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dissbib.bib
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@Article{ dreze_evidence_2011,
title = {Evidence for {Network} {Evolution} in an {Arabidopsis}
{Interactome} {Map}},
volume = {333},
issn = {0036-8075, 1095-9203},
language = {en},
number = {6042},
urldate = {2015-05-04},
journal = {Science},
author = {Dreze, Matija and Carvunis, Anne-Ruxandra and Charloteaux,
Benoit and Galli, Mary and Pevzner, Samuel J. and Tasan,
Murat and Ahn, Yong-Yeol and Balumuri, Padmavathi and
Barabási, Albert-László and Bautista, Vanessa and Braun,
Pascal and Byrdsong, Danielle and Chen, Huaming and
Chesnut, Jonathan D. and Cusick, Michael E. and Dangl,
Jeffery L. and Reyes, Chris de los and Dricot, Amélie and
Duarte, Melissa and Ecker, Joseph R. and Fan, Changyu and
Gai, Lantian and Gebreab, Fana and Ghoshal, Gourab and
Gilles, Patrick and Gutierrez, Bryan J. and Hao, Tong and
Hill, David E. and Kim, Christopher J. and Kim, Rosa Cheuk
and Lurin, Claire and MacWilliams, Andrew and Matrubutham,
Uday and Milenkovic, Tijana and Mirchandani, Jyotika and
Monachello, Dario and Moore, Jonathan and Mukhtar, M.
Shahid and Olivares, Eric and Patnaik, Suswapna and Poulin,
Matthew M. and Przulj, Natasa and Quan, Rosa and Rabello,
Sabrina and Ramaswamy, Gopalakrishna and Reichert, Patrick
and Rietman, Edward A. and Rolland, Thomas and Romero,
Viviana and Roth, Frederick P. and Santhanam, Balaji and
Schmitz, Robert J. and Shinn, Paul and Spooner, William and
Stein, Joshua and Swamilingiah, Geetha M. and Tam, Stanley
and Vandenhaute, Jean and Vidal, Marc and Waaijers, Selma
and Ware, Doreen and Weiner, Evan M. and Wu, Stacy and
Yazaki, Junshi},
month = jul,
year = {2011},
pmid = {21798944},
pages = {601--607},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/TZ886B67/Dreze
et al. - 2011 - Evidence for Network Evolution in an
Arabidopsis
I.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/GJTXG838/601.html:text/html}
}
@Article{ jolma_dna-binding_2013,
title = {{DNA}-{Binding} {Specificities} of {Human} {Transcription}
{Factors}},
volume = {152},
issn = {0092-8674},
language = {English},
number = {1},
urldate = {2015-12-21},
journal = {Cell},
author = {Jolma, Arttu and Yan, Jian and Whitington, Thomas and
Toivonen, Jarkko and Nitta, Kazuhiro R. and Rastas, Pasi
and Morgunova, Ekaterina and Enge, Martin and Taipale,
Mikko and Wei, Gonghong and Palin, Kimmo and Vaquerizas,
Juan M. and Vincentelli, Renaud and Luscombe, Nicholas M.
and Hughes, Timothy R. and Lemaire, Patrick and Ukkonen,
Esko and Kivioja, Teemu and Taipale, Jussi},
month = jan,
year = {2013},
pmid = {23332764},
pages = {327--339},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/RAEB5SNN/Jolma
et al. - 2013 - DNA-Binding Specificities of Human
Transcription
F.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/KD6TFSVN/S0092-8674(12)01496-1.html:text/html}
}
@Article{ brooks_evolution_2002,
title = {Evolution of {Amino} {Acid} {Frequencies} in {Proteins}
{Over} {Deep} {Time}: {Inferred} {Order} of {Introduction}
of {Amino} {Acids} into the {Genetic} {Code}},
volume = {19},
issn = {0737-4038, 1537-1719},
shorttitle = {Evolution of {Amino} {Acid} {Frequencies} in {Proteins}
{Over} {Deep} {Time}},
language = {en},
number = {10},
urldate = {2015-12-01},
journal = {Molecular Biology and Evolution},
author = {Brooks, Dawn J. and Fresco, Jacques R. and Lesk, Arthur M.
