TY - JOUR AU - Bartel, D. P. PY - 2018 DA - 2018// TI - Metazoan micrornas JO - Cell. VL - 173 UR - https://doi.org/10.1016/j.cell.2018.03.006 DO - 10.1016/j.cell.2018.03.006 ID - Bartel2018 ER - TY - JOUR AU - Ross, J. PY - 1995 DA - 1995// TI - mRNA stability in mammalian cells JO - Microbiol Mol Biol Rev VL - 59 ID - Ross1995 ER - TY - JOUR AU - Bartel, D. P. PY - 2004 DA - 2004// TI - MicroRNAs: genomics, biogenesis, mechanism, and function JO - Cell VL - 116 UR - https://doi.org/10.1016/S0092-8674(04)00045-5 DO - 10.1016/S0092-8674(04)00045-5 ID - Bartel2004 ER - TY - JOUR AU - Batista, P. J. AU - Molinie, B. AU - Wang, J. AU - Qu, K. AU - Zhang, J. AU - Li, L. PY - 2014 DA - 2014// TI - m6A RNA modification controls cell fate transition in mammalian embryonic stem cells JO - Cell Stem Cell VL - 15 UR - https://doi.org/10.1016/j.stem.2014.09.019 DO - 10.1016/j.stem.2014.09.019 ID - Batista2014 ER - TY - JOUR AU - Tadros, W. AU - Lipshitz, H. D. PY - 2009 DA - 2009// TI - The maternal-to-zygotic transition: a play in two acts JO - Development. VL - 136 UR - https://doi.org/10.1242/dev.033183 DO - 10.1242/dev.033183 ID - Tadros2009 ER - TY - JOUR AU - Mayr, C. PY - 2017 DA - 2017// TI - Regulation by 3′-untranslated regions JO - Annu Rev Genet VL - 51 UR - https://doi.org/10.1146/annurev-genet-120116-024704 DO - 10.1146/annurev-genet-120116-024704 ID - Mayr2017 ER - TY - JOUR AU - Laver, J. D. AU - Li, X. AU - Ray, D. AU - Cook, K. B. AU - Hahn, N. A. AU - Nabeel-Shah, S. PY - 2015 DA - 2015// TI - Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0659-4 DO - 10.1186/s13059-015-0659-4 ID - Laver2015 ER - TY - JOUR AU - Chen, L. AU - Dumelie, J. G. AU - Li, X. AU - Cheng, M. H. AU - Yang, Z. AU - Laver, J. D. PY - 2014 DA - 2014// TI - Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-1-r4 DO - 10.1186/gb-2014-15-1-r4 ID - Chen2014 ER - TY - JOUR AU - Laver, J. D. AU - Ly, J. AU - Winn, A. K. AU - Karaiskakis, A. AU - Lin, S. AU - Nie, K. PY - 2020 DA - 2020// TI - The RNA-binding protein Rasputin/G3BP enhances the stability and translation of its target mRNAs JO - Cell Rep VL - 30 UR - https://doi.org/10.1016/j.celrep.2020.02.066 DO - 10.1016/j.celrep.2020.02.066 ID - Laver2020 ER - TY - JOUR AU - Zhao, B. S. AU - Wang, X. AU - Beadell, A. V. AU - Lu, Z. AU - Shi, H. AU - Kuuspalu, A. PY - 2017 DA - 2017// TI - m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition JO - Nature. VL - 542 UR - https://doi.org/10.1038/nature21355 DO - 10.1038/nature21355 ID - Zhao2017 ER - TY - JOUR AU - Schoenberg, D. R. AU - Maquat, L. E. PY - 2012 DA - 2012// TI - Regulation of cytoplasmic mRNA decay JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3160 DO - 10.1038/nrg3160 ID - Schoenberg2012 ER - TY - JOUR AU - Hanson, G. AU - Coller, J. PY - 2018 DA - 2018// TI - Codon optimality, bias and usage in translation and mRNA decay JO - Nat Rev Mol Cell Biol VL - 19 UR - https://doi.org/10.1038/nrm.2017.91 DO - 10.1038/nrm.2017.91 ID - Hanson2018 ER - TY - JOUR AU - Pinder, B. D. AU - Smibert, C. A. PY - 2013 DA - 2013// TI - Smaug: an unexpected journey into the mechanisms of post-transcriptional regulation JO - Fly. VL - 7 UR - https://doi.org/10.4161/fly.24336 