-
1
-
-
0035816218
-
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
-
Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 2001, 310:311-325.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 311-325
-
-
Apic, G.1
Gough, J.2
Teichmann, S.A.3
-
2
-
-
12344261833
-
The relationship between domain duplication and recombination
-
Vogel C., Teichmann S., Pereira-Leal J. The relationship between domain duplication and recombination. J. Mol. Biol. 2005, 346:355-365.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 355-365
-
-
Vogel, C.1
Teichmann, S.2
Pereira-Leal, J.3
-
3
-
-
26844454995
-
Domain rearrangements in protein evolution
-
Björklund Å.K., Ekman D., Light S., Frey-Skött J., Elofsson A. Domain rearrangements in protein evolution. J. Mol. Biol. 2005, 353:911-923.
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 911-923
-
-
Björklund, Å.K.1
Ekman, D.2
Light, S.3
Frey-Skött, J.4
Elofsson, A.5
-
4
-
-
33646268799
-
Domain deletions and substitutions in the modular protein evolution
-
Weiner J., Beaussart F., Bornberg-Bauer E. Domain deletions and substitutions in the modular protein evolution. FEBS J. 2006, 273:2037-2047.
-
(2006)
FEBS J.
, vol.273
, pp. 2037-2047
-
-
Weiner, J.1
Beaussart, F.2
Bornberg-Bauer, E.3
-
5
-
-
16244423379
-
Multi-domain proteins in the three kingdoms of like-orphan domains and other unassigned regions
-
Ekman D., Björklund Å.K., Frey-Skött J., Elofsson A. Multi-domain proteins in the three kingdoms of like-orphan domains and other unassigned regions. J. Mol. Biol. 2005, 348:231-243.
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 231-243
-
-
Ekman, D.1
Björklund, Å.K.2
Frey-Skött, J.3
Elofsson, A.4
-
7
-
-
0033569354
-
A census of protein repeats
-
Marcotte E., Pellegrini M., Yeates T.O., Eisenberg D. A census of protein repeats. J. Mol. Biol. 1999, 293:151-160.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 151-160
-
-
Marcotte, E.1
Pellegrini, M.2
Yeates, T.O.3
Eisenberg, D.4
-
8
-
-
33745686603
-
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
-
Ekman D., Light S., Björklund Å.K., Elofsson A. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?. Genome Biol. 2006, 7:R45.
-
(2006)
Genome Biol.
, vol.7
-
-
Ekman, D.1
Light, S.2
Björklund, Å.K.3
Elofsson, A.4
-
9
-
-
0035946941
-
Comparison of ARM and HEAT protein repeats
-
Andrade M.A., Petosa C., O'Donoghue S.I., Müller C.W., Bork P. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 2001, 309:1-18.
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 1-18
-
-
Andrade, M.A.1
Petosa, C.2
O'Donoghue, S.I.3
Müller, C.W.4
Bork, P.5
-
10
-
-
0028347405
-
Nebulin, a helical actin binding protein
-
Pfuhl M., Winder S., Pastore A. Nebulin, a helical actin binding protein. EMBO J. 1994, 13:1782-1789.
-
(1994)
EMBO J.
, vol.13
, pp. 1782-1789
-
-
Pfuhl, M.1
Winder, S.2
Pastore, A.3
-
11
-
-
0038353769
-
Nebulin: the nebulous, multifunctional giant of striated muscle
-
McElhinny A.S., Kazmierski S.T., Labeit S., Gregorio C.C. Nebulin: the nebulous, multifunctional giant of striated muscle. Trends Cardiovasc. Med. 2003, 13:195-201.
-
(2003)
Trends Cardiovasc. Med.
, vol.13
, pp. 195-201
-
-
McElhinny, A.S.1
Kazmierski, S.T.2
Labeit, S.3
Gregorio, C.C.4
-
12
-
-
0035814795
-
High-affinity actin-binding nebulin fragments influence the actoS1 complex
-
Root D., Wang K. High-affinity actin-binding nebulin fragments influence the actoS1 complex. Biochemistry 2001, 40:1171-1186.
-
(2001)
Biochemistry
, vol.40
, pp. 1171-1186
-
-
Root, D.1
Wang, K.2
-
13
-
-
4644306059
-
Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts
-
Donner K., Sandbacka M., Lehtokari V., Wallgren-Pettersson C., Pelin K. Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts. Eur. J. Hum. Genet. 2004, 12:744-751. 10.1038/sj.ejhg.5201242.
