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Evolution of protein complexes by duplication of homomeric interactions
Jose B Pereira-Leal, Emmanuel D Levy, Christel Kamp, Sarah A Teichmann
Genome Biol. 2007; 8(4): R51. Published online 2007 April 5. doi: 10.1186/gb-2007-8-4-r51
PMCID:
PMC1895999
Abstract Full Text PDF–576K Supplementary Material
 Is Cited by the Following 28 Articles in this Archive:
Modularity in Protein Complex and Drug Interactions Reveals New Polypharmacological Properties
Jose C. Nacher, Jean-Marc Schwartz
PLoS One. 2012; 7(1): e30028. Published online 2012 January 18. doi: 10.1371/journal.pone.0030028
PMCID:
PMC3261189
Abstract Full Text PDF–1.9M Supplementary Material
The Human Genome Retains Relics of Its Prokaryotic Ancestry: Human Genes of Archaebacterial and Eubacterial Origin Exhibit Remarkable Differences
David Alvarez-Ponce, James O. McInerney
Genome Biol Evol. 2011; 3: 782–790. Published online 2011 July 27. doi: 10.1093/gbe/evr073
PMCID:
PMC3163467
Abstract Full Text PDF–193K
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs
Zhongyang Liu, Qijun Liu, Hanchang Sun, Lin Hou, Hao Guo, Yunping Zhu, Dong Li, Fuchu He
BMC Evol Biol. 2011; 11: 133. Published online 2011 May 20. doi: 10.1186/1471-2148-11-133
PMCID:
PMC3128043
Abstract Full Text PDF–911K Supplementary Material
Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization
Martin Seizl, Laurent Larivière, Toni Pfaffeneder, Larissa Wenzeck, Patrick Cramer
Nucleic Acids Res. 2011 August; 39(14): 6291–6304. Published online 2011 April 15. doi: 10.1093/nar/gkr229
PMCID:
PMC3152362
Abstract Full Text PDF–14M Supplementary Material
Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions
Saket Navlakha, Carl Kingsford
PLoS Comput Biol. 2011 April; 7(4): e1001119. Published online 2011 April 14. doi: 10.1371/journal.pcbi.1001119
PMCID:
PMC3077358
Abstract Full Text PDF–1.8M
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Todd J. Treangen, Eduardo P. C. Rocha
PLoS Genet. 2011 January; 7(1): e1001284. Published online 2011 January 27. doi: 10.1371/journal.pgen.1001284
PMCID:
PMC3029252
Abstract Full Text PDF–713K Supplementary Material
Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR
Nan Hao, Murray L. Whitelaw, Keith E. Shearwin, Ian B. Dodd, Anne Chapman-Smith
Nucleic Acids Res. 2011 May; 39(9): 3695–3709. Published online 2011 January 17. doi: 10.1093/nar/gkq1336
PMCID:
PMC3089468
Abstract Full Text PDF–9.8M Supplementary Material
The role of exon shuffling in shaping protein-protein interaction networks
Douglas V Cancherini, Gustavo S França, Sandro J de Souza
BMC Genomics. 2010; 11(Suppl 5): S11. Published online 2010 December 22. doi: 10.1186/1471-2164-11-S5-S11
PMCID:
PMC3045794
Abstract Full Text PDF–460K Supplementary Material
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
Kosuke Hashimoto, Anna R. Panchenko
Proc Natl Acad Sci U S A. 2010 November 23; 107(47): 20352–20357. Published online 2010 November 3. doi: 10.1073/pnas.1012999107
PMCID:
PMC2996646
Abstract Full Text PDF–703K Supplementary Material
Duplicability of self-interacting human genes
Åsa Pérez-Bercoff, Takashi Makino, Aoife McLysaght
BMC Evol Biol. 2010; 10: 160. Published online 2010 May 28. doi: 10.1186/1471-2148-10-160
PMCID:
PMC2894830
Abstract Full Text PDF–686K Supplementary Material
The Role of Recently Derived FT Paralogs in Sunflower Domestication
Benjamin K. Blackman, Jared L. Strasburg, Andrew R. Raduski, Scott D. Michaels, Loren H. Rieseberg
Curr Biol. Author manuscript; available in PMC 2011 April 13.
Published in final edited form as: Curr Biol. 2010 April 13; 20(7): 629–635. Published online 2010 March 18. doi: 10.1016/j.cub.2010.01.059
PMCID:
PMC2898918
Abstract Full Text PDF–1.4M Supplementary Material
Comparative evolutionary analysis of protein complexes in E. coli and yeast
Adam J Reid, Juan AG Ranea, Christine A Orengo
BMC Genomics. 2010; 11: 79. Published online 2010 February 1. doi: 10.1186/1471-2164-11-79
PMCID:
PMC2837643
Abstract Full Text PDF–708K Supplementary Material
Evolution of Protein Binding Modes in Homooligomers
Judith E. Dayhoff, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko
J Mol Biol. Author manuscript; available in PMC 2010 January 29.