and Singh, Mona},
month = oct,
year = {2002},
pmid = {12270892},
pages = {1645--1655},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/7DVV6JJE/Brooks
et al. - 2002 - Evolution of Amino Acid Frequencies in
Proteins
Ov.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/AV9STCAK/1645.html:text/html}
}
@Article{ pal_integrated_2006,
title = {An integrated view of protein evolution},
volume = {7},
copyright = {© 2006 Nature Publishing Group},
issn = {1471-0056},
language = {en},
number = {5},
urldate = {2015-12-01},
journal = {Nature Reviews Genetics},
author = {Pál, Csaba and Papp, Balázs and Lercher, Martin J.},
month = may,
year = {2006},
pages = {337--348},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/ARZWQB7I/Pál
et al. - 2006 - An integrated view of protein
evolution.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/6M6JTK6R/nrg1838.html:text/html}
}
@Article{ heo_topology_2011,
title = {Topology of protein interaction network shapes protein
abundances and strengths of their functional and
nonspecific interactions},
volume = {108},
issn = {0027-8424, 1091-6490},
language = {en},
number = {10},
urldate = {2015-12-01},
journal = {Proceedings of the National Academy of Sciences},
author = {Heo, Muyoung and Maslov, Sergei and Shakhnovich, Eugene},
month = mar,
year = {2011},
pmid = {21368118},
keywords = {a multi-scale evolutionary model cell, evolution of
protein interface, genotype-phenotype relationship},
pages = {4258--4263},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/2RRAQ82A/Heo
et al. - 2011 - Topology of protein interaction network
shapes
pro.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/5UR2TNMN/4258.html:text/html}
}
@Article{ mannige_universal_2012,
title = {A {Universal} {Trend} among {Proteomes} {Indicates} an
{Oily} {Last} {Common} {Ancestor}},
volume = {8},
number = {12},
urldate = {2015-12-01},
journal = {PLoS Comput Biol},
author = {Mannige, Ranjan V. and Brooks, Charles L. and Shakhnovich,
Eugene I.},
month = dec,
year = {2012},
pages = {e1002839},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/6RJ4RZJF/Mannige
et al. - 2012 - A Universal Trend among Proteomes Indicates
an Oil.pdf:application/pdf}
}
@Article{ lehmann_consensus_2002,
title = {The consensus concept for thermostability engineering of
proteins: further proof of concept},
volume = {15},
issn = {1741-0126, 1741-0134},
shorttitle = {The consensus concept for thermostability engineering of
proteins},
language = {en},
number = {5},
urldate = {2015-12-01},
journal = {Protein Engineering},
author = {Lehmann, Martin and Loch, Claudia and Middendorf, Anke and
Studer, Dominik and Lassen, Søren F. and Pasamontes, Luis
and Loon, Adolphus P. G. M. van and Wyss, Markus},
month = may,
year = {2002},
pmid = {12034860},
keywords = {consensus sequence, phytase, protein engineering,
thermostabilization},
pages = {403--411},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/TE56BH4J/Lehmann
et al. - 2002 - The consensus concept for thermostability
engineer.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/NF4CTX53/403.html:text/html}
}
@Article{ sayou_promiscuous_2014,
title = {A {Promiscuous} {Intermediate} {Underlies} the {Evolution}
of {LEAFY} {DNA} {Binding} {Specificity}},
volume = {343},
issn = {0036-8075, 1095-9203},
language = {en},
number = {6171},
urldate = {2015-12-01},
journal = {Science},
author = {Sayou, Camille and Monniaux, Marie and Nanao, Max H. and
Moyroud, Edwige and Brockington, Samuel F. and Thévenon,
Emmanuel and Chahtane, Hicham and Warthmann, Norman and
Melkonian, Michael and Zhang, Yong and Wong, Gane Ka-Shu
and Weigel, Detlef and Parcy, François and Dumas, Renaud},
month = feb,
year = {2014},
pmid = {24436181},