-
(2004)
Eur. J. Hum. Genet.
, vol.12
, pp. 744-751
-
-
Donner, K.1
Sandbacka, M.2
Lehtokari, V.3
Wallgren-Pettersson, C.4
Pelin, K.5
-
14
-
-
0036061465
-
Targeted disruption of Nebulette protein expression alters cardiac myofibril assembly and function
-
Moncman C., Wang K. Targeted disruption of Nebulette protein expression alters cardiac myofibril assembly and function. Exp. Cell Res. 2002, 273:204-218. 10.1006/excr.2001.5423.
-
(2002)
Exp. Cell Res.
, vol.273
, pp. 204-218
-
-
Moncman, C.1
Wang, K.2
-
15
-
-
2442576932
-
Zyxin interacts with the SH3 domains of the cytoskeletal proteins LIM-Nebulette and Lasp-1
-
Li B., Zhuang L., Trueb B. Zyxin interacts with the SH3 domains of the cytoskeletal proteins LIM-Nebulette and Lasp-1. J. Biol. Chem. 2004, 279:20401-20410.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 20401-20410
-
-
Li, B.1
Zhuang, L.2
Trueb, B.3
-
16
-
-
37549035082
-
Lasp-2 expression, localization, and ligand interactions: a new Z-disc scaffolding protein
-
Zieseniss A., Terasaki A.G., Gregorio C.C. Lasp-2 expression, localization, and ligand interactions: a new Z-disc scaffolding protein. Cell Motil. Cytoskeleton 2008, 65:59-72.
-
(2008)
Cell Motil. Cytoskeleton
, vol.65
, pp. 59-72
-
-
Zieseniss, A.1
Terasaki, A.G.2
Gregorio, C.C.3
-
17
-
-
62849089983
-
Characterization of amphioxus nebulin and its similarity to human nebulin
-
Hanashima A., Kubokawa K., Kimura S. Characterization of amphioxus nebulin and its similarity to human nebulin. J. Exp. Biol. 2009, 212:668-672. 10.1242/jeb.022681.
-
(2009)
J. Exp. Biol.
, vol.212
, pp. 668-672
-
-
Hanashima, A.1
Kubokawa, K.2
Kimura, S.3
-
18
-
-
0030925920
-
Pfam: a comprehensive database of protein domain families based on seed alignments
-
Sonnhammer E., Eddy S., Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins Struct. Funct. Genet. 1997, 28:405-420.
-
(1997)
Proteins Struct. Funct. Genet.
, vol.28
, pp. 405-420
-
-
Sonnhammer, E.1
Eddy, S.2
Durbin, R.3
-
19
-
-
70349670977
-
Muscle giants: molecular scaffolds in sarcomerogenesis
-
Kontrogianni-Konstantopoulos A., Ackermann M., Bowman A., Yap S., Bloch R. Muscle giants: molecular scaffolds in sarcomerogenesis. Physiol. Rev. 2009, 89:1217-1267.
-
(2009)
Physiol. Rev.
, vol.89
, pp. 1217-1267
-
-
Kontrogianni-Konstantopoulos, A.1
Ackermann, M.2
Bowman, A.3
Yap, S.4
Bloch, R.5
-
20
-
-
0031962157
-
Expression and purification of large nebulin fragments and their interaction with actin
-
Zhang J., Weisberg A., Horowits R. Expression and purification of large nebulin fragments and their interaction with actin. Biophys J. 1998, 74:349-359.
-
(1998)
Biophys J.
, vol.74
, pp. 349-359
-
-
Zhang, J.1
Weisberg, A.2
Horowits, R.3
-
21
-
-
1642464839
-
Protein structure prediction using Rosetta
-
Rohl C., Strauss C., Misura K., Baker D. Protein structure prediction using Rosetta. Methods Enzymol. 2004, 383:66-93.
-
(2004)
Methods Enzymol.
, vol.383
, pp. 66-93
-
-
Rohl, C.1
Strauss, C.2
Misura, K.3
Baker, D.4
-
22
-
-
0034831138
-
Segmental duplications: organization and impact within the current human genome project assembly
-
Bailey J., Yavor A., Massa H., Trask B., Eichler E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 2001, 11:1005-1017. 10.1101/gr.187101.
-
(2001)
Genome Res.
