-
1
-
-
84913548467
-
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
-
Adey, A., Kitzman, J. O., Burton, J. N., Daza, R., Kumar, A., Christiansen, L., et al. (2014). In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 24, 2041-2049. doi: 10.1101/gr.178319.114.
-
(2014)
Genome Res
, vol.24
, pp. 2041-2049
-
-
Adey, A.1
Kitzman, J.O.2
Burton, J.N.3
Daza, R.4
Kumar, A.5
Christiansen, L.6
-
2
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey, A., Morrison, H. G., Asan, Xun, X., Kitzman, J. O., Turner, E. H., et al. (2010). Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11:R119. doi: 10.1186/gb-2010-11-12-r119.
-
(2010)
Genome Biol
, vol.11
, pp. R119
-
-
Adey, A.1
Morrison, H.G.2
Asan Xun, X.3
Kitzman, J.O.4
Turner, E.H.5
-
3
-
-
78650909427
-
Limitations of next-generation genome sequence assembly
-
Alkan, C., Sajjadian, S., and Eichler, E. E. (2011). Limitations of next-generation genome sequence assembly. Nat. Methods 8, 61-65. doi: 10.1038/nmeth.1527.
-
(2011)
Nat. Methods
, vol.8
, pp. 61-65
-
-
Alkan, C.1
Sajjadian, S.2
Eichler, E.E.3
-
4
-
-
84922537404
-
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
-
Amini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., et al. (2014). Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat. Genet. 46, 1343-1349. doi: 10.1038/ng.3119.
-
(2014)
Nat. Genet
, vol.46
, pp. 1343-1349
-
-
Amini, S.1
Pushkarev, D.2
Christiansen, L.3
Kostem, E.4
Royce, T.5
Turk, C.6
-
5
-
-
54449098752
-
Rapid SNP discovery and genetic mapping using sequenced RAD markers
-
Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. doi: 10.1371/journal.pone.0003376.
-
(2008)
PLoS ONE
, vol.3
-
-
Baird, N.A.1
Etter, P.D.2
Atwood, T.S.3
Currey, M.C.4
Shiver, A.L.5
Lewis, Z.A.6
-
6
-
-
84859178440
-
De novo genome assembly: what every biologist should know
-
Baker, M. (2012). De novo genome assembly: what every biologist should know. Nat. Methods 9, 333-337. doi: 10.1038/nmeth.1935.
-
(2012)
Nat. Methods
, vol.9
, pp. 333-337
-
-
Baker, M.1
-
7
-
-
84928902472
-
High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly
-
Bartholome, J., Mandrou, E., Mabiala, A., Jenkins, J., Nabihoudine, I., Klopp, C., et al. (2015). High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol. 206, 1283-1296. doi: 10.1111/nph.13150.
-
(2015)
New Phytol
, vol.206
, pp. 1283-1296
-
-
Bartholome, J.1
Mandrou, E.2
Mabiala, A.3
Jenkins, J.4
Nabihoudine, I.5
Klopp, C.6
-
8
-
-
0036144823
-
ARACHE: a whole-genome shotgun assembler
-
Batzoglou, S., Jaffe, D. B., Stanley, K., Butler, J., Gnerre, S., Mauceli, E., et al. (2002). ARACHE: a whole-genome shotgun assembler. Genome Res. 12, 177-189. doi: 10.1101/gr.208902.
-
(2002)
Genome Res
, vol.12
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.B.2
Stanley, K.3
Butler, J.4
Gnerre, S.5
Mauceli, E.6
-
9
-
-
84991528460
-
Assemblathon 2, evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., et al. (2013). Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2:10. doi: 10.1186/2047-217X-2-10.
-
(2013)
Gigascience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
Fass, J.N.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
Birol, I.6
-
10
-
-
0037958742
-
R/qtl: QTL mapping in experimental crosses
-
Broman, K. W., Wu, H., Sen, S., and Churchill, G. A. (2003). R/qtl: QTL mapping in experimental crosses. Bioinformatics 19, 889-890. doi: 10.1093/bioinformatics/btg112.
