TY - JOUR PY - 2002 DA - 2002// TI - Initial sequencing and comparative analysis of the mouse genome JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01262 DO - 10.1038/nature01262 ID - ref1 ER - TY - JOUR AU - Margulies, E. H. AU - Blanchette, M. AU - Haussler, D. AU - Green, E. D. PY - 2003 DA - 2003// TI - Identification and characterization of multi-species conserved sequences JO - Genome Research VL - 13 UR - https://doi.org/10.1101/gr.1602203 DO - 10.1101/gr.1602203 ID - Margulies2003 ER - TY - JOUR AU - Blanchette, M. AU - Bataille, A. AU - Chen, X. AU - Poitras, C. AU - Laganiere, J. AU - Lefebvre, C. AU - Deblois, G. AU - Giguere, V. AU - Ferretti, V. AU - Bergeron, D. AU - Coulombe, B. AU - Robert, F. PY - 2006 DA - 2006// TI - Genome-wide computation prediction of transcriptional regulatory modules reveals new insights into human gene expression JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.4866006 DO - 10.1101/gr.4866006 ID - Blanchette2006 ER - TY - JOUR AU - King, D. C. AU - Taylor, J. AU - Elnitski, L. AU - Chiaromonte, F. AU - Miller, W. AU - Hardison, R. C. PY - 2005 DA - 2005// TI - Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3642605 DO - 10.1101/gr.3642605 ID - King2005 ER - TY - JOUR AU - Hastings, M. AU - Krainer, A. PY - 2001 DA - 2001// TI - Pre-mRNA splicing in the new millenium JO - Current Opinion in Cell Biology VL - 13 UR - https://doi.org/10.1016/S0955-0674(00)00212-X DO - 10.1016/S0955-0674(00)00212-X ID - Hastings2001 ER - TY - JOUR AU - Fairbrother, W. AU - Yeh, R. AU - Sharp, P. AU - Burge, C. PY - 2002 DA - 2002// TI - Predictive identification of exonic splicing enhancers in human genes JO - Science VL - 297 UR - https://doi.org/10.1126/science.1073774 DO - 10.1126/science.1073774 ID - Fairbrother2002 ER - TY - JOUR AU - Meisner, N. C. AU - Hackermuller, J. AU - Uhl, V. AU - Aszodi, A. AU - Jaritz, M. AU - Auer, M. PY - 2004 DA - 2004// TI - mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure JO - Chembiochem VL - 5 UR - https://doi.org/10.1002/cbic.200400219 DO - 10.1002/cbic.200400219 ID - Meisner2004 ER - TY - JOUR AU - Jansen, R. P. PY - 2001 DA - 2001// TI - mRNA localization: message on the move JO - Nat Rev Mol Cell Biol VL - 2 UR - https://doi.org/10.1038/35067016 DO - 10.1038/35067016 ID - Jansen2001 ER - TY - JOUR AU - Kozak, M. PY - 1994 DA - 1994// TI - Determinants of translational fidelity and efficiency in vertebrate mRNAs JO - Biochimie VL - 76 UR - https://doi.org/10.1016/0300-9084(94)90182-1 DO - 10.1016/0300-9084(94)90182-1 ID - Kozak1994 ER - TY - JOUR AU - Kozak, M. PY - 2005 DA - 2005// TI - Regulation of translation via mRNA structure in prokaryotes and eukaryotes JO - Gene VL - 361 UR - https://doi.org/10.1016/j.gene.2005.06.037 DO - 10.1016/j.gene.2005.06.037 ID - Kozak2005 ER - TY - JOUR AU - Meyer, I. M. AU - Miklos, I. PY - 2005 DA - 2005// TI - Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki923 DO - 10.1093/nar/gki923 ID - Meyer2005 ER - TY - JOUR AU - Lin, C. AU - Tam, R. C. PY - 2001 DA - 2001// TI - Transcriptional regulation of CD28 expression by CD28GR, a novel promoter element located in exon 1 of the CD28 gene JO - J Immunol VL - 166 UR - https://doi.org/10.4049/jimmunol.166.10.6134 DO - 10.4049/jimmunol.166.10.6134 ID - Lin2001 ER - TY - JOUR AU - Tagle, D. AU - Koop, B. AU - Goodman, M. AU - Slightom, J. AU - Hess, D. AU - Jones, R. PY - 1988 DA - 1988// TI - Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus) nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints JO - Journal of Molecular Biology VL - 203 UR - https://doi.org/10.1016/0022-2836(88)90011-3 DO - 10.1016/0022-2836(88)90011-3 ID - Tagle1988 ER - TY - JOUR AU - Blanchette, M. AU - Tompa, M. PY - 2002 DA - 2002// TI - Discovery of Regulatory elements by a computational method for phylogenetic footprinting JO - Genome Research VL - 12 UR - https://doi.org/10.1101/gr.6902 