TY - JOUR AU - Golding, G. B. PY - 1999 DA - 1999// TI - Simple sequence is abundant in eukaryotic proteins JO - Protein Sci VL - 8 UR - https://doi.org/10.1110/ps.8.6.1358 DO - 10.1110/ps.8.6.1358 ID - Golding1999 ER - TY - JOUR AU - Wootton, J. C. AU - Federhen, S. PY - 1996 DA - 1996// TI - Analysis of compositionally biased regions in sequence databases JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66035-2 DO - 10.1016/S0076-6879(96)66035-2 ID - Wootton1996 ER - TY - JOUR AU - Green, H. AU - Wang, N. PY - 1994 DA - 1994// TI - Codon reiteration and the evolution of proteins JO - Proc Natl Acad Sci U S A VL - 91 UR - https://doi.org/10.1073/pnas.91.10.4298 DO - 10.1073/pnas.91.10.4298 ID - Green1994 ER - TY - JOUR AU - Karlin, S. AU - Brocchieri, L. AU - Bergman, A. AU - Mrazek, J. AU - Gentles, A. J. PY - 2002 DA - 2002// TI - Amino acid runs in eukaryotic proteomes and disease associations JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.012608599 DO - 10.1073/pnas.012608599 ID - Karlin2002 ER - TY - JOUR AU - Alba, M. M. AU - Guigo, R. PY - 2004 DA - 2004// TI - Comparative analysis of amino acid repeats in rodents and humans JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1925704 DO - 10.1101/gr.1925704 ID - Alba2004 ER - TY - JOUR AU - Alba, M. M. AU - Tompa, P. AU - Veitia, R. A. PY - 2007 DA - 2007// TI - Amino acid repeats and the structure and evolution of proteins JO - Genome Dyn VL - 3 UR - https://doi.org/10.1159/000107607 DO - 10.1159/000107607 ID - Alba2007 ER - TY - JOUR AU - Nishizawa, K. AU - Nishizawa, M. AU - Kim, K. S. PY - 1999 DA - 1999// TI - Tendency for local repetitiveness in amino acid usages in modern proteins JO - J Mol Biol VL - 294 UR - https://doi.org/10.1006/jmbi.1999.3275 DO - 10.1006/jmbi.1999.3275 ID - Nishizawa1999 ER - TY - JOUR AU - Alba, M. M. AU - Laskowski, R. A. AU - Hancock, J. M. PY - 2002 DA - 2002// TI - Detecting cryptically simple protein sequences using the SIMPLE algorithm JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.5.672 DO - 10.1093/bioinformatics/18.5.672 ID - Alba2002 ER - TY - JOUR AU - Levinson, G. AU - Gutman, G. A. PY - 1987 DA - 1987// TI - Slipped-strand mispairing: a major mechanism for DNA sequence evolution JO - Mol Biol Evol VL - 4 ID - Levinson1987 ER - TY - JOUR AU - Alba, M. M. AU - Santibanez-Koref, M. F. AU - Hancock, J. M. PY - 1999 DA - 1999// TI - Conservation of polyglutamine tract size between mice and humans depends on codon interruption JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026077 DO - 10.1093/oxfordjournals.molbev.a026077 ID - Alba1999 ER - TY - JOUR AU - Mularoni, L. AU - Veitia, R. A. AU - Alba, M. M. PY - 2007 DA - 2007// TI - Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats JO - Genomics VL - 89 UR - https://doi.org/10.1016/j.ygeno.2006.11.011 DO - 10.1016/j.ygeno.2006.11.011 ID - Mularoni2007 ER - TY - JOUR AU - Rorick, M. M. AU - Wagner, G. P. PY - 2010 DA - 2010// TI - The origin of conserved protein domains and amino acid repeats via adaptive competition for control over amino acid residues JO - J Mol Evol VL - 70 UR - https://doi.org/10.1007/s00239-009-9305-7 DO - 10.1007/s00239-009-9305-7 ID - Rorick2010 ER - TY - JOUR AU - Faux, N. G. AU - Bottomley, S. P. AU - Lesk, A. M. AU - Irving, J. A. AU - Morrison, J. R. AU - de la Banda, M. G. AU - Whisstock, J. C. PY - 2005 DA - 2005// TI - Functional insights from the distribution and role of homopeptide repeat-containing proteins JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3096505 DO - 10.1101/gr.3096505 ID - Faux2005 ER - TY - JOUR AU - Brown, L. AU - Paraso, M. AU - Arkell, R. AU - Brown, S. PY - 2005 DA - 2005// TI - In vitro analysis of partial loss-of-function ZIC2 