-
1
-
-
79951694175
-
Analyzing and minimizing pcr amplification bias in illumina sequencing libraries
-
Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, et al: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12:R18 (2011).
-
(2011)
Genome Biol
, vol.12
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Et Al.6
-
2
-
-
78650909427
-
Limitations of next-generation genome sequence assembly
-
Alkan C, Sajjadian S, Eichler EE: Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65 (2011).
-
(2011)
Nat Methods
, vol.8
, pp. 61-65
-
-
Alkan, C.1
Sajjadian, S.2
Eichler, E.E.3
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al: Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389- 3402 (1997). (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, 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
-
-
79959438245
-
Systematic exploration of error sources in pyrosequencing flowgram data
-
Balzer S, Malde K, Jonassen I: Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 27:i304-i309 (2011).
-
(2011)
Bioinformatics
, vol.27
-
-
Balzer, S.1
Malde, K.2
Jonassen, I.3
-
5
-
-
84861548193
-
Summarizing and correcting the gc content bias in high-throughput sequencing
-
Benjamini Y, Speed TP: Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40:e72 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Benjamini, Y.1
Speed, T.P.2
-
7
-
-
46449095516
-
Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: Resolution, sensitivity, and banding paint development
-
Danilova TV, Birchler JA: Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 117: 345- 356 (2008).
-
(2008)
Chromosoma
, vol.117
, pp. 345-356
-
-
Danilova, T.V.1
Birchler, J.A.2
-
8
-
-
0032033746
-
Cytogenetics for the model system Arabidopsis thaliana
-
DOI 10.1046/j.1365-313X.1998.00086.x
-
Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G: Cytogenetics for the model system Arabidopsis thaliana . Plant J 13: 867-876 (1998). (Pubitemid 28178648)
-
(1998)
Plant Journal
, vol.13
, Issue.6
, pp. 867-876
-
-
Fransz, P.1
Armstrong, S.2
Alonso-Blanco, C.3
Fischer, T.C.4
Torres-Ruiz, R.A.5
Jones, G.6
-
9
-
-
79952334224
-
A new repeat-masking method enables specific detection of homologous sequences
-
Frith MC: A new repeat-masking method enables specific detection of homologous sequences. Nucleic Acids Res 39:e23 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Frith, M.C.1
-
10
-
-
0028369699
-
Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes
-
Fukui K, Kamisugi Y, Sakai F: Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes. Genome 37: 105-111 (1994). (Pubitemid 2068484)
-
(1994)
Genome
, vol.37
, Issue.1
, pp. 105-111
-
-
Fukui, K.1
Kamisugi, Y.2
Sakai, F.3
-
11
-
-
84869876659
-
The effect of strand bias in illumina shortread sequencing data
-
Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y: The effect of strand bias in Illumina shortread sequencing data. BMC Genomics 13: 666 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 666
-
-
Guo, Y.1
Li, J.2
Li, C.I.3
Long, J.4
Samuels, D.C.5
Shyr, Y.6
-
12
-
-
33744489394
-
Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization
-
DOI 10.1534/genetics.105.049726
-
Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, et al: Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173: 349-362 (2006). (Pubitemid 43800207)
-
(2006)
Genetics
, vol.173
, Issue.1
, pp. 349-362
-
-
Hasterok, R.1
Marasek, A.2
Donnison, I.S.3
Armstead, I.4
Thomas, A.5
King, I.P.6
Wolny, E.7
Idziak, D.8
Draper, J.9
Jenkins, G.10
-
13
-
-
84870265846
-
International barley genome sequencing consortium: A physical, genetic and functional sequence assembly of the barley genome
-
International Barley Genome Sequencing Consortium: A physical, genetic and functional sequence assembly of the barley genome. Nature 491: 711-716 (2012).
-
(2012)
Nature
, vol.491
, pp. 711-716
-
-
-
14
-
-
0029050636
-
Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes
-
Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC: Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92: 4487-4491 (1995).