DO - 10.1101/gr.6902 ID - Blanchette2002 ER - TY - JOUR AU - Sorek, R. AU - Ast, G. PY - 2003 DA - 2003// TI - Intronic sequences flanking alternatively spliced exons are conserved between human and mouse JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1208803 DO - 10.1101/gr.1208803 ID - Sorek2003 ER - TY - JOUR AU - Margulies, E. H. AU - Vinson, J. P. AU - Miller, W. AU - Jaffe, D. B. AU - Lindblad-Toh, K. AU - Chang, J. L. AU - Green, E. D. AU - Lander, E. S. AU - Mullikin, J. C. AU - Clamp, M. PY - 2005 DA - 2005// TI - An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409882102 DO - 10.1073/pnas.0409882102 ID - Margulies2005 ER - TY - JOUR AU - Siepel, A. AU - Bejerano, G. AU - Pedersen, J. S. AU - Hinrichs, A. S. AU - Hou, M. AU - Rosenbloom, K. AU - Clawson, H. AU - Spieth, J. AU - Hillier, L. W. AU - Richards, S. AU - Weinstock, G. M. AU - Wilson, R. K. AU - Gibbs, R. A. AU - Kent, W. J. AU - Miller, W. AU - Haussler, D. PY - 2005 DA - 2005// TI - Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3715005 DO - 10.1101/gr.3715005 ID - Siepel2005 ER - TY - CHAP AU - Blanchette, M. PY - 2003 DA - 2003// TI - A comparative analysis method for detecting binding sites in coding regions BT - Proceedings of the seventh annual international conference on computational molecular biology ID - Blanchette2003 ER - TY - JOUR AU - Stojanovic, N. AU - Florea, L. AU - Riemer, C. AU - Gumucio, D. AU - Slightom, J. AU - Goodman, M. AU - Miller, W. AU - Hardison, R. PY - 1999 DA - 1999// TI - Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.19.3899 DO - 10.1093/nar/27.19.3899 ID - Stojanovic1999 ER - TY - JOUR AU - Bailey, T. L. AU - Elkan, C. PY - 1995 DA - 1995// TI - Unsupervised learning of multiple motifs in biopolymers using expectation maximization JO - Machine Learning VL - 21 ID - Bailey1995 ER - TY - JOUR AU - Fitch, W. M. PY - 1971 DA - 1971// TI - Toward Defining the Course of Evolution: Minimum Change for a Specified Tree Topology JO - Systematic Zoology VL - 20 UR - https://doi.org/10.2307/2412116 DO - 10.2307/2412116 ID - Fitch1971 ER - TY - JOUR AU - Sankoff, D. D. PY - 1975 DA - 1975// TI - Minimal mutation trees of sequences JO - SIAM Journal on Applied Mathematics VL - 28 UR - https://doi.org/10.1137/0128004 DO - 10.1137/0128004 ID - Sankoff1975 ER - TY - JOUR AU - Lartillot, N. AU - Philippe, H. PY - 2004 DA - 2004// TI - A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh112 DO - 10.1093/molbev/msh112 ID - Lartillot2004 ER - TY - STD TI - Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res. 2004, D138-D141. 10.1093/nar/gkh121. 32 Database ID - ref24 ER - TY - JOUR AU - Sjolander, K. AU - Karplus, K. AU - Brown, M. AU - Hughey, R. AU - Krogh, A. AU - Mian, I. S. AU - Haussler, D. PY - 1996 DA - 1996// TI - Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology JO - Comput Appl Biosci VL - 12 ID - Sjolander1996 ER - TY - JOUR AU - Nakamura, Y. AU - Gojobori, T. AU - Ikemura, T. PY - 2000 DA - 2000// TI - Codon usage tabulated from international DNA sequence databases: status for the year 2000 JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.292 DO - 10.1093/nar/28.1.292 ID - Nakamura2000 ER - TY - BOOK AU - Karlin, S. AU - Taylor, H. PY - 1975 DA - 1975// TI - A first course in stochastic processes ID - Karlin1975 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - Journal of Molecular Evolution VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Dirksen, W. P. AU - Li, X. AU - Mayeda, A. AU - Krainer, A. R. AU - Rottman, F. M. PY - 2000 DA - 2000// TI - Mapping the SF2/ASF binding sites in the bovine growth hormone exonic splicing enhancer JO - J Biol Chem VL - 275 UR - https://doi.org/10.1074/jbc.M001126200 DO - 10.1074/jbc.M001126200 ID - Dirksen2000 ER - TY - STD TI - Supplemental material. [http://www.mcb.mcgill.ca/~blanchem/CRUNCS] UR - http://www.mcb.mcgill.ca/~blanchem/CRUNCS ID - ref30 ER -