R. Bijlsma, and P. W. Hedrick 2010. Conservation genetics in transition to conservation genomics. Trends in Genetics 26:177-187.
-
(2010)
Trends in Genetics
, vol.26
, pp. 177-187
-
-
Ouborg, N.J.1
Pertoldi, C.2
Loeschcke, V.3
Bijlsma, R.4
Hedrick, P.W.5
-
85
-
-
19944416873
-
Genetic analyses from ancient DNA
-
Pääbo, S., H. Poinar, D. Serre, V. Jaenicke-Despres, J. Hebler, N. Rohland, M. Kuch et al. 2004. Genetic analyses from ancient DNA. Annual review of genetics 38:645-679.
-
(2004)
Annual review of genetics
, vol.38
, pp. 645-679
-
-
Pääbo, S.1
Poinar, H.2
Serre, D.3
Jaenicke-Despres, V.4
Hebler, J.5
Rohland, N.6
Kuch, M.7
-
86
-
-
84885574505
-
Genome-wide signatures of convergent evolution in echolocating mammals
-
Parker, J., G. Tsagkogeorga, J. A. Cotton, Y. Liu, P. Provero, E. Stupka, and S. J. Rossiter 2013. Genome-wide signatures of convergent evolution in echolocating mammals. Nature 502:228-231.
-
(2013)
Nature
, vol.502
, pp. 228-231
-
-
Parker, J.1
Tsagkogeorga, G.2
Cotton, J.A.3
Liu, Y.4
Provero, P.5
Stupka, E.6
Rossiter, S.J.7
-
87
-
-
34249848751
-
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
-
Parra, G., K. Bradnam, and I. Korf 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061-1067.
-
(2007)
Bioinformatics
, vol.23
, pp. 1061-1067
-
-
Parra, G.1
Bradnam, K.2
Korf, I.3
-
88
-
-
84856468953
-
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
-
Patel, R. K., and M. Jain 2012. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619.
-
(2012)
PLoS One
, vol.7
, pp. e30619
-
-
Patel, R.K.1
Jain, M.2
-
89
-
-
84865818257
-
A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar
-
Perry, G. H., D. Reeves, P. Melsted, A. Ratan, W. Miller, K. Michelini, E. E. Louis et al. 2012. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution 4:126-135.
-
(2012)
Genome Biology and Evolution
, vol.4
, pp. 126-135
-
-
Perry, G.H.1
Reeves, D.2
Melsted, P.3
Ratan, A.4
Miller, W.5
Michelini, K.6
Louis, E.E.7
-
90
-
-
84876061150
-
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar
-
Perry, G. H., E. E. Louis, A. Ratan, O. C. Bedoya-Reina, R. C. Burhans, R. Lei, S. E. Johnson et al. 2013. Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proceedings of the National Academy of Sciences 110:5823-5828.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. 5823-5828
-
-
Perry, G.H.1
Louis, E.E.2
Ratan, A.3
Bedoya-Reina, O.C.4
Burhans, R.C.5
Lei, R.6
Johnson, S.E.7
-
91
-
-
45549109750
-
Genome assembly forensics: finding the elusive mis-assembly
-
Phillippy, A., M. Schatz, and M. Pop 2008. Genome assembly forensics: finding the elusive mis-assembly. Genome Biology 9:R55.
-
(2008)
Genome Biology
, vol.9
, pp. R55
-
-
Phillippy, A.1
Schatz, M.2
Pop, M.3
-
92
-
-
67449095888
-
Genome assembly reborn: recent computational challenges
-
Pop, M. 2009. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10:354-366.
-
(2009)
Briefings in Bioinformatics
, vol.10
, pp. 354-366
-
-
Pop, M.1
-
93
-
-
66149113352
-
From conservation genetics to conservation genomics
-
Primmer, C. R. 2009. From conservation genetics to conservation genomics. Annals of the New York Academy of Sciences 1162:357-368.
-
(2009)
Annals of the New York Academy of Sciences
, vol.1162
, pp. 357-368
-
-
Primmer, C.R.1
-
94
-
-
84879015776
-
Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research
-
Primmer, C. R., S. Papakostas, E. H. Leder, M. J. Davis, and M. A. Ragan 2013. Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology 22:3216-3241.
