-
1
-
-
85016096622
-
Ensembl 2017
-
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, et al. 2017. Ensembl 2017. Nucleic Acids Res 45: D635–D642.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D635-D642
-
-
Aken, B.L.1
Achuthan, P.2
Akanni, W.3
Amode, M.R.4
Bernsdorff, F.5
Bhai, J.6
Billis, K.7
Carvalho-Silva, D.8
Cummins, C.9
Clapham, P.10
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403–410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
84864439921
-
FastML: A web server for probabilistic reconstruction of ancestral sequences
-
Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T. 2012. FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res 40: W580–W584.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W580-W584
-
-
Ashkenazy, H.1
Penn, O.2
Doron-Faigenboim, A.3
Cohen, O.4
Cannarozzi, G.5
Zomer, O.6
Pupko, T.7
-
4
-
-
84881176167
-
Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat
-
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, et al. 2013. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 154: 691–703.
-
(2013)
Cell
, vol.154
, pp. 691-703
-
-
Atanur, S.S.1
Diaz, A.G.2
Maratou, K.3
Sarkis, A.4
Rotival, M.5
Game, L.6
Tschannen, M.R.7
Kaisaki, P.J.8
Otto, G.W.9
Ma, M.C.10
-
5
-
-
4444264564
-
Hotspots of mammalian chromosomal evolution
-
Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. 2004. Hotspots of mammalian chromosomal evolution. Genome Biol 5: R23.
-
(2004)
Genome Biol
, vol.5
, pp. R23
-
-
Bailey, J.A.1
Baertsch, R.2
Kent, W.J.3
Haussler, D.4
Eichler, E.E.5
-
7
-
-
0036250811
-
Alu repeats and human genomic diversity
-
Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3: 370–379.
-
(2002)
Nat Rev Genet
, vol.3
, pp. 370-379
-
-
Batzer, M.A.1
Deininger, P.L.2
-
8
-
-
79956349420
-
Reinforcement selection acting on the European house mouse hybrid zone
-
Bimova BV, Macholan M, Baird SJ, Munclinger P, Dufkova P, Laukaitis CM, Karn RC, Luzynski K, Tucker PK, Pialek J. 2011. Reinforcement selection acting on the European house mouse hybrid zone. Mol Ecol 20: 2403–2424.
-
(2011)
Mol Ecol
, vol.20
, pp. 2403-2424
-
-
Bimova, B.V.1
Macholan, M.2
Baird, S.J.3
Munclinger, P.4
Dufkova, P.5
Laukaitis, C.M.6
Karn, R.C.7
Luzynski, K.8
Tucker, P.K.9
Pialek, J.10
-
9
-
-
84901305512
-
BEAST 2: A software platform for Bayesian evolutionary analysis
-
Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10: e1003537.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003537
-
-
Bouckaert, R.1
Heled, J.2
Kuhnert, D.3
Vaughan, T.4
Wu, C.H.5
Xie, D.6
Suchard, M.A.7
Rambaut, A.8
Drummond, A.J.9
-
10
-
-
55549117831
-
Evolution of the mammalian transcription factor binding repertoire via transposable elements
-
Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, et al. 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18: 1752–1762.
-
(2008)
Genome Res
, vol.18
, pp. 1752-1762
-
-
Bourque, G.1
Leong, B.2
Vega, V.B.3
Chen, X.4
Lee, Y.L.5
Srinivasan, K.G.6
Chew, J.L.7
Ruan, Y.8
Wei, C.L.9
Ng, H.H.10
-
11
-
-
77951621301
-
The genome sequence of taurine cattle: A window to ruminant biology and evolution
-
The Bovine Genome Sequencing and Analysis Consortium. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522–528.
-
(2009)
Science
, vol.324
, pp. 522-528
-
-
-
12
-
-
67649130520
-
Why do species vary in their rate of molecular evolution?
-
Bromham L. 2009. Why do species vary in their rate of molecular evolution? Biol Lett 5: 401–404.
-
(2009)
Biol Lett
, vol.5
, pp. 401-404
-
-
Bromham, L.1
-
13
-
-
85014383066
-
Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia
-
Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. 2016. Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia. Genome Biol Evol 8: 3703–3717.
-
(2016)
Genome Biol Evol
, vol.8
, pp. 3703-3717
-
-
Capilla, L.1
Sánchez-Guillén, R.A.2
Farre, M.3
Paytuví-Gallart, A.4
Malinverni, R.5
Ventura, J.6
Larkin, D.M.7
Ruiz-Herrera, A.8
-
14
-
-
84907284157
-
Gibbon genome and the fast karyotype evolution of small apes
-
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, et al. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature 513: 195–201.
