-
1
-
-
84890829647
-
The Amborella genome and the evolution of flowering plants
-
Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science 342:1241089.
-
(2013)
Science
, vol.342
, pp. 1241089
-
-
Amborella Genome Project1
-
2
-
-
84858194655
-
Gene capture by Helitron transposons reshuffles the transcriptome of maize
-
Barbaglia AM, et al. 2012. Gene capture by Helitron transposons reshuffles the transcriptome of maize. Genetics 190:965-975.
-
(2012)
Genetics
, vol.190
, pp. 965-975
-
-
Barbaglia, A.M.1
-
3
-
-
84870664380
-
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants
-
Baxter L, et al. 2012. Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell 24:3949-3965.
-
(2012)
Plant Cell
, vol.24
, pp. 3949-3965
-
-
Baxter, L.1
-
4
-
-
0037468758
-
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
-
Bowers JE, Chapman BA, Rong J, Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.
-
(2003)
Nature
, vol.422
, pp. 433-438
-
-
Bowers, J.E.1
Chapman, B.A.2
Rong, J.3
Paterson, A.H.4
-
5
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne KP, Wolfe KH. 2005. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456-1461.
-
(2005)
Genome Res.
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
6
-
-
79952706998
-
MicroSyn: A user friendly tool for detection of microsynteny in a gene family
-
Cai B, Yang X, Tuskan GA, Cheng ZM. 2011. MicroSyn: a user friendly tool for detection of microsynteny in a gene family. BMC Bioinformatics 12:79.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 79
-
-
Cai, B.1
Yang, X.2
Tuskan, G.A.3
Cheng, Z.M.4
-
7
-
-
84906689347
-
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
-
Chalhoub B, et al. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950-953.
-
(2014)
Science
, vol.345
, pp. 950-953
-
-
Chalhoub, B.1
-
8
-
-
67649331694
-
Sixty million years in evolution of soft grain trait in grasses: Emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae
-
Charles M, et al. 2009. Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol Biol Evol. 26:1651-1661.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 1651-1661
-
-
Charles, M.1
-
9
-
-
84864475788
-
Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution
-
Davidson RM, et al. 2012. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 71:492-502.
-
(2012)
Plant J.
, vol.71
, pp. 492-502
-
-
Davidson, R.M.1
-
10
-
-
80053195352
-
Positional orthology: Putting genomic evolutionary relationships into context
-
Dewey CN. 2011. Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinformatics 12:401-412.
-
(2011)
Brief Bioinformatics
, vol.12
, pp. 401-412
-
-
Dewey, C.N.1
-
11
-
-
70350029560
-
Synorth: Exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
-
Dong X, Fredman D, Lenhard B. 2009. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 10:R86.
-
(2009)
Genome Biol.
, vol.10
, pp. R86
-
-
Dong, X.1
Fredman, D.2
Lenhard, B.3
-
12
-
-
38849112675
-
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
-
Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. 2007. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17:1898-1908.
-
(2007)
Genome Res.
, vol.17
, pp. 1898-1908
-
-
Engstrom, P.G.1
Ho Sui, S.J.2
Drivenes, O.3
Becker, T.S.4
Lenhard, B.5
-
13
-
-
57149120510
-
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
-
Freeling M, et al. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18:1924-1937.
-
(2008)
Genome Res.
, vol.18
, pp. 1924-1937
-
-
Freeling, M.1
-
14
-
-
84902506954
-
Evaluating synteny for improved comparative studies
-
Ghiurcuta CG, Moret BM. 2014. Evaluating synteny for improved comparative studies. Bioinformatics 30:i9-i18.
-
(2014)
Bioinformatics
, vol.30
, pp. i9-i18
-
-
Ghiurcuta, C.G.1
Moret, B.M.2
-
15
-
-
84858593012
-
The iPlant collaborative: Cyberinfrastructure for plant biology
-
Goff SA, et al. 2011. The iPlant collaborative: cyberinfrastructure for plant biology. Front Plant Sci. 2:34.
-
(2011)
Front Plant Sci.
, vol.2
, pp. 34
-
-
Goff, S.A.1
-
16
-
-
84917697073
-
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
-
Green RE, et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449.
-
(2014)
Science
, vol.346
, pp. 1254449
-
-
Green, R.E.1
-
17
-
-
84881028642
-
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
-
Haudry A, et al. 2013. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet. 45:891-898.
-
(2013)
Nat Genet.
, vol.45
, pp. 891-898
-
-
Haudry, A.1
-
18
-
-
38549148421
-
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
-
Heger A, Ponting CP. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17:1837-1849.
-
(2007)
Genome Res.
, vol.17
, pp. 1837-1849
-
-
Heger, A.1
Ponting, C.P.2
-
19
-
-
84892641918
-
Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family
-
Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric SchranzM. 2013. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biol Evol. 5:2155-2173.
-
(2013)
Genome Biol Evol.
