-
1
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491: 56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
2
-
-
84887617108
-
Teneurin-3 specifies morphological and functional connectivity of retinal ganglion cells in the vertebrate visual system
-
Antinucci P, Nikolaou N, Meyer MP, Hindges R. 2013. Teneurin-3 specifies morphological and functional connectivity of retinal ganglion cells in the vertebrate visual system. Cell Rep 5: 582-592.
-
(2013)
Cell Rep
, vol.5
, pp. 582-592
-
-
Antinucci, P.1
Nikolaou, N.2
Meyer, M.P.3
Hindges, R.4
-
3
-
-
33646244720
-
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome
-
Arbiza L, Dopazo J, Dopazo H. 2006. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2: E38.
-
(2006)
PLoS Comput Biol
, vol.2
, pp. e38
-
-
Arbiza, L.1
Dopazo, J.2
Dopazo, H.3
-
4
-
-
34547632934
-
Widely distributed noncoding purifying selection in the human genome
-
Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. 2007. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci 104: 12410-12415.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 12410-12415
-
-
Asthana, S.1
Noble, W.S.2
Kryukov, G.3
Grant, C.E.4
Sunyaev, S.5
Stamatoyannopoulos, J.A.6
-
5
-
-
84895541597
-
Function of YY1 in long-distance DNA interactions
-
Atchison ML. 2014. Function of YY1 in long-distance DNA interactions. Front Immunol 5: 45.
-
(2014)
Front Immunol
, vol.5
, pp. 45
-
-
Atchison, M.L.1
-
6
-
-
84901838628
-
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
-
Ay F, Bailey TL, Noble WS. 2014. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res 24: 999-1011.
-
(2014)
Genome Res
, vol.24
, pp. 999-1011
-
-
Ay, F.1
Bailey, T.L.2
Noble, W.S.3
-
7
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, et al. 2010. The NIH roadmap epigenomics mapping consortium. Nat Biotechnol 28: 1045-1048.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
Stamatoyannopoulos, J.A.2
Costello, J.F.3
Ren, B.4
Milosavljevic, A.5
Meissner, A.6
Kellis, M.7
Marra, M.A.8
Beaudet, A.L.9
Ecker, J.R.10
-
8
-
-
0014690698
-
Gene regulation for higher cells: A theory
-
Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: A theory. Science 165: 349-357.
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
9
-
-
39049088628
-
A genome-wide screen for noncoding elements important in primate evolution
-
Bush EC, Lahn BT. 2008. A genome-wide screen for noncoding elements important in primate evolution. BMC Evol Biol 8: 17.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 17
-
-
Bush, E.C.1
Lahn, B.T.2
-
10
-
-
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
-
11
-
-
0028222304
-
The effect of background selection against deleterious mutations on weakly selected, linked variants
-
Charlesworth B. 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet Res 63: 213-227.
-
(1994)
Genet Res
, vol.63
, pp. 213-227
-
-
Charlesworth, B.1
-
12
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
Chimpanzee Sequencing and Analysis Consortium
-
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
-
-
-
13
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Chinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LW, Mardis ER, McPherson JD, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Chinwalla, A.T.1
Cook, L.L.2
Delehaunty, K.D.3
Fewell, G.A.4
Fulton, L.A.5
Fulton, R.S.6
Graves, T.A.7
Hillier, L.W.8
Mardis, E.R.9
McPherson, J.D.10
-
14
-
-
0346243805
-
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios
-
Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
-
(2003)
Science
, vol.302
, pp. 1960-1963
-
-
Clark, A.G.1
Glanowski, S.2
Nielsen, R.3
Thomas, P.D.4
Kejariwal, A.5
Todd, M.A.6
Tanenbaum, D.M.7
Civello, D.8
Lu, F.9
Murphy, B.10
-
15
-
-
84879911829
-
The evolution of lineage-specific regulatory activities in the human embryonic limb
-
Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. 2013. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154: 185-196.
