-
1
-
-
26444603772
-
Two rounds of whole genome duplication in the ancestral vertebrate
-
PMID: 16128622
-
Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS biology 3: e314. PMID: 16128622
-
(2005)
PLoS Biology
, vol.3
, pp. e314
-
-
Dehal, P.1
Boore, J.L.2
-
2
-
-
45749086679
-
The amphioxus genome and the evolution of the chordate karyotype
-
PMID: 18563158
-
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-1071. doi: 10.1038/nature06967 PMID: 18563158
-
(2008)
Nature
, vol.453
, pp. 1064-1071
-
-
Putnam, N.H.1
Butts, T.2
Ferrier, D.E.3
Furlong, R.F.4
Hellsten, U.5
-
3
-
-
0036613237
-
Extensive genomic duplication during early chordate evolution
-
PMID: 12032567
-
McLysaght A, Hokamp K, Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nature genetics 31: 200-204. PMID: 12032567
-
(2002)
Nature Genetics
, vol.31
, pp. 200-204
-
-
McLysaght, A.1
Hokamp, K.2
Wolfe, K.H.3
-
4
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
PMID: 10101175
-
Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545. PMID: 10101175
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
Amores, A.4
Yan, Y.L.5
-
5
-
-
21344439563
-
Subfunctionalization of duplicated genes as a transition state to neofunctionalization
-
PMID: 15831095
-
Rastogi S, Liberles DA (2005) Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC evolutionary biology 5: 28. PMID: 15831095
-
(2005)
BMC Evolutionary Biology
, vol.5
, pp. 28
-
-
Rastogi, S.1
Liberles, D.A.2
-
6
-
-
0003515251
-
-
Berlin, New York, Springer-Verlag. PMID: 25077213
-
Ohno S (1970) Evolution by Gene Duplication. Berlin, New York, Springer-Verlag. PMID: 25077213
-
(1970)
Evolution by Gene Duplication
-
-
Ohno, S.1
-
7
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
PMID: 19015660
-
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics 10: 57-63. doi: 10.1038/nrg2484 PMID: 19015660
-
(2009)
Nature Reviews Genetics
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
8
-
-
84875923909
-
Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris
-
PMID: 23593398
-
Mooney M, Bond J, Monks N, Eugster E, Cherba D, et al. (2013) Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris. PloS one 8: e61088. doi: 10.1371/journal.pone.0061088 PMID: 23593398
-
(2013)
PloS One
, vol.8
, pp. e61088
-
-
Mooney, M.1
Bond, J.2
Monks, N.3
Eugster, E.4
Cherba, D.5
-
9
-
-
84869014474
-
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: A case study in Saccharomyces cerevisiae
-
PMID: 22965124
-
Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, et al. (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic acids research 40: 10084-10097. doi: 10.1093/nar/gks804 PMID: 22965124
-
(2012)
Nucleic Acids Research
, vol.40
, pp. 10084-10097
-
-
Nookaew, I.1
Papini, M.2
Pornputtapong, N.3
Scalcinati, G.4
Fagerberg, L.5
-
10
-
-
67449141880
-
RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing
-
PMID: 19336255
-
Wilhelm BT, Landry JR (2009) RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48: 249-257. doi: 10.1016/j.ymeth.2009.03.016 PMID: 19336255
-
(2009)
Methods
, vol.48
, pp. 249-257
-
-
Wilhelm, B.T.1
Landry, J.R.2
-
11
-
-
84871410405
-
The evolutionary landscape of alternative splicing in vertebrate species
-
PMID: 23258890
-
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, et al. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338: 1587-1593. doi: 10.1126/science.1230612 PMID: 23258890
-
(2012)
Science
, vol.338
, pp. 1587-1593
-
-
Barbosa-Morais, N.L.1
Irimia, M.2
Pan, Q.3
Xiong, H.Y.4
Gueroussov, S.5
-
12
-
-
84871436996
-
Evolutionary dynamics of gene and isoform regulation in Mammalian tissues
-
PMID: 23258891
-
Merkin J, Russell C, Chen P, Burge CB (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338: 1593-1599. doi: 10.1126/science.1228186 PMID: 23258891
-
(2012)
Science
, vol.338
, pp. 1593-1599
-
-
Merkin, J.1
Russell, C.2
Chen, P.3
Burge, C.B.4
-
13
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
PMID: 22012392
-
Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348. doi: 10.1038/nature10532 PMID: 22012392
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
Soumillon, M.2
Necsulea, A.3
Julien, P.4
Csardi, G.5
-
14
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
PMID: 19033363
-
Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 37: 1-13. doi: 10.1093/nar/gkn923 PMID: 19033363
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
15
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
PMID: 19131956
-
Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 4: 44-57. doi: 10.1038/nprot.2008.211 PMID: 19131956
-
(2009)
Nature Protocols
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
16
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
PMID: 19029536
-
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome research 19: 327-335. doi: 10.1101/gr.073585.107 PMID: 19029536
-
(2009)
Genome Research
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
-
17
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
PMID: 15034147
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32: 1792-1797. PMID: 15034147
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
18
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
PMID: 19377059
-
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular biology and evolution 26: 1641-1650. doi: 10.1093/molbev/msp077 PMID: 19377059
-
(2009)
Molecular Biology and Evolution
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
19
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