, vol.5
, pp. 2155-2173
-
-
Hofberger, J.A.1
Lyons, E.2
Edger, P.P.3
Chris Pires, J.4
Eric Schranz, M.5
-
20
-
-
84878713991
-
Architecture and evolution of a minute plant genome
-
Ibarra-Laclette E, et al. 2013. Architecture and evolution of a minute plant genome. Nature 498:94-98.
-
(2013)
Nature
, vol.498
, pp. 94-98
-
-
Ibarra-Laclette, E.1
-
21
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
Jin Q, et al. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
-
22
-
-
79952256999
-
Adaptive seeds tame genomic sequence comparison
-
Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. 2011. Adaptive seeds tame genomic sequence comparison. Genome Res. 21:487-493.
-
(2011)
Genome Res.
, vol.21
, pp. 487-493
-
-
Kielbasa, S.M.1
Wan, R.2
Sato, K.3
Horton, P.4
Frith, M.C.5
-
23
-
-
21144454436
-
Gene movement by Helitron transposons contributes to the haplotype variability of maize
-
Lai J, Li Y, Messing J, Dooner HK. 2005. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci U S A. 102:9068-9073.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 9068-9073
-
-
Lai, J.1
Li, Y.2
Messing, J.3
Dooner, H.K.4
-
24
-
-
84920188663
-
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGenv3 gene models and identifies new genes
-
Law M, et al. 2015. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGenv3 gene models and identifies new genes. Plant Physiol. 167:25-39.
-
(2015)
Plant Physiol.
, vol.167
, pp. 25-39
-
-
Law, M.1
-
25
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
-
(2003)
Genome Res.
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
26
-
-
61449125108
-
Detecting gene clusters under evolutionary constraint in a large number of genomes
-
Ling X, He X, Xin D. 2009. Detecting gene clusters under evolutionary constraint in a large number of genomes. Bioinformatics 25:571-577.
-
(2009)
Bioinformatics
, vol.25
, pp. 571-577
-
-
Ling, X.1
He, X.2
Xin, D.3
-
27
-
-
84928135172
-
For big-data scientists, "Janitor Work" is key hurdle to insights
-
New York City Aug 18
-
Lohr S. 2014 Aug 18. For big-data scientists, "Janitor Work" is key hurdle to insights. The New York Times. New York City. Available from: http://www.nytimes.com/2014/08/18/technology/for-big-datascientists-hurdle-to-insights-is-janitor-work.html?-r=0.
-
(2014)
The New York Times
-
-
Lohr, S.1
-
28
-
-
38949151064
-
How to usefully compare homologous plant genes and chromosomes as DNA sequences
-
Lyons E, Freeling M. 2008. How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53:661-673.
-
(2008)
Plant J.
, vol.53
, pp. 661-673
-
-
Lyons, E.1
Freeling, M.2
-
29
-
-
57749096814
-
The value of nonmodel genomes and an example using synmap within coge to dissect the hexaploidy that predates the rosids
-
Lyons E, Pedersen B, Kane J, Freeling M. 2008. The value of nonmodel genomes and an example using synmap within coge to dissect the hexaploidy that predates the rosids. Trop Plant Biol. 1:181-190.
-
(2008)
Trop Plant Biol.
, vol.1
, pp. 181-190
-
-
Lyons, E.1
Pedersen, B.2
Kane, J.3
Freeling, M.4
-
30
-
-
0035313453
-
Transcription unit conservation in the three domains of life: A perspective from Escherichia coli
-
Moreno-Hagelsieb G, Trevino V, Perez-Rueda E, Smith TF, Collado-Vides J. 2001. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends Genet. 17:175-177.
-
(2001)
Trends Genet.
, vol.17
, pp. 175-177
-
-
Moreno-Hagelsieb, G.1
Trevino, V.2
Perez-Rueda, E.3
Smith, T.F.4
Collado-Vides, J.5
-
31
-
-
67650961327
-
OrthoClusterDB: An online platform for synteny blocks
-
Ng MP, et al. 2009. OrthoClusterDB: an online platform for synteny blocks. BMC Bioinformatics 10:192.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 192
-
-
Ng, M.P.1
-
32
-
-
75549086594
-
InParanoid 7: New algorithms and tools for eukaryotic orthology analysis
-
Ostlund G, et al. 2010. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38:D196-D203.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D196-D203
-
-
Ostlund, G.1
-
33
-
-
42649133497
-
The determinants of gene order conservation in yeasts
-
Poyatos JF, Hurst LD. 2007. The determinants of gene order conservation in yeasts. Genome Biol. 8:R233.
-
(2007)
Genome Biol.
, vol.8
, pp. R233
-
-
Poyatos, J.F.1
Hurst, L.D.2
-
34
-
-
84855884044
-
I-ADHoRe 3.0 - Fast and sensitive detection of genomic homology in extremely large data sets
-
Proost S, et al. 2012. i-ADHoRe 3.0 - fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. 40:e11.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e11
-
-
Proost, S.1
-
35
-
-
84864444502
-
A web-based multi-genome synteny viewer for customized data
-
Revanna KV, et al. 2012. A web-based multi-genome synteny viewer for customized data. BMC Bioinformatics 13:190.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 190
-
-
Revanna, K.V.1
-
36
-
-
77749246134
-
CYNTENATOR: Progressive gene order alignment of 17 vertebrate genomes
-
Rodelsperger C, Dieterich C. 2010. CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PLoS One 5:e8861.