-
(2013)
Cell
, vol.154
, pp. 185-196
-
-
Cotney, J.1
Leng, J.2
Yin, J.3
Reilly, S.K.4
DeMare, L.E.5
Emera, D.6
Ayoub, A.E.7
Rakic, P.8
Noonan, J.P.9
-
16
-
-
84860860685
-
Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication
-
Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, et al. 2012.Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149: 912-922.
-
(2012)
Cell
, vol.149
, pp. 912-922
-
-
Dennis, M.Y.1
Nuttle, X.2
Sudmant, P.H.3
Antonacci, F.4
Graves, T.A.5
Nefedov, M.6
Rosenfeld, J.A.7
Sajjadian, S.8
Malig, M.9
Kotkiewicz, H.10
-
17
-
-
0035986888
-
Evolution of transcription factor binding sites inmammalian gene regulatory regions: Conservation and turnover
-
Dermitzakis ET, Clark AG. 2002. Evolution of transcription factor binding sites inmammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19: 1114-1121.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1114-1121
-
-
Dermitzakis, E.T.1
Clark, A.G.2
-
18
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376-380.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
Hu, M.7
Liu, J.S.8
Ren, B.9
-
19
-
-
84875847924
-
Is junk DNA bunk? A critique of ENCODE
-
Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci 110: 5294-5300.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 5294-5300
-
-
Doolittle, W.F.1
-
20
-
-
20844435623
-
High-throughput localization of functional elements by quantitative chromatin profiling
-
Dorschner MO, Hawrylycz M, Humbert R, Wallace JC, Shafer A, Kawamoto J, Mack J, Hall R, Goldy J, Sabo PJ, et al. 2004. High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods 1: 219-225.
-
(2004)
Nat Methods
, vol.1
, pp. 219-225
-
-
Dorschner, M.O.1
Hawrylycz, M.2
Humbert, R.3
Wallace, J.C.4
Shafer, A.5
Kawamoto, J.6
Mack, J.7
Hall, R.8
Goldy, J.9
Sabo, P.J.10
-
21
-
-
59849104053
-
Comment on "Human-specific gain of function in a developmental enhancer"
-
Duret L, Galtier N. 2009. Comment on "Human-specific gain of function in a developmental enhancer". Science 323: 714.
-
(2009)
Science
, vol.323
, pp. 714
-
-
Duret, L.1
Galtier, N.2
-
22
-
-
84868550433
-
The C-value paradox, junk DNA and ENCODE
-
Eddy SR. 2012. The C-value paradox, junk DNA and ENCODE. Curr Biol 22: R898-R899.
-
(2012)
Curr Biol
, vol.22
, pp. R898-R899
-
-
Eddy, S.R.1
-
23
-
-
0037158715
-
Molecular evolution of FOXP2, a gene involved in speech and language
-
Enard W, Przeworski M, Fisher SE, Lai CSL, Wiebe V, Kitano T, Monaco AP, Pääbo S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-872.
-
(2002)
Nature
, vol.418
, pp. 869-872
-
-
Enard, W.1
Przeworski, M.2
Fisher, S.E.3
Lai, C.S.L.4
Wiebe, V.5
Kitano, T.6
Monaco, A.P.7
Pääbo, S.8
-
24
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
25
-
-
84891768365
-
Ensembl 2014
-
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. 2014. Ensembl 2014. Nucleic Acids Res 42: D749-D755.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D749-D755
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
26
-
-
0018199224
-
DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
-
Galas D, Schmitz A. 1978. DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5: 3157-3170.
-
(1978)
Nucleic Acids Res
, vol.5
, pp. 3157-3170
-
-
Galas, D.1
Schmitz, A.2
-
27
-
-
34248641119
-
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution
-
Galtier N, Duret L. 2007. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet 23: 273-277.
-
(2007)
Trends Genet
, vol.23
, pp. 273-277
-
-
Galtier, N.1
Duret, L.2
-
28
-
-
0041321057
-
Development of the pharyngeal arches
-
Graham A. 2003. Development of the pharyngeal arches. Am J Med Genet A 119A: 251-256.
-
(2003)
Am J Med Genet A
, vol.119 A
, pp. 251-256
-
-
Graham, A.1
-
29
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018.