-
(2003)
Bioinformatics
, vol.19
, pp. 889-890
-
-
Broman, K.W.1
Wu, H.2
Sen, S.3
Churchill, G.A.4
-
11
-
-
0025958321
-
Recombinant inbreds for molecular mapping in maize
-
Burr, B., and Burr, F. A. (1991). Recombinant inbreds for molecular mapping in maize. Trends Genet. 7, 55-60.
-
(1991)
Trends Genet
, vol.7
, pp. 55-60
-
-
Burr, B.1
Burr, F.A.2
-
12
-
-
0023968729
-
Gene mapping with recombinant inbreds in maize
-
Burr, B., Burr, F. A., Thompson, K. H., Albertson, M. C., and Stuber, C. W. (1988). Gene mapping with recombinant inbreds in maize. Genetics 118, 519-526.
-
(1988)
Genetics
, vol.118
, pp. 519-526
-
-
Burr, B.1
Burr, F.A.2
Thompson, K.H.3
Albertson, M.C.4
Stuber, C.W.5
-
13
-
-
84890034912
-
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
-
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., and Shendure, J. (2013). Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125. doi: 10.1038/nbt.2727.
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 1119-1125
-
-
Burton, J.N.1
Adey, A.2
Patwardhan, R.P.3
Qiu, R.4
Kitzman, J.O.5
Shendure, J.6
-
14
-
-
84923794054
-
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
-
Cao, H., Hastie, A. R., Cao, D., Lam, E. T., Sun, Y., Huang, H., et al. (2014). Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience 3:34. doi: 10.1186/2047-217X-3-34.
-
(2014)
Gigascience
, vol.3
, pp. 34
-
-
Cao, H.1
Hastie, A.R.2
Cao, D.3
Lam, E.T.4
Sun, Y.5
Huang, H.6
-
15
-
-
84925513772
-
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
-
Chapman, J. A., Mascher, M., Buluc, A., Barry, K., Georganas, E., Session, A., et al. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 16, 26. doi: 10.1186/s13059-015-0582-8.
-
(2015)
Genome Biol
, vol.16
, pp. 26
-
-
Chapman, J.A.1
Mascher, M.2
Buluc, A.3
Barry, K.4
Georganas, E.5
Session, A.6
-
16
-
-
70450280981
-
Computational approaches and software tools for genetic linkage map estimation in plants
-
Cheema, J., and Dicks, J. (2009). Computational approaches and software tools for genetic linkage map estimation in plants. Brief. Bioinformatics 10, 595-608. doi: 10.1093/bib/bbp045.
-
(2009)
Brief. Bioinformatics
, vol.10
, pp. 595-608
-
-
Cheema, J.1
Dicks, J.2
-
17
-
-
84876936831
-
Effects of GC bias in next-generation-sequencing data on de novo genome assembly
-
Chen, Y., Liu, T., Yu, C., Chiang, T., and Hwang, C. (2013). Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS ONE 8:e62856. doi: 10.1371/journal.pone.0062856.
-
(2013)
PLoS ONE
, vol.8
-
-
Chen, Y.1
Liu, T.2
Yu, C.3
Chiang, T.4
Hwang, C.5
-
18
-
-
0005292858
-
Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads, Proc
-
Collins, J., and Hohn, B. (1978). Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads, Proc. Natl. Acad. Sci. U.S.A. 75, 4242-4246.
-
(1978)
Natl. Acad. Sci. U.S.A
, vol.75
, pp. 4242-4246
-
-
Collins, J.1
Hohn, B.2
-
19
-
-
84855297335
-
A decade of 3C technologies: insights into nuclear organization
-
de Wit, E., and de Laat, W. (2012). A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11-24. doi: 10.1101/gad.179804.111.
-
(2012)
Genes Dev
, vol.26
, pp. 11-24
-
-
de Wit, E.1
de Laat, W.2
-
20
-
-
84919629313
-
Extensive error in the number of genes inferred from draft genome assemblies
-
Denton, J. F., Lugo-Martinez, J., Tucker, A. E., Schrider, D. R., Warren, W. C., and Hahn, M. W. (2014). Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput. Biol. 10:e1003998. doi: 10.1371/journal.pcbi.1003998.
