-
1
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating go graph structure
-
Alexa A, Rahnenführer J, Lengauer T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenführer, J.2
Lengauer, T.3
-
2
-
-
84892554083
-
Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders
-
Babarinde IA, Saitou N. (2013). Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol. 5: 2330-2343
-
(2013)
Genome Biol Evol
, vol.5
, pp. 2330-2343
-
-
Babarinde, I.A.1
Saitou, N.2
-
3
-
-
85016147805
-
Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics
-
Babarinde IA, Saitou N. (2016). Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Mol Biol Evol. 33: 1807-1817
-
(2016)
Mol Biol Evol
, vol.33
, pp. 1807-1817
-
-
Babarinde, I.A.1
Saitou, N.2
-
4
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. (2004). Ultraconserved elements in the human genome. Science 304: 1321-1325
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
Mattick, J.S.6
Haussler, D.7
-
5
-
-
39049157173
-
Fast-evolving noncoding sequences in the human genome
-
Bird C, Stranger B, Liu M, Thomas D, Ingle C, Beazley C, Miller W, Hurles M, Dermitzakis E. (2007). Fast-evolving noncoding sequences in the human genome. Genome Biol 8: R118
-
(2007)
Genome Biol
, vol.8
, pp. R118
-
-
Bird, C.1
Stranger, B.2
Liu, M.3
Thomas, D.4
Ingle, C.5
Beazley, C.6
Miller, W.7
Hurles, M.8
Dermitzakis, E.9
-
6
-
-
10344265486
-
Conserved and acquired features of neurogenin1 regulation
-
Blader P, Lam CS, Rastegar S, Scardigli R, Nicod J-C, Simplicio N, Plessy C, Fischer N, Schuurmans C, Guillemot F, et al. (2004). Conserved and acquired features of neurogenin1 regulation. Development 131: 5627-5637
-
(2004)
Development
, vol.131
, pp. 5627-5637
-
-
Blader, P.1
Lam, C.S.2
Rastegar, S.3
Scardigli, R.4
Nicod, J.-C.5
Simplicio, N.6
Plessy, C.7
Fischer, N.8
Schuurmans, C.9
Guillemot, F.10
-
7
-
-
3042740671
-
Comparative genomics at the vertebrate extremes
-
Boffelli D, Nobrega MA, Rubin EM. (2004). Comparative genomics at the vertebrate extremes. Nat Rev Genet. 5: 456-465
-
(2004)
Nat Rev Genet
, vol.5
, pp. 456-465
-
-
Boffelli, D.1
Nobrega, M.A.2
Rubin, E.M.3
-
8
-
-
84926420296
-
Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex
-
Boyd JL, Skove SL, Rouanet JP, Pilaz L-J, Bepler T, Gordan R, Wray GA, Silver DL. (2015). Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol. 25: 772-779
-
(2015)
Curr Biol
, vol.25
, pp. 772-779
-
-
Boyd, J.L.1
Skove, S.L.2
Rouanet, J.P.3
Pilaz, L.-J.4
Bepler, T.5
Gordan, R.6
Wray, G.A.7
Silver, D.L.8
-
9
-
-
84887496761
-
Many human accelerated regions are developmental enhancers
-
Capra JA, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS. (2013). Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci. 368: 20130025
-
(2013)
Philos Trans R Soc Lond B Biol Sci
, vol.368
, pp. 20130025
-
-
Capra, J.A.1
Erwin, G.D.2
McKinsey, G.3
Rubenstein, J.L.R.4
Pollard, K.S.5
-
10
-
-
46149104377
-
Evo-devo and an expanding evolutionary syn thesis a genetic theory of morphological evolution
-
Carroll SB. (2008). Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25-36
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
11
-
-
84866453386
-
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
-
Dimitrieva S, Bucher P. (2012). Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics 28: i395-i401
-
(2012)
Bioinformatics
, vol.28
, pp. i395-i401
-
-
Dimitrieva, S.1
Bucher, P.2
-
12
-
-
84966295083
-
Origin and evolution of developmental enhancers in themammalian neocortex
-
Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. (2016). Origin and evolution of developmental enhancers in themammalian neocortex. Proc Natl Acad Sci U S A. 113: E2617-E2626
-
(2016)
Proc Natl Acad Sci U S A.