DO - 10.4161/fly.24336 ID - Pinder2013 ER - TY - JOUR AU - Ambros, V. PY - 2011 DA - 2011// TI - MicroRNAs and developmental timing JO - Curr Opin Genet Dev VL - 21 UR - https://doi.org/10.1016/j.gde.2011.04.003 DO - 10.1016/j.gde.2011.04.003 ID - Ambros2011 ER - TY - JOUR AU - Vastenhouw, N. L. AU - Cao, W. X. AU - Lipshitz, H. D. PY - 2019 DA - 2019// TI - The maternal-to-zygotic transition revisited JO - Development VL - 146 UR - https://doi.org/10.1242/dev.161471 DO - 10.1242/dev.161471 ID - Vastenhouw2019 ER - TY - JOUR AU - Laver, J. D. AU - Marsolais, A. J. AU - Smibert, C. A. AU - Lipshitz, H. D. PY - 2015 DA - 2015// TI - Regulation and function of maternal gene products during the maternal-to-zygotic transition in Drosophila JO - Curr Top Dev Biol VL - 113 UR - https://doi.org/10.1016/bs.ctdb.2015.06.007 DO - 10.1016/bs.ctdb.2015.06.007 ID - Laver2015 ER - TY - JOUR AU - Bushati, N. AU - Stark, A. AU - Brennecke, J. AU - Cohen, S. M. PY - 2008 DA - 2008// TI - Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila JO - Curr Biol VL - 18 UR - https://doi.org/10.1016/j.cub.2008.02.081 DO - 10.1016/j.cub.2008.02.081 ID - Bushati2008 ER - TY - JOUR AU - Giraldez, A. J. AU - Mishima, Y. AU - Rihel, J. AU - Grocock, R. J. AU - Dongen, S. AU - Inoue, K. PY - 2006 DA - 2006// TI - Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs JO - Science VL - 312 UR - https://doi.org/10.1126/science.1122689 DO - 10.1126/science.1122689 ID - Giraldez2006 ER - TY - JOUR AU - Lund, E. AU - Liu, M. AU - Hartley, R. S. AU - Sheets, M. D. AU - Dahlberg, J. E. PY - 2009 DA - 2009// TI - Deadenylation of maternal mRNAs mediated by miR-427 in Xenopus laevis embryos JO - Rna. VL - 15 UR - https://doi.org/10.1261/rna.1882009 DO - 10.1261/rna.1882009 ID - Lund2009 ER - TY - JOUR AU - Bazzini, A. A. AU - Lee, M. T. AU - Giraldez, A. J. PY - 2012 DA - 2012// TI - Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish JO - Science. VL - 336 UR - https://doi.org/10.1126/science.1215704 DO - 10.1126/science.1215704 ID - Bazzini2012 ER - TY - JOUR AU - Ivanova, I. AU - Much, C. AU - Giacomo, M. AU - Azzi, C. AU - Morgan, M. AU - Moreira, P. N. PY - 2017 DA - 2017// TI - The RNA m6A reader YTHDF2 is essential for the post-transcriptional regulation of the maternal transcriptome and oocyte competence JO - Mol Cell VL - 67 UR - https://doi.org/10.1016/j.molcel.2017.08.003 DO - 10.1016/j.molcel.2017.08.003 ID - Ivanova2017 ER - TY - JOUR AU - Bazzini, A. A. AU - Viso, F. AU - Moreno-Mateos, M. A. AU - Johnstone, T. G. AU - Vejnar, C. E. AU - Qin, Y. PY - 2016 DA - 2016// TI - Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition JO - EMBO J VL - 35 UR - https://doi.org/10.15252/embj.201694699 DO - 10.15252/embj.201694699 ID - Bazzini2016 ER - TY - JOUR AU - Mishima, Y. AU - Tomari, Y. PY - 2016 DA - 2016// TI - Codon usage and 3′ UTR length determine maternal mRNA stability in zebrafish JO - Mol Cell VL - 61 UR - https://doi.org/10.1016/j.molcel.2016.02.027 DO - 10.1016/j.molcel.2016.02.027 ID - Mishima2016 ER - TY - JOUR AU - Wu, Q. AU - Medina, S. G. AU - Kushawah, G. AU - DeVore, M. L. AU - Castellano, L. A. AU - Hand, J. M. PY - 2019 DA - 2019// TI - Translation affects