-
(2010)
PLoS One
, vol.5
-
-
Rodelsperger, C.1
Dieterich, C.2
-
37
-
-
84928887792
-
Genome evolution in maize: From genomes back to genes
-
Schnable JC. 2015. Genome evolution in maize: from genomes back to genes. Annu Rev Plant Biol. 66:329-343.
-
(2015)
Annu Rev Plant Biol.
, vol.66
, pp. 329-343
-
-
Schnable, J.C.1
-
38
-
-
79952495788
-
Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize
-
Schnable JC, Freeling M. 2011. Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One 6:e17855.
-
(2011)
PLoS One
, vol.6
-
-
Schnable, J.C.1
Freeling, M.2
-
39
-
-
84863210911
-
Genome-wide analysis of syntenic gene deletion in the grasses
-
Schnable JC, FreelingM, Lyons E. 2012. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol. 4:265-277.
-
(2012)
Genome Biol Evol.
, vol.4
, pp. 265-277
-
-
Schnable, J.C.1
Freeling, M.2
Lyons, E.3
-
40
-
-
33947408098
-
Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organisms
-
Sinha AU, Meller J. 2007. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 8:82.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 82
-
-
Sinha, A.U.1
Meller, J.2
-
41
-
-
79961194036
-
SyMAP v3.4: A turnkey synteny system with application to plant genomes
-
Soderlund C, Bomhoff M, Nelson WM. 2011. SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res. 39:e68.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. e68
-
-
Soderlund, C.1
Bomhoff, M.2
Nelson, W.M.3
-
42
-
-
42549120705
-
Synteny and collinearity in plant genomes
-
Tang H, Bowers JE, et al. 2008. Synteny and collinearity in plant genomes. Science 320:486-488.
-
(2008)
Science
, vol.320
, pp. 486-488
-
-
Tang, H.1
Bowers, J.E.2
-
43
-
-
79955111350
-
Screening synteny blocks in pairwise genome comparisons through integer programming
-
Tang H, et al. 2011. Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 12:102.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 102
-
-
Tang, H.1
-
44
-
-
84879472582
-
Unleashing the genome of Brassica rapa
-
Tang H, Lyons E. 2012. Unleashing the genome of Brassica rapa. Front Plant Sci. 3:172.
-
(2012)
Front Plant Sci.
, vol.3
, pp. 172
-
-
Tang, H.1
Lyons, E.2
-
45
-
-
57149102681
-
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
-
Tang H, Wang X, et al. 2008. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18:1944-1954.
-
(2008)
Genome Res.
, vol.18
, pp. 1944-1954
-
-
Tang, H.1
Wang, X.2
-
46
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pangenome"
-
Tettelin H, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pangenome." Proc Natl Acad Sci U S A. 102:13950-13955.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 13950-13955
-
-
Tettelin, H.1
-
48
-
-
77956926876
-
Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster
-
Vergara IA, Chen N. 2010. Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genomics 11:516.
-
(2010)
BMC Genomics
, vol.11
, pp. 516
-
-
Vergara, I.A.1
Chen, N.2
-
49
-
-
33750489449
-
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
-
Wang X, et al. 2006. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 7:447.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 447
-
-
Wang, X.1
-
50
-
-
84860137835
-
MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity
-
Wang Y, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40:e49.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e49
-
-
Wang, Y.1
-
51
-
-
84888377186
-
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
-
Waters AJ, et al. 2013. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proc Natl Acad Sci U S A. 110:19639-19644.
-
(2013)
Proc Natl Acad Sci U S A.
, vol.110
, pp. 19639-19644
-
-
Waters, A.J.1
-
52
-
-
0035344021
-
Yesterday's polyploids and the mystery of diploidization
-
Wolfe KH. 2001. Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet. 2:333-341.
-
(2001)
Nat Rev Genet.
, vol.2
, pp. 333-341
-
-
Wolfe, K.H.1
-
53
-
-
77953179573
-
Transposed genes in Arabidopsis are often associated with flanking repeats
-
Woodhouse MR, Pedersen B, Freeling M. 2010. Transposed genes in Arabidopsis are often associated with flanking repeats. PLoS Genet. 6:e1000949.
-
(2010)
PLoS Genet.
, vol.6
-
-
Woodhouse, M.R.1
Pedersen, B.2
Freeling, M.3
-
54
-
-
84856480832
-
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids
-
Woodhouse MR, Tang H, Freeling M. 2011. Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell 23:4241-4253.
-
(2011)
Plant Cell
, vol.23
, pp. 4241-4253
-
-
Woodhouse, M.R.1
Tang, H.2
Freeling, M.3
|