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diff --git a/academic/meme-suite/References b/academic/meme-suite/References index 242a70d914..871bc591a7 100644 --- a/academic/meme-suite/References +++ b/academic/meme-suite/References @@ -1,22 +1,4 @@ -Authors - -The MEME Suite was developed by - -Timothy Bailey at the Institute for Molecular Bioscience at the University of Queensland, -William Stafford Noble in the Department of Genome Sciences at the University of Washington and -with input from - -Charles Elkan and -Michael Gribskov. -Development of portions of the MEME Suite have previously been supported by - -Columbia University, -the Computational Biology Research Center at the National Institute of Advanced Industrial Science and Technology, Japan, -the National Biomedical Computation Resource, and -the San Diego Supercomputer Center. - Citing MEME Suite Programs - To cite the full MEME Suite Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text] To cite individual tools @@ -25,27 +7,31 @@ Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning AME Robert C. McLeay, Timothy L. Bailey, "Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data", BMC Bioinformatics, 11:165, 2010. [full text] CentriMo -Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Abstract and Full Text] +Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Full Text] +T-Gene +Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019. DREME Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text] FIMO -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text] +Charles E. Grant, Timothy L. Bailey and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text] GLAM2 and GLAM2SCAN -Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text] +Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text] GOMO Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26(7), 860-866, 2010. [full text] MAST Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(1):48-54, 1998. [pdf] +MCAST +Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text] MEME -Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf] +Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf] MEME-ChIP Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics 27(12):1696-1697, 2011. [full text] +MoMo +Alice Cheng, Charles Grant, Timothy L. Bailey and William Noble, "MoMo: Discovery of statistically significant post-translational modification motifs", Bioinformatics, 2018. [full text] PSPs -Timothy L. Bailey, Mikael Bodén, Tom Whitington, and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text] -MCAST -Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text] +Timothy L. Bailey, Mikael Bodén, Tom Whitington and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text] SpaMo -Tom Whitington, Martin C. Frith, James Johnson, and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text] +Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text] Tomtom Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007. [full text] Related papers @@ -55,24 +41,24 @@ MAST related Timothy L. Bailey and Michael Gribskov, "Score distributions for simultaneous matching to multiple motifs" Journal of Computational Biology, Vol. 4, pp. 45-59, 1997. [pdf] Timothy L. Bailey and Michael Gribskov, "Methods and statistics for combining motif match scores" Journal of Computational Biology, Vol. 5, pp. 211-221, 1998. [pdf] MEME related -Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf] +Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf] Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", UCSD Technical Report, CS94-351, March, 1994, University of California at San Diego. [pdf] Timothy L. Bailey, "Discovering motifs in DNA and protein sequences: The approximate common substring problem", Ph.D. dissertation, University of California at San Diego, 1995. [pdf] Timothy L. Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers using EM" Machine Learning, 21(1-2):51-80, October, 1995. [pdf] Timothy L. Bailey and Charles Elkan, "The value of prior knowledge in discovering motifs with MEME", Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 21-29, AAAI Press, Menlo Park, California, 1995. [pdf] Timothy L. Bailey and Michael Gribskov, "The megaprior heuristic for discovering protein sequence patterns"", Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 15-24 AAAI Press, Menlo Park, California, 1996. [pdf] William N. Grundy, Timothy L. Bailey and Charles P. Elkan, "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool", Computer Applications in the Biological Sciences (CABIOS), Vol. 12(4), pp. 303-310, 1996. [pdf] -Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997. +Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steroid dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997. Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov,, William S. Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye and Zhou Zhu. "Assessing computational tools for the discovery of transcription factor binding sites." Nature Biotechnology, 23(1), 137-144, 2005. [full text] -Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf] +Timothy L. Bailey, Nadya Williams, Chris Misleh and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf] Wenxiu Ma, William Stafford Noble and Timothy L. Bailey, "Motif-based analysis of large nucleotide datasets using MEME-ChIP" Nature Protocols, 9(6):1428-1450, 2014. [html] Tomtom related -Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble, and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text] +Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text] Other William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs" Biochemical and Biophysical Research Communications, Vol 231, pp. 760-766, 1997. [pdf] William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based Hidden Markov Models of Protein Families" Computer Applications in the Biological Sciences (CABIOS), Vol. 13(4), pp. 397-406, 1997. [pdf] -Michael E. Baker, William N. Grundy, and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf] -Michael E. Baker, William N. Grundy, and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999. -John Hawkins, Charles Grant, William S. Noble, and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text] -Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf] -Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Resesearch, 43(W1):W39-49, 2015 [full text] +Michael E. Baker, William N. Grundy and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf] +Michael E. Baker, William N. Grundy and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999. +John Hawkins, Charles Grant, William S. Noble and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text] +Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf] +Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Research, 43(W1):W39-49, 2015 [full text] |