-
(2014)
Nature
, vol.513
, pp. 195-201
-
-
Carbone, L.1
Harris, R.A.2
Gnerre, S.3
Veeramah, K.R.4
Lorente-Galdos, B.5
Huddleston, J.6
Meyer, T.J.7
Herrero, J.8
Roos, C.9
Aken, B.10
-
15
-
-
60349093708
-
Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation
-
Charlesworth B. 2009. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10: 195–205.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 195-205
-
-
Charlesworth, B.1
-
16
-
-
84902590955
-
A phy-logeographic survey of the pygmy mouse Mus minutoides in South Africa: Taxonomic and karyotypic inference from cytochrome b sequences of museum specimens
-
Chevret P, Robinson TJ, Perez J, Veyrunes F, Britton-Davidian J. 2014. A phy-logeographic survey of the pygmy mouse Mus minutoides in South Africa: taxonomic and karyotypic inference from cytochrome b sequences of museum specimens. PLoS One 9: e98499.
-
(2014)
PLoS One
, vol.9
, pp. e98499
-
-
Chevret, P.1
Robinson, T.J.2
Perez, J.3
Veyrunes, F.4
Britton-Davidian, J.5
-
17
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
18
-
-
84960194716
-
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
-
Chuong EB, Elde NC, Feschotte C. 2016. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351: 1083–1087.
-
(2016)
Science
, vol.351
, pp. 1083-1087
-
-
Chuong, E.B.1
Elde, N.C.2
Feschotte, C.3
-
19
-
-
66249148986
-
Lineage-specific biology revealed by a finished genome assembly of the mouse
-
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, et al. 2009. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7: e1000112.
-
(2009)
PLoS Biol
, vol.7
, pp. e1000112
-
-
Church, D.M.1
Goodstadt, L.2
Hillier, L.W.3
Zody, M.C.4
Goldstein, S.5
She, X.6
Bult, C.J.7
Agarwala, R.8
Cherry, J.L.9
DiCuccio, M.10
-
21
-
-
0034079713
-
Human LINE retrotransposons generate processed pseudogenes
-
Esnault C, Maestre J, Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363–367.
-
(2000)
Nat Genet
, vol.24
, pp. 363-367
-
-
Esnault, C.1
Maestre, J.2
Heidmann, T.3
-
23
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29–W37.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W29-W37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
24
-
-
84924078627
-
Convergent evolution of the genomes of marine mammals
-
Foote AD, Liu Y, Thomas GW, Vinar T, Alfoldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, et al. 2015. Convergent evolution of the genomes of marine mammals. Nat Genet 47: 272–275.
-
(2015)
Nat Genet
, vol.47
, pp. 272-275
-
-
Foote, A.D.1
Liu, Y.2
Thomas, G.W.3
Vinar, T.4
Alfoldi, J.5
Deng, J.6
Dugan, S.7
Van Elk, C.E.8
Hunter, M.E.9
Joshi, V.10
-
25
-
-
33751374466
-
Genomic selective constraints in murid noncoding DNA
-
Gaffney DJ, Keightley PD. 2006. Genomic selective constraints in murid noncoding DNA. PLoS Genet 2: e204.
-
(2006)
PLoS Genet
, vol.2
, pp. e204
-
-
Gaffney, D.J.1
Keightley, P.D.2
-
26
-
-
84934294825
-
The Robertsonian phenomenon in the house mouse: Mutation, meiosis and speciation
-
Garagna S, Page J, Fernandez-Donoso R, Zuccotti M, Searle JB. 2014. The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation. Chromosoma 123: 529–544.
-
(2014)
Chromosoma
, vol.123
, pp. 529-544
-
-
Garagna, S.1
Page, J.2
Fernandez-Donoso, R.3
Zuccotti, M.4
Searle, J.B.5
-
27
-
-
80053542924
-
Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
-
Gazave E, Darre F, Morcillo-Suarez C, Petit-Marty N, Carreno A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, et al. 2011. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res 21: 1626–1639.
-
(2011)
Genome Res
, vol.21
, pp. 1626-1639
-
-
Gazave, E.1
Darre, F.2
Morcillo-Suarez, C.3
Petit-Marty, N.4
Carreno, A.5
Marigorta, U.M.6
Ryder, O.A.7
Blancher, A.8
Rocchi, M.9
Bosch, E.10
-
28
-
-
80054090252
-
Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination
-
Geraldes A, Basset P, Smith KL, Nachman MW. 2011. Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination. Mol Ecol 20: 4722–4736.
-
(2011)
Mol Ecol
, vol.20
, pp. 4722-4736
-
-
Geraldes, A.1
Basset, P.2
Smith, K.L.3
Nachman, M.W.4
-
29
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci 108: 1513–1518.
