-
1
-
-
79957658264
-
Genetic analysis of complex traits in the emerging Collaborative Cross
-
COI: 1:CAS:528:DC%2BC3MXpvFeqs74%3D, PID: 21406540
-
Aylor DL, Valdar W, Foulds-Mathes W et al (2011) Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21:1213–1222. doi:10.1101/gr.111310.110
-
(2011)
Genome Res
, vol.21
, pp. 1213-1222
-
-
Aylor, D.L.1
Valdar, W.2
Foulds-Mathes, W.3
-
2
-
-
0037047628
-
Recent segmental duplications in the human genome
-
COI: 1:CAS:528:DC%2BD38Xmt1Cktr4%3D, PID: 12169732
-
Bailey JA, Gu Z, Clark RA et al (2002) Recent segmental duplications in the human genome. Science 297:1003–1007. doi:10.1126/science.1072047
-
(2002)
Science
, vol.297
, pp. 1003-1007
-
-
Bailey, J.A.1
Gu, Z.2
Clark, R.A.3
-
3
-
-
4444264564
-
Hotspots of mammalian chromosomal evolution
-
PID: 15059256
-
Bailey JA, Baertsch R, Kent WJ et al (2004) Hotspots of mammalian chromosomal evolution. Genome Biol 5:R23. doi:10.1186/gb-2004-5-4-r23
-
(2004)
Genome Biol
, vol.5
, pp. 23
-
-
Bailey, J.A.1
Baertsch, R.2
Kent, W.J.3
-
4
-
-
84924388025
-
PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination
-
PID: 25568937
-
Baker CL, Kajita S, Walker M et al (2015) PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination. PLoS Genet 11:e1004916. doi:10.1371/journal.pgen.1004916
-
(2015)
PLoS Genet
, vol.11
, pp. 1004916
-
-
Baker, C.L.1
Kajita, S.2
Walker, M.3
-
5
-
-
84876410333
-
Lightweight algorithms for constructing and inverting the BWT of string collections
-
Bauer MJ, Cox AJ, Rosone G et al (2013) Lightweight algorithms for constructing and inverting the BWT of string collections. Theor Comput Sci 483:134–148. doi:10.1016/j.tcs.2012.02.002
-
(2013)
Theor Comput Sci
, vol.483
, pp. 134-148
-
-
Bauer, M.J.1
Cox, A.J.2
Rosone, G.3
-
6
-
-
0000342467
-
Statistical inference for probabilistic functions of finite state Markov chains
-
Baum LE, Petrie T (1966) Statistical inference for probabilistic functions of finite state Markov chains. Ann Math Stat 37:1554–1563
-
(1966)
Ann Math Stat
, vol.37
, pp. 1554-1563
-
-
Baum, L.E.1
Petrie, T.2
-
7
-
-
0033989159
-
Genealogies of mouse inbred strains
-
COI: 1:CAS:528:DC%2BD3cXks1emsg%3D%3D, PID: 10615122
-
Beck JA, Lloyd S, Hafezparast M et al (2000) Genealogies of mouse inbred strains. Nat Genet 24:23–25. doi:10.1038/71641
-
(2000)
Nat Genet
, vol.24
, pp. 23-25
-
-
Beck, J.A.1
Lloyd, S.2
Hafezparast, M.3
-
8
-
-
0001677717
-
Controlling the false-discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y et al (1995) Controlling the false-discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300
-
(1995)
J R Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
9
-
-
75649122259
-
A high-resolution association mapping panel for the dissection of complex traits in mice
-
COI: 1:CAS:528:DC%2BC3cXhs1Ghtbk%3D, PID: 20054062
-
Bennett BJ, Farber CR, Orozco L et al (2010) A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 20:281–290. doi:10.1101/gr.099234.109
-
(2010)
Genome Res
, vol.20
, pp. 281-290
-
-
Bennett, B.J.1
Farber, C.R.2
Orozco, L.3
-
11
-
-
0037958742
-
R/qtl: QTL mapping in experimental crosses
-
COI: 1:CAS:528:DC%2BD3sXjsVKmtb0%3D, PID: 12724300
-
Broman KW, Wu H, Sen S, Churchill GA et al (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890
-
(2003)
Bioinformatics
, vol.19
, pp. 889-890
-
-
Broman, K.W.1
Wu, H.2
Sen, S.3
Churchill, G.A.4
-
12
-
-
84887276151
-
Genetic architecture of skewed X inactivation in the laboratory mouse
-
PID: 24098153
-
Calaway JD, Lenarcic AB, Didion JP et al (2013) Genetic architecture of skewed X inactivation in the laboratory mouse. PLoS Genet 9:e1003853. doi:10.1371/journal.pgen.1003853
-
(2013)
PLoS Genet
, vol.9
, pp. 1003853
-
-
Calaway, J.D.1
Lenarcic, A.B.2
Didion, J.P.3
-
13
-
-
84863115856
-
The genome architecture of the Collaborative Cross mouse genetic reference population
-
CCC (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190:389–401. doi:10.1534/genetics.111.132639
-
(2012)
Genetics
, vol.190
, pp. 389-401
-
-
-
14
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
COI: 1:CAS:528:DC%2BD1cXhvVSrtro%3D, PID: 18083777
-
Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18:324–330. doi:10.1101/gr.7088808
-
(2008)
Genome Res
, vol.18
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
15
-
-
84895866508
-
Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research
-
PID: 24272351
-
Chesler EJ et al (2014) Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research. Mamm Genome 25:3–11. doi:10.1007/s00335-013-9492-9
-
(2014)
Mamm Genome