pages = {645--648},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/ECJMVW4A/Sayou
et al. - 2014 - A Promiscuous Intermediate Underlies the
Evolution.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/ZMKTTUHH/645.html:text/html}
}
@Article{ hyland_model_2014,
title = {A {Model} for the {Evolution} of {Biological}
{Specificity}: a {Cross}-{Reacting} {DNA}-{Binding}
{Protein} {Causes} {Plasmid} {Incompatibility}},
volume = {196},
issn = {0021-9193, 1098-5530},
shorttitle = {A {Model} for the {Evolution} of {Biological}
{Specificity}},
language = {en},
number = {16},
urldate = {2015-12-01},
journal = {Journal of Bacteriology},
author = {Hyland, Edel M. and Wallace, Edward W. J. and Murray,
Andrew W.},
month = aug,
year = {2014},
pmid = {24914185},
pages = {3002--3011},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/V4AJ73EC/Hyland
et al. - 2014 - A Model for the Evolution of Biological
Specificit.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/CBBUXCC7/3002.html:text/html}
}
@Article{ stewart_evolution_2013,
title = {The evolution of complex gene regulation by
low-specificity binding sites},
volume = {280},
copyright = {© 2013 The Author(s) Published by the Royal Society. All
rights reserved.},
issn = {0962-8452, 1471-2954},
language = {en},
number = {1768},
urldate = {2015-12-01},
journal = {Proceedings of the Royal Society of London B: Biological
Sciences},
author = {Stewart, Alexander J. and Plotkin, Joshua B.},
month = oct,
year = {2013},
pmid = {23945682},
pages = {20131313},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/8T8N9MJW/Stewart
and Plotkin - 2013 - The evolution of complex gene
regulation by
low-sp.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/X5IDF3ZR/20131313.html:text/html}
}
@Article{ jager_global_2012,
title = {Global landscape of {HIV}-human protein complexes},
volume = {481},
copyright = {© 2011 Nature Publishing Group, a division of Macmillan
Publishers Limited. All Rights Reserved.},
issn = {0028-0836},
language = {en},
number = {7381},
urldate = {2015-12-01},
journal = {Nature},
author = {Jäger, Stefanie and Cimermancic, Peter and Gulbahce,
Natali and Johnson, Jeffrey R. and McGovern, Kathryn E. and
Clarke, Starlynn C. and Shales, Michael and Mercenne,
Gaelle and Pache, Lars and Li, Kathy and Hernandez, Hilda
and Jang, Gwendolyn M. and Roth, Shoshannah L. and Akiva,
Eyal and Marlett, John and Stephens, Melanie and D’Orso,
Iván and Fernandes, Jason and Fahey, Marie and Mahon,
Cathal and O’Donoghue, Anthony J. and Todorovic,
Aleksandar and Morris, John H. and Maltby, David A. and
Alber, Tom and Cagney, Gerard and Bushman, Frederic D. and
Young, John A. and Chanda, Sumit K. and Sundquist, Wesley
I. and Kortemme, Tanja and Hernandez, Ryan D. and Craik,
Charles S. and Burlingame, Alma and Sali, Andrej and
Frankel, Alan D. and Krogan, Nevan J.},
month = jan,
year = {2012},
keywords = {Biochemistry, Cell Biology, Computing science, Virology},
pages = {365--370},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/53G6WIBH/Jäger
et al. - 2012 - Global landscape of HIV-human protein
complexes.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/UX5PE33E/nature10719.html:text/html}
}
@Article{ amoutzias_one_2007,
title = {One {Billion} {Years} of {bZIP} {Transcription} {Factor}
{Evolution}: {Conservation} and {Change} in {Dimerization}
and {DNA}-{Binding} {Site} {Specificity}},
volume = {24},
issn = {0737-4038, 1537-1719},
shorttitle = {One {Billion} {Years} of {bZIP} {Transcription} {Factor}
{Evolution}},
language = {en},
number = {3},
urldate = {2015-12-01},
journal = {Molecular Biology and Evolution},
author = {Amoutzias, G. D. and Veron, A. S. and Weiner, J. and
Robinson-Rechavi, M. and Bornberg-Bauer, E. and Oliver, S.
