TY - JOUR AU - Luo, H. AU - Nijveen, H. PY - 2014 DA - 2014// TI - Understanding and identifying amino acid repeats JO - Brief Bioinform VL - 15 UR - https://doi.org/10.1093/bib/bbt003 DO - 10.1093/bib/bbt003 ID - Luo2014 ER - TY - JOUR AU - Golding, G. B. AU - Haerty, W. PY - 2010 DA - 2010// TI - Low-complexity sequences and single amino acid repeats: not just “junk” peptide sequences JO - Genome VL - 53 UR - https://doi.org/10.1139/G10-063 DO - 10.1139/G10-063 ID - Golding2010 ER - TY - JOUR AU - Nussenzweig, R. S. AU - Nussenzweig, V. AU - Freeman, R. R. PY - 1984 DA - 1984// TI - Development of Sporozoite Vaccines [and Discussion] JO - Philos Trans R Soc Lond B Biol Sci VL - 307 UR - https://doi.org/10.1098/rstb.1984.0113 DO - 10.1098/rstb.1984.0113 ID - Nussenzweig1984 ER - TY - JOUR AU - Ferreira, M. U. AU - Nunes, M. d. S. AU - Wunderlich, G. PY - 2004 DA - 2004// TI - Antigenic diversity and immune evasion by malaria parasites JO - Clin Diagn Lab Immunol VL - 11 ID - Ferreira2004 ER - TY - JOUR AU - Verra, F. AU - Hughes, A. L. PY - 1999 DA - 1999// TI - Biased amino acid composition in repeat regions of Plasmodium antigens JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026145 DO - 10.1093/oxfordjournals.molbev.a026145 ID - Verra1999 ER - TY - JOUR AU - Hughes, A. L. PY - 2004 DA - 2004// TI - The evolution of amino acid repeat arrays in Plasmodium and other organisms JO - J Mol Evol VL - 59 UR - https://doi.org/10.1007/s00239-004-2645-4 DO - 10.1007/s00239-004-2645-4 ID - Hughes2004 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 - Pizzi, E. AU - Frontali, C. PY - 2001 DA - 2001// TI - Low-complexity regions in plasmodium falciparum proteins JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.GR-1522R DO - 10.1101/gr.GR-1522R ID - Pizzi2001 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 - Xue, H. Y. AU - Forsdyke, D. R. PY - 2003 DA - 2003// TI - Low-complexity segments in plasmodium falciparum proteins are primarily nucleic acid level adaptations JO - Mol Biochem Parasitol VL - 128 UR - https://doi.org/10.1016/S0166-6851(03)00039-2 DO - 10.1016/S0166-6851(03)00039-2 ID - Xue2003 ER - TY - JOUR AU - Frugier, M. AU - Bour, T. AU - Ayach, M. AU - Santos, M. A. S. AU - Rudinger-Thirion, J. AU - Théobald-Dietrich, A. AU - Pizzi, E. PY - 2010 DA - 2010// TI - Low complexity regions behave as tRNA sponges to help co-translational folding of plasmodial proteins JO - FEBS Lett VL - 584 UR - https://doi.org/10.1016/j.febslet.2009.11.004 DO - 10.1016/j.febslet.2009.11.004 ID - Frugier2010 ER - TY - JOUR AU - Haerty, W. AU - Golding, G. B. PY - 2011 DA - 2011// TI - Increased polymorphism near low-complexity sequences across the genomes of plasmodium falciparum isolates JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evr045 DO - 10.1093/gbe/evr045 ID - Haerty2011 ER - TY - JOUR AU - Wootton, J. C. AU - Federhen, S. PY - 1993 DA - 1993// TI - Statistics of local complexity in amino acid sequences and sequence databases JO - Comput Chem VL - 17 UR - https://doi.org/10.1016/0097-8485(93)85006-X DO - 10.1016/0097-8485(93)85006-X ID - Wootton1993 ER - TY - JOUR AU - Coletta, A. AU - Pinney, J. AU - Solís, D. AU - Marsh, J. AU - Pettifer, S. AU - Attwood, T. PY - 2010 DA - 2010// TI - Low-complexity regions within protein sequences have position-dependent roles JO - BMC Syst Biol VL - 4 UR - https://doi.org/10.1186/1752-0509-4-43 DO - 10.1186/1752-0509-4-43 ID - Coletta2010 ER - TY - JOUR AU - Huntley, M. A. AU - Golding, G. B. PY - 2002 DA - 2002// TI - Simple sequences are rare in the protein data bank JO - Proteins Struct Funct Bioinforma VL - 48 UR - https://doi.org/10.1002/prot.10150 DO - 10.1002/prot.10150 ID - Huntley2002 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 - 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 - King, D. G. AU - Soller, M. AU - Kashi, Y. PY - 1997 DA - 1997// TI - Evolutionary tuning knobs JO - Endeavour VL - 21 UR - https://doi.org/10.1016/S0160-9327(97)01005-3 DO - 10.1016/S0160-9327(97)01005-3 ID - King1997 ER - TY - JOUR AU - Fondon, J. W. AU - Garner, H. R. PY - 2004 DA - 2004// TI - Molecular origins of rapid and continuous morphological evolution JO - Proc Natl Acad Sci VL - 101 UR - https://doi.org/10.1073/pnas.0408118101 DO - 10.1073/pnas.0408118101 ID - Fondon2004 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 - Kashi, Y. AU - King, D. G. PY - 2006 DA - 2006// TI - Simple sequence repeats as advantageous mutators in evolution JO - Trends Genet VL - 22 UR - https://doi.org/10.1016/j.tig.2006.03.005 DO - 10.1016/j.tig.2006.03.005 ID - Kashi2006 ER - TY - JOUR AU - Toll-Riera, M. AU - Radó-Trilla, N. AU - Martys, F. AU - Albà, 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 - Kirmitzoglou, I. AU - Promponas, V. J. PY - 2015 DA - 2015// TI - LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv115 DO - 10.1093/bioinformatics/btv115 ID - Kirmitzoglou2015 ER - TY - JOUR AU - Press, M. O. AU - Carlson, K. D. AU - Queitsch, C. PY - 2014 DA - 2014// TI - The overdue promise of short tandem repeat variation for heritability JO - Trends Genet VL - 30 UR - https://doi.org/10.1016/j.tig.2014.07.008 DO - 10.1016/j.tig.2014.07.008 ID - Press2014 ER - TY - JOUR AU - Gemayel, R. AU - Vinces, M. D. AU - Legendre, M. AU - Verstrepen, K. J. PY - 2010 DA - 2010// TI - Variable tandem repeats accelerate evolution of coding and regulatory sequences JO - Annu Rev Genet VL - 44 UR - https://doi.org/10.1146/annurev-genet-072610-155046 DO - 10.1146/annurev-genet-072610-155046 ID - Gemayel2010 ER - TY - JOUR AU - Gemayel, R. AU - Cho, J. AU - Boeynaems, S. AU - Verstrepen, K. J. PY - 2012 DA - 2012// TI - Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences JO - Genes VL - 3 UR - https://doi.org/10.3390/genes3030461 DO - 10.3390/genes3030461 ID - Gemayel2012 ER - TY - JOUR AU - Dalby, A. R. PY - 2009 DA - 2009// TI - A comparative proteomic analysis of the simple amino acid repeat distributions in plasmodia reveals lineage specific amino acid selection JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0006231 DO - 10.1371/journal.pone.0006231 ID - Dalby2009 ER - TY - JOUR AU - Albà, M. M. AU - Guigó, 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 - Albà2004 ER - TY - JOUR AU - Behura, S. K. AU - Severson, D. W. PY - 2012 DA - 2012// TI - Genome-wide comparative analysis of simple sequence coding repeats among 25 insect species JO - Gene VL - 504 UR - https://doi.org/10.1016/j.gene.2012.05.020 DO - 10.1016/j.gene.2012.05.020 ID - Behura2012 ER - TY - JOUR AU - Faux, N. G. AU - Bottomley, S. P. AU - Lesk, A. M. AU - Irving, J. A. AU - Morrison, J. R. AU - 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 - Faux, N. G. AU - Huttley, G. A. AU - Mahmood, K. AU - Webb, G. I. AU - Garcia de la Banda, M. AU - Whisstock, J. C. PY - 2007 DA - 2007// TI - RCPdb: an evolutionary classification and codon usage database for repeat-containing proteins JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6255407 DO - 10.1101/gr.6255407 ID - Faux2007 ER - TY - JOUR AU - Dunker, A. K. AU - Lawson, J. D. AU - Brown, C. J. AU - Williams, R. M. AU - Romero, P. AU - Oh, J. S. AU - Oldfield, C. J. AU - Campen, A. M. AU - Ratliff, C. M. AU - Hipps, K. W. AU - Ausio, J. AU - Nissen, M. S. AU - Reeves, R. AU - Kang, C. AU - Kissinger, C. R. AU - Bailey, R. W. AU - Griswold, M. D. AU - Chiu, W. AU - Garner, E. C. AU - Obradovic, Z. PY - 2001 DA - 2001// TI - Intrinsically disordered protein JO - J Mol