-
(2011)
Proc Natl Acad Sci
, 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
Sharpe, T.7
Hall, G.8
Shea, T.P.9
Sykes, S.10
-
30
-
-
33750236839
-
Mammalian Male mutation bias: Impacts of generation time and regional variation in substitution rates
-
Goetting-Minesky MP, Makova KD. 2006. Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates. J Mol Evol 63: 537–544.
-
(2006)
J Mol Evol
, vol.63
, pp. 537-544
-
-
Goetting-Minesky, M.P.1
Makova, K.D.2
-
31
-
-
84963548310
-
Long-read sequence assembly of the gorilla genome
-
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, et al. 2016. Long-read sequence assembly of the gorilla genome. Science 352: aae0344.
-
(2016)
Science
, vol.352
, pp. aae0344
-
-
Gordon, D.1
Huddleston, J.2
Chaisson, M.J.3
Hill, C.M.4
Kronenberg, Z.N.5
Munson, K.M.6
Malig, M.7
Raja, A.8
Fiddes, I.9
Hillier, L.W.10
-
32
-
-
84869003221
-
Analyses of pig genomes provide insight into porcine demography and evolution
-
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491: 393–398.
-
(2012)
Nature
, vol.491
, pp. 393-398
-
-
Groenen, M.A.1
Archibald, A.L.2
Uenishi, H.3
Tuggle, C.K.4
Takeuchi, Y.5
Rothschild, M.F.6
Rogel-Gaillard, C.7
Park, C.8
Milan, D.9
Megens, H.J.10
-
33
-
-
84865760395
-
GENCODE: The reference human genome annotation for The ENCODE Project
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22: 1760–1774.
-
(2012)
Genome Res
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
34
-
-
33846704345
-
Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity
-
Hedges DJ, Deininger PL. 2007. Inviting instability: transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res 616: 46–59.
-
(2007)
Mutat Res
, vol.616
, pp. 46-59
-
-
Hedges, D.J.1
Deininger, P.L.2
-
35
-
-
84964765606
-
Ensembl comparative genomics resources
-
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, et al. 2016. Ensembl comparative genomics resources. Database (Oxford) 2016: bav096.
-
(2016)
Database (Oxford)
, vol.2016
, pp. bav096
-
-
Herrero, J.1
Muffato, M.2
Beal, K.3
Fitzgerald, S.4
Gordon, L.5
Pignatelli, M.6
Vilella, A.J.7
Searle, S.M.8
Amode, R.9
Brent, S.10
-
36
-
-
84992700410
-
An LTR retrotransposon-derived gene displays lineage-specific structural and putative species-specific functional variations in eutherians
-
Irie M, Koga A, Kaneko-Ishino T, Ishino F. 2016. An LTR retrotransposon-derived gene displays lineage-specific structural and putative species-specific functional variations in eutherians. Front Chem 4: 26.
-
(2016)
Front Chem
, vol.4
, pp. 26
-
-
Irie, M.1
Koga, A.2
Kaneko-Ishino, T.3
Ishino, F.4
-
37
-
-
41049092113
-
Of mice… again: The Siwalik rodent record, murine distribution, and molecular clocks
-
(ed. Lieberman D, et al.), Brill Academic Publishers, Boston
-
Jacobs L, Flynn L. 2005. Of mice… again: the Siwalik rodent record, murine distribution, and molecular clocks. In Interpreting the past: essays on human, primate, and mammal evolution in honor of David Pilbeam (ed. Lieberman D, et al.), pp. 63–80. Brill Academic Publishers, Boston.
-
(2005)
Interpreting The Past: Essays on Human, Primate, and Mammal Evolution in Honor of David Pilbeam
, pp. 63-80
-
-
Jacobs, L.1
Flynn, L.2
-
38
-
-
84878522936
-
The majority of primate-specific regulatory sequences are derived from transposable elements
-
Jacques PE, Jeyakani J, Bourque G. 2013. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet 9: e1003504.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003504
-
-
Jacques, P.E.1
Jeyakani, J.2
Bourque, G.3
-
39
-
-
84878230681
-
The role of retrotransposons in gene family expansions: Insights from the mouse Abp gene family
-
Janoušek V, Karn RC, Laukaitis CM. 2013. The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family. BMC Evol Biol 13: 107.
-
(2013)
BMC Evol Biol
, vol.13
, pp. 107
-
-
Janoušek, V.1
Karn, R.C.2
Laukaitis, C.M.3
-
40
-
-
84995394519
-
The role of retrotransposons in gene family expansions in the human and mouse genomes
-
Janoušek V, Laukaitis CM, Yanchukov A, Karn RC. 2016. The role of retrotransposons in gene family expansions in the human and mouse genomes. Genome Biol Evol 8: 2632–2650.