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 4487-4491
-
-
Jiang, J.1
Gill, B.S.2
Wang, G.L.3
Ronald, P.C.4
Ward, D.C.5
-
15
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
DOI 10.1159/000084979
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467 (2005). (Pubitemid 41159923)
-
(2005)
Cytogenetic and Genome Research
, vol.110
, Issue.1-4
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
16
-
-
79958256572
-
High-Density fluorescence in situ hybridization signal detection on barley (hordeum vulgare l.) Chromosomes with improved probe screening and reprobing procedures
-
Kato A: High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures. Genome 54: 151-159 (2011).
-
(2011)
Genome
, vol.54
, pp. 151-159
-
-
Kato, A.1
-
17
-
-
33745424117
-
Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration dna polymerase nick translation
-
Kato A, Albert PS, Vega JM, Birchler JA: Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81: 71-78 (2006).
-
(2006)
Biotech Histochem
, vol.81
, pp. 71-78
-
-
Kato, A.1
Albert, P.S.2
Vega, J.M.3
Birchler, J.A.4
-
18
-
-
0036009443
-
Integrated karyotyping of sorghum by in situ hybridization of landed BACs
-
DOI 10.1139/g01-141
-
Kim JS, Childs KL, Islam-Faridi MN, Menz MA, Klein RR, et al: Integrated karyotyping of sorghum by in situ hybridization of landed BACs. Genome 45: 402-412 (2002). (Pubitemid 34253914)
-
(2002)
Genome
, vol.45
, Issue.2
, pp. 402-412
-
-
Kim, J.-S.1
Childs, K.L.2
Islam-Faridi, M.N.3
Menz, M.A.4
Klein, R.R.5
Klein, P.E.6
Price, H.J.7
Mullet, J.E.8
Stelly, D.M.9
-
19
-
-
56549086632
-
A new method to compute k-mer frequencies and its application to annotate large repetitive plant genomes
-
Kurtz S, Narechania A, Stein JC, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9: 517 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 517
-
-
Kurtz, S.1
Narechania, A.2
Stein, J.C.3
Ware, D.4
-
20
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander ES, Waterman S: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231-239 (1988).
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, S.2
-
21
-
-
0031037470
-
FISH physical mapping with barley BAC clones
-
DOI 10.1046/j.1365-313X.1997.11010149.x
-
Lapitan NLV, Brown SE, Kennard W, Stephens JL, Knudson DL: FISH physical mapping with barley BAC clones. Plant J 11: 149-156 (1997). (Pubitemid 27108366)
-
(1997)
Plant Journal
, vol.11
, Issue.1
, pp. 149-156
-
-
Lapitan, N.L.V.1
Brown, S.E.2
Kennard, W.3
Stephens, J.L.4
Knudson, D.L.5
-
22
-
-
77949587649
-
Fast and accurate long-read alignment with burrows-wheeler transform
-
Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
23
-
-
0030994539
-
The barley genome and its relationship with the wheat genomes. A survey with an internationally agreed recommendation for barley chromosome nomenclature
-
Linde-Laursen I, Heslop-Harrison JS, Shepherd KW, Taketa S: The barley genome and its relationship with the wheat genomes. A survey with an internationally agreed recommendation for barley chromosome nomenclature. Hereditas 126: 1-16 (1997). (Pubitemid 27219867)
-
(1997)
Hereditas
, vol.126
, Issue.1
, pp. 1-16
-
-
Linde-Laursen, I.1
Heslop-Harrison, J.S.2
Shepherd, K.W.3
Taketa, S.4
-
24
-
-
78649976495
-
Synteny between brachypodium distachyon and hordeum vulgare as revealed by fish
-
Ma L, Vu GT, Schubert V, Watanabe K, Stein N, Houben A, Schubert I: Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18: 841-850 (2010).
-
(2010)
Chromosome Res
, vol.18
, pp. 841-850
-
-
Ma, L.1
Vu, G.T.2
Schubert, V.3
Watanabe, K.4
Stein, N.5
Houben, A.6
Schubert, I.7
-
25
-
-
70349635850
-
Gene content and virtual gene order of barley chromosome 1h
-
Mayer KFX, Taudien S, Martis M, Simková H, Suchá nková P, et al: Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151: 496-505 (2009).