mutations in holoprosencephaly: alanine tract expansion modulates DNA binding and transactivation JO - Hum Mol Genet VL - 14 UR - https://doi.org/10.1093/hmg/ddi037 DO - 10.1093/hmg/ddi037 ID - Brown2005 ER - TY - JOUR AU - Gerber, H. P. AU - Seipel, K. AU - Georgiev, O. AU - Hofferer, M. AU - Hug, M. AU - Rusconi, S. AU - Schaffner, W. PY - 1994 DA - 1994// TI - Transcriptional activation modulated by homopolymeric glutamine and proline stretches JO - Science VL - 263 UR - https://doi.org/10.1126/science.8303297 DO - 10.1126/science.8303297 ID - Gerber1994 ER - TY - JOUR AU - Galant, R. AU - Carroll, S. B. PY - 2002 DA - 2002// TI - Evolution of a transcriptional repression domain in an insect Hox protein JO - Nature VL - 415 UR - https://doi.org/10.1038/nature717 DO - 10.1038/nature717 ID - Galant2002 ER - TY - JOUR AU - Gatchel, J. R. AU - Zoghbi, H. Y. PY - 2005 DA - 2005// TI - Diseases of unstable repeat expansion: mechanisms and common principles JO - Nat Rev Genet VL - 6 UR - https://doi.org/10.1038/nrg1691 DO - 10.1038/nrg1691 ID - Gatchel2005 ER - TY - JOUR AU - Brown, L. Y. AU - Brown, S. A. PY - 2004 DA - 2004// TI - Alanine tracts: the expanding story of human illness and trinucleotide repeats JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2003.11.002 DO - 10.1016/j.tig.2003.11.002 ID - Brown2004 ER - TY - JOUR AU - Simon, M. AU - Hancock, J. M. PY - 2009 DA - 2009// TI - Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-6-r59 DO - 10.1186/gb-2009-10-6-r59 ID - Simon2009 ER - TY - JOUR AU - Zilversmit, M. M. AU - Volkman, S. K. AU - DePristo, M. A. AU - Wirth, D. F. AU - Awadalla, P. AU - Hartl, D. L. PY - 2010 DA - 2010// TI - Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msq108 DO - 10.1093/molbev/msq108 ID - Zilversmit2010 ER - TY - JOUR AU - Salichs, E. AU - Ledda, A. AU - Mularoni, L. AU - Alba, M. M. AU - de la Luna, S. PY - 2009 DA - 2009// TI - Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000397 DO - 10.1371/journal.pgen.1000397 ID - Salichs2009 ER - TY - JOUR AU - Shepard, P. J. AU - Hertel, K. J. PY - 2009 DA - 2009// TI - The SR protein family JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-10-242 DO - 10.1186/gb-2009-10-10-242 ID - Shepard2009 ER - TY - JOUR AU - Janody, F. AU - Sturny, R. AU - Schaeffer, V. AU - Azou, Y. AU - Dostatni, N. PY - 2001 DA - 2001// TI - Two distinct domains of Bicoid mediate its transcriptional downregulation by the Torso pathway JO - Development VL - 128 ID - Janody2001 ER - TY - JOUR AU - Hanna-Rose, W. AU - Hansen, U. PY - 1996 DA - 1996// TI - Active repression mechanisms of eukaryotic transcription repressors JO - Trends Genet VL - 12 UR - https://doi.org/10.1016/0168-9525(96)10022-6 DO - 10.1016/0168-9525(96)10022-6 ID - Hanna-Rose1996 ER - TY - JOUR AU - Tompa, P. PY - 2003 DA - 2003// TI - Intrinsically unstructured proteins evolve by repeat expansion JO - Bioessays VL - 25 UR - https://doi.org/10.1002/bies.10324 DO - 10.1002/bies.10324 ID - Tompa2003 ER - TY - JOUR AU - Jorda, J. AU - Xue, B. AU - Uversky, V. N. AU - Kajava, A. V. PY - 2010 DA - 2010// TI - Protein tandem repeats - the more perfect, the less structured JO - FEBS J VL - 277 UR - https://doi.org/10.1111/j.1742-4658.2010.07684.x DO - 10.1111/j.1742-4658.2010.07684.x ID - Jorda2010 ER - TY - JOUR AU - Laurie, S. AU - Toll-Riera, M. AU - Rado-Trilla, N. AU - Alba, M. M. PY - 2012 DA - 2012// TI - Sequence shortening in the rodent ancestor JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.121897.111 DO - 10.1101/gr.121897.111 ID - Laurie2012 ER - TY - JOUR AU - Chakraborty, R. AU - Kimmel, M. AU - Stivers, D. N. AU - Davison, L. J. AU - Deka, R. PY - 1997 DA - 1997// TI - Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci JO - Proc Nat Acad Sci U S A VL - 94 UR - https://doi.org/10.1073/pnas.94.3.1041 DO - 10.1073/pnas.94.3.1041 ID - Chakraborty1997 ER - TY - JOUR AU - Rooney, A. P. AU - Zhang, J. AU - Nei, M. PY - 2000 DA - 2000// TI - An unusual form of purifying selection in a sperm protein JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026307 DO - 10.1093/oxfordjournals.molbev.a026307 ID - Rooney2000 ER - TY - JOUR AU - Hancock, J. M. AU - Simon, M. PY - 2005 DA - 2005// TI - Simple sequence repeats in proteins and their significance for network evolution JO - Gene VL - 345 UR - https://doi.org/10.1016/j.gene.2004.11.023 DO - 10.1016/j.gene.2004.11.023 ID - Hancock2005 ER - TY - JOUR AU - Wren, J. D. AU - Forgacs, E. AU - Fondon, J. W. AU - Pertsemlidis, A. AU - Cheng, S. Y. AU - Gallardo, T. AU - Williams, R. S. AU - Shohet, R. V. AU - Minna, J. D. AU - Garner, H. R. PY - 2000 DA - 2000// TI - Repeat polymorphisms within gene regions: phenotypic and evolutionary implications JO - Am J Hum Genet VL - 67 UR - https://doi.org/10.1086/303013 DO - 10.1086/303013 ID - Wren2000 ER - TY - JOUR AU - Mularoni, L. AU - Guigo, R. AU - Alba, M. M. PY - 2006 DA - 2006// TI - Mutation patterns of amino acid tandem repeats in the human proteome JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-4-r33 DO - 10.1186/gb-2006-7-4-r33 ID - Mularoni2006 ER - TY - JOUR AU - Li, Y. C. AU - Korol, A. B. AU - Fahima, T. AU - Nevo, E. PY - 2004 DA - 2004// TI - Microsatellites within genes: structure, function, and evolution JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh073 DO - 10.1093/molbev/msh073 ID - Li2004 ER - TY - JOUR AU - Mularoni, L. AU - Ledda, A. AU - Toll-Riera, M. AU - Alba, M. M. PY - 2010 DA - 2010// TI - Natural selection drives the accumulation of amino acid tandem repeats in human proteins JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.101261.109 DO - 10.1101/gr.101261.109 ID - Mularoni2010 ER - TY - JOUR AU - Vilella, A. J. AU - Severin, J. AU - Ureta-Vidal, A. AU - Heng, L. AU - Durbin, R. AU - Birney, E. PY - 2009 DA - 2009// TI - EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.073585.107 DO - 10.1101/gr.073585.107 ID - Vilella2009 ER - TY - JOUR AU - Donoghue, P. C. AU - Benton, M. J. PY - 2007 DA - 2007// TI - Rocks and clocks: calibrating the Tree of Life using fossils and molecules JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2007.05.005 DO - 10.1016/j.tree.2007.05.005 ID - Donoghue2007 ER - TY - JOUR AU - Haerty, W. AU - Golding, G. B. PY - 2010 DA - 2010// TI - Genome-wide evidence for selection acting on single amino acid repeats JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.101246.109 DO - 10.1101/gr.101246.109 ID - Haerty2010 ER - TY - JOUR AU - Swire, J. PY - 2007 DA - 2007// TI - Selection on synthesis cost affects interprotein amino acid usage in all three domains of life JO - J Mol Evol VL - 64 UR - https://doi.org/10.1007/s00239-006-0206-8 DO - 10.1007/s00239-006-0206-8 ID - Swire2007 ER - TY - JOUR AU - Chi, L. M. AU - Lam, S. L. PY - 2005 DA - 2005// TI - Structural roles of CTG repeats in slippage expansion during DNA replication JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki307 DO - 10.1093/nar/gki307 ID - Chi2005 ER - TY - JOUR AU - Mar Alba, M. AU - Santibanez-Koref, M. F. AU - Hancock, J. M. PY - 1999 DA - 1999// TI - Amino acid reiterations in yeast are overrepresented in particular classes of proteins and show evidence of a slippage-like mutational process JO - J Mol Evol VL - 49 UR - https://doi.org/10.1007/PL00006601 DO - 10.1007/PL00006601 ID - Mar Alba1999 ER - TY - JOUR AU - Huntley, M. A. AU - Clark, A. G. PY - 2007 DA - 2007// TI - Evolutionary Analysis of Amino Acid Repeats Across the Genomes