, vol.25
, pp. 3-11
-
-
Chesler, E.J.1
-
16
-
-
84939129835
-
Extending reference assembly models
-
PID: 25651527
-
Church DM, Schneider VA, Steinberg KM et al (2015) Extending reference assembly models. Genome Biol 16:13. doi:10.1186/s13059-015-0587-3
-
(2015)
Genome Biol
, vol.16
, pp. 13
-
-
Church, D.M.1
Schneider, V.A.2
Steinberg, K.M.3
-
17
-
-
0028151261
-
Empirical threshold values for quantitative trait mapping
-
COI: 1:STN:280:DyaK2M7lsVOiug%3D%3D, PID: 7851788
-
Churchill GA, Doerge RW et al (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
-
(1994)
Genetics
, vol.138
, pp. 963-971
-
-
Churchill, G.A.1
Doerge, R.W.2
-
18
-
-
14644441018
-
The Collaborative Cross, a community resource for the genetic analysis of complex traits
-
COI: 1:CAS:528:DC%2BD2cXptVOht7o%3D, PID: 15514660
-
Churchill GA, Airey DC, Allayee H et al (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133–1137. doi:10.1038/ng1104-1133
-
(2004)
Nat Genet
, vol.36
, pp. 1133-1137
-
-
Churchill, G.A.1
Airey, D.C.2
Allayee, H.3
-
19
-
-
27544474337
-
Ascertainment bias in studies of human genome-wide polymorphism
-
COI: 1:CAS:528:DC%2BD2MXhtF2itb7M, PID: 16251459
-
Clark AG, Hubisz MJ, Bustamante CD et al (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Res 15:1496–1502. doi:10.1101/gr.4107905
-
(2005)
Genome Res
, vol.15
, pp. 1496-1502
-
-
Clark, A.G.1
Hubisz, M.J.2
Bustamante, C.D.3
-
20
-
-
0035990464
-
Behavioral differences among 129 substrains: implications for knockout and transgenic mice
-
Cook MN, Bolivar V, McFadyen MP, Flaherty L et al (2002) Behavioral differences among 129 substrains: implications for knockout and transgenic mice. BehavNeurosci 116:600–611. doi:10.1037/0735-7044.116.4.600
-
(2002)
BehavNeurosci
, vol.116
, pp. 600-611
-
-
Cook, M.N.1
Bolivar, V.2
McFadyen, M.P.3
Flaherty, L.4
-
21
-
-
84925842188
-
Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
-
Crowley JJ, Zhabotynsky V, Sun W et al (2015) Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. doi:10.1038/ng.3222
-
(2015)
Nat Genet
-
-
Crowley, J.J.1
Zhabotynsky, V.2
Sun, W.3
-
22
-
-
84876361750
-
Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking
-
PID: 23222650
-
Daetwyler HD, Calus MPL, Pong-Wong R et al (2013) Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. Genetics 193:347–365. doi:10.1534/genetics.112.147983
-
(2013)
Genetics
, vol.193
, pp. 347-365
-
-
Daetwyler, H.D.1
Calus, M.P.L.2
Pong-Wong, R.3
-
23
-
-
84855886780
-
Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
-
COI: 1:CAS:528:DC%2BC38Xls1Git7w%3D
-
Didion JP, Yang H, Sheppard K et al (2012) Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genom 13:34. doi:10.1186/1471-2164-13-34
-
(2012)
BMC Genom
, vol.13
, pp. 34
-
-
Didion, J.P.1
Yang, H.2
Sheppard, K.3
-
24
-
-
84873315046
-
Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse
-
COI: 1:CAS:528:DC%2BC3sXitVOisb4%3D, PID: 23223940
-
Didion JP, de Villena FP-M et al (2013) Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome 24:1–20. doi:10.1007/s00335-012-9441-z
-
(2013)
Mamm Genome
, vol.24
, pp. 1-20
-
-
Didion, J.P.1
de Villena, F.P.-M.2
-
25
-
-
0001232092
-
Studies on hybrid sterility. II Localization of sterility factors in Drosophila pseudoobscura hybrids
-
COI: 1:STN:280:DC%2BD2s%2FmsVOlsA%3D%3D, PID: 17246786
-
Dobzhansky T et al (1936) Studies on hybrid sterility. II Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 21:113–135
-
(1936)
Genetics
, vol.21
, pp. 113-135
-
-
Dobzhansky, T.1
-
26
-
-
84930088305
-
Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression
-
PID: 25088201
-
Ferguson B, Ram R, Handoko HY et al (2014) Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression. Oncogene. doi:10.1038/onc.2014.227
-
(2014)
Oncogene
-
-
Ferguson, B.1
Ram, R.2
Handoko, H.Y.3
-
27
-
-
84880944577
-
Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross
-
PID: 23468633
-
Ferris MT, Aylor DL, Bottomly D et al (2013) Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross. PLoS Pathog 9:e1003196. doi:10.1371/journal.ppat.1003196
-
(2013)
PLoS Pathog
, vol.9
, pp. 1003196
-
-
Ferris, M.T.1
Aylor, D.L.2
Bottomly, D.3
-
28
-
-
84875391572
-
Ensembl 2013
-
COI: 1:CAS:528:DC%2BC38XhvV2ktrbO, PID: 23203987
-
Flicek P, Ahmed I, Amode MR et al (2013) Ensembl 2013. Nucleic Acids Res 41:D48–D55. doi:10.1093/nar/gks1236
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 48-55
-
-
Flicek, P.1
Ahmed, I.2
Amode, M.R.3
-
29
-
-
0016184741
-
Genetic studies on male sterility of hybrids between laboratory and wild mice (Mus musculus L.)