-
(2014)
PLoS Comput. Biol
, vol.10
-
-
Denton, J.F.1
Lugo-Martinez, J.2
Tucker, A.E.3
Schrider, D.R.4
Warren, W.C.5
Hahn, M.W.6
-
21
-
-
52649157765
-
Substanial biases in ultra-short read data sets from high-throughput dna sequencing
-
Dohm, J. C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2008). Substanial biases in ultra-short read data sets from high-throughput dna sequencing. Nucleic Acids Res. 36:e105. doi: 10.1093/nar/gkn425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
22
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Drosophila 12 Genomes Consortium. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218. doi: 10.1038/nature06341.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
-
23
-
-
83055181941
-
Assemblathon 1, a competitive assessment of de novo short read assembly methods
-
Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D., Fass, J., et al. (2011). Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21, 2224-2241. doi: 10.1101/gr.126599.111.
-
(2011)
Genome Res
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St John, J.3
Darling, A.4
Lin, D.5
Fass, J.6
-
24
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., et al. (2008). Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138. doi: 10.1126/science.1162986.
-
(2008)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
-
25
-
-
84911882712
-
A field guide to whole-genome sequencing, assembly and annotation, Evol
-
Ekblom, R., and Wolf, J. B. W. (2014). A field guide to whole-genome sequencing, assembly and annotation, Evol. Appl. 7, 1026-1042. doi: 10.1111/eva.12178.
-
(2014)
Appl
, vol.7
, pp. 1026-1042
-
-
Ekblom, R.1
Wolf, J.B.W.2
-
26
-
-
79955783956
-
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
-
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., et al. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi: 10.1371/journal.pone.0019379.
-
(2011)
PLoS ONE
, vol.6
-
-
Elshire, R.J.1
Glaubitz, J.C.2
Sun, Q.3
Poland, J.A.4
Kawamoto, K.5
Buckler, E.S.6
-
27
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., et al. (2011). High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U.S.A. 108, 1513-1518. doi: 10.1073/pnas.1017351108.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A
, 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
-
28
-
-
0030972827
-
2× genomes-Does depth matter?
-
Green, P. (1997). 2× genomes-Does depth matter? Genome Res. 7:410.
-
(1997)
Genome Res
, vol.7
, pp. 410
-
-
Green, P.1
-
29
-
-
84898855509
-
Sequencing, assembling, and correcting draft genomes using recombinant populations
-
Hahn, M. W., Zhang, S. V., and Moyle, L. C. (2014). Sequencing, assembling, and correcting draft genomes using recombinant populations. G3 (Bethesda) 4, 669-679. doi: 10.1534/g3.114.010264.
-
(2014)
G3 (Bethesda)
, vol.4
, pp. 669-679
-
-
Hahn, M.W.1
Zhang, S.V.2
Moyle, L.C.3
-
30
-
-
84924286023
-
Flexible and scalable genotyping-by-sequencing strategies for population studies
-
Heffelfinger, C., Fragoso, C. A., Moreno, M. A., Overton, J. D., Mottinger, J. P., Zhao, H., et al. (2014). Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics 15:979. doi: 10.1186/1471-2164-15-979.
-
(2014)
BMC Genomics
, vol.15
, pp. 979
-
-
Heffelfinger, C.1
Fragoso, C.A.2
Moreno, M.A.3
Overton, J.D.4
Mottinger, J.P.5
Zhao, H.6
-
31
-
-
84878076144
-
REAPR: a universal tool for genome assembly evaluation
-
Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., and Otto, T. (2013). REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14:R47. doi: 10.1186/gb-2013-14-5-r47.
-
(2013)
Genome Biol
, vol.14
, pp. R47
-
-
Hunt, M.1
Kikuchi, T.2
Sanders, M.3
Newbold, C.4
Berriman, M.5
Otto, T.6
-
32
-
-
0034978066
-
Constructing dense genetic linkage maps
-
Jansen, J., de Jong, A. G., and van Ooijen, J. W. (2001). Constructing dense genetic linkage maps. Theor. Appl. Genet. 102, 1113-1122. doi: 10.1007/s001220000489.