-
(2013)
Molecular Ecology
, vol.22
, pp. 3216-3241
-
-
Primmer, C.R.1
Papakostas, S.2
Leder, E.H.3
Davis, M.J.4
Ragan, M.A.5
-
95
-
-
84862980012
-
The bonobo genome compared with the chimpanzee and human genomes
-
Prufer, K., K. Munch, I. Hellmann, K. Akagi, J. R. Miller, B. Walenz, S. Koren et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486:527-531.
-
(2012)
Nature
, vol.486
, pp. 527-531
-
-
Prufer, K.1
Munch, K.2
Hellmann, I.3
Akagi, K.4
Miller, J.R.5
Walenz, B.6
Koren, S.7
-
96
-
-
84864398778
-
The yak genome and adaptation to life at high altitude
-
Qiu, Q., G. Zhang, T. Ma, W. Qian, J. Wang, Z. Ye, C. Cao et al. 2012. The yak genome and adaptation to life at high altitude. Nature Genetics 44:946-949.
-
(2012)
Nature Genetics
, vol.44
, pp. 946-949
-
-
Qiu, Q.1
Zhang, G.2
Ma, T.3
Qian, W.4
Wang, J.5
Ye, Z.6
Cao, C.7
-
97
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan, A. R., and I. M. Hall 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
98
-
-
84873700991
-
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
-
Rands, C., A. Darling, M. Fujita, L. Kong, M. Webster, C. Clabaut, R. Emes et al. 2013. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14:95.
-
(2013)
BMC Genomics
, vol.14
, pp. 95
-
-
Rands, C.1
Darling, A.2
Fujita, M.3
Kong, L.4
Webster, M.5
Clabaut, C.6
Emes, R.7
-
99
-
-
67649258849
-
The value of avian genomics to the conservation of wildlife
-
Romanov, M. N., E. M. Tuttle, M. L. Houck, W. S. Modi, L. G. Chemnick, M. L. Korody, E. M. S. Mork et al. 2009. The value of avian genomics to the conservation of wildlife. BMC Genomics 10(Suppl 2):S10.
-
(2009)
BMC Genomics
, vol.10
, pp. S10
-
-
Romanov, M.N.1
Tuttle, E.M.2
Houck, M.L.3
Modi, W.S.4
Chemnick, L.G.5
Korody, M.L.6
Mork, E.M.S.7
-
100
-
-
84863230553
-
Insights into hominid evolution from the gorilla genome sequence
-
Scally, A., J. Y. Dutheil, L. W. Hillier, G. E. Jordan, I. Goodhead, J. Herrero, A. Hobolth et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.
-
(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
-
101
-
-
77956279237
-
Assembly of large genomes using second-generation sequencing
-
Schatz, M. C., A. L. Delcher, and S. L. Salzberg 2010a. Assembly of large genomes using second-generation sequencing. Genome Research 20:1165-1173.
-
(2010)
Genome Research
, vol.20
, pp. 1165-1173
-
-
Schatz, M.C.1
Delcher, A.L.2
Salzberg, S.L.3
-
103
-
-
84860342753
-
Current challenges in de novo plant genome sequencing and assembly
-
Schatz, M., J. Witkowski, and W. R. McCombie 2012. Current challenges in de novo plant genome sequencing and assembly. Genome Biology 13:243.
-
(2012)
Genome Biology
, vol.13
, pp. 243
-
-
Schatz, M.1
Witkowski, J.2
McCombie, W.R.3
-
104
-
-
84875591702
-
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
-
Schatz, M. C., A. M. Phillippy, D. D. Sommer, A. L. Delcher, D. Puiu, G. Narzisi, S. L. Salzberg et al. 2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics 14:213-224.
-
(2013)
Briefings in Bioinformatics
, vol.14
, pp. 213-224
-
-
Schatz, M.C.1
Phillippy, A.M.2
Sommer, D.D.3
Delcher, A.L.4
Puiu, D.5
Narzisi, G.6
Salzberg, S.L.7
-
105
-
-
79959974750
-
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
-
Schneeberger, K., S. Ossowski, F. Ott, J. D. Klein, X. Wang, C. Lanz, L. M. Smith et al. 2011. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proceedings of the National Academy of Sciences 108:10249-10254.