-
(2016)
Genome Biol Evol
, vol.8
, pp. 2632-2650
-
-
Janoušek, V.1
Laukaitis, C.M.2
Yanchukov, A.3
Karn, R.C.4
-
41
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497–1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
42
-
-
34247494315
-
Karyotypic diversity and speciation in Agrodiaetus butterflies
-
Kandul NP, Lukhtanov VA, Pierce NE. 2007. Karyotypic diversity and speciation in Agrodiaetus butterflies. Evolution 61: 546–559.
-
(2007)
Evolution
, vol.61
, pp. 546-559
-
-
Kandul, N.P.1
Lukhtanov, V.A.2
Pierce, N.E.3
-
44
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772–780.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
45
-
-
80855165387
-
Genome sequencing reveals insights into physiology and longevity of the naked mole rat
-
Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, et al. 2011. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479: 223–227.
-
(2011)
Nature
, vol.479
, pp. 223-227
-
-
Kim, E.B.1
Fang, X.2
Fushan, A.A.3
Huang, Z.4
Lobanov, A.V.5
Han, L.6
Marino, S.M.7
Sun, X.8
Turanov, A.A.9
Yang, P.10
-
46
-
-
0141596080
-
The dog genome: Survey sequencing and comparative analysis
-
Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, et al. 2003. The dog genome: survey sequencing and comparative analysis. Science 301: 1898–1903.
-
(2003)
Science
, vol.301
, pp. 1898-1903
-
-
Kirkness, E.F.1
Bafna, V.2
Halpern, A.L.3
Levy, S.4
Remington, K.5
Rusch, D.B.6
Delcher, A.L.7
Pop, M.8
Wang, W.9
Fraser, C.M.10
-
48
-
-
85030691763
-
Chromosome assembly of large and complex genomes using multiple references
-
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane T, Thybert D, et al. 2016. Chromosome assembly of large and complex genomes using multiple references. bioRxiv doi:10.1101/ 088435.
-
(2016)
bioRxiv
-
-
Kolmogorov, M.1
Armstrong, J.2
Raney, B.J.3
Streeter, I.4
Dunn, M.5
Yang, F.6
Odom, D.7
Flicek, P.8
Keane, T.9
Thybert, D.10
-
50
-
-
77954100084
-
Transposable elements have rewired the core regulatory network of human embryonic stem cells
-
Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G. 2010. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42: 631–634.
-
(2010)
Nat Genet
, vol.42
, pp. 631-634
-
-
Kunarso, G.1
Chia, N.Y.2
Jeyakani, J.3
Hwang, C.4
Lu, X.5
Chan, Y.S.6
Ng, H.H.7
Bourque, G.8
-
51
-
-
41349085816
-
CGHweb: A tool for comparing DNA copy number segmentations from multiple algorithms
-
Lai W, Choudhary V, Park PJ. 2008. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics 24: 1014–1015.
-
(2008)
Bioinformatics
, vol.24
, pp. 1014-1015
-
-
Lai, W.1
Choudhary, V.2
Park, P.J.3
-
52
-
-
84866856766
-
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
-
Langergraber KE, Prufer K, Rowney C, Boesch C, Crockford C, Fawcett K, Inoue E, Inoue-Muruyama M, Mitani JC, Muller MN, et al. 2012. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci 109: 15716–15721.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 15716-15721
-
-
Langergraber, K.E.1
Prufer, K.2
Rowney, C.3
Boesch, C.4
Crockford, C.5
Fawcett, K.6
Inoue, E.7
Inoue-Muruyama, M.8
Mitani, J.C.9
Muller, M.N.10
-
53
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
54
-
-
84867682989
-
Recognition of subspecies status mediated by androgen-binding protein (ABP) in the evolution of incipient reinforcement on the European house mouse hybrid zone
-
(ed. Macholan M, et al.), Cambridge University Press, Cambridge, UK
-
Laukaitis C, Karn RC. 2012. Recognition of subspecies status mediated by androgen-binding protein (ABP) in the evolution of incipient reinforcement on the European house mouse hybrid zone. In Evolution of the house mouse (ed. Macholan M, et al.), pp. 150–190. Cambridge University Press, Cambridge, UK.
-
(2012)
Evolution of The House Mouse
, pp. 150-190
-
-
Laukaitis, C.1
Karn, R.C.2
-
55
-
-
41849131787
-
Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
-
Laukaitis CM, Heger A, Blakley TD, Munclinger P, Ponting CP, Karn RC. 2008. Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals. BMC Evol Biol 8: 46.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 46
-
-
Laukaitis, C.M.1
Heger, A.2
Blakley, T.D.3
Munclinger, P.4
Ponting, C.P.5
Karn, R.C.6
-
56
-
-
0023263979
-
The molecular clock runs more slowly in man than in apes and monkeys
-
Li WH, Tanimura M. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93–96.