G. and Robertson, D. L.},
month = mar,
year = {2007},
pmid = {17194801},
keywords = {bilateria, bZIP, dimerization, molecular evolution,
network, transcription factor},
pages = {827--835},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/MP9HUGNK/Amoutzias
et al. - 2007 - One Billion Years of bZIP Transcription
Factor
Evo.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/6NH2A3VQ/827.html:text/html}
}
@Article{ kim_rewiring_2012,
title = {Rewiring of {PDZ} {Domain}-{Ligand} {Interaction}
{Network} {Contributed} to {Eukaryotic} {Evolution}},
volume = {8},
number = {2},
urldate = {2015-12-01},
journal = {PLoS Genet},
author = {Kim, Jinho and Kim, Inhae and Yang, Jae-Seong and Shin,
Young-Eun and Hwang, Jihye and Park, Solip and Choi, Yoon
Sup and Kim, Sanguk},
month = feb,
year = {2012},
pages = {e1002510},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/7R39DNFP/Kim
et al. - 2012 - Rewiring of PDZ Domain-Ligand Interaction
Network .pdf:application/pdf}
}
@Article{ chica_evidence_2009,
title = {Evidence for the {Concerted} {Evolution} between {Short}
{Linear} {Protein} {Motifs} and {Their} {Flanking}
{Regions}},
volume = {4},
issn = {1932-6203},
number = {7},
urldate = {2015-12-01},
journal = {PLoS ONE},
author = {Chica, Claudia and Diella, Francesca and Gibson, Toby J.},
month = jul,
year = {2009},
pmid = {19584925},
pmcid = {PMC2702822},
file = {PubMed Central Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/KPF4XSE5/Chica
et al. - 2009 - Evidence for the Concerted Evolution
between Short.pdf:application/pdf}
}
@Article{ kapopoulou_evolution_2015,
title = {The evolution of gene expression and binding specificity
of the largest transcription factor family in primates},
copyright = {This article is protected by copyright. All rights
reserved},
issn = {1558-5646},
language = {en},
urldate = {2015-12-04},
journal = {Evolution},
author = {Kapopoulou, Adamandia and Mathew, Lisha and Wong, Alex and
Trono, Didier and Jensen, Jeffrey D.},
month = nov,
year = {2015},
keywords = {DNA-contacting residues, endogenous retroelements,
KRAB-containing zinc-finger genes, population genetics,
regulatory evolution, transcription factors},
pages = {n/a--n/a},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/VXFRSCVF/Kapopoulou
et al. - 2015 - The evolution of gene expression and
binding
speci.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/NPIMGPTR/abstract.html:text/html}
}
@Article{ verschueren_evolution_2015,
title = {Evolution of the {SH}3 {Domain} {Specificity} {Landscape}
in {Yeasts}},
volume = {10},
number = {6},
urldate = {2015-12-04},
journal = {PLoS ONE},
author = {Verschueren, Erik and Spiess, Matthias and Gkourtsa, Areti
and Avula, Teja and Landgraf, Christiane and Mancilla,
Victor Tapia and Huber, Aline and Volkmer, Rudolf and
Winsor, Barbara and Serrano, Luis and Hochstenbach, Frans
and Distel, Ben},
month = jun,
year = {2015},
pages = {e0129229},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/U64GK5BS/Verschueren
et al. - 2015 - Evolution of the SH3 Domain Specificity
Landscape .pdf:application/pdf}
}
@Article{ hong_molecular_2014,
title = {Molecular {Specificity}, {Convergence} and {Constraint}
{Shape} {Adaptive} {Evolution} in {Nutrient}-{Poor}
{Environments}},
volume = {10},
number = {1},
urldate = {2015-12-04},
journal = {PLoS Genet},
author = {Hong, Jungeui and Gresham, David},
month = jan,
year = {2014},
pages = {e1004041},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/9C5J9JVK/Hong
and Gresham - 2014 - Molecular Specificity, Convergence and
Constraint .pdf:application/pdf}
}
@Article{ taylor_directed_2015,
title = {Directed evolution of the substrate specificity of
dialkylglycine decarboxylase},
volume = {1854},
issn = {1570-9639},
number = {2},
urldate = {2015-12-04},
journal = {Biochimica et Biophysica Acta (BBA) - Proteins and
Proteomics},
author = {Taylor, Jared L. and Price, Joseph E. and Toney, Michael
D.},
month = feb,
year = {2015},
keywords = {Conformational change, Dialkylglycine decarboxylase,