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 10249-10254
-
-
Schneeberger, K.1
Ossowski, S.2
Ott, F.3
Klein, J.D.4
Wang, X.5
Lanz, C.6
Smith, L.M.7
-
106
-
-
84859625932
-
Next-generation sequencing technologies for environmental DNA research
-
Shokralla, S., J. L. Spall, J. F. Gibson, and M. Hajibabaei 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21:1794-1805.
-
(2012)
Molecular Ecology
, vol.21
, pp. 1794-1805
-
-
Shokralla, S.1
Spall, J.L.2
Gibson, J.F.3
Hajibabaei, M.4
-
107
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson, J. T., and R. Durbin 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Research 22:549-556.
-
(2012)
Genome Research
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
108
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
Simpson, J. T., K. Wong, S. D. Jackman, J. E. Schein, S. J. M. Jones, and I˙. Birol 2009. ABySS: a parallel assembler for short read sequence data. Genome Research 19:1117-1123.
-
(2009)
Genome Research
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
109
-
-
84892728434
-
Sequencing depth and coverage: key considerations in genomic analyses
-
Sims, D., I. Sudbery, N. E. Ilott, A. Heger, and C. P. Ponting 2014. Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics 15:121-132.
-
(2014)
Nature Reviews Genetics
, vol.15
, pp. 121-132
-
-
Sims, D.1
Sudbery, I.2
Ilott, N.E.3
Heger, A.4
Ponting, C.P.5
-
110
-
-
80054784996
-
ConDeTri - a content dependent read trimmer for Illumina data
-
Smeds, L., and A. Künstner 2011. ConDeTri - a content dependent read trimmer for Illumina data. PLoS One 6:e26314.
-
(2011)
PLoS One
, vol.6
, pp. e26314
-
-
Smeds, L.1
Künstner, A.2
-
111
-
-
33747830848
-
AUGUSTUS: ab initio prediction of alternative transcripts
-
Stanke, M., O. Keller, I. Gunduz, A. Hayes, S. Waack, and B. Morgenstern 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research 34(Suppl 2):W435-W439.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. W435-W439
-
-
Stanke, M.1
Keller, O.2
Gunduz, I.3
Hayes, A.4
Waack, S.5
Morgenstern, B.6
-
112
-
-
80052606169
-
The genome sequence of Atlantic cod reveals a unique immune system
-
Star, B., A. J. Nederbragt, S. Jentoft, U. Grimholt, M. Malmstrom, T. F. Gregers, T. B. Rounge et al. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477:207-210.
-
(2011)
Nature
, vol.477
, pp. 207-210
-
-
Star, B.1
Nederbragt, A.J.2
Jentoft, S.3
Grimholt, U.4
Malmstrom, M.5
Gregers, T.F.6
Rounge, T.B.7
-
113
-
-
84893741469
-
Conservation genomics of threatened animal species
-
Steiner, C. C., A. S. Putnam, P. E. A. Hoeck, and O. A. Ryder 2013. Conservation genomics of threatened animal species. Annual Review of Animal Biosciences 1:261-281.
-
(2013)
Annual Review of Animal Biosciences
, vol.1
, pp. 261-281
-
-
Steiner, C.C.1
Putnam, A.S.2
Hoeck, P.E.A.3
Ryder, O.A.4
-
114
-
-
79951810290
-
The importance of phase information for human genomics
-
Tewhey, R., V. Bansal, A. Torkamani, E. J. Topol, and N. J. Schork 2011. The importance of phase information for human genomics. Nature Reviews Genetics 12:215-223.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 215-223
-
-
Tewhey, R.1
Bansal, V.2
Torkamani, A.3
Topol, E.J.4
Schork, N.J.5
-
115
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
116
-
-
84863496231
-
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
-
The Heliconius Genome Consortium
-
The Heliconius Genome Consortium 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94-98.
-
(2012)
Nature
, vol.487
, pp. 94-98
-
-
-
117
-
-
66149192669
-
How to map billions of short reads onto genomes
-
Trapnell, C., and S. L. Salzberg 2009. How to map billions of short reads onto genomes. Nature Biotechnology 27:455-457.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 455-457
-
-
Trapnell, C.1
Salzberg, S.L.2
-
118
-
-
77950658346
-
Method improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
-
Tsai, I. J., T. D. Otto, and M. Berriman 2010. Method improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology 11:R41.
