Albà, M.M., Santibáñez-Koref, M.F. & Hancock, J.M. (2001). The comparative genomics of polyglutamine repeats: extreme differences in the codon organization of repeat-encoding regions between mammals and Drosophila. J. Mol. Evol. 52, 249-259.
Bhattacharyya, A., Thakur, A.K., Chellgren, V.M., Thiagarajan, G., Williams, A.D., Chellgren, B.W. et al. (2006). Oligoproline effects on polyglutamine conformation and aggregation. J. Mol. Biol. 355, 524-535.
Blum, E.S., Schwendeman, A.R. & Shaham, S. (2013). PolyQ disease: misfiring of a developmental cell death program? Trends Cell Biol. 23, 168-174.
Cuff, J.A. & Barton, G.J. (1999). Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34, 508-519.
Darnell, G., Orgel J.P.R.O., Pahl, R. & Meredith, S.C. (2007). Flanking polyproline sequences inhibit beta-sheet structure in polyglutamine segments by inducing PPII-like helix structure. J. Mol. Biol. 374, 688-704.
Drozdetskiy, A., Cole, C., Procter, J. & Barton, G.J. (2015). JPred4: a protein secondary structure prediction server. Nucleic Acids Res. 43, W389-W394.
Eftekharzadeh, B., Piai, A., Chiesa, G., Mungianu, D., García, J., Pierattelli, R. et al. (2016). Sequence context influences the structure and aggregation behavior of a polyQ tract. Biophys. J. 110, 2361-2366.
Escobedo, A., Topal, B., Kunze, M.B.A., Aranda, J., Chiesa, G., Mungianu, D. et al. (2019). Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor. Nat. Commun. 10, 2034.
Faux, N.G., Bottomley, S.P., Lesk, A.M., Irving, J.A., Morrison, J.R., Garcia de la Banda, M., et al. (2005). Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Res. 15, 537-551.
Ferrante, M.I., Zullo, A., Barra, A., Bimonte, S., Messaddeq, N., Studer, M. et al. (2006). Oral-facial-digital type I protein is required for primary cilia formation and left-right axis specification. Nat. Genet. 38, 112-117.
Guemez-Gamboa, A., Coufal, N.G. & Gleeson, J.G. (2014). Primary cilia in the developing and mature brain. Neuron 82, 511-521.
Huang, D.W., Sherman, B.T. & Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.
Huang, H., McGarvey, P.B., Suzek, B.E., Mazumder, R., Zhang, J., Chen, Y. et al. (2011). A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics 27, 1190-1191.
Jorda, J. & Kajava, A.V. (2010). Protein homorepeats sequences, structures, evolution, and functions. Adv. Protein Chem. Struct. Biol. 79, 59-88.
Katoh, K. & Standley, D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780.
Lobanov, M.Y. & Galzitskaya, O.V. (2012). Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes. Mol. Biosyst. 8, 327-337.
Lobanov, M.Y., Sokolovskiy, I.V. & Galzitskaya, O.V. (2014). HRaP: database of occurrence of homorepeats and patterns in proteomes. Nucleic Acid Res. 42, D273-D278.
Ludwiczak, J., Winski, A., Szczepaniak, K., Alva, V. & Dunin-Horkawicz, S. (2019). DeepCoil-a fast and accurate prediction of coiled-coil domains in protein sequences. Bioinformatics 35, 2790-2795.
McMurdie, P.J. & Holmes, S. (2013). Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217.
McMurray, C.T. (2010). Mechanisms of trinucleotide repeat instability during human development. Nat. Rev. Genet. 11, 786-799.
Mier, P., Alanis-Lobato, G. & Andrade-Navarro, M.A. (2017). Context characterization of amino acid homorepeats using evolution, position, and order. Proteins 85, 709-719.
Mier, P. & Andrade-Navarro, M.A. (2018). Glutamine codon usage and polyQ evolution in primates depend on the Q stretch length. Genome Biol. Evol. 10, 816-825.
Mier, P., Pérez-Pulido, A.J. & Andrade-Navarro, M.A. (2018). Automated selection of homologs to track the evolutionary history of proteins. BMC Bioinformatics 19, 431.
Mier, P., Elena-Real, C., Urbanek, A., Bernadó, P. & Andrade-Navarro, M.A. (2020). The importance of definitions in the study of polyQ regions: a tale of thresholds, impurities and sequence context. Comput. Struct. Biotechnol. J. https://doi.org/10.1016/j.csbj.2020.01.012. In press.
O’Donoghue, S., Sabir, K.S., Kalemanov, M., Stolte, C., Wellmann, B., Ho, V. et al. (2015). Aquaria: simplifying discovery and insight from protein structures. Nat. Methods 12, 98-99.
Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V. et al. (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37, D5-D15.
Schaefer, M.H., Wanker, E.E. & Andrade-Navarro, M.A. (2012). Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res. 40, 4273-4287.
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Weizhong, L. et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539.
Singla, V., Romaguera-Ros, M., Garcia-Verdugo, J.M. & Reiter, J.F. (2010). Ofd1, a human disease gene, regulates the length and distal structure of centrioles. Dev. Cell 18, 410-424.
Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J. et al. (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607-D613.
Thurmond, J., Goodman, J.L., Strelets, V.B., Attrill, H., Gramates, L.S., Marygold, S.J. et al. (2019). FlyBase 2.0: the next generation. Nucleic Acids Res. 47, D759-D765.
Totzeck, F., Andrade-Navarro, M.A. & Mier, P. (2017). The protein structure context of polyQ regions. PloS One 12, e0170801.
Ward, N. & Moreno-Hagelsieb, G. (2014). Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PLoS One 9, e101850.
Yushchenko, T., Deuerling, E. & Hauser, K. (2018). Insights into the aggregation mechanism of polyQ proteins with different glutamine repeat lengths. Biophys. J. 114, 1847-1857.
Zerbino, D.R., Achuthan, P., Akanni, W., Amode M.R., Barrel, D., Bhai, J. et al. (2018). Ensembl 2018. Nucleic Acids Res. 46, D754-D761.