-
(2001)
Theor. Appl. Genet
, vol.102
, pp. 1113-1122
-
-
Jansen, J.1
de Jong, A.G.2
van Ooijen, J.W.3
-
33
-
-
84890032321
-
High-throughput genome scaffolding from in vivo DNA interaction frequency
-
Kaplan, N., and Dekker, J. (2013). High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31, 1143-1147. doi: 10.1038/nbt.2768.
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 1143-1147
-
-
Kaplan, N.1
Dekker, J.2
-
34
-
-
84905465421
-
A high-density linkage map enables a second-generation collared flycatcher assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
-
Kawakami, T., Smeds, L., Backstrom, N., Husby, A., Qvarnstrom, A., Mugal, C. F., et al. (2014). A high-density linkage map enables a second-generation collared flycatcher assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol. Ecol. 23, 4035-4058. doi: 10.1111/mec.12810.
-
(2014)
Mol. Ecol
, vol.23
, pp. 4035-4058
-
-
Kawakami, T.1
Smeds, L.2
Backstrom, N.3
Husby, A.4
Qvarnstrom, A.5
Mugal, C.F.6
-
35
-
-
0026594245
-
Stable propagation of cosmid-sized human DNA inserts in an F-factor based vector
-
Kim, U., Shizuya, H., De Jong, P. J., Birren, B., and Simon, M. I. (1992). Stable propagation of cosmid-sized human DNA inserts in an F-factor based vector. Nucleic Acids Res. 20, 1083-1085.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 1083-1085
-
-
Kim, U.1
Shizuya, H.2
De Jong, P.J.3
Birren, B.4
Simon, M.I.5
-
36
-
-
84913554630
-
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
-
Koren, S., and Phillippy, A. M. (2015). One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110-120. doi: 10.1016/j.mib.2014.11.014.
-
(2015)
Curr. Opin. Microbiol
, vol.23
, pp. 110-120
-
-
Koren, S.1
Phillippy, A.M.2
-
37
-
-
84883664726
-
Reducing assembly complexity of microbial genomes with single-molecule sequencing
-
Koren, S., Harhay, G. P., Smith, T. P., Bono, J. L., Harhay, D. M., McVey, S. D., et al. (2013). Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol. 14:R101. doi: 10.1186/gb-2013-14-9-r101.
-
(2013)
Genome Biol
, vol.14
, pp. R101
-
-
Koren, S.1
Harhay, G.P.2
Smith, T.P.3
Bono, J.L.4
Harhay, D.M.5
McVey, S.D.6
-
38
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
Kozarewa, I., Ning, Z., Quail, M. A., Sanders, M. J., and Berriman, M. (2009). Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6, 291-295. doi: 10.1038/nmeth.1311.
-
(2009)
Nat. Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
Ning, Z.2
Quail, M.A.3
Sanders, M.J.4
Berriman, M.5
-
39
-
-
0024508964
-
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps
-
Lander, E. S., and Botstein, D. (1989). Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121, 185-199.
-
(1989)
Genetics
, vol.121
, pp. 185-199
-
-
Lander, E.S.1
Botstein, D.2
-
40
-
-
84907086311
-
Initial De novo assemblies of the D. melanogaster genome using long-read
-
Landolin, J., Chin, J., Kim, K., Yu, C., Fisher, W. W., Wan, K. H., et al. (2014). Initial De novo assemblies of the D. melanogaster genome using long-read PacBio sequencing. doi: 10.6084/m9.figshare.976097.
-
(2014)
PacBio sequencing
-
-
Landolin, J.1
Chin, J.2
Kim, K.3
Yu, C.4
Fisher, W.W.5
Wan, K.H.6
-
41
-
-
84880943505
-
Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy
-
Levy-Sakin, M., and Ebenstein, Y. (2013). Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. Curr. Opin. Biotechnol. 24, 690-698. doi: 10.1016/j.copbio.2013.01.009.