-
(2010)
Genome Biology
, vol.11
, pp. R41
-
-
Tsai, I.J.1
Otto, T.D.2
Berriman, M.3
-
119
-
-
84896009017
-
From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
-
Van der Auwera, G. A., M. O. Carneiro, C. Hartl, R. Poplin, G. del Angel, A. Levy-Moonshine, T. Jordan et al. 2013. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics 43:11.10.1-11.10.33.
-
(2013)
Current Protocols in Bioinformatics
, vol.43
, pp. 11101-111033
-
-
Van der Auwera, G.A.1
Carneiro, M.O.2
Hartl, C.3
Poplin, R.4
del Angel, G.5
Levy-Moonshine, A.6
Jordan, T.7
-
120
-
-
40149098690
-
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
-
Van Tassell, C. P., T. P. L. Smith, L. K. Matukumalli, J. F. Taylor, R. D. Schnabel, C. T. Lawley, C. D. Haudenschild et al. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5:247-252.
-
(2008)
Nature Methods
, vol.5
, pp. 247-252
-
-
Van Tassell, C.P.1
Smith, T.P.L.2
Matukumalli, L.K.3
Taylor, J.F.4
Schnabel, R.D.5
Lawley, C.T.6
Haudenschild, C.D.7
-
121
-
-
84872483518
-
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments
-
Vijay, N., J. W. Poelstra, A. Künstner, and J. B. W. Wolf 2013. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology 22:620-634.
-
(2013)
Molecular Ecology
, vol.22
, pp. 620-634
-
-
Vijay, N.1
Poelstra, J.W.2
Künstner, A.3
Wolf, J.B.W.4
-
122
-
-
84890842764
-
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
-
Vonk, F. J., N. R. Casewell, C. V. Henkel, A. M. Heimberg, H. J. Jansen, R. J. R. McCleary, H. M. E. Kerkkamp et al. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences 110:20651-20656.
-
(2013)
Proceedings of the National Academy of Sciences
, vol.110
, pp. 20651-20656
-
-
Vonk, F.J.1
Casewell, N.R.2
Henkel, C.V.3
Heimberg, A.M.4
Jansen, H.J.5
McCleary, R.J.R.6
Kerkkamp, H.M.E.7
-
123
-
-
84867363902
-
Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC
-
Wang, B., R. Ekblom, T. Strand, S. Portela-Bens, and J. Hoglund 2012. Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC. BMC Genomics 13:553.
-
(2012)
BMC Genomics
, vol.13
, pp. 553
-
-
Wang, B.1
Ekblom, R.2
Strand, T.3
Portela-Bens, S.4
Hoglund, J.5
-
124
-
-
84878729685
-
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
-
Wang, Z., J. Pascual-Anaya, A. Zadissa, W. Li, Y. Niimura, Z. Huang, C. Li et al. 2013. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics 45:701-706.
-
(2013)
Nature Genetics
, vol.45
, pp. 701-706
-
-
Wang, Z.1
Pascual-Anaya, J.2
Zadissa, A.3
Li, W.4
Niimura, Y.5
Huang, Z.6
Li, C.7
-
125
-
-
84899476884
-
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
-
Wang, B., R. Ekblom, I. Bunikis, H. Siitari, and J. Hoglund 2014. Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics 15:180.
-
(2014)
BMC Genomics
, vol.15
, pp. 180
-
-
Wang, B.1
Ekblom, R.2
Bunikis, I.3
Siitari, H.4
Hoglund, J.5
-
126
-
-
33847307402
-
Assembling millions of short DNA sequences using SSAKE
-
Warren, R. L., G. G. Sutton, S. J. M. Jones, and R. A. Holt 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500-501.
-
(2007)
Bioinformatics
, vol.23
, pp. 500-501
-
-
Warren, R.L.1
Sutton, G.G.2
Jones, S.J.M.3
Holt, R.A.4
-
127
-
-
84870255864
-
Black and white and read all over: the past, present and future of giant panda genetics
-
Wei, F., Y. Hu, L. Zhu, M. W. Bruford, X. Zhan, and L. Zhang 2012. Black and white and read all over: the past, present and future of giant panda genetics. Molecular Ecology 21:5660-5674.