, vol.11
, pp. 1005-1017
-
-
Bailey, J.1
Yavor, A.2
Massa, H.3
Trask, B.4
Eichler, E.5
-
24
-
-
41149140876
-
The fine-scale and complex architecture of human copy-number variation
-
Perry G., Ben-Dor A., Tsalenko A., Sampas N., Rodriguez-Revenga L., Tran C., et al. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 2008, 82:685-695. 10.1016/j.ajhg.2007.12.010.
-
(2008)
Am. J. Hum. Genet.
, vol.82
, pp. 685-695
-
-
Perry, G.1
Ben-Dor, A.2
Tsalenko, A.3
Sampas, N.4
Rodriguez-Revenga, L.5
Tran, C.6
-
25
-
-
22844451617
-
Fine-scale structural variation of the human genome
-
Tuzun E., Sharp A., Bailey J., Kaul R., Morrison V., Pertz L., et al. Fine-scale structural variation of the human genome. Nat. Genet. 2005, 37:727-732. 10.1038/ng1562.
-
(2005)
Nat. Genet.
, vol.37
, pp. 727-732
-
-
Tuzun, E.1
Sharp, A.2
Bailey, J.3
Kaul, R.4
Morrison, V.5
Pertz, L.6
-
26
-
-
77950461601
-
Origins and functional impact of copy number variation in the human genome
-
Conrad D., Pinto D., Redon R., Feuk L., Gokcumen O., Zhang Y., et al. Origins and functional impact of copy number variation in the human genome. Nature 2010, 464:704-712. 10.1038/nature08516.
-
(2010)
Nature
, vol.464
, pp. 704-712
-
-
Conrad, D.1
Pinto, D.2
Redon, R.3
Feuk, L.4
Gokcumen, O.5
Zhang, Y.6
-
27
-
-
48249127189
-
Nebulin interacts with CapZ and regulates thin filament architecture within the Z-disc
-
Pappas C., Bhattacharya N., Cooper J., Gregorio C. Nebulin interacts with CapZ and regulates thin filament architecture within the Z-disc. Mol. Biol. Cell 2008, 5:1837-1847.
-
(2008)
Mol. Biol. Cell
, vol.5
, pp. 1837-1847
-
-
Pappas, C.1
Bhattacharya, N.2
Cooper, J.3
Gregorio, C.4
-
28
-
-
33748058496
-
Nebulin regulates thin filament length, contractility, and Z-disk structure in vivo
-
Witt C., Burkart C., Labeit D., McNabb M., Wu Y., Granzier H., Labeit S. Nebulin regulates thin filament length, contractility, and Z-disk structure in vivo. EMBO J. 2006, 25:3843-3855.
-
(2006)
EMBO J.
, vol.25
, pp. 3843-3855
-
-
Witt, C.1
Burkart, C.2
Labeit, D.3
McNabb, M.4
Wu, Y.5
Granzier, H.6
Labeit, S.7
-
29
-
-
61549130938
-
A prominent role for segmental duplications in modeling eukaryotic genomes
-
Koszul R., Fischer G. A prominent role for segmental duplications in modeling eukaryotic genomes. C. R. Biol. 2009, 332:254-266.
-
(2009)
C. R. Biol.
, vol.332
, pp. 254-266
-
-
Koszul, R.1
Fischer, G.2
-
30
-
-
0142059650
-
An Alu transposition model for the origin and expansion of human segmental duplications
-
Bailey J., Liu G., Eichler E. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 2003, 73:823-834.
-
(2003)
Am. J. Hum. Genet.
, vol.73
, pp. 823-834
-
-
Bailey, J.1
Liu, G.2
Eichler, E.3
-
31
-
-
0032478140
-
The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia
-
Strout M.P., Marcucci G., Bloomfield C.D., Caligiuri M.A. The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia. Proc. Natl Acad. Sci. 1998, 95:2390.
-
(1998)
Proc. Natl Acad. Sci.
, vol.95
, pp. 2390
-
-
Strout, M.P.1
Marcucci, G.2
Bloomfield, C.D.3
Caligiuri, M.A.4
-
32
-
-
0031857253
-
Analysis of two duplications of the LDL receptor gene affecting intracellular transport, catabolism, and surface binding of the LDL receptor
-
Patel D. Analysis of two duplications of the LDL receptor gene affecting intracellular transport, catabolism, and surface binding of the LDL receptor. J. Lipid Res. 1998, 39:1466.