, vol.113
, pp. E2617-E2626
-
-
Emera, D.1
Yin, J.2
Reilly, S.K.3
Gockley, J.4
Noonan, J.P.5
-
13
-
-
33645833857
-
Conservation of RET regulatory function from human to zebrafish without sequence similarity
-
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. (2006). Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312: 276-279
-
(2006)
Science
, vol.312
, pp. 276-279
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
McCallion, A.S.5
-
15
-
-
79951528195
-
Minor change, major difference: Divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events
-
Goode DK, Callaway HA, Cerda GA, Lewis KE, Elgar G. (2011). Minor change, major difference: Divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. Development 138: 879-884
-
(2011)
Development
, vol.138
, pp. 879-884
-
-
Goode, D.K.1
Callaway, H.A.2
Cerda, G.A.3
Lewis, K.E.4
Elgar, G.5
-
16
-
-
46249134068
-
Sepsid evenskipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
-
Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. (2008). Sepsid evenskipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 4: e1000106
-
(2008)
Plos Genet
, vol.4
, pp. e1000106
-
-
Hare, E.E.1
Peterson, B.K.2
Iyer, V.N.3
Meier, R.4
Eisen, M.B.5
-
18
-
-
77952359315
-
Contrasts between adaptive coding and noncoding changes during human evolution
-
Haygood R, Babbitt CC, Fedrigo O, Wray GA. (2010). Contrasts between adaptive coding and noncoding changes during human evolution. Proc Natl Acad Sci U S A. 107: 7853-7857
-
(2010)
Proc Natl Acad Sci U S A.
, vol.107
, pp. 7853-7857
-
-
Haygood, R.1
Babbitt, C.C.2
Fedrigo, O.3
Wray, G.A.4
-
19
-
-
34548346860
-
Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution
-
Haygood R, Fedrigo O, Hanson B, Yokoyama K-D, Wray GA. (2007). Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution. Nat Genet. 39: 1140-1144
-
(2007)
Nat Genet
, vol.39
, pp. 1140-1144
-
-
Haygood, R.1
Fedrigo, O.2
Hanson, B.3
Yokoyama, K.-D.4
Wray, G.A.5
-
20
-
-
84871254993
-
Hundreds of conserved noncoding genomic regions are independently lost in mammals
-
Hiller M, Schaar BT, Bejerano G. (2012). Hundreds of conserved noncoding genomic regions are independently lost in mammals. Nucleic Acids Res. 40: 11463-11476
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11463-11476
-
-
Hiller, M.1
Schaar, B.T.2
Bejerano, G.3
-
21
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
Hunter JD. (2007). Matplotlib: a 2D graphics environment. Comput Sci Eng. 9: 90-95
-
(2007)
Comput Sci Eng
, vol.9
, pp. 90-95
-
-
Hunter, J.D.1
-
22
-
-
84954262110
-
Evolving new skeletal traits by cisregulatory changes in bone morphogenetic proteins
-
Indjeian VB, Kingman GA, Jones FC, Guenther CA, Grimwood J, Schmutz J, Myers RM, Kingsley DM. (2016). Evolving new skeletal traits by cisregulatory changes in bone morphogenetic proteins. Cell 164: 45-56
-
(2016)
Cell
, vol.164
, pp. 45-56
-
-
Indjeian, V.B.1
Kingman, G.A.2
Jones, F.C.3
Guenther, C.A.4
Grimwood, J.5
Schmutz, J.6
Myers, R.M.7
Kingsley, D.M.8
-
23
-
-
65649112466
-
Functional and evolutionary insights into human brain development through global transcriptome analysis
-
Johnson MB, Kawasawa YI, Mason CE, Krsnikž, Coppola G, Bogdanovič D, Geschwind DH, Mane SM, State MW, Šestan N. (2009). Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62: 494-509
-
(2009)
Neuron
, vol.62