Directed evolution, Genetic selection, Pyridoxal phosphate,
Stereoelectronic effect},
pages = {146--155},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/QAVRFZVM/S1570963914003197.html:text/html}
}
@Article{ ito_evolution_2014,
title = {Evolution of a {New} {Chlorophyll} {Metabolic} {Pathway}
{Driven} by the {Dynamic} {Changes} in {Enzyme}
{Promiscuous} {Activity}},
volume = {55},
issn = {0032-0781, 1471-9053},
language = {en},
number = {3},
urldate = {2015-12-04},
journal = {Plant and Cell Physiology},
author = {Ito, Hisashi and Tanaka, Ayumi},
month = mar,
year = {2014},
pmid = {24399236},
keywords = {Chlorophyll biosynthesis, Divinyl chlorophyll, Pathway
evolution, Promiscuous activity, Synechocystis},
pages = {593--603},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/HVWGKM34/Ito
and Tanaka - 2014 - Evolution of a New Chlorophyll
Metabolic Pathway
D.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/M9J2W3EH/593.html:text/html}
}
@Article{ fuentes_thermodynamic_2015,
title = {Thermodynamic and {Dynamic} {Basis} for the {Broadened}
{Ligand} {Specificity} of a {Tiam}2 {PDZ} {Domain}
{Mutant}},
volume = {108},
issn = {0006-3495},
language = {English},
number = {2},
urldate = {2015-12-04},
journal = {Biophysical Journal},
author = {Fuentes, Ernesto J. and Liu, Xu and Golden, Lisa C. and
Yu, Liping},
month = jan,
year = {2015},
pages = {60a},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/X2WEG4SW/Fuentes
et al. - 2015 - Thermodynamic and Dynamic Basis for the
Broadened
.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/TP4FWQ7S/S0006-3495(14)01569-0.html:text/html}
}
@Article{ jarvela_modular_2014,
title = {Modular {Evolution} of {DNA}-{Binding} {Preference} of a
{Tbrain} {Transcription} {Factor} {Provides} a {Mechanism}
for {Modifying} {Gene} {Regulatory} {Networks}},
volume = {31},
issn = {0737-4038, 1537-1719},
language = {en},
number = {10},
urldate = {2015-12-04},
journal = {Molecular Biology and Evolution},
author = {Jarvela, Alys M. Cheatle and Brubaker, Lisa and Vedenko,
Anastasia and Gupta, Anisha and Armitage, Bruce A. and
Bulyk, Martha L. and Hinman, Veronica F.},
month = oct,
year = {2014},
pmid = {25016582},
keywords = {echinoderm, evo-devo, Evolution, gene regulatory networks,
T-box, transcription factors},
pages = {2672--2688},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/UV4SVB9G/Jarvela
et al. - 2014 - Modular Evolution of DNA-Binding Preference
of a
T.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/C5AS5NJ3/2672.html:text/html}
}
@Article{ hudson_structure_2014,
title = {The structure, function and evolution of proteins that
bind {DNA} and {RNA}},
volume = {15},
copyright = {© 2014 Nature Publishing Group, a division of Macmillan
Publishers Limited. All Rights Reserved.},
issn = {1471-0072},
language = {en},
number = {11},
urldate = {2015-12-04},
journal = {Nature Reviews Molecular Cell Biology},
author = {Hudson, William H. and Ortlund, Eric A.},
month = nov,
year = {2014},
keywords = {DNA-binding proteins, Long non-coding RNAs, RNA-binding
proteins, X-ray crystallography},
pages = {749--760},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/3ADW976T/Hudson
and Ortlund - 2014 - The structure, function and evolution
of proteins
.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/N6XGTEVS/nrm3884.html:text/html}
}
@Article{ yamamoto_integrative_2014,
title = {An integrative evolution theory of histo-blood group {ABO}
and related genes},
volume = {4},
issn = {2045-2322},
urldate = {2015-12-04},
journal = {Scientific Reports},
author = {Yamamoto, Fumiichiro and Cid, Emili and Yamamoto, Miyako
and Saitou, Naruya and Bertranpetit, Jaume and Blancher,
Antoine},
month = oct,
year = {2014},
pages = {6601}
}
@Article{ kaltenbach_dynamics_2014,
title = {Dynamics and constraints of enzyme evolution},
volume = {322},
copyright = {© 2014 Wiley Periodicals, Inc.},
issn = {1552-5015},
language = {en},
number = {7},
urldate = {2015-12-04},