Graph Model VL - 19 UR - https://doi.org/10.1016/S1093-3263(00)00138-8 DO - 10.1016/S1093-3263(00)00138-8 ID - Dunker2001 ER - TY - JOUR AU - Brown, C. J. AU - Takayama, S. AU - Campen, A. M. AU - Vise, P. AU - Marshall, T. W. AU - Oldfield, C. J. AU - Williams, C. J. AU - Keith Dunker, A. PY - 2002 DA - 2002// TI - Evolutionary rate heterogeneity in proteins with long disordered regions JO - J Mol Evol VL - 55 UR - https://doi.org/10.1007/s00239-001-2309-6 DO - 10.1007/s00239-001-2309-6 ID - Brown2002 ER - TY - JOUR AU - Brown, C. J. AU - Johnson, A. K. AU - Dunker, A. K. AU - Daughdrill, G. W. PY - 2011 DA - 2011// TI - Evolution and disorder JO - Curr Opin Struct Biol VL - 21 UR - https://doi.org/10.1016/j.sbi.2011.02.005 DO - 10.1016/j.sbi.2011.02.005 ID - Brown2011 ER - TY - JOUR AU - Nakachi, Y. AU - Hayakawa, T. AU - Ootah, H. 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 - 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 - 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 - Mularoni, L. AU - Ledda, A. AU - Toll-Riera, M. AU - Albà, 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 - Mularoni, L. AU - Veitia, R. A. AU - Albà, 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 - Salichs, E. AU - Ledda, A. AU - Mularoni, L. AU - Albà, M. M. AU - 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 - Yu, F. PY - 2005 DA - 2005// TI - Positive selection of a pre-expansion CAG repeat of the human SCA2 gene JO - PLoS Genet VL - 1 UR - https://doi.org/10.1371/journal.pgen.0010041 DO - 10.1371/journal.pgen.0010041 ID - Yu2005 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 - Ellegren, H. PY - 2004 DA - 2004// TI - Microsatellites: simple sequences with complex evolution JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1348 DO - 10.1038/nrg1348 ID - Ellegren2004 ER - TY - JOUR AU - Romero, P. AU - Obradovic, Z. AU - Li, X. AU - Garner, E. C. AU - Brown, C. J. AU - Dunker, A. K. PY - 2001 DA - 2001// TI - Sequence complexity of disordered protein JO - Proteins VL - 42 UR - https://doi.org/3.0.CO;2-3 DO - 3.0.CO;2-3 ID - Romero2001 ER - TY - STD TI - Tompa P, Fersht A. Structure and Function of Intrinsically Disordered Proteins. Boca Raton, FL: CRC Press; 2009. ID - ref45 ER - TY - JOUR AU - Tompa, P. PY - 2012 DA - 2012// TI - Intrinsically disordered proteins: a 10-year recap JO - Trends Biochem Sci VL - 37 UR - https://doi.org/10.1016/j.tibs.2012.08.004 DO - 10.1016/j.tibs.2012.08.004 ID - Tompa2012 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 - BOOK PY - 2008 DA - 2008// TI - SASSTAT 92 Users Guide ID - ref48 ER - TY - STD TI - Fox J, Weisberg S. An R Companion to Applied Regression. 2nd edition. Thousand Oaks, California: Sage; 2011. ID - ref49 ER - TY - JOUR AU - Kendall, M. G. PY - 1938 DA - 1938// TI - A new measure of rank correlation JO - Biometrika VL - 30 UR - https://doi.org/10.1093/biomet/30.1-2.81 DO - 10.1093/biomet/30.1-2.81 ID - Kendall1938 ER - TY - JOUR AU - Efron, B. AU - Tibshirani, R. PY - 1986 DA - 1986// TI - Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy JO - Stat Sci VL - 1 UR - https://doi.org/10.1214/ss/1177013815 DO - 10.1214/ss/1177013815 ID - Efron1986 ER - TY - CHAP AU - Midford, P. E. AU - Garland, T. AU - Maddison, W. P. PY - 2005 DA - 2005// TI - PDAP package of Mesquite BT - Version 107 ID - Midford2005 ER - TY - STD TI - Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Version 2.5 http://mesquiteproject.org. 2008. UR - http://mesquiteproject.org ID - ref53 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - STD TI - Kuo C-H, Wares JP, Kissinger JC. The apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol. 2008;25:2689–98. ID - ref55 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER -