-
1
-
-
1642512344
-
Evolution of eyes and photoreceptor cell types
-
Arendt D. 2003. Evolution of eyes and photoreceptor cell types. Int J Dev Biol. 47:563-571.
-
(2003)
Int J Dev Biol.
, vol.47
, pp. 563-571
-
-
Arendt, D.1
-
2
-
-
54149090863
-
The evolution of cell types in animals: Emerging principles from molecular studies
-
Arendt D. 2008. The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet. 9:868-882.
-
(2008)
Nat Rev Genet.
, vol.9
, pp. 868-882
-
-
Arendt, D.1
-
3
-
-
68849123047
-
Methods for analyzing deep sequencing expression data: Constructing the human and mouse promoterome with deepCAGE data
-
Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, Van Nimwegen E. 2009. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol. 10:R79.
-
(2009)
Genome Biol.
, vol.10
-
-
Balwierz, P.J.1
Carninci, P.2
Daub, C.O.3
Kawai, J.4
Hayashizaki, Y.5
Van Belle, W.6
Beisel, C.7
Van Nimwegen, E.8
-
4
-
-
84871410405
-
The evolutionary landscape of alternative splicing in vertebrate species
-
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, et al. 2012. The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587-1593.
-
(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
Lee, L.J.6
Slobodeniuc, V.7
Kutter, C.8
Watt, S.9
Colak, R.10
-
5
-
-
84879172714
-
Dynamics and adaptive benefits of modular protein evolution
-
Bornberg-Bauer E, Albà MM. 2013. Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol. 23: 466-459.
-
(2013)
Curr Opin Struct Biol.
, vol.23
, pp. 466-459
-
-
Bornberg-Bauer, E.1
Albà, M.M.2
-
7
-
-
84862992463
-
Tissue-specific splicing of disordered segments that Embed binding motifs rewires protein interaction networks
-
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM. 2012. Tissue-specific splicing of disordered segments that Embed binding motifs rewires protein interaction networks. Mol Cell. 46:871-883.
-
(2012)
Mol Cell.
, vol.46
, pp. 871-883
-
-
Buljan, M.1
Chalancon, G.2
Eustermann, S.3
Wagner, G.P.4
Fuxreiter, M.5
Bateman, A.6
Babu, M.M.7
-
8
-
-
84155175837
-
Quantifying the mechanisms of domain gain in animal proteins
-
Buljan M, Frankish A, Bateman A. 2010. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 11:R74.
-
(2010)
Genome Biol.
, vol.11
-
-
Buljan, M.1
Frankish, A.2
Bateman, A.3
-
9
-
-
72949113702
-
How did our complex immune system evolve?
-
Cooper MD, Herrin BR. 2010. How did our complex immune system evolve? Nat Rev Immunol. 10:2-3.
-
(2010)
Nat Rev Immunol.
, vol.10
, pp. 2-3
-
-
Cooper, M.D.1
Herrin, B.R.2
-
10
-
-
0037126639
-
Mono-ADP-ribosylation: A tool for modulating immune response and cell signaling
-
Corda D, Di Girolamo M. 2002. Mono-ADP-ribosylation: a tool for modulating immune response and cell signaling. Sci STKE. 2002:pe53.
-
(2002)
Sci STKE.
-
-
Corda, D.1
Di Girolamo, M.2
-
11
-
-
71749086711
-
RNAi-mediated silencing of insulin receptor substrate-4 enhances actinomycin D-and tumor necrosis factor-alpha-induced cell death in hepatocarcinoma cancer cell lines
-
Cuevas EP, Escribano O, Monserrat J, Mart?́nez-Botas J, Sánchez MG, Chiloeches A, Hernández-Breijo B, Sánchez- Alonso V, Román ID, Fernández-Moreno MD, et al. 2009. RNAi-mediated silencing of insulin receptor substrate-4 enhances actinomycin D-and tumor necrosis factor-alpha-induced cell death in hepatocarcinoma cancer cell lines. J Cell Biochem. 108:1292-1301.
-
(2009)
J Cell Biochem.
, vol.108
, pp. 1292-1301
-
-
Cuevas, E.P.1
Escribano, O.2
Monserrat, J.3
Martínez-Botas, J.4
Sánchez, M.G.5
Chiloeches, A.6
Hernández-Breijo, B.7
Sánchez-Alonso, V.8
Román, I.D.9
Fernández-Moreno, M.D.10
-
12
-
-
9444255105
-
Formin homology 2 domains occur in multiple contexts in angiosperms
-
Cvrcková F, Novotný M, Pícková D, Zárský V. 2004. Formin homology 2 domains occur in multiple contexts in angiosperms. BMC Genomics 5:44.
-
(2004)
BMC Genomics
, vol.5
, pp. 44
-
-
Cvrcková, F.1
Novotný, M.2
Pícková, D.3
Zárský, V.4
-
14
-
-
78651274743
-
SUPERFAMILY 1.75 including a domain-centric gene ontology method
-
De Lima Morais DA, Fang H, Rackham OJL, Wilson D, Pethica R, Chothia C, Gough J. 2011. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res. 39: D427-D434.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
De Lima Morais, D.A.1
Fang, H.2
Rackham, O.J.L.3
Wilson, D.4
Pethica, R.5
Chothia, C.6
Gough, J.7
-
15
-
-
35748936426
-
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
-
Domazet-Loso T, Brajković J, Tautz D. 2007. A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet. 23:533-539.
-
(2007)
Trends Genet.
, vol.23
, pp. 533-539
-
-
Domazet-Loso, T.1
Brajković, J.2
Tautz, D.3
-
16
-
-
84876528480
-
DcGO: Database of domain-centric ontologies on functions, phenotypes, diseases and more
-
Fang H, Gough J. 2013. dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res. 41: D536-D544.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Fang, H.1
Gough, J.2
-
17
-
-
84856562355
-
The NCBI taxonomy database
-
Federhen S. 2012. The NCBI taxonomy database. Nucleic Acids Res. 40: D136-D143.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Federhen, S.1
-
18
-
-
84897406127
-
A promoter level mammalian expression atlas
-
Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, et al. 2014. A promoter level mammalian expression atlas. Nature 507:462-470.
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
Forrest, A.R.R.1
Kawaji, H.2
Rehli, M.3
Baillie, J.K.4
De Hoon, M.J.L.5
Haberle, V.6
Lassmann, T.7
Kulakovskiy, I.V.8
Lizio, M.9
Itoh, M.10
-
20
-
-
17544367678
-
Convergent evolution of domain architectures (is rare)
-
Gough J. 2005. Convergent evolution of domain architectures (is rare). Bioinformatics 21:1464-1471.
-
(2005)
Bioinformatics
, vol.21
, pp. 1464-1471
-
-
Gough, J.1
-
21
-
-
84868280094
-
A functional selectionmodel explains evolutionary robustness despite plasticity in regulatory networks
-
Habib N, Wapinski I, Margalit H, Regev A, Friedman N. 2012. A functional selectionmodel explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol. 8:619.
-
(2012)
Mol Syst Biol.
, vol.8
, pp. 619
-
-
Habib, N.1
Wapinski, I.2
Margalit, H.3
Regev, A.4
Friedman, N.5
-
22
-
-
0033591428
-
Phylogenetic perspectives in innate immunity
-
Hoffmann JA. 1999. Phylogenetic Perspectives in Innate Immunity. Science 284:1313-1318.
-
(1999)
Science
, vol.284
, pp. 1313-1318
-
-
Hoffmann, J.A.1
-
23
-
-
70349318376
-
Structure is three to ten times more conserved than sequence - A study of structural response in protein cores
-
Illerga°rd K, Ardell DH, Elofsson A. 2009. Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins 77:499-508.
-
(2009)
Proteins
, vol.77
, pp. 499-508
-
-
Illergard, K.1
Ardell, D.H.2
Elofsson, A.3
-
25
-
-
83155181907
-
The SH2 domain-containing proteins in 21 species establish the provenance and scope of phosphotyrosine signaling in eukaryotes
-
Liu BA, Shah E, Jablonowski K, Stergachis A, Engelmann B, Nash PD. 2011. The SH2 domain-containing proteins in 21 species establish the provenance and scope of phosphotyrosine signaling in eukaryotes. Sci Signal. 4:ra83.
-
(2011)
Sci Signal.
, vol.4
-
-
Liu, B.A.1
Shah, E.2
Jablonowski, K.3
Stergachis, A.4
Engelmann, B.5
Nash, P.D.6
-
26
-
-
0036796379
-
A comparison of profile hidden Markov model procedures for remote homology detection
-
Madera M, Gough J. 2002. A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res. 30:4321-4328.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4321-4328
-
-
Madera, M.1
Gough, J.2
-
27
-
-
69249217275
-
Expression and function of the insulin receptor substrate proteins in cancer
-
Mardilovich K, Pankratz SL, Shaw LM. 2009. Expression and function of the insulin receptor substrate proteins in cancer. Cell Commun Signal. 7:14.
-
(2009)
Cell Commun Signal.
, vol.7
, pp. 14
-
-
Mardilovich, K.1
Pankratz, S.L.2
Shaw, L.M.3
-
28
-
-
84880213068
-
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
-
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. 2013. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 41:e121.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Mistry, J.1
Finn, R.D.2
Eddy, S.R.3
Bateman, A.4
Punta, M.5
-
29
-
-
50849114838
-
Arrangements in themodular evolution of proteins
-
Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. 2008. Arrangements in themodular evolution of proteins. Trends Biochem Sci. 33:444-451.
-
(2008)
Trends Biochem Sci.
, vol.33
, pp. 444-451
-
-
Moore, A.D.1
Björklund, A.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
30
-
-
84876281976
-
Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree
-
Moore AD, Grath S, Schüler A, Huylmans AK, Bornberg-Bauer E. 2013. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. Biochim Biophys Acta. 1834: 898-907.
-
(2013)
Biochim Biophys Acta.
, vol.1834
, pp. 898-907
-
-
Moore, A.D.1
Grath, S.2
Schüler, A.3
Huylmans, A.K.4
Bornberg-Bauer, E.5
-
32
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin A, Brenner S, Hubbard T, Chothia C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:536-540.
-
(1995)
J Mol Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.1
Brenner, S.2
Hubbard, T.3
Chothia, C.4
-
33
-
-
84876524220
-
D2P2: Database of disordered protein predictions
-
(Database issue)
-
Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, et al. 2013. D2P2: database of disordered protein predictions. Nucleic Acids Res. 41(Database issue):D508-D516.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Oates, M.E.1
Romero, P.2
Ishida, T.3
Ghalwash, M.4
Mizianty, M.J.5
Xue, B.6
Dosztányi, Z.7
Uversky, V.N.8
Obradovic, Z.9
Kurgan, L.10
-
34
-
-
0035895992
-
Nod2, a Nod1/Apaf-1 family member that is restricted to monocytes and activates NF-kappaB
-
Ogura Y, Inohara N, Benito A, Chen FF, Yamaoka S, Nunez G. 2001. Nod2, a Nod1/Apaf-1 family member that is restricted to monocytes and activates NF-kappaB. J Biol Chem. 276:4812-4818.
-
(2001)
J Biol Chem.
, vol.276
, pp. 4812-4818
-
-
Ogura, Y.1
Inohara, N.2
Benito, A.3
Chen, F.F.4
Yamaoka, S.5
Nunez, G.6
-
35
-
-
49949090861
-
The functional repertoires of metazoan genomes
-
Ponting CP. 2008. The functional repertoires of metazoan genomes. Nat Rev Genet. 9:689-698.
-
(2008)
Nat Rev Genet.
, vol.9
, pp. 689-698
-
-
Ponting, C.P.1
-
36
-
-
0033615620
-
Insulin receptor substrate-4 enhances insulin-like growth factor-I-induced cell proliferation
-
Qu BH, Karas M, Koval A, LeRoith D. 1999. Insulin receptor substrate-4 enhances insulin-like growth factor-I-induced cell proliferation. J Biol Chem. 274:31179-31184.
-
(1999)
J Biol Chem.
, vol.274
, pp. 31179-31184
-
-
Qu, B.H.1
Karas, M.2
Koval, A.3
Leroith, D.4
-
37
-
-
49449091882
-
Splenic nerve is required for cholinergic antiinflammatory pathway control of TNF in endotoxemia
-
Rosas-BallinaM, OchaniM, ParrishWR, Ochani K, Harris YT,Huston JM, Chavan S, Tracey KJ. 2008. Splenic nerve is required for cholinergic antiinflammatory pathway control of TNF in endotoxemia. Proc Natl Acad Sci USA. 105:11008-11013.
-
(2008)
Proc Natl Acad Sci USA.
, vol.105
, pp. 11008-11013
-
-
Rosas-Ballina, M.1
Ochani, M.2
Parrish, W.R.3
Ochani, K.4
Harris, Y.T.5
Huston, J.M.6
Chavan, S.7
Tracey, K.J.8
-
38
-
-
70349816648
-
The neurology of the immune system: Neural reflexes regulate immunity
-
Rosas-Ballina M, Tracey KJ. 2009. The neurology of the immune system: neural reflexes regulate immunity. Neuron 64:28-32.
-
(2009)
Neuron
, vol.64
, pp. 28-32
-
-
Rosas-Ballina, M.1
Tracey, K.J.2
-
39
-
-
0028774720
-
The crystal structure of citrate synthase from the thermophilic Archaeon, Thermoplasma acidophilum
-
Russell RJ, Hough DW, DansonMJ, Taylor GL. 1994. The crystal structure of citrate synthase from the thermophilic Archaeon, Thermoplasma acidophilum. Structure 2:1157-1167.
-
(1994)
Structure
, vol.2
, pp. 1157-1167
-
-
Russell, R.J.1
Hough, D.W.2
Danson, M.J.3
Taylor, G.L.4
-
40
-
-
0037390484
-
Insulin receptor substrate-4 is expressed in muscle tissue without acting as a substrate for the insulin receptor
-
Schreyer S. 2003. Insulin receptor substrate-4 is expressed in muscle tissue without acting as a substrate for the insulin receptor. Endocrinology 144:1211-1218.
-
(2003)
Endocrinology
, vol.144
, pp. 1211-1218
-
-
Schreyer, S.1
-
41
-
-
0021919786
-
On the evolution of the spleen
-
Tischendorf F. 1985. On the evolution of the spleen. Experientia 41: 145-152.
-
(1985)
Experientia
, vol.41
, pp. 145-152
-
-
Tischendorf, F.1
-
42
-
-
60149097110
-
Origin of primate orphan genes: A comparative genomics approach
-
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM. 2009. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol. 26:603-612.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 603-612
-
-
Toll-Riera, M.1
Bosch, N.2
Bellora, N.3
Castelo, R.4
Armengol, L.5
Estivill, X.6
Albà, M.M.7
-
43
-
-
75849153303
-
The universal protein resource (UniProt) in 2010
-
UniProt Consortium
-
UniProt Consortium. 2010. The universal protein resource (UniProt) in 2010. Nucleic Acids Res. 38:D142-D148.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
-
44
-
-
38049168357
-
SOM-based data visualization methods
-
Vesanto J. 1999. SOM-based data visualization methods. Intelligent Data Anal. 3:111-126.
-
(1999)
Intelligent Data Anal.
, vol.3
, pp. 111-126
-
-
Vesanto, J.1
-
45
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
(London, England: 1993)
-
Wang M, Caetano-Anollés G. 2009. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure (London, England: 1993) 17:66-78.
-
(2009)
Structure
, vol.17
, pp. 66-78
-
-
Wang, M.1
Caetano-Anollés, G.2
-
46
-
-
84870492989
-
Overexpression of Uromodulin-like1 accelerates follicle depletion and subsequent ovarian degeneration
-
Wang W, Tang Y, Ni L, Kim E, Jongwutiwes T, Hourvitz A, Zhang R, Xiong H, Liu HC, Rosenwaks Z. 2012. Overexpression of Uromodulin-like1 accelerates follicle depletion and subsequent ovarian degeneration. Cell Death Dis. 3:e433.
-
(2012)
Cell Death Dis.
, vol.3
-
-
Wang, W.1
Tang, Y.2
Ni, L.3
Kim, E.4
Jongwutiwes, T.5
Hourvitz, A.6
Zhang, R.7
Xiong, H.8
Liu, H.C.9
Rosenwaks, Z.10
-
47
-
-
0037434889
-
Component plane presentation integrated self-organizing map for microarray data analysis
-
Xiao L, Wang K, Teng Y, Zhang J. 2003. Component plane presentation integrated self-organizing map for microarray data analysis. FEBS Lett. 538:117-124.
-
(2003)
FEBS Lett.
, vol.538
, pp. 117-124
-
-
Xiao, L.1
Wang, K.2
Teng, Y.3
Zhang, J.4
-
48
-
-
33748470085
-
Alternative splicing in human transcriptome: Functional and structural influence on proteins
-
Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, et al. 2006. Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene 380:63-71.
-
(2006)
Gene
, vol.380
, pp. 63-71
-
-
Yura, K.1
Shionyu, M.2
Hagino, K.3
Hijikata, A.4
Hirashima, Y.5
Nakahara, T.6
Eguchi, T.7
Shinoda, K.8
Yamaguchi, A.9
Takahashi, K.10
|