-
COI: 1:STN:280:DyaE2M7htlCksA%3D%3D, PID: 4452481
-
Forejt J, Ivanyi P et al (1974) Genetic studies on male sterility of hybrids between laboratory and wild mice (Mus musculus L.). Genet Res 24:189–206
-
(1974)
Genet Res
, vol.24
, pp. 189-206
-
-
Forejt, J.1
Ivanyi, P.2
-
30
-
-
34548295740
-
A sequence-based variation map of 8.27 million SNPs in inbred mouse strains
-
COI: 1:CAS:528:DC%2BD2sXps12nsLw%3D, PID: 17660834
-
Frazer KA, Eskin E, Kang HM et al (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448:1050–1053. doi:10.1038/nature06067
-
(2007)
Nature
, vol.448
, pp. 1050-1053
-
-
Frazer, K.A.1
Eskin, E.2
Kang, H.M.3
-
31
-
-
84869392652
-
-
ACM Press, New York
-
Fu C-P, Welsh CE, Villena FP-M de, McMillan L et al (2012) Inferring ancestry in admixed populations using microarray probe intensities. In: Proceedings of the ACM conference on bioinformatics, computational biology and biomedicine—bCB’12. ACM Press, New York, pp 105–112
-
(2012)
Inferring ancestry in admixed populations using microarray probe intensities. In: Proceedings of the ACM conference on bioinformatics, computational biology and biomedicine—bCB’12
, pp. 105-112
-
-
Fu, C.-P.1
Welsh, C.E.2
de Villena, F.P.-M.3
McMillan, L.4
-
34
-
-
57349140938
-
Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes
-
PID: 19121002
-
Geraldes A, Basset P, Gibson B et al (2008) Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol 17:5349–5363. doi:10.1111/j.1365-294X.2008.04005.x
-
(2008)
Mol Ecol
, vol.17
, pp. 5349-5363
-
-
Geraldes, A.1
Basset, P.2
Gibson, B.3
-
35
-
-
84867332713
-
Hybrid Mouse Diversity Panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits
-
COI: 1:CAS:528:DC%2BC38XhsVKrtrfE, PID: 22892838
-
Ghazalpour A, Rau CD, Farber CR et al (2012) Hybrid Mouse Diversity Panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome 23:680–692. doi:10.1007/s00335-012-9411-5
-
(2012)
Mamm Genome
, vol.23
, pp. 680-692
-
-
Ghazalpour, A.1
Rau, C.D.2
Farber, C.R.3
-
36
-
-
84905568645
-
Fine-mapping QTLs in advanced intercross lines and other outbred populations
-
PID: 24906874
-
Gonzales NM, Palmer AA et al (2014) Fine-mapping QTLs in advanced intercross lines and other outbred populations. Mamm Genome 25:271–292. doi:10.1007/s00335-014-9523-1
-
(2014)
Mamm Genome
, vol.25
, pp. 271-292
-
-
Gonzales, N.M.1
Palmer, A.A.2
-
37
-
-
55749092472
-
A complex genetic basis to X-linked hybrid male sterility between two species of house mice
-
PID: 18689897
-
Good JM, Dean MD, Nachman MW et al (2008) A complex genetic basis to X-linked hybrid male sterility between two species of house mice. Genetics 179:2213–2228. doi:10.1534/genetics.107.085340
-
(2008)
Genetics
, vol.179
, pp. 2213-2228
-
-
Good, J.M.1
Dean, M.D.2
Nachman, M.W.3
-
38
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
COI: 1:CAS:528:DC%2BC3MXmtV2hsbc%3D, PID: 21572440
-
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. doi:10.1038/nbt.1883
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
-
39
-
-
84891797984
-
Mouse phenome database
-
COI: 1:CAS:528:DC%2BC2cXoslWj, PID: 24243846
-
Grubb SC, Bult CJ, Bogue MA et al (2014) Mouse phenome database. Nucleic Acids Res 42:D825–D834. doi:10.1093/nar/gkt1159
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 825-834
-
-
Grubb, S.C.1
Bult, C.J.2
Bogue, M.A.3
-
40
-
-
33646942472
-
A simple regression method for mapping quantitative trait loci in line crosses using flanking markers
-
COI: 1:STN:280:DC%2BD283ovFaltQ%3D%3D, PID: 16718932
-
Haley CS, Knott SA et al (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324. doi:10.1038/hdy.1992.131