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
30
-
-
84875275808
-
On the immortality of television sets: "Function" in the human genome according to the evolution-free gospel of ENCODE
-
Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5: 578-590.
-
(2013)
Genome Biol Evol
, vol.5
, pp. 578-590
-
-
Graur, D.1
Zheng, Y.2
Price, N.3
Azevedo, R.B.R.4
Zufall, R.A.5
Elhaik, E.6
-
31
-
-
77952136530
-
A draft sequence of the Neandertal genome
-
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, ZhaiW, Fritz MH-Y, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.
-
(2010)
Science
, vol.328
, pp. 710-722
-
-
Green, R.E.1
Krause, J.2
Briggs, A.W.3
Maricic, T.4
Stenzel, U.5
Kircher, M.6
Patterson, N.7
Li, H.8
Zhai, W.9
Fritz, M.H.-Y.10
-
32
-
-
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
-
33
-
-
79551634894
-
PHAST and RPHAST: Phylogenetic analysis with space/time models
-
Hubisz MJ, Pollard KS, Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform 12: 41-51.
-
(2011)
Brief Bioinform
, vol.12
, pp. 41-51
-
-
Hubisz, M.J.1
Pollard, K.S.2
Siepel, A.3
-
34
-
-
84866997011
-
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
-
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. 2012. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9: 999-1003.
-
(2012)
Nat Methods
, vol.9
, pp. 999-1003
-
-
Imakaev, M.1
Fudenberg, G.2
McCord, R.P.3
Naumova, N.4
Goloborodko, A.5
Lajoie, B.R.6
Dekker, J.7
Mirny, L.A.8
-
35
-
-
79952279828
-
DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors
-
Jiao Y, Shi C, Edil BH, de Wilde RF, Klimstra DS, Maitra A, Schulick RD, Tang LH, Wolfgang CL, Choti MA, et al. 2011. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331: 1199-1203.
-
(2011)
Science
, vol.331
, pp. 1199-1203
-
-
Jiao, Y.1
Shi, C.2
Edil, B.H.3
De Wilde, R.F.4
Klimstra, D.S.5
Maitra, A.6
Schulick, R.D.7
Tang, L.H.8
Wolfgang, C.L.9
Choti, M.A.10
-
36
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264-268.
-
(2011)
Nat Genet
, vol.43
, pp. 264-268
-
-
John, S.1
Sabo, P.J.2
Thurman, R.E.3
Sung, M.-H.4
Biddie, S.C.5
Johnson, T.A.6
Hager, G.L.7
Stamatoyannopoulos, J.A.8
-
37
-
-
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. 2013. 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
-
38
-
-
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: 1572-1586.
-
(2007)
PLoS Genet
, vol.3
, pp. 1572-1586
-
-
Kim, S.Y.1
Pritchard, J.K.2
-
39
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
40
-
-
84857214297
-
The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome
-
Kostka D, Hubisz MJ, Siepel A, Pollard KS. 2012. The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol 29: 1047-1057.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1047-1057
-
-
Kostka, D.1
Hubisz, M.J.2
Siepel, A.3
Pollard, K.S.4
-
41
-
-
0032189223
-
A new long form of Sox5 (LSox5), Sox6 and Sox9 are coexpressed in chondrogenesis and cooperatively activate the type II collagen gene
-
Lefebvre V, Li P, de Crombrugghe B. 1998. A new long form of Sox5 (LSox5), Sox6 and Sox9 are coexpressed in chondrogenesis and cooperatively activate the type II collagen gene. EMBO J 17: 5718-5733.
-
(1998)
EMBO J
, vol.17
, pp. 5718-5733
-
-
Lefebvre, V.1
Li, P.2
De Crombrugghe, B.3
-
42
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
43
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh KK, Garber MM, Zuk OO, Lin MFM, Parker BJB, Washietl SS, Kheradpour PP, Ernst JJ, Jordan GG, Mauceli EE, 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.K.1
Garber, M.M.2
Zuk, O.O.3
Lin, M.F.M.4
Parker, B.J.B.5
Washietl, S.S.6
Kheradpour, P.P.7
Ernst, J.J.8
Jordan, G.G.9
Mauceli, E.E.10
-
44
-
-
80051914599
-
Three periods of regulatory innovation during vertebrate evolution
-
Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. 2011. Three periods of regulatory innovation during vertebrate evolution. Science 333: 1019-1024.
-
(2011)
Science
, vol.333
, pp. 1019-1024
-
-
Lowe, C.B.1
Kellis, M.2
Siepel, A.3
Raney, B.J.4
Clamp, M.5
Salama, S.R.6
Kingsley, D.M.7
Lindblad-Toh, K.8
Haussler, D.9
-
45
-
-
33645798112
-
Genome-wide identification of human functional DNA using a neutral indel model
-
Lunter G, Ponting CP, Hein J. 2006. Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2: E5.
-
(2006)
PLoS Comput Biol
, vol.2
, pp. e5
-
-
Lunter, G.1
Ponting, C.P.2
Hein, J.3
-
46
-
-
84875614116
-
A recent evolutionary change affects a regulatory element in the human FOXP2 gene
-
Maricic T, Günther V, Georgiev O, Gehre S, Curlin M, Schreiweis C, Naumann R, Burbano HA, Meyer M, Lalueza-Fox C, et al. 2013. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Mol Biol Evol 30: 844-852.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 844-852
-
-
Maricic, T.1
Günther, V.2
Georgiev, O.3
Gehre, S.4
Curlin, M.5
Schreiweis, C.6
Naumann, R.7
Burbano, H.A.8
Meyer, M.9
Lalueza-Fox, C.10
-
47
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, et al. 2012. Systematic localization of common disease-associated variation in regulatory DNA. Science 337: 1190-1195.
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
Humbert, R.2
Rynes, E.3
Thurman, R.E.4
Haugen, E.5
Wang, H.6
Reynolds, A.P.7
Sandstrom, R.8
Qu, H.9
Brody, J.10
-
48
-
-
77952214662
-
GREAT improves functional interpretation of cisregulatory regions
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cisregulatory 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
-
49
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, et al. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216-219.
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
Reno, P.L.2
Pollen, A.A.3
Bassan, A.I.4
Capellini, T.D.5
Guenther, C.6
Indjeian, V.B.7
Lim, X.8
Menke, D.B.9
Schaar, B.T.10
-
50
-
-
78149408021
-
Massive turnover of functional sequence in human and other mammalian genomes
-
Meader S, Ponting CP, Lunter G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res 20: 1335-1343.
-
(2010)
Genome Res
, vol.20
, pp. 1335-1343
-
-
Meader, S.1
Ponting, C.P.2
Lunter, G.3
-
51
-
-
84875171933
-
Deletion of Ten-m3 induces the formation of eye dominance domains in mouse visual cortex
-
Merlin S, Horng S, Marotte LR, Sur M, Sawatari A, Leamey CA. 2013. Deletion of Ten-m3 induces the formation of eye dominance domains in mouse visual cortex. Cereb Cortex 23: 763-774.
-
(2013)
Cereb Cortex
, vol.23
, pp. 763-774
-
-
Merlin, S.1
Horng, S.2
Marotte, L.R.3
Sur, M.4
Sawatari, A.5
Leamey, C.A.6
-
52
-
-
75749124332
-
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
-
Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, et al. 2010. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 42: 181-185.
-
(2010)
Nat Genet
, vol.42
, pp. 181-185
-
-
Morin, R.D.1
Johnson, N.A.2
Severson, T.M.3
Mungall, A.J.4
An, J.5
Goya, R.6
Paul, J.E.7
Boyle, M.8
Woolcock, B.W.9
Kuchenbauer, F.10
-
53
-
-
84864147180
-
BEDOPS: High-performance genomic feature operations
-
Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, et al. 2012. BEDOPS: high-performance genomic feature operations. Bioinformatics 28: 1919-1920.
-
(2012)
Bioinformatics
, vol.28
, pp. 1919-1920
-
-
Neph, S.1
Kuehn, M.S.2
Reynolds, A.P.3
Haugen, E.4
Thurman, R.E.5
Johnson, A.K.6
Rynes, E.7
Maurano, M.T.8
Vierstra, J.9
Thomas, S.10
-
54
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: E170.
-
(2005)
PLoS Biol
, vol.3
, pp. e170
-
-
Nielsen, R.1
Bustamante, C.2
Clark, A.G.3
Glanowski, S.4
Sackton, T.B.5
Hubisz, M.J.6
Fledel-Alon, A.7
Tanenbaum, D.M.8
Civello, D.9
White, T.J.10
-
55
-
-
84872861423
-
Can ENCODE tell us how much junk DNA we carry in our genome?
-
Niu D-K, Jiang L. 2013. Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 430: 1340-1343.
-
(2013)
Biochem Biophys Res Commun
, vol.430
, pp. 1340-1343
-
-
Niu, D.-K.1
Jiang, L.2
-
56
-
-
84869479375
-
Evolution of genetic and genomic features unique to the human lineage
-
O'Bleness M, Searles VB, Varki A, Gagneux P, Sikela JM. 2012. Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet 13: 853-866.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 853-866
-
-
O'Bleness, M.1
Searles, V.B.2
Varki, A.3
Gagneux, P.4
Sikela, J.M.5
-
57
-
-
54949108148
-
Enredo and Pecan: Genomewide mammalian consistency-based multiple alignment with paralogs
-
Paten B, Herrero J, Beal K, Fitzgerald S. 2008. Enredo and Pecan: genomewide mammalian consistency-based multiple alignment with paralogs. Genome Res 18: 1814-1828.
-
(2008)
Genome Res
, vol.18
, pp. 1814-1828
-
-
Paten, B.1
Herrero, J.2
Beal, K.3
Fitzgerald, S.4
-
58
-
-
79959789752
-
Detection of lineage-specific evolutionary changes among primate species
-
Pertea M, Pertea GM, Salzberg SL. 2011. Detection of lineage-specific evolutionary changes among primate species. BMC Bioinformatics 12: 274.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 274
-
-
Pertea, M.1
Pertea, G.M.2
Salzberg, S.L.3
-
59
-
-
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
-
60
-
-
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
-
61
-
-
74949092081
-
Detection of nonneutral substitution rates on mammalian phylogenies
-
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20: 110-121.
-
(2010)
Genome Res
, vol.20
, pp. 110-121
-
-
Pollard, K.S.1
Hubisz, M.J.2
Rosenbloom, K.R.3
Siepel, A.4
-
62
-
-
80555142991
-
What fraction of the human genome is functional?
-
Ponting CP, Hardison RC. 2011. What fraction of the human genome is functional? Genome Res 21: 1769-1776.
-
(2011)
Genome Res
, vol.21
, pp. 1769-1776
-
-
Ponting, C.P.1
Hardison, R.C.2
-
63
-
-
33750737061
-
Accelerated evolution of conserved noncoding sequences in humans
-
Prabhakar S, Noonan JP, Paabo S, Rubin EM. 2006. Accelerated evolution of conserved noncoding sequences in humans. Science 314: 786.
-
(2006)
Science
, vol.314
, pp. 786
-
-
Prabhakar, S.1
Noonan, J.P.2
Paabo, S.3
Rubin, E.M.4
-
64
-
-
51149097366
-
Human-specific 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. Human-specific 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
Fitzpatrick, D.R.9
Afzal, V.10
-
65
-
-
84907095419
-
R: A language and environment for statistical computing
-
R Core Team., Vienna, Austria
-
R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
-
(2014)
R Foundation for Statistical Computing
-
-
-
66
-
-
84924561748
-
Evolutionary genomics: 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 genomics: 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
-
67
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
Sanyal A, Lajoie BR, Jain G, Dekker J. 2012. The long-range interaction landscape of gene promoters. Nature 489: 109-113.
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
-
68
-
-
84864073098
-
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection
-
Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee B-K, Iyer VR, et al. 2012. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet 8: E1002789.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002789
-
-
Shibata, Y.1
Sheffield, N.C.2
Fedrigo, O.3
Babbitt, C.C.4
Wortham, M.5
Tewari, A.K.6
London, D.7
Song, L.8
Lee, B.-K.9
Iyer, V.R.10
-
69
-
-
70350644759
-
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium
-
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, et al. 2009. A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet 41: 1182-1190.