-
(1987)
Nature
, vol.326
, pp. 93-96
-
-
Li, W.H.1
Tanimura, M.2
-
57
-
-
0030076124
-
Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis
-
Li WH, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylogenet Evol 5: 182–187.
-
(1996)
Mol Phylogenet Evol
, vol.5
, pp. 182-187
-
-
Li, W.H.1
Ellsworth, D.L.2
Krushkal, J.3
Chang, B.H.4
Hewett-Emmett, D.5
-
58
-
-
85015691214
-
Identification of critical base pairs required for CTCF binding in motif M1 and M2
-
Li W, Shang L, Huang K, Li J, Wang Z, Yao H. 2017. Identification of critical base pairs required for CTCF binding in motif M1 and M2. Protein Cell 8: 544–549.
-
(2017)
Protein Cell
, vol.8
, pp. 544-549
-
-
Li, W.1
Shang, L.2
Huang, K.3
Li, J.4
Wang, Z.5
Yao, H.6
-
59
-
-
85046123514
-
Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
-
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennet R, Chow W, Collins J, Czechanski A, Danecek P, et al. 2018. Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci. bioRxiv doi: 10.1101/235838.
-
(2018)
bioRxiv
-
-
Lilue, J.1
Doran, A.G.2
Fiddes, I.T.3
Abrudan, M.4
Armstrong, J.5
Bennet, R.6
Chow, W.7
Collins, J.8
Czechanski, A.9
Danecek, P.10
-
60
-
-
55249106663
-
Diverse splicing patterns of exonized Alu elements in human tissues
-
Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. 2008. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet 4: e1000225.
-
(2008)
PLoS Genet
, vol.4
, pp. e1000225
-
-
Lin, L.1
Shen, S.2
Tye, A.3
Cai, J.J.4
Jiang, P.5
Davidson, B.L.6
Xing, Y.7
-
61
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ III, Zody MC, et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803–819.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
Kamal, M.6
Clamp, M.7
Chang, J.L.8
Kulbokas, E.J.9
Zody, M.C.10
-
62
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, et al. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476–482.
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
Kheradpour, P.7
Ernst, J.8
Jordan, G.9
Mauceli, E.10
-
63
-
-
66049147797
-
Comparative analysis of Alu repeats in primate genomes
-
Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. 2009. Comparative analysis of Alu repeats in primate genomes. Genome Res 19: 876–885.
-
(2009)
Genome Res
, vol.19
, pp. 876-885
-
-
Liu, G.E.1
Alkan, C.2
Jiang, L.3
Zhao, S.4
Eichler, E.E.5
-
64
-
-
84900301308
-
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
-
Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, et al. 2014. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157: 785–794.
-
(2014)
Cell
, vol.157
, pp. 785-794
-
-
Liu, S.1
Lorenzen, E.D.2
Fumagalli, M.3
Li, B.4
Harris, K.5
Xiong, Z.6
Zhou, L.7
Korneliussen, T.S.8
Somel, M.9
Babbitt, C.10
-
65
-
-
79251553493
-
Comparative and demographic analysis of orang-utan genomes
-
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469: 529–533.
-
(2011)
Nature
, vol.469
, pp. 529-533
-
-
Locke, D.P.1
Hillier, L.W.2
Warren, W.C.3
Worley, K.C.4
Nazareth, L.V.5
Muzny, D.M.6
Yang, S.P.7
Wang, Z.8
Chinwalla, A.T.9
Minx, P.10
-
66
-
-
78649319201
-
WebPRANK: A phylogeny-aware multiple sequence aligner with interactive alignment browser
-
Loytynoja A, Goldman N. 2010. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11: 579.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 579
-
-
Loytynoja, A.1
Goldman, N.2
-
67
-
-
80055010534
-
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
-
Lynch VJ, Leclerc RD, May G, Wagner GP. 2011. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43: 1154–1159.
-
(2011)
Nat Genet
, vol.43
, pp. 1154-1159
-
-
Lynch, V.J.1
Leclerc, R.D.2
May, G.3
Wagner, G.P.4
-
68
-
-
60149083509
-
A burst of segmental duplications in the genome of the African great ape ancestor
-
Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, et al. 2009. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877–881.
-
(2009)
Nature
, vol.457
, pp. 877-881
-
-
Marques-Bonet, T.1
Kidd, J.M.2
Ventura, M.3
Graves, T.A.4
Cheng, Z.5
Hillier, L.W.6
Jiang, Z.7
Baker, C.8
Malfavon-Borja, R.9
Fulton, L.A.10
-
69
-
-
84957535518
-
How retrotransposons shape genome regulation
-
Mita P, Boeke JD. 2016. How retrotransposons shape genome regulation. Curr Opin Genet Dev 37: 90–100.
-
(2016)
Curr Opin Genet Dev
, vol.37
, pp. 90-100
-
-
Mita, P.1
Boeke, J.D.2
-
70
-
-
33749389932
-
Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
-
Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B. 2006. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res 16: 1208–1221.