-
(2013)
Curr. Opin. Biotechnol
, vol.24
, pp. 690-698
-
-
Levy-Sakin, M.1
Ebenstein, Y.2
-
42
-
-
70350714429
-
Every genome sequence needs a good map
-
Lewin, H. A., Larkin, D. M., Pontius, J., and O'Brien, S. J. (2009). Every genome sequence needs a good map. Genome Res. 19, 1925-1928. doi: 10.1101/gr.094557.109.
-
(2009)
Genome Res
, vol.19
, pp. 1925-1928
-
-
Lewin, H.A.1
Larkin, D.M.2
Pontius, J.3
O'Brien, S.J.4
-
43
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293. doi: 10.1126/science.1181369.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
-
44
-
-
84871823801
-
Comparison of next-generation sequencing systems
-
Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., et al. (2012). Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 1-11. doi: 10.1155/2012/373945.
-
(2012)
J. Biomed. Biotechnol
, vol.2012
, pp. 1-11
-
-
Liu, L.1
Li, Y.2
Li, S.3
Hu, N.4
He, Y.5
Pong, R.6
-
45
-
-
84902590946
-
Construction and analysis of high-density linkage map using high-throughput sequencing data
-
Liu, D., Ma, C., Hong, W., Huang, L., Liu, M., Liu, H., et al. (2014). Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS ONE 9:e98855. doi: 10.1371/journal.pone.0098855.
-
(2014)
PLoS ONE
, vol.9
-
-
Liu, D.1
Ma, C.2
Hong, W.3
Huang, L.4
Liu, M.5
Liu, H.6
-
46
-
-
34547190185
-
Onemap: software for genetic mapping in outcrossing species
-
Margarido, G. R. A., Souza, A. P., and Garcia, A. A. F. (2007). Onemap: software for genetic mapping in outcrossing species. Hereditas 144, 78-79. doi: 10.1111/j.2007.0018-0661.02000.x.
-
(2007)
Hereditas
, vol.144
, pp. 78-79
-
-
Margarido, G.R.A.1
Souza, A.P.2
Garcia, A.A.F.3
-
47
-
-
84906215015
-
Genetic anchoring of whole-genome shotgun assemblies
-
Mascher, M., and Stein, N. (2014). Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5:208. doi: 10.3389/fgene.2014.00208.
-
(2014)
Front. Genet
, vol.5
, pp. 208
-
-
Mascher, M.1
Stein, N.2
-
48
-
-
84886793453
-
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
-
Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., et al. (2013). Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76, 718-727. doi: 10.1111/tpj.12319.
-
(2013)
Plant J
, vol.76
, pp. 718-727
-
-
Mascher, M.1
Muehlbauer, G.J.2
Rokhsar, D.S.3
Chapman, J.4
Schmutz, J.5
Barry, K.6
-
49
-
-
84907087679
-
Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements
-
McCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., et al. (2014). Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS ONE 9:e106689. doi: 10.1371/journal.pone.0106689.
-
(2014)
PLoS ONE
, vol.9
-
-
McCoy, R.C.1
Taylor, R.W.2
Blauwkamp, T.A.3
Kelley, J.L.4
Kertesz, M.5
Pushkarev, D.6
-
50
-
-
70549083922
-
Evaluation of algorithms used to order markers on genetic maps
-
Mollinari, M., Margarido, G. R. A., Vencovsky, R., and Garcia, A. A. F. (2009). Evaluation of algorithms used to order markers on genetic maps. Heredity 103, 494-502. doi: 10.1038/hdy.2009.96.
-
(2009)
Heredity
, vol.103
, pp. 494-502
-
-
Mollinari, M.1
Margarido, G.R.A.2
Vencovsky, R.3
Garcia, A.A.F.4
-
51
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., et al. (2000). A whole-genome assembly of Drosophila. Science 287, 2196-2204. doi: 10.1126/science.287.5461.2196.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
Dew, I.M.4
Fasulo, D.P.5
Flanigan, M.J.6
-
52
-
-
84905989520
-
Joint assembly and genetic mapping of the atlantic horseshoe crab genome reveals ancient whole genome duplication
-
Nossa, C. W., Havlak, P., Yue, J., Lv, J., Vincent, K. Y., Brockmann, H. J., et al. (2014). Joint assembly and genetic mapping of the atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience 3:9. doi: 10.1186/2047-217X-3-9.