journal = {Journal of Experimental Zoology Part B: Molecular and
Developmental Evolution},
author = {Kaltenbach, Miriam and Tokuriki, Nobuhiko},
month = nov,
year = {2014},
pages = {468--487},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/43RV6JS3/Kaltenbach
and Tokuriki - 2014 - Dynamics and constraints of enzyme
evolution.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/FW3P7I4G/abstract.html:text/html}
}
@Article{ nadimpalli_pervasive_2015,
title = {Pervasive {Variation} of {Transcription} {Factor}
{Orthologs} {Contributes} to {Regulatory} {Network}
{Evolution}},
volume = {11},
number = {3},
urldate = {2015-12-04},
journal = {PLoS Genet},
author = {Nadimpalli, Shilpa and Persikov, Anton V. and Singh,
Mona},
month = mar,
year = {2015},
pages = {e1005011},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/V4GKRUR6/Nadimpalli
et al. - 2015 - Pervasive Variation of Transcription Factor
Orthol.pdf:application/pdf}
}
@Article{ martinezcuesta_classification_2015,
title = {The {Classification} and {Evolution} of {Enzyme}
{Function}},
volume = {109},
issn = {0006-3495},
number = {6},
urldate = {2015-12-04},
journal = {Biophysical Journal},
author = {Martínez Cuesta, Sergio and Rahman, Syed Asad and
Furnham, Nicholas and Thornton, Janet M.},
month = sep,
year = {2015},
pages = {1082--1086},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/MGMEIJ2I/S0006349515004002.html:text/html}
}
@Article{ eick_evolution_2012,
title = {Evolution of {Minimal} {Specificity} and {Promiscuity} in
{Steroid} {Hormone} {Receptors}},
volume = {8},
issn = {1553-7390},
number = {11},
urldate = {2015-12-07},
journal = {PLoS Genetics},
author = {Eick, Geeta N. and Colucci, Jennifer K. and Harms, Michael
J. and Ortlund, Eric A. and Thornton, Joseph W.},
month = nov,
year = {2012},
pmid = {23166518},
pmcid = {PMC3499368},
file = {PubMed Central Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/WN628SSI/Eick
et al. - 2012 - Evolution of Minimal Specificity and
Promiscuity i.pdf:application/pdf}
}
@Article{ crocker_low_2015,
title = {Low {Affinity} {Binding} {Site} {Clusters} {Confer} {Hox}
{Specificity} and {Regulatory} {Robustness}},
volume = {160},
issn = {0092-8674},
number = {1–2},
urldate = {2015-12-04},
journal = {Cell},
author = {Crocker, Justin and Abe, Namiko and Rinaldi, Lucrezia and
McGregor, Alistair P. and Frankel, Nicolás and Wang, Shu
and Alsawadi, Ahmad and Valenti, Philippe and Plaza, Serge
and Payre, François and Mann, Richard S. and Stern,
David L.},
month = jan,
year = {2015},
pages = {191--203},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/XMQEZT9A/S0092867414015189.html:text/html}
}
@Article{ noda-garcia_insights_2015,
title = {Insights into the evolution of enzyme substrate
promiscuity after the discovery of (βα)8 isomerase
evolutionary intermediates from a diverse metagenome},
volume = {15},
copyright = {2015 Noda-García et al.},
issn = {1471-2148},
language = {en},
number = {1},
urldate = {2015-12-04},
journal = {BMC Evolutionary Biology},
author = {Noda-García, Lianet and Juárez-Vázquez, Ana L. and
Ávila-Arcos, María C. and Verduzco-Castro, Ernesto A. and
Montero-Morán, Gabriela and Gaytán, Paul and
Carrillo-Tripp, Mauricio and Barona-Gómez, Francisco},
month = jun,
year = {2015},
pmid = {26058375},
pages = {107},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/S7A78QIS/Noda-García
et al. - 2015 - Insights into the evolution of enzyme
substrate
pr.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/7E43BWRK/107.html:text/html}
}
@Article{ murren_constraints_2015,
title = {Constraints on the evolution of phenotypic plasticity:
limits and costs of phenotype and plasticity},
volume = {115},
copyright = {© 2015 Nature Publishing Group},
issn = {0018-067X},
shorttitle = {Constraints on the evolution of phenotypic plasticity},
language = {en},
number = {4},
urldate = {2015-12-04},
journal = {Heredity},
author = {Murren, C. J. and Auld, J. R. and Callahan, H. and
Ghalambor, C. K. and Handelsman, C. A. and Heskel, M. A.