-
(2012)
Molecular Ecology
, vol.21
, pp. 5660-5674
-
-
Wei, F.1
Hu, Y.2
Zhu, L.3
Bruford, M.W.4
Zhan, X.5
Zhang, L.6
-
128
-
-
42249087308
-
The complete genome of an individual by massively parallel DNA sequencing
-
Wheeler, D. A., M. Srinivasan, M. Egholm, Y. Shen, L. Chen, A. McGuire, W. He et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872-876.
-
(2008)
Nature
, vol.452
, pp. 872-876
-
-
Wheeler, D.A.1
Srinivasan, M.2
Egholm, M.3
Shen, Y.4
Chen, L.5
McGuire, A.6
He, W.7
-
129
-
-
84879330562
-
Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial
-
Wolf, J. B. W. 2013. Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Molecular Ecology Resources 13:559-572.
-
(2013)
Molecular Ecology Resources
, vol.13
, pp. 559-572
-
-
Wolf, J.B.W.1
-
130
-
-
84906944019
-
Tissue sampling methods and standards for vertebrate genomics
-
Wong, P., E. Wiley, W. Johnson, O. Ryder, S. O'Brien, D. Haussler, K.-P. Koepfli et al. 2012. Tissue sampling methods and standards for vertebrate genomics. GigaScience 1:8.
-
(2012)
GigaScience
, vol.1
, pp. 8
-
-
Wong, P.1
Wiley, E.2
Johnson, W.3
Ryder, O.4
O'Brien, S.5
Haussler, D.6
Koepfli, K.-P.7
-
131
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell, M., and D. Ence 2012. A beginner's guide to eukaryotic genome annotation. Nature Reviews Genetics 13:329-342.
-
(2012)
Nature Reviews Genetics
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
132
-
-
84891372280
-
Minke whale genome and aquatic adaptation in cetaceans
-
Yim, H.-S., Y. S. Cho, X. Guang, S. G. Kang, J.-Y. Jeong, S.-S. Cha, H.-M. Oh et al. 2014. Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics 46:88-92.
-
(2014)
Nature Genetics
, vol.46
, pp. 88-92
-
-
Yim, H.-S.1
Cho, Y.S.2
Guang, X.3
Kang, S.G.4
Jeong, J.-Y.5
Cha, S.-S.6
Oh, H.-M.7
-
133
-
-
84876308901
-
Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation
-
Zavodna, M., C. E. Grueber, and N. J. Gemmell 2013. Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation. PLoS One 8:e61471.
-
(2013)
PLoS One
, vol.8
, pp. e61471
-
-
Zavodna, M.1
Grueber, C.E.2
Gemmell, N.J.3
-
134
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D. R., and E. Birney 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.
-
(2008)
Genome Research
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
135
-
-
84878588665
-
Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle
-
Zhan, X., S. Pan, J. Wang, A. Dixon, J. He, M. G. Muller, P. Ni et al. 2013. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics 45:563-566.
-
(2013)
Nature Genetics
, vol.45
, pp. 563-566
-
-
Zhan, X.1
Pan, S.2
Wang, J.3
Dixon, A.4
He, J.5
Muller, M.G.6
Ni, P.7
-
136
-
-
84867088834
-
The oyster genome reveals stress adaptation and complexity of shell formation
-
Zhang, G., X. Fang, X. Guo, L. Li, R. Luo, F. Xu, P. Yang et al. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490:49-54.
-
(2012)
Nature
, vol.490
, pp. 49-54
-
-
Zhang, G.1
Fang, X.2
Guo, X.3
Li, L.4
Luo, R.5
Xu, F.6
Yang, P.7
-
137
-
-
84897111313
-
Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
-
Zhou, X., and A. Rokas 2014. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Molecular Ecology 23:1679-1700.
-
(2014)
Molecular Ecology
, vol.23
, pp. 1679-1700
-
-
Zhou, X.1
Rokas, A.2
-
138
-
-
84885968059
-
The MaSuRCA genome Assembler
-
Zimin, A., G. Marçais, D. Puiu, M. Roberts, S. L. Salzberg, and J. A. Yorke 2013. The MaSuRCA genome Assembler. Bioinformatics 29:2669-2677.
-
(2013)
Bioinformatics
, vol.29
, pp. 2669-2677
-
-
Zimin, A.1
Marçais, G.2
Puiu, D.3
Roberts, M.4
Salzberg, S.L.5
Yorke, J.A.6
|