-
(2014)
Gigascience
, vol.3
, pp. 9
-
-
Nossa, C.W.1
Havlak, P.2
Yue, J.3
Lv, J.4
Vincent, K.Y.5
Brockmann, H.J.6
-
53
-
-
0024390820
-
Construction of large DNA segments in Escherichia coli
-
O'Connor, M., Peifer, M., and Bender, W. (1989). Construction of large DNA segments in Escherichia coli. Science 4910, 1307-1312.
-
(1989)
Science
, vol.4910
, pp. 1307-1312
-
-
O'Connor, M.1
Peifer, M.2
Bender, W.3
-
54
-
-
58249138817
-
Generations of sequencing technologies
-
Petterson, E., Lundeberg, J., and Ahmadian, A. (2009). Generations of sequencing technologies. Genomics 93, 105-111. doi: 10.1016/j.ygeno.2008.10.003.
-
(2009)
Genomics
, vol.93
, pp. 105-111
-
-
Petterson, E.1
Lundeberg, J.2
Ahmadian, A.3
-
55
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner, P. A., Tang, H., and Waterman, M. S. (2001). An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A. 98, 9748-9753. doi: 10.1073/pnas.171285098.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A
, vol.98
, pp. 9748-9753
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
56
-
-
39649084637
-
Bioinformatics challenges of new sequencing technology
-
Pop, M., and Salzberg, S. L. (2008). Bioinformatics challenges of new sequencing technology. Trends Genet. 24, 142-149. doi: 10.1016/j.tig.2007.12.006.
-
(2008)
Trends Genet
, vol.24
, pp. 142-149
-
-
Pop, M.1
Salzberg, S.L.2
-
57
-
-
84977623941
-
'De novo identification of 'heterotigs" towards accurate and in-phase assemby of complex plant genomes,"
-
(Las Vegas, NV)
-
Price, J. C., Udall, J. A., Bodily, P. M., Ward, J. A., Schatz, M. C., Page, J. T., et al. (2012). "De novo identification of "heterotigs" towards accurate and in-phase assemby of complex plant genomes," in Proceedings of The 2012 International Conference on Bioinformatics and Computational Biology (BIOCOMP12) (Las Vegas, NV).
-
(2012)
Proceedings of The 2012 International Conference on Bioinformatics and Computational Biology (BIOCOMP12)
-
-
Price, J.C.1
Udall, J.A.2
Bodily, P.M.3
Ward, J.A.4
Schatz, M.C.5
Page, J.T.6
-
58
-
-
84929516809
-
-
Putnam, N. H., O'Connell, B., Stites, J. C., Rice, B. J., Fields, A., Hartley, P. D., et al. (2015). Chromsome-scale shotgun assembly using an in vitro method for long-range linkage. Available online at: http://arxiv.org/abs/1502.05331.
-
(2015)
Chromsome-scale shotgun assembly using an in vitro method for long-range linkage
-
-
Putnam, N.H.1
O'Connell, B.2
Stites, J.C.3
Rice, B.J.4
Fields, A.5
Hartley, P.D.6
-
59
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina miseq sequencers
-
Quail, M. A., Smith, M., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., et al. (2012). A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina miseq sequencers. BMC Genomics 13:341. doi: 10.1186/1471-2164-13-341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
Smith, M.2
Coupland, P.3
Otto, T.D.4
Harris, S.R.5
Connor, T.R.6
-
60
-
-
84942520038
-
A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer
-
Quick, J., Quinlan, A., and Loman, N. (2014). A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer. Gigascience 3, 22. doi: 10.1101/009613.
-
(2014)
Gigascience
, vol.3
, pp. 22
-
-
Quick, J.1
Quinlan, A.2
Loman, N.3
-
61
-
-
84898539524
-
Lep-MAP: fast and accurate linkage map construction for large SNP datasets
-
Rastas, P., Paulin, L., Hanski, I., Lehtonen, R., and Auvinen, P. (2013). Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics 29, 3128-3134. doi: 10.1093/bioinformatics/btt563.