and Kingsolver, J. G. and Maclean, H. J. and Masel, J. and
Maughan, H. and Pfennig, D. W. and Relyea, R. A. and
Seiter, S. and Snell-Rood, E. and Steiner, U. K. and
Schlichting, C. D.},
month = oct,
year = {2015},
pages = {293--301},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/WHJEPKPX/Murren
et al. - 2015 - Constraints on the evolution of phenotypic
plastic.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/K6TTB753/hdy20158a.html:text/html}
}
@Article{ lathe_steroid_2015,
series = {Steroid/{Sterol} {Signaling} – {Promiscuity} and
{Diversity}},
title = {Steroid promiscuity: {Diversity} of enzyme action},
volume = {151},
issn = {0960-0760},
shorttitle = {Steroid promiscuity},
urldate = {2015-12-05},
journal = {The Journal of Steroid Biochemistry and Molecular
Biology},
author = {Lathe, Richard and Kotelevtsev, Yuri and Mason, J. Ian},
month = jul,
year = {2015},
keywords = {promiscuity, Steroid},
pages = {1--2},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/CMRWQ4IQ/S0960076015000102.html:text/html}
}
@Article{ moghe_something_2015,
title = {Something {Old}, {Something} {New}: {Conserved} {Enzymes}
and the {Evolution} of {Novelty} in {Plant} {Specialized}
{Metabolism}},
volume = {169},
issn = {, 1532-2548},
shorttitle = {Something {Old}, {Something} {New}},
language = {en},
number = {3},
urldate = {2015-12-05},
journal = {Plant Physiology},
author = {Moghe, Gaurav D. and Last, Robert L.},
month = nov,
year = {2015},
pmid = {26276843},
pages = {1512--1523},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/US4G447F/Moghe
and Last - 2015 - Something Old, Something New Conserved
Enzymes
an.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/4IZU6NFU/1512.html:text/html}
}
@Article{ voordeckers_reconstruction_2012,
title = {Reconstruction of {Ancestral} {Metabolic} {Enzymes}
{Reveals} {Molecular} {Mechanisms} {Underlying}
{Evolutionary} {Innovation} through {Gene} {Duplication}},
volume = {10},
number = {12},
urldate = {2015-12-07},
journal = {PLoS Biol},
author = {Voordeckers, Karin and Brown, Chris A. and Vanneste, Kevin
and van der Zande, Elisa and Voet, Arnout and Maere, Steven
and Verstrepen, Kevin J.},
month = dec,
year = {2012},
pages = {e1001446},
file = {PLoS Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/64UHHSX2/Voordeckers
et al. - 2012 - Reconstruction of Ancestral Metabolic
Enzymes Reve.pdf:application/pdf}
}
@Article{ glembo_collective_2012,
title = {Collective {Dynamics} {Differentiates} {Functional}
{Divergence} in {Protein} {Evolution}},
volume = {8},
issn = {1553-734X},
number = {3},
urldate = {2015-12-08},
journal = {PLoS Computational Biology},
author = {Glembo, Tyler J. and Farrell, Daniel W. and Gerek, Z.
Nevin and Thorpe, M. F. and Ozkan, S. Banu},
month = mar,
year = {2012},
pmid = {22479170},
pmcid = {PMC3315450},
file = {PubMed Central Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/XGKP7NS9/Glembo
et al. - 2012 - Collective Dynamics Differentiates
Functional Dive.pdf:application/pdf}
}
@Article{ khersonsky_enzyme_2010,
title = {Enzyme {Promiscuity}: {A} {Mechanistic} and {Evolutionary}
{Perspective}},
volume = {79},
shorttitle = {Enzyme {Promiscuity}},
number = {1},
urldate = {2015-12-08},
journal = {Annual Review of Biochemistry},
author = {Khersonsky, Olga and Tawfik, Dan S.},
year = {2010},
pmid = {20235827},
keywords = {enzyme mechanism, protein evolution, superfamilies},
pages = {471--505},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/3GP3PCZI/Khersonsky
and Tawfik - 2010 - Enzyme Promiscuity A Mechanistic and
Evolutionary.pdf:application/pdf}
}
@Article{ nobeli_protein_2009,
title = {Protein promiscuity and its implications for
biotechnology},
volume = {27},
copyright = {© 2009 Nature Publishing Group},
issn = {1087-0156},
language = {en},
number = {2},
urldate = {2015-12-08},
journal = {Nature Biotechnology},
author = {Nobeli, Irene and Favia, Angelo D. and Thornton, Janet
M.},
month = feb,
year = {2009},
pages = {157--167},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/CI4Q7855/Nobeli
et al. - 2009 - Protein promiscuity and its implications
for
biote.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/M62A2ITK/nbt1519.html:text/html}
}
@Article{ aharoni_evolvability_2005,
title = {The 'evolvability' of promiscuous protein functions},
volume = {37},
copyright = {© 2004 Nature Publishing Group},