PMID: 11319253
-
Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular biology and evolution 18: 691-699. PMID: 11319253
-
(2001)
Molecular Biology and Evolution
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
20
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
PMID: 22955619
-
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100. doi: 10.1038/nature11245 PMID: 22955619
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Landt, S.G.4
Yan, K.K.5
-
21
-
-
84876566914
-
ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
-
PMID: 23161675
-
Yang JH, Li JH, Jiang S, Zhou H, Qu LH (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic acids research 41: D177-187. doi: 10.1093/nar/gks1060 PMID: 23161675
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D177-D187
-
-
Yang, J.H.1
Li, J.H.2
Jiang, S.3
Zhou, H.4
Qu, L.H.5
-
22
-
-
33646182934
-
An integrated view of protein evolution
-
PMID: 16619049
-
Pal C, Papp B, Lercher MJ (2006) An integrated view of protein evolution. Nature reviews Genetics 7: 337-348. PMID: 16619049
-
(2006)
Nature Reviews Genetics
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
23
-
-
70349636360
-
Evaluating the affective component of the cerebellar cognitive affective syndrome
-
PMID: 19776302
-
Wolf U, Rapoport MJ, Schweizer TA (2009) Evaluating the affective component of the cerebellar cognitive affective syndrome. The Journal of neuropsychiatry and clinical neurosciences 21: 245-253. doi: 10.1176/appi.neuropsych.21.3.245 PMID: 19776302
-
(2009)
The Journal of Neuropsychiatry and Clinical Neurosciences
, vol.21
, pp. 245-253
-
-
Wolf, U.1
Rapoport, M.J.2
Schweizer, T.A.3
-
24
-
-
0028934541
-
REST: A mammalian silencer protein that restricts sodium channel gene expression to neurons
-
PMID: 7697725
-
Chong JA, Tapia-Ramirez J, Kim S, Toledo-Aral JJ, Zheng Y, et al. (1995) REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell 80: 949-957. PMID: 7697725
-
(1995)
Cell
, vol.80
, pp. 949-957
-
-
Chong, J.A.1
Tapia-Ramirez, J.2
Kim, S.3
Toledo-Aral, J.J.4
Zheng, Y.5
-
25
-
-
0028968802
-
The neuron-restrictive silencer factor (NRSF): A coordinate repressor of multiple neuron-specific genes
-
PMID: 7871435
-
Schoenherr CJ, Anderson DJ (1995) The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science 267: 1360-1363. PMID: 7871435
-
(1995)
Science
, vol.267
, pp. 1360-1363
-
-
Schoenherr, C.J.1
Anderson, D.J.2
-
26
-
-
34250767817
-
Chromatin crosstalk in development and disease: Lessons from REST
-
PMID: 17572692
-
Ooi L, Wood IC (2007) Chromatin crosstalk in development and disease: lessons from REST. Nature reviews Genetics 8: 544-554. PMID: 17572692
-
(2007)
Nature Reviews Genetics
, vol.8
, pp. 544-554
-
-
Ooi, L.1
Wood, I.C.2
-
27
-
-
84879795456
-
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis
-
PMID: 23791531
-
Soumillon M, Necsulea A, Weier M, Brawand D, Zhang X, et al. (2013) Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell reports 3: 2179-2190. doi: 10.1016/j.celrep.2013.05.031 PMID: 23791531
-
(2013)
Cell Reports
, vol.3
, pp. 2179-2190
-
-
Soumillon, M.1
Necsulea, A.2
Weier, M.3
Brawand, D.4
Zhang, X.5
-
29
-
-
84856700596
-
Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations
-
PMID: 22233631
-
Eizaguirre C, Lenz TL, Kalbe M, Milinski M (2012) Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations. Nature communications 3: 621. doi: 10.1038/ncomms1632 PMID: 22233631
-
(2012)
Nature Communications
, vol.3
, pp. 621
-
-
Eizaguirre, C.1
Lenz, T.L.2
Kalbe, M.3
Milinski, M.4
-
33
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
PMID: 14525925
-
Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome research 13: 2229-2235. PMID: 14525925
-
(2003)
Genome Research
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
35
-
-
79951572053
-
Evidences for increased expression variation of duplicate genes in budding yeast: From cis- to trans-regulation effects
-
PMID: 20935054
-
Dong D, Yuan Z, Zhang Z (2011) Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. Nucleic acids research 39: 837-847. doi: 10.1093/nar/gkq874 PMID: 20935054
-
(2011)
Nucleic Acids Research
, vol.39
, pp. 837-847
-
-
Dong, D.1
Yuan, Z.2
Zhang, Z.3
-
36
-
-
78649231644
-
Origins, evolution, and phenotypic impact of new genes
-
PMID: 20651121
-
Kaessmann H (2010) Origins, evolution, and phenotypic impact of new genes. Genome research 20: 1313-1326. doi: 10.1101/gr.101386.109 PMID: 20651121
-
(2010)
Genome Research
, vol.20
, pp. 1313-1326
-
-
Kaessmann, H.1
-
37
-
-
0037015176
-
Exploring genetic regulatory networks in metazoan development: Methods and models
-
PMID: 12209016
-
Halfon MS, Michelson AM (2002) Exploring genetic regulatory networks in metazoan development: methods and models. Physiological genomics 10: 131-143. PMID: 12209016
-
(2002)
Physiological Genomics
, vol.10
, pp. 131-143
-
-
Halfon, M.S.1
Michelson, A.M.2
-
38
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
PMID: 22955616
-
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74. doi: 10.1038/nature11247 PMID: 22955616
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
-
39
-
-
79953046943
-
A cis-regulatory map of the Drosophila genome
-
PMID: 21430782
-
Negre N, Brown CD, Ma L, Bristow CA, Miller SW, et al. (2011) A cis-regulatory map of the Drosophila genome. Nature 471: 527-531. doi: 10.1038/nature09990 PMID: 21430782
-
(2011)
Nature
, vol.471
, pp. 527-531
-
-
Negre, N.1
Brown, C.D.2
Ma, L.3
Bristow, C.A.4
Miller, S.W.5
|