mRNA stability in a codon-dependent manner in human cells JO - Elife. VL - 8 UR - https://doi.org/10.7554/eLife.45396 DO - 10.7554/eLife.45396 ID - Wu2019 ER - TY - JOUR AU - Presnyak, V. AU - Alhusaini, N. AU - Chen, Y. -. H. AU - Martin, S. AU - Morris, N. AU - Kline, N. PY - 2015 DA - 2015// TI - Codon optimality is a major determinant of mRNA stability JO - Cell. VL - 160 UR - https://doi.org/10.1016/j.cell.2015.02.029 DO - 10.1016/j.cell.2015.02.029 ID - Presnyak2015 ER - TY - JOUR AU - Boël, G. AU - Letso, R. AU - Neely, H. AU - Price, W. N. AU - Wong, K. -. H. AU - Su, M. PY - 2016 DA - 2016// TI - Codon influence on protein expression in E. coli correlates with mRNA levels JO - Nature. VL - 529 UR - https://doi.org/10.1038/nature16509 DO - 10.1038/nature16509 ID - Boël2016 ER - TY - JOUR AU - Cheng, J. AU - Maier, K. C. AU - Avsec, Ž. AU - Rus, P. AU - Gagneur, J. PY - 2017 DA - 2017// TI - Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast JO - Rna. VL - 23 UR - https://doi.org/10.1261/rna.062224.117 DO - 10.1261/rna.062224.117 ID - Cheng2017 ER - TY - JOUR AU - Tibshirani, R. PY - 1996 DA - 1996// TI - Regression shrinkage and selection via the lasso JO - J R Stat Soc Ser B Methodol VL - 58 ID - Tibshirani1996 ER - TY - JOUR AU - Herzog, V. A. AU - Reichholf, B. AU - Neumann, T. AU - Rescheneder, P. AU - Bhat, P. AU - Burkard, T. R. PY - 2017 DA - 2017// TI - Thiol-linked alkylation of RNA to assess expression dynamics JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4435 DO - 10.1038/nmeth.4435 ID - Herzog2017 ER - TY - JOUR AU - Radhakrishnan, A. AU - Chen, Y. -. H. AU - Martin, S. AU - Alhusaini, N. AU - Green, R. AU - Coller, J. PY - 2016 DA - 2016// TI - The DEAD-box protein Dhh1p couples mRNA decay and translation by monitoring codon optimality JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.08.053 DO - 10.1016/j.cell.2016.08.053 ID - Radhakrishnan2016 ER - TY - JOUR AU - Wu, Q. AU - Bazzini, A. A. PY - 2018 DA - 2018// TI - Systems to study codon effect on post-transcriptional regulation of gene expression JO - Methods (San Diego) VL - 137 UR - https://doi.org/10.1016/j.ymeth.2017.11.006 DO - 10.1016/j.ymeth.2017.11.006 ID - Wu2018 ER - TY - JOUR AU - Vehtari, A. AU - Gelman, A. AU - Gabry, J. PY - 2017 DA - 2017// TI - Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC JO - Stat Comput VL - 27 UR - https://doi.org/10.1007/s11222-016-9696-4 DO - 10.1007/s11222-016-9696-4 ID - Vehtari2017 ER - TY - JOUR AU - Owens, N. D. AU - Blitz, I. L. AU - Lane, M. A. AU - Patrushev, I. AU - Overton, J. D. AU - Gilchrist, M. J. PY - 2016 DA - 2016// TI - Measuring absolute RNA copy numbers at high temporal resolution reveals transcriptome kinetics in development JO - Cell Rep VL - 14 UR - https://doi.org/10.1016/j.celrep.2015.12.050 DO - 10.1016/j.celrep.2015.12.050 ID - Owens2016 ER - TY - BOOK AU - Vehtari, A. AU - Simpson, D. AU - Gelman, A. AU - Yao, Y. AU - Gabry, J. PY - 2015 DA - 2015// TI - Pareto smoothed importance sampling ID - Vehtari2015 ER - TY - JOUR AU - Dongen, S. AU - Abreu-Goodger, C. AU - Enright, A. J. PY - 2008 DA - 2008// TI - Detecting microRNA binding and siRNA off-target effects from expression data JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1267 DO - 10.1038/nmeth.1267 ID - Dongen2008 ER - TY - JOUR AU - Yang, Y. AU - Wang, L. AU - Han, X. AU - Yang, W. -. L. AU - Zhang, M. AU - Ma, H. -. L. PY - 2019 DA - 2019// TI - RNA 5-methylcytosine facilitates the maternal-to-zygotic transition by preventing maternal mRNA decay JO - Mol Cell VL - 75 UR - https://doi.org/10.1016/j.molcel.2019.06.033 DO - 10.1016/j.molcel.2019.06.033 ID - Yang2019 ER - TY - JOUR AU - Guo, H. AU - Ingolia, N. T. AU - Weissman, J. S. AU - Bartel, D. P. PY - 2010 DA - 2010// TI - Mammalian microRNAs predominantly act to decrease target mRNA levels JO - Nature. VL - 466 UR - https://doi.org/10.1038/nature09267 DO - 10.1038/nature09267 ID - Guo2010 ER - TY - JOUR AU - Lichner, Z. AU - Páll, E. AU - Kerekes, A. AU - Pállinger, É. AU - Maraghechi, P. AU - Bősze, Z. PY - 2011 DA - 2011// TI - The miR-290-295 cluster promotes pluripotency maintenance by regulating cell cycle phase distribution in mouse embryonic stem cells JO - Differentiation. VL - 81 UR - https://doi.org/10.1016/j.diff.2010.08.002 DO - 10.1016/j.diff.2010.08.002 ID - Lichner2011 ER - TY - JOUR AU - Cifuentes, D. AU - Xue, H. AU - Taylor, D. W. AU - Patnode, H. AU - Mishima, Y. AU - Cheloufi, S. PY - 2010 DA - 2010// TI - A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity JO - Science. VL - 328 UR - https://doi.org/10.1126/science.1190809 DO - 10.1126/science.1190809 ID - Cifuentes2010 ER - TY - BOOK AU - Efron, B. AU - Tibshirani, R. J. PY - 1994 DA - 1994// TI - An introduction to the bootstrap PB - CRC Press CY - Boca Raton UR - https://doi.org/10.1201/9780429246593 DO - 10.1201/9780429246593 ID - Efron1994 ER - TY - BOOK AU - Hastie, T. J. AU - Tibshirani, R. J. PY - 1990 DA - 1990// TI - Generalized additive models PB - CRC Press CY - Boca Raton ID - Hastie1990 ER - TY - JOUR AU - Laue, K. AU - Rajshekar, S. AU - Courtney, A. J. AU - Lewis, Z. A. AU - Goll, M. G. PY - 2019 DA - 2019// TI - The maternal to zygotic transition regulates genome-wide heterochromatin establishment in the zebrafish embryo JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-019-09582-3 DO - 10.1038/s41467-019-09582-3 ID - Laue2019 ER - TY - JOUR AU - Rabani, M. AU - Pieper, L. AU - Chew, G. -. L. AU - Schier, A. F. PY - 2017 DA - 2017// TI - A massively parallel reporter assay of 3′ UTR sequences identifies in vivo rules for mRNA degradation JO - Mol Cell VL - 68 UR - https://doi.org/10.1016/j.molcel.2017.11.014 DO - 10.1016/j.molcel.2017.11.014 ID - Rabani2017 ER - TY - JOUR AU - Vejnar, C. E. AU - Messih, M. A. AU - Takacs, C. M. AU - Yartseva, V. AU - Oikonomou, P. AU - Christiano, R. PY - 2019 DA - 2019// TI - Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.245159.118 DO - 10.1101/gr.245159.118 ID - Vejnar2019 ER - TY - JOUR AU - Yartseva, V. AU - Takacs, C. M. AU - Vejnar, C. E. AU - Lee, M. T. AU - Giraldez, A. J. PY - 2017 DA - 2017// TI - RESA identifies mRNA-regulatory sequences at high resolution JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4121 DO - 10.1038/nmeth.4121 ID - Yartseva2017 ER - TY - JOUR AU - McGeary, S. E. AU - Lin, K. S. AU - Shi, C. Y. AU - Pham, T. M. AU - Bisaria, N. AU - Kelley, G. M. PY - 2019 DA - 2019// TI - The biochemical basis of microRNA targeting efficacy JO - Science VL - 366 UR - https://doi.org/10.1126/science.aav1741 DO - 10.1126/science.aav1741 ID - McGeary2019 ER - TY - JOUR AU - Seok, H. AU - Ham, J. AU - Jang, E. -. S. AU - Chi, S. W. PY - 2016 DA - 2016// TI - MicroRNA target recognition: insights from transcriptome-wide non-canonical interactions JO - Mol Cells VL - 39 UR - https://doi.org/10.14348/molcells.2016.0013 DO - 10.14348/molcells.2016.0013 ID - Seok2016 ER - TY - JOUR AU - Sheu-Gruttadauria, J. AU - Xiao, Y. AU - Gebert, L. F. AU - MacRae, I. J. PY - 2019 DA - 2019// TI - Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2 JO - Embo j. VL - 38 UR - https://doi.org/10.15252/embj.2018101153 DO - 10.15252/embj.2018101153 ID - Sheu-Gruttadauria2019 ER - TY - JOUR AU - Kushawah, G. AU - Hernandez-Huertas, L. AU - Abugattas-Nuñez Del Prado, J. AU - Martinez-Morales, J. R. AU - DeVore, M. L. AU - Hassan, H. PY - 2020 DA - 2020// TI - CRISPR-Cas13d Induces Efficient mRNA Knockdown in Animal Embryos JO - Dev Cell. VL - 54 UR - https://doi.org/10.1016/j.devcel.2020.07.013 DO - 10.1016/j.devcel.2020.07.013 ID - Kushawah2020 ER - TY - STD TI - iCodon: designing “ideal” coding (iCodon) sequences for customized expression level. 2020. [Zenodo repository]. https://doi.org/10.5281/zenodo.3788015. ID - ref50 ER - TY - STD TI - iCodon: designing “ideal” coding (iCodon) sequences for customized expression level. 2020. [Web application]. Available from: https://bazzinilab.shinyapps.io/icodon/. UR - https://bazzinilab.shinyapps.io/icodon/ ID - ref51 ER - TY - JOUR AU - Rutkowski, A. J. AU - Erhard, F. AU - L’Hernault, A. AU - Bonfert, T. AU - Schilhabel, M. AU - Crump, C. PY - 2015 DA - 2015// TI - Widespread disruption of host transcription termination in HSV-1 infection JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms8126 DO - 10.1038/ncomms8126 ID - Rutkowski2015 ER - TY - JOUR AU - Bazzini, A. A. AU - Johnstone, T. G. AU - Christiano, R. AU - Mackowiak, S. D. AU - Obermayer, B. AU - Fleming, E. S. PY - 2014 DA - 2014// TI - Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation JO - EMBO J VL - 33 UR - https://doi.org/10.1002/embj.201488411 DO - 10.1002/embj.201488411 ID - Bazzini2014 ER - TY - JOUR AU - Wu, Q. AU - Wright, M. AU - Gogol, M. M. AU - Bradford, W. D. AU - Zhang, N. AU - Bazzini, A. A. PY - 2020 DA - 2020// TI - Translation of small downstream ORFs enhances translation of canonical main open reading frames JO - Embo J. VL - 39 UR - https://doi.org/10.15252/embj.2020104763 DO - 10.15252/embj.2020104763 ID - Wu2020 ER - TY - JOUR AU - Johnstone, T. G. AU - Bazzini, A. A. AU - Giraldez, A. J. PY - 2016 DA - 2016// TI - Upstream ORFs are prevalent translational repressors in vertebrates JO - EMBO J VL - 35 UR - https://doi.org/10.15252/embj.201592759 DO - 10.15252/embj.201592759 ID - Johnstone2016 ER - TY - STD TI - Despic V, Neugebauer KM. RNA tales–how embryos read and discard messages from mom. J Cell Sci. 2018;131(5):jcs201996. ID - ref56 ER - TY - JOUR AU - Aanes, H. AU - Winata, C. L. AU - Lin, C. H. AU - Chen, J. P. AU - Srinivasan, K. G. AU - Lee, S. G. PY - 2011 DA - 2011// TI - Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.116012.110 DO - 10.1101/gr.116012.110 ID - Aanes2011 ER - TY - JOUR AU - Lee, M. T. AU - Bonneau, A. R. AU - Takacs, C. M. AU - Bazzini, A. A. AU - DiVito, K. R. AU - Fleming, E. S. PY - 2013 DA - 2013// TI - Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition JO - Nature. VL - 503 UR - https://doi.org/10.1038/nature12632 DO - 10.1038/nature12632 ID - Lee2013 ER - TY - JOUR AU - Pedregosa, F. AU - Varoquaux, G. AU - Gramfort, A. AU - Michel, V. AU - Thirion, B. AU - Grisel, O. PY - 2011 DA - 2011// TI - Scikit-learn: machine learning in Python JO - J Mach Learn Res VL - 12 ID - Pedregosa2011 ER - TY - JOUR AU - Carneiro, R. L. AU - Requião, R. D. AU - Rossetto, S. AU - Domitrovic, T. AU - Palhano, F. L. PY - 2019 DA - 2019// TI - Codon stabilization coefficient as a metric to gain insights into mRNA stability and codon bias and their relationships with translation JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gkz033 DO - 10.1093/nar/gkz033 ID - Carneiro2019 ER - TY - JOUR AU - Abdi, H. PY - 2010 DA - 2010// TI - Partial least squares regression and projection on latent structure regression (PLS Regression) JO - Wiley interdisciplinary reviews: computational statistics. VL - 2 UR - https://doi.org/10.1002/wics.51 DO - 10.1002/wics.51 ID - Abdi2010 ER - TY - BOOK AU - Kuhn, M. AU - Johnson, K. PY - 2013 DA - 2013// TI - Applied predictive modeling PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4614-6849-3 DO - 10.1007/978-1-4614-6849-3 ID - Kuhn2013 ER - TY - JOUR AU - Bürkner, P. -. C. PY - 2017 DA - 2017// TI - brms: an R package for Bayesian multilevel models using Stan JO - J Stat Softw VL - 80 UR - https://doi.org/10.18637/jss.v080.i01 DO - 10.18637/jss.v080.i01 ID - Bürkner2017 ER - TY - JOUR AU - Yao, Y. AU - Vehtari, A. AU - Simpson, D. AU - Gelman, A. PY - 2018 DA - 2018// TI - Using stacking to average Bayesian predictive distributions (with discussion) JO - Bayesian Anal VL - 13 UR - https://doi.org/10.1214/17-BA1091 DO - 10.1214/17-BA1091 ID - Yao2018 ER - TY - JOUR AU - Flicek, P. AU - Amode, M. R. AU - Barrell, D. AU - Beal, K. AU - Billis, K. AU - Brent, S. PY - 2014 DA - 2014// TI - Ensembl 2014 JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1196 DO - 10.1093/nar/gkt1196 ID - Flicek2014 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - STD TI - Medina-Muñoz SG, Kushawah G, Castellano LA, Diez M, DeVore ML, Salazar MJB, et al. 2020. Crosstalk between codon optimality and 3′ UTR ciselementsdictates mRNA stability. Datasets. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148391. 2020. UR - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148391 ID - ref69 ER - TY - STD TI - Medina-Muñoz SG. Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability 2020 [GitHub repository]. Available from: https://github.com/santiago1234/MZT-rna-stability. UR - https://github.com/santiago1234/MZT-rna-stability ID - ref70 ER - TY - STD TI - Medina-Muñoz SG, Kushawah G, Castellano LA, Diez M, DeVore ML, Salazar MJB, et al. Crosstalk between codon optimality and 3′ UTR cis-elements dictates mRNA stability; 2020 [Zenodo repository]. https://doi.org/10.5281/zenodo.4313561. ID - ref71 ER -