-
(2009)
Nat Genet
, vol.41
, pp. 1182-1190
-
-
Soranzo, N.1
Spector, T.D.2
Mangino, M.3
Kühnel, B.4
Rendon, A.5
Teumer, A.6
Willenborg, C.7
Wright, B.8
Chen, L.9
Li, M.10
-
70
-
-
12144288568
-
Myosin gene mutation correlates with anatomical changes in the human lineage
-
Stedman HH, Kozyak BW, Nelson A, Thesier DM, Su LT, Low DW, Bridges CR, Shrager JB, Minugh-Purvis N, Mitchell MA. 2004. Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 428: 415-418.
-
(2004)
Nature
, vol.428
, pp. 415-418
-
-
Stedman, H.H.1
Kozyak, B.W.2
Nelson, A.3
Thesier, D.M.4
Su, L.T.5
Low, D.W.6
Bridges, C.R.7
Shrager, J.B.8
Minugh-Purvis, N.9
Mitchell, M.A.10
-
71
-
-
33845336846
-
Peroxisome biogenesis disorders
-
Steinberg SJ, Dodt G, Raymond GV, Braverman NE, Moser AB, Moser HW. 2006. Peroxisome biogenesis disorders. Biochim Biophys Acta 1763: 1733-1748.
-
(2006)
Biochim Biophys Acta
, vol.1763
, pp. 1733-1748
-
-
Steinberg, S.J.1
Dodt, G.2
Raymond, G.V.3
Braverman, N.E.4
Moser, A.B.5
Moser, H.W.6
-
72
-
-
84883682103
-
Evolution and diversity of copy number variation in the great ape lineage
-
Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW, Baker C, Mohajeri K, Kondova I, Bontrop RE, Persengiev S, et al. 2013.Evolution and diversity of copy number variation in the great ape lineage. Genome Res 23: 1373-1382.
-
(2013)
Genome Res
, vol.23
, pp. 1373-1382
-
-
Sudmant, P.H.1
Huddleston, J.2
Catacchio, C.R.3
Malig, M.4
Hillier, L.W.5
Baker, C.6
Mohajeri, K.7
Kondova, I.8
Bontrop, R.E.9
Persengiev, S.10
-
73
-
-
55049123524
-
Rapidly evolving human promoter regions
-
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CAM. 2008. Rapidly evolving human promoter regions. Nat Genet 40: 1262-1263.
-
(2008)
Nat Genet
, vol.40
, pp. 1262-1263
-
-
Taylor, M.S.1
Massingham, T.2
Hayashizaki, Y.3
Carninci, P.4
Goldman, N.5
Semple, C.A.M.6
-
74
-
-
84927641804
-
In search of the determinants of enhancer-promoter interaction specificity
-
van Arensbergen J, van Steensel B, Bussemaker HJ. 2014. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol 24: 695-702.
-
(2014)
Trends Cell Biol
, vol.24
, pp. 695-702
-
-
Van Arensbergen, J.1
Van Steensel, B.2
Bussemaker, H.J.3
-
75
-
-
84864627693
-
Personal and population genomics of human regulatory variation
-
Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. 2012. Personal and population genomics of human regulatory variation. Genome Res 22: 1689-1697.
-
(2012)
Genome Res
, vol.22
, pp. 1689-1697
-
-
Vernot, B.1
Stergachis, A.B.2
Maurano, M.T.3
Vierstra, J.4
Neph, S.5
Thurman, R.E.6
Stamatoyannopoulos, J.A.7
Akey, J.M.8
-
76
-
-
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
-
78
-
-
84880617636
-
WEB-based gene set analysis toolkit (WebGestalt): Update 2013
-
Wang J, Duncan D, Shi Z, Zhang B. 2013. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res 41: W77-W83.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. W77-W83
-
-
Wang, J.1
Duncan, D.2
Shi, Z.3
Zhang, B.4
-
79
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20: 1377-1419.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
|