-
(1998)
J. Lipid Res.
, vol.39
, pp. 1466
-
-
Patel, D.1
-
33
-
-
0031026976
-
Duplication of seven exons in the lysyl hydroxylase gene is associated with longer forms of a repetitive sequence within the gene and is a common cause for the type VI variant of Ehlers-Danlos syndrome
-
Heikkinen J., Toppinen T., Yeowell H., Krieg T., Steinmann B., Kivirikko K., Myllylä R. Duplication of seven exons in the lysyl hydroxylase gene is associated with longer forms of a repetitive sequence within the gene and is a common cause for the type VI variant of Ehlers-Danlos syndrome. Am. J. Hum. Genet. 1997, 60:48.
-
(1997)
Am. J. Hum. Genet.
, vol.60
, pp. 48
-
-
Heikkinen, J.1
Toppinen, T.2
Yeowell, H.3
Krieg, T.4
Steinmann, B.5
Kivirikko, K.6
Myllylä, R.7
-
34
-
-
36248946195
-
Identification of an Alu-mediated tandem duplication of exons 8 and 9 in a patient with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency
-
Fukao T., Zhang G., Rolland M.O., Zabot M.T., Guffon N., Aoki Y., Kondo N. Identification of an Alu-mediated tandem duplication of exons 8 and 9 in a patient with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency. Mol. Genet. Metab. 2007, 92:375-378.
-
(2007)
Mol. Genet. Metab.
, vol.92
, pp. 375-378
-
-
Fukao, T.1
Zhang, G.2
Rolland, M.O.3
Zabot, M.T.4
Guffon, N.5
Aoki, Y.6
Kondo, N.7
-
35
-
-
33751329250
-
Global variation in copy number in the human genome
-
Redon R., Ishikawa S., Fitch K., Feuk L., Perry G., Andrews T., et al. Global variation in copy number in the human genome. Nature 2006, 444:444-454.
-
(2006)
Nature
, vol.444
, pp. 444-454
-
-
Redon, R.1
Ishikawa, S.2
Fitch, K.3
Feuk, L.4
Perry, G.5
Andrews, T.6
-
36
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
37
-
-
0036087630
-
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer A., Panchenko A., Shoemaker B., Thiessen P., Geer L., Bryant S. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002, 30:281.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 281
-
-
Marchler-Bauer, A.1
Panchenko, A.2
Shoemaker, B.3
Thiessen, P.4
Geer, L.5
Bryant, S.6
-
38
-
-
45749086679
-
The amphioxus genome and the evolution of the chordate karyotype
-
Putnam N., Butts T., Ferrier D., Furlong R., Hellsten U., Kawashima T., et al. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008, 453:1064-1071.
-
(2008)
Nature
, vol.453
, pp. 1064-1071
-
-
Putnam, N.1
Butts, T.2
Ferrier, D.3
Furlong, R.4
Hellsten, U.5
Kawashima, T.6
-
39
-
-
0034201441
-
EMBOSS: the European Molecular Biology Open Software Suite
-
Rice P., Longden I., Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16:276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
40
-
-
63349085641
-
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
-
Lassmann T., Frings O., Sonnhammer E. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res. 2009, 37:858-865. 10.1093/nar/gkn1006.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 858-865
-
-
Lassmann, T.1
Frings, O.2
Sonnhammer, E.3
-
41
-
-
1342288004
-
The Jalview Java alignment editor
-
Clamp M., Cuff J., Searle S., Barton G. The Jalview Java alignment editor. Bioinformatics 2004, 20:426.
-
(2004)
Bioinformatics
, vol.20
, pp. 426
-
-
Clamp, M.1
Cuff, J.2
Searle, S.3
Barton, G.4
-
42
-
-
0029654258
-
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis
-
Sonnhammer E., Durbin R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 1995, 167:1-2.
-
(1995)
Gene
, vol.167
, pp. 1-2
-
-
Sonnhammer, E.1
Durbin, R.2
-
43
-
-
0003437299
-
-
Department of Genome Sciences, University of Washington, Seattle, WA, distributed by the author
-
Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6 2004, Department of Genome Sciences, University of Washington, Seattle, WA, distributed by the author.
-
(2004)
PHYLIP (Phylogeny Inference Package) Version 3.6
-
-
Felsenstein, J.1
-
44
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks G., Hon G., Chandonia J., Brenner S. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188.
-
(2004)
Genome Res.
, vol.14
, pp. 1188
-
-
Crooks, G.1
Hon, G.2
Chandonia, J.3
Brenner, S.4
|