of 12 Drosophila Species JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm129 DO - 10.1093/molbev/msm129 ID - Huntley2007 ER - TY - JOUR AU - Herskovits, J. S. AU - Shpetner, H. S. AU - Burgess, C. C. AU - Vallee, R. B. PY - 1993 DA - 1993// TI - Microtubules and Src homology 3 domains stimulate the dynamin GTPase via its C-terminal domain JO - Proc Natl Acad Sci U S A VL - 90 UR - https://doi.org/10.1073/pnas.90.24.11468 DO - 10.1073/pnas.90.24.11468 ID - Herskovits1993 ER - TY - JOUR AU - Trifonov, E. N. AU - Bettecken, T. PY - 1997 DA - 1997// TI - Sequence fossils, triplet expansion, and reconstruction of earliest codons JO - Gene VL - 205 UR - https://doi.org/10.1016/S0378-1119(97)00479-4 DO - 10.1016/S0378-1119(97)00479-4 ID - Trifonov1997 ER - TY - JOUR AU - Trifonov, E. N. PY - 2009 DA - 2009// TI - The origin of the genetic code and of the earliest oligopeptides JO - Res Microbiol VL - 160 UR - https://doi.org/10.1016/j.resmic.2009.05.004 DO - 10.1016/j.resmic.2009.05.004 ID - Trifonov2009 ER - TY - JOUR AU - Ohno, S. AU - Epplen, J. T. PY - 1983 DA - 1983// TI - The primitive code and repeats of base oligomers as the primordial protein-encoding sequence JO - Proc Natl Acad Sci U S A VL - 80 UR - https://doi.org/10.1073/pnas.80.11.3391 DO - 10.1073/pnas.80.11.3391 ID - Ohno1983 ER - TY - JOUR AU - Toll-Riera, M. AU - Rado-Trilla, N. AU - Martys, F. AU - Alba, M. M. PY - 2012 DA - 2012// TI - Role of low-complexity sequences in the formation of novel protein coding sequences JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/msr263 DO - 10.1093/molbev/msr263 ID - Toll-Riera2012 ER - TY - JOUR AU - Caburet, S. AU - Cocquet, J. AU - Vaiman, D. AU - Veitia, R. A. PY - 2005 DA - 2005// TI - Coding repeats and evolutionary "agility" JO - Bioessays VL - 27 UR - https://doi.org/10.1002/bies.20248 DO - 10.1002/bies.20248 ID - Caburet2005 ER - TY - JOUR AU - Nakachi, Y. AU - Hayakawa, T. AU - Oota, H. AU - Sumiyama, K. AU - Wang, L. AU - Ueda, S. PY - 1997 DA - 1997// TI - Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025710 DO - 10.1093/oxfordjournals.molbev.a025710 ID - Nakachi1997 ER - TY - JOUR AU - Sumiyama, K. AU - Washio-Watanabe, K. AU - Saitou, N. AU - Hayakawa, T. AU - Ueda, S. PY - 1996 DA - 1996// TI - Class III POU genes: generation of homopolymeric amino acid repeats under GC pressure in mammals JO - J Mol Evol VL - 43 UR - https://doi.org/10.1007/BF02338824 DO - 10.1007/BF02338824 ID - Sumiyama1996 ER - TY - JOUR AU - Zhou, Y. AU - Liu, J. AU - Han, L. AU - Li, Z. G. AU - Zhang, Z. PY - 2011 DA - 2011// TI - Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-632 DO - 10.1186/1471-2164-12-632 ID - Zhou2011 ER - TY - JOUR AU - DePristo, M. A. AU - Zilversmit, M. M. AU - Hartl, D. L. PY - 2006 DA - 2006// TI - On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins JO - Gene VL - 378 UR - https://doi.org/10.1016/j.gene.2006.03.023 DO - 10.1016/j.gene.2006.03.023 ID - DePristo2006 ER - TY - JOUR AU - Flicek, P. AU - Aken, B. L. AU - Beal, K. AU - Ballester, B. AU - Caccamo, M. AU - Chen, Y. AU - Clarke, L. AU - Coates, G. AU - Cunningham, F. AU - Cutts, T. PY - 2008 DA - 2008// TI - Ensembl 2008 JO - Nucleic Acids Res VL - 36 ID - Flicek2008 ER - TY - JOUR AU - Notredame, C. AU - Higgins, D. G. AU - Heringa, J. PY - 2000 DA - 2000// TI - T-Coffee: a novel method for fast and accurate multiple sequence alignment JO - J Mol Biol VL - 302 UR - https://doi.org/10.1006/jmbi.2000.4042 DO - 10.1006/jmbi.2000.4042 ID - Notredame2000 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - BOOK PY - 2007 DA - 2007// TI - A languange and environment for statistical computing PB - R fundation for statistical computing CY - Vienna (Austria) ID - ref55 ER -