-
(2006)
Genome Res
, vol.16
, pp. 1208-1221
-
-
Mortazavi, A.1
Leeper Thompson, E.C.2
Garcia, S.T.3
Myers, R.M.4
Wold, B.5
-
71
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
-
72
-
-
22744440499
-
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
-
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613–617.
-
(2005)
Science
, vol.309
, pp. 613-617
-
-
Murphy, W.J.1
Larkin, D.M.2
Everts-Van Der Wind, A.3
Bourque, G.4
Tesler, G.5
Auvil, L.6
Beever, J.E.7
Chowdhary, B.P.8
Galibert, F.9
Gatzke, L.10
-
73
-
-
84886293630
-
RCPedia: A database of retrocopied genes
-
Navarro FC, Galante PA. 2013. RCPedia: a database of retrocopied genes. Bioinformatics 29: 1235–1237.
-
(2013)
Bioinformatics
, vol.29
, pp. 1235-1237
-
-
Navarro, F.C.1
Galante, P.A.2
-
74
-
-
84954328457
-
A genome-wide landscape of retrocopies in primate genomes
-
Navarro FC, Galante PA. 2015. A genome-wide landscape of retrocopies in primate genomes. Genome Biol Evol 7: 2265–2275.
-
(2015)
Genome Biol Evol
, vol.7
, pp. 2265-2275
-
-
Navarro, F.C.1
Galante, P.A.2
-
75
-
-
84862203271
-
The genomic landscape shaped by selection on transposable elements across 18 mouse strains
-
Nellaker C, Keane TM, Yalcin B, Wong K, Agam A, Belgard TG, Flint J, Adams DJ, Frankel WN, Ponting CP. 2012. The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol 13: R45.
-
(2012)
Genome Biol
, vol.13
, pp. R45
-
-
Nellaker, C.1
Keane, T.M.2
Yalcin, B.3
Wong, K.4
Agam, A.5
Belgard, T.G.6
Flint, J.7
Adams, D.J.8
Frankel, W.N.9
Ponting, C.P.10
-
76
-
-
34147105638
-
The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage
-
Pace JK II, Feschotte C. 2007. The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res 17: 422–432.
-
(2007)
Genome Res
, vol.17
, pp. 422-432
-
-
Pace, J.K.1
Feschotte, C.2
-
77
-
-
84876580265
-
SwissRegulon, a database of genome-wide annotations of regulatory sites: Recent updates
-
Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. 2013. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res 41: D214–D220.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D214-D220
-
-
Pachkov, M.1
Balwierz, P.J.2
Arnold, P.3
Ozonov, E.4
Van Nimwegen, E.5
-
78
-
-
84894535837
-
An improved approach to mate-paired library preparation for Illumina sequencing
-
Park N, Shirley L, Gu Y, Keane T, Swerdlow H, Quail M. 2013. An improved approach to mate-paired library preparation for Illumina sequencing. Methods Next Generation Seq 1: 10–20.
-
(2013)
Methods Next Generation Seq
, vol.1
, pp. 10-20
-
-
Park, N.1
Shirley, L.2
Gu, Y.3
Keane, T.4
Swerdlow, H.5
Quail, M.6
-
79
-
-
80052551536
-
Cactus: Algorithms for genome multiple sequence alignment
-
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. 2011. Cactus: algorithms for genome multiple sequence alignment. Genome Res 21: 1512–1528.
-
(2011)
Genome Res
, vol.21
, pp. 1512-1528
-
-
Paten, B.1
Earl, D.2
Nguyen, N.3
Diekhans, M.4
Zerbino, D.5
Haussler, D.6
-
80
-
-
84865726286
-
The GENCODE pseudogene resource
-
Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, et al. 2012. The GENCODE pseudogene resource. Genome Biol 13: R51.
-
(2012)
Genome Biol
, vol.13
, pp. R51
-
-
Pei, B.1
Sisu, C.2
Frankish, A.3
Howald, C.4
Habegger, L.5
Mu, X.J.6
Harte, R.7
Balasubramanian, S.8
Tanzer, A.9
Diekhans, M.10
-
81
-
-
84979851907
-
Insights into mammalian biology from the wild house mouse Mus musculus
-
Phifer-Rixey M, Nachman MW. 2015. Insights into mammalian biology from the wild house mouse Mus musculus. eLife 4. doi: 10.7554/ eLife.05959.001.
-
(2015)
eLife
, vol.4
-
-
Phifer-Rixey, M.1
Nachman, M.W.2
-
82
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, et al. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167–172.
-
(2006)
Nature
, vol.443
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.A.4
Coppens, S.5
Pedersen, J.S.6
Katzman, S.7
King, B.8
Onodera, C.9
Siepel, A.10
-
83
-
-
77949718257
-
FastTree 2 – Approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
-
(2010)
PLoS One
, vol.5
, pp. e9490
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
84
-
-
1842684068
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
-
Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493–521.
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
-
85
-
-
33847633354
-
Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis
-
Ray DA, Pagan HJ, Thompson ML, Stevens RD. 2007. Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol 24: 632–639.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 632-639
-
-
Ray, D.A.1
Pagan, H.J.2
Thompson, M.L.3
Stevens, R.D.4
-
86
-
-
34247352040
-
Evolutionary and biomedical insights from the rhesus macaque genome
-
Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234.
-
(2007)
Science
, vol.316
, pp. 222-234
-
-
-
87
-
-
84874608346
-
Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations
-
Robberecht C, Voet T, Zamani Esteki M, Nowakowska BA, Vermeesch JR. 2013. Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. Genome Res 23: 411–418.
-
(2013)
Genome Res
, vol.23
, pp. 411-418
-
-
Robberecht, C.1
Voet, T.2
Zamani Esteki, M.3
Nowakowska, B.A.4
Vermeesch, J.R.5
-
88
-
-
84863230553
-
Insights into hominid evolution from the gorilla genome sequence
-
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169–175.
-
(2012)
Nature
, vol.483
, pp. 169-175
-
-
Scally, A.1
Dutheil, J.Y.2
Hillier, L.W.3
Jordan, G.E.4
Goodhead, I.5
Herrero, J.6
Hobolth, A.7
Lappalainen, T.8
Mailund, T.9
Marques-Bonet, T.10
-
89
-
-
67649834440
-
ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
-
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. 2009. ChIP-seq: using high-throughput sequencing to discover protein–DNA interactions. Methods 48: 240–248.
-
(2009)
Methods
, vol.48
, pp. 240-248
-
-
Schmidt, D.1
Wilson, M.D.2
Spyrou, C.3
Brown, G.D.4
Hadfield, J.5
Odom, D.T.6
-
90
-
-
84863393570
-
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
-
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. 2012. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335–348.
-
(2012)
Cell
, vol.148
, pp. 335-348
-
-
Schmidt, D.1
Schwalie, P.C.2
Wilson, M.D.3
Ballester, B.4
Gonçalves, A.5
Kutter, C.6
Brown, G.D.7
Marshall, A.8
Flicek, P.9
Odom, D.T.10
-
91
-
-
85019127944
-
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
-
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, et al. 2017. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res 27: 849–864.
-
(2017)
Genome Res
, vol.27
, pp. 849-864
-
-
Schneider, V.A.1
Graves-Lindsay, T.2
Howe, K.3
Bouk, N.4
Chen, H.C.5
Kitts, P.A.6
Murphy, T.D.7
Pruitt, K.D.8
Thibaud-Nissen, F.9
Albracht, D.10
-
92
-
-
84891793509
-
The effective population sizes of the anthropoid ancestors of the human-chimpanzee lineage provide insights on the historical biogeography of the great apes
-
Schrago CG. 2014. The effective population sizes of the anthropoid ancestors of the human-chimpanzee lineage provide insights on the historical biogeography of the great apes. Mol Biol Evol 31: 37–47.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 37-47
-
-
Schrago, C.G.1
-
93
-
-
84891352724
-
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
-
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. 2013. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol 14: R148.
-
(2013)
Genome Biol
, vol.14
, pp. R148
-
-
Schwalie, P.C.1
Ward, M.C.2
Cain, C.E.3
Faure, A.J.4
Gilad, Y.5
Odom, D.T.6
Flicek, P.7
-
94
-
-
84907267727
-
Comparative analysis of pseudogenes across three phyla
-
Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, et al. 2014. Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci 111: 13361–13366.
-
(2014)
Proc Natl Acad Sci
, vol.111
, pp. 13361-13366
-
-
Sisu, C.1
Pei, B.2
Leng, J.3
Frankish, A.4
Zhang, Y.5
Balasubramanian, S.6
Harte, R.7
Wang, D.8
Rutenberg-Schoenberg, M.9
Clark, W.10
-
95
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
Slater GS, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
97
-
-
33748674197
-
AUGUSTUS at EGASP: Using EST, protein and genomic alignments for improved gene prediction in the human genome
-
Stanke M, Tzvetkova A, Morgenstern B. 2006. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol 7(Suppl 1): S11.1–S11.8.
-
(2006)
Genome Biol
, vol.7
, pp. S111-S118
-
-
Stanke, M.1
Tzvetkova, A.2
Morgenstern, B.3
-
98
-
-
40049091292
-
Using native and syn-tenically mapped cDNA alignments to improve de novo gene finding
-
Stanke M, Diekhans M, Baertsch R, Haussler D. 2008. Using native and syn-tenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637–644.