Published in final edited form as: J Mol Biol. 2010 January 29; 395(4): 860. Published online 2009 October 30. doi: 10.1016/j.jmb.2009.10.052
PMCID:
PMC2813322
Abstract Full Text PDF–2.0M Supplementary Material
From evidence to inference: probing the evolution of protein interaction networks
Oliver Ratmann, Carsten Wiuf, John W. Pinney
HFSP J. 2009 October; 3(5): 290–306. Published online 2009 October 19. doi: 10.2976/1.3167215
PMCID:
PMC2801530
Abstract Full Text PDF–380K
The Modular Organization of Protein Interactions in Escherichia coli
José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson
PLoS Comput Biol. 2009 October; 5(10): e1000523. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000523
PMCID:
PMC2739439
Abstract Full Text PDF–1.0M Supplementary Material
A complex-centric view of protein network evolution
Nir Yosef, Martin Kupiec, Eytan Ruppin, Roded Sharan
Nucleic Acids Res. 2009 July; 37(12): e88. Published online 2009 July. doi: 10.1093/nar/gkp414
PMCID:
PMC2709590
Abstract Full Text PDF–644K Supplementary Material
Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species
Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, Nevan J. Krogan
PLoS Biol. 2009 June; 7(6): e1000134. Published online 2009 June 23. doi: 10.1371/journal.pbio.1000134
Correction in:
PLoS Biol. 2009 November; 7(11): 10.1371/annotation/66479889-5e57-4213-bf25-c4e8cf3d933b.
PMCID:
PMC2691599
Abstract Full Text PDF–659K Supplementary Material Correction
Is protein classification necessary? Towards alternative approaches to function annotation
Donald Petrey, Barry Honig
Curr Opin Struct Biol. Author manuscript; available in PMC 2009 December 1.
Published in final edited form as: Curr Opin Struct Biol. 2009 June; 19(3): 363–368. Published online 2009 March 5. doi: 10.1016/j.sbi.2009.02.001
PMCID:
PMC2745633
Abstract Full Text PDF–380K
Questioning the Ubiquity of Neofunctionalization
Todd A. Gibson, Debra S. Goldberg
PLoS Comput Biol. 2009 January; 5(1): e1000252. Published online 2009 January 2. doi: 10.1371/journal.pcbi.1000252
PMCID:
PMC2597716
Abstract Full Text PDF–391K Supplementary Material
An evolutionary and structural characterization of mammalian protein complex organization
Philip Wong, Sonja Althammer, Andrea Hildebrand, Andreas Kirschner, Philipp Pagel, Bernd Geissler, Pawel Smialowski, Florian Blöchl, Matthias Oesterheld, Thorsten Schmidt, Normann Strack, Fabian J Theis, Andreas Ruepp, Dmitrij Frishman
BMC Genomics. 2008; 9: 629. Published online 2008 December 23. doi: 10.1186/1471-2164-9-629
PMCID:
PMC2645396
Abstract Full Text PDF–1.1M Supplementary Material
Complex fate of paralogs
Radek Szklarczyk, Martijn A Huynen, Berend Snel
BMC Evol Biol. 2008; 8: 337. Published online 2008 December 18. doi: 10.1186/1471-2148-8-337
PMCID:
PMC2628386
Abstract Full Text PDF–1.9M Supplementary Material
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
Wan Kyu Kim, Edward M. Marcotte
PLoS Comput Biol. 2008 November; 4(11): e1000232. Published online 2008 November 28. doi: 10.1371/journal.pcbi.1000232
PMCID:
PMC2583957
Abstract Full Text PDF–402K Supplementary Material
Assembly reflects evolution of protein complexes
Emmanuel D. Levy, Elisabetta Boeri Erba, Carol V. Robinson, Sarah A. Teichmann
Nature. Author manuscript; available in PMC 2009 March 19.
Published in final edited form as: Nature. 2008 June 26; 453(7199): 1262–1265. Published online 2008 June 18. doi: 10.1038/nature06942
PMCID:
PMC2658002
Abstract Full Text PDF–1.5M Supplementary Material
Large-scale screening for novel low-affinity extracellular protein interactions
K. Mark Bushell, Christian Söllner, Benjamin Schuster-Boeckler, Alex Bateman, Gavin J. Wright
Genome Res. 2008 April; 18(4): 622–630. doi: 10.1101/gr.7187808
PMCID:
PMC2279249
Abstract Full Text PDF–776K
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
Aviva Presser, Michael B. Elowitz, Manolis Kellis, Roy Kishony
Proc Natl Acad Sci U S A. 2008 January 22; 105(3): 950–954. Published online 2008 January 16. doi: 10.1073/pnas.0707293105
PMCID:
PMC2242688
Abstract Full Text PDF–438K Supplementary Material
A simple principle concerning the robustness of protein complex activity to changes in gene expression
Jennifer I Semple, Tanya Vavouri, Ben Lehner
BMC Syst Biol. 2008; 2: 1. Published online 2008 January 2. doi: 10.1186/1752-0509-2-1
PMCID:
PMC2242779
Abstract Full Text PDF–401K Supplementary Material
Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution
Filipe G Vieira, Alejandro Sánchez-Gracia, Julio Rozas
Genome Biol. 2007; 8(11): R235. Published online 2007 November 8. doi: 10.1186/gb-2007-8-11-r235
PMCID:
PMC2258175
Abstract Full Text PDF–1.4M Supplementary Material
Multiple domain insertions and losses in the evolution of the Rab prenylation complex
Rita Rasteiro, Jose B Pereira-Leal
BMC Evol Biol. 2007; 7: 140. Published online 2007 August 17. doi: 10.1186/1471-2148-7-140
PMCID:
PMC1994686
Abstract Full Text PDF–610K Supplementary Material
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