-
(1992)
Heredity
, vol.69
, pp. 315-324
-
-
Haley, C.S.1
Knott, S.A.2
-
41
-
-
33748645500
-
GENCODE: producing a reference annotation for ENCODE
-
Harrow J, Denoeud F, Frankish A et al (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7(Suppl 1):S4 1–S4 9. doi:10.1186/gb-2006-7-s1-s4
-
(2006)
Genome Biol
, vol.7
, pp. 4 1-4 9
-
-
Harrow, J.1
Denoeud, F.2
Frankish, A.3
-
42
-
-
84922709802
-
Merging of multi-string BWTs with applications
-
COI: 1:CAS:528:DC%2BC2MXisFaltr0%3D, PID: 25172922
-
Holt J, McMillan L et al (2014) Merging of multi-string BWTs with applications. Bioinformatics 30:3524–3531. doi:10.1093/bioinformatics/btu584
-
(2014)
Bioinformatics
, vol.30
, pp. 3524-3531
-
-
Holt, J.1
McMillan, L.2
-
43
-
-
84986915866
-
A novel multi-alignment pipeline for high-throughput sequencing data
-
PID: 24948510
-
Huang S, Holt J, Kao C-Y et al (2014) A novel multi-alignment pipeline for high-throughput sequencing data. Database 2014:bau057. doi:10.1093/database/bau057
-
(2014)
Database
, vol.2014
, pp. 57
-
-
Huang, S.1
Holt, J.2
Kao, C.-Y.3
-
44
-
-
0022211482
-
Statistical properties of the number of recombination events in the history of a sample of DNA sequences
-
COI: 1:STN:280:DyaL2M3os1ejug%3D%3D, PID: 4029609
-
Hudson RR, Kaplan NL et al (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164
-
(1985)
Genetics
, vol.111
, pp. 147-164
-
-
Hudson, R.R.1
Kaplan, N.L.2
-
45
-
-
84897116193
-
Heritability and coefficient of genetic variation analyses of phenotypic traits provide strong basis for high-resolution QTL mapping in the Collaborative Cross mouse genetic reference population
-
PID: 24445421
-
Iraqi FA, Athamni H, Dorman A et al (2014) Heritability and coefficient of genetic variation analyses of phenotypic traits provide strong basis for high-resolution QTL mapping in the Collaborative Cross mouse genetic reference population. Mamm Genome 25:109–119. doi:10.1007/s00335-014-9503-5
-
(2014)
Mamm Genome
, vol.25
, pp. 109-119
-
-
Iraqi, F.A.1
Athamni, H.2
Dorman, A.3
-
46
-
-
45149105926
-
Efficient control of population structure in model organism association mapping
-
PID: 18385116
-
Kang HM, Zaitlen NA, Wade CM et al (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723. doi:10.1534/genetics.107.080101
-
(2008)
Genetics
, vol.178
, pp. 1709-1723
-
-
Kang, H.M.1
Zaitlen, N.A.2
Wade, C.M.3
-
47
-
-
84891771466
-
The UCSC genome browser database: 2014 update
-
COI: 1:CAS:528:DC%2BC2cXoslCr, PID: 24270787
-
Karolchik D, Barber GP, Casper J et al (2014) The UCSC genome browser database: 2014 update. Nucleic Acids Res 42:D764–D770. doi:10.1093/nar/gkt1168
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 764-770
-
-
Karolchik, D.1
Barber, G.P.2
Casper, J.3
-
48
-
-
80052851950
-
Mouse genomic variation and its effect on phenotypes and gene regulation
-
COI: 1:CAS:528:DC%2BC3MXhtFOlsL7N, PID: 21921910
-
Keane TM, Goodstadt L, Danecek P et al (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477:289–294. doi:10.1038/nature10413
-
(2011)
Nature
, vol.477
, pp. 289-294
-
-
Keane, T.M.1
Goodstadt, L.2
Danecek, P.3
-
49
-
-
84857383489
-
Genetic analysis of hematological parameters in incipient lines of the Collaborative Cross
-
PID: 22384394
-
Kelada SNP, Aylor DL, Peck BCE et al (2012) Genetic analysis of hematological parameters in incipient lines of the Collaborative Cross. G3 2:157–165. doi:10.1534/g3.111.001776
-
(2012)
G3
, vol.2
, pp. 157-165
-
-
Kelada, S.N.P.1
Aylor, D.L.2
Peck, B.C.E.3
-
50
-
-
84906860214
-
Integrative genetic analysis of allergic inflammation in the murine lung
-
COI: 1:CAS:528:DC%2BC2cXhs1yqt7rM, PID: 24693920
-
Kelada SNP, Carpenter DE, Aylor DL et al (2014) Integrative genetic analysis of allergic inflammation in the murine lung. Am J Respir Cell Mol Biol 51:436–445. doi:10.1165/rcmb.2013-0501OC
-
(2014)
Am J Respir Cell Mol Biol
, vol.51
, pp. 436-445
-
-
Kelada, S.N.P.1
Carpenter, D.E.2
Aylor, D.L.3
-
51
-
-
84857405495
-
A general Bayesian approach to analyzing diallel crosses of inbred strains
-
PID: 22345610
-
Lenarcic AB, Svenson KL, Churchill GA, Valdar W et al (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190:413–435. doi:10.1534/genetics.111.132563
-
(2012)
Genetics
, vol.190
, pp. 413-435
-
-
Lenarcic, A.B.1
Svenson, K.L.2
Churchill, G.A.3
Valdar, W.4
-
52
-
-
80053372166
-
FaST linear mixed models for genome-wide association studies
-
COI: 1:CAS:528:DC%2BC3MXhtFWku7nF, PID: 21892150
-
Lippert C, Listgarten J, Liu Y et al (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8:833–835. doi:10.1038/nmeth.1681
-
(2011)
Nat Methods
, vol.8
, pp. 833-835
-
-
Lippert, C.1
Listgarten, J.2
Liu, Y.3
-
53
-
-
77954187717
-
Efficient genome ancestry inference in complex pedigrees with inbreeding
-
COI: 1:CAS:528:DC%2BC3cXnsVOksLs%3D, PID: 20529906
-
Liu EY, Zhang Q, McMillan L et al (2010) Efficient genome ancestry inference in complex pedigrees with inbreeding. Bioinformatics 26:i199–i207. doi:10.1093/bioinformatics/btq187
-
(2010)
Bioinformatics
, vol.26
, pp. 199-207
-
-
Liu, E.Y.1
Zhang, Q.2
McMillan, L.3
-
54
-
-
84901303111
-
High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline
-
PID: 24578350
-
Liu EY, Morgan AP, Chesler EJ et al (2014) High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics 197:91–106. doi:10.1534/genetics.114.161653
-
(2014)
Genetics
, vol.197
, pp. 91-106
-
-
Liu, E.Y.1
Morgan, A.P.2
Chesler, E.J.3
-
55
-
-
77955405475
-
Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor
-
COI: 1:CAS:528:DC%2BC3cXpvFSlsLc%3D, PID: 20562413
-
McLaren W, Pritchard B, Rios D et al (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics 26:2069–2070. doi:10.1093/bioinformatics/btq330
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
-
56
-
-
0034619331
-
A method for fine mapping quantitative trait loci in outbred animal stocks
-
PID: 11050180
-
Mott R, Talbot CJ, Turri MG et al (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci USA 97:12649–12654. doi:10.1073/pnas.230304397
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12649-12654
-
-
Mott, R.1
Talbot, C.J.2
Turri, M.G.3
-
57
-
-
84908008732
-
RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations
-
PID: 25236449
-
Munger SC, Raghupathy N, Choi K et al (2014) RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics 198:59–73. doi:10.1534/genetics.114.165886
-
(2014)
Genetics
, vol.198
, pp. 59-73
-
-
Munger, S.C.1
Raghupathy, N.2
Choi, K.3
-
58
-
-
0031832438
-
Natural hybridization between two subspecies of the house mouse, Mus musculus domesticus and Mus musculus castaneus, near Lake Casitas, California
-
COI: 1:STN:280:DyaK1c3htVajtg%3D%3D, PID: 9549063
-
Orth A, Adama T, Din W, Bonhomme F et al (1998) Natural hybridization between two subspecies of the house mouse, Mus musculusdomesticus and Mus musculus castaneus, near Lake Casitas, California. Genome 41:104–110
-
(1998)
Genome
, vol.41
, pp. 104-110
-
-
Orth, A.1
Adama, T.2
Din, W.3
Bonhomme, F.4
-
59
-
-
84900328038
-
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
-
COI: 1:CAS:528:DC%2BC2cXmsVKmtr8%3D, PID: 24752080
-
Patro R, Mount SM, Kingsford C (2014) Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat Biotechnol 32:462–646. doi:10.1038/nbt.2862
-
(2014)
Nat Biotechnol
, vol.32
, pp. 462-646
-
-
Patro, R.1
Mount, S.M.2
Kingsford, C.3
-
60
-
-
4644292674
-
An efficient SNP system for mouse genome scanning and elucidating strain relationships
-
COI: 1:CAS:528:DC%2BD2cXnsFGjtr8%3D, PID: 15342563
-
Petkov PM, Ding Y, Cassell MA et al (2004) An efficient SNP system for mouse genome scanning and elucidating strain relationships. Genome Res 14:1806–1811. doi:10.1101/gr.2825804
-
(2004)
Genome Res
, vol.14
, pp. 1806-1811
-
-
Petkov, P.M.1
Ding, Y.2
Cassell, M.A.3
-
61
-
-
84895886695
-
Using the emerging Collaborative Cross to probe the immune system
-
COI: 1:CAS:528:DC%2BC3sXhslGntL7I, PID: 24195963
-
Phillippi J, Xie Y, Miller DR et al (2014) Using the emerging Collaborative Cross to probe the immune system. Genes Immun 15:38–46. doi:10.1038/gene.2013.59
-
(2014)
Genes Immun
, vol.15
, pp. 38-46
-
-
Phillippi, J.1
Xie, Y.2
Miller, D.R.3
-
62
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77:257–286
-
(1989)
Proc IEEE
, vol.77
, pp. 257-286
-
-
Rabiner, L.R.1
-
63
-
-
84911371938
-
Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance
-
Rasmussen AL, Okumura A, Ferris MT et al (2014) Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance. Science. doi:10.1126/science.1259595
-
(2014)
Science
-
-
Rasmussen, A.L.1
Okumura, A.2
Ferris, M.T.3
-
64
-
-
84897108137
-
The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis
-
PID: 24487921
-
Rogala AR, Morgan AP, Christensen AM et al (2014) The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mamm Genome 25:95–108. doi:10.1007/s00335-013-9499-2
-
(2014)
Mamm Genome
, vol.25
, pp. 95-108
-
-
Rogala, A.R.1
Morgan, A.P.2
Christensen, A.M.3
-
65
-
-
46249114293
-
Mouse segmental duplication and copy number variation
-
COI: 1:CAS:528:DC%2BD1cXnslKku7o%3D, PID: 18500340
-
She X, Cheng Z, Zöllner S et al (2008) Mouse segmental duplication and copy number variation. Nat Genet 40:909–914. doi:10.1038/ng.172
-
(2008)
Nat Genet
, vol.40
, pp. 909-914
-
-
She, X.1
Cheng, Z.2
Zöllner, S.3
-
67
-
-
84910036383
-
Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes
-
COI: 1:CAS:528:DC%2BC2cXhvVGks7nP, PID: 25417157
-
Soh YQS, Alföldi J, Pyntikova T et al (2014) Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159:800–813. doi:10.1016/j.cell.2014.09.052
-
(2014)
Cell
, vol.159
, pp. 800-813
-
-
Soh, Y.Q.S.1
Alföldi, J.2
Pyntikova, T.3
-
68
-
-
84857410370
-
High-resolution genetic mapping using the mouse Diversity Outbred population
-
COI: 1:CAS:528:DC%2BC38XnsVSmsbY%3D, PID: 22345611
-
Svenson KL, Gatti DM, Valdar W et al (2012) High-resolution genetic mapping using the mouse Diversity Outbred population. Genetics 190:437–447. doi:10.1534/genetics.111.132597
-
(2012)
Genetics
, vol.190
, pp. 437-447
-
-
Svenson, K.L.1
Gatti, D.M.2
Valdar, W.3
-
69
-
-
0015796924
-
Genetic analysis of resistance to cadmium-induced testicular damage in mice
-
COI: 1:CAS:528:DyaE3sXltVWht7c%3D, PID: 4719448
-
Taylor BA, Heiniger HJ, Meier H et al (1973) Genetic analysis of resistance to cadmium-induced testicular damage in mice. Proc Soc Exp Biol Med 143:629–633
-
(1973)
Proc Soc Exp Biol Med
, vol.143
, pp. 629-633
-
-
Taylor, B.A.1
Heiniger, H.J.2
Meier, H.3
-
70
-
-
0043177667
-
Occurrence of voles, mice, and rats (Muridae) in Denmark, with a special note on a zone of intergradation between two subspecies of the house mouse (Mus musculus L.)
-
Ursin E (1952) Occurrence of voles, mice, and rats (Muridae) in Denmark, with a special note on a zone of intergradation between two subspecies of the house mouse (Mus musculus L.). Vid Medd Dansk Naturhist Foren 114:217–244
-
(1952)
Vid Medd Dansk Naturhist Foren
, vol.114
, pp. 217-244
-
-
Ursin, E.1
-
71
-
-
33645217146
-
Simulating the Collaborative Cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice
-
COI: 1:CAS:528:DC%2BD28XjvV2lurk%3D, PID: 16361245
-
Valdar W, Flint J, Mott R et al (2006a) Simulating the Collaborative Cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172:1783–1797. doi:10.1534/genetics.104.039313
-
(2006)
Genetics
, vol.172
, pp. 1783-1797
-
-
Valdar, W.1
Flint, J.2
Mott, R.3
-
72
-
-
33746540478
-
Genome-wide genetic association of complex traits in heterogeneous stock mice
-
COI: 1:CAS:528:DC%2BD28XnsVCgsr4%3D, PID: 16832355
-
Valdar W, Solberg LC, Gauguier D et al (2006b) Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat Genet 38:879–887. doi:10.1038/ng1840
-
(2006)
Nat Genet
, vol.38
, pp. 879-887
-
-
Valdar, W.1
Solberg, L.C.2
Gauguier, D.3
-
73
-
-
68249130288
-
Mapping in structured populations by resample model averaging
-
PID: 19474203
-
Valdar W, Holmes CC, Mott R, Flint J et al (2009) Mapping in structured populations by resample model averaging. Genetics 182:1263–1277. doi:10.1534/genetics.109.100727
-
(2009)
Genetics
, vol.182
, pp. 1263-1277
-
-
Valdar, W.1
Holmes, C.C.2
Mott, R.3
Flint, J.4
-
74
-
-
0037028155
-
The mosaic structure of variation in the laboratory mouse genome
-
COI: 1:CAS:528:DC%2BD38Xpt1WhsL4%3D, PID: 12466852
-
Wade CM, Kulbokas EJ, Kirby AW et al (2002) The mosaic structure of variation in the laboratory mouse genome. Nature 420:574–578. doi:10.1038/nature01252
-
(2002)
Nature
, vol.420
, pp. 574-578
-
-
Wade, C.M.1
Kulbokas, E.J.2
Kirby, A.W.3
-
75
-
-
0043267974
-
Haplotype blocks and linkage disequilibrium in the human genome
-
COI: 1:CAS:528:DC%2BD3sXlvFaqtrc%3D, PID: 12897771
-
Wall JD, Pritchard JK et al (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 4:587–597. doi:10.1038/nrg1123
-
(2003)
Nat Rev Genet
, vol.4
, pp. 587-597
-
-
Wall, J.D.1
Pritchard, J.K.2
-
77
-
-
84863150047
-
Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny
-
COI: 1:CAS:528:DC%2BC38XnsVSmsbc%3D, PID: 22345612
-
Wang JR, de Villena FP-M, Lawson HA et al (2012a) Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny. Genetics 190:449–458. doi:10.1534/genetics.111.132381
-
(2012)
Genetics
, vol.190
, pp. 449-458
-
-
Wang, J.R.1
de Villena, F.P.-M.2
Lawson, H.A.3
-
78
-
-
84867328380
-
Comparative analysis and visualization of multiple collinear genomes
-
Wang JR, de Villena FP-M, McMillan L et al (2012b) Comparative analysis and visualization of multiple collinear genomes. BMC Bioinform 13(Suppl 3):S13. doi:10.1186/1471-2105-13-S3-S13
-
(2012)
BMC Bioinform
, vol.13
, pp. 13
-
-
Wang, J.R.1
de Villena, F.P.-M.2
McMillan, L.3
-
79
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
COI: 1:CAS:528:DC%2BD38Xpt1WhsLw%3D, PID: 12466850
-
Waterston RH, Lindblad-Toh K, Birney E et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562. doi:10.1038/nature01262
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
-
80
-
-
84936076024
-
Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations
-
PID: 25230953
-
Weiser M, Mukherjee S, Furey TS et al (2014) Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics 198:879–893. doi:10.1534/genetics.114.167791
-
(2014)
Genetics
, vol.198
, pp. 879-893
-
-
Weiser, M.1
Mukherjee, S.2
Furey, T.S.3
-
81
-
-
0035233644
-
The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis
-
Williams RW, Gu J, Qi S, Lu L et al (2001) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol 2:46. doi:10.1186/gb-2001-2-11-research0046
-
(2001)
Genome Biol
, vol.2
, pp. 46
-
-
Williams, R.W.1
Gu, J.2
Qi, S.3
Lu, L.4
-
82
-
-
3943093151
-
Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis
-
COI: 1:CAS:528:DC%2BD2cXnt1Ont7k%3D, PID: 15457343
-
Williams RW, Bennett B, Lu L et al (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mamm Genome 15:637–647. doi:10.1007/s00335-004-2380-6
-
(2004)
Mamm Genome
, vol.15
, pp. 637-647
-
-
Williams, R.W.1
Bennett, B.2
Lu, L.3
-
83
-
-
38549148703
-
The vertebrate genome annotation (Vega) database
-
COI: 1:CAS:528:DC%2BD1cXhtVWjs70%3D, PID: 18003653
-
Wilming LG, Gilbert JGR, Howe K et al (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36:D753–D760. doi:10.1093/nar/gkm987
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 753-760
-
-
Wilming, L.G.1
Gilbert, J.G.R.2
Howe, K.3
-
84
-
-
34548348147
-
On the subspecific origin of the laboratory mouse
-
COI: 1:CAS:528:DC%2BD2sXps12gtLs%3D, PID: 17660819
-
Yang H, Bell TA, Churchill GA, de Villena FPM et al (2007) On the subspecific origin of the laboratory mouse. Nat Genet 39:1100–1107. doi:10.1038/ng2087
-
(2007)
Nat Genet
, vol.39
, pp. 1100-1107
-
-
Yang, H.1
Bell, T.A.2
Churchill, G.A.3
de Villena, F.P.M.4
-
85
-
-
69549102945
-
A customized and versatile high-density genotyping array for the mouse
-
COI: 1:CAS:528:DC%2BD1MXps1ahu74%3D, PID: 19668205
-
Yang H, Ding Y, Hutchins LN et al (2009) A customized and versatile high-density genotyping array for the mouse. Nat Methods 6:663–666. doi:10.1038/nmeth.1359
-
(2009)
Nat Methods
, vol.6
, pp. 663-666
-
-
Yang, H.1
Ding, Y.2
Hutchins, L.N.3
-
86
-
-
79959735506
-
Subspecific origin and haplotype diversity in the laboratory mouse
-
COI: 1:CAS:528:DC%2BC3MXmslSktL8%3D, PID: 21623374
-
Yang H, Wang JR, Didion JP et al (2011) Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 43:648–655. doi:10.1038/ng.847
-
(2011)
Nat Genet
, vol.43
, pp. 648-655
-
-
Yang, H.1
Wang, J.R.2
Didion, J.P.3
-
87
-
-
84907912911
-
Bayesian modeling of haplotype effects in multiparent populations
-
PID: 25236455
-
Zhang Z, Wang W, Valdar W et al (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198:139–156. doi:10.1534/genetics.114.166249
-
(2014)
Genetics
, vol.198
, pp. 139-156
-
-
Zhang, Z.1
Wang, W.2
Valdar, W.3
-
88
-
-
84943819248
-
-
BAGPIPE
-
BAGPIPE. http://valdarlab.unc.edu/software/bagpipe
-
-
-
-
89
-
-
84943818502
-
-
BAGPHENOTYPE
-
BAGPHENOTYPE. http://valdarlab.unc.edu/bagphenotype.html
-
-
-
-
90
-
-
84943820926
-
-
Collaborative Cross Status website
-
Collaborative Cross Status website. http://www.csbio.unc.edu/CCstatus/
-
-
-
-
91
-
-
84943816411
-
-
Collaborative Cross Viewer
-
Collaborative Cross Viewer. http://www.csbio.unc.edu/CCstatus/index.py?run=CCV
-
-
-
-
92
-
-
84943817899
-
-
DOQTL
-
DOQTL. http://www.bioconductor.org/packages/release/bioc/html/DOQTL.html
-
-
-
-
93
-
-
84943820087
-
-
GECCO gene expression browser
-
GECCO gene expression browser. http://csbio.unc.edu/gecco/
-
-
-
-
94
-
-
84943818647
-
-
MDA genotypes for 100 inbred strains
-
MDA genotypes for 100 inbred strains. http://cgd.jax.org/datasets/popgen/diversityarray/yang2011.shtml
-
-
-
-
95
-
-
84943819108
-
-
MegaMUGA genotypes for CC founder strains
-
MegaMUGA genotypes for CC founder strains. http://csbio.unc.edu/CCstatus/index.py?run=GeneseekMM
-
-
-
-
96
-
-
84943815047
-
-
modtools + lapels + suspenders pipeline
-
modtools + lapels + suspenders pipeline. http://www.csbio.unc.edu/CCstatus/index.py?run=Pseudo
-
-
-
-
97
-
-
84943815479
-
-
Mouse Imputation Resource
-
Mouse Imputation Resource. http://csbio.unc.edu/imputation/
-
-
-
-
98
-
-
84943820877
-
-
Mouse Phylogeny Viewer
-
Mouse Phylogeny Viewer. http://msub.csbio.unc.edu/
-
-
-
-
99
-
-
84943814884
-
-
Sanger Mouse Genomes Project
-
Sanger Mouse Genomes Project. http://www.sanger.ac.uk/resources/mouse/genomes/
-
-
-
-
100
-
-
84943820251
-
-
Searchable index of sequencing reads from CC founder strains
-
Searchable index of sequencing reads from CC founder strains. http://www.csbio.unc.edu/CEGSseq/index.py?run=MsbwtTools
-
-
-
-
101
-
-
84943814593
-
-
Seqnature
-
Seqnature. https://github.com/jaxcs/Seqnature
-
-
-
|