issn = {1061-4036},
language = {en},
number = {1},
urldate = {2015-12-08},
journal = {Nature Genetics},
author = {Aharoni, Amir and Gaidukov, Leonid and Khersonsky, Olga
and Gould, Stephen McQ and Roodveldt, Cintia and Tawfik,
Dan S.},
month = jan,
year = {2005},
pages = {73--76},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/V9XQHJ2P/Aharoni
et al. - 2005 - The 'evolvability' of promiscuous protein
function.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/P38VAMCN/ng1482.html:text/html}
}
@Article{ zou_evolution_2015,
title = {Evolution of {Conformational} {Dynamics} {Determines} the
{Conversion} of a {Promiscuous} {Generalist} into a
{Specialist} {Enzyme}},
volume = {32},
issn = {0737-4038, 1537-1719},
language = {en},
number = {1},
urldate = {2015-12-08},
journal = {Molecular Biology and Evolution},
author = {Zou, Taisong and Risso, Valeria A. and Gavira, Jose A. and
Sanchez-Ruiz, Jose M. and Ozkan, S. Banu},
month = jan,
year = {2015},
pmid = {25312912},
keywords = {ancestral enzyme, molecular dynamics, protein dynamics and
structure},
pages = {132--143},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/G2ASA3WD/Zou
et al. - 2015 - Evolution of Conformational Dynamics
Determines
th.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/DCT8SQJF/132.html:text/html}
}
@Article{ chemes_convergent_2015,
series = {New constructs and expression of proteins / {Sequences}
and topology},
title = {Convergent evolution and mimicry of protein linear motifs
in host–pathogen interactions},
volume = {32},
issn = {0959-440X},
urldate = {2015-12-08},
journal = {Current Opinion in Structural Biology},
author = {Chemes, Lucía Beatriz and de Prat-Gay, Gonzalo and
Sánchez, Ignacio Enrique},
month = jun,
year = {2015},
pages = {91--101},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/Q6EF7PDS/S0959440X15000317.html:text/html}
}
@Article{ via_how_2015,
title = {How pathogens use linear motifs to perturb host cell
networks},
volume = {40},
issn = {0968-0004},
number = {1},
urldate = {2015-12-08},
journal = {Trends in Biochemical Sciences},
author = {Via, Allegra and Uyar, Bora and Brun, Christine and
Zanzoni, Andreas},
month = jan,
year = {2015},
keywords = {host–pathogen interactions, molecular mimicry, short
linear motifs, SLiMs, virulence},
pages = {36--48},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/SIQHEE5V/S0968000414002059.html:text/html}
}
@Article{ peleg_evolution_2014,
title = {Evolution of {Specificity} in {Protein}-{Protein}
{Interactions}},
volume = {107},
issn = {0006-3495},
number = {7},
urldate = {2015-12-08},
journal = {Biophysical Journal},
author = {Peleg, Orit and Choi, Jeong-Mo and Shakhnovich,
Eugene I.},
month = oct,
year = {2014},
pages = {1686--1696},
file = {ScienceDirect
Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/PZDVF9EQ/S0006349514008418.html:text/html}
}
@Article{ lukatsky_sequence_2011,
title = {Sequence correlations shape protein promiscuity},
volume = {135},
issn = {0021-9606, 1089-7690},
number = {6},
urldate = {2015-12-08},
journal = {The Journal of Chemical Physics},
author = {Lukatsky, David B. and Afek, Ariel and Shakhnovich, Eugene
I.},
month = aug,
year = {2011},
keywords = {Acids, Protein folding, Proteins, Sequence analysis,
Statistical properties},
pages = {065104},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/G66I3BXK/Lukatsky
et al. - 2011 - Sequence correlations shape protein
promiscuity.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/VQTV52C9/1.html:text/html}
}
@Article{ mosca_role_2012,
title = {The {Role} of {Structural} {Disorder} in the {Rewiring} of
{Protein} {Interactions} through {Evolution}},
volume = {11},
issn = {1535-9476, 1535-9484},
language = {en},
number = {7},
urldate = {2015-12-10},
journal = {Molecular \& Cellular Proteomics},
author = {Mosca, Roberto and Pache, Roland A. and Aloy, Patrick},
month = jul,
year = {2012},
pmid = {22389433},
pages = {M111.014969},
file = {Full Text
PDF:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/JPFF572N/Mosca
et al. - 2012 - The Role of Structural Disorder in the
Rewiring
of.pdf:application/pdf;Snapshot:/home/luke/.zotero/zotero/1fr5c5dx.default/zotero/storage/6C3DQHFK/M111.014969.html:text/html}
}
@Article{ capra_spatial_2012,
title = {Spatial tethering of kinases to their substrates relaxes
evolutionary constraints on specificity},
volume = {86},