-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathreferences.bib
184 lines (171 loc) · 7.98 KB
/
references.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
@Article{DiTommaso2017nextflow,
author={Di Tommaso, Paolo
and Chatzou, Maria
and Floden, Evan W.
and Barja, Pablo Prieto
and Palumbo, Emilio
and Notredame, Cedric},
title={Nextflow enables reproducible computational workflows},
journal={Nature Biotechnology},
year={2017},
month={Apr},
day={11},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. SN -},
volume={35},
pages={316 EP -},
url={http://dx.doi.org/10.1038/nbt.3820}
}
@Article{Steinegger2017mmseqs2,
author={Steinegger, Martin
and S{\"o}ding, Johannes},
title={MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets},
journal={Nature Biotechnology},
year={2017},
month={Oct},
day={16},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. SN -},
volume={35},
pages={1026 EP -},
url={http://dx.doi.org/10.1038/nbt.3988}
}
@Article{Wang2014,
author={Wang, Shichen
and Wong, Debbie
and Forrest, Kerrie
and Allen, Alexandra
and Chao, Shiaoman
and Huang, Bevan E.
and Maccaferri, Marco
and Salvi, Silvio
and Milner, Sara G.
and Cattivelli, Luigi
and Mastrangelo, Anna M.
and Whan, Alex
and Stephen, Stuart
and Barker, Gary
and Wieseke, Ralf
and Plieske, Joerg
and Consortium, International Wheat Genome Sequencing
and Lillemo, Morten
and Mather, Diane
and Appels, Rudi
and Dolferus, Rudy
and Brown-Guedira, Gina
and Korol, Abraham
and Akhunova, Alina R.
and Feuillet, Catherine
and Salse, Jerome
and Morgante, Michele
and Pozniak, Curtis
and Luo, Ming-Cheng
and Dvorak, Jan
and Morell, Matthew
and Dubcovsky, Jorge
and Ganal, Martin
and Tuberosa, Roberto
and Lawley, Cindy
and Mikoulitch, Ivan
and Cavanagh, Colin
and Edwards, Keith J.
and Hayden, Matthew
and Akhunov, Eduard},
title={Characterization of polyploid wheat genomic diversity using a high-density {90 000} single nucleotide polymorphism array},
journal={Plant Biotechnol J},
year={2014},
month={Aug},
day={20},
publisher={BlackWell Publishing Ltd},
address={Oxford, UK},
volume={12},
number={6},
pages={787-796},
abstract={High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90?000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46?977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.},
note={24646323[pmid]},
issn={1467-7644},
doi={10.1111/pbi.12183},
url={http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265271/}
}
@Article{Gardner2016,
author={Gardner, Keith A.
and Wittern, Lukas M.
and Mackay, Ian J.},
title={A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments},
journal={Plant Biotechnol J},
year={2016},
month={Jun},
day={23},
publisher={John Wiley and Sons Inc.},
address={Hoboken},
volume={14},
number={6},
pages={1406-1417},
abstract={Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight-parent MAGIC genetic map for wheat, comprising 18?601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20?cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high-marker-density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.},
note={PBI12504[PII]},
note={26801965[pmid]},
issn={1467-7644},
doi={10.1111/pbi.12504},
url={http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985697/}
}
@ARTICLE{Wen2017,
AUTHOR={Wen, Weie and He, Zhonghu and Gao, Fengmei and Liu, Jindong and Jin, Hui and Zhai, Shengnan and Qu, Yanying and Xia, Xianchun},
TITLE={A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array},
JOURNAL={Frontiers in Plant Science},
VOLUME={8},
PAGES={1389},
YEAR={2017},
URL={https://www.frontiersin.org/article/10.3389/fpls.2017.01389},
DOI={10.3389/fpls.2017.01389},
ISSN={1664-462X}
}
@article{Bayer2011,
author = {Bayer, Micha and Milne, Iain and Stephen, Gordon and Shaw, Paul and Cardle, Linda and Wright, Frank and Marshall, David},
title = {Comparative visualization of genetic and physical maps with Strudel},
journal = {Bioinformatics},
volume = {27},
number = {9},
pages = {1307-1308},
year = {2011},
doi = {10.1093/bioinformatics/btr111},
URL = {http://dx.doi.org/10.1093/bioinformatics/btr111},
eprint = {/oup/backfile/content_public/journal/bioinformatics/27/9/10.1093/bioinformatics/btr111/2/btr111.pdf}
}
@article{Holtz2017,
author = {Holtz, Yan and David, Jacques Léon and Ranwez, Vincent},
title = {The genetic map comparator: a user-friendly application to display and compare genetic maps},
journal = {Bioinformatics},
volume = {33},
number = {9},
pages = {1387-1388},
year = {2017},
doi = {10.1093/bioinformatics/btw816},
URL = {http://dx.doi.org/10.1093/bioinformatics/btw816},
eprint = {/oup/backfile/content_public/journal/bioinformatics/33/9/10.1093_bioinformatics_btw816/3/btw816.pdf}
}
@article{fang2003cmap,
title={cMap: the comparative genetic map viewer},
author={Fang, Zhiwei and Polacco, M and Chen, S and Schroeder, S and Hancock, D and Sanchez, H and Coe, E},
journal={Bioinformatics},
volume={19},
number={3},
pages={416--417},
year={2003},
publisher={Oxford University Press}
}
@article{stein2002generic,
title={The generic genome browser: a building block for a model organism system database},
author={Stein, Lincoln D and Mungall, Christopher and Shu, ShengQiang and Caudy, Michael and Mangone, Marco and Day, Allen and Nickerson, Elizabeth and Stajich, Jason E and Harris, Todd W and Arva, Adrian and others},
journal={Genome research},
volume={12},
number={10},
pages={1599--1610},
year={2002},
publisher={Cold Spring Harbor Lab}
}
@article{skinner2009jbrowse,
title={JBrowse: a next-generation genome browser},
author={Skinner, Mitchell E and Uzilov, Andrew V and Stein, Lincoln D and Mungall, Christopher J and Holmes, Ian H},
journal={Genome research},
pages={gr--094607},
year={2009},
publisher={Cold Spring Harbor Lab}
}