-
(2009)
Plant Physiol
, vol.151
, pp. 496-505
-
-
Mayer, K.F.X.1
Taudien, S.2
Martis, M.3
Simková, H.4
Suchá nková, P.5
Et Al.6
-
26
-
-
79957676864
-
Unlocking the barley genome by chromosomal and comparative genomics
-
Mayer KFX, Martis M, Hedley PE, Hana S, Steuernagel B, et al: Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23: 1249-1263 (2011).
-
(2011)
Plant Cell
, vol.23
, pp. 1249-1263
-
-
Mayer, K.F.X.1
Martis, M.2
Hedley, P.E.3
Hana, S.4
Steuernagel, B.5
Et Al.6
-
27
-
-
33745617710
-
A fast and symmetric DUST implementation to mask low-complexity DNA sequences
-
DOI 10.1089/cmb.2006.13.1028
-
Morgulis A, Gertz EM, Schäffer AA, Agarwala R: A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13: 1028-1040 (2006). (Pubitemid 43993449)
-
(2006)
Journal of Computational Biology
, vol.13
, Issue.5
, pp. 1028-1040
-
-
Morgulis, A.1
Gertz, E.M.2
Schaffer, A.A.3
Agarwala, R.4
-
28
-
-
77954854627
-
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
-
Novák P, Neumann P, Macas J: Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11: 378 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 378
-
-
Novák, P.1
Neumann, P.2
Macas, J.3
-
29
-
-
77955287614
-
Development of a molecular cytogenetic recombination assay for barley
-
Phillips D, Nibau C, Ramsay L, Waugh R, Jenkins G: Development of a molecular cytogenetic recombination assay for barley. Cytogenet Genome Res 129: 154-161 (2010).
-
(2010)
Cytogenet Genome Res
, vol.129
, pp. 154-161
-
-
Phillips, D.1
Nibau, C.2
Ramsay, L.3
Waugh, R.4
Jenkins, G.5
-
30
-
-
84860342753
-
Current challenges in de novo plant genome sequencing and assembly
-
Schatz MC, Witkowski J, McCombie WR: Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13: 243 (2012).
-
(2012)
Genome Biol
, vol.13
, pp. 243
-
-
Schatz, M.C.1
Witkowski, J.2
McCombie, W.R.3
-
31
-
-
70349564537
-
Visual search strategies of tag clouds - Results from an eyetracking study
-
Gross T, Gulliksen J, Kotzé P, Oestreicher L, Palanque P, et al (eds) (Springer, Berlin 2009)
-
Schrammel J, Deutsch S, Tscheligi M: Visual search strategies of tag clouds - results from an eyetracking study, in Gross T, Gulliksen J, Kotzé P, Oestreicher L, Palanque P, et al (eds): Human-Computer Interaction - INTERACT 2009, pp 819-831 (Springer, Berlin 2009).
-
(2009)
Human-Computer Interaction - INTERACT
, pp. 819-831
-
-
Schrammel, J.1
Deutsch, S.2
Tscheligi, M.3
-
32
-
-
1942424050
-
Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique
-
DOI 10.1139/g03-084
-
Stephens JL, Brown SE, Lapitan NL, Knudson DL: Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47: 179-189 (2004). (Pubitemid 38504143)
-
(2004)
Genome
, vol.47
, Issue.1
, pp. 179-189
-
-
Stephens, J.L.1
Brown, S.E.2
Lapitan, N.L.V.3
Knudson, D.L.4
-
33
-
-
71549121654
-
De novo 454 sequencing of barcoded bac pools for comprehensive gene survey and genome analysis in the complex genome of barley
-
Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, et al: De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 10: 547 (2009).
-
(2009)
BMC Genomics
, vol.10
, pp. 547
-
-
Steuernagel, B.1
Taudien, S.2
Gundlach, H.3
Seidel, M.4
Ariyadasa, R.5
Et Al.6
-
34
-
-
70350094296
-
Plant bac libraries as tools for molecular cytogenetics
-
Williams CR (ed) (Nova Science Publishers, New York
-
Suzuki G, Mukai Y: Plant BAC libraries as tools for molecular cytogenetics, in Williams CR (ed): Focus on Genome Research, pp 195-210 (Nova Science Publishers, New York 2004).