-
(2008)
Bioinformatics
, vol.24
, pp. 637-644
-
-
Stanke, M.1
Diekhans, M.2
Baertsch, R.3
Haussler, D.4
-
99
-
-
84941127294
-
Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination
-
Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. 2015. Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination. Nucleic Acids Res 43: 2188–2198.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 2188-2198
-
-
Startek, M.1
Szafranski, P.2
Gambin, T.3
Campbell, I.M.4
Hixson, P.5
Shaw, C.A.6
Stankiewicz, P.7
Gambin, A.8
-
100
-
-
85014955691
-
Integration site selection by retroviruses and transposable elements in eukaryotes
-
Sultana T, Zamborlini A, Cristofari G, Lesage P. 2017. Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 18: 292–308.
-
(2017)
Nat Rev Genet
, vol.18
, pp. 292-308
-
-
Sultana, T.1
Zamborlini, A.2
Cristofari, G.3
Lesage, P.4
-
101
-
-
84938870216
-
Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
-
Uchimura A, Higuchi M, Minakuchi Y, Ohno M, Toyoda A, Fujiyama A, Miura I, Wakana S, Nishino J, Yagi T. 2015. Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice. Genome Res 25: 1125–1134.
-
(2015)
Genome Res
, vol.25
, pp. 1125-1134
-
-
Uchimura, A.1
Higuchi, M.2
Minakuchi, Y.3
Ohno, M.4
Toyoda, A.5
Fujiyama, A.6
Miura, I.7
Wakana, S.8
Nishino, J.9
Yagi, T.10
-
102
-
-
20444406113
-
Molecular phylogeny of the African pygmy mice, subgenus Nannomys (Rodentia, Murinae, Mus): Implications for chromosomal evolution
-
Veyrunes F, Britton-Davidian J, Robinson TJ, Calvet E, Denys C, Chevret P. 2005. Molecular phylogeny of the African pygmy mice, subgenus Nannomys (Rodentia, Murinae, Mus): implications for chromosomal evolution. Mol Phylogenet Evol 36: 358–369.
-
(2005)
Mol Phylogenet Evol
, vol.36
, pp. 358-369
-
-
Veyrunes, F.1
Britton-Davidian, J.2
Robinson, T.J.3
Calvet, E.4
Denys, C.5
Chevret, P.6
-
103
-
-
33847682098
-
Phylogenomics of the genus Mus (Rodentia; Muridae): Extensive genome repatterning is not restricted to the house mouse
-
Veyrunes F, Dobigny G, Yang F, O’Brien PC, Catalan J, Robinson TJ, Britton-Davidian J. 2006. Phylogenomics of the genus Mus (Rodentia; Muridae): Extensive genome repatterning is not restricted to the house mouse. Proc Biol Sci 273: 2925–2934.
-
(2006)
Proc Biol Sci
, vol.273
, pp. 2925-2934
-
-
Veyrunes, F.1
Dobigny, G.2
Yang, F.3
O’Brien, P.C.4
Catalan, J.5
Robinson, T.J.6
Britton-Davidian, J.7
-
104
-
-
84923172778
-
Camelid genomes reveal evolution and adaptation to desert environments
-
Wu H, Guang X, Al-Fageeh MB, Cao J, Pan S, Zhou H, Zhang L, Abutarboush MH, Xing Y, Xie Z, et al. 2014. Camelid genomes reveal evolution and adaptation to desert environments. Nat Commun 5: 5188.
-
(2014)
Nat Commun
, vol.5
, pp. 5188
-
-
Wu, H.1
Guang, X.2
Al-Fageeh, M.B.3
Cao, J.4
Pan, S.5
Zhou, H.6
Zhang, L.7
Abutarboush, M.H.8
Xing, Y.9
Xie, Z.10
-
105
-
-
33745614319
-
PseudoPipe: An automated pseudogene identification pipeline
-
Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. 2006. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22: 1437–1439.
-
(2006)
Bioinformatics
, vol.22
, pp. 1437-1439
-
-
Zhang, Z.1
Carriero, N.2
Zheng, D.3
Karro, J.4
Harrison, P.M.5
Gerstein, M.6
-
106
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
107
-
-
6344222248
-
Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation
-
Zhao S, Shetty J, Hou L, Delcher A, Zhu B, Osoegawa K, de Jong P, Nierman WC, Strausberg RL, Fraser CM. 2004. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res 14: 1851–1860.
-
(2004)
Genome Res
, vol.14
, pp. 1851-1860
-
-
Zhao, S.1
Shetty, J.2
Hou, L.3
Delcher, A.4
Zhu, B.5
Osoegawa, K.6
De Jong, P.7
Nierman, W.C.8
Strausberg, R.L.9
Fraser, C.M.10
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