-
(2013)
Bioinformatics
, vol.29
, pp. 3128-3134
-
-
Rastas, P.1
Paulin, L.2
Hanski, I.3
Lehtonen, R.4
Auvinen, P.5
-
62
-
-
0016800090
-
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
-
Sanger, F., and Coulson, A. R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94, 441-448.
-
(1975)
J. Mol. Biol
, vol.94
, pp. 441-448
-
-
Sanger, F.1
Coulson, A.R.2
-
63
-
-
0017681196
-
DNA sequencing with chain-terminating inhibitors
-
Sanger, F., Nicklen, S., and Couson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467.
-
(1977)
Proc. Natl. Acad. Sci. U.S.A
, vol.74
, pp. 5463-5467
-
-
Sanger, F.1
Nicklen, S.2
Couson, A.R.3
-
64
-
-
84859633774
-
DNA sequencing with nanopores
-
Schneider, G. F., and Dekker, C. (2012). DNA sequencing with nanopores. Nat. Biotechnol. 30, 326-328. doi: 10.1038/nbt.2181.
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 326-328
-
-
Schneider, G.F.1
Dekker, C.2
-
65
-
-
0027485082
-
Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping
-
Schwartz, D. C., Li, X., Hernandez, L., Ramnarain, S. P., Huff, E. J., and Wang, Y. K. (1993). Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262, 110-114.
-
(1993)
Science
, vol.262
, pp. 110-114
-
-
Schwartz, D.C.1
Li, X.2
Hernandez, L.3
Ramnarain, S.P.4
Huff, E.J.5
Wang, Y.K.6
-
66
-
-
67349103634
-
Principles, requirements and prospects of genetic mapping in plants
-
Semagn, K., Bjørnstad, A., and Ndjiondjop, M. J. (2006). Principles, requirements and prospects of genetic mapping in plants. Afr. J. Biotechnol. 5, 2569-2587.
-
(2006)
Afr. J. Biotechnol
, vol.5
, pp. 2569-2587
-
-
Semagn, K.1
Bjørnstad, A.2
Ndjiondjop, M.J.3
-
67
-
-
0026703169
-
Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector
-
Shizuy, H., Birren, B., Kim, U., Mancino, V., Slepak, T., Tachiiri, Y., et al. (1992). Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. U.S.A. 89, 8794-8797.
-
(1992)
Proc. Natl. Acad. Sci. U.S.A
, vol.89
, pp. 8794-8797
-
-
Shizuy, H.1
Birren, B.2
Kim, U.3
Mancino, V.4
Slepak, T.5
Tachiiri, Y.6
-
68
-
-
7344254829
-
Construction of integrated genetic linkage maps by means of a new computer package: joinmap
-
Stam, P. (1993). Construction of integrated genetic linkage maps by means of a new computer package: joinmap. Plant J. 3, 739-744.
-
(1993)
Plant J
, vol.3
, pp. 739-744
-
-
Stam, P.1
-
69
-
-
84922773775
-
'Efficient and accurate clustering for large-scale genetic mapping,'
-
(Belfast: IEEE)
-
Strnadova, V., Buluc, A., Chapman, J., Gilbert, J. R., Gonzalez, J., Jegelka, S., et al. (2014). "Efficient and accurate clustering for large-scale genetic mapping," in 2014 IEEE International Conference on Bioinformatics and Biomedicine (Belfast: IEEE), 3-10. doi: 10.1109/BIBM.2014.6999119.
-
(2014)
2014 IEEE International Conference on Bioinformatics and Biomedicine
, pp. 3-10
-
-
Strnadova, V.1
Buluc, A.2
Chapman, J.3
Gilbert, J.R.4
Gonzalez, J.5
Jegelka, S.6
-
70
-
-
84956762643
-
The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association
-
Sturtevant, A. H. (1913a). The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J. Exp. Zool. 14, 43-59.
-
(1913)
J. Exp. Zool
, vol.14
, pp. 43-59
-
-
Sturtevant, A.H.1
-
71
-
-
33750074514
-
A third group of linked genes in Drosophila ampelophila
-
Sturtevant, A. H. (1913b). A third group of linked genes in Drosophila ampelophila. Science 37, 990-992.