-
(2004)
Focus on Genome Research
, pp. 195-210
-
-
Suzuki, G.1
Mukai, Y.2
-
35
-
-
58149216719
-
High-resolution chromosome mapping of bacs using multi-colour fish and pooled-bac fish as a backbone for sequencing tomato chromosome 6
-
Szinay D, Chang SB, Khrustaleva L, Peters S, Schijlen E, et al: High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J 56: 627-637 (2008).
-
(2008)
Plant J
, vol.56
, pp. 627-637
-
-
Szinay, D.1
Chang, S.B.2
Khrustaleva, L.3
Peters, S.4
Schijlen, E.5
Et Al.6
-
36
-
-
80053981849
-
Sequencing of bac pools by different next generation sequencing platforms and strategies
-
Taudien S, Steuernagel B, Ariyadasa R, Schulte D, Schmutzer T, et al: Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes 4: 411 (2011).
-
(2011)
BMC Res Notes
, vol.4
, pp. 411
-
-
Taudien, S.1
Steuernagel, B.2
Ariyadasa, R.3
Schulte, D.4
Schmutzer, T.5
Et Al.6
-
37
-
-
34447262605
-
Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by bac-fish
-
Wang K, Guo W, Zhang T: Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by BAC-FISH. BMC Genomics 8: 178 (2007).
-
(2007)
BMC Genomics
, vol.8
, pp. 178
-
-
Wang, K.1
Guo, W.2
Zhang, T.3
-
38
-
-
0037700013
-
TREP: A database for Triticeae repetitive elements
-
DOI 10.1016/S1360-1385(02)02372-5, PII S1360138502023725
-
Wicker T, Matthews DE, Keller B: TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7: 561-562 (2002). (Pubitemid 36725981)
-
(2002)
Trends in Plant Science
, vol.7
, Issue.12
, pp. 561-562
-
-
Wicker, T.1
Matthews, D.E.2
Keller, B.3
-
39
-
-
56549090030
-
Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats
-
Wicker T, Narechania A, Sabot F, Stein J, Vu GT, et al: Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9: 518 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 518
-
-
Wicker, T.1
Narechania, A.2
Sabot, F.3
Stein, J.4
Vu, G.T.5
Et Al.6
-
40
-
-
77956284088
-
Patching gaps in plant genomes results in gene movement and erosion of colinearity
-
Wicker T, Buchmann JP, Keller B: Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res 20: 1229-1237 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 1229-1237
-
-
Wicker, T.1
Buchmann, J.P.2
Keller, B.3
-
41
-
-
46049108350
-
Batchprimer3: A high throughput web application for pcr and sequencing primer design
-
You FM, Huo N, Gu YQ, Luo MC, Ma Y, et al: BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9: 253 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 253
-
-
You, F.M.1
Huo, N.2
Gu, Y.Q.3
Luo, M.C.4
Ma, Y.5
Et Al.6
-
42
-
-
11144326220
-
Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH
-
DOI 10.1139/G04-042
-
Zhang P, Li WL, Friebe B, Gill BS: Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH. Genome 47: 979-987 (2004a). (Pubitemid 40033911)
-
(2004)
Genome
, vol.47
, Issue.5
, pp. 979-987
-
-
Zhang, P.1
Li, W.2
Friebe, B.3
Gill, B.S.4
-
43
-
-
1842741224
-
BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements
-
DOI 10.1007/s00412-004-0273-9
-
Zhang P, Li WL, Fellers J, Friebe B, Gill BS: BACFISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112: 288-299 (2004b). (Pubitemid 38477258)
-
(2004)
Chromosoma
, vol.112
, Issue.6
, pp. 288-299
-
-
Zhang, P.1
Li, W.2
Fellers, J.3
Friebe, B.4
Gill, B.S.5
-
44
-
-
0034053725
-
A greedy algorithm for aligning DNA sequences
-
DOI 10.1089/10665270050081478
-
Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214 (2000). (Pubitemid 30412170)
-
(2000)
Journal of Computational Biology
, vol.7
, Issue.1-2
, pp. 203-214
-
-
Zhang, Z.1
Schwartz, S.2
Wagner, L.3
Miller, W.4
|