, pp. 494-509
-
-
Johnson, M.B.1
Kawasawa, Y.I.2
Mason, C.E.3
Krsnikž Coppola, G.4
Bogdanovič, D.5
Geschwind, D.H.6
Mane, S.M.7
State, M.W.8
Šestan, N.9
-
24
-
-
78649716038
-
Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among drosophila species
-
Kalay G, Wittkopp PJ. (2010). Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet. 6: e1001222
-
(2010)
Plos Genet
, vol.6
, pp. e1001222
-
-
Kalay, G.1
Wittkopp, P.J.2
-
25
-
-
84887497668
-
A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice
-
Kamm GB, López-Leal R, Lorenzo JR, Franchini LF. (2013a). A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice. Philos Trans R Soc Lond B Biol Sci. 368: 20130019
-
(2013)
Philos Trans R Soc Lond B Biol Sci
, vol.368
, pp. 20130019
-
-
Kamm, G.B.1
López-Leal, R.2
Lorenzo, J.R.3
Franchini, L.F.4
-
26
-
-
84876520556
-
The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome
-
Kamm GB, Pisciottano F, Kliger R, Franchini LF. (2013b). The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol Biol Evol. 30: 1088-1102
-
(2013)
Mol Biol Evol
, vol.30
, pp. 1088-1102
-
-
Kamm, G.B.1
Pisciottano, F.2
Kliger, R.3
Franchini, L.F.4
-
27
-
-
80054993342
-
Spatio-temporal transcriptome of the human brain
-
Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AMM, Pletikos M, Meyer KA, Sedmak G, et al. (2011). Spatio-temporal transcriptome of the human brain. Nature 478: 483-489
-
(2011)
Nature
, vol.478
, pp. 483-489
-
-
Kang, H.J.1
Kawasawa, Y.I.2
Cheng, F.3
Zhu, Y.4
Xu, X.5
Li, M.6
Sousa, A.M.M.7
Pletikos, M.8
Meyer, K.A.9
Sedmak, G.10
-
28
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, et al. (2007). Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17: 545-555
-
(2007)
Genome Res
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
Komisarczuk, A.Z.4
Engström, P.G.5
Fredman, D.6
Akalin, A.7
Caccamo, M.8
Sealy, I.9
Howe, K.10
-
29
-
-
34848901059
-
Adaptive evolution of conserved noncoding elements in mammals
-
Kim SY, Pritchard JK. (2007). Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet. 3: e147
-
(2007)
Plos Genet
, vol.3
, pp. e147
-
-
Kim, S.Y.1
Pritchard, J.K.2
-
30
-
-
84867306721
-
Snakemake-A scalable bioinformatics workflow engine
-
Köster J, Rahmann S. (2012). Snakemake-A scalable bioinformatics workflow engine. Bioinformatics 28: 2520-2522
-
(2012)
Bioinformatics
, vol.28
, pp. 2520-2522
-
-
Köster, J.1
Rahmann, S.2
-
31
-
-
79952801550
-
Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution
-
Lambert N, Lambot M-A, Bilheu A, Albert V, Englert Y, Libert F, Noel J-C, Sotiriou C, Holloway AK, Pollard KS, et al. (2011). Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PloS One 6: e17753
-
(2011)
Plos One
, vol.6
, pp. e17753
-
-
Lambert, N.1
Lambot, M.-A.2
Bilheu, A.3
Albert, V.4
Englert, Y.5
Libert, F.6
Noel, J.-C.7
Sotiriou, C.8
Holloway, A.K.9
Pollard, K.S.10
-
32
-
-
84896735766
-
Voom: Precisionweightsunlocklinear model analysis tools for RNA-seq read counts
-
Law C, Chen Y, Shi W, Smyth G. (2014). voom: precisionweightsunlocklinear model analysis tools for RNA-seq read counts. Genome Biol. 15: R29
-
(2014)
Genome Biol
, vol.15
, pp. R29
-
-
Law, C.1
Chen, Y.2
Shi, W.3
Smyth, G.4
-
33
-
-
80054973803
-
A highresolution 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 highresolution 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
-
34
-
-
84874963219
-
Adaptive evolution of multiple traits through multiple mutations at a single gene
-
Linnen CR, Poh Y-P, Peterson BK, Barrett RDH, Larson JG, Jensen JD, Hoekstra HE. (2013). Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312-1316
-
(2013)
Science
, vol.339
, pp. 1312-1316
-
-
Linnen, C.R.1
Poh, Y.-P.2
Peterson, B.K.3
Barrett, R.D.H.4
Larson, J.G.5
Jensen, J.D.6
Hoekstra, H.E.7
-
35
-
-
84876569149
-
Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain
-
Matsunami M, Saitou N. (2013). Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. Genome Biol. Evol. 5: 140-150
-
(2013)
Genome Biol. Evol
, vol.5
, pp. 140-150
-
-
Matsunami, M.1
Saitou, N.2
-
36
-
-
62549109118
-
Testing significance relative to a foldchange threshold is a treat
-
McCarthy DJ, Smyth GK. (2009). Testing significance relative to a foldchange threshold is a TREAT. Bioinformatics 25: 765-771
-
(2009)
Bioinformatics
, vol.25
, pp. 765-771
-
-
McCarthy, D.J.1
Smyth, G.K.2
-
37
-
-
74249085481
-
Early evolution of conserved regulatory sequences associated with development in vertebrates
-
McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. (2009). Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet. 5: e1000762
-
(2009)
Plos Genet
, vol.5
, pp. e1000762
-
-
McEwen, G.K.1
Goode, D.K.2
Parker, H.J.3
Woolfe, A.4
Callaway, H.5
Elgar, G.6
-
38
-
-
77952214662
-
Great improves functional interpretation of cis-regulatory regions
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. (2010). GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 28: 495-501
-
(2010)
Nat Biotechnol
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
-
39
-
-
84900303453
-
Transcriptional landscape of the prenatal human brain
-
Miller JA, Ding S-L, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, et al. (2014). Transcriptional landscape of the prenatal human brain. Nature 508: 199-206
-
(2014)
Nature
, vol.508
, pp. 199-206
-
-
Miller, J.A.1
Ding, S.-L.2
Sunkin, S.M.3
Smith, K.A.4
Ng, L.5
Szafer, A.6
Ebbert, A.7
Riley, Z.L.8
Royall, J.J.9
Aiona, K.10
-
40
-
-
84875082455
-
Conserved non-coding elements and cis regulation: Actions speak louder than words
-
Nelson AC, Wardle FC. (2013). Conserved non-coding elements and cis regulation: Actions speak louder than words. Development 140: 1385-1395
-
(2013)
Development
, vol.140
, pp. 1385-1395
-
-
Nelson, A.C.1
Wardle, F.C.2
-
42
-
-
84894598129
-
Rapid and pervasive changes in genome-wide enhancer usage during mammalian development
-
Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, et al. (2013). Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155: 1521-1531
-
(2013)
Cell
, vol.155
, pp. 1521-1531
-
-
Nord, A.S.1
Blow, M.J.2
Attanasio, C.3
Akiyama, J.A.4
Holt, A.5
Hosseini, R.6
Phouanenavong, S.7
Plajzer-Frick, I.8
Shoukry, M.9
Afzal, V.10
-
43
-
-
47649125626
-
Widespread ultraconservation divergence in primates
-
Ovcharenko I. (2008). Widespread ultraconservation divergence in primates. Mol Biol Evol. 25: 1668-1676
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1668-1676
-
-
Ovcharenko, I.1
-
44
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, et al. (2006). In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
Minovitsky, S.7
Dubchak, I.8
Holt, A.9
Lewis, K.D.10
-
45
-
-
15244341767
-
Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes
-
Plessy C, Dickmeis T, Chalmel F, Strähle U. (2005). Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet. 21: 207-210
-
(2005)
Trends Genet
, vol.21
, pp. 207-210
-
-
Plessy, C.1
Dickmeis, T.2
Chalmel, F.3
Strähle, U.4
-
46
-
-
33750428182
-
Forces shaping the fastest evolving regions in the human genome
-
Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, et al. (2006a). Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2: e168
-
(2006)
Plos Genet
, vol.2
, pp. e168
-
-
Pollard, K.S.1
Salama, S.R.2
King, B.3
Kern, A.D.4
Dreszer, T.5
Katzman, S.6
Siepel, A.7
Pedersen, J.S.8
Bejerano, G.9
Baertsch, R.10
-
47
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, et al. (2006b). 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
-
48
-
-
18844376318
-
In vivo characterization of a vertebrate ultraconserved enhancer
-
Poulin F, Nobrega MA, Plajzer-Frick I, Holt A, Afzal V, Rubin EM, Pennacchio LA. (2005). In vivo characterization of a vertebrate ultraconserved enhancer. Genomics 85: 774-781
-
(2005)
Genomics
, vol.85
, pp. 774-781
-
-
Poulin, F.1
Nobrega, M.A.2
Plajzer-Frick, I.3
Holt, A.4
Afzal, V.5
Rubin, E.M.6
Pennacchio, L.A.7
-
49
-
-
33750737061
-
Acceleratedevolution of conservednoncoding sequences inhumans
-
Prabhakar S, Noonan JP, Pääbo S, Rubin EM. (2006a). Acceleratedevolution of conservednoncoding sequences inhumans. Science 314: 786-786
-
(2006)
Science
, vol.314
, pp. 786
-
-
Prabhakar, S.1
Noonan, J.P.2
Pääbo, S.3
Rubin, E.M.4
-
50
-
-
33745628791
-
Close sequence comparisons are sufficient to identify human cis-regulatory elements
-
Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA. (2006b). Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res 16: 855-863
-
(2006)
Genome Res
, vol.16
, pp. 855-863
-
-
Prabhakar, S.1
Poulin, F.2
Shoukry, M.3
Afzal, V.4
Rubin, E.M.5
Couronne, O.6
Pennacchio, L.A.7
-
51
-
-
51149097366
-
Humanspecific gain of function in a developmental enhancer
-
Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, et al. (2008). Humanspecific gain of function in a developmental enhancer. Science 321: 1346-1350
-
(2008)
Science
, vol.321
, pp. 1346-1350
-
-
Prabhakar, S.1
Visel, A.2
Akiyama, J.A.3
Shoukry, M.4
Lewis, K.D.5
Holt, A.6
Plajzer-Frick, I.7
Morrison, H.8
Fitz Patrick, D.R.9
Afzal, V.10
-
52
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
53
-
-
84975753826
-
-
R Core Team. R Foundation for Statistical Computing, Vienna, Austria. Available from last accessed November 6, 2016
-
R Core Team. (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available from: https://www.R-project.org/, last accessed November 6, 2016
-
(2016)
R A Language and Environment for Statistical Computing
-
-
-
54
-
-
84924561748
-
Evolutionary changes in promoter and enhancer activity during human corticogenesis
-
Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. (2015). Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 347: 1155-1159
-
(2015)
Science
, vol.347
, pp. 1155-1159
-
-
Reilly, S.K.1
Yin, J.2
Ayoub, A.E.3
Emera, D.4
Leng, J.5
Cotney, J.6
Sarro, R.7
Rakic, P.8
Noonan, J.P.9
-
55
-
-
79952323416
-
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences
-
Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, et al. (2011). Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 6: e17634
-
(2011)
Plos One
, vol.6
, pp. e17634
-
-
Robyr, D.1
Friedli, M.2
Gehrig, C.3
Arcangeli, M.4
Marin, M.5
Guipponi, M.6
Farinelli, L.7
Barde, I.8
Verp, S.9
Trono, D.10
-
57
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
Sandelin A, Bailey P, Bruce S, Engström P, Klos J, Wasserman W, Ericson J, Lenhard B. (2004). Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99
-
(2004)
BMC Genomics
, vol.5
, pp. 99
-
-
Sandelin, A.1
Bailey, P.2
Bruce, S.3
Engström, P.4
Klos, J.5
Wasserman, W.6
Ericson, J.7
Lenhard, B.8
-
58
-
-
84982180013
-
Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain
-
Schrider DR, Kern AD. (2015). Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain. Genome Biol Evol. 7: 3511-3528
-
(2015)
Genome Biol Evol
, vol.7
, pp. 3511-3528
-
-
Schrider, D.R.1
Kern, A.D.2
-
59
-
-
1942455815
-
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks
-
Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, Jónsson B, Schluter D, Kingsley DM. (2004). Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717-723
-
(2004)
Nature
, vol.428
, pp. 717-723
-
-
Shapiro, M.D.1
Marks, M.E.2
Peichel, C.L.3
Blackman, B.K.4
Nereng, K.S.5
Jónsson, B.6
Schluter, D.7
Kingsley, D.M.8
-
60
-
-
84921714149
-
From trans to cis: Transcriptional regulatory networks in neocortical development
-
Shibata M, Gulden FO, Sestan N. (2015). From trans to cis: Transcriptional regulatory networks in neocortical development. Trends Genet. 31: 77-87
-
(2015)
Trends Genet
, vol.31
, pp. 77-87
-
-
Shibata, M.1
Gulden, F.O.2
Sestan, N.3
-
61
-
-
84861932338
-
Cis-regulatory control of corticospinal system development and evolution
-
Shim S, Kwan KY, Li M, Lefebvre V, Sestan N. (2012). Cis-regulatory control of corticospinal system development and evolution. Nature 486: 74-79
-
(2012)
Nature
, vol.486
, pp. 74-79
-
-
Shim, S.1
Kwan, K.Y.2
Li, M.3
Lefebvre, V.4
Sestan, N.5
-
62
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-1050
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
63
-
-
84996504468
-
The cellular and molecular landscapes of the developing human central nervous system
-
Silbereis JC, Pochareddy S, Zhu Y, Li M, Sestan N. (2016). The cellular and molecular landscapes of the developing human central nervous system. Neuron 89: 248-268
-
(2016)
Neuron
, vol.89
, pp. 248-268
-
-
Silbereis, J.C.1
Pochareddy, S.2
Zhu, Y.3
Li, M.4
Sestan, N.5
-
64
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth GK. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3: 1-25
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, pp. 1-25
-
-
Smyth, G.K.1
-
65
-
-
84954389263
-
-
Stan Development Team. Available from last accessed March 18, 2015
-
Stan Development Team. (2015). Stan: A C++ library for probability and sampling. Available from: http://mc-stan.org/, last accessed March 18, 2015
-
(2015)
Stan: A C++ Library for Probability and Sampling
-
-
-
66
-
-
80155192425
-
Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
-
Sumiyama K, Saitou N. (2011). Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1. Mol Biol Evol. 28: 3005-3007
-
(2011)
Mol Biol Evol
, vol.28
, pp. 3005-3007
-
-
Sumiyama, K.1
Saitou, N.2
-
67
-
-
61449212191
-
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
-
Taher L, Ovcharenko I. (2009). Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics 25: 578-584
-
(2009)
Bioinformatics
, vol.25
, pp. 578-584
-
-
Taher, L.1
Ovcharenko, I.2
-
68
-
-
84929001104
-
The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
The GTEx Consortium
-
The GTEx Consortium. (2015). The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348: 648-660
-
(2015)
Science
, vol.348
, pp. 648-660
-
-
-
69
-
-
84959157387
-
Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
-
Vermunt MW, Tan SC, Castelijns B, Geeven G, Reinink P, De Bruijn E, Kondova I, Persengiev S, Bontrop R, et al. (2016). Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 19: 494-503
-
(2016)
Nat Neurosci
, vol.19
, pp. 494-503
-
-
Vermunt, M.W.1
Tan, S.C.2
Castelijns, B.3
Geeven, G.4
Reinink, P.5
De Bruijn, E.6
Kondova, I.7
Persengiev, S.8
Bontrop, R.9
-
70
-
-
84899453734
-
Evolution of transcription factor binding in metazoans-Mechanisms and functional implications
-
Villar D, Flicek P, Odom DT. (2014). Evolution of transcription factor binding in metazoans-Mechanisms and functional implications. Nat Rev Genet. 15: 221-233
-
(2014)
Nat Rev Genet
, vol.15
, pp. 221-233
-
-
Villar, D.1
Flicek, P.2
Odom, D.T.3
-
71
-
-
38649123306
-
Ultraconservation identifies a small subset of extremely constrained developmental enhancers
-
Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA. (2008). Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet. 40: 158-160
-
(2008)
Nat Genet
, vol.40
, pp. 158-160
-
-
Visel, A.1
Prabhakar, S.2
Akiyama, J.A.3
Shoukry, M.4
Lewis, K.D.5
Holt, A.6
Plajzer-Frick, I.7
Afzal, V.8
Rubin, E.M.9
Pennacchio, L.A.10
-
72
-
-
84884656824
-
The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option
-
Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. (2013). The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genet. 9: e1003728
-
(2013)
Plos Genet
, vol.9
, pp. e1003728
-
-
Wenger, A.M.1
Clarke, S.L.2
Notwell, J.H.3
Chung, T.4
Tuteja, G.5
Guturu, H.6
Schaar, B.T.7
Bejerano, G.8
-
73
-
-
78650862532
-
Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models
-
Wood SN. (2011). Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J R Stat Soc B. 73: 3-36
-
(2011)
J R Stat Soc B.
, vol.73
, pp. 3-36
-
-
Wood, S.N.1
-
74
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, et al. (2004). Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3: e7
-
(2004)
Plos Biol
, vol.3
, pp. e7
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
Snell, P.4
McEwen, G.K.5
Vavouri, T.6
Smith, S.F.7
North, P.8
Callaway, H.9
Kelly, K.10
-
75
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA. (2007). The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 8: 206-216
-
(2007)
Nat Rev Genet
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
76
-
-
0342635450
-
A highly conserved enhancer in the Dlx5/Dlx6 intergenic region is the site of crossregulatory interactions between Dlx genes in the embryonic forebrain
-
Zerucha T, Stühmer T, Hatch G, Park BK, Long Q, Yu G, Gambarotta A, Schultz JR, Rubenstein JLR, Ekker M. (2000). A highly conserved enhancer in the Dlx5/Dlx6 intergenic region is the site of crossregulatory interactions between Dlx genes in the embryonic forebrain. J Neurosci. 20: 709-721
-
(2000)
J Neurosci
, vol.20
, pp. 709-721
-
-
Zerucha, T.1
Stühmer, T.2
Hatch, G.3
Park, B.K.4
Long, Q.5
Yu, G.6
Gambarotta, A.7
Schultz, J.R.8
Rubenstein, J.L.R.9
Ekker, M.10
|