-
(1913)
Science
, vol.37
, pp. 990-992
-
-
Sturtevant, A.H.1
-
72
-
-
85005608771
-
Achiasmatic oogenesis in the heliconiine butterflies
-
Suomalainen, E., Cook, L. M., and Turner, J. R. G. (1973). Achiasmatic oogenesis in the heliconiine butterflies. Hereditas 74, 302-304.
-
(1973)
Hereditas
, vol.74
, pp. 302-304
-
-
Suomalainen, E.1
Cook, L.M.2
Turner, J.R.G.3
-
73
-
-
84904382612
-
A chromsome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
-
The International Wheat Genome Sequencing Consortium. (2014). A chromsome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1-11. doi: 10.1126/science.1251788.
-
(2014)
Science
, vol.345
, pp. 1-11
-
-
-
74
-
-
84894033853
-
Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
-
van Oers, K., Santure, A. W., De Cauwer, I., van Bers, N. E. M., Crooijmans, R. P. M. A., Shelder, B. C., et al. (2014). Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates. Heredity 112, 307-316. doi: 10.1038/hdy.2013.107.
-
(2014)
Heredity
, vol.112
, pp. 307-316
-
-
van Oers, K.1
Santure, A.W.2
De Cauwer, I.3
van Bers, N.E.M.4
Crooijmans, R.P.M.A.5
Shelder, B.C.6
-
75
-
-
80054890337
-
Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species
-
van Ooijen, J. W. (2011). Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet. Res. 93, 343-349. doi: 10.1017/S0016672311000279.
-
(2011)
Genet. Res
, vol.93
, pp. 343-349
-
-
van Ooijen, J.W.1
-
76
-
-
0030950735
-
Human whole-genome shotgun sequencing
-
Weber, J., and Myers, H. (1997). Human whole-genome shotgun sequencing. Genome Res. 7:401.
-
(1997)
Genome Res
, vol.7
, pp. 401
-
-
Weber, J.1
Myers, H.2
-
77
-
-
55449100528
-
Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph
-
Wu, Y., Bhat, P. R., Close, T. J., and Lonardi, S. (2008). Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 4:e1000212. doi: 10.1371/journal.pgen.1000212.
-
(2008)
PLoS Genet
, vol.4
-
-
Wu, Y.1
Bhat, P.R.2
Close, T.J.3
Lonardi, S.4
-
78
-
-
79961170068
-
Comparisons of four approximation algorithms for large-scale linkage map construction
-
Wu, J., Jenkins, J. N., McCarty, J. C., and Lou, X. (2011). Comparisons of four approximation algorithms for large-scale linkage map construction. Theor. Appl. Genet. 123, 649-655. doi: 10.1007/s00122-011-1614-8.
-
(2011)
Theor. Appl. Genet
, vol.123
, pp. 649-655
-
-
Wu, J.1
Jenkins, J.N.2
McCarty, J.C.3
Lou, X.4
-
79
-
-
84925052582
-
De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana
-
Xie, T., Zheng, J. F., Liu, S., Peng, C., Zhou, Y. M., Yang, Q. Y., et al. (2015). De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Mol. Plant 8, 489-492. doi: 10.1016/j.molp.2014.12.015.
-
(2015)
Mol. Plant
, vol.8
, pp. 489-492
-
-
Xie, T.1
Zheng, J.F.2
Liu, S.3
Peng, C.4
Zhou, Y.M.5
Yang, Q.Y.6
-
80
-
-
79960422847
-
Genome sequence and analysis of the tuber crop potato
-
Xu, X., Pan, S., Cheng, S., Zhang, B., Mu, D., Ni, P., et al. (2011). Genome sequence and analysis of the tuber crop potato Nature 475, 189-195. doi: 10.1038/nature10158.
-
(2011)
Nature
, vol.475
, pp. 189-195
-
-
Xu, X.1
Pan, S.2
Cheng, S.3
Zhang, B.4
Mu, D.5
Ni, P.6
-
81
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D. R., and Birney, E. (2010). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829. doi: 10.1101/